class Ui_ChildWindow(object):
def setupUi(self, MainWindow, params):
#app = QtGui.QApplication([])
#self.win = QtGui.QMainWindow()
self.area = DockArea()
MainWindow.setCentralWidget(self.area)
MainWindow.resize(500, 700)
MainWindow.setWindowTitle('Action construct')
self.seq_cntr = Dock("Sequence", size=(150, 200))
self.area.addDock(self.seq_cntr, 'left')
## first dock gets save/restore buttons
self.t = ParameterTree()
if params != None:
self.p_child = Parameter.create(name='params',
type='group',
children=params)
self.t.setParameters(self.p_child, showTop=False)
self.t.setWindowTitle('pyqtgraph example: Parameter Tree')
self.seq_cntr.addWidget(self.t)
self.seq = pg.LayoutWidget()
self.label = QtGui.QLabel("""Controls""")
self.saveBtn = QtGui.QPushButton('Add Action')
self.restoreBtn = QtGui.QPushButton('Modify table')
self.restoreBtn.setEnabled(False)
self.seq.addWidget(self.label, row=0, col=0)
self.seq.addWidget(self.saveBtn, row=1, col=0)
self.seq.addWidget(self.restoreBtn, row=2, col=0)
self.seq_cntr.addWidget(self.seq)
class Ui_ChildWindow(object):
def setupUi(self, MainWindow, params):
#app = QtGui.QApplication([])
#self.win = QtGui.QMainWindow()
self.area = DockArea()
MainWindow.setCentralWidget(self.area)
MainWindow.resize(500, 700)
MainWindow.setWindowTitle('Action construct')
self.seq_cntr = Dock("Sequence", size=(150,200))
self.area.addDock(self.seq_cntr, 'left')
## first dock gets save/restore buttons
self.t = ParameterTree()
if params != None:
self.p_child = Parameter.create(name='params', type='group', children=params)
self.t.setParameters(self.p_child, showTop=False)
self.t.setWindowTitle('pyqtgraph example: Parameter Tree')
self.seq_cntr.addWidget(self.t)
self.seq = pg.LayoutWidget()
self.label = QtGui.QLabel("""Controls""")
self.saveBtn = QtGui.QPushButton('Add Action')
self.restoreBtn = QtGui.QPushButton('Modify table')
self.restoreBtn.setEnabled(False)
self.seq.addWidget(self.label, row=0, col=0)
self.seq.addWidget(self.saveBtn, row=1, col=0)
self.seq.addWidget(self.restoreBtn, row=2, col=0)
self.seq_cntr.addWidget(self.seq)
def start_gui(self):
from PyQt5 import QtGui
from PyQt5 import QtWidgets
# import QApplication, QFileDialog
app = QtWidgets.QApplication(sys.argv)
self.parameters.param('Input', 'Select').sigActivated.connect(self.select_input_dir_gui)
self.parameters.param('Make dir with image files').sigActivated.connect(self.make_dir_with_files)
self.parameters.param("Make PDF's").sigActivated.connect(self.make_pdfs)
self.parameters.param("Make PDF", "Automatic title recognition").sigActivated.connect(self.auto_split_file_names)
t = ParameterTree()
t.setParameters(self.parameters, showTop=False)
t.setWindowTitle('pyqtgraph example: Parameter Tree')
# t.show()
print("run scaffan")
win = QtGui.QWidget()
layout = QtGui.QGridLayout()
win.setLayout(layout)
# layout.addWidget(QtGui.QLabel("These are two views of the same data. They should always display the same values."), 0, 0, 1, 2)
layout.addWidget(t, 1, 0, 1, 1)
# layout.addWidget(t2, 1, 1, 1, 1)
win.show()
win.resize(800, 800)
app.exec_()
def main(camera):
app = Qt.QApplication([])
t = ParameterTree()
t.resize(600, 800)
t.show()
def value_changed(param, value):
try:
setattr(camera, param.name(), value)
except Exception as err:
Qt.QMessageBox.critical(None,
"Error setting {}".format(param.name()),
repr(err))
def connect(param, slot):
param.sigValueChanged.connect(slot)
for child in param.children():
connect(child, slot)
with camera:
t.setWindowTitle(camera.device_info.GetFriendlyName())
data = parameter_dict(camera)
# limits are dynamic (ex: max offset-x depends on current value
# of width).
strip_limits(data)
p = Parameter.create(**data)
t.setParameters(p, showTop=False)
connect(p, value_changed)
app.exec_()
class EyeTrackingExperimentWindow(SimpleExperimentWindow):
"""Window for controlling an experiment where the tail and the eyes
of an embedded fish are tracked.
Parameters
----------
Returns
-------
"""
def __init__(self, *args, **kwargs):
self.camera_display = CameraEyesSelection(
experiment=kwargs["experiment"])
self.camera_splitter = QSplitter(Qt.Horizontal)
self.monitoring_widget = QWidget()
self.monitoring_layout = QVBoxLayout()
self.monitoring_widget.setLayout(self.monitoring_layout)
# Stream plot:
self.stream_plot = MultiStreamPlot(time_past=30)
self.monitoring_layout.addWidget(self.stream_plot)
# Tracking params button:
self.button_tracking_params = QPushButton("Tracking params")
self.button_tracking_params.clicked.connect(
self.open_tracking_params_tree)
self.monitoring_layout.addWidget(self.button_tracking_params)
self.track_params_wnd = None
# self.tracking_layout.addWidget(self.camera_display)
# self.tracking_layout.addWidget(self.button_tracking_params)
super().__init__(*args, **kwargs)
def construct_ui(self):
""" """
self.stream_plot.add_stream(self.experiment.data_acc,
["th_e0", "th_e1"])
self.experiment.gui_timer.timeout.connect(self.stream_plot.update)
previous_widget = super().construct_ui()
self.monitoring_layout.addWidget(previous_widget)
self.monitoring_layout.setStretch(1, 1)
self.monitoring_layout.setStretch(0, 1)
self.camera_splitter.addWidget(self.camera_display)
self.camera_splitter.addWidget(self.monitoring_widget)
return self.camera_splitter
def open_tracking_params_tree(self):
""" """
self.track_params_wnd = ParameterTree()
self.track_params_wnd.setParameters(
self.experiment.tracking_method.params, showTop=False)
self.track_params_wnd.setWindowTitle("Tracking data")
self.track_params_wnd.show()
def do_stuff(self):
p = Parameter.create(name='params', type='group', children=self.params)
def change(param, changes):
print("tree changes:")
for param, change, data in changes:
path = p.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
print(' parameter: %s' % childName)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
p.sigTreeStateChanged.connect(change)
# create a parameter tree widget
t = ParameterTree()
t.setParameters(p, showTop=False)
t.setWindowTitle('pyqtgraph example: Parameter Tree')
# plot some data
plot = pg.PlotWidget()
n = 1000
xv = np.arange(n)
yv = 1 * pg.gaussianFilter(np.random.random(size=n), 10)
plot.plot(xv, yv, pen='r')
# make a second plot
plot2 = pg.PlotWidget()
plot2.plot(xv, yv, pen='g')
# set the layout of the widget
layout = QtGui.QGridLayout()
# layout.columnStretch(5)
layout.setColumnStretch(2, 2)
# NOTE: (widget, # y_row, x_row, y_span, x_span)
# layout.addWidget(QtGui.QLabel("Data monitor thing"), 0, 0, 1, 2)
layout.addWidget(t, 0, 0, 2, 1)
layout.addWidget(plot, 0, 2)
layout.addWidget(plot2, 1, 2)
self.setLayout(layout)
# test save/restore
s = p.saveState()
p.restoreState(s)
def valueChanging(param, value):
# print("Value changing (not finalized): %s %s" % (param, value))
# Too lazy for recursion:
for child in p.children():
child.sigValueChanging.connect(valueChanging)
for ch2 in child.children():
ch2.sigValueChanging.connect(valueChanging)
def save():
global state
state = p.saveState()
def restore():
global state
add = p['Save/Restore functionality', 'Restore State', 'Add missing items']
rem = p['Save/Restore functionality', 'Restore State', 'Remove extra items']
p.restoreState(state, addChildren=add, removeChildren=rem)
p.param('Save/Restore functionality', 'Save State').sigActivated.connect(save)
p.param('Save/Restore functionality', 'Restore State').sigActivated.connect(restore)
## Create two ParameterTree widgets, both accessing the same data
t = ParameterTree()
t.setParameters(p, showTop=False)
t.setWindowTitle('pyqtgraph example: Parameter Tree')
t2 = ParameterTree()
t2.setParameters(p, showTop=False)
win = QtGui.QWidget()
layout = QtGui.QGridLayout()
win.setLayout(layout)
layout.addWidget(QtGui.QLabel("These are two views of the same data. They should always display the same values."), 0, 0, 1, 2)
layout.addWidget(t, 1, 0, 1, 1)
layout.addWidget(t2, 1, 1, 1, 1)
win.show()
win.resize(800,800)
## test save/restore
s = p.saveState()
p.restoreState(s)
## Start Qt event loop unless running in interactive mode or using pyside.
if __name__ == '__main__':
import sys
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()
class NetworkInterface(QWidget):
def __init__(self, params):
super().__init__()
self.param = Parameter.create(name='params',
type='group',
children=params)
self.tree = ParameterTree()
self.tree.setParameters(self.param, showTop=False)
self.tree.setWindowTitle('Network Interface')
self.window = QWidget()
self.layout = QGridLayout()
self.window.setLayout(self.layout)
l = QLabel("Network Interface")
l.setAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.layout.addWidget(l)
self.layout.addWidget(self.tree)
self.window.setWindowFlags(QtCore.Qt.WindowStaysOnTopHint)
self.window.setGeometry(500, 800, 800, 500)
def updataParameter(self, params, opt):
self.param = Parameter.create(name='params',
type='group',
children=params)
self.tree.setParameters(self.param, showTop=False)
self.layout.addWidget(self.tree)
if opt == 1:
print('Please wait for a moment, I am working in progress')
else:
print('interface updated')
QtWidgets.QApplication.processEvents()
def closeEvent(self, closeEvent):
reply = QtWidgets.QMessageBox.question(
self, 'Warning', 'Are you sure to exit?',
QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No,
QtWidgets.QMessageBox.No)
if reply == QtWidgets.QMessageBox.Yes:
QCloseEvent.accept()
else:
QCloseEvent.ignore()
class GuiMetadata(HasPyQtGraphParams):
"""General class for a group of metadata that can be controlled via
a GUI.
Parameters
----------
Returns
-------
"""
def __init__(self):
super().__init__()
self.protocol_params_tree = ParameterTree(showHeader=False)
def get_param_dict(self):
""" Return values of the parameters.
Returns
-------
OrderedDict with the params values
"""
return self.params.getValues()
def show_metadata_gui(self):
""" Create and return a ParameterTree window (documented
`here <http://www.pyqtgraph.org/documentation/parametertree/index.html/>`_
)
Returns
-------
ParameterTree object to control the metadata
"""
self.protocol_params_tree = ParameterTree(showHeader=False)
self.protocol_params_tree.setParameters(self.params)
self.protocol_params_tree.setWindowTitle("Metadata")
self.protocol_params_tree.resize(450,
600) # TODO figure out this window
return self.protocol_params_tree
class MainWindow(Qt.QWidget):
''' Main Window '''
def __init__(self):
# 'Super' is used to initialize the class from which this class
# depends, in this case MainWindow depends on Qt.Widget class
super(MainWindow, self).__init__()
# buscar esto que son cosas de la ventana de la gui
self.setFocusPolicy(Qt.Qt.WheelFocus)
layout = Qt.QVBoxLayout(self)
# Qt.QPushButton is used to generate a button in the GUI
self.btnStart = Qt.QPushButton("Start Gen and Adq!")
layout.addWidget(self.btnStart)
self.btnStartSingleAdq = Qt.QPushButton("Single Adq!")
layout.addWidget(self.btnStartSingleAdq)
self.ResetGraph = Qt.QPushButton("Reset Graphics")
layout.addWidget(self.ResetGraph)
#Eliminar########################################
self.btnSaveData = Qt.QPushButton("Save Data")
layout.addWidget(self.btnSaveData)
#################################################
# Set threads as None
self.threadGeneration = None
self.threadPlotter = None
self.threadPsdPlotter = None
self.threadSave = None
self.threadCharact = None
# #############################Save##############################
self.SaveStateParams = FileMod.SaveSateParameters(
QTparent=self, name='FileState', title='Save/load config')
# With this line, it is initize the group of parameters that are
# going to be part of the full GUI
self.Parameters = Parameter.create(name='params',
type='group',
children=(self.SaveStateParams, ))
# #############################File##############################
self.FileParams = FileMod.SaveFileParameters(QTparent=self,
name='Record File')
self.Parameters.addChild(self.FileParams)
# #############################Plot Parameters#### REVISARRRR
self.PlotParams = TimePltPars(name='TimePlt',
title='Time Plot Options')
self.Parameters.addChild(self.PlotParams)
self.PsdPlotParams = PSDPltPars(name='PSDPlt',
title='PSD Plot Options')
self.Parameters.addChild(self.PsdPlotParams)
# #############################ASIC##############################
self.ASICParams = ASICConfig.ASICParameters(QTparent=self,
name='ASIC Configuration')
self.Parameters.addChild(self.ASICParams)
##ASIC 2 Class
if DEBUG == 0:
self.ASIC_C = AS(DEBUG=1)
self.ParamChange = 1
# #############################Sweep Config##############################
self.SwParams = Charact.SweepsConfig(QTparent=self,
name='Sweeps Configuration')
self.Parameters.addChild(self.SwParams)
# ################################EVENTS#############################
# Connect event for managing event
self.ASICParams.NewConf.connect(self.on_NewASICConf)
self.PsdPlotParams.NewConf.connect(self.on_NewPSDConf)
self.PlotParams.NewConf.connect(self.on_NewPlotConf)
# Event for debug print of changes
# self.Parameters.sigTreeStateChanged.connect(self.on_Params_changed)
# First call of some events for initializations
self.on_NewASICConf()
# Event of main button start and stop
self.ResetGraph.clicked.connect(self.on_ResetGraph)
self.btnStart.clicked.connect(self.on_btnStart)
#Boton adicional
self.btnStartSingleAdq.clicked.connect(self.on_btnStartSingleAdq)
self.btnSaveData.clicked.connect(self.on_btnSaveData)
self.SwParams.param('SweepsConfig').param(
'Start/Stop Sweep').sigActivated.connect(self.on_Sweep_start)
# self.SwParams.param('SweepsConfig').param('Pause Sweep').sigActivated.connect(self.on_Sweep_paused)
self.ASICParams.param('Global_VREFE').param(
'Start/Stop Sweep').sigActivated.connect(
self.on_VREF_E_Sweep_start)
# ############################GuiConfiguration##############################
# Is the same as before functions but for 'Parameters' variable,
# which conatins all the trees of all the Gui, so on_Params_changed
# will be execute for any change in the Gui
self.Parameters.sigTreeStateChanged.connect(self.on_Params_changed)
# EXPLICAR ESTO TAMBIEN QUE TIENE QUE VER CON LA GUI
self.treepar = ParameterTree()
self.treepar.setParameters(self.Parameters, showTop=False)
self.treepar.setWindowTitle('pyqtgraph example: Parameter Tree')
layout.addWidget(self.treepar)
self.setGeometry(550, 10, 500, 700)
self.setWindowTitle('MainWindow')
# ############################Changes Control##############################
def on_Params_changed(self, param, changes):
'''
This function is used to print in the consol the changes that have
been done.
'''
print("tree changes:")
for param, change, data in changes:
path = self.Parameters.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
print(' parameter: %s' % childName)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
#Flag
self.ParamChange
def on_NewASICConf(self):
self.PlotParams.SetChannels(self.ASICParams.GetChannels())
self.PsdPlotParams.ChannelConf = self.PlotParams.ChannelConf
nChannels = self.PlotParams.param('nChannels').value()
self.PsdPlotParams.param('nChannels').setValue(nChannels)
Fs = self.ASICParams.Fs
print(Fs)
nCols = self.ASICParams.nCols
Fs = Fs / 2.0 / 32.0 / nCols
self.PlotParams.param('Fs').setValue(Fs)
self.PsdPlotParams.param('Fs').setValue(Fs)
def on_NewPSDConf(self):
if self.threadPsdPlotter is not None:
nFFT = self.PsdPlotParams.param('nFFT').value()
nAvg = self.PsdPlotParams.param('nAvg').value()
self.threadPsdPlotter.InitBuffer(nFFT=nFFT, nAvg=nAvg)
def on_NewPlotConf(self):
if self.threadPlotter is not None:
ViewTime = self.PlotParams.param('ViewTime').value()
self.threadPlotter.SetViewTime(ViewTime)
RefreshTime = self.PlotParams.param('RefreshTime').value()
self.threadPlotter.SetRefreshTime(RefreshTime)
def on_ResetGraph(self):
if self.threadGeneration is None:
return
# Plot and PSD threads are stopped
if self.threadPlotter is not None:
self.threadPlotter.stop()
self.threadPlotter = None
if self.threadPsdPlotter is not None:
self.threadPsdPlotter.stop()
self.threadPsdPlotter = None
if self.PlotParams.param('PlotEnable').value():
Pltkw = self.PlotParams.GetParams()
self.threadPlotter = TimePlt(**Pltkw)
self.threadPlotter.start()
if self.PsdPlotParams.param('PlotEnable').value():
PSDKwargs = self.PsdPlotParams.GetParams()
self.threadPsdPlotter = PSDPlt(**PSDKwargs)
self.threadPsdPlotter.start()
# ############################START##############################
def on_btnStart(self):
'''
This function is executed when the 'start' button is pressed. It is
used to initialize the threads, emit signals and data that are
necessary durint the execution of the program. Also in this function
the different threads starts.
'''
if self.threadGeneration is None:
print('########## Starting Adquisition ##########')
#Actualizacion de los parametros de configuracion
DIC_C = self.ASICParams.GetGenParams()
DIC_R = self.ASICParams.GetRowsParams()
#Solo aplicar cambios si es necesario
self.ASIC_C.Dict_To_InstructionSimple(DIC_C)
self.ASIC_C.Dict_To_InstructionSimple(DIC_R)
#Chapuza
# self.threadGeneration = self.ASIC_C
self.threadGeneration = AS_Thread(
ASP=self.ASIC_C,
nChannels=self.ASICParams.nChannels,
nCols=self.ASICParams.nCols,
DIC_C=DIC_C,
DIC_R=DIC_R)
#Runs completos
self.ASIC_C.Runs_Completos = self.ASICParams.RunsCompletos
self.ASIC_C.tInterrupt = 1000
self.threadGeneration.NewGenData.connect(self.on_NewSample)
if self.FileParams.param('Enabled').value():
FilekwArgs = {
'FileName': self.FileParams.FilePath(),
'nChannels': self.ASICParams.nChannels,
'Fs': None,
'ChnNames': None,
'MaxSize': self.FileParams.param('MaxSize').value(),
'dtype': 'float',
}
self.threadSave = FileMod.DataSavingThread(**FilekwArgs)
self.threadSave.start()
#Reset Plots
self.on_ResetGraph()
# Start generation
self.OldTime = time.time()
self.threadGeneration.start()
self.btnStart.setText("Stop Gen and Adq!")
else:
print('########## Stoping Adquisition ##########')
#Pone el ASIC en Standby
self.ASIC_C.StopRun()
# Thread is terminated and set to None
self.threadGeneration.NewGenData.disconnect()
self.threadGeneration.terminate()
self.threadGeneration = None
# Plot and PSD threads are stopped
if self.threadPlotter is not None:
self.threadPlotter.stop()
self.threadPlotter = None
if self.threadPsdPlotter is not None:
self.threadPsdPlotter.stop()
self.threadPsdPlotter = None
# Also save thread is stopped
if self.threadSave is not None:
self.threadSave.stop()
self.threadSave = None
# Button text is changed again
self.btnStart.setText("Start Gen and Adq!")
# ############################Single Adquisition Long##############################
def on_btnStartSingleAdq(self):
'''
This function is executed when the 'start' button is pressed. It is
used to initialize the threads, emit signals and data that are
necessary durint the execution of the program. Also in this function
the different threads starts.
'''
print('########## Starting single Adq ##########')
if self.threadGeneration is None:
#Actualizacion de los parametros de configuracion
DIC_C = self.ASICParams.GetGenParams()
DIC_R = self.ASICParams.GetRowsParams()
#Chapuza
self.threadGeneration = self.ASIC_C
self.threadGeneration.Dict_To_InstructionSimple(DIC_C)
self.threadGeneration.Dict_To_InstructionSimple(DIC_R)
# self.ASIC_C.Dict_To_InstructionSimple(DIC_C)
# self.ASIC_C.Dict_To_InstructionSimple(DIC_R)
# #Short Run Adquisicion
self.Error, self.Col, self.Sar_0, self.Sar_1, self.Sar_2, self.Sar_3 = self.ASIC_C.ReadAcqS(
)
# self.Error,self.Col,self.Sar_0,self.Sar_1,self.Sar_2,self.Sar_3 = self.ASIC_C.ReadAcqL()
Sar_0_I = 2.0 * (self.Sar_0 - (2**(13.0 - 1)) + 0.5) / 2**13.0
Sar_1_I = 2.0 * (self.Sar_1 - (2**(13.0 - 1)) + 0.5) / 2**13.0
Sar_2_I = 2.0 * (self.Sar_2 - (2**(13.0 - 1)) + 0.5) / 2**13.0
Sar_3_I = 2.0 * (self.Sar_3 - (2**(13.0 - 1)) + 0.5) / 2**13.0
# Sar_0_I = Sar_0_I/(4*25e3)
# a[0]
plt.figure(1001)
plt.plot(Sar_0_I)
plt.plot(Sar_1_I)
plt.plot(Sar_2_I)
plt.plot(Sar_3_I)
#Pone el ASIC en Standby
self.threadGeneration.StopRun()
self.threadGeneration = None
else:
print('########## Stoping single Adq ##########')
def on_NewSample(self):
"""To call when new data ready to read."""
Ts = time.time() - self.OldTime
self.OldTime = time.time()
# Debug print of interruption time
print('Sample time', Ts)
# print('Data ', self.threadGeneration.OutData)
if self.threadPlotter is not None:
self.threadPlotter.AddData(self.threadGeneration.OutData)
if self.threadSave is not None:
self.threadSave.AddData(self.threadGeneration.OutData)
if self.threadPsdPlotter is not None:
self.threadPsdPlotter.AddData(self.threadGeneration.OutData)
if self.threadCharact is not None:
self.threadCharact.AddData(self.threadGeneration.OutData)
# #############################VREF_E GLOBAL ##############################
def on_VREF_E_Sweep_start(self):
Vmin = self.ASICParams.Vmin
Vmax = self.ASICParams.Vmax
Steps = self.ASICParams.NSweeps
nChannels = self.ASICParams.nChannels
nCols = self.ASICParams.nCols
DIC_C = self.ASICParams.GetGenParams()
VREF_E_G = self.ASIC_C.GlobalVREFE(Vmin, Vmax, Steps, nChannels, nCols,
DIC_C)
self.ASIC_C.StopRun()
self.ASICParams.GenConfig.param('DAC E').setValue(VREF_E_G)
# #############################START Sweep Acquisition ####################
def on_Sweep_start(self):
if self.threadGeneration is None:
print('Sweep started')
self.treepar.setParameters(self.Parameters, showTop=False)
self.SweepsKwargs = self.SwParams.GetConfigSweepsParams()
self.DcSaveKwargs = self.SwParams.GetSaveSweepsParams()
self.VdSweepVals = self.SweepsKwargs['VdSweep']
self.VgSweepVals = self.SweepsKwargs['VgSweep']
self.ASICParams.GenConfig.param('DAC EL').setValue(
0.9 + self.VgSweepVals[0]) ####DESCOMENTAR
self.ASICParams.GenConfig.param('DAC COL').setValue(
0.9 + self.VdSweepVals[0])
#Actualizacion de los parametros de configuracion
DIC_C = self.ASICParams.GetGenParams()
DIC_R = self.ASICParams.GetRowsParams()
# print(DIC_C)
self.threadGeneration = AS_Thread(
ASP=self.ASIC_C,
nChannels=self.ASICParams.nChannels,
nCols=self.ASICParams.nCols,
DIC_C=DIC_C,
DIC_R=DIC_R)
self.ASIC_C.Dict_To_InstructionSimple(DIC_C)
self.ASIC_C.Dict_To_InstructionSimple(DIC_R)
#Runs completos
self.ASIC_C.Runs_Completos = self.ASICParams.RunsCompletos
self.ASIC_C.tInterrupt = 1000
self.threadGeneration.NewGenData.connect(self.on_NewSample)
self.threadGeneration.Lista = None
#Reset Plots
self.on_ResetGraph()
self.threadCharact = Charact.StbDetThread(
nChannels=self.ASICParams.nChannels,
ChnName=self.ASICParams.GetChannels(),
PlotterDemodKwargs=self.PsdPlotParams.GetParams(),
**self.SweepsKwargs)
self.threadCharact.NextVg.connect(self.on_NextVg)
self.threadCharact.NextVd.connect(self.on_NextVd)
self.threadCharact.CharactEnd.connect(self.on_CharactEnd)
self.threadCharact.Timer.start(self.SweepsKwargs['TimeOut'] * 1000)
self.threadCharact.start()
# Start generation
self.threadGeneration.start()
self.OldTime = time.time()
else:
print('########## Stoping Adquisition ##########')
#Pone el ASIC en Standby
self.ASIC_C.StopRun()
# Thread is terminated and set to None
self.threadGeneration.NewGenData.disconnect()
self.threadGeneration.terminate()
self.threadGeneration = None
# Plot and PSD threads are stopped
if self.threadPlotter is not None:
self.threadPlotter.stop()
self.threadPlotter = None
if self.threadPsdPlotter is not None:
self.threadPsdPlotter.stop()
self.threadPsdPlotter = None
# Also save thread is stopped
if self.threadSave is not None:
self.threadSave.stop()
self.threadSave = None
# Button text is changed again
if self.threadCharact is not None:
self.threadCharact.NextVg.disconnect()
self.threadCharact.NextVd.disconnect()
self.threadCharact.CharactEnd.disconnect()
self.threadCharact.stop()
self.threadCharact = None
def on_NextVg(self):
print('HUEVO VGS ')
while (self.threadGeneration.EndCap == 1):
print("Esperando a que acabe de cojer datos...")
# self.ASIC_C.StopRun()
# # Thread is terminated and set to None
# self.threadGeneration.NewGenData.disconnect()
# self.threadGeneration.terminate()
# self.threadGeneration = None
DIC_C = {'DAC EL': 0.9 + self.threadCharact.NextVgs} ####DESCOMENTAR
#Actualizacion de los parametros de configuracion
# self.ASIC_C.Dict_To_InstructionSimple(DIC_C) ####DESCOMENTAR
# self.threadGeneration = AS_Thread(ASP = self.ASIC_C,nChannels = self.ASICParams.nChannels,nCols = self.ASICParams.nCols,Scale = [2,2,2,2])
# self.threadGeneration.NewGenData.connect(self.on_NewSample)
# self.threadGeneration.start()
self.threadGeneration.Lista = DIC_C
print('VG ', self.threadCharact.NextVgs)
# self.threadCharact.Timer.start(self.SweepsKwargs['TimeOut']*1000)
print('NEXT VGS SWEEP')
def on_NextVd(self):
while (self.threadGeneration.EndCap == 1):
print("Esperando a que acabe de cojer datos...")
# self.ASIC_C.StopRun()
# Thread is terminated and set to None
# self.threadGeneration.NewGenData.disconnect()
# self.threadGeneration.terminate()
# self.threadGeneration = None
DIC_C = {'DAC COL': 0.9 + self.threadCharact.NextVds}
#Actualizacion de los parametros de configuracion
# self.ASIC_C.Dict_To_InstructionSimple(DIC_C)
# self.threadGeneration = AS_Thread(ASP = self.ASIC_C,nChannels = self.ASICParams.nChannels,nCols = self.ASICParams.nCols,Scale = [2,2,2,2])
# self.threadGeneration.NewGenData.connect(self.on_NewSample)
# self.threadGeneration.start()
self.threadGeneration.Lista = DIC_C
print('VD ', self.threadCharact.NextVds)
# self.threadCharact.Timer.timeout.connect(self.threadCharact.printTime)
# self.threadCharact.Timer.start(self.SweepsKwargs['TimeOut']*1000)
def on_CharactEnd(self):
while (self.threadGeneration.EndCap == 1):
print("Esperando a que acabe de cojer datos...")
#Pone el ASIC en Standby
self.threadGeneration.EndCap = 2
self.ASIC_C.StopRun()
# Thread is terminated and set to None
self.threadGeneration.NewGenData.disconnect()
self.threadGeneration.terminate()
self.threadGeneration = None
print('END Charact')
self.threadCharact.NextVg.disconnect()
self.threadCharact.NextVd.disconnect()
self.threadCharact.CharactEnd.disconnect()
CharactDCDict = self.threadCharact.DCDict
CharactACDict = self.threadCharact.ACDict
self.threadCharact.SaveDCAC.SaveDicts(Dcdict=CharactDCDict,
Acdict=CharactACDict,
**self.DcSaveKwargs)
# Plot and PSD threads are stopped
if self.threadPlotter is not None:
self.threadPlotter.stop()
self.threadPlotter = None
if self.threadPsdPlotter is not None:
self.threadPsdPlotter.stop()
self.threadPsdPlotter = None
# Also save thread is stopped
if self.threadSave is not None:
self.threadSave.stop()
self.threadSave = None
# Button text is changed again
if self.threadCharact is not None:
self.threadCharact.stop()
self.threadCharact = None
###########ELIMINAR
def on_btnSaveData(self):
print("SAVING DATA")
print("Len Sar 0", len(self.Sar_0))
print("Len Sar 1", len(self.Sar_1))
print("Len Sar 2", len(self.Sar_2))
print("Len Sar 3", len(self.Sar_3))
letra = '2000504_Sar_CDS_999999999'
path_f = "/home/jcisneros/Downloads/DAta_rouleta"
file_name = "SAR_0_AS2t" + letra + ".txt"
self.ASIC_C.Gravar_M_Conversion(path=path_f,
filename=file_name,
Data=self.Sar_0,
Limite=len(self.Sar_0),
Conversion=1)
file_name = "SAR_1_AS2t" + letra + ".txt"
self.ASIC_C.Gravar_M_Conversion(path=path_f,
filename=file_name,
Data=self.Sar_1,
Limite=len(self.Sar_1),
Conversion=1)
file_name = "SAR_2_AS2t" + letra + ".txt"
self.ASIC_C.Gravar_M_Conversion(path=path_f,
filename=file_name,
Data=self.Sar_2,
Limite=len(self.Sar_2),
Conversion=1)
file_name = "SAR_3_AS2t" + letra + ".txt"
self.ASIC_C.Gravar_M_Conversion(path=path_f,
filename=file_name,
Data=self.Sar_3,
Limite=len(self.Sar_3),
Conversion=1)
print("END SAVING DATA")
'name': 'ADD SINGLE',
'type': 'action'
}, {
'name': 'REMOVE SINGLE',
'type': 'action'
}, {
'name': 'SAVE OBJECT',
'type': 'action'
}]
pars_action = Parameter.create(name='params_action',
type='group',
children=params_action)
t_action.setParameters(pars_action, showTop=False)
t_action.setWindowTitle('Parameter Action')
def reset_button():
global mode
mode = "reset"
p2.setTitle("mode: %s" % (mode))
#clear the upper right image
zeros = np.asarray([[0] * 80 for _ in range(60)])
img2.setImage(make_color_img(zeros), autoLevels=False)
draw_contours()
pars.param('RESET').sigActivated.connect(reset_button)
class RTSmainView(mainViewBase,mainViewForm):
def __init__(self, parent = None):
super().__init__()
self.params_filename = "params.dat"
self.loaded_data = None
self.parameters = None
self.setupUi()
self.setupParameterTree()
#self.timetrace_filename = ""
settings = QtCore.QSettings("foo","foo")
self.timetrace_filename = settings.value('filename', type=str)#.toString()
if self.timetrace_filename:
self.load_data(self.timetrace_filename)
def setupUi(self):
super().setupUi(self)
self.plot1 = self.ui_plot_area.addPlot(row=1, col=0)
self.plot2 = self.ui_plot_area.addPlot(row=2, col=0, colspan =2)
self.histogram_plot = self.ui_plot_area.addPlot(row = 1, col = 1)
self.label = pg.LabelItem(justify='right')
self.region = pg.LinearRegionItem()
self.region.setZValue(10)
self.region.sigRegionChanged.connect(self.update)
## Add the LinearRegionItem to the ViewBox, but tell the ViewBox to exclude this
## item when doing auto-range calculations.
self.plot2.addItem(self.region, ignoreBounds=True)
self.plot1.setAutoVisible(y=True)
self.general_curve = self.plot2.plot(pen = pg.mkColor("g"))
self.general_curve.setVisible(True)
self.analysis_curve = self.plot1.plot(pen = pg.mkColor("y"))
self.analysis_curve.setVisible(True)
self.histogram_curve = self.histogram_plot.plot(pen = pg.mkColor("b"), fillLevel=0, fillBrush=(255,255,255,30))
self.histogram_curve.setVisible(True)
self.rts_curve = self.plot1.plot(pen = pg.mkPen("r", width = 3)) #pg.mkColor("r"),width = 3)
self.rts_curve.setVisible(True)
self.rts_curve.setZValue(100)
#self.plot1.addItem(pg.MultiRectROI([[0, 0], [20,0 ], [40, 0]], width = 1e-06))
#roi = pg.MultiRectROI(, width=5, pen=(2,9))
#self.plot1.addItem(roi)
print("init")
def getDefaultParams(self):
return [ {'name': 'Automated RTS recognition', 'type': 'group', 'children': [
{'name': 'Error', 'type': 'float', 'value': 1e-06},
{'name': 'Weights', 'type': 'str', 'value': '2'}
#WeightParamGroup(name="Weights", children=[
#])
]},
{'name':'Window', 'type': 'int', 'value':10},
{'name': 'Filtering', 'type': 'group', 'children':[
{'name':'Filter design', 'type':'list', 'values': {"Butterworth":0,
"Chebyshev I":1,
"Chebyshev II":2,
"Elliptic":3,
"Bessel":4
}},
{'name':'Order', 'type': 'int', 'value': 1},
{'name':'Type', 'type':'list', 'values': {"lowpass":0,
"highpass":1 }},
{'name':'Frequency','type': 'float', 'value':100.0},
{'name':'Apply', 'type':'action'}
]}
]
def save_state(self, filename,state):
"""Save a tree as a pickle file
"""
with open(filename, 'wb') as fid:
pickle.dump(state,fid)
def load_state(self, filename):
"""Load a tree state to a pickle file
"""
try:
with open(filename, 'rb') as fid:
data = pickle.load(fid)
return data
except FileNotFoundError as e:
print("File Not Found")
return None
def setupParameterTree(self):
self.param_tree = ParameterTree()
self.param_tree.setWindowTitle('pyqtgraph example: Parameter Tree')
#self.param_tree.setFixedWidth(300)
self.parameterTreeLayout.addWidget(self.param_tree)
self.parameterTreeLayout.setSizes([500,150])
#self.parameterTreeLayour.
self.parameters = Parameter.create(name='params', type='group')
params = self.getDefaultParams()
self.parameters.addChildren(params)
state = self.load_state(self.params_filename)
if state:
self.parameters.restoreState(state)
#else:
#params = self.getDefaultParams()
#self.parameters.addChildren(params)
self.parameters.sigTreeStateChanged.connect(self.action_signaled)
self.param_tree.setParameters(self.parameters, showTop=False)
def action_signaled(self, *args, **kwargs):
print(args)
print(kwargs)
def closeEvent(self,event):
print("closing")
settings = QtCore.QSettings("foo","foo")
if self.timetrace_filename:
settings.setValue("filename", self.timetrace_filename)
if self.parameters:
self.save_state(self.params_filename, self.parameters.saveState())
def update(self):
minX, maxX = self.region.getRegion()
self.plot1.setXRange(minX, maxX, padding=0)
region_data = self.loaded_data.loc[lambda df: (df.time > minX) & (df.time < maxX),:]
time = region_data.time
data = region_data.data
hist, bin_edges = np.histogram(data, bins = 'rice') #bins = 'auto')
bin_centers = 0.5*(bin_edges[1:]+bin_edges[:-1]) #0.5*(x[1:] + x[:-1])
self.histogram_curve.setData(bin_centers, hist)
print("data points selected: {0}".format(len(time)))
#rts_values = self.calc_levels(data)
#self.rts_curve.setData(time, rts_values)
@QtCore.pyqtSlot()
def on_actionConvolve_triggered(self):
print("convolution")
minX, maxX = self.region.getRegion()
region_data = self.loaded_data.loc[lambda df: (df.time > minX) & (df.time < maxX),:]
time = region_data.time.values
data = region_data.data.values
win_size = self.parameters['Window']
win = self.generate_window(win_size) #signal.hann(win_size)
pg.plot(win, title = "Window size: {0}".format(win_size))
#filtered = self.fit_using_pearson(data,win)
#fit_using_pearson
mean_value = np.mean(data)
std = np.std(data)
signal_to_noise = mean_value / std
print("MEAN = {0}".format(mean_value))
print("STD = {0}".format(std))
print("SNR = {0}".format(signal_to_noise))
filtered = signal.convolve(data,win, mode='same')/sum(win)
fourier_filter(data, time[1]-time[0])
#pearsonr, p_val = stats.pearsonr(data, filtered)
#print("PearsonR = {0}".format(pearsonr))
#optimal_wnd_size, pearsonr = self.fit_data_with_pulses(data, [3,5,10,15,20,25,30,50,100,200])
#print("STD = {0}".format(std))
#print("wnd_size = {0}".format(optimal_wnd_size))
#win = signal.hann(optimal_wnd_size)
#filtered = signal.convolve(data,win, mode='same')/sum(win)
#filtered = data - filtered
self.rts_curve.setData(time,filtered)
def generate_window(self, wnd_size, front_size = 3):
#wnd = np.hstack((np.zeros(wnd_size),np.ones(wnd_size)))
wnd = signal.hann(2*front_size)
wnd = np.insert(wnd,front_size,signal.boxcar(wnd_size))
wnd = np.insert(np.zeros(2*front_size),front_size, wnd)
return wnd
def fit_using_pearson(self, data, wnd):
wnd_size = len(wnd)
half_wnd_size = wnd_size/2
data_size = len(data)
result_size = data_size - wnd_size
result = np.zeros(data_size, dtype = np.float)
for i in range(result_size):
pearsonr,p_val =stats.pearsonr(data[i:i+wnd_size], wnd)
result[i+half_wnd_size] = pearsonr * 1e-04
return result
def fit_data_with_pulses(self, data, wnd_length_arr:list):
#current_std = 0
current_pearsonr_to_one_dist = 1
current_wnd_len = None
for i, wnd_size in enumerate(wnd_length_arr):
wnd = self.generate_window(wnd_size) #signal.hann(wnd_size)
print(wnd)
#filtered = data - signal.convolve(data,wnd, mode='same')/sum(wnd)
#std = np.std(filtered)
pg.plot(wnd, title = "Window size: {0}".format(wnd_size))
filtered = signal.convolve(data,wnd, mode='same')/sum(wnd)
pearsonr, p_val = stats.pearsonr(data, filtered)
dist = 1 - pearsonr
print("PearsonR = {0}".format(pearsonr))
print("wnd_size = {0}".format(wnd_size))
if i == 0:
#current_std = std
current_pearsonr_to_one_dist = dist
current_wnd_len = wnd_size
elif dist < current_pearsonr_to_one_dist:
current_pearsonr_to_one_dist = dist
current_wnd_len = wnd_size
return (current_wnd_len, current_pearsonr_to_one_dist)
@QtCore.pyqtSlot()
def on_actionSelectedArea_triggered(self):
minX, maxX = self.region.getRegion()
region_data = self.loaded_data.loc[lambda df: (df.time > minX) & (df.time < maxX),:]
time = region_data.time.values
data = region_data.data.values
#weights = self.parameters.va
weights = list(map(float, self.parameters["Automated RTS recognition","Weights"].split(';')))#.items()
error = self.parameters["Automated RTS recognition","Error"]
rts_values = self.calc_levels(data, weights, error)
self.rts_curve.setData(time,rts_values)
@QtCore.pyqtSlot()
def on_actionFull_Set_triggered(self):
time = self.loaded_data.time.values
data = self.loaded_data.data.values
rts_values = self.calc_levels(data)
self.rts_curve.setData(time,rts_values)
@QtCore.pyqtSlot()
def on_actionOpen_triggered(self):
print("opening")
print("Select folder")
self.timetrace_filename = os.path.abspath(QtGui.QFileDialog.getOpenFileName(self,caption="Select File"))#, directory = self._settings.working_directory))
msg = QtGui.QMessageBox()
msg.setIcon(QtGui.QMessageBox.Information)
msg.setText("This is a message box")
msg.setInformativeText("This is additional information")
msg.setWindowTitle("MessageBox demo")
msg.setDetailedText(self.timetrace_filename)
msg.setStandardButtons(QtGui.QMessageBox.Ok | QtGui.QMessageBox.Cancel)
retval = msg.exec_()
if retval:
self.load_data(self.timetrace_filename)
def load_data(self, filename):
print("loading file: {0}".format(filename))
try:
self.loaded_data = pd.read_csv(filename, delimiter = "\t", names=["time", "data"])
time = self.loaded_data.time #["time"]
rts = self.generate_rts(len(self.loaded_data.index), 100, time[1], 5e-05)
rts2 = self.generate_rts(len(self.loaded_data.index), 10, time[1], 5e-06)
self.loaded_data.data = self.loaded_data.data + rts# + rts2
data = self.loaded_data.data #["data"]
#time,data = np.loadtxt(filename).T
self.general_curve.setData(time,data)
self.analysis_curve.setData(time,data)
self.update()
except Exception as e:
print("failed to load data")
def generate_rts(self, nelem, k,dt, amplitude = 1):
k = float(k)
ra = np.random.rand(nelem)
# exponentially distributed jumps:
t = np.log(1./ra)/k
tr = np.floor(t/dt)
x = []
s = amplitude
ones = np.ones(len(tr))
ones[::2] = -1
ones = ones * s
arr =np.vstack((ones, tr)).T
#np.apply_along_axis(generate_arr, 1, arr)
result = np.zeros(nelem)
current_idx = 0
for val, n in arr:
next_idx = current_idx+int(n)
result[current_idx: next_idx] = val
current_idx = next_idx
return result
def calc_levels(self,current_arr, weights= [1,0.7,0.4], error = 1e-06):
L = len(current_arr)
result = np.zeros(L)
r_weights = weights #[1,0.7,0.4]#,0.8,0.7]
l_weights = r_weights.reverse()
N_half_wnd = len(r_weights)
sigma = error
left_avg = np.average(current_arr[0:N_half_wnd])
right_arv = 0
prev_val = 0
result[:N_half_wnd] = left_avg
## prev_time = 0
## time_counter = 0
for i in range(N_half_wnd,L-N_half_wnd):
left_avg = np.average(current_arr[i-N_half_wnd:i],weights=l_weights)
right_avg= np.average(current_arr[i:i+N_half_wnd],weights=r_weights)
diff = right_avg - left_avg
abs_diff = abs(diff)
if abs_diff > sigma or abs(right_avg - prev_val) > sigma:
## if time_counter >1:
## amplitude_time_list.append([prev_val,prev_time])
prev_val = right_avg
## prev_time =0
## time_counter =0
result[i] = prev_val
## prev_time += dt
## time_counter += 1
## print(i)
result[-N_half_wnd:] = prev_val
return result
class MainWindow(Qt.QWidget):
''' Main Window '''
def __init__(self):
super(MainWindow, self).__init__()
self.threadAcq = None
self.threadSave = None
self.threadPlotter = None
self.threadPSDPlotter = None
self.threadPlotterRaw = None
layout = Qt.QVBoxLayout(self)
self.btnAcq = Qt.QPushButton("Start Acq!")
layout.addWidget(self.btnAcq)
self.ResetGraph = Qt.QPushButton("Reset Graphics")
layout.addWidget(self.ResetGraph)
self.SamplingPar = AcqMod.SampSetParam(name='SampSettingConf')
self.Parameters = Parameter.create(name='App Parameters',
type='group',
children=(self.SamplingPar, ))
self.SamplingPar.NewConf.connect(self.on_NewConf)
self.SamplingPar.Fs.sigValueChanged.connect(self.on_FsChanged)
self.SamplingPar.FsxCh.sigValueChanged.connect(self.on_FsxChChanged)
self.SamplingPar.Vds.sigValueChanged.connect(self.on_BiasChanged)
self.SamplingPar.Vgs.sigValueChanged.connect(self.on_BiasChanged)
self.PlotParams = TimePltPars(name='TimePlt',
title='Time Plot Options')
self.PlotParams.NewConf.connect(self.on_NewPlotConf)
self.Parameters.addChild(self.PlotParams)
self.RawPlotParams = TimePltPars(name='RawPlot')
self.Parameters.addChild(self.RawPlotParams)
self.PsdPlotParams = PSDPltPars(name='PSDPlt',
title='PSD Plot Options')
self.Parameters.addChild(self.PsdPlotParams)
self.PsdPlotParams.NewConf.connect(self.on_NewPSDConf)
self.treepar = ParameterTree()
self.treepar.setParameters(self.Parameters, showTop=False)
self.treepar.setWindowTitle('pyqtgraph example: Parameter Tree')
layout.addWidget(self.treepar)
self.setGeometry(650, 20, 400, 800)
self.setWindowTitle('MainWindow')
self.btnAcq.clicked.connect(self.on_btnStart)
self.ResetGraph.clicked.connect(self.on_ResetGraph)
self.FileParameters = FileMod.SaveFileParameters(QTparent=self,
name='Record File')
self.Parameters.addChild(self.FileParameters)
self.ConfigParameters = FileMod.SaveSateParameters(
QTparent=self, name='Configuration File')
self.Parameters.addChild(self.ConfigParameters)
self.on_FsChanged()
self.on_FsxChChanged()
self.on_NewConf()
def on_BiasChanged(self):
if self.threadAcq:
Vgs = self.SamplingPar.Vgs.value()
Vds = self.SamplingPar.Vds.value()
Ao2 = None
Ao3 = None
if self.SamplingPar.Ao2:
Ao2 = self.SamplingPar.Ao2.value()
if self.SamplingPar.Ao3:
Ao3 = self.SamplingPar.Ao3.value()
self.threadAcq.DaqInterface.SetBias(Vgs=Vgs,
Vds=Vds,
ChAo2=Ao2,
ChAo3=Ao3)
def on_FsChanged(self):
self.RawPlotParams.param('Fs').setValue(self.SamplingPar.Fs.value())
def on_FsxChChanged(self):
print('FSXCH', self.SamplingPar.FsxCh.value())
self.PlotParams.param('Fs').setValue(self.SamplingPar.FsxCh.value())
self.PsdPlotParams.param('Fs').setValue(self.SamplingPar.FsxCh.value())
def on_NewPSDConf(self):
if self.threadPSDPlotter is not None:
nFFT = self.PsdPlotParams.param('nFFT').value()
nAvg = self.PsdPlotParams.param('nAvg').value()
self.threadPSDPlotter.InitBuffer(nFFT=nFFT, nAvg=nAvg)
def on_NewConf(self):
print('NewConf')
self.PlotParams.SetChannels(self.SamplingPar.GetChannelsNames())
self.RawPlotParams.SetChannels(self.SamplingPar.GetRowNames())
self.PsdPlotParams.ChannelConf = self.PlotParams.ChannelConf
nChannels = self.PlotParams.param('nChannels').value()
self.PsdPlotParams.param('nChannels').setValue(nChannels)
if self.SamplingPar.Ao2:
self.SamplingPar.Ao2.sigValueChanged.connect(self.on_BiasChanged)
if self.SamplingPar.Ao3:
self.SamplingPar.Ao3.sigValueChanged.connect(self.on_BiasChanged)
def on_NewPlotConf(self):
if self.threadPlotter is not None:
ViewTime = self.PlotParams.param('ViewTime').value()
self.threadPlotter.SetViewTime(ViewTime)
RefreshTime = self.PlotParams.param('RefreshTime').value()
self.threadPlotter.SetRefreshTime(RefreshTime)
def on_ResetGraph(self):
if self.threadAcq is None:
return
# Plot and PSD threads are stopped
if self.threadPlotter is not None:
self.threadPlotter.stop()
self.threadPlotter = None
if self.threadPSDPlotter is not None:
self.threadPSDPlotter.stop()
self.threadPSDPlotter = None
if self.threadPlotterRaw is not None:
self.threadPlotterRaw.stop()
self.threadPlotterRaw = None
if self.PlotParams.param('PlotEnable').value():
Pltkw = self.PlotParams.GetParams()
self.threadPlotter = TimePlt(**Pltkw)
self.threadPlotter.start()
if self.PsdPlotParams.param('PlotEnable').value():
PSDKwargs = self.PsdPlotParams.GetParams()
self.threadPSDPlotter = PSDPlt(**PSDKwargs)
self.threadPSDPlotter.start()
if self.RawPlotParams.param('PlotEnable').value():
RwPltkw = self.RawPlotParams.GetParams()
self.threadPlotterRaw = TimePlt(**RwPltkw)
self.threadPlotterRaw.start()
def on_btnStart(self):
if self.threadAcq is None:
GenKwargs = self.SamplingPar.GetSampKwargs()
GenChanKwargs = self.SamplingPar.GetChannelsConfigKwargs()
AvgIndex = self.SamplingPar.SampSet.param('nAvg').value()
self.threadAcq = AcqMod.DataAcquisitionThread(
ChannelsConfigKW=GenChanKwargs,
SampKw=GenKwargs,
AvgIndex=AvgIndex,
)
self.threadAcq.NewMuxData.connect(self.on_NewSample)
self.threadAcq.start()
PlotterRawKwargs = self.RawPlotParams.GetParams()
print(PlotterRawKwargs['nChannels'])
FileName = self.FileParameters.FilePath()
print('Filename', FileName)
if FileName == '':
print('No file')
else:
if os.path.isfile(FileName):
print('Remove File')
os.remove(FileName)
MaxSize = self.FileParameters.param('MaxSize').value()
self.threadSave = FileMod.DataSavingThread(
FileName=FileName,
nChannels=PlotterRawKwargs['nChannels'],
MaxSize=MaxSize)
self.threadSave.start()
self.on_ResetGraph()
self.btnAcq.setText("Stop Gen")
self.OldTime = time.time()
self.Tss = []
else:
self.threadAcq.DaqInterface.Stop()
self.threadAcq = None
if self.threadSave is not None:
self.threadSave.terminate()
self.threadSave = None
if self.PlotParams.param('PlotEnable').value():
self.threadPlotter.terminate()
self.threadPlotter = None
if self.threadPSDPlotter is not None:
self.threadPSDPlotter.stop()
self.threadPSDPlotter = None
if self.threadPlotterRaw is not None:
self.threadPlotterRaw.stop()
self.threadPlotterRaw = None
self.btnAcq.setText("Start Gen")
def on_NewSample(self):
''' Visualization of streaming data-WorkThread. '''
Ts = time.time() - self.OldTime
self.Tss.append(Ts)
self.OldTime = time.time()
if self.threadSave is not None:
self.threadSave.AddData(self.threadAcq.aiData.transpose())
if self.threadPlotter is not None:
self.threadPlotter.AddData(self.threadAcq.OutData.transpose())
if self.threadPSDPlotter is not None:
self.threadPSDPlotter.AddData(self.threadAcq.OutData.transpose())
if self.threadPlotterRaw is not None:
self.threadPlotterRaw.AddData(self.threadAcq.aiData.transpose())
global state
state = p.saveState()
def restore():
global state
add = p['Save/Restore functionality', 'Restore State', 'Add missing items']
rem = p['Save/Restore functionality', 'Restore State', 'Remove extra items']
p.restoreState(state, addChildren=add, removeChildren=rem)
p.param('Save/Restore functionality', 'Save State').sigActivated.connect(save)
p.param('Save/Restore functionality', 'Restore State').sigActivated.connect(restore)
## Create two ParameterTree widgets, both accessing the same data
t = ParameterTree()
t.setParameters(p, showTop=False)
t.setWindowTitle('pyqtgraph example: Parameter Tree')
t2 = ParameterTree()
t2.setParameters(p, showTop=False)
win = QtGui.QWidget()
layout = QtGui.QGridLayout()
win.setLayout(layout)
layout.addWidget(QtGui.QLabel("These are two views of the same data. They should always display the same values."), 0, 0, 1, 2)
layout.addWidget(t, 1, 0, 1, 1)
layout.addWidget(t2, 1, 1, 1, 1)
win.show()
win.resize(800,800)
## test save/restore
s = p.saveState()
p.restoreState(s)
def __init__(self):
#==========================================
super(GUIMainWindow, self).__init__()
# CHANGE HERE -------------------------------------------------
# -------------------------------------------------------------
area = DockArea()
self.setCentralWidget(area)
self.resize(1280, 800)
self.setWindowTitle('Demo: How to use HARP with Python')
## Create docks, place them into the window one at a time.
## Note that size arguments are only a suggestion; docks will still have to
## fill the entire dock area and obey the limits of their internal widgets.
d1 = Dock("Control", size=(300,200)) ## give this dock the minimum possible size
d2 = Dock("Description", size=(300,800))
d31 = Dock("INTRA frame - Prediction Units", size=(500,300))
d32 = Dock("INTER frame - Prediction Units", size=(500,300))
#d33 = Dock("Dock3 - Transform Units", size=(500,300))
d41 = Dock("Frame Difference ", size=(100,100))
d42 = Dock("Current Frame ", size=(100,100))
d51 = Dock("CU Depths", size=(200,100))
d52 = Dock("MVs X Component", size=(200,100))
d53 = Dock("MVs Y Component", size=(200,100))
area.addDock(d2, 'left') ## place d1 at left edge of dock area (it will fill the whole space since there are no other docks yet)
area.addDock(d1, 'bottom', d2) ## place d2 at right edge of dock area
area.addDock(d31, 'right')
area.addDock(d32, 'bottom', d31)
#area.addDock(d33, 'bottom', d32)
area.addDock(d41, 'right')
area.addDock(d51, 'bottom', d41)
area.addDock(d42, 'right', d41)
area.addDock(d52, 'right', d51)
area.addDock(d53, 'right', d52)
#==========================================
def dock_ImageItem(self, Dock):
#==========================================
pgGLWidget = pg.GraphicsLayoutWidget()
ViewBox = pgGLWidget.addViewBox(invertY = True)
#ViewBox.setBackgroundColor((255,255,255))
ViewBox.setAspectLocked(True)
pgImageItem = pg.ImageItem(border='w')
ViewBox.addItem(pgImageItem)
Dock.addWidget(pgGLWidget)
return pgImageItem
#==========================================
def dock_CurveItem(self, Dock, Title, LabelX, LabelY):
#==========================================
pgGWindow= pg.GraphicsLayoutWidget()
pgPlot = pgGWindow.addPlot(title=Title)
x =[0,0,0]
y = [0,0]
pgCurveItem = pg.PlotCurveItem(x, y, stepMode=True, fillLevel=0, brush=(0, 255, 0, 80))
pgPlot.addItem(pgCurveItem)
pgPlot.setLabel('bottom', LabelX)
pgPlot.setLabel('left', LabelY)
Dock.addWidget(pgGWindow)
return pgCurveItem
self.ImageItem_d2 = dock_ImageItem(self, d2)
self.ImageItem_d31 = dock_ImageItem(self, d31)
self.ImageItem_d32 = dock_ImageItem(self, d32)
self.ImageItem_d41 = dock_ImageItem(self, d41)
self.ImageItem_d42 = dock_ImageItem(self, d42)
self.CurveItem_d51 = dock_CurveItem(self, d51, "CU Depths", "CU Depth", "Number of Occurences")
self.CurveItem_d52 = dock_CurveItem(self, d52, "MVs X Component", "Magnitude", "Number of Occurences")
self.CurveItem_d53 = dock_CurveItem(self, d53, "MVs Y Component", "Magnitude", "Number of Occurences")
params = [
{'name': 'Basic settings', 'type': 'group', 'children':
[
{'name': 'QP', 'type': 'int', 'value': 30},
{'name': 'x265', 'type': 'bool', 'value': True},
{'name': 'Show CUs', 'type': 'bool', 'value': True},
{'name': 'Show PUs', 'type': 'bool', 'value': True},
{'name': 'Show Modes', 'type': 'bool', 'value': True},
]},
]
## Create tree of Parameter objects
p = Parameter.create(name='params', type='group', children=params, readonly=False, enabled=True)
t = ParameterTree()
t.setParameters(p, showTop=False)
t.setWindowTitle('pyqtgraph example: Parameter Tree')
self.p = p
d1.addWidget(t)
MyWorkThread = WorkThread(self)
MyWorkThread.start()
Description = readImg(ProjectDir + "/Various/Resources/Special/LMS_Demo.png")
Description = cv2.transpose(cv2.cvtColor(Description, cv2.COLOR_BGR2RGB))
self.ImageItem_d2.setImage(Description, autoDownsample=True, border=(255,255,255) )
class ProjectSettingsDialog(QtGui.QDialog):
path2key=dict()
def __init__(self, parent = None, savedstate=None):
global SETTINGS
super(ProjectSettingsDialog, self).__init__(parent)
self.setWindowTitle("Application Settings")
layout = QtGui.QVBoxLayout(self)
self.setLayout(layout)
if savedstate:
for key,val in savedstate.items():
if flattenned_settings_dict.get(key):
flattenned_settings_dict[key]['value'] = val
#self._settings.restoreState(savedstate)
self.initKeyParamMapping()
self._settings = Parameter.create(name='params', type='group', children=settings_params)
# Holds settings keys that have changed by the user when the
# dialog is closed. Used to update any needed gui values..
self._updated_settings={}
self._invalid_settings={}
self._settings.sigTreeStateChanged.connect(self.handleSettingChange)
self.initSettingsValues()
self._settings.param('Default Settings', 'Save As').sigActivated.connect(self.saveToFile)
self._settings.param('Default Settings', 'Load').sigActivated.connect(self.loadFromFile)
self.ptree = ParameterTree()
self.ptree.setParameters(self._settings, showTop=False)
self.ptree.setWindowTitle('MarkWrite Application Settings')
layout.addWidget(self.ptree)
# OK and Cancel buttons
self.buttons = QtGui.QDialogButtonBox(
QtGui.QDialogButtonBox.Ok | QtGui.QDialogButtonBox.Cancel,
QtCore.Qt.Horizontal, self)
layout.addWidget(self.buttons)
self.buttons.accepted.connect(self.accept)
self.buttons.rejected.connect(self.reject)
wscreen = QtGui.QDesktopWidget().screenGeometry()
if savedstate and savedstate.get(SETTINGS_DIALOG_SIZE_SETTING):
w, h = savedstate.get(SETTINGS_DIALOG_SIZE_SETTING)
self.resize(w, h)
SETTINGS[SETTINGS_DIALOG_SIZE_SETTING]=(w, h)
if savedstate.get(APP_WIN_SIZE_SETTING):
SETTINGS[APP_WIN_SIZE_SETTING]=savedstate.get(APP_WIN_SIZE_SETTING)
else:
if parent:
wscreen = QtGui.QDesktopWidget().screenGeometry(parent)
self.resize(min(500,int(wscreen.width()*.66)),min(700,int(wscreen.height()*.66)))
# center dialog on same screen as is being used by markwrite app.
qr = self.frameGeometry()
cp = wscreen.center()
qr.moveCenter(cp)
self.move(qr.topLeft())
def saveToFile(self):
from markwrite.gui.dialogs import fileSaveDlg, ErrorDialog
from markwrite import writePickle, current_settings_path
save_to_path=fileSaveDlg(
initFilePath=current_settings_path,
initFileName=u"markwrite_settings.pkl",
prompt=u"Save MarkWrite Settings",
allowed="Python Pickle file (*.pkl)",
parent=self)
if save_to_path:
import os
from markwrite import default_settings_file_name, current_settings_file_name
ff, fn = os.path.split(save_to_path)
if fn in [default_settings_file_name, current_settings_file_name]:
ErrorDialog.info_text = u"%s a is reserved file name." \
u" Save again using a different name."%(fn)
ErrorDialog().display()
else:
writePickle(ff, fn, SETTINGS)
def loadFromFile(self):
global settings
from markwrite.gui.dialogs import fileOpenDlg
from markwrite import appdirs as mwappdirs
from markwrite import readPickle, writePickle
from markwrite import current_settings_file_name, current_settings_path
if self.parent:
mws_file = fileOpenDlg(current_settings_path,
None, "Select MarkWrite Settings File",
"Python Pickle file (*.pkl)", False)
if mws_file:
import os
ff, fn = os.path.split(mws_file[0])
mw_setting = readPickle(ff, fn)
_ = ProjectSettingsDialog(savedstate=mw_setting)
self.parent().updateApplicationFromSettings(mw_setting, mw_setting)
writePickle(current_settings_path,current_settings_file_name, SETTINGS)
def initKeyParamMapping(self):
if len(self.path2key)==0:
def replaceGroupKeys(paramlist, parent_path=[]):
for i,p in enumerate(paramlist):
if isinstance(p,basestring):
pdict=flattenned_settings_dict[p]
paramlist[i]=pdict
self.path2key['.'.join(parent_path+[pdict['name'],])]=p
elif isinstance(p,dict):
replaceGroupKeys(p.get('children'),parent_path+[p.get('name'),])
replaceGroupKeys(settings_params)
def initSettingsValues(self, pgroup=None):
global SETTINGS
if pgroup is None:
pgroup = self._settings
for child in pgroup.children():
if child.hasChildren():
self.initSettingsValues(child)
else:
path = self._settings.childPath(child)
if path is not None:
childName = '.'.join(path)
else:
childName = child.name()
if self.path2key.has_key(childName):
SETTINGS[self.path2key[childName]]=child.value()
child.orgvalue = child.value()
## If anything changes in the tree
def handleSettingChange(self, param, changes):
global SETTINGS
for param, change, data in changes:
path = self._settings.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
if change == 'value':
setting_key = self.path2key[childName]
if setting_key.startswith('kbshortcut_'):
qks=QtGui.QKeySequence(data)
if (len(data)>0 and qks.isEmpty()) or qks.toString() in SETTINGS.values():
self._invalid_settings[setting_key]=param
continue
else:
data = u''+qks.toString()
SETTINGS[setting_key]=data
self._updated_settings[setting_key] = data
param.orgvalue=data
def resizeEvent(self, event):
global SETTINGS
w, h = self.size().width(), self.size().height()
SETTINGS[SETTINGS_DIALOG_SIZE_SETTING] = (w, h)
self._updated_settings[SETTINGS_DIALOG_SIZE_SETTING] = (w, h)
return super(QtGui.QDialog, self).resizeEvent(event)
@staticmethod
def getProjectSettings(parent = None, usersettings = None):
if usersettings is None:
usersettings=SETTINGS
dialog = ProjectSettingsDialog(parent, usersettings)
result = dialog.exec_()
for k, v in dialog._invalid_settings.items():
v.setValue(v.orgvalue)
dialog._invalid_settings.clear()
usersettings=dialog._settings.saveState()
return dialog._updated_settings,SETTINGS, usersettings, result == QtGui.QDialog.Accepted
class CrystalIndexing(object):
def __init__(self, parent = None):
self.parent = parent
## Dock: Indexing
self.dock = Dock("Indexing", size=(1, 1))
self.win = ParameterTree()
self.win.setWindowTitle('Indexing')
self.dock.addWidget(self.win)
self.winL = pg.LayoutWidget()
self.launchIndexBtn = QtGui.QPushButton('Launch indexing')
self.winL.addWidget(self.launchIndexBtn, row=0, col=0)
self.synchBtn = QtGui.QPushButton('Deploy CrystFEL geometry')
self.winL.addWidget(self.synchBtn, row=1, col=0)
self.dock.addWidget(self.winL)
self.index_grp = 'Crystal indexing'
self.index_on_str = 'Indexing on'
self.index_geom_str = 'CrystFEL geometry'
self.index_peakMethod_str = 'Peak method'
self.index_intRadius_str = 'Integration radii'
self.index_pdb_str = 'Unitcell'
self.index_method_str = 'Indexing method'
self.index_tolerance_str = 'Tolerance'
self.index_extra_str = 'Extra CrystFEL parameters'
self.index_condition_str = 'Index condition'
self.launch_grp = 'Batch'
self.outDir_str = 'Output directory'
self.runs_str = 'Runs(s)'
self.sample_str = 'Sample name'
self.tag_str = 'Tag'
self.queue_str = 'Queue'
self.chunkSize_str = 'Chunk size'
self.cpu_str = 'CPUs'
self.keepData_str = 'Keep CXI images'
self.noe_str = 'Number of events to process'
(self.psanaq_str,self.psnehq_str,self.psfehq_str,self.psnehprioq_str,self.psfehprioq_str,self.psnehhiprioq_str,self.psfehhiprioq_str,self.psdebugq_str) = \
('psanaq','psnehq','psfehq','psnehprioq','psfehprioq','psnehhiprioq','psfehhiprioq','psdebugq')
self.noQueue_str = 'N/A'
self.outDir = self.parent.psocakeDir
self.outDir_overridden = False
self.runs = ''
self.sample = 'crystal'
self.tag = ''
self.queue = self.psanaq_str
self.chunkSize = 500
self.cpu = 12
self.noe = -1
# Indexing
if self.parent.facility == self.parent.facilityLCLS:
self.showIndexedPeaks = False
self.indexedPeaks = None
self.hiddenCXI = '.temp.cxi'
self.hiddenCrystfelStream = '.temp.stream'
self.hiddenCrystfelList = '.temp.lst'
self.indexingOn = False
self.numIndexedPeaksFound = 0
self.geom = '.temp.geom'
self.peakMethod = 'cxi'
self.intRadius = '3,4,5'
self.pdb = ''
self.indexingMethod = 'mosflm,dirax'
self.tolerance = '5,5,5,1.5'
self.extra = ''
self.condition = ''
self.keepData = True
elif self.parent.facility == self.parent.facilityPAL:
self.showIndexedPeaks = False
self.indexedPeaks = None
self.hiddenCXI = '.temp.cxi'
self.hiddenCrystfelStream = '.temp.stream'
self.hiddenCrystfelList = '.temp.lst'
self.indexingOn = False
self.numIndexedPeaksFound = 0
self.geom = '.temp.geom'
self.peakMethod = 'cxi'
self.intRadius = '4,5,6'
self.pdb = ''
self.indexingMethod = 'mosflm,dirax'
self.tolerance = '5,5,5,1.5'
self.extra = ''
self.condition = ''
self.keepData = True
#######################
# Mandatory parameter #
#######################
if self.parent.facility == self.parent.facilityLCLS:
self.params = [
{'name': self.index_grp, 'type': 'group', 'children': [
{'name': self.index_on_str, 'type': 'bool', 'value': self.indexingOn, 'tip': "Turn on indexing"},
{'name': self.index_geom_str, 'type': 'str', 'value': self.geom, 'tip': "CrystFEL geometry file"},
#{'name': self.index_peakMethod_str, 'type': 'str', 'value': self.peakMethod, 'tip': "Turn on indexing"},
{'name': self.index_intRadius_str, 'type': 'str', 'value': self.intRadius, 'tip': "Integration radii"},
{'name': self.index_pdb_str, 'type': 'str', 'value': self.pdb, 'tip': "(Optional) CrystFEL unitcell file"},
{'name': self.index_method_str, 'type': 'str', 'value': self.indexingMethod, 'tip': "comma separated indexing methods"},
{'name': self.index_tolerance_str, 'type': 'str', 'value': self.tolerance,
'tip': "Indexing tolerance, default: 5,5,5,1.5"},
{'name': self.index_extra_str, 'type': 'str', 'value': self.extra,
'tip': "Other indexing parameters, comma separated (e.g. --multi,--no-check-peaks)"},
{'name': self.index_condition_str, 'type': 'str', 'value': self.condition,
'tip': "indexing condition e.g. 41 in #evr1# and #eventNumber# > 3"},
]},
{'name': self.launch_grp, 'type': 'group', 'children': [
{'name': self.outDir_str, 'type': 'str', 'value': self.outDir},
{'name': self.runs_str, 'type': 'str', 'value': self.runs, 'tip': "comma separated or use colon for a range, e.g. 1,3,5:7 = runs 1,3,5,6,7"},
{'name': self.sample_str, 'type': 'str', 'value': self.sample, 'tip': "name of the sample saved in the cxidb file, e.g. lysozyme"},
{'name': self.tag_str, 'type': 'str', 'value': self.tag, 'tip': "attach tag to stream, e.g. cxitut13_0010_tag.stream"},
{'name': self.queue_str, 'type': 'list', 'values': {self.psfehhiprioq_str: self.psfehhiprioq_str,
self.psnehhiprioq_str: self.psnehhiprioq_str,
self.psfehprioq_str: self.psfehprioq_str,
self.psnehprioq_str: self.psnehprioq_str,
self.psfehq_str: self.psfehq_str,
self.psnehq_str: self.psnehq_str,
self.psanaq_str: self.psanaq_str,
self.psdebugq_str: self.psdebugq_str},
'value': self.queue, 'tip': "Choose queue"},
{'name': self.chunkSize_str, 'type': 'int', 'value': self.chunkSize, 'tip': "number of patterns to process per worker"},
{'name': self.keepData_str, 'type': 'bool', 'value': self.keepData, 'tip': "Do not delete cxidb images in cxi file"},
]},
]
elif self.parent.facility == self.parent.facilityPAL:
self.params = [
{'name': self.index_grp, 'type': 'group', 'children': [
{'name': self.index_on_str, 'type': 'bool', 'value': self.indexingOn, 'tip': "Turn on indexing"},
{'name': self.index_geom_str, 'type': 'str', 'value': self.geom, 'tip': "CrystFEL geometry file"},
{'name': self.index_intRadius_str, 'type': 'str', 'value': self.intRadius, 'tip': "Integration radii"},
{'name': self.index_pdb_str, 'type': 'str', 'value': self.pdb, 'tip': "(Optional) CrystFEL unitcell file"},
{'name': self.index_method_str, 'type': 'str', 'value': self.indexingMethod, 'tip': "comma separated indexing methods"},
{'name': self.index_tolerance_str, 'type': 'str', 'value': self.tolerance,
'tip': "Indexing tolerance, default: 5,5,5,1.5"},
{'name': self.index_extra_str, 'type': 'str', 'value': self.extra,
'tip': "Other CrystFEL indexing parameters"},
]},
{'name': self.launch_grp, 'type': 'group', 'children': [
{'name': self.outDir_str, 'type': 'str', 'value': self.outDir},
{'name': self.runs_str, 'type': 'str', 'value': self.runs, 'tip': "comma separated or use colon for a range, e.g. 1,3,5:7 = runs 1,3,5,6,7"},
{'name': self.sample_str, 'type': 'str', 'value': self.sample, 'tip': "name of the sample saved in the cxidb file, e.g. lysozyme"},
{'name': self.tag_str, 'type': 'str', 'value': self.tag, 'tip': "attach tag to stream, e.g. cxitut13_0010_tag.stream"},
{'name': self.queue_str, 'type': 'list', 'values': {self.noQueue_str: self.noQueue_str},
'value': self.queue, 'tip': "Choose queue"},
{'name': self.cpu_str, 'type': 'int', 'value': self.cpu, 'tip': "number of cores to use for indexing per run"},
{'name': self.keepData_str, 'type': 'bool', 'value': self.keepData, 'tip': "Do not delete cxidb images in cxi file"},
]},
]
self.p9 = Parameter.create(name='paramsCrystalIndexing', type='group', \
children=self.params, expanded=True)
self.win.setParameters(self.p9, showTop=False)
self.p9.sigTreeStateChanged.connect(self.change)
if using_pyqt4:
self.parent.connect(self.launchIndexBtn, QtCore.SIGNAL("clicked()"), self.indexPeaks)
self.parent.connect(self.synchBtn, QtCore.SIGNAL("clicked()"), self.syncGeom)
else:
self.launchIndexBtn.clicked.connect(self.indexPeaks)
self.synchBtn.clicked.connect(self.syncGeom)
# Launch indexing
def indexPeaks(self):
self.parent.thread.append(LaunchIndexer.LaunchIndexer(self.parent)) # send parent parameters with self
self.parent.thread[self.parent.threadCounter].launch(self.parent.experimentName, self.parent.detInfo)
self.parent.threadCounter += 1
# Update psana geometry
def syncGeom(self):
if self.parent.facility == self.parent.facilityLCLS:
with pg.BusyCursor():
print "#################################################"
print "Updating psana geometry with CrystFEL geometry"
print "#################################################"
self.parent.geom.findPsanaGeometry()
psanaGeom = self.parent.psocakeRunDir + "/.temp.data"
if self.parent.args.localCalib:
cmd = ["crystfel2psana",
"-e", self.parent.experimentName,
"-r", str(self.parent.runNumber),
"-d", str(self.parent.det.name),
"--rootDir", '.',
"-c", self.geom,
"-p", psanaGeom,
"-z", str(self.parent.clen)]
else:
cmd = ["crystfel2psana",
"-e", self.parent.experimentName,
"-r", str(self.parent.runNumber),
"-d", str(self.parent.det.name),
"--rootDir", self.parent.rootDir,
"-c", self.geom,
"-p", psanaGeom,
"-z", str(self.parent.clen)]
if self.parent.args.v >= 0: print "cmd: ", cmd
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
output = p.communicate()[0]
p.stdout.close()
# Reload new psana geometry
cmts = {'exp': self.parent.experimentName, 'app': 'psocake', 'comment': 'converted from crystfel geometry'}
if self.parent.args.localCalib:
calibDir = './calib'
elif self.parent.args.outDir is None:
calibDir = self.parent.rootDir + '/calib'
else:
calibDir = self.parent.dir + self.parent.experimentName[:3] + '/' + self.parent.experimentName + '/calib'
deploy_calib_file(cdir=calibDir, src=str(self.parent.det.name), type='geometry',
run_start=self.parent.runNumber, run_end=None, ifname=psanaGeom, dcmts=cmts, pbits=0)
self.parent.exp.setupExperiment()
self.parent.img.getDetImage(self.parent.eventNumber)
self.parent.geom.updateRings()
self.parent.index.updateIndex()
self.parent.geom.drawCentre()
# Show mask
self.parent.mk.updatePsanaMaskOn()
elif self.parent.facility == self.parent.facilityPAL:
print "deploy crystfel geom is not implemented for PAL"
# If anything changes in the parameter tree, print a message
def change(self, panel, changes):
for param, change, data in changes:
path = panel.childPath(param)
if self.parent.args.v >= 1:
print(' path: %s' % path)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
self.paramUpdate(path, change, data)
##############################
# Mandatory parameter update #
##############################
def paramUpdate(self, path, change, data):
if path[1] == self.index_on_str:
self.updateIndexStatus(data)
elif path[1] == self.index_geom_str:
self.updateGeom(data)
elif path[1] == self.index_peakMethod_str:
self.updatePeakMethod(data)
elif path[1] == self.index_intRadius_str:
self.updateIntegrationRadius(data)
elif path[1] == self.index_pdb_str:
self.updatePDB(data)
elif path[1] == self.index_method_str:
self.updateIndexingMethod(data)
elif path[1] == self.index_tolerance_str:
self.updateTolerance(data)
elif path[1] == self.index_extra_str:
self.updateExtra(data)
elif path[1] == self.index_condition_str:
self.updateCondition(data)
# launch grp
elif path[1] == self.outDir_str:
self.updateOutputDir(data)
elif path[1] == self.runs_str:
self.updateRuns(data)
elif path[1] == self.sample_str:
self.updateSample(data)
elif path[1] == self.tag_str:
self.updateTag(data)
elif path[1] == self.queue_str:
self.updateQueue(data)
elif path[1] == self.chunkSize_str:
self.updateChunkSize(data)
elif path[1] == self.cpu_str:
self.updateCpu(data)
elif path[1] == self.noe_str:
self.updateNoe(data)
elif path[1] == self.keepData_str:
self.keepData = data
def updateIndexStatus(self, data):
self.indexingOn = data
self.showIndexedPeaks = data
self.updateIndex()
def updateGeom(self, data):
self.geom = data
self.updateIndex()
def updatePeakMethod(self, data):
self.peakMethod = data
if self.indexingOn:
self.updateIndex()
def updateIntegrationRadius(self, data):
self.intRadius = data
self.updateIndex()
def updatePDB(self, data):
self.pdb = data
self.updateIndex()
def updateIndexingMethod(self, data):
self.indexingMethod = data
self.updateIndex()
def updateTolerance(self, data):
self.tolerance = data
self.updateIndex()
def updateExtra(self, data):
self.extra = data.replace(" ","")
self.updateIndex()
def updateCondition(self, data):
self.condition = data
self.updateIndex()
def updateIndex(self):
if self.indexingOn:
if self.parent.pk.peaks is None:
self.parent.index.clearIndexedPeaks()
else:
self.indexer = IndexHandler(parent=self.parent)
self.indexer.computeIndex(self.parent.experimentName, self.parent.runNumber, self.parent.detInfo,
self.parent.eventNumber, self.geom, self.peakMethod, self.intRadius, self.pdb,
self.indexingMethod, self.parent.pk.minPeaks, self.parent.pk.maxPeaks, self.parent.pk.minRes,
self.tolerance, self.extra, self.outDir, queue=None)
else:
# do not display predicted spots
self.parent.index.clearIndexedPeaks()
def updateOutputDir(self, data):
self.outDir = data
self.outDir_overridden = True
def updateRuns(self, data):
self.runs = data
def updateSample(self, data):
self.sample = data
def updateTag(self, data):
self.tag = data
def updateQueue(self, data):
self.queue = data
def updateChunkSize(self, data):
self.chunkSize = data
def updateCpu(self, data):
self.cpu = data
def updateNoe(self, data):
self.noe = data
def clearIndexedPeaks(self):
self.parent.img.win.getView().removeItem(self.parent.img.abc_text)
self.parent.img.indexedPeak_feature.setData([], [], pxMode=False)
if self.parent.args.v >= 1: print "Done clearIndexedPeaks"
def displayWaiting(self):
if self.showIndexedPeaks:
if self.numIndexedPeaksFound == 0: # indexing proceeding
xMargin = 5 # pixels
if self.parent.facility == self.parent.facilityLCLS:
maxX = np.max(self.parent.det.indexes_x(self.parent.evt)) + xMargin
maxY = np.max(self.parent.det.indexes_y(self.parent.evt))
elif self.parent.facility == self.parent.facilityPAL:
yMargin = 0 # pixels
(dim0, dim1) = self.parent.calib.shape
self.iy = np.tile(np.arange(dim0), [dim1, 1])
self.ix = np.transpose(self.iy)
maxX = np.max(self.ix) + xMargin
maxY = np.max(self.iy) - yMargin
# Draw a big X
cenX = np.array((self.parent.cx,)) + 0.5
cenY = np.array((self.parent.cy,)) + 0.5
diameter = 256 # self.peakRadius*2+1
self.parent.img.indexedPeak_feature.setData(cenX, cenY, symbol='t', \
size=diameter, brush=(255, 255, 255, 0), \
pen=pg.mkPen({'color': "#FF00FF", 'width': 3}),
pxMode=False)
self.parent.img.abc_text = pg.TextItem(html='', anchor=(0, 0))
self.parent.img.win.getView().addItem(self.parent.img.abc_text)
self.parent.img.abc_text.setPos(maxX, maxY)
def drawIndexedPeaks(self, latticeType=None, centering=None, unitCell=None):
self.clearIndexedPeaks()
if self.showIndexedPeaks:
if self.indexedPeaks is not None and self.numIndexedPeaksFound > 0: # indexing succeeded
cenX = self.indexedPeaks[:,0]+0.5
cenY = self.indexedPeaks[:,1]+0.5
cenX = np.concatenate((cenX,cenX,cenX))
cenY = np.concatenate((cenY,cenY,cenY))
diameter = np.ones_like(cenX)
diameter[0:self.numIndexedPeaksFound] = float(self.intRadius.split(',')[0])*2
diameter[self.numIndexedPeaksFound:2*self.numIndexedPeaksFound] = float(self.intRadius.split(',')[1])*2
diameter[2*self.numIndexedPeaksFound:3*self.numIndexedPeaksFound] = float(self.intRadius.split(',')[2])*2
self.parent.img.indexedPeak_feature.setData(cenX, cenY, symbol='o', \
size=diameter, brush=(255,255,255,0), \
pen=pg.mkPen({'color': "#FF00FF", 'width': 1.5}), pxMode=False)
# Write unit cell parameters
if unitCell is not None:
xMargin = 5
yMargin = 400
if self.parent.facility == self.parent.facilityLCLS:
maxX = np.max(self.parent.det.indexes_x(self.parent.evt)) + xMargin
maxY = np.max(self.parent.det.indexes_y(self.parent.evt)) - yMargin
elif self.parent.facility == self.parent.facilityPAL:
(dim0, dim1) = self.parent.calib.shape
self.iy = np.tile(np.arange(dim0), [dim1, 1])
self.ix = np.transpose(self.iy)
maxX = np.max(self.ix) + xMargin
maxY = np.max(self.iy) - yMargin
#myMessage = '<div style="text-align: center"><span style="color: #FF00FF; font-size: 12pt;">lattice='+\
# str(latticeType) +'<br>centering=' + str(centering) + '<br>a='+\
# str(round(float(unitCell[0])*10,2))+'A <br>b='+str(round(float(unitCell[1])*10,2))+'A <br>c='+\
# str(round(float(unitCell[2])*10,2))+'A <br>α='+str(round(float(unitCell[3]),2))+\
# '° <br>β='+str(round(float(unitCell[4]),2))+'° <br>γ='+\
# str(round(float(unitCell[5]),2))+'° <br></span></div>'
myMessage = '<div style="text-align: center"><span style="color: #FF00FF; font-size: 12pt;">lattice='+\
str(latticeType) +'<br>centering=' + str(centering) + '<br></span></div>'
self.parent.img.abc_text = pg.TextItem(html=myMessage, anchor=(0,0))
self.parent.img.win.getView().addItem(self.parent.img.abc_text)
self.parent.img.abc_text.setPos(maxX, maxY)
else: # Failed indexing
#xMargin = 5 # pixels
#if self.parent.facility == self.parent.facilityLCLS:
# maxX = np.max(self.parent.det.indexes_x(self.parent.evt))+xMargin
# maxY = np.max(self.parent.det.indexes_y(self.parent.evt))
#elif self.parent.facility == self.parent.facilityPAL:
# yMargin = 0 # pixels
# (dim0, dim1) = self.parent.calib.shape
# self.iy = np.tile(np.arange(dim0), [dim1, 1])
# self.ix = np.transpose(self.iy)
# maxX = np.max(self.ix) + xMargin
# maxY = np.max(self.iy) - yMargin
# Draw a big X
cenX = np.array((self.parent.cx,))+0.5
cenY = np.array((self.parent.cy,))+0.5
diameter = 256 #self.peakRadius*2+1
self.parent.img.indexedPeak_feature.setData(cenX, cenY, symbol='x', \
size=diameter, brush=(255,255,255,0), \
pen=pg.mkPen({'color': "#FF00FF", 'width': 3}), pxMode=False)
self.parent.img.abc_text = pg.TextItem(html='', anchor=(0,0))
self.parent.img.win.getView().addItem(self.parent.img.abc_text)
self.parent.img.abc_text.setPos(0,0)
else:
self.parent.img.indexedPeak_feature.setData([], [], pxMode=False)
self.parent.img.abc_text = pg.TextItem(html='', anchor=(0, 0))
self.parent.img.win.getView().addItem(self.parent.img.abc_text)
self.parent.img.abc_text.setPos(0, 0)
if self.parent.args.v >= 1: print "Done drawIndexedPeaks"
# This function probably doesn't get called
def launchIndexing(self, requestRun=None):
self.batchIndexer = IndexHandler(parent=self.parent)
if requestRun is None:
self.batchIndexer.computeIndex(self.parent.experimentName, self.parent.runNumber, self.parent.detInfo,
self.parent.eventNumber, self.geom, self.peakMethod, self.intRadius, self.pdb,
self.indexingMethod, self.parent.pk.minPeaks, self.parent.pk.maxPeaks, self.parent.pk.minRes,
self.tolerance, self.extra, self.outDir, self.runs, self.sample, self.tag, self.queue, self.chunkSize, self.noe)
else:
self.batchIndexer.computeIndex(self.parent.experimentName, requestRun, self.parent.detInfo,
self.parent.eventNumber, self.geom, self.peakMethod, self.intRadius, self.pdb,
self.indexingMethod, self.parent.pk.minPeaks, self.parent.pk.maxPeaks, self.parent.pk.minRes,
self.tolerance, self.extra, self.outDir, self.runs, self.sample, self.tag, self.queue, self.chunkSize, self.noe)
if self.parent.args.v >= 1: print "Done updateIndex"
class JsonReader(QWidget):
""" """
def __init__(self):
super().__init__()
self.title = "Json metadata reader"
self.left = 100
self.top = 100
self.width = 500
self.height = 500
self.initUI()
def initUI(self):
""" """
self.setWindowTitle(self.title)
self.setGeometry(self.left, self.top, self.width, self.height)
self.getbtn = QPushButton("Select file")
self.getbtn.clicked.connect(self.get_file)
self.draglbl = DragDropLabel(self)
self.draglbl.setText("... or drop .{} file here".format(
DragDropLabel.acceptedFormat.upper()))
self.draglbl.setAlignment(QtCore.Qt.AlignCenter)
self.draglbl.droppedFile.connect(self.open_file)
self.layout = QGridLayout(self)
self.layout.addWidget(self.getbtn, 0, 0)
self.layout.addWidget(self.draglbl, 1, 0)
self.layout.setColumnMinimumWidth(0, 500)
self.setLayout(self.layout)
self.show()
def get_file(self):
""" """
self.path, _ = QFileDialog.getOpenFileName(
filter="Json files (*.json)")
if not self.path:
pass
else:
self.open_file(self.path)
def open_file(self, filename):
"""
Parameters
----------
filename :
Returns
-------
"""
self.filename = filename
with open(filename) as json_file:
self.metadata_dict = json.load(json_file)
self.display_tree_widget(self.metadata_dict)
def display_tree_widget(self, metadata):
"""Display the parameter tree from the experiment metadata.
Parameters
----------
metadata :
json metadata
Returns
-------
"""
# Close previous tree widget
self.close_tree()
# Create a variable checking whether changes have been made to the parameter tree values
self.has_changed = False
# Create list with parameters for the tree
self.parameters = self.create_parameters(self.fix_types(metadata))
# Add parameters for Save buttons and Image options
self.parameters.append({
"name":
"Metadata Image Options",
"type":
"group",
"children": [
{
"name": "Append Image",
"type": "action"
},
{
"name": "View Image",
"type": "action"
},
],
})
self.parameters.append({
"name":
"Save/Reset metadata",
"type":
"group",
"children": [
{
"name": "Save changes",
"type": "action"
},
{
"name": "Reset changes",
"type": "action"
},
],
})
# Create tree of Parameter objects
self.p = Parameter.create(name="params",
type="group",
children=self.parameters)
# Check if Image parameters already exist. If they don't,
# add them and update Parameter object
self.children_list = []
for child in self.p.children():
self.children_list.append(str(child).split("'")[1])
# Save original state
self.original_state = self.p.saveState()
# Connect Save/Reset buttons to respective functions
self.p.param("Save/Reset metadata",
"Save changes").sigActivated.connect(self.save_treevals)
self.p.param("Save/Reset metadata",
"Reset changes").sigActivated.connect(self.reset)
# Create ParameterTree widget
self.tree = ParameterTree()
self.tree.setParameters(self.p, showTop=False)
self.tree.setWindowTitle("pyqtgraph example: Parameter Tree")
# Display tree widget
self.layout.addWidget(self.tree, 2, 0)
# Send signal when any entry is changed
self.p.sigTreeStateChanged.connect(self.change)
def append_img(self):
"""Attach a .png image to the metadata file."""
self.imagefile, _ = QFileDialog.getOpenFileName(
filter="png images (*.png)")
if not self.imagefile:
pass
else:
with open(self.imagefile, "rb") as f:
self.img = f.read()
self.encoded_img = base64.b64encode(self.img)
self.encoded_img = self.encoded_img.decode("utf8")
self.p.param("Metadata Image").setValue(self.encoded_img)
self.p.param("Metadata Image").setDefault(self.encoded_img)
def display_img(self):
"""Show image appended to the metadata file"""
try:
self.layout.removeWidget(self.imglbl)
self.imglbl.deleteLater()
self.imglbl = None
except AttributeError:
pass
if not self.p.param("Metadata Image").defaultValue():
self.imglbl = QLabel("No image associated to this metadata")
self.layout.addWidget(self.imglbl, 2, 1)
try:
self.layout.removeWidget(self.viewbtn)
self.viewbtn.deleteLater()
self.viewbtn = None
except AttributeError:
pass
else:
self.figstring = self.p.param("Metadata Image").defaultValue()
self.figbytes = self.figstring.encode("utf8")
self.figbytes = base64.b64decode(self.figbytes)
self.viewbtn = QPushButton("Zoom image")
self.viewbtn.clicked.connect(self.image_viewer)
self.image = QtGui.QPixmap()
self.image.loadFromData(self.figbytes)
self.image = self.image.scaledToHeight(500)
self.imglbl = QLabel()
self.imglbl.setPixmap(self.image)
self.layout.addWidget(self.imglbl, 0, 1, 3, 1)
self.layout.addWidget(self.viewbtn, 3, 1)
def image_viewer(self):
"""Open metadata image in the Image Viewer from PyQtGraph."""
self.win = QtGui.QMainWindow()
self.win.resize(800, 800)
self.fignp = np.array(Image.open(io.BytesIO(self.figbytes)))
self.fignp = np.swapaxes(self.fignp, 0, 1)
self.imv = pg.ImageView()
self.imv.setImage(self.fignp)
self.win.setCentralWidget(self.imv)
self.win.setWindowTitle("Metadata Image")
self.win.show()
def save_treevals(self):
"""Save current values of the parameter tree into a dictionary."""
# Recover data from tree and store it in a dict
self.treevals_dict = self.p.getValues()
self.metadata_dict_mod = self.get_mod_dict(self.treevals_dict)
# Nasty way to make new dict (with modified metadata) with same structure as the original one
self.metadata_dict_mod.pop("Save/Reset metadata")
self.metadata_dict_mod.pop("Metadata Image Options")
self.metadata_dict_mod["stimulus"]["log"] = self.metadata_dict[
"stimulus"]["log"]
self.metadata_dict_mod["stimulus"]["display_params"][
"pos"] = json.loads(
self.metadata_dict_mod["stimulus"]["display_params"]["pos"])
self.metadata_dict_mod["stimulus"]["display_params"][
"size"] = json.loads(
self.metadata_dict_mod["stimulus"]["display_params"]["size"])
self.show_warning()
def show_warning(self):
"""Upon saving, display a warning message
to choose whether to create a new metadata file or replace the existing one.
Parameters
----------
Returns
-------
"""
if self.has_changed:
self.msg = QMessageBox()
self.msg.setIcon(QMessageBox.Warning)
self.setWindowTitle("Saving Warning")
self.msg.setText("Some parameters have changed")
self.msg.setInformativeText(
"Do you want to overwrite the original .json metadata file?")
self.msg.addButton("Create new file", QMessageBox.AcceptRole)
self.msg.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
self.ret = self.msg.exec_()
if self.ret == QMessageBox.Yes:
self.overwrite_metadata_file(self.metadata_dict_mod)
elif self.ret == QMessageBox.AcceptRole:
self.create_metadata_file(self.metadata_dict_mod)
else:
pass
else:
self.msg2 = QMessageBox()
self.msg2.setIcon(QMessageBox.Information)
self.setWindowTitle("Saving Warning")
self.msg2.setText("No changes have been made.")
self.msg2.addButton("OK", QMessageBox.AcceptRole)
self.ret = self.msg2.exec_()
def overwrite_metadata_file(self, metadata_dict_mod):
"""
Parameters
----------
metadata_dict_mod :
Returns
-------
"""
# Overwritte original metadata file
with open(self.filename, "w") as file:
json.dump(metadata_dict_mod, file)
def create_metadata_file(self, metadata_dict_mod):
"""
Parameters
----------
metadata_dict_mod :
Returns
-------
"""
# Overwritte original metadata file
self.name, self.ext = self.filename.split(".")
with open("{}_modified.{}".format(self.name, self.ext), "w") as file:
json.dump(metadata_dict_mod, file)
def reset(self):
"""Reset parameter tree values to the original state after loading."""
self.p.restoreState(self.original_state, recursive=True)
self.tree.setParameters(self.p, showTop=False)
def fix_types(self, datadict):
"""Modify metadata dict so only accepted types are found.
Parameters
----------
datadict :
Returns
-------
"""
param_dict = dict()
for key, value in datadict.items():
if isinstance(value, list):
param_dict[key] = str(value)
elif isinstance(value, dict):
param_dict[key] = self.fix_types(value)
else:
param_dict[key] = value
return param_dict
def create_parameters(self, datadict):
"""Create list with parameters and Children to which the tree will be built from.
Parameters
----------
datadict :
Returns
-------
"""
parameters = []
for key, value in datadict.items():
if key == "log":
pass
else:
if isinstance(value, dict):
parameters.append({
"name":
"{}".format(key),
"type":
"group",
"children":
self.create_parameters(value),
})
else:
parameters.append({
"name": "{}".format(key),
"type": "{}".format(type(value).__name__),
"value": value,
})
return parameters
def get_mod_dict(self, treevals_dict):
"""Recursive function to convert into dict output of getValues function.
Parameters
----------
treevals_dict :
Returns
-------
"""
metadata_dict_mod = dict()
for key, value in treevals_dict.items():
if value[0] is None:
metadata_dict_mod[key] = dict(self.get_mod_dict(value[1]))
else:
metadata_dict_mod[key] = value[0]
return metadata_dict_mod
def change(self, param, changes):
"""
Parameters
----------
param :
changes :
Returns
-------
"""
print("tree changes:")
for param, change, data in changes:
path = self.p.childPath(param)
if path is not None:
childName = ".".join(path)
else:
childName = param.name()
print(" parameter: %s" % childName)
print(" change: %s" % change)
print(" data: %s" % str(data))
print(" ----------")
if change == "activated":
pass
else:
self.has_changed = True
def close_tree(self):
""" """
try:
self.layout.removeWidget(self.tree)
self.tree.deleteLater()
self.tree = None
except AttributeError:
pass
class MainWindow(Qt.QWidget):
''' Main Window '''
def __init__(self):
super(MainWindow, self).__init__()
layout = Qt.QVBoxLayout(self)
self.btnGen = Qt.QPushButton("Start Gen!")
layout.addWidget(self.btnGen)
self.SaveStateParams = FileMod.SaveSateParameters(self, name='State')
self.Parameters = Parameter.create(name='params',
type='group',
children=(self.SaveStateParams, ))
self.DataGenParams = SampGen.DataGeneratorParameters(
name='Data Generator')
self.DataGenParams.param('Col0').param('Freq').setValue(75e3)
self.DataGenParams.param('Col1').param('Freq').setValue(100e3)
self.DataGenParams.param('Col2').param('Freq').setValue(125e3)
self.DataGenParams.param('Col3').param('Freq').setValue(150e3)
self.DataGenParams.param('Col0').param('Fsig').setValue(1e3)
self.DataGenParams.param('Col1').param('Fsig').setValue(800)
self.DataGenParams.param('Col2').param('Fsig').setValue(250)
self.DataGenParams.param('Col3').param('Fsig').setValue(10)
self.Parameters.addChild(self.DataGenParams)
self.FileParameters = FileMod.SaveFileParameters(QTparent=self,
name='Record File')
self.Parameters.addChild(self.FileParameters)
self.PSDParams = PltMod.PSDParameters(name='PSD Options')
self.PSDParams.param('Fs').setValue(
self.DataGenParams.param('Fs').value())
self.PSDParams.param('Fmin').setValue(50)
self.PSDParams.param('nAvg').setValue(50)
self.Parameters.addChild(self.PSDParams)
self.PlotParams = PltMod.PlotterParameters(name='Plot options')
self.PlotParams.SetChannels(self.DataGenParams.GetChannels())
self.PlotParams.param('Fs').setValue(
self.DataGenParams.param('Fs').value())
self.Parameters.addChild(self.PlotParams)
self.Parameters.sigTreeStateChanged.connect(self.on_pars_changed)
self.treepar = ParameterTree()
self.treepar.setParameters(self.Parameters, showTop=False)
self.treepar.setWindowTitle('pyqtgraph example: Parameter Tree')
layout.addWidget(self.treepar)
self.setGeometry(550, 10, 300, 700)
self.setWindowTitle('MainWindow')
self.btnGen.clicked.connect(self.on_btnGen)
self.threadGen = None
self.threadSave = None
self.threadPlotter = None
def on_pars_changed(self, param, changes):
print("tree changes:")
for param, change, data in changes:
path = self.Parameters.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
print(' parameter: %s' % childName)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
if childName == 'Data Generator.nChannels':
self.PlotParams.SetChannels(self.DataGenParams.GetChannels())
if childName == 'Data Generator.Fs':
self.PlotParams.param('Fs').setValue(data)
self.PSDParams.param('Fs').setValue(data)
if childName == 'Plot options.RefreshTime':
if self.threadPlotter is not None:
self.threadPlotter.SetRefreshTime(data)
if childName == 'Plot options.ViewTime':
if self.threadPlotter is not None:
self.threadPlotter.SetViewTime(data)
def on_btnGen(self):
if self.threadGen is None:
GenKwargs = self.DataGenParams.GetParams()
self.threadGen = SampGen.DataSamplingThread(**GenKwargs)
self.threadGen.NewSample.connect(self.on_NewSample)
self.threadGen.start()
FileName = self.FileParameters.param('File Path').value()
if FileName == '':
print('No file')
else:
if os.path.isfile(FileName):
print('Remove File')
os.remove(FileName)
MaxSize = self.FileParameters.param('MaxSize').value()
self.threadSave = FileMod.DataSavingThread(
FileName=FileName,
nChannels=GenKwargs['Rows'],
MaxSize=MaxSize)
self.threadSave.start()
PlotterKwargs = self.PlotParams.GetParams()
print(PlotterKwargs)
self.threadPlotter = PltMod.Plotter(**PlotterKwargs)
self.threadPlotter.start()
self.threadPSDPlotter = PltMod.PSDPlotter(
ChannelConf=PlotterKwargs['ChannelConf'],
nChannels=GenKwargs['Rows'],
**self.PSDParams.GetParams())
self.threadPSDPlotter.start()
self.btnGen.setText("Stop Gen")
self.OldTime = time.time()
self.Tss = []
else:
self.threadGen.NewSample.disconnect()
self.threadGen.terminate()
self.threadGen = None
if self.threadSave is not None:
self.threadSave.terminate()
self.threadSave = None
self.threadPlotter.terminate()
self.threadPlotter = None
self.btnGen.setText("Start Gen")
def on_NewSample(self):
''' Visualization of streaming data-WorkThread. '''
Ts = time.time() - self.OldTime
self.Tss.append(Ts)
self.OldTime = time.time()
if self.threadSave is not None:
self.threadSave.AddData(self.threadGen.OutData)
self.threadPlotter.AddData(self.threadGen.OutData)
self.threadPSDPlotter.AddData(self.threadGen.OutData)
print('Sample time', Ts, np.mean(self.Tss))
class GuiManager(QtGui.QMainWindow):
def __init__(self):
super(GuiManager, self).__init__()
self.createLayout()
def closeEvent(self, event):
print 'User asked to close the app'
self.stopAcquisition()
Parameters.isAppKilled = True
#time.sleep(0.1) #Wait for the worker death
event.accept() # let the window close
def startAcquisition(self):
if Parameters.isConnected == False:
return
Parameters.isSaving = Parameters.paramObject.child("Saving parameters", "saveResults").value()
if Parameters.isSaving == True:
theDate = datetime.datetime.today() .strftime('%Y%m%d')
theTime = datetime.datetime.today() .strftime('%H%M%S')
theName=Parameters.paramObject.child("Saving parameters", "Experiment name").value()
#Check counter increment
folderParent = 'C:/InterferometryResults/' + theDate
counter = 1
folderFound = False
theFolder = folderParent + '/' + theName + '_' + str(counter).zfill(3)
if not os.path.exists(folderParent): #Make sure parent exist
os.makedirs(folderParent)
while folderFound == False and counter < 1000: #Loop until folder is found
if not os.path.exists(theFolder): #Make sure parent exist
os.makedirs(theFolder)
folderFound = True
else:
counter = counter + 1
theFolder = folderParent + '/' + theName + '_' + str(counter).zfill(3)
if counter < 1000:
Parameters.savingFolder = theFolder
if not os.path.exists(theFolder):
os.makedirs(theFolder)
else:
Parameters.isSaving = False; #Should not happen.
self.btStart.setEnabled(False)
self.btStop.setEnabled(True)
self.btOpen.setEnabled(False)
#Get the parameter values
Parameters.nSamples=Parameters.paramObject.child("Acquisition Parameters", "Number of samples to acquire").value()
acqMode=Parameters.paramObject.child("Trigger Options", "Acquisition mode").value()
triggerAmplitude=Parameters.paramObject.child("Trigger Options", "Trigger amplitude").value()
motorSpeed=Parameters.paramObject.child("Acquisition Parameters", "Rotation speed (%)").value()+28 #28 is calibration
nBlocks=int(math.ceil(float(Parameters.nSamples)/512)) #Must be a multiple of 512
Parameters.nSamples = nBlocks*512
Parameters.paramObject.child("Acquisition Parameters", "Number of samples to acquire").setValue(Parameters.nSamples)
#Set frequency in free mode. These settings could be optimized depending on the computer.
freq=2500000 #10im/s
if Parameters.nSamples > 100352:
freq=5000000 #5im/s
if Parameters.nSamples > 300032:
freq=12500000 #2im/s
if Parameters.nSamples > 1000000:
freq=25000000 #1im/s
if Parameters.nSamples > 2000000:
freq=50000000 #0.5im/s
#Start the acquisition on the FPGA
data = []
data = array('i')
data.append(1)
data.append(freq)
data.append(2)
data.append(acqMode)
data.append(3)
data.append(nBlocks)
data.append(4)
data.append(motorSpeed)
data.append(5)
data.append(triggerAmplitude)
data.append(6)
data.append(0)
theBytes = struct.pack('i' * len(data), *data)
buf = bytearray(theBytes)
Parameters.dev.WriteToPipeIn(128, buf)
Parameters.dev.SetWireInValue(0, 1+2+8, 1+2+8);Parameters.dev.UpdateWireIns() #Enable DDR2 reading and writing and activate memory.
time.sleep(0.1); #Wait to make sure everything is ready. TODO: Reduce this.
Parameters.dev.SetWireInValue(0, 4, 4);Parameters.dev.UpdateWireIns() #Start acquisition clock.
#self.plotTr.enableAutoRange('xy', True) ## stop auto-scaling after the first data set is plotted
Parameters.theQueue = Queue.Queue() #Create the queue
#self.DisplayUpdater(0)
self.workThread.start(); #Start the display worker
def stopAcquisition(self):
print 'Stopping...'
if hasattr(self,'tDisplay'):
self.tDisplay.cancel()
self.workThread.exitWorker();
while self.workThread.isRunning == True:
time.sleep(0.01) #Wait for the worker death, before resetting the board
Parameters.dev.SetWireInValue(0, 0, 1+2+4+8);Parameters.dev.UpdateWireIns() #Reset board.
#Save format: Results / YYMMDD / ExperimentName_Counter. Could also use the time.
if Parameters.isSaving == True:
#global state
state = Parameters.paramObject.saveState()
file = open(Parameters.savingFolder + '\Parameters.txt', 'w')
pickle.dump(state, file)
file.close()
print 'Stopped.'
self.btStart.setEnabled(True)
self.btStop.setEnabled(False)
self.btOpen.setEnabled(True)
'''
def DisplayUpdater(self,dummy):
if Parameters.isAppKilled == True:
return;
if Parameters.theQueue.empty():
print 'no data...'
while not Parameters.theQueue.empty(): #Empty the display queue
data = Parameters.theQueue.get()
#print 'data available!'
if 'data' in locals():
#print 'display data' + str(data[2])
self.setDataCurveTr(data)
tDisplay = Timer(2, self.DisplayUpdater, [0],{})
tDisplay.start()
'''
def motorSpeedChanged(self,value):
newSpeed=Parameters.paramObject.child("Acquisition Parameters", "Rotation speed (%)").value()
newSpeed=newSpeed+28 #Calibration
#Debug
#Parameters.paramObject.child("Acquisition Parameters", "Rotation speed (%)").setOpts(enabled=False)
#Parameters.paramObject.child("Acquisition Parameters", "Rotation speed (%)").setOpts(visible=False)
#Parameters.paramObject.child("Acquisition Parameters", "Rotation speed (%)").setOpts(value=200)
data = []
data = array('i')
data.append(4)
data.append(newSpeed)
data.append(0) #Minimum size is 8 'int'
data.append(0)
data.append(0)
data.append(0)
data.append(0)
data.append(0)
theBytes = struct.pack('i' * len(data), *data)
Parameters.bufferToDev = bytearray(theBytes)
Parameters.bufferToDevReady = True
def triggerChanged(self,value):
acqMode=Parameters.paramObject.child("Trigger Options", "Acquisition mode").value()
triggerAmplitude=Parameters.paramObject.child("Trigger Options", "Trigger amplitude").value()
data = []
data = array('i')
data.append(2)
data.append(acqMode)
data.append(5)
data.append(triggerAmplitude)
data.append(0)
data.append(0)
data.append(0)
data.append(0)
theBytes = struct.pack('i' * len(data), *data)
print str(theBytes)
Parameters.bufferToDev = bytearray(theBytes)
Parameters.bufferToDevReady = True
def triggerHalfSwitch(self):
Parameters.triggerToDev = True
def saveParam(self):
#global state
state = Parameters.paramObject.saveState()
file = open('dump.txt', 'w')
pickle.dump(state, file)
file.close()
def restoreParam(self):
#lobal state
file = open('dump.txt', 'r')
state = pickle.load(file)
#add = Parameters.paramObject['Save/Restore functionality', 'Restore State', 'Add missing items']
#rem = Parameters.paramObject['Save/Restore functionality', 'Restore State', 'Remove extra items']
Parameters.paramObject.restoreState(state, addChildren=False, removeChildren=False)
#Set the status text (system connected or not)
def setStatus(self, isConnected, isError = False):
def dotChange(item, nDots): #Timer function to display a varying number of dots after "retrying"
if Parameters.isConnected == True:
return;
if Parameters.isAppKilled == True:
return;
textNotConnected = "System not connected, retrying"
item.setText(textNotConnected+".")
#Number of dots varies from 1 to 5
if nDots == 1:
textDots = "."
nDots = 2
elif nDots == 2:
textDots = ".."
nDots = 3
elif nDots == 3:
textDots = "..."
nDots = 4
elif nDots == 4:
textDots = "...."
nDots = 5
else:
textDots = "....."
nDots = 1
item.setForeground(QtGui.QColor("red"))
item.setText(textNotConnected+textDots)
self.timerDotChange = Timer(0.25, dotChange, [self.itemStatus, nDots])
self.timerDotChange.start()
if (isError == True): #System not connected
print "Error"
if hasattr(self,'timerDotChange'):
self.timerDotChange.cancel()
time.sleep(0.5)
self.itemStatus.setForeground(QtGui.QColor("red"))
self.itemStatus.setText("Error with system. Please restart the application and the system.")
elif (isConnected == False): #System not connected
nDots = 1
if hasattr(self,'timerDotChange'):
self.timerDotChange.cancel()
self.timerDotChange = Timer(0.25, dotChange, [self.itemStatus, nDots])
self.timerDotChange.start()
else:
print "Connected"
if hasattr(self,'timerDotChange'):
self.timerDotChange.cancel()
time.sleep(0.1)
self.itemStatus.setForeground(QtGui.QColor("green"))
self.itemStatus.setText("System connected.")
print "Connected2"
#Set the status text (system connected or not)
def setCameraStatus(self, isConnected):
def dotChange(item, nDots): #Timer function to display a varying number of dots after "retrying"
if Parameters.isCameraConnected == True:
return;
if Parameters.isAppKilled == True:
return;
textNotConnected = "Camera not connected, retrying"
item.setText(textNotConnected+".")
#Number of dots varies from 1 to 5
if nDots == 1:
textDots = "."
nDots = 2
elif nDots == 2:
textDots = ".."
nDots = 3
elif nDots == 3:
textDots = "..."
nDots = 4
elif nDots == 4:
textDots = "...."
nDots = 5
else:
textDots = "....."
nDots = 1
item.setForeground(QtGui.QColor("red"))
item.setText(textNotConnected+textDots)
self.timerDotChangeCamera = Timer(0.25, dotChange, [self.itemCameraStatus, nDots])
self.timerDotChangeCamera.start()
if (isConnected == False): #System not connected
print 'cam oups'
nDots = 1
if hasattr(self,'timerDotChangeCamera'):
self.timerDotChangeCamera.cancel()
self.timerDotChangeCamera = Timer(0.25, dotChange, [self.itemCameraStatus, nDots])
self.timerDotChangeCamera.start()
else:
print "Camera connected"
if hasattr(self,'timerDotChangeCamera'):
self.timerDotChangeCamera.cancel()
time.sleep(0.1)
self.itemCameraStatus.setForeground(QtGui.QColor("green"))
self.itemCameraStatus.setText("Camera connected.")
print "Camera connected2"
#Set the status text (system connected or not)
def setInfo(self, text):
self.tbInfo.append(text)
#Set the status text (system connected or not)
def setWire(self, mem1, mem2, mem3, mem4, maxValPos):
self.itemMemory.setText("Acquisition board memory usage:\nDDR2: " + str(mem1) + " bytes.\nFIFO in: " + str(mem2) + " bytes.\nFIFO out: " + str(mem3) + " bytes.\nFIFO out (minimum): " + str(mem4) + " bytes.")
self.itemMaxValPos.setText("Maximum RF value position: " + str(maxValPos))
def createLayout(self):
print 'Creating layout...'
self.setWindowTitle('Interferometry Acquisition GUI')
#self.widget = QtGui.QWidget()
#self.setCentralWidget(self.widget)
self.layout = pg.LayoutWidget()
#self.widget.setLayout(self.layout)
self.setCentralWidget(self.layout)
#Create GUI
sizePolicyBt = QtGui.QSizePolicy(1, 1)
sizePolicyBt.setHorizontalStretch(0)
sizePolicyBt.setVerticalStretch(0)
self.btOpen = QtGui.QPushButton("Open\nprevious results")
sizePolicyBt.setHeightForWidth(self.btOpen.sizePolicy().hasHeightForWidth())
self.btOpen.setSizePolicy(sizePolicyBt);
self.btOpen.setStyleSheet("background-color: yellow; font-size: 16px; font: bold")
self.btStart = QtGui.QPushButton("Start\nacquisition")
sizePolicyBt.setHeightForWidth(self.btStart.sizePolicy().hasHeightForWidth())
self.btStart.setSizePolicy(sizePolicyBt);
self.btStart.setStyleSheet("background-color: green; font-size: 16px; font: bold")
self.btStart.clicked.connect(self.startAcquisition)
self.btStop = QtGui.QPushButton("Stop\nacquisition")
sizePolicyBt.setHeightForWidth(self.btStop.sizePolicy().hasHeightForWidth())
self.btStop.setSizePolicy(sizePolicyBt);
self.btStop.setStyleSheet("background-color: red; font-size: 16px; font: bold")
self.btStop.clicked.connect(self.stopAcquisition)
self.btStop.setEnabled(False)
self.paramTree = ParameterTree()
self.paramTree.setParameters(Parameters.paramObject, showTop=False)
self.paramTree.setWindowTitle('pyqtgraph example: Parameter Tree')
self.paramTree.setMinimumWidth(350)
self.paramTree.setMaximumWidth(350)
sizePolicyPt = QtGui.QSizePolicy(1,1)
sizePolicyPt.setHorizontalStretch(QtGui.QSizePolicy.Fixed)
sizePolicyPt.setVerticalStretch(1)
self.paramTree.setSizePolicy(sizePolicyPt);
## Create random 2D data
data = np.random.normal(size=(512, 512)) + pg.gaussianFilter(np.random.normal(size=(512, 512)), (5, 5)) * 20 + 100
data = data[:,:,np.newaxis]
data = data.repeat(3,2)
self.plotTl = pg.GraphicsView()
self.plotTlImage = pg.ImageItem(data[:,:,:]) #parent=self.plotTl
self.plotTlViewBox = pg.ViewBox()
self.plotTl.setCentralWidget(self.plotTlViewBox)
self.plotTlViewBox.addItem(self.plotTlImage)
self.plotTr = pg.PlotWidget(title="Interferometry", labels={'left': 'Signal amplitude (A.U.)', 'bottom': 'Distance (mm)'})
#self.plotTlViewBox2.addItem(self.plotTr)
self.plotTrCurve = self.plotTr.plot(pen=(255,0,0),name='C1') #Red
self.plotTrCurve2 = self.plotTr.plot(pen=(0,255,0),name='C2') #Green
#self.plotTlViewBox2.enableAutoRange('xy', True) ## stop auto-scaling after the first data set is plotted
#self.plotTr.addLegend('Test')
self.plotTr.setYRange(-1000, 1000)
self.plotBl = pg.PlotWidget(title="Distance", labels={'left': 'Distance (mm)', 'bottom': 'Number of acquisitions'})
self.plotBlCurve = self.plotBl.plot(pen=(255,0,0),name='C1')
self.plotBl.enableAutoRange('xy', True) ## stop auto-scaling after the first data set is plotted
self.plotBl.setMaximumWidth(3500)
self.tbInfo = QtGui.QTextEdit()
self.tbInfo.setEnabled(False)
palette = self.tbInfo.palette()
palette.setColor(QtGui.QPalette.Base, QtGui.QColor("white")) #White background
self.tbInfo.setPalette(palette)
self.tbInfo.setTextColor(QtGui.QColor("black"))
self.tbInfo.insertPlainText("Useful information will appear here.")
#Create list view of multiple items
self.tbStatus = QtGui.QListView()
self.tbStatus.setEnabled(False)
palette = self.tbStatus.palette()
palette.setColor(QtGui.QPalette.Base, QtGui.QColor("white")) #White background
self.tbStatus.setPalette(palette)
itemModelStatus = QtGui.QStandardItemModel(self.tbStatus)
self.tbStatus.setModel(itemModelStatus)
#Add system status
self.itemStatus = QtGui.QStandardItem()
self.setStatus(False)
itemModelStatus.appendRow(self.itemStatus)
#Add camera status
self.itemCameraStatus = QtGui.QStandardItem()
self.setCameraStatus(False)
itemModelStatus.appendRow(self.itemCameraStatus)
#Add memory usage
self.itemMemory = QtGui.QStandardItem("Acquisition board memory usage: N/A")
self.itemMemory.setForeground(QtGui.QColor("black"))
itemModelStatus.appendRow(self.itemMemory)
#Add max value position
self.itemMaxValPos = QtGui.QStandardItem("Maximum RF value position: N/A")
self.itemMaxValPos.setForeground(QtGui.QColor("black"))
itemModelStatus.appendRow(self.itemMaxValPos)
#layout.addWidget(QtGui.QLabel("These are two views of the same data. They should always display the same values."), 0, 0, 1, 2)
self.layout.addWidget(self.btOpen, 9, 6, 1, 1)
self.layout.addWidget(self.btStart, 9, 7, 1, 1)
self.layout.addWidget(self.btStop, 9, 8, 1, 1)
self.layout.addWidget(self.paramTree, 0, 0, 10, 3)
self.layout.addWidget(self.plotTl, 0, 3, 5, 3)
self.layout.addWidget(self.plotTr, 0, 6, 5, 3)
self.layout.addWidget(self.plotBl, 5, 3, 5, 3)
self.layout.addWidget(self.tbInfo, 5, 6, 2, 3)
self.layout.addWidget(self.tbStatus, 7, 6, 2, 3)
self.layout.layout.setColumnStretch(3,1)
self.layout.layout.setColumnStretch(4,1)
self.layout.layout.setColumnStretch(5,1)
self.layout.layout.setColumnStretch(6,1)
self.layout.layout.setColumnStretch(7,1)
self.layout.layout.setColumnStretch(8,1)
self.show()
self.resize(1500,800)
self.move(100,100)
Parameters.paramObject.param('Save/Restore functionality', 'Save State').sigActivated.connect(self.saveParam)
Parameters.paramObject.param('Save/Restore functionality', 'Restore State').sigActivated.connect(self.restoreParam)
Parameters.paramObject.child("Acquisition Parameters", "Rotation speed (%)").sigValueChanged.connect(self.motorSpeedChanged)
Parameters.paramObject.child("Trigger Options", "Acquisition mode").sigValueChanged.connect(self.triggerChanged)
Parameters.paramObject.child("Trigger Options", "Trigger amplitude").sigValueChanged.connect(self.triggerChanged)
Parameters.paramObject.child("Trigger Options", "Trigger switch 1/2").sigActivated.connect(self.triggerHalfSwitch)
# adding by emitting signal in different thread
self.workThread = AcquisitionWorker()
self.workThread.updateDataCamera.connect(self.setDataCurveTl)
self.workThread.updateDataInterf.connect(self.setDataCurveTr)
self.workThread.updateDataDistance.connect(self.setDataCurveBl)
self.workThread.updateDataDistance2.connect(self.setDataCurveBl2)
self.workThread.updateWire.connect(self.setWire)
self.workThread.setStatus.connect(self.setStatus)
self.workThread.setInfo.connect(self.setInfo)
self.testCount = 0;
#Fill the plots with dummy data
self.data = np.random.normal(size=(10,1000))
self.plotTrXAxis = np.arange(1000) * (0.01)
self.plotBlXAxis = np.arange(1000) * (1)
self.plotTrCurve.setData(x=self.plotTrXAxis,y=self.data[2%10],name='C1')
self.plotTrCurve2.setData(x=self.plotTrXAxis,y=self.data[3%10],name='C2')
self.plotBlCurve.setData(x=self.plotBlXAxis,y=self.data[4%10],name='C1')
self.valueTest = 1
def setDataCurveTl(self, data):
self.dataImage1 = data
self.plotTlImage.setImage(data)
self.testCount = self.testCount + 1;
def setDataCurveTr(self, dataIn):
self.plotTrCurve.setData(dataIn[0:len(dataIn):2],name='C1')
self.plotTrCurve2.setData(dataIn[1:len(dataIn):2],name='C2')
def setDataCurveBl(self, dataIn):
self.plotBlCurve.setData(dataIn,name='C1')
def setDataCurveBl2(self, xIn, dataIn):
self.plotBlCurve.setData(x=xIn,y=dataIn,name='C1')
class DiffractionGeometry(object):
def __init__(self, parent = None):
self.parent = parent
#############################
## Dock 3: Diffraction geometry
#############################
self.d3 = Dock("Diffraction Geometry", size=(1, 1))
self.w3 = ParameterTree()
self.w3.setWindowTitle('Diffraction geometry')
self.d3.addWidget(self.w3)
self.w3a = pg.LayoutWidget()
self.deployGeomBtn = QtGui.QPushButton('Deploy manually centred geometry')
self.w3a.addWidget(self.deployGeomBtn, row=0, col=0)
self.deployAutoGeomBtn = QtGui.QPushButton('Deploy automatically centred geometry')
self.w3a.addWidget(self.deployAutoGeomBtn, row=1, col=0)
self.d3.addWidget(self.w3a)
self.resolutionRingList = np.array([100.,300.,500.,700.,900.,1100.])
self.resolutionText = []
self.hasUserDefinedResolution = False
self.geom_grp = 'Diffraction geometry'
self.geom_detectorDistance_str = 'Detector distance'
self.geom_clen_str = 'Home to Detector (clen)'
self.geom_coffset_str = 'Sample to Home (coffset)'
self.geom_photonEnergy_str = 'Photon energy'
self.geom_wavelength_str = "Wavelength"
self.geom_pixelSize_str = 'Pixel size'
self.geom_resolutionRings_str = 'Resolution rings'
self.geom_resolution_str = 'Resolution (pixels)'
self.geom_resolutionUnits_str = 'Units'
self.geom_unitA_crystal_str = 'Crystallography (Angstrom)'
self.geom_unitNm_crystal_str = 'Crystallography (Nanometre)'
self.geom_unitQ_crystal_str = 'Crystallography Reciprocal Space (q)'
self.geom_unitA_physics_str = 'Physics (Angstrom)'
self.geom_unitNm_physics_str = 'Physics (Nanometre)'
self.geom_unitQ_physics_str = 'Physics Reciprocal Space (q)'
self.geom_unitTwoTheta_str = 'Scattering Angle 2Theta'
(self.unitA_c,self.unitNm_c,self.unitQ_c,self.unitA_p,self.unitNm_p,self.unitQ_p,self.unitTwoTheta) = (0,1,2,3,4,5,6)
#######################
# Mandatory parameter #
#######################
self.params = [
{'name': self.geom_grp, 'type': 'group', 'children': [
{'name': self.geom_detectorDistance_str, 'type': 'float', 'value': 0.0, 'precision': 6, 'minVal': 0.0001, 'siFormat': (6,6), 'siPrefix': True, 'suffix': 'mm'},
{'name': self.geom_clen_str, 'type': 'float', 'value': 0.0, 'step': 1e-6, 'siPrefix': True,
'suffix': 'm', 'readonly': True},
{'name': self.geom_coffset_str, 'type': 'float', 'value': 0.0, 'step': 1e-6, 'siPrefix': True,
'suffix': 'm', 'readonly': True},
{'name': self.geom_photonEnergy_str, 'type': 'float', 'value': 0.0, 'step': 1e-6, 'siPrefix': True, 'suffix': 'eV'},
{'name': self.geom_wavelength_str, 'type': 'float', 'value': 0.0, 'step': 1e-6, 'siPrefix': True, 'suffix': 'm', 'readonly': True},
{'name': self.geom_pixelSize_str, 'type': 'float', 'value': 0.0, 'precision': 12, 'minVal': 1e-6, 'siPrefix': True, 'suffix': 'm'},
{'name': self.geom_resolutionRings_str, 'type': 'bool', 'value': False, 'tip': "Display resolution rings", 'children': [
{'name': self.geom_resolution_str, 'type': 'str', 'value': None},
{'name': self.geom_resolutionUnits_str, 'type': 'list', 'values': {self.geom_unitA_crystal_str: self.unitA_c,
self.geom_unitNm_crystal_str: self.unitNm_c,
self.geom_unitQ_crystal_str: self.unitQ_c,
self.geom_unitA_physics_str: self.unitA_p,
self.geom_unitNm_physics_str: self.unitNm_p,
self.geom_unitQ_physics_str: self.unitQ_p,
self.geom_unitTwoTheta_str: self.unitTwoTheta},
'value': self.unitA_c},
]},
]},
]
self.p1 = Parameter.create(name='paramsDiffractionGeometry', type='group', \
children=self.params, expanded=True)
self.p1.sigTreeStateChanged.connect(self.change)
self.w3.setParameters(self.p1, showTop=False)
self.deployGeomBtn.clicked.connect(self.deploy)
self.deployAutoGeomBtn.clicked.connect(self.autoDeploy)
# If anything changes in the parameter tree, print a message
def change(self, panel, changes):
for param, change, data in changes:
path = panel.childPath(param)
if self.parent.args.v >= 1:
print(' path: %s' % path)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
self.paramUpdate(path, change, data)
##############################
# Mandatory parameter update #
##############################
def paramUpdate(self, path, change, data):
if path[1] == self.geom_detectorDistance_str:
self.updateDetectorDistance(data)
elif path[1] == self.geom_clen_str:
pass
elif path[1] == self.geom_coffset_str:
pass
elif path[1] == self.geom_photonEnergy_str:
self.updatePhotonEnergy(data)
elif path[1] == self.geom_pixelSize_str:
self.updatePixelSize(data)
elif path[1] == self.geom_wavelength_str:
pass
elif path[1] == self.geom_resolutionRings_str and len(path) == 2:
self.updateResolutionRings(data)
elif path[2] == self.geom_resolution_str:
self.updateResolution(data)
elif path[2] == self.geom_resolutionUnits_str:
self.updateResolutionUnits(data)
def findPsanaGeometry(self):
try:
self.source = Detector.PyDetector.map_alias_to_source(self.parent.detInfo,
self.parent.exp.ds.env()) # 'DetInfo(CxiDs2.0:Cspad.0)'
self.calibSource = self.source.split('(')[-1].split(')')[0] # 'CxiDs2.0:Cspad.0'
self.detectorType = gu.det_type_from_source(self.source) # 1
self.calibGroup = gu.dic_det_type_to_calib_group[self.detectorType] # 'CsPad::CalibV1'
self.detectorName = gu.dic_det_type_to_name[self.detectorType].upper() # 'CSPAD'
if self.parent.args.localCalib:
self.calibPath = "./calib/" + self.calibGroup + "/" + self.calibSource + "/geometry"
else:
self.calibPath = "/reg/d/psdm/" + self.parent.experimentName[0:3] + \
"/" + self.parent.experimentName + "/calib/" + \
self.calibGroup + "/" + self.calibSource + "/geometry"
if self.parent.args.v >= 1: print "### calibPath: ", self.calibPath
# Determine which calib file to use
geometryFiles = os.listdir(self.calibPath)
if self.parent.args.v >= 1: print "geom: ", geometryFiles
self.calibFile = None
minDiff = -1e6
for fname in geometryFiles:
if fname.endswith('.data'):
endValid = False
startNum = int(fname.split('-')[0])
endNum = fname.split('-')[-1].split('.data')[0]
diff = startNum - self.parent.runNumber
# Make sure it's end number is valid too
if 'end' in endNum:
endValid = True
else:
try:
if self.parent.runNumber <= int(endNum):
endValid = True
except:
continue
if diff <= 0 and diff > minDiff and endValid is True:
minDiff = diff
self.calibFile = fname
except:
if self.parent.args.v >= 1: print "Couldn't find psana geometry"
self.calibFile = None
def deployCrystfelGeometry(self, arg):
if arg == 'lcls':
self.findPsanaGeometry()
if self.calibFile is not None and self.parent.writeAccess:
# Convert psana geometry to crystfel geom
if 'cspad' in self.parent.detInfo.lower() and 'cxi' in self.parent.experimentName:
if '.temp.geom' in self.parent.index.geom:
self.parent.index.p9.param(self.parent.index.index_grp, self.parent.index.index_geom_str).setValue(
self.parent.psocakeRunDir + '/.temp.geom')
cmd = ["psana2crystfel", self.calibPath + '/' + self.calibFile,
self.parent.psocakeRunDir + "/.temp.geom", str(self.parent.coffset)]
if self.parent.args.v >= 1: print "cmd: ", cmd
try:
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
p.communicate()[0]
p.stdout.close()
except:
print "Warning! deployCrystfelGeometry() failed."
elif 'rayonix' in self.parent.detInfo.lower() and 'mfx' in self.parent.experimentName:
if '.temp.geom' in self.parent.index.geom:
# Set GUI field to .temp.geom
self.parent.index.p9.param(self.parent.index.index_grp,
self.parent.index.index_geom_str).setValue(
self.parent.psocakeRunDir + '/.temp.geom')
cmd = ["psana2crystfel", self.calibPath + '/' + self.calibFile,
self.parent.psocakeRunDir + "/.temp.geom", str(self.parent.coffset)]
if self.parent.args.v >= 1: print "cmd: ", cmd
try:
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
p.communicate()[0]
p.stdout.close()
except:
print "Warning! deployCrystfelGeometry() failed."
elif 'rayonix' in self.parent.detInfo.lower() and 'xpp' in self.parent.experimentName:
if '.temp.geom' in self.parent.index.geom:
# Set GUI field to .temp.geom
self.parent.index.p9.param(self.parent.index.index_grp,
self.parent.index.index_geom_str).setValue(
self.parent.psocakeRunDir + '/.temp.geom')
cmd = ["psana2crystfel", self.calibPath + '/' + self.calibFile,
self.parent.psocakeRunDir + "/.temp.geom", str(self.parent.coffset)]
if self.parent.args.v >= 1: print "cmd: ", cmd
try:
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
p.communicate()[0]
p.stdout.close()
except:
print "Warning! deployCrystfelGeometry() failed."
else:
if self.parent.args.v >= 1: print "deployCrystfelGeometry not implemented", self.parent.detInfo.lower(), self.parent.experimentName
def updateClen(self, arg):
if arg == 'lcls':
if ('cspad' in self.parent.detInfo.lower() and 'cxi' in self.parent.experimentName) or \
('rayonix' in self.parent.detInfo.lower() and 'mfx' in self.parent.experimentName) or \
('rayonix' in self.parent.detInfo.lower() and 'xpp' in self.parent.experimentName):
self.p1.param(self.geom_grp, self.geom_clen_str).setValue(self.parent.clen)
self.parent.coffset = self.parent.detectorDistance - self.parent.clen
self.p1.param(self.geom_grp, self.geom_coffset_str).setValue(self.parent.coffset)
if self.parent.args.v >= 1: print "Done updateClen: ", self.parent.coffset, self.parent.detectorDistance, self.parent.clen
else:
if self.parent.args.v >= 1: print "updateClen not implemented"
def updateDetectorDistance(self, data):
self.parent.detectorDistance = data / 1000. # mm to metres
self.updateClen('lcls')
if self.parent.args.v >= 1: print "!!!!!!coffset (m), detectorDistance (m), clen (m): ", self.parent.coffset, self.parent.detectorDistance, self.parent.clen
self.writeCrystfelGeom('lcls')
if self.hasGeometryInfo():
if self.parent.args.v >= 1: print "has geometry info"
self.updateGeometry()
self.parent.img.updatePolarizationFactor()
if self.parent.exp.image_property == self.parent.exp.disp_radialCorrection:
self.parent.img.updateImage()
if self.parent.pk.showPeaks: self.parent.pk.updateClassification()
if self.parent.args.v >= 1: print "Done updateDetectorDistance"
def updatePhotonEnergy(self, data):
if data > 0:
self.parent.photonEnergy = data
# E = hc/lambda
h = 6.626070e-34 # J.m
c = 2.99792458e8 # m/s
joulesPerEv = 1.602176621e-19 #J/eV
if self.parent.photonEnergy > 0:
self.parent.wavelength = (h/joulesPerEv*c)/self.parent.photonEnergy
else:
self.parent.wavelength = 0
self.p1.param(self.geom_grp,self.geom_wavelength_str).setValue(self.parent.wavelength)
if self.hasGeometryInfo():
self.updateGeometry()
def updatePixelSize(self, data):
self.parent.pixelSize = data
if self.hasGeometryInfo():
self.updateGeometry()
def hasGeometryInfo(self):
if self.parent.detectorDistance is not None \
and self.parent.photonEnergy is not None \
and self.parent.pixelSize is not None:
return True
else:
return False
def writeCrystfelGeom(self, arg):
if arg == 'lcls':
if ('cspad' in self.parent.detInfo.lower() and 'cxi' in self.parent.experimentName) or \
('rayonix' in self.parent.detInfo.lower() and 'mfx' in self.parent.experimentName) or \
('rayonix' in self.parent.detInfo.lower() and 'xpp' in self.parent.experimentName):
if self.parent.index.hiddenCXI is not None:
if os.path.isfile(self.parent.index.hiddenCXI):
f = h5py.File(self.parent.index.hiddenCXI,'r')
encoderVal = f['/LCLS/detector_1/EncoderValue'][0] / 1000. # metres
f.close()
else:
encoderVal = self.parent.clen # metres
coffset = self.parent.detectorDistance - encoderVal
if self.parent.args.v >= 1: print "&&&&&& coffset (m),detectorDistance (m) ,encoderVal (m): ", coffset, self.parent.detectorDistance, encoderVal
# Replace coffset value in geometry file
if '.temp.geom' in self.parent.index.geom and os.path.exists(self.parent.index.geom):
for line in fileinput.input(self.parent.index.geom, inplace=True):
if 'coffset' in line and line.strip()[0] is not ';':
coffsetStr = line.split('=')[0]+"= "+str(coffset)+"\n"
print coffsetStr, # comma is required
else:
print line, # comma is required
else:
if self.parent.args.v >= 1: print "writeCrystfelGeom not implemented"
def updateGeometry(self):
if self.hasUserDefinedResolution:
self.myResolutionRingList = self.parent.resolution
else:
self.myResolutionRingList = self.resolutionRingList
self.thetaMax = np.zeros_like(self.myResolutionRingList)
self.dMin_crystal = np.zeros_like(self.myResolutionRingList)
self.qMax_crystal = np.zeros_like(self.myResolutionRingList)
self.dMin_physics = np.zeros_like(self.myResolutionRingList)
self.qMax_physics = np.zeros_like(self.myResolutionRingList)
for i, pix in enumerate(self.myResolutionRingList):
if self.parent.detectorDistance > 0 and self.parent.wavelength is not None:
self.thetaMax[i] = np.arctan(pix*self.parent.pixelSize/self.parent.detectorDistance)
self.qMax_crystal[i] = 2/self.parent.wavelength*np.sin(self.thetaMax[i]/2)
self.dMin_crystal[i] = 1/self.qMax_crystal[i]
self.qMax_physics[i] = 4*np.pi/self.parent.wavelength*np.sin(self.thetaMax[i]/2)
self.dMin_physics[i] = np.pi/self.qMax_physics[i]
if self.parent.args.v >= 1:
print "updateGeometry: ", i, self.thetaMax[i], self.dMin_crystal[i], self.dMin_physics[i]
if self.parent.resolutionRingsOn:
self.updateRings()
if self.parent.args.v >= 1: print "Done updateGeometry"
def updateDock42(self, data):
a = ['a','b','c','d','e','k','m','n','r','s']
myStr = a[5]+a[8]+a[0]+a[5]+a[4]+a[7]
if myStr in data:
self.d42 = Dock("Console", size=(100,100))
# build an initial namespace for console commands to be executed in (this is optional;
# the user can always import these modules manually)
namespace = {'pg': pg, 'np': np, 'self': self}
# initial text to display in the console
text = "You have awoken the "+myStr+"\nWelcome to psocake IPython: dir(self)\n" \
"Here are some commonly used variables:\n" \
"unassembled detector: self.parent.calib\n" \
"assembled detector: self.parent.data\n" \
"user-defined mask: self.parent.mk.userMask\n" \
"streak mask: self.parent.mk.streakMask\n" \
"psana mask: self.parent.mk.psanaMask"
self.w42 = pg.console.ConsoleWidget(parent=None,namespace=namespace, text=text)
self.d42.addWidget(self.w42)
self.parent.area.addDock(self.d42, 'bottom')
def updateResolutionRings(self, data):
self.parent.resolutionRingsOn = data
if self.parent.exp.hasExpRunDetInfo():
self.updateRings()
if self.parent.args.v >= 1:
print "Done updateResolutionRings"
def updateResolution(self, data):
# convert to array of floats
_resolution = data.split(',')
self.parent.resolution = np.zeros((len(_resolution,)))
self.updateDock42(data)
if data != '':
for i in range(len(_resolution)):
self.parent.resolution[i] = float(_resolution[i])
if data != '':
self.hasUserDefinedResolution = True
else:
self.hasUserDefinedResolution = False
self.myResolutionRingList = self.parent.resolution
self.dMin = np.zeros_like(self.myResolutionRingList)
if self.hasGeometryInfo():
self.updateGeometry()
if self.parent.exp.hasExpRunDetInfo():
self.updateRings()
if self.parent.args.v >= 1:
print "Done updateResolution"
def updateResolutionUnits(self, data):
# convert to array of floats
self.parent.resolutionUnits = data
if self.hasGeometryInfo():
self.updateGeometry()
if self.parent.exp.hasExpRunDetInfo():
self.updateRings()
if self.parent.args.v >= 1:
print "Done updateResolutionUnits"
def updateRings(self):
if self.parent.resolutionRingsOn:
self.clearRings()
cenx = np.ones_like(self.myResolutionRingList)*self.parent.cx
ceny = np.ones_like(self.myResolutionRingList)*self.parent.cy
diameter = 2*self.myResolutionRingList
self.parent.img.ring_feature.setData(cenx, ceny, symbol='o', \
size=diameter, brush=(255,255,255,0), \
pen='r', pxMode=False)
for i,val in enumerate(self.dMin_crystal):
if self.parent.resolutionUnits == self.unitA_c:
self.resolutionText.append(pg.TextItem(text='%s A' % float('%.3g' % (val*1e10)), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitNm_c:
self.resolutionText.append(pg.TextItem(text='%s nm' % float('%.3g' % (val*1e9)), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitQ_c:
self.resolutionText.append(pg.TextItem(text='%s m^-1' % float('%.3g' % (self.qMax_crystal[i])), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitA_p:
self.resolutionText.append(pg.TextItem(text='%s A' % float('%.3g' % (self.dMin_physics[i]*1e10)), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitNm_p:
self.resolutionText.append(pg.TextItem(text='%s nm' % float('%.3g' % (self.dMin_physics[i]*1e9)), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitQ_p:
self.resolutionText.append(pg.TextItem(text='%s m^-1' % float('%.3g' % (self.qMax_physics[i])), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitTwoTheta:
self.resolutionText.append(pg.TextItem(text='%s degrees' % float('%.3g' % (self.thetaMax[i]*180/np.pi)), border='w', fill=(0, 0, 255, 100)))
self.parent.img.w1.getView().addItem(self.resolutionText[i])
self.resolutionText[i].setPos(self.myResolutionRingList[i]+self.parent.cx, self.parent.cy)
else:
self.clearRings()
if self.parent.args.v >= 1: print "Done updateRings"
def drawCentre(self):
# Always indicate centre of detector
try:
self.parent.img.centre_feature.setData(np.array([self.parent.cx]), np.array([self.parent.cy]), symbol='o', \
size=6, brush=(255, 255, 255, 0), pen='r', pxMode=False)
if self.parent.args.v >= 1: print "Done drawCentre"
except:
pass
def clearRings(self):
if self.resolutionText:
cen = [0,]
self.parent.img.ring_feature.setData(cen, cen, size=0)
for i,val in enumerate(self.resolutionText):
self.parent.img.w1.getView().removeItem(self.resolutionText[i])
self.resolutionText = []
def deploy(self):
with pg.BusyCursor():
# Calculate detector translation in x and y
dx = self.parent.pixelSize * 1e6 * (self.parent.cx - self.parent.roi.centreX) # microns
dy = self.parent.pixelSize * 1e6 * (self.parent.cy - self.parent.roi.centreY) # microns
dz = np.mean(self.parent.det.coords_z(self.parent.evt)) - self.parent.detectorDistance*1e6 # microns
geo = self.parent.det.geometry(self.parent.evt)
if 'cspad' in self.parent.detInfo.lower() and 'cxi' in self.parent.experimentName:
geo.move_geo('CSPAD:V1', 0, dx=dx, dy=dy, dz=-dz)
elif 'rayonix' in self.parent.detInfo.lower() and 'mfx' in self.parent.experimentName:
top = geo.get_top_geo()
children = top.get_list_of_children()[0]
geo.move_geo(children.oname, 0, dx=dx, dy=dy, dz=-dz)
elif 'rayonix' in self.parent.detInfo.lower() and 'xpp' in self.parent.experimentName:
top = geo.get_top_geo()
children = top.get_list_of_children()[0]
geo.move_geo(children.oname, 0, dx=dx, dy=dy, dz=-dz)
else:
print "deploy not implemented"
fname = self.parent.psocakeRunDir + "/"+str(self.parent.runNumber)+'-end.data'
geo.save_pars_in_file(fname)
print "#################################################"
print "Deploying psana detector geometry: ", fname
print "#################################################"
cmts = {'exp': self.parent.experimentName, 'app': 'psocake', 'comment': 'recentred geometry'}
if self.parent.args.localCalib:
calibDir = './calib'
elif self.parent.args.outDir is None:
calibDir = self.parent.rootDir + '/calib'
else:
calibDir = '/reg/d/psdm/'+self.parent.experimentName[:3]+'/'+self.parent.experimentName+'/calib'
deploy_calib_file(cdir=calibDir, src=str(self.parent.det.name), type='geometry',
run_start=self.parent.runNumber, run_end=None, ifname=fname, dcmts=cmts, pbits=0)
# Reload new psana geometry
self.parent.exp.setupExperiment()
self.parent.img.getDetImage(self.parent.eventNumber)
self.updateRings()
self.parent.index.updateIndex()
self.drawCentre()
def autoDeploy(self):
with pg.BusyCursor():
powderHits = np.load(self.parent.psocakeRunDir + '/' + self.parent.experimentName + '_' + str(self.parent.runNumber).zfill(4) + '_maxHits.npy')
powderMisses = np.load(self.parent.psocakeRunDir + '/' + self.parent.experimentName + '_' + str(self.parent.runNumber).zfill(4) + '_maxMisses.npy')
powderImg = self.parent.det.image(self.parent.evt, np.maximum(powderHits,powderMisses))
centreRow, centreCol = findDetectorCentre(np.log(abs(powderImg)), self.parent.cx, self.parent.cy, range=200)
print("Current centre along row,centre along column: ", self.parent.cx, self.parent.cy)
print("Optimum centre along row,centre along column: ", centreRow, centreCol)
allowedDeviation = 175 # pixels
if abs(self.parent.cx - centreRow) <= allowedDeviation and \
abs(self.parent.cy - centreCol) <= allowedDeviation:
deploy = True
else:
deploy = False
print "Too far away from current centre. I will not deploy the auto centred geometry."
if deploy:
# Calculate detector translation in x and y
dx = self.parent.pixelSize * 1e6 * (self.parent.cx - centreRow) # microns
dy = self.parent.pixelSize * 1e6 * (self.parent.cy - centreCol) # microns
dz = np.mean(self.parent.det.coords_z(self.parent.evt)) - self.parent.detectorDistance * 1e6 # microns
geo = self.parent.det.geometry(self.parent.evt)
if 'cspad' in self.parent.detInfo.lower() and 'cxi' in self.parent.experimentName:
geo.move_geo('CSPAD:V1', 0, dx=dx, dy=dy, dz=-dz)
elif 'rayonix' in self.parent.detInfo.lower() and 'mfx' in self.parent.experimentName:
top = geo.get_top_geo()
children = top.get_list_of_children()[0]
geo.move_geo(children.oname, 0, dx=dx, dy=dy, dz=-dz)
elif 'rayonix' in self.parent.detInfo.lower() and 'xpp' in self.parent.experimentName:
top = geo.get_top_geo()
children = top.get_list_of_children()[0]
geo.move_geo(children.oname, 0, dx=dx, dy=dy, dz=-dz)
else:
print "autoDeploy not implemented"
fname = self.parent.psocakeRunDir + "/" + str(self.parent.runNumber) + '-end.data'
geo.save_pars_in_file(fname)
print "#################################################"
print "Deploying psana detector geometry: ", fname
print "#################################################"
cmts = {'exp': self.parent.experimentName, 'app': 'psocake', 'comment': 'auto recentred geometry'}
if self.parent.args.localCalib:
calibDir = './calib'
elif self.parent.args.outDir is None:
calibDir = self.parent.rootDir + '/calib'
else:
calibDir = '/reg/d/psdm/' + self.parent.experimentName[:3] + '/' + self.parent.experimentName + '/calib'
deploy_calib_file(cdir=calibDir, src=str(self.parent.det.name), type='geometry',
run_start=self.parent.runNumber, run_end=None, ifname=fname, dcmts=cmts, pbits=0)
# Reload new psana geometry
self.parent.exp.setupExperiment()
self.parent.img.getDetImage(self.parent.eventNumber)
self.updateRings()
self.parent.index.updateIndex()
self.drawCentre()
class TrackingExperimentWindow(SimpleExperimentWindow):
"""Window for controlling an experiment where the tail of an
embedded fish is tracked.
Parameters
----------
Returns
-------
"""
def __init__(self, tracking=True, tail=False, eyes=False, *args, **kwargs):
# TODO refactor movement detection
self.tracking = tracking
self.tail = tail
self.eyes = eyes
if tail or eyes:
self.camera_display = CameraEmbeddedTrackingSelection(
experiment=kwargs["experiment"], tail=tail, eyes=eyes)
else:
self.camera_display = CameraViewWidget(
experiment=kwargs["experiment"])
self.camera_splitter = QSplitter(Qt.Horizontal)
self.monitoring_widget = QWidget()
self.monitoring_layout = QVBoxLayout()
self.monitoring_widget.setLayout(self.monitoring_layout)
# Stream plot:
# if eyes:
time_past = 30
# else:
# time_past = 5
self.stream_plot = MultiStreamPlot(time_past=time_past)
self.monitoring_layout.addWidget(self.stream_plot)
# Tracking params button:
self.button_tracking_params = QPushButton(
"Tracking params" if tracking else "Movement detection params")
self.button_tracking_params.clicked.connect(
self.open_tracking_params_tree)
self.monitoring_layout.addWidget(self.button_tracking_params)
self.track_params_wnd = None
super().__init__(*args, **kwargs)
def construct_ui(self):
""" """
self.experiment.gui_timer.timeout.connect(self.stream_plot.update)
previous_widget = super().construct_ui()
previous_widget.layout().setContentsMargins(0, 0, 0, 0)
self.monitoring_layout.addWidget(previous_widget)
self.monitoring_layout.setStretch(1, 1)
self.monitoring_layout.setStretch(0, 1)
self.camera_splitter.addWidget(self.camera_display)
self.camera_splitter.addWidget(self.monitoring_widget)
return self.camera_splitter
def open_tracking_params_tree(self):
""" """
self.track_params_wnd = ParameterTree()
self.track_params_wnd.addParameters(
self.experiment.tracking_method.params)
self.track_params_wnd.addParameters(
self.experiment.preprocessing_method.params)
self.track_params_wnd.setWindowTitle("Tracking parameters")
self.track_params_wnd.show()
def _init_extra(self,**kw):
self.neuron=kw.get('base_neuron')
self.neuron_params=kw.get('neuron_params')
for d in self.neuron_params[0]['children']:
if 'children' in d.keys():
for dd in d['children']:
self.__dict__[dd['name']] = dd['value']
else:
pp(d)
if 'value' in d.keys():
self.__dict__[d['name']] = d['value']
self.dyn_xticks=[[100*i,i*0.1] for i in range(0,22,4)]
self.script_name=kw.get('script_name', __file__.split('/')[-1][0:-3])
self.p.param('store_state', 'save').sigActivated.connect(self.save)
self.p.param('stimulate', 'start').sigActivated.connect(self.stimulate)
# Comet for recovery current vs time plot
w=pg.PlotWidget()
w.plotItem.getAxis('bottom').setScale(0.001)
w.plotItem.getAxis('left').setLabel('Current', units='A')
w.plotItem.getAxis('left').setScale(0.000000000001)
w.setWindowTitle('Recovery current')
w.setRange(QtCore.QRectF(0, -200, self.n_history, 400))
w.setLabel('bottom', 'Time', units='s')
w.plotItem.layout.setContentsMargins(20, 20, 20, 20)
color=self.kw.get('curve_uv_color',(0,0,0))
pen=pg.mkPen(color, width=self.kw.get('curve_uv_width',5))
self.curve_ut = w.plot(pen=pen)
self.widgets.append(w)
# Comet for voltage recovery current plot
w=pg.PlotWidget()
w.plotItem.getAxis('bottom').setScale(0.001)
w.plotItem.getAxis('left').setLabel('Recovery current u', units='A')
w.plotItem.getAxis('left').setScale(0.000000000001)
w.setWindowTitle('Recovery current/voltage')
w.setRange(QtCore.QRectF(-100, -50, 100, 200))
w.setLabel('bottom', 'Voltage', units='V')
w.plotItem.layout.setContentsMargins(10, 10, 10, 10)
self.widgets.append(w)
color=self.kw.get('curve_uv_color',(0,0,0))
pen=pg.mkPen(color, width=self.kw.get('curve_uv_width',5) )
self.curve_uv = w.plot(pen=pen)
# x,y=self.get_nullcline_extreme_points()
# self.curve_uv_extreme_point = w.plot(x,y, pen=pen)
color=self.kw.get('curve_uv_color',(0,0,0))
self.curve_uv_nullcline0 = w.plot(pen=pen)
self.curve_uv_nullcline1 = w.plot(pen=pen)
color=self.kw.get('curve_uv_color',(255,0,0))
brush=pg.mkBrush(color=color)
self.curve_uv_comet= w.plot(symbolBrush= brush, symbol='o', symbolSize=15.)
# Parameters base_neuron
self.p2 = Parameter.create(name='params', type='group', children=self.neuron_params)
self.p2.sigTreeStateChanged.connect(self.change)
self.p2.param('IV, IF, nullcline, etc', 'run base_neuron').sigActivated.connect(self.run_neuron_thread)
self.p2.param('IV, IF, nullcline, etc', 'run GP-ST network').sigActivated.connect(self.run_GP_STN_network_thread)
pt = ParameterTree()
pt.setParameters(self.p2, showTop=False)
pt.setWindowTitle('Parameters')
self.widgets.append(pt)
# Threshold type
w=pg.PlotWidget()
# w.plotItem.getAxis('bottom').setScale(0.001)
w.plotItem.getAxis('left').setLabel('a/g_L')
# w.plotItem.getAxis('left').setScale(0.000000000001)
w.setWindowTitle('Recovery current/voltage')
w.setRange(QtCore.QRectF(0, 0, 4, 1))
w.setLabel('bottom', 'tau_m/tau_w')
w.plotItem.layout.setContentsMargins(10, 10, 10, 10)
self.widgets.append(w)
color=self.kw.get('curve_uv_color',(0,0,0))
pen=pg.mkPen(color, width=self.kw.get('curve_uv_width',5) )
c1,c2=self.get_threshold_oscillation_curves()
x, y=self.get_threshold_oscilltion_point()
color=self.kw.get('curve_uv_color',(255,0,0))
brush=pg.mkBrush(color=color)
self.curve_oscillation1 = w.plot(c1[0],c1[1],pen=pen)
self.curve_oscillation2 = w.plot(c2[0],c2[1],pen=pen)
self.curve_oscillation_points1 = w.plot([x[0]], [y[0]],
symbolBrush= brush,
symbol='o',
symbolSize=25.)
color=self.kw.get('curve_uv_color',(0,0,255))
brush=pg.mkBrush(color=color)
self.curve_oscillation_points2 = w.plot([x[1]], [y[1]],
symbolBrush= brush,
symbol='o',
symbolSize=15.)
self.draw()
def __init__(self, **kw):
self.app=kw.pop('app')
self.data_label=''
self.date_time=dt.datetime.now().strftime('%Y_%m_%d-%H_%M')
self.h=kw.pop('h', .1) #integration step size
self.n_state_variables=kw.pop('n_state_variables', 2)
self.n_history=kw.pop('n_history', 2000)
self.kw=kw
self.params=kw.get('params') #qt paramters, se tree parameter class
self.update_time=kw.pop('update_time', 0)
self.widgets=[]
self.script_name=kw.pop('script_name',__file__.split('/')[-1][0:-3])
self.start_stim=-10000.0
self.scale_plot=10
for key, value in kw.items():
self.__dict__[key] = value
for d in self.params[0]['children']:
self.__dict__[d['name']] = d['value']
for d in self.params[1]['children']:
if 'value' in d.keys():
self.__dict__[d['name']] = d['value']
self.x=self.n_history
self.y=numpy.zeros(self.n_state_variables)
self.y[0]=-70
self.dy=numpy.zeros(self.n_state_variables)
self.x_history=numpy.arange(0,self.n_history, self.scale_plot*self.h)
self.y_history=numpy.random.rand( self.n_state_variables, self.n_history/(self.scale_plot*self.h))
self.y_history[0,:]=-70
# Parameters
self.p = Parameter.create(name='params', type='group', children=self.params)
self.p.sigTreeStateChanged.connect(self.change)
pt = ParameterTree()
pt.setParameters(self.p, showTop=False)
pt.setWindowTitle('Parameters')
self.widgets.append(pt)
# Voltage time plot
w=pg.PlotWidget()
w.setWindowTitle('Voltage/time')
w.setRange(QtCore.QRectF(0, -90, self.n_history, 100))
w.setLabel('bottom', 'Time', units='s')
w.plotItem.layout.setContentsMargins(20, 20, 20, 20)
ax=w.plotItem.getAxis('left')
l=[[ (0.0,'0'), (-30, -30), (-60, -60), (-90, -90) ], ]
ax.setTicks(l)
w.plotItem.getAxis('bottom').setScale(0.001)
ax.setLabel('Voltage', units='V')
ax.setScale(0.001)
# ax.setWidth(w=2)
# ax.setRange(500,1500)
color=self.kw.get('curve_uv_color',(0,0,0))
pen=pg.mkPen(color, width=self.kw.get('curve_uv_width',5))
self.curve_vt = w.plot(pen=pen)
self.curve_vt.setData(self.x_history, self.y_history[0,:])
self.widgets.append(w)
self.timer = QtCore.QTimer()
self.timer.timeout.connect(self.update)
self.timer.start(self.update_time)
# self.timer.start(1000.)
self._init_extra(**kw)
mars_mis = mars1_disable | mars2_disable | mars3_disable | mars_delays
print("mars clock %04X" % mars_clock)
zc.write(52, mars_clock)
print("test pulser %X" % test_pulse)
zc.write(32, test_pulse)
print("MARS mis %X" % mars_mis)
zc.write(56, mars_mis)
p2.param('Global actons', 'Set actions').sigActivated.connect(global_set)
p2.param('Load MARS', 'Load State').sigActivated.connect(load_MARS)
p2.param('Load MARS', 'Global reset').sigActivated.connect(MARS_reset)
# Create two ParameterTree widgets, both accessing the same data
t = ParameterTree()
t.setParameters(p, showTop=False)
t.setWindowTitle('MARS settings')
t2 = ParameterTree()
t2.setParameters(p2, showTop=False)
win = QtGui.QWidget()
layout = QtGui.QGridLayout()
win.setLayout(layout)
layout.addWidget(QtGui.QLabel(" MARS Parameters "), 0, 0, 1, 2)
layout.addWidget(t, 1, 0, 1, 1)
layout.addWidget(t2, 1, 1, 1, 1)
win.show()
win.resize(800, 800)
# test save/restore
s = p.saveState()
p.restoreState(s)
def setupGUI(self):
"""Setup GUI"""
self.layout = QtGui.QVBoxLayout()
self.layout.setContentsMargins(0,0,0,0)
self.setLayout(self.layout)
self.splitter = QtGui.QSplitter()
self.splitter.setOrientation(QtCore.Qt.Vertical)
self.splitter.setSizes([int(self.height()*0.5), int(self.height()*0.5)]);
self.layout.addWidget(self.splitter)
self.splitter2 = QtGui.QSplitter()
self.splitter2.setOrientation(QtCore.Qt.Horizontal)
#self.splitter2.setSizes([int(self.width()*0.5), int(self.width()*0.5)]);
self.splitter.addWidget(self.splitter2);
self.splitter3 = QtGui.QSplitter()
self.splitter3.setOrientation(QtCore.Qt.Horizontal)
#self.splitter2.setSizes([int(self.width()*0.5), int(self.width()*0.5)]);
self.splitter.addWidget(self.splitter3);
# various matrix like plots: state, goal, weights, p
self.nStates = 20; #number of states in the past to remember
self.matrixdata = [np.zeros((self.network.nInputs, self.nStates)),
np.zeros((self.network.nOutputs, self.nStates)),
np.zeros((self.network.nOutputs, self.nStates)),
np.zeros((self.network.nNodes, self.nStates)),
np.zeros(self.network.weights.shape)];
#np.zeros(self.network.a.shape)
#np.zeros(self.network.b.shape)];
self.images = [];
for j in range(len(self.matrixdata)):
l = pg.GraphicsLayoutWidget()
self.splitter2.addWidget(l);
v = pg.ViewBox();
l.addItem(v, 0, 1);
i = pg.ImageItem(self.matrixdata[j]);
v.addItem(i);
self.images.append(i);
for i in [0,1,2,3]:
self.images[i].setLevels([0,1]);
#output and error
self.plotlayout = pg.GraphicsLayoutWidget();
self.splitter3.addWidget(self.plotlayout);
self.plot = [];
for i in range(2):
self.plot.append(self.plotlayout.addPlot());
self.plot[i].setYRange(0, 1, padding=0);
self.plotlength = 10000;
self.output = np.zeros((self.network.nOutputs, self.plotlength));
#self.goal = np.zeros((self.network.nOutputs, self.plotlength));
self.errorlength = 10000;
self.error = np.zeros(self.errorlength);
self.curves = []
for i in range(self.network.nOutputs):
c = self.plot[0].plot(self.output[i,:], pen = (i, self.network.nOutputs));
#c.setPos(0,0*i*6);
self.curves.append(c);
c = self.plot[1].plot(self.error, pen = (2,3));
self.curves.append(c);
# parameter controls
self.steps = 0;
params = [
{'name': 'Controls', 'type': 'group', 'children': [
{'name': 'Simulate', 'type': 'bool', 'value': True, 'tip': "Run the network simulation"},
{'name': 'Plot', 'type': 'bool', 'value': True, 'tip': "Check to plot network evolution"},
{'name': 'Plot Interval', 'type': 'int', 'value': 10, 'tip': "Step between plot updates"},
{'name': 'Timer', 'type': 'int', 'value': 10, 'tip': "Pause between plot is updated"},
]}
,
{'name': 'Network Parameter', 'type': 'group', 'children': [
{'name': 'Eta', 'type': 'float', 'value': self.network.eta, 'tip': "Learning rate"},
{'name': 'Gamma', 'type': 'float', 'value': self.network.gamma, 'tip': "Learning rate"}#,
]}
,
{'name': 'Status', 'type': 'group', 'children': [
{'name': 'Steps', 'type': 'int', 'value': self.steps, 'tip': "Actual iteration step", 'readonly': True}
]}
];
self.parameter = Parameter.create(name = 'Parameter', type = 'group', children = params);
print self.parameter
print self.parameter.children()
self.parameter.sigTreeStateChanged.connect(self.updateParameter);
## Create two ParameterTree widgets, both accessing the same data
t = ParameterTree();
t.setParameters(self.parameter, showTop=False)
t.setWindowTitle('Parameter');
self.splitter3.addWidget(t);
# draw network
self.nsteps = 100;
self.updateView();
def run_gui(path=None, data=None):
"""
Loads PCF or CNMF data object from a provided path and loads the CaImAn GUI for component inspection.
This GUI was tweaked to not require any storage-intensive mmap files, but can therefore not show individual frames.
:param path: optional str, directory of the PCF or CNMF object from which component data should be loaded. If None
and data=None, a window prompt will open to select a directory where to look for a CNMF/PCF file.
:param data: optional, data in form of an already loaded cnm object can be provided directly
:return:
"""
try:
cv2.setNumThreads(1)
except:
print('Open CV is naturally single threaded')
try:
if __IPYTHON__:
# print(1)
# this is used for debugging purposes only. allows to reload classes
# when changed
get_ipython().magic('load_ext autoreload')
get_ipython().magic('autoreload 2')
except NameError:
print('Not launched under iPython')
def make_color_img(img, gain=255, min_max=None, out_type=np.uint8):
if min_max is None:
min_ = img.min()
max_ = img.max()
else:
min_, max_ = min_max
img = (img - min_) / (max_ - min_) * gain
img = img.astype(out_type)
img = np.dstack([img] * 3)
return img
### FIND DATA ###
if data is None: # different conditions on file loading (not necessary if data was already provided)
if path is None: # if no path has been given, open a window prompt to select a directory
F = FileDialog()
# load object saved by CNMF
path = F.getExistingDirectory(
caption='Select folder from which to load a PCF or CNMF file')
try: # first try to get CNMF data from a PCF object (should be most up-to-date)
cnm_obj = pipe.load_pcf(path).cnmf
except FileNotFoundError:
try:
cnm_obj = pipe.load_cnmf(path)
except FileNotFoundError:
raise FileNotFoundError(
f'Could not find data to load in {path}!')
else:
cnm_obj = data
# movie NOT NEEDED IN VERSION WITHOUT MMAP FILE
# if not os.path.exists(cnm_obj.mmap_file):
# M = FileDialog()
# cnm_obj.mmap_file = M.getOpenFileName(caption='Load memory mapped file', filter='*.mmap')[0]
#
# if fpath[-3:] == 'nwb':
# mov = cm.load(cnm_obj.mmap_file, var_name_hdf5='acquisition/TwoPhotonSeries')
# else:
# mov = cm.load(cnm_obj.mmap_file)
estimates = cnm_obj.estimates
params_obj = cnm_obj.params
# min_mov = np.min(mov)
# max_mov = np.max(mov)
if not hasattr(estimates, 'Cn'):
if not os.path.exists(cnm_obj.mmap_file):
M = FileDialog()
cnm_obj.mmap_file = M.getOpenFileName(
caption='Load memory mapped file', filter='*.mmap')[0]
mov = cm.load(cnm_obj.mmap_file)
estimates.Cn = cm.local_correlations(mov, swap_dim=False)
Cn = estimates.Cn
# min_mov_denoise = np.min(estimates.A)*estimates.C.min()
# max_mov_denoise = np.max(estimates.A)*estimates.C.max()
background_num = -1
neuron_selected = False
nr_index = 0
min_background = np.min(estimates.b, axis=0) * np.min(estimates.f, axis=1)
max_background = np.max(estimates.b, axis=0) * np.max(estimates.f, axis=1)
if not hasattr(estimates, 'accepted_list'):
# if estimates.discarded_components.A.shape[-1] > 0:
# estimates.restore_discarded_components()
estimates.accepted_list = np.array([], dtype=np.int)
estimates.rejected_list = np.array([], dtype=np.int)
estimates.img_components = estimates.A.toarray().reshape(
(estimates.dims[0], estimates.dims[1], -1),
order='F').transpose([2, 0, 1])
estimates.cms = np.array([
scipy.ndimage.measurements.center_of_mass(comp)
for comp in estimates.img_components
])
estimates.idx_components = np.arange(estimates.nr)
estimates.idx_components_bad = np.array([])
estimates.background_image = make_color_img(estimates.Cn)
# Generate image data
estimates.img_components /= estimates.img_components.max(
axis=(1, 2))[:, None, None]
estimates.img_components *= 255
estimates.img_components = estimates.img_components.astype(np.uint8)
def draw_contours_overall(md):
if md is "reset":
draw_contours()
elif md is "neurons":
if neuron_selected is True:
#if a specific neuron has been selected, only one contour should be changed while thrshcomp_line is changing
if nr_index is 0:
#if user does not start to move through the frames
draw_contours_update(estimates.background_image, img)
draw_contours_update(comp2_scaled, img2)
else:
# NEVER CALLED IN THIS VERSION WITHOUT MMAP SINCE NR_INDEX NEVER CHANGES (NO NR_VLINE)
draw_contours_update(raw_mov_scaled, img)
draw_contours_update(frame_denoise_scaled, img2)
else:
#if no specific neuron has been selected, all the contours are changing
draw_contours()
else:
#md is "background":
return
def draw_contours():
global thrshcomp_line, estimates, img
bkgr_contours = estimates.background_image.copy()
if len(estimates.idx_components) > 0:
contours = [
cv2.findContours(
cv2.threshold(img, np.int(thrshcomp_line.value()), 255,
0)[1], cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)[0]
for img in estimates.img_components[estimates.idx_components]
]
SNRs = np.array(estimates.r_values)
iidd = np.array(estimates.idx_components)
idx1 = np.where(SNRs[iidd] < 0.1)[0]
idx2 = np.where((SNRs[iidd] >= 0.1) & (SNRs[iidd] < 0.25))[0]
idx3 = np.where((SNRs[iidd] >= 0.25) & (SNRs[iidd] < 0.5))[0]
idx4 = np.where((SNRs[iidd] >= 0.5) & (SNRs[iidd] < 0.75))[0]
idx5 = np.where((SNRs[iidd] >= 0.75) & (SNRs[iidd] < 0.9))[0]
idx6 = np.where(SNRs[iidd] >= 0.9)[0]
cv2.drawContours(bkgr_contours,
sum([contours[jj] for jj in idx1], []), -1,
(255, 0, 0), 1)
cv2.drawContours(bkgr_contours,
sum([contours[jj] for jj in idx2], []), -1,
(0, 255, 0), 1)
cv2.drawContours(bkgr_contours,
sum([contours[jj] for jj in idx3], []), -1,
(0, 0, 255), 1)
cv2.drawContours(bkgr_contours,
sum([contours[jj] for jj in idx4], []), -1,
(255, 255, 0), 1)
cv2.drawContours(bkgr_contours,
sum([contours[jj] for jj in idx5], []), -1,
(255, 0, 255), 1)
cv2.drawContours(bkgr_contours,
sum([contours[jj] for jj in idx6], []), -1,
(0, 255, 255), 1)
img.setImage(bkgr_contours, autoLevels=False)
# pg.setConfigOptions(imageAxisOrder='row-major')
def draw_contours_update(cf, im):
global thrshcomp_line, estimates
curFrame = cf.copy()
if len(estimates.idx_components) > 0:
contours = [
cv2.findContours(
cv2.threshold(img, np.int(thrshcomp_line.value()), 255,
0)[1], cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)[0]
for img in estimates.img_components[estimates.idx_components]
]
SNRs = np.array(estimates.r_values)
iidd = np.array(estimates.idx_components)
idx1 = np.where(SNRs[iidd] < 0.1)[0]
idx2 = np.where((SNRs[iidd] >= 0.1) & (SNRs[iidd] < 0.25))[0]
idx3 = np.where((SNRs[iidd] >= 0.25) & (SNRs[iidd] < 0.5))[0]
idx4 = np.where((SNRs[iidd] >= 0.5) & (SNRs[iidd] < 0.75))[0]
idx5 = np.where((SNRs[iidd] >= 0.75) & (SNRs[iidd] < 0.9))[0]
idx6 = np.where(SNRs[iidd] >= 0.9)[0]
if min_dist_comp in idx1:
cv2.drawContours(curFrame, contours[min_dist_comp], -1,
(255, 0, 0), 1)
if min_dist_comp in idx2:
cv2.drawContours(curFrame, contours[min_dist_comp], -1,
(0, 255, 0), 1)
if min_dist_comp in idx3:
cv2.drawContours(curFrame, contours[min_dist_comp], -1,
(0, 0, 255), 1)
if min_dist_comp in idx4:
cv2.drawContours(curFrame, contours[min_dist_comp], -1,
(255, 255, 0), 1)
if min_dist_comp in idx5:
cv2.drawContours(curFrame, contours[min_dist_comp], -1,
(255, 0, 255), 1)
if min_dist_comp in idx6:
cv2.drawContours(curFrame, contours[min_dist_comp], -1,
(0, 255, 255), 1)
im.setImage(curFrame, autoLevels=False)
#%% START BUILDING THE APPLICATION WINDOW
# Always start by initializing Qt (only once per application)
app = QtGui.QApplication([])
# Define a top-level widget to hold everything
w = QtGui.QWidget()
# Create some widgets to be placed inside
btn = QtGui.QPushButton('press me')
text = QtGui.QLineEdit('enter text')
# Histogram controller (win)
win = pg.GraphicsLayoutWidget()
win.setMaximumWidth(300)
win.setMinimumWidth(200)
hist = pg.HistogramLUTItem() # Contrast/color control
win.addItem(hist)
# Plotting windows
p1 = pg.PlotWidget(
) # raw movie window (top-mid), all contours are drawn here
p2 = pg.PlotWidget(
) # trace window (bottom-mid), calcium trace of the selected component
p3 = pg.PlotWidget(
) # denoised movie window (top-right), only selected contour is drawn here
# parameter table for online evaluation and mode change
t = ParameterTree()
# parameter table for neuron selection/sorting
t_action = ParameterTree()
action_layout = QtGui.QGridLayout()
## Create a grid layout to manage the widgets size and position
layout = QtGui.QGridLayout()
w.setLayout(layout)
# A plot area (ViewBox + axes) for displaying the image
#p1 = win.addPlot(title="Image here")
# Item for displaying image data
img = pg.ImageItem()
p1.addItem(img)
img2 = pg.ImageItem()
p3.addItem(img2)
hist.setImageItem(img)
# Draggable line for setting isocurve level
thrshcomp_line = pg.InfiniteLine(angle=0, movable=True, pen='g')
hist.vb.addItem(thrshcomp_line)
hist.vb.setMouseEnabled(y=False) # makes user interaction a little easier
thrshcomp_line.setValue(100)
thrshcomp_line.setZValue(1000) # bring iso line above contrast controls
## Add widgets to the layout in their proper positions
layout.addWidget(win, 1, 0) # histogram
layout.addWidget(p3, 0, 2) # denoised movie
layout.addWidget(t, 0, 0) # upper-right table
layout.addWidget(t_action, 1, 2) # bottom-right table
layout.addWidget(p1, 0, 1) # raw movie
layout.addWidget(p2, 1, 1) # calcium trace window
#enable only horizontal zoom for the traces component
p2.setMouseEnabled(x=True, y=False)
## Display the widget as a new window
w.show()
## Start the Qt event loop
app.exec_()
draw_contours()
hist.setLevels(estimates.background_image.min(),
estimates.background_image.max())
# Another plot area for displaying ROI data
#win.nextRow()
#p2 = win.addPlot(colspan=2)
p2.setMaximumHeight(250)
#win.resize(800, 800)
#win.show()
# set position and scale of image
img.scale(1, 1)
# img.translate(-50, 0)
# zoom to fit image
p1.autoRange()
mode = "reset"
p2.setTitle("mode: %s" % (mode))
thrshcomp_line.sigDragged.connect(lambda: draw_contours_overall(mode))
def imageHoverEvent(event):
#Show the position, pixel, and value under the mouse cursor.
global x, y, i, j, val
pos = event.pos()
i, j = pos.y(), pos.x()
i = int(np.clip(i, 0, estimates.background_image.shape[0] - 1))
j = int(np.clip(j, 0, estimates.background_image.shape[1] - 1))
val = estimates.background_image[i, j, 0]
ppos = img.mapToParent(pos)
x, y = ppos.x(), ppos.y()
# Monkey-patch the image to use our custom hover function.
# This is generally discouraged (you should subclass ImageItem instead),
# but it works for a very simple use like this.
img.hoverEvent = imageHoverEvent
def mouseClickEvent(event):
global mode
global x, y, i, j, val
pos = img.mapFromScene(event.pos())
x = int(pos.x())
y = int(pos.y())
if x < 0 or x > mov.shape[1] or y < 0 or y > mov.shape[2]:
# if the user click outside of the movie, do nothing and jump out of the function
return
i, j = pos.y(), pos.x()
i = int(np.clip(i, 0, estimates.background_image.shape[0] - 1))
j = int(np.clip(j, 0, estimates.background_image.shape[1] - 1))
val = estimates.background_image[i, j, 0]
if mode is "neurons":
show_neurons_clicked()
p1.mousePressEvent = mouseClickEvent
#A general rule in Qt is that if you override one mouse event handler, you must override all of them.
def release(event):
pass
p1.mouseReleaseEvent = release
def move(event):
pass
p1.mouseMoveEvent = move
## PARAMS
params = [{
'name': 'min_cnn_thr',
'type': 'float',
'value': 0.99,
'limits': (0, 1),
'step': 0.01
}, {
'name': 'cnn_lowest',
'type': 'float',
'value': 0.1,
'limits': (0, 1),
'step': 0.01
}, {
'name': 'rval_thr',
'type': 'float',
'value': 0.85,
'limits': (-1, 1),
'step': 0.01
}, {
'name': 'rval_lowest',
'type': 'float',
'value': -1,
'limits': (-1, 1),
'step': 0.01
}, {
'name': 'min_SNR',
'type': 'float',
'value': 2,
'limits': (0, 20),
'step': 0.1
}, {
'name': 'SNR_lowest',
'type': 'float',
'value': 0,
'limits': (0, 20),
'step': 0.1
}, {
'name': 'RESET',
'type': 'action'
}, {
'name': 'SHOW BACKGROUND',
'type': 'action'
}, {
'name': 'SHOW NEURONS',
'type': 'action'
}]
## Create tree of Parameter objects
pars = Parameter.create(name='params', type='group', children=params)
params_action = [{
'name': 'Filter components',
'type': 'bool',
'value': True,
'tip': "Filter components"
}, {
'name': 'View components',
'type': 'list',
'values': ['All', 'Accepted', 'Rejected', 'Unassigned'],
'value': 'All'
}, {
'name': 'ADD GROUP',
'type': 'action'
}, {
'name': 'REMOVE GROUP',
'type': 'action'
}, {
'name': 'ADD SINGLE',
'type': 'action'
}, {
'name': 'REMOVE SINGLE',
'type': 'action'
}, {
'name': 'SAVE OBJECT',
'type': 'action'
}]
pars_action = Parameter.create(name='params_action',
type='group',
children=params_action)
t_action.setParameters(pars_action, showTop=False)
t_action.setWindowTitle('Parameter Action')
def reset_button():
global mode
mode = "reset"
p2.setTitle("mode: %s" % (mode))
#clear the upper right image
zeros = np.asarray([[0] * 80 for _ in range(60)])
img2.setImage(make_color_img(zeros), autoLevels=False)
draw_contours()
pars.param('RESET').sigActivated.connect(reset_button)
def show_background_button():
global bg_vline, min_background, max_background, background_num
global mode, background_first_frame_scaled
#clear thhe upper right image
zeros = np.asarray([[0] * 80 for _ in range(60)])
img2.setImage(make_color_img(zeros), autoLevels=False)
background_num = (background_num + 1) % estimates.f.shape[0]
mode = "background"
p2.setTitle("mode: %s %d" % (mode, background_num))
# display the first frame of the background
background_first_frame = estimates.b[:, background_num].reshape(
estimates.dims, order='F')
min_background_first_frame = np.min(background_first_frame)
max_background_first_frame = np.max(background_first_frame)
background_first_frame_scaled = make_color_img(
background_first_frame,
min_max=(min_background_first_frame, max_background_first_frame))
img.setImage(background_first_frame_scaled, autoLevels=False)
# draw the trace and the infinite line
trace_background = estimates.f[background_num]
p2.plot(trace_background, clear=True)
bg_vline = pg.InfiniteLine(angle=90, movable=True)
p2.addItem(bg_vline, ignoreBounds=True)
bg_vline.setValue(0)
bg_vline.sigPositionChanged.connect(show_background_update)
def show_background_update():
global bg_index, min_background, max_background, background_scaled
bg_index = int(bg_vline.value())
if bg_index > -1 and bg_index < estimates.f.shape[-1]:
# upper left component scrolls through the frames of the background
background = estimates.b[:, background_num].dot(
estimates.f[background_num, bg_index]).reshape(estimates.dims,
order='F')
background_scaled = make_color_img(
background,
min_max=(min_background[background_num],
max_background[background_num]))
img.setImage(background_scaled, autoLevels=False)
pars.param('SHOW BACKGROUND').sigActivated.connect(show_background_button)
def show_neurons_button():
global mode, neuron_selected
mode = "neurons"
neuron_selected = False
p2.setTitle("mode: %s" % (mode))
#clear the upper right image
zeros = np.asarray([[0] * 80 for _ in range(60)])
img2.setImage(make_color_img(zeros), autoLevels=False)
def show_neurons_clicked():
global nr_index
global x, y, i, j, val, min_dist_comp, contour_single, neuron_selected, comp2_scaled
neuron_selected = True
distances = np.sum(
((x, y) - estimates.cms[estimates.idx_components])**2, axis=1)**0.5
min_dist_comp = np.argmin(distances)
contour_all = [
cv2.threshold(img, np.int(thrshcomp_line.value()), 255, 0)[1]
for img in estimates.img_components[estimates.idx_components]
]
contour_single = contour_all[min_dist_comp]
# draw the traces (lower left component)
estimates.components_to_plot = estimates.idx_components[min_dist_comp]
p2.plot(estimates.C[estimates.components_to_plot] +
estimates.YrA[estimates.components_to_plot],
clear=True)
# plot img (upper left component)
img.setImage(estimates.background_image, autoLevels=False)
draw_contours_update(estimates.background_image, img)
# plot img2 (upper right component)
comp2 = np.multiply(estimates.Cn, contour_single > 0)
comp2_scaled = make_color_img(comp2,
min_max=(np.min(comp2), np.max(comp2)))
img2.setImage(comp2_scaled, autoLevels=False)
draw_contours_update(comp2_scaled, img2)
# set title for the upper two components
p3.setTitle("pos: (%0.1f, %0.1f) component: %d value: %g dist:%f" %
(x, y, estimates.components_to_plot, val,
distances[min_dist_comp]))
p1.setTitle("pos: (%0.1f, %0.1f) component: %d value: %g dist:%f" %
(x, y, estimates.components_to_plot, val,
distances[min_dist_comp]))
# draw the infinite line (INACTIVE IN THIS VERSION WITHOUT MMAP FILES)
# nr_vline = pg.InfiniteLine(angle=90, movable=True)
# p2.addItem(nr_vline, ignoreBounds=True)
# nr_vline.setValue(0)
# nr_vline.sigPositionChanged.connect(show_neurons_update)
nr_index = 0
def show_neurons_update(): # NOT CALLED IN THIS VERSION
global nr_index, frame_denoise_scaled, estimates, raw_mov_scaled
global min_mov, max_mov, min_mov_denoise, max_mov_denoise
if neuron_selected is False:
return
nr_index = int(nr_vline.value())
if nr_index > 0 and nr_index < mov[:, 0, 0].shape[0]:
# upper left component scrolls through the raw movie
raw_mov = mov[nr_index, :, :]
raw_mov_scaled = make_color_img(raw_mov,
min_max=(min_mov, max_mov))
img.setImage(raw_mov_scaled, autoLevels=False)
draw_contours_update(raw_mov_scaled, img)
# upper right component scrolls through the denoised movie
frame_denoise = estimates.A[:, estimates.idx_components].dot(
estimates.C[estimates.idx_components,
nr_index]).reshape(estimates.dims, order='F')
frame_denoise_scaled = make_color_img(frame_denoise,
min_max=(min_mov_denoise,
max_mov_denoise))
img2.setImage(frame_denoise_scaled, autoLevels=False)
draw_contours_update(frame_denoise_scaled, img2)
pars.param('SHOW NEURONS').sigActivated.connect(show_neurons_button)
def add_group():
estimates.accepted_list = np.union1d(estimates.accepted_list,
estimates.idx_components)
estimates.rejected_list = np.setdiff1d(estimates.rejected_list,
estimates.idx_components)
change(None, None)
pars_action.param('ADD GROUP').sigActivated.connect(add_group)
def remove_group():
estimates.rejected_list = np.union1d(estimates.rejected_list,
estimates.idx_components)
estimates.accepted_list = np.setdiff1d(estimates.accepted_list,
estimates.idx_components)
change(None, None)
pars_action.param('REMOVE GROUP').sigActivated.connect(remove_group)
def add_single():
estimates.accepted_list = np.union1d(estimates.accepted_list,
estimates.components_to_plot)
estimates.rejected_list = np.setdiff1d(estimates.rejected_list,
estimates.components_to_plot)
change(None, None)
pars_action.param('ADD SINGLE').sigActivated.connect(add_single)
def remove_single():
estimates.rejected_list = np.union1d(estimates.rejected_list,
estimates.components_to_plot)
estimates.accepted_list = np.setdiff1d(estimates.accepted_list,
estimates.components_to_plot)
change(None, None)
pars_action.param('REMOVE SINGLE').sigActivated.connect(remove_single)
def save_object():
print('Saving')
ffll = F.getSaveFileName(filter='*.hdf5')
print(ffll[0])
cnm_obj.estimates = estimates
cnm_obj.save(ffll[0])
pars_action.param('SAVE OBJECT').sigActivated.connect(save_object)
def action_pars_activated(param, changes):
change(None, None)
pars_action.sigTreeStateChanged.connect(action_pars_activated)
## If anything changes in the tree, print a message
def change(param, changes):
global estimates, pars, pars_action
set_par = pars.getValues()
if pars_action.param('Filter components').value():
for keyy in set_par.keys():
params_obj.quality.update({keyy: set_par[keyy][0]})
else:
params_obj.quality.update({
'cnn_lowest': .1,
'min_cnn_thr': 0.99,
'rval_thr': 0.85,
'rval_lowest': -1,
'min_SNR': 2,
'SNR_lowest': 0
})
estimates.filter_components(
mov,
params_obj,
dview=None,
select_mode=pars_action.param('View components').value())
if mode is "background":
return
else:
draw_contours()
pars.sigTreeStateChanged.connect(change)
change(None, None) # set params to default
t.setParameters(pars, showTop=False)
t.setWindowTitle('Parameter Quality')
## END PARAMS
## Display the widget as a new window
w.show()
## Start the Qt event loop
app.exit(app.exec_())
class ProjectSettingsDialog(QtGui.QDialog):
path2key=dict()
def __init__(self, parent = None, savedstate=None):
super(ProjectSettingsDialog, self).__init__(parent)
self.setWindowTitle("Application Settings")
layout = QtGui.QVBoxLayout(self)
self.initKeyParamMapping()
self._settings = Parameter.create(name='params', type='group', children=settings_params)
if savedstate:
self._settings.restoreState(savedstate)
# Holds settings keys that have changed by the user when the
# dialog is closed. Used to update any needed gui values..
self._updated_settings={}
self._settings.sigTreeStateChanged.connect(self.handleSettingChange)
self.initSettingsValues()
self.ptree = ParameterTree()
self.ptree.setParameters(self._settings, showTop=False)
self.ptree.setWindowTitle('MarkWrite Application Settings')
layout.addWidget(self.ptree)
self.ptree.adjustSize()
# OK and Cancel buttons
self.buttons = QtGui.QDialogButtonBox(
QtGui.QDialogButtonBox.Ok | QtGui.QDialogButtonBox.Cancel,
QtCore.Qt.Horizontal, self)
layout.addWidget(self.buttons)
self.buttons.accepted.connect(self.accept)
self.buttons.rejected.connect(self.reject)
self.resize(500,700)
def initKeyParamMapping(self):
if len(self.path2key)==0:
def replaceGroupKeys(paramlist, parent_path=[]):
for i,p in enumerate(paramlist):
if isinstance(p,basestring):
pdict=flattenned_settings_dict[p]
paramlist[i]=pdict
self.path2key['.'.join(parent_path+[pdict['name'],])]=p
elif isinstance(p,dict):
replaceGroupKeys(p.get('children'),parent_path+[p.get('name'),])
replaceGroupKeys(settings_params)
def initSettingsValues(self, pgroup=None):
global SETTINGS
if pgroup is None:
pgroup = self._settings
for child in pgroup.children():
if child.hasChildren():
self.initSettingsValues(child)
else:
path = self._settings.childPath(child)
if path is not None:
childName = '.'.join(path)
else:
childName = child.name()
if self.path2key.has_key(childName):
SETTINGS[self.path2key[childName]]=child.value()
## If anything changes in the tree, print a message
def handleSettingChange(self, param, changes):
global SETTINGS
for param, change, data in changes:
path = self._settings.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
if change == 'value':
setting_key = self.path2key[childName]
SETTINGS[setting_key]=data
self._updated_settings[setting_key] = data
#print 'settings_state:',self.settings_state
# static method to create the dialog and return (date, time, accepted)
@staticmethod
def getProjectSettings(parent = None, usersettings = None):
dialog = ProjectSettingsDialog(parent, usersettings)
result = dialog.exec_()
usersettings=dialog._settings.saveState()
return dialog._updated_settings,SETTINGS, usersettings, result == QtGui.QDialog.Accepted
class Labels(object):
def __init__(self, parent = None):
#print "init!!!!!"
self.parent = parent
## Dock: Labels
self.dLabels = Dock("Labels", size=(1, 1))
self.wLabels = ParameterTree()
self.wLabels.setWindowTitle('Labels')
self.dLabels.addWidget(self.wLabels)
self.labels_grp = 'Labels'
self.labels_A_str = 'Single'
self.labels_B_str = 'Multi'
self.labels_C_str = 'Dunno'
self.labelA = False
self.labelB = False
self.labelC = False
#######################
# Mandatory parameter #
#######################
self.params = [
{'name': self.labels_grp, 'type': 'group', 'children': [
{'name': self.labels_A_str, 'type': 'bool', 'value': self.labelA, 'tip': "Single"},
{'name': self.labels_B_str, 'type': 'bool', 'value': self.labelB, 'tip': "Multi"},
{'name': self.labels_C_str, 'type': 'bool', 'value': self.labelC, 'tip': "Dunno"},
]},
]
self.pLabels = Parameter.create(name='paramsLabel', type='group', \
children=self.params, expanded=True)
self.pLabels.sigTreeStateChanged.connect(self.change)
self.wLabels.setParameters(self.pLabels, showTop=False)
# If anything changes in the parameter tree, print a message
def change(self, panel, changes):
for param, change, data in changes:
path = panel.childPath(param)
if self.parent.args.v >= 1:
print(' path: %s' % path)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
self.paramUpdate(path, data)
##############################
# Mandatory parameter update #
##############################
def paramUpdate(self, path, data):
global dset
if path[1] == self.labels_A_str:
self.labelA = data
if data:
dset[self.parent.eventNumber] = 1
else:
dset[self.parent.eventNumber] = 0
elif path[1] == self.labels_B_str:
self.labelB = data
if data:
dset[self.parent.eventNumber] = 2
else:
dset[self.parent.eventNumber] = 0
elif path[1] == self.labels_C_str:
self.labelC = data
if data:
dset[self.parent.eventNumber] = 3
else:
dset[self.parent.eventNumber] = 0
def refresh(self):
fname = self.parent.psocakeRunDir + '/' + self.parent.experimentName + '_' + str(self.parent.runNumber).zfill(4) + '_labels.h5'
global dset
print "##### fname: ", fname
if self.parent.runNumber > 0:
if os.path.exists(fname):
labels = h5py.File(fname, 'r+', dtype = 'i8')
else:
labels = h5py.File(fname, 'w', dtype = 'i8')
try:
dset = labels["labels"]
except: # corrupt dataset, so create a new one
print labels
dset = labels.create_dataset("labels", (self.parent.exp.eventTotal, 1))
#print dset.shape
self.labelA = False
self.labelB = False
self.labelC = False
if dset[self.parent.eventNumber] == 1:
self.labelA = True
elif dset[self.parent.eventNumber] == 2:
self.labelB = True
elif dset[self.parent.eventNumber] == 3:
self.labelC = True
self.pLabels.param(self.labels_grp, self.labels_A_str).setValue(self.labelA)
self.pLabels.param(self.labels_grp, self.labels_B_str).setValue(self.labelB)
self.pLabels.param(self.labels_grp, self.labels_C_str).setValue(self.labelC)
def selected(text):
global sz, t
sz=SzenenTreeInputs(False,text)
t.setParameters(sz.p, showTop=False)
win = QtGui.QWidget()
comboBox = QtGui.QComboBox(win)
for cmdLst in cmdLsts:
comboBox.addItem(cmdLst)
comboBox.activated[str].connect(selected)
t = ParameterTree()
sz=SzenenTreeInputs(False,cmdLsts[0])
#print sz
t.setParameters(sz.p, showTop=False)
t.setWindowTitle('Szenen Setup:')
#t2 = ParameterTree()
#t2.setParameters(p, showTop=False)
layout = QtGui.QGridLayout()
win.setLayout(layout)
layout.addWidget(QtGui.QLabel(""), 1, 1, 1, 2)
layout.addWidget(comboBox, 0, 0, 1, 1)
layout.addWidget(t, 20, 0, 1, 1)
#layout.addWidget(t2, 1, 1, 1, 1)
win.show()
win.resize(800,800)
class MainWindow(Qt.QWidget):
''' Main Window '''
def __init__(self):
super(MainWindow, self).__init__()
layout = Qt.QVBoxLayout(self)
self.btnGen = Qt.QPushButton("Start Gen!")
layout.addWidget(self.btnGen)
self.StateParams = FileMod.SaveSateParameters(QTparent=self,
name='State')
self.Parameters = Parameter.create(name='params',
type='group',
children=(self.StateParams, ))
self.NifGenParams = FMacq.NifGeneratorParameters(name='NifGenerator')
self.Parameters.addChild(self.NifGenParams)
self.NiScopeParams = FMacq.NiScopeParameters(name='Scope')
self.Parameters.addChild(self.NiScopeParams)
#
self.FileParameters = FileMod.SaveFileParameters(QTparent=self,
name='Record File')
self.Parameters.addChild(self.FileParameters)
self.PSDParams = PltMod.PSDParameters(name='PSD Options')
self.PSDParams.param('Fs').setValue(self.NifGenParams.Fs.value())
self.PSDParams.param('Fmin').setValue(50)
self.PSDParams.param('nAvg').setValue(50)
self.PSDEnable = self.PSDParams.param('PSDEnable').value()
self.Parameters.addChild(self.PSDParams)
self.PlotParams = PltMod.PlotterParameters(name='Plot options')
self.PlotParams.SetChannels(self.NiScopeParams.GetChannels())
self.PlotParams.param('Fs').setValue(self.NifGenParams.Fs.value())
self.PltEnable = self.PlotParams.param('PlotEnable').value()
self.Parameters.addChild(self.PlotParams)
self.Parameters.sigTreeStateChanged.connect(self.on_pars_changed)
self.treepar = ParameterTree()
self.treepar.setParameters(self.Parameters, showTop=False)
self.treepar.setWindowTitle('pyqtgraph example: Parameter Tree')
layout.addWidget(self.treepar)
self.setGeometry(550, 10, 300, 700)
self.setWindowTitle('MainWindow')
self.btnGen.clicked.connect(self.on_btnGen)
self.threadAqc = None
self.threadSave = None
self.threadPlotter = None
self.threadPSDPlotter = None
def on_pars_changed(self, param, changes):
print("tree changes:")
for param, change, data in changes:
path = self.Parameters.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
print(' parameter: %s' % childName)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
if childName == 'NifGenerator.SamplingConfig.Fs':
self.NiScopeParams.Fs.setValue(data)
self.PlotParams.param('Fs').setValue(data)
self.PSDParams.param('Fs').setValue(data)
if childName == 'Scope.FetchConfig.NRow':
self.PlotParams.SetChannels(self.NiScopeParams.GetChannels())
if childName == 'Plot options.RefreshTime':
if self.threadPlotter is not None:
self.threadPlotter.SetRefreshTime(data)
if childName == 'Plot options.ViewTime':
if self.threadPlotter is not None:
self.threadPlotter.SetViewTime(data)
if childName == 'Plot options.PlotEnable':
self.PltEnable = data
if self.threadAqc is not None:
self.UpdatePlots()
if childName == 'PSD Options.PSDEnable':
self.PSDEnable = data
if self.threadAqc is not None:
self.UpdatePlots()
def on_btnGen(self):
print('h')
if self.threadAqc is None:
self.GenKwargs = self.NifGenParams.GetParams()
self.ScopeKwargs = self.NiScopeParams.GetParams()
self.threadAqc = FMacq.DataAcquisitionThread(
**self.GenKwargs, **self.ScopeKwargs)
self.threadAqc.NewData.connect(self.on_NewSample)
self.SaveFiles()
self.GenPlots()
self.threadAqc.start()
self.btnGen.setText("Stop Gen")
self.OldTime = time.time()
else:
self.threadAqc.NewData.disconnect()
self.threadAqc.stopSessions()
self.threadAqc.terminate()
self.threadAqc = None
if self.threadSave is not None:
self.threadSave.stop()
self.threadSave = None
self.DestroyPlotter()
self.DestroyPSD()
self.btnGen.setText("Start Gen")
def on_NewSample(self):
''' Visualization of streaming data-WorkThread. '''
Ts = time.time() - self.OldTime
self.OldTime = time.time()
if self.threadSave is not None:
self.threadSave.AddData(self.threadAqc.IntData)
if self.threadPlotter is not None:
self.threadPlotter.AddData(self.threadAqc.OutData)
if self.threadPSDPlotter is not None:
self.threadPSDPlotter.AddData(self.threadAqc.OutData)
print('Sample time', Ts)
def GenPlots(self):
PlotterKwargs = self.PlotParams.GetParams()
ScopeKwargs = self.NiScopeParams.GetParams()
if self.threadPlotter is None:
if self.PltEnable == True:
self.threadPlotter = PltMod.Plotter(**PlotterKwargs)
self.threadPlotter.start()
if self.threadPSDPlotter is None:
if self.PSDEnable == True:
self.threadPSDPlotter = PltMod.PSDPlotter(
ChannelConf=PlotterKwargs['ChannelConf'],
nChannels=ScopeKwargs['NRow'],
**self.PSDParams.GetParams())
self.threadPSDPlotter.start()
def DestroyPlotter(self):
if self.threadPlotter is not None:
self.threadPlotter.stop()
self.threadPlotter = None
def DestroyPSD(self):
if self.threadPSDPlotter is not None:
self.threadPSDPlotter.stop()
self.threadPSDPlotter = None
def UpdatePlots(self):
if self.PltEnable == False:
self.DestroyPlotter()
if self.PSDEnable == False:
self.DestroyPSD()
else:
self.GenPlots()
def SaveFiles(self):
FileName = self.FileParameters.param('File Path').value()
if FileName == '':
print('No file')
else:
if os.path.isfile(FileName):
print('Remove File')
os.remove(FileName)
MaxSize = self.FileParameters.param('MaxSize').value()
self.threadSave = FileMod.DataSavingThread(
FileName=FileName,
nChannels=self.ScopeKwargs['NRow'],
MaxSize=MaxSize)
self.threadSave.start()
GenName = FileName + '_GenConfig.dat'
ScopeName = FileName + '_ScopeConfig.dat'
if os.path.isfile(GenName):
print('Overwriting file')
OutGen = input('y/n + press(Enter)')
if OutGen == 'y':
self.GenArchivo(GenName, self.GenKwargs)
else:
self.GenArchivo(GenName, self.GenKwargs)
if os.path.isfile(ScopeName):
print('Overwriting file')
OutScope = input('y/n + press(Enter)')
if OutScope == 'y':
self.GenArchivo(ScopeName, self.ScopeKwargs)
else:
self.GenArchivo(ScopeName, self.ScopeKwargs)
def GenArchivo(self, name, dic2Save):
with open(name, "wb") as f:
pickle.dump(dic2Save, f)
'name': 'MAX RADIUS',
'type': 'int',
'value': 10
}, {
'name': 'ROUGHNESS',
'type': 'int',
'value': 1
}]
}]
pars_action = Parameter.create(name='params_action',
type='group',
children=params_action)
neuron_action.setParameters(pars_action, showTop=False)
neuron_action.setWindowTitle('Parameter Action')
mode = pars_action.getValues()['MODE'][0]
def mouseClickEvent(event):
global mode, x, y, i, j, pts, roi, cur_image
if mode == "POLYGON":
pos = img.mapFromScene(event.pos())
x = int(pos.x())
y = int(pos.y())
j, i = pos.y(), pos.x()
i = int(np.clip(i, 0, dims[0] - 1))
j = int(np.clip(j, 0, dims[1] - 1))
p1.plot(x=[i],
y=[j],
symbol='o',
class ProtocolControlWidget(QWidget):
"""GUI for controlling a ProtocolRunner.
This class implements:
- selection box of the Protocol to be run;
- window for controlling Protocol parameters;
- toggle button for starting/stopping the Protocol;
- progress bar to display progression of the Protocol.
Parameters
----------
protocol_runner: :class:`ProtocolRunner <stytra.stimulation.ProtocolRunner>` object
ProtocolRunner that is controlled by the GUI.
**Signals**
"""
sig_start_protocol = pyqtSignal()
""" Emitted via the toggle button click, meant to
start the protocol """
sig_stop_protocol = pyqtSignal()
""" Emitted via the toggle button click, meant to
abort the protocol"""
def __init__(self, protocol_runner=None, *args):
""" """
super().__init__(*args)
self.protocol_runner = protocol_runner
# Create parametertree for protocol parameter control
self.protocol_params_tree = ParameterTree(showHeader=False)
# Layout for selecting the protocol:
self.lyt_prot_selection = QHBoxLayout()
# Dropdown menu with the protocol classes found in the Experiment:
self.combo_prot = QComboBox()
self.combo_prot.addItems(
list(self.protocol_runner.prot_class_dict.keys()))
self.combo_prot.currentIndexChanged.connect(self.set_protocol)
self.lyt_prot_selection.addWidget(self.combo_prot)
# Window with the protocol parameters:
self.protocol_params_butt = QPushButton("Protocol parameters")
self.protocol_params_butt.clicked.connect(self.show_stim_params_gui)
self.lyt_prot_selection.addWidget(self.protocol_params_butt)
# Layout for protocol start and progression report:
self.lyt_run = QHBoxLayout()
# Button for startup:
self.button_toggle_prot = QPushButton("▶")
self.button_toggle_prot.clicked.connect(self.toggle_protocol_running)
self.lyt_run.addWidget(self.button_toggle_prot)
# Progress bar for monitoring the protocol:
self.progress_bar = QProgressBar()
self.progress_bar.setFormat("%p% %v/%m")
self.lyt_run.addWidget(self.progress_bar)
# Global layout:
self.lyt = QVBoxLayout()
self.lyt.setContentsMargins(0, 0, 0, 0)
self.lyt.addLayout(self.lyt_run)
self.lyt.addLayout(self.lyt_prot_selection)
self.setLayout(self.lyt)
self.timer = None
# Connect events and signals from the ProtocolRunner to update the GUI:
self.protocol_runner.sig_protocol_updated.connect(
self.update_stim_duration)
self.protocol_runner.sig_timestep.connect(self.update_progress)
self.protocol_runner.sig_protocol_started.connect(self.toggle_icon)
self.protocol_runner.sig_protocol_finished.connect(self.toggle_icon)
self.protocol_runner.sig_protocol_updated.connect(
self.update_stim_duration)
# If a previous protocol was already set in the protocol runner
# change the GUI values accordingly:
if protocol_runner.protocol is not None:
self.combo_prot.setCurrentText(protocol_runner.protocol.name)
else:
self.set_protocol()
def show_stim_params_gui(self):
"""Create and show window to update protocol parameters.
"""
if self.protocol_runner.protocol.params is not None:
self.protocol_params_tree.setParameters(
self.protocol_runner.protocol.params)
self.protocol_params_tree.show()
self.protocol_params_tree.setWindowTitle("Protocol parameters")
self.protocol_params_tree.resize(300, 600)
def toggle_protocol_running(self):
"""Emit the start and stop signals. These can be used in the Experiment
class or directly connected with the respective ProtocolRunner
start() and stop() methods.
Parameters
----------
Returns
-------
"""
# Start/stop the protocol:
if not self.protocol_runner.running:
self.sig_start_protocol.emit()
else:
self.sig_stop_protocol.emit()
self.toggle_icon()
def toggle_icon(self):
"""Change the play/stop icon of the GUI.
"""
if self.button_toggle_prot.text() == "■":
self.button_toggle_prot.setText("▶")
self.progress_bar.setValue(0)
else:
self.button_toggle_prot.setText("■")
def update_stim_duration(self):
""" """
self.progress_bar.setMaximum(int(self.protocol_runner.duration))
self.progress_bar.setValue(0)
def update_progress(self):
""" """
self.progress_bar.setValue(int(self.protocol_runner.t))
def set_protocol(self):
"""Use value in the dropdown menu to change the protocol.
"""
protocol_name = self.combo_prot.currentText()
self.protocol_runner.set_new_protocol(protocol_name)
self.button_toggle_prot.setEnabled(True)
class CrystalIndexing(object):
def __init__(self, parent = None):
self.parent = parent
## Dock 14: Indexing
self.d14 = Dock("Indexing", size=(1, 1))
self.w21 = ParameterTree()
self.w21.setWindowTitle('Indexing')
self.d14.addWidget(self.w21)
self.w22 = pg.LayoutWidget()
self.launchIndexBtn = QtGui.QPushButton('Launch indexing')
self.w22.addWidget(self.launchIndexBtn, row=0, col=0)
self.synchBtn = QtGui.QPushButton('Deploy CrystFEL geometry')
self.w22.addWidget(self.synchBtn, row=1, col=0)
self.d14.addWidget(self.w22)
self.index_grp = 'Crystal indexing'
self.index_on_str = 'Indexing on'
self.index_geom_str = 'CrystFEL geometry'
self.index_peakMethod_str = 'Peak method'
self.index_intRadius_str = 'Integration radii'
self.index_pdb_str = 'PDB'
self.index_method_str = 'Indexing method'
#self.index_minPeaks_str = 'Minimum number of peaks'
#self.index_maxPeaks_str = 'Maximum number of peaks'
#self.index_minRes_str = 'Minimum resolution (pixels)'
self.index_tolerance_str = 'Tolerance'
self.index_extra_str = 'Extra CrystFEL parameters'
self.launch_grp = 'Batch'
self.outDir_str = 'Output directory'
self.runs_str = 'Runs(s)'
self.sample_str = 'Sample name'
self.tag_str = 'Tag'
self.queue_str = 'Queue'
self.chunkSize_str = 'Chunk size'
self.keepData_str = 'Keep CXI images'
self.noe_str = 'Number of events to process'
(self.psanaq_str,self.psnehq_str,self.psfehq_str,self.psnehprioq_str,self.psfehprioq_str,self.psnehhiprioq_str,self.psfehhiprioq_str,self.psdebugq_str) = \
('psanaq','psnehq','psfehq','psnehprioq','psfehprioq','psnehhiprioq','psfehhiprioq','psdebugq')
self.outDir = self.parent.psocakeDir
self.outDir_overridden = False
self.runs = ''
self.sample = 'crystal'
self.tag = ''
self.queue = self.psanaq_str
self.chunkSize = 500
self.noe = -1
# Indexing
self.showIndexedPeaks = False
self.indexedPeaks = None
self.hiddenCXI = '.temp.cxi'
self.hiddenCrystfelStream = '.temp.stream'
self.hiddenCrystfelList = '.temp.lst'
self.indexingOn = False
self.numIndexedPeaksFound = 0
self.geom = '.temp.geom'
self.peakMethod = 'cxi'
self.intRadius = '2,3,4'
self.pdb = ''
self.indexingMethod = 'mosflm-noretry,dirax'
#self.minPeaks = 15
#self.maxPeaks = 2048
#self.minRes = 0
self.tolerance = '5,5,5,1.5'
self.extra = ''
self.keepData = True
#######################
# Mandatory parameter #
#######################
self.params = [
{'name': self.index_grp, 'type': 'group', 'children': [
{'name': self.index_on_str, 'type': 'bool', 'value': self.indexingOn, 'tip': "Turn on indexing"},
{'name': self.index_geom_str, 'type': 'str', 'value': self.geom, 'tip': "CrystFEL geometry file"},
#{'name': self.index_peakMethod_str, 'type': 'str', 'value': self.peakMethod, 'tip': "Turn on indexing"},
{'name': self.index_intRadius_str, 'type': 'str', 'value': self.intRadius, 'tip': "Integration radii"},
{'name': self.index_pdb_str, 'type': 'str', 'value': self.pdb, 'tip': "(Optional) CrystFEL unitcell file"},
{'name': self.index_method_str, 'type': 'str', 'value': self.indexingMethod, 'tip': "comma separated indexing methods"},
{'name': self.index_tolerance_str, 'type': 'str', 'value': self.tolerance,
'tip': "Indexing tolerance, default: 5,5,5,1.5"},
{'name': self.index_extra_str, 'type': 'str', 'value': self.extra,
'tip': "Other indexing parameters"},
#{'name': self.index_minPeaks_str, 'type': 'int', 'value': self.minPeaks,
# 'tip': "Index only if there are more Bragg peaks found"},
#{'name': self.index_maxPeaks_str, 'type': 'int', 'value': self.maxPeaks,
# 'tip': "Index only if there are less Bragg peaks found"},
#{'name': self.index_minRes_str, 'type': 'int', 'value': self.minRes,
# 'tip': "Index only if Bragg peak resolution is at least this"},
]},
{'name': self.launch_grp, 'type': 'group', 'children': [
{'name': self.outDir_str, 'type': 'str', 'value': self.outDir},
{'name': self.runs_str, 'type': 'str', 'value': self.runs, 'tip': "comma separated or use colon for a range, e.g. 1,3,5:7 = runs 1,3,5,6,7"},
{'name': self.sample_str, 'type': 'str', 'value': self.sample, 'tip': "name of the sample saved in the cxidb file, e.g. lysozyme"},
{'name': self.tag_str, 'type': 'str', 'value': self.tag, 'tip': "attach tag to stream, e.g. cxitut13_0010_tag.stream"},
{'name': self.queue_str, 'type': 'list', 'values': {self.psfehhiprioq_str: self.psfehhiprioq_str,
self.psnehhiprioq_str: self.psnehhiprioq_str,
self.psfehprioq_str: self.psfehprioq_str,
self.psnehprioq_str: self.psnehprioq_str,
self.psfehq_str: self.psfehq_str,
self.psnehq_str: self.psnehq_str,
self.psanaq_str: self.psanaq_str,
self.psdebugq_str: self.psdebugq_str},
'value': self.queue, 'tip': "Choose queue"},
{'name': self.chunkSize_str, 'type': 'int', 'value': self.chunkSize, 'tip': "number of patterns to process per worker"},
{'name': self.keepData_str, 'type': 'bool', 'value': self.keepData, 'tip': "Do not delete cxidb images in cxi file"},
]},
]
self.p9 = Parameter.create(name='paramsCrystalIndexing', type='group', \
children=self.params, expanded=True)
self.w21.setParameters(self.p9, showTop=False)
self.p9.sigTreeStateChanged.connect(self.change)
self.launchIndexBtn.clicked.connect(self.indexPeaks)
self.synchBtn.clicked.connect(self.syncGeom)
# Launch indexing
def indexPeaks(self):
self.parent.thread.append(LaunchIndexer.LaunchIndexer(self.parent)) # send parent parameters with self
self.parent.thread[self.parent.threadCounter].launch(self.parent.experimentName, self.parent.detInfo)
self.parent.threadCounter += 1
# Update psana geometry
def syncGeom(self):
with pg.BusyCursor():
print "#################################################"
print "Updating psana geometry with CrystFEL geometry"
print "#################################################"
self.parent.geom.findPsanaGeometry()
psanaGeom = self.parent.psocakeRunDir + "/.temp.data"
if self.parent.args.localCalib:
cmd = ["crystfel2psana",
"-e", self.parent.experimentName,
"-r", str(self.parent.runNumber),
"-d", str(self.parent.det.name),
"--rootDir", '.',
"-c", self.geom,
"-p", psanaGeom,
"-z", str(self.parent.clen)]
else:
cmd = ["crystfel2psana",
"-e", self.parent.experimentName,
"-r", str(self.parent.runNumber),
"-d", str(self.parent.det.name),
"--rootDir", self.parent.rootDir,
"-c", self.geom,
"-p", psanaGeom,
"-z", str(self.parent.clen)]
if self.parent.args.v >= 0: print "cmd: ", cmd
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
output = p.communicate()[0]
p.stdout.close()
# Reload new psana geometry
cmts = {'exp': self.parent.experimentName, 'app': 'psocake', 'comment': 'converted from crystfel geometry'}
if self.parent.args.localCalib:
calibDir = './calib'
elif self.parent.args.outDir is None:
calibDir = self.parent.rootDir + '/calib'
else:
calibDir = '/reg/d/psdm/' + self.parent.experimentName[:3] + '/' + self.parent.experimentName + '/calib'
deploy_calib_file(cdir=calibDir, src=str(self.parent.det.name), type='geometry',
run_start=self.parent.runNumber, run_end=None, ifname=psanaGeom, dcmts=cmts, pbits=0)
self.parent.exp.setupExperiment()
self.parent.img.getDetImage(self.parent.eventNumber)
self.parent.geom.updateRings()
self.parent.index.updateIndex()
self.parent.geom.drawCentre()
# If anything changes in the parameter tree, print a message
def change(self, panel, changes):
for param, change, data in changes:
path = panel.childPath(param)
if self.parent.args.v >= 1:
print(' path: %s' % path)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
self.paramUpdate(path, change, data)
##############################
# Mandatory parameter update #
##############################
def paramUpdate(self, path, change, data):
if path[1] == self.index_on_str:
self.updateIndexStatus(data)
elif path[1] == self.index_geom_str:
self.updateGeom(data)
elif path[1] == self.index_peakMethod_str:
self.updatePeakMethod(data)
elif path[1] == self.index_intRadius_str:
self.updateIntegrationRadius(data)
elif path[1] == self.index_pdb_str:
self.updatePDB(data)
elif path[1] == self.index_method_str:
self.updateIndexingMethod(data)
#elif path[1] == self.index_minPeaks_str:
# self.updateMinPeaks(data)
#elif path[1] == self.index_maxPeaks_str:
# self.updateMaxPeaks(data)
#elif path[1] == self.index_minRes_str:
# self.updateMinRes(data)
elif path[1] == self.index_tolerance_str:
self.updateTolerance(data)
elif path[1] == self.index_extra_str:
self.updateExtra(data)
# launch grp
elif path[1] == self.outDir_str:
self.updateOutputDir(data)
elif path[1] == self.runs_str:
self.updateRuns(data)
elif path[1] == self.sample_str:
self.updateSample(data)
elif path[1] == self.tag_str:
self.updateTag(data)
elif path[1] == self.queue_str:
self.updateQueue(data)
elif path[1] == self.chunkSize_str:
self.updateChunkSize(data)
elif path[1] == self.noe_str:
self.updateNoe(data)
elif path[1] == self.keepData_str:
self.keepData = data
def updateIndexStatus(self, data):
self.indexingOn = data
self.showIndexedPeaks = data
self.updateIndex()
def updateGeom(self, data):
self.geom = data
self.updateIndex()
def updatePeakMethod(self, data):
self.peakMethod = data
if self.indexingOn:
self.updateIndex()
def updateIntegrationRadius(self, data):
self.intRadius = data
self.updateIndex()
def updatePDB(self, data):
self.pdb = data
self.updateIndex()
def updateIndexingMethod(self, data):
self.indexingMethod = data
self.updateIndex()
#def updateMinPeaks(self, data):
# self.minPeaks = data
# self.updateIndex()
#def updateMaxPeaks(self, data):
# self.maxPeaks = data
# self.updateIndex()
#def updateMinRes(self, data):
# self.minRes = data
# self.updateIndex()
def updateTolerance(self, data):
self.tolerance = data
self.updateIndex()
def updateExtra(self, data):
self.extra = data
self.updateIndex()
def updateIndex(self):
if self.indexingOn:
self.indexer = IndexHandler(parent=self.parent)
self.indexer.computeIndex(self.parent.experimentName, self.parent.runNumber, self.parent.detInfo,
self.parent.eventNumber, self.geom, self.peakMethod, self.intRadius, self.pdb,
self.indexingMethod, self.parent.pk.minPeaks, self.parent.pk.maxPeaks, self.parent.pk.minRes,
self.tolerance, self.extra, self.outDir, queue=None)
def updateOutputDir(self, data):
self.outDir = data
self.outDir_overridden = True
def updateRuns(self, data):
self.runs = data
def updateSample(self, data):
self.sample = data
def updateTag(self, data):
self.tag = data
def updateQueue(self, data):
self.queue = data
def updateChunkSize(self, data):
self.chunkSize = data
def updateNoe(self, data):
self.noe = data
def clearIndexedPeaks(self):
self.parent.img.w1.getView().removeItem(self.parent.img.abc_text)
self.parent.img.indexedPeak_feature.setData([], [], pxMode=False)
if self.parent.args.v >= 1: print "Done clearIndexedPeaks"
def displayWaiting(self):
if self.showIndexedPeaks:
if self.numIndexedPeaksFound == 0: # indexing proceeding
xMargin = 5 # pixels
maxX = np.max(self.parent.det.indexes_x(self.parent.evt)) + xMargin
maxY = np.max(self.parent.det.indexes_y(self.parent.evt))
# Draw a big X
cenX = np.array((self.parent.cx,)) + 0.5
cenY = np.array((self.parent.cy,)) + 0.5
diameter = 256 # self.peakRadius*2+1
self.parent.img.indexedPeak_feature.setData(cenX, cenY, symbol='t', \
size=diameter, brush=(255, 255, 255, 0), \
pen=pg.mkPen({'color': "#FF00FF", 'width': 3}),
pxMode=False)
self.parent.img.abc_text = pg.TextItem(html='', anchor=(0, 0))
self.parent.img.w1.getView().addItem(self.parent.img.abc_text)
self.parent.img.abc_text.setPos(maxX, maxY)
def drawIndexedPeaks(self, latticeType=None, centering=None, numSaturatedPeaks=None, unitCell=None):
self.clearIndexedPeaks()
if self.showIndexedPeaks:
if self.indexedPeaks is not None and self.numIndexedPeaksFound > 0: # indexing succeeded
cenX = self.indexedPeaks[:,0]+0.5
cenY = self.indexedPeaks[:,1]+0.5
cenX = np.concatenate((cenX,cenX,cenX))
cenY = np.concatenate((cenY,cenY,cenY))
diameter = np.ones_like(cenX)
diameter[0:self.numIndexedPeaksFound] = float(self.intRadius.split(',')[0])*2
diameter[self.numIndexedPeaksFound:2*self.numIndexedPeaksFound] = float(self.intRadius.split(',')[1])*2
diameter[2*self.numIndexedPeaksFound:3*self.numIndexedPeaksFound] = float(self.intRadius.split(',')[2])*2
self.parent.img.indexedPeak_feature.setData(cenX, cenY, symbol='o', \
size=diameter, brush=(255,255,255,0), \
pen=pg.mkPen({'color': "#FF00FF", 'width': 1.5}), pxMode=False)
# Write unit cell parameters
if unitCell is not None:
xMargin = 5
yMargin = 400
maxX = np.max(self.parent.det.indexes_x(self.parent.evt)) + xMargin
maxY = np.max(self.parent.det.indexes_y(self.parent.evt)) - yMargin
myMessage = '<div style="text-align: center"><span style="color: #FF00FF; font-size: 12pt;">lattice='+\
latticeType +'<br>centering=' + centering + '<br>a='+\
str(round(float(unitCell[0])*10,2))+'A <br>b='+str(round(float(unitCell[1])*10,2))+'A <br>c='+\
str(round(float(unitCell[2])*10,2))+'A <br>α='+str(round(float(unitCell[3]),2))+\
'° <br>β='+str(round(float(unitCell[4]),2))+'° <br>γ='+\
str(round(float(unitCell[5]),2))+'° <br></span></div>'
self.parent.img.abc_text = pg.TextItem(html=myMessage, anchor=(0,0))
self.parent.img.w1.getView().addItem(self.parent.img.abc_text)
self.parent.img.abc_text.setPos(maxX, maxY)
else: # Failed indexing
xMargin = 5 # pixels
maxX = np.max(self.parent.det.indexes_x(self.parent.evt))+xMargin
maxY = np.max(self.parent.det.indexes_y(self.parent.evt))
# Draw a big X
cenX = np.array((self.parent.cx,))+0.5
cenY = np.array((self.parent.cy,))+0.5
diameter = 256 #self.peakRadius*2+1
self.parent.img.indexedPeak_feature.setData(cenX, cenY, symbol='x', \
size=diameter, brush=(255,255,255,0), \
pen=pg.mkPen({'color': "#FF00FF", 'width': 3}), pxMode=False)
self.parent.img.abc_text = pg.TextItem(html='', anchor=(0,0))
self.parent.img.w1.getView().addItem(self.parent.img.abc_text)
self.parent.img.abc_text.setPos(maxX,maxY)
else:
self.parent.img.indexedPeak_feature.setData([], [], pxMode=False)
if self.parent.args.v >= 1: print "Done updatePeaks"
# This function probably doesn't get called
def launchIndexing(self, requestRun=None):
self.batchIndexer = IndexHandler(parent=self.parent)
if requestRun is None:
self.batchIndexer.computeIndex(self.parent.experimentName, self.parent.runNumber, self.parent.detInfo,
self.parent.eventNumber, self.geom, self.peakMethod, self.intRadius, self.pdb,
self.indexingMethod, self.parent.pk.minPeaks, self.parent.pk.maxPeaks, self.parent.pk.minRes,
self.tolerance, self.extra, self.outDir, self.runs, self.sample, self.tag, self.queue, self.chunkSize, self.noe)
else:
self.batchIndexer.computeIndex(self.parent.experimentName, requestRun, self.parent.detInfo,
self.parent.eventNumber, self.geom, self.peakMethod, self.intRadius, self.pdb,
self.indexingMethod, self.parent.pk.minPeaks, self.parent.pk.maxPeaks, self.parent.pk.minRes,
self.tolerance, self.extra, self.outDir, self.runs, self.sample, self.tag, self.queue, self.chunkSize, self.noe)
if self.parent.args.v >= 1: print "Done updateIndex"
def start_gui(self, skip_exec=False, qapp=None):
from PyQt5 import QtWidgets
# import scaffan.qtexceptionhook
# import QApplication, QFileDialog
if not skip_exec and qapp == None:
qapp = QtWidgets.QApplication(sys.argv)
self.parameters.param("Input", "Select").sigActivated.connect(
self.select_file_gui)
# self.parameters.param("Output", "Select").sigActivated.connect(
# self.select_output_dir_gui
# )
self.parameters.param(
"Output", "Select Common Spreadsheet File").sigActivated.connect(
self.select_output_spreadsheet_gui)
self.parameters.param("Run").sigActivated.connect(self.run)
self.parameters.param("Input", "X-Axis").sigValueChanged.connect(
self._on_param_change)
self.parameters.param("Input", "Y-Axis").sigValueChanged.connect(
self._on_param_change)
self.parameters.param("Input", "Time Axis").sigValueChanged.connect(
self._on_param_change)
self.parameters.param("Input", "C-Axis").sigValueChanged.connect(
self._on_param_change)
self.parameters.param("Input",
"Tracked Channel").sigValueChanged.connect(
self._on_param_change)
self.parameters.param("Input", "Preview Time").sigValueChanged.connect(
self._on_param_change)
# self.parameters.param("Processing", "Open output dir").setValue(True)
t = ParameterTree()
t.setParameters(self.parameters, showTop=False)
t.setWindowTitle("pyqtgraph example: Parameter Tree")
t.show()
# print("run scaffan")
win = QtGui.QWidget()
win.setWindowTitle("CellTrack {}".format(celltrack.__version__))
logo_fn = op.join(op.dirname(__file__), "celltrack_icon512.png")
logo_fav_fn = op.join(op.dirname(__file__), "logo_fav.png")
logo_prifuk = op.join(op.dirname(__file__), "logo_prifuk.png")
app_icon = QtGui.QIcon()
# app_icon.addFile(logo_fn, QtCore.QSize(16, 16))
app_icon.addFile(logo_fn)
win.setWindowIcon(app_icon)
# qapp.setWindowIcon(app_icon)
layout = QtGui.QGridLayout()
layout.setColumnStretch(0, 2)
layout.setColumnStretch(1, 3)
win.setLayout(layout)
# layout.setColumnStretch(2, 3)
logolink = QGroupBox("Created by")
logolink_layout = QtGui.QGridLayout()
logolink.setLayout(logolink_layout)
pic = QtGui.QLabel()
urlLink = "<a href=\"http://www.google.com\">'Click this link to go to Google'</a>"
pic.setText(urlLink)
pic.setPixmap(QtGui.QPixmap(logo_fav_fn).scaled(50, 50))
pic.setOpenExternalLinks(True)
pic.show()
urlLink = "<a href=\"http://www.google.com\">'Click this link to go to Google'</a>"
pic2 = QtGui.QLabel()
pic2.setText(urlLink)
pic2.setPixmap(QtGui.QPixmap(logo_prifuk).scaled(50, 50))
pic2.setOpenExternalLinks(True)
pic2.show()
# self.image1 = PlotCanvas()
# self.image1.axes.set_axis_off()
# self.image1.imshow(plt.imread(logo_fn))
# self.image1.plot()
self.image2 = PlotCanvas()
self.image2.axes.text(0.1, 0.6, "Load Tiff file")
self.image2.axes.text(0.1, 0.5, "Check pixelsize")
self.image2.axes.text(0.1, 0.4, "Run")
# self.image2.axes.text(0.1, 0.3, "Use Comparative Annotation (optimal in further iterations)")
self.image2.axes.set_axis_off()
self.image2.draw()
# self.image2.plot()
# self.addToolBar(NavigationToolbar(self.image1, self))
# self.image1.setPixmap(QtGui.QPixmap(logo_fn).scaled(100, 100))
# self.image1.show()
# self.image2 = QtGui.QLabel()
# self.image2.setPixmap(QtGui.QPixmap(logo_fn).scaled(100, 100))
# self.image2.show()
# layout.addWidget(QtGui.QLabel("These are two views of the same data. They should always display the same values."), 0, 0, 1, 2)
logolink_layout.addWidget(pic, 1, 0, 1, 1)
logolink_layout.addWidget(pic2, 1, 1, 1, 1)
layout.addWidget(logolink, 1, 0, 1, 1)
layout.addWidget(t, 2, 0, 1, 1)
# layout.addWidget(NavigationToolbar(self.image2, win),1, 2, 1, 1)
layout.addWidget(NavigationToolbar(self.image2, win), 1, 1, 1, 1)
layout.addWidget(self.image2, 2, 1, 1, 1)
# layout.addWidget(self.image2, 2, 2, 1, 1)
# layout.addWidget(t2, 1, 1, 1, 1)
win.show()
win.resize(1200, 800)
self.win = win
# win.
self.qapp = qapp
if not skip_exec:
qapp.exec_()
class MainWindow(Qt.QWidget):
''' Main Window '''
def __init__(self):
# 'Super' is used to initialize the class from which this class
# depends, in this case MainWindow depends on Qt.Widget class
super(MainWindow, self).__init__()
# buscar esto que son cosas de la ventana de la gui
self.setFocusPolicy(Qt.Qt.WheelFocus)
layout = Qt.QVBoxLayout(self)
# Qt.QPushButton is used to generate a button in the GUI
self.btnStart = Qt.QPushButton("Start Gen and Adq!")
layout.addWidget(self.btnStart)
# #############################Save##############################
self.SaveStateParams = FileMod.SaveTreeSateParameters(QTparent=self,
name='State')
# With this line, it is initize the group of parameters that are
# going to be part of the full GUI
self.Parameters = Parameter.create(name='params',
type='group',
children=(self.SaveStateParams,))
# #############################File##############################
self.FileParams = FileMod.SaveFileParameters(QTparent=self,
name='Record File')
self.Parameters.addChild(self.FileParams)
# ############################SignalConfig##############################
# QTparent indicades that is going to be added a tree in the actual
# GUI that has already been created.
# Name is the name that you want as title of your tree in the GUI
self.SigParams = SigConfig.SignalConfig(QTparent=self,
name='Signal SetUp')
self.Parameters.addChild(self.SigParams)
# You can create variables of the main class with the values of
# an specific tree you have created in a concret GroupParameter class
self.GenParams = self.SigParams.param('GeneralConfig')
self.CarrParams = self.SigParams.param('CarrierConfig')
self.ModParams = self.SigParams.param('ModConfig')
# ############################LockInConfig##############################
# It is added the tree of LockIn_Config to the actual GUI
self.LockInParams = LockInConfig.LockIn_Config(QTparent=self,
name='LockIn SetUp')
# And its parameters are added to Parameters variable
self.Parameters.addChild(self.LockInParams)
# A variable with LockInConfig parameters is created
self.LockInConf = self.LockInParams.param('LockInConfig')
# ############################LPFConfig##############################
# It is added the tree of LPFilterConfig to the actual GUI
self.LPFParams = LPFilter.LPFilterConfig(QTparent=self,
name='LPF SetUp')
# And its parameters are added to Parameters variable
self.Parameters.addChild(self.LPFParams)
# A variable with LPFConfig parameters is created
self.LPFConf = self.LPFParams.param('LPFConfig')
# #############################Plots##############################
self.PsdPlotParams = PSDPlt.PSDParameters(name='PSD Plot Options')
self.PsdPlotParams.param('Fmin').setValue(50)
self.PsdPlotParams.param('nAvg').setValue(50)
self.Parameters.addChild(self.PsdPlotParams)
self.PlotParams = TimePlt.PlotterParameters(name='Plot options')
self.PlotParams.SetChannels({'Row1': 0,})
self.Parameters.addChild(self.PlotParams)
# ############################Shared Configs##############################
# It can be seen that some parameters of different trees are
# the same, so they need to have the same value.
# To force a value in a parameter it is used the statement setValue
# With the form XX.param('param') you access to a concrete param value
# With the form self.XX.param.value() you acced to the value of a
# SELF variable created in the XX class
self.LockInConf.param('Fs').setValue(self.SigParams.Fs.value())
self.LPFConf.param('Fs').setValue(self.SigParams.Fs.value())
self.PlotParams.param('Fs').setValue(self.LockInParams.OutFs.value())
self.PsdPlotParams.param('Fs').setValue(self.LockInParams.OutFs.value())
self.LockInConf.param(
'CarrFrequency').setValue(
self.SigParams.CarrFreq.value())
self.LPFConf.param(
'CuttOffFreq').setValue(
self.LockInParams.OutFs.value())
self.LockInConf.param(
'nSamples').setValue(
self.SigParams.nSamples.value())
# ############################Instancias for Changes######################
# Statement sigValueChanged.connect is used to execute a function
# if the indicated value (param('param')) changes
# Statement sigTreeStateChanged.connect is used to execute a function
# if any parameter of the indicated tree changes
self.CarrParams.param('CarrFrequency').sigValueChanged.connect(self.on_Fc_changed)
self.GenParams.sigTreeStateChanged.connect(self.on_GenConfig_changed)
self.CarrParams.sigTreeStateChanged.connect(self.on_CarrierConfig_changed)
self.ModParams.sigTreeStateChanged.connect(self.on_ModConfig_changed)
self.LockInConf.param('OutFs').sigValueChanged.connect(self.on_OutFs_changed)
self.PlotParams.param('PlotEnable').sigValueChanged.connect(self.on_PlotEnable_changed)
self.PlotParams.param('RefreshTime').sigValueChanged.connect(self.on_RefreshTimePlt_changed)
self.PlotParams.param('ViewTime').sigValueChanged.connect(self.on_SetViewTimePlt_changed)
self.PsdPlotParams.param('PSDEnable').sigValueChanged.connect(self.on_PSDEnable_changed)
# ############################GuiConfiguration##############################
# Is the same as before functions but for 'Parameters' variable,
# which conatins all the trees of all the Gui, so on_Params_changed
# will be execute for any change in the Gui
self.Parameters.sigTreeStateChanged.connect(self.on_Params_changed)
# EXPLICAR ESTO TAMBIEN QUE TIENE QUE VER CON LA GUI
self.treepar = ParameterTree()
self.treepar.setParameters(self.Parameters, showTop=False)
self.treepar.setWindowTitle('pyqtgraph example: Parameter Tree')
layout.addWidget(self.treepar)
self.setGeometry(550, 10, 300, 700)
self.setWindowTitle('MainWindow')
# It is connected the action of click a button with a function
self.btnStart.clicked.connect(self.on_btnStart)
# Threads are startes as None
self.threadGeneration = None
self.threadLockIn = None
self.threadPlotter = None
self.threadPsdPlotter = None
self.threadDemodSave = None
# ############################Changes Control##############################
def on_Params_changed(self, param, changes):
'''
This function is used to print in the consol the changes that have
been done.
'''
print("tree changes:")
for param, change, data in changes:
path = self.Parameters.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
print(' parameter: %s' % childName)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
# ############################Changes Emits##############################
def on_Fc_changed(self):
'''
This function is used to change the Carrier Frequency value of
Lock In tree to the same value specified in Signal Configuration tree
'''
self.LockInConf.param(
'CarrFrequency').setValue(
self.SigParams.CarrFreq.value())
if self.threadLockIn is not None:
self.threadLockIn.LockIn.GenerateVcoiSignal(
self.SigParams.CarrFreq.value())
def on_OutFs_changed(self):
'''
This function is used to change the Cutoff Frequency value of
Low pass filter tree to the same value specified in Lock In
Configuration tree
'''
self.LPFConf.param(
'CuttOffFreq').setValue(
self.LockInParams.OutFs.value())
self.PlotParams.param('Fs').setValue(self.LockInParams.OutFs.value())
self.PsdPlotParams.param('Fs').setValue(self.LockInParams.OutFs.value())
self.PlotParams.param('ViewBuffer').setValue(
self.SigParams.nSamples.value()/self.LockInParams.OutFs.value())
def on_GenConfig_changed(self):
'''
This function is used to change the Sampling frequency value and
nSamples value of Lock In and Low pass Filter trees to the ones
specified in the signal configuration
'''
self.LockInConf.param('Fs').setValue(self.SigParams.Fs.value())
self.LPFConf.param('Fs').setValue(self.SigParams.Fs.value())
self.PlotParams.param('Fs').setValue(self.LockInParams.OutFs.value())
self.PsdPlotParams.param('Fs').setValue(self.LockInParams.OutFs.value())
self.LockInConf.param(
'nSamples').setValue(
self.SigParams.nSamples.value())
self.PlotParams.param('ViewBuffer').setValue(
self.SigParams.nSamples.value()/self.LockInParams.OutFs.value())
def on_CarrierConfig_changed(self):
'''
This function is used to change the Carrier parameters while the
program is running
'''
# It is checked if the Thread of generation is active
if self.threadGeneration is not None:
# Gen Carrier function is called and appropiate parameters are
# sent to generate the new waveform
SigGen.GenAMSignal(**self.SigParams.Get_SignalConf_Params())
def on_ModConfig_changed(self):
'''
This function is used to change the Modulation parameters while the
program is running
'''
# It is checked if the Thread of generation is active
if self.threadGeneration is not None:
if self.ModParams.param('ModType').value() == 'sinusoidal':
# GenModulation for a sinusoidal waveform function is called
# and appropiate parameters are sent to generate the new
# waveform
SigGen.GenAMSignal(**self.SigParams.Get_SignalConf_Params())
if self.ModParams.param('ModType').value() == 'square':
# GenModulation for an square waveform function is called
# and appropiate parameters are sent to generate the new
# waveform
SigGen.GenAMSignal(**self.SigParams.Get_SignalConf_Params())
def on_PSDEnable_changed(self):
'''
This function is used to Generate or destroy the PSD plot
'''
if self.threadGeneration is not None:
self.Gen_Destroy_PsdPlotter()
def on_PlotEnable_changed(self):
'''
This function is used to Generate or destroy the Time plot
'''
if self.threadGeneration is not None:
self.Gen_Destroy_Plotters()
def on_RefreshTimePlt_changed(self):
'''
This function is used to change the refresh time of Time Plot
'''
if self.threadPlotter is not None:
self.threadPlotter.SetRefreshTime(self.PlotParams.param('RefreshTime').value())
def on_SetViewTimePlt_changed(self):
'''
This function is used to change the View time of Time Plot
'''
if self.threadPlotter is not None:
self.threadPlotter.SetViewTime(self.PlotParams.param('ViewTime').value())
# ############################START##############################
def on_btnStart(self):
'''
This function is executed when the 'start' button is pressed. It is
used to initialize the threads, emit signals and data that are
necessary durint the execution of the program. Also in this function
the different threads starts.
'''
# It is checked if the thread of generation is running
if self.threadGeneration is None: # If it is not running
# A dictionary created by the function Get_SignalConf_Params, with
# all the parameters and values of Signal configuration class is
# saved in a class variable. This dictionary can be used as kwargs
self.SignalConfigKwargs = self.SigParams.Get_SignalConf_Params()
# The function Get_LockInConf_Params generates a dictioanry that
# is saved to pass to other functions as dictionary or kwargs
self.LockInConfigKwargs = self.LockInParams.Get_LockInConf_Params()
# The function Get_LPF_Params generates a dictioanry that
# is saved to pass to other functions as dictionary or kwargs
self.LPFConfigKwargs = self.LPFParams.Get_LPF_Params()
# The dictionary is passed to the genration thread
self.threadGeneration = SigGen.GenerationThread(**self.SignalConfigKwargs)
# As LPF is used in Lock In process, both dictionaries are passed
# to the LockIn Thread
self.threadLockIn = LockIn.LockInThread(self.LockInConfigKwargs,
self.LPFConfigKwargs,
tWait=self.SigParams.tInterrput.value()
)
# the Qt signal of the generation thread is connected to a
# function (on_NewSample) so, when the thread emits this signal
# the specified function will be executed
self.threadGeneration.NewGenData.connect(self.on_NewSample)
self.threadLockIn.NewDemodData.connect(self.on_NewDemodSample)
# Time and PSD Plots threads are initialized and started
self.Gen_Destroy_PsdPlotter()
self.Gen_Destroy_Plotters()
# Also save thread is initialize and started
self.SaveFiles()
# The thread is started, so run function is executed in loop
self.threadGeneration.start()
self.threadLockIn.start()
# Falta iniciar plot y PSD cuando javi los haga para 1
# Text of the button is changed to 'stop'
self.btnStart.setText("Stop Gen")
# The exact time the thread starts is saved
self.OldTime = time.time()
else:
# stopped is printed in the console
print('Stopped')
# Thread is terminated and set to None
self.threadGeneration.NewGenData.disconnect()
self.threadLockIn.NewDemodData.disconnect()
self.threadGeneration.terminate()
self.threadGeneration = None
self.threadLockIn = None
if self.threadPlotter is not None:
self.threadPlotter.stop()
self.threadPlotter = None
if self.threadPsdPlotter is not None:
self.threadPsdPlotter.stop()
self.threadPsdPlotter = None
# Also save thread is stopped
if self.threadDemodSave is not None:
self.threadDemodSave.stop()
self.threadDemodSave = None
# Button text is changed again
self.btnStart.setText("Start Gen and Adq!")
def on_NewSample(self):
'''
This function is executed when a new amount of values of the signal
generated are ready so they can be read and processed
'''
# It is calculated the period of Generation Thread with the actual
# time and the one saved in the last iteration
Ts = time.time() - self.OldTime
# Time is saved again to calculate the next periot of the thread
self.OldTime = time.time()
# period is printed in the console
print('Sample time', Ts)
# to read clean signal
self.threadLockIn.AddData(NewData=self.threadGeneration.OutData)
# to read noisy signal
# self.threadLockIn.AddData(NewData=self.threadGeneration.OutNoiseData)
def on_NewDemodSample(self):
print('demodDone')
if self.threadDemodSave is not None:
self.threadDemodSave.AddData(self.threadLockIn.OutDemodDataReShape)
if self.LockInConf.param('OutType').value() == 'Abs':
OutDemodData = np.abs(self.threadLockIn.OutDemodDataReShape)
elif self.LockInConf.param('OutType').value() == 'Real':
OutDemodData = np.real(self.threadLockIn.OutDemodDataReShape)
elif self.LockInConf.param('OutType').value() == 'Imag':
OutDemodData = np.imag(self.threadLockIn.OutDemodDataReShape)
elif self.LockInConf.param('OutType').value() == 'Angle':
OutDemodData = np.angle(self.threadLockIn.OutDemodDataReShape,
deg=True)
if self.threadPlotter is not None:
self.threadPlotter.AddData(OutDemodData)
if self.threadPsdPlotter is not None:
self.threadPsdPlotter.AddData(OutDemodData)
# #############################Plots##############################
def Gen_Destroy_Plotters(self):
'''
This function is executed to initialize and start or destroy time plot
'''
# If Time plot thread does not exist
if self.threadPlotter is None:
# And the plot enable checkbox is selected
if self.PlotParams.param('PlotEnable').value() is True:
# A dictionary obtained with Get Params function is saved
PlotterKwargs = self.PlotParams.GetParams()
# And is sent to Plotter thread to initialize it
self.threadPlotter = TimePlt.Plotter(**PlotterKwargs)
# Then thread is started
self.threadPlotter.start()
# If time plot thread exists
if self.threadPlotter is not None:
# And plot enable checkbox is not selected
if self.PlotParams.param('PlotEnable').value() is False:
# The thread is stopped and set to None
self.threadPlotter.stop()
self.threadPlotter = None
def Gen_Destroy_PsdPlotter(self):
'''
This function is executed to initialize and start or destroy PSD plot
'''
# If PSD plot thread does not exist
if self.threadPsdPlotter is None:
# And the plot enable checkbox is selected
if self.PsdPlotParams.param('PSDEnable').value() is True:
# A dictionary obtained with Get Params function is saved
PlotterKwargs = self.PlotParams.GetParams()
# And is sent to PSDPlotter thread to initialize it
self.threadPsdPlotter = PSDPlt.PSDPlotter(ChannelConf=PlotterKwargs['ChannelConf'],
nChannels=1,
**self.PsdPlotParams.GetParams())
# Then thread is started
self.threadPsdPlotter.start()
# If PSD plot thread exists
if self.threadPsdPlotter is not None:
# And plot enable checkbox is not selected
if self.PsdPlotParams.param('PSDEnable').value() is False:
# The thread is stopped and set to None
self.threadPsdPlotter.stop()
self.threadPsdPlotter = None
# #############################Saving Files##############################
def SaveFiles(self):
'''
This function is executed to initialize and start save thread
'''
# The File Name is obtained from the GUI File Path
FileName = self.FileParams.param('File Path').value()
# If the is no file name, No file is printed
if FileName == '':
print('No file')
# If there is file name
else:
# It is checked if the file exists, if it exists is removed
if os.path.isfile(FileName):
print('Remove File')
os.remove(FileName)
# Maximum size alowed for the new file is obtained from the GUI
MaxSize = self.FileParams.param('MaxSize').value()
# The threas is initialized
self.threadDemodSave = FileMod.DataSavingThread(FileName=FileName,
nChannels=1,
MaxSize=MaxSize,
Fs = self.SigParams.Fs.value(),
tWait=self.SigParams.tInterrput.value(),
dtype='float')
# And then started
self.threadDemodSave.start()
class ProjectSettingsDialog(QtGui.QDialog):
path2key = dict()
def __init__(self, parent=None, savedstate=None):
global SETTINGS
super(ProjectSettingsDialog, self).__init__(parent)
self.setWindowTitle("Application Settings")
layout = QtGui.QVBoxLayout(self)
self.setLayout(layout)
if savedstate:
for key, val in savedstate.items():
if flattenned_settings_dict.get(key):
flattenned_settings_dict[key]['value'] = val
#self._settings.restoreState(savedstate)
self.initKeyParamMapping()
self._settings = Parameter.create(name='params',
type='group',
children=settings_params)
# Holds settings keys that have changed by the user when the
# dialog is closed. Used to update any needed gui values..
self._updated_settings = {}
self._invalid_settings = {}
self._settings.sigTreeStateChanged.connect(self.handleSettingChange)
self.initSettingsValues()
self._settings.param('Default Settings',
'Save As').sigActivated.connect(self.saveToFile)
self._settings.param('Default Settings',
'Load').sigActivated.connect(self.loadFromFile)
self.ptree = ParameterTree()
self.ptree.setParameters(self._settings, showTop=False)
self.ptree.setWindowTitle('MarkWrite Application Settings')
layout.addWidget(self.ptree)
# OK and Cancel buttons
self.buttons = QtGui.QDialogButtonBox(
QtGui.QDialogButtonBox.Ok | QtGui.QDialogButtonBox.Cancel,
QtCore.Qt.Horizontal, self)
layout.addWidget(self.buttons)
self.buttons.accepted.connect(self.accept)
self.buttons.rejected.connect(self.reject)
wscreen = QtGui.QDesktopWidget().screenGeometry()
if savedstate and savedstate.get(SETTINGS_DIALOG_SIZE_SETTING):
w, h = savedstate.get(SETTINGS_DIALOG_SIZE_SETTING)
self.resize(w, h)
SETTINGS[SETTINGS_DIALOG_SIZE_SETTING] = (w, h)
if savedstate.get(APP_WIN_SIZE_SETTING):
SETTINGS[APP_WIN_SIZE_SETTING] = savedstate.get(
APP_WIN_SIZE_SETTING)
else:
if parent:
wscreen = QtGui.QDesktopWidget().screenGeometry(parent)
self.resize(min(500, int(wscreen.width() * .66)),
min(700, int(wscreen.height() * .66)))
# center dialog on same screen as is being used by markwrite app.
qr = self.frameGeometry()
cp = wscreen.center()
qr.moveCenter(cp)
self.move(qr.topLeft())
def saveToFile(self):
from markwrite.gui.dialogs import fileSaveDlg, ErrorDialog
from markwrite import writePickle, current_settings_path
save_to_path = fileSaveDlg(initFilePath=current_settings_path,
initFileName=u"markwrite_settings.pkl",
prompt=u"Save MarkWrite Settings",
allowed="Python Pickle file (*.pkl)",
parent=self)
if save_to_path:
import os
from markwrite import default_settings_file_name, current_settings_file_name
ff, fn = os.path.split(save_to_path)
if fn in [default_settings_file_name, current_settings_file_name]:
ErrorDialog.info_text = u"%s a is reserved file name." \
u" Save again using a different name."%(fn)
ErrorDialog().display()
else:
writePickle(ff, fn, SETTINGS)
def loadFromFile(self):
global settings
from markwrite.gui.dialogs import fileOpenDlg
from markwrite import appdirs as mwappdirs
from markwrite import readPickle, writePickle
from markwrite import current_settings_file_name, current_settings_path
if self.parent:
mws_file = fileOpenDlg(current_settings_path, None,
"Select MarkWrite Settings File",
"Python Pickle file (*.pkl)", False)
if mws_file:
import os
ff, fn = os.path.split(mws_file[0])
mw_setting = readPickle(ff, fn)
_ = ProjectSettingsDialog(savedstate=mw_setting)
self.parent().updateApplicationFromSettings(
mw_setting, mw_setting)
writePickle(current_settings_path, current_settings_file_name,
SETTINGS)
def initKeyParamMapping(self):
if len(self.path2key) == 0:
def replaceGroupKeys(paramlist, parent_path=[]):
for i, p in enumerate(paramlist):
if isinstance(p, basestring):
pdict = flattenned_settings_dict[p]
paramlist[i] = pdict
self.path2key['.'.join(parent_path + [
pdict['name'],
])] = p
elif isinstance(p, dict):
replaceGroupKeys(p.get('children'), parent_path + [
p.get('name'),
])
replaceGroupKeys(settings_params)
def initSettingsValues(self, pgroup=None):
global SETTINGS
if pgroup is None:
pgroup = self._settings
for child in pgroup.children():
if child.hasChildren():
self.initSettingsValues(child)
else:
path = self._settings.childPath(child)
if path is not None:
childName = '.'.join(path)
else:
childName = child.name()
if self.path2key.has_key(childName):
SETTINGS[self.path2key[childName]] = child.value()
child.orgvalue = child.value()
## If anything changes in the tree
def handleSettingChange(self, param, changes):
global SETTINGS
for param, change, data in changes:
path = self._settings.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
if change == 'value':
setting_key = self.path2key[childName]
if setting_key.startswith('kbshortcut_'):
qks = QtGui.QKeySequence(data)
if (len(data) > 0 and qks.isEmpty()
) or qks.toString() in SETTINGS.values():
self._invalid_settings[setting_key] = param
continue
else:
data = u'' + qks.toString()
SETTINGS[setting_key] = data
self._updated_settings[setting_key] = data
param.orgvalue = data
def resizeEvent(self, event):
global SETTINGS
w, h = self.size().width(), self.size().height()
SETTINGS[SETTINGS_DIALOG_SIZE_SETTING] = (w, h)
self._updated_settings[SETTINGS_DIALOG_SIZE_SETTING] = (w, h)
return super(QtGui.QDialog, self).resizeEvent(event)
@staticmethod
def getProjectSettings(parent=None, usersettings=None):
if usersettings is None:
usersettings = SETTINGS
dialog = ProjectSettingsDialog(parent, usersettings)
result = dialog.exec_()
for k, v in dialog._invalid_settings.items():
v.setValue(v.orgvalue)
dialog._invalid_settings.clear()
usersettings = dialog._settings.saveState()
return dialog._updated_settings, SETTINGS, usersettings, result == QtGui.QDialog.Accepted
def __init__(self, **kw):
self.app = kw.pop('app')
self.data_label = ''
self.date_time = dt.datetime.now().strftime('%Y_%m_%d-%H_%M')
self.h = kw.pop('h', .1) #integration step size
self.n_state_variables = kw.pop('n_state_variables', 2)
self.n_history = kw.pop('n_history', 2000)
self.kw = kw
self.params = kw.get('params') #qt paramters, se tree parameter class
self.update_time = kw.pop('update_time', 0)
self.widgets = []
self.script_name = kw.pop('script_name', __file__.split('/')[-1][0:-3])
self.start_stim = -10000.0
self.scale_plot = 10
for key, value in kw.items():
self.__dict__[key] = value
for d in self.params[0]['children']:
self.__dict__[d['name']] = d['value']
for d in self.params[1]['children']:
if 'value' in d.keys():
self.__dict__[d['name']] = d['value']
self.x = self.n_history
self.y = numpy.zeros(self.n_state_variables)
self.y[0] = -70
self.dy = numpy.zeros(self.n_state_variables)
self.x_history = numpy.arange(0, self.n_history,
self.scale_plot * self.h)
self.y_history = numpy.random.rand(
self.n_state_variables,
self.n_history / (self.scale_plot * self.h))
self.y_history[0, :] = -70
# Parameters
self.p = Parameter.create(name='params',
type='group',
children=self.params)
self.p.sigTreeStateChanged.connect(self.change)
pt = ParameterTree()
pt.setParameters(self.p, showTop=False)
pt.setWindowTitle('Parameters')
self.widgets.append(pt)
# Voltage time plot
w = pg.PlotWidget()
w.setWindowTitle('Voltage/time')
w.setRange(QtCore.QRectF(0, -90, self.n_history, 100))
w.setLabel('bottom', 'Time', units='s')
w.plotItem.layout.setContentsMargins(20, 20, 20, 20)
ax = w.plotItem.getAxis('left')
l = [
[(0.0, '0'), (-30, -30), (-60, -60), (-90, -90)],
]
ax.setTicks(l)
w.plotItem.getAxis('bottom').setScale(0.001)
ax.setLabel('Voltage', units='V')
ax.setScale(0.001)
# ax.setWidth(w=2)
# ax.setRange(500,1500)
color = self.kw.get('curve_uv_color', (0, 0, 0))
pen = pg.mkPen(color, width=self.kw.get('curve_uv_width', 5))
self.curve_vt = w.plot(pen=pen)
self.curve_vt.setData(self.x_history, self.y_history[0, :])
self.widgets.append(w)
self.timer = QtCore.QTimer()
self.timer.timeout.connect(self.update)
self.timer.start(self.update_time)
# self.timer.start(1000.)
self._init_extra(**kw)
class MainWindow(Qt.QWidget):
''' Main Window '''
def __init__(self):
super(MainWindow, self).__init__()
layout = Qt.QVBoxLayout(self)
self.btnAcq = Qt.QPushButton("Start Acq!")
layout.addWidget(self.btnAcq)
self.SamplingPar = AcqMod.SampSetParam(name='SampSettingConf')
self.Parameters = Parameter.create(name='App Parameters',
type='group',
children=(self.SamplingPar, ))
self.SamplingPar.NewConf.connect(self.on_NewConf)
self.PlotParams = PltMod.PlotterParameters(name='Plot options')
self.PlotParams.SetChannels(self.SamplingPar.GetChannelsNames())
self.PlotParams.param('Fs').setValue(self.SamplingPar.Fs.value())
self.Parameters.addChild(self.PlotParams)
self.PSDParams = PltMod.PSDParameters(name='PSD Options')
self.PSDParams.param('Fs').setValue(self.SamplingPar.Fs.value())
self.Parameters.addChild(self.PSDParams)
self.Parameters.sigTreeStateChanged.connect(self.on_pars_changed)
self.treepar = ParameterTree()
self.treepar.setParameters(self.Parameters, showTop=False)
self.treepar.setWindowTitle('pyqtgraph example: Parameter Tree')
layout.addWidget(self.treepar)
self.setGeometry(650, 20, 400, 800)
self.setWindowTitle('MainWindow')
self.btnAcq.clicked.connect(self.on_btnStart)
self.threadAcq = None
self.threadSave = None
self.threadPlotter = None
self.FileParameters = FileMod.SaveFileParameters(QTparent=self,
name='Record File')
self.Parameters.addChild(self.FileParameters)
self.ConfigParameters = FileMod.SaveSateParameters(
QTparent=self, name='Configuration File')
self.Parameters.addChild(self.ConfigParameters)
def on_pars_changed(self, param, changes):
print("tree changes:")
for param, change, data in changes:
path = self.Parameters.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
print(' parameter: %s' % childName)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
if childName == 'SampSettingConf.Sampling Settings.Fs':
self.PlotParams.param('Fs').setValue(data)
self.PSDParams.param('Fs').setValue(data)
if childName == 'SampSettingConf.Sampling Settings.Vgs':
if self.threadAcq:
Vds = self.threadAcq.DaqInterface.Vds
self.threadAcq.DaqInterface.SetBias(Vgs=data, Vds=Vds)
if childName == 'SampSettingConf.Sampling Settings.Vds':
if self.threadAcq:
Vgs = self.threadAcq.DaqInterface.Vgs
self.threadAcq.DaqInterface.SetBias(Vgs=Vgs, Vds=data)
if childName == 'Plot options.RefreshTime':
if self.threadPlotter is not None:
self.threadPlotter.SetRefreshTime(data)
if childName == 'Plot options.ViewTime':
if self.threadPlotter is not None:
self.threadPlotter.SetViewTime(data)
if childName == 'Raw Plot.ViewTime':
if self.threadPlotterRaw is not None:
self.threadPlotterRaw.SetViewTime(data)
if childName == 'Raw Plot.RefreshTime':
if self.threadPlotterRaw is not None:
self.threadPlotterRaw.SetRefreshTime(data)
def on_NewConf(self):
self.Parameters.sigTreeStateChanged.disconnect()
self.PlotParams.SetChannels(self.SamplingPar.GetChannelsNames())
self.Parameters.sigTreeStateChanged.connect(self.on_pars_changed)
def on_btnStart(self):
if self.threadAcq is None:
GenKwargs = self.SamplingPar.GetSampKwargs()
GenChanKwargs = self.SamplingPar.GetChannelsConfigKwargs()
self.threadAcq = AcqMod.DataAcquisitionThread(
ChannelsConfigKW=GenChanKwargs, SampKw=GenKwargs)
self.threadAcq.NewTimeData.connect(self.on_NewSample)
self.threadAcq.start()
PlotterKwargs = self.PlotParams.GetParams()
# FileName = self.Parameters.param('File Path').value()
FileName = self.FileParameters.FilePath()
print('Filename', FileName)
if FileName == '':
print('No file')
else:
if os.path.isfile(FileName):
print('Remove File')
os.remove(FileName)
MaxSize = self.FileParameters.param('MaxSize').value()
self.threadSave = FileMod.DataSavingThread(
FileName=FileName,
nChannels=PlotterKwargs['nChannels'],
MaxSize=MaxSize)
self.threadSave.start()
self.threadPlotter = PltMod.Plotter(**PlotterKwargs)
self.threadPlotter.start()
self.threadPSDPlotter = PltMod.PSDPlotter(
ChannelConf=PlotterKwargs['ChannelConf'],
nChannels=PlotterKwargs['nChannels'],
**self.PSDParams.GetParams())
self.threadPSDPlotter.start()
self.btnAcq.setText("Stop Gen")
self.OldTime = time.time()
self.Tss = []
else:
self.threadAcq.DaqInterface.Stop()
self.threadAcq = None
if self.threadSave is not None:
self.threadSave.terminate()
self.threadSave = None
self.threadPlotter.terminate()
self.threadPlotter = None
self.btnAcq.setText("Start Gen")
def on_NewSample(self):
''' Visualization of streaming data-WorkThread. '''
Ts = time.time() - self.OldTime
self.Tss.append(Ts)
self.OldTime = time.time()
if self.threadSave is not None:
self.threadSave.AddData(self.threadAcq.aiData)
self.threadPlotter.AddData(self.threadAcq.aiData)
self.threadPSDPlotter.AddData(self.threadAcq.aiData)
print('Sample time', Ts, np.mean(self.Tss))
def _init_extra(self, **kw):
self.neuron = kw.get('base_neuron')
self.neuron_params = kw.get('neuron_params')
for d in self.neuron_params[0]['children']:
if 'children' in d.keys():
for dd in d['children']:
self.__dict__[dd['name']] = dd['value']
else:
pp(d)
if 'value' in d.keys():
self.__dict__[d['name']] = d['value']
self.dyn_xticks = [[100 * i, i * 0.1] for i in range(0, 22, 4)]
self.script_name = kw.get('script_name', __file__.split('/')[-1][0:-3])
self.p.param('store_state', 'save').sigActivated.connect(self.save)
self.p.param('stimulate', 'start').sigActivated.connect(self.stimulate)
# Comet for recovery current vs time plot
w = pg.PlotWidget()
w.plotItem.getAxis('bottom').setScale(0.001)
w.plotItem.getAxis('left').setLabel('Current', units='A')
w.plotItem.getAxis('left').setScale(0.000000000001)
w.setWindowTitle('Recovery current')
w.setRange(QtCore.QRectF(0, -200, self.n_history, 400))
w.setLabel('bottom', 'Time', units='s')
w.plotItem.layout.setContentsMargins(20, 20, 20, 20)
color = self.kw.get('curve_uv_color', (0, 0, 0))
pen = pg.mkPen(color, width=self.kw.get('curve_uv_width', 5))
self.curve_ut = w.plot(pen=pen)
self.widgets.append(w)
# Comet for voltage recovery current plot
w = pg.PlotWidget()
w.plotItem.getAxis('bottom').setScale(0.001)
w.plotItem.getAxis('left').setLabel('Recovery current u', units='A')
w.plotItem.getAxis('left').setScale(0.000000000001)
w.setWindowTitle('Recovery current/voltage')
w.setRange(QtCore.QRectF(-100, -50, 100, 200))
w.setLabel('bottom', 'Voltage', units='V')
w.plotItem.layout.setContentsMargins(10, 10, 10, 10)
self.widgets.append(w)
color = self.kw.get('curve_uv_color', (0, 0, 0))
pen = pg.mkPen(color, width=self.kw.get('curve_uv_width', 5))
self.curve_uv = w.plot(pen=pen)
# x,y=self.get_nullcline_extreme_points()
# self.curve_uv_extreme_point = w.plot(x,y, pen=pen)
color = self.kw.get('curve_uv_color', (0, 0, 0))
self.curve_uv_nullcline0 = w.plot(pen=pen)
self.curve_uv_nullcline1 = w.plot(pen=pen)
color = self.kw.get('curve_uv_color', (255, 0, 0))
brush = pg.mkBrush(color=color)
self.curve_uv_comet = w.plot(symbolBrush=brush,
symbol='o',
symbolSize=15.)
# Parameters base_neuron
self.p2 = Parameter.create(name='params',
type='group',
children=self.neuron_params)
self.p2.sigTreeStateChanged.connect(self.change)
self.p2.param('IV, IF, nullcline, etc',
'run base_neuron').sigActivated.connect(
self.run_neuron_thread)
self.p2.param('IV, IF, nullcline, etc',
'run GP-ST network').sigActivated.connect(
self.run_GP_STN_network_thread)
pt = ParameterTree()
pt.setParameters(self.p2, showTop=False)
pt.setWindowTitle('Parameters')
self.widgets.append(pt)
# Threshold type
w = pg.PlotWidget()
# w.plotItem.getAxis('bottom').setScale(0.001)
w.plotItem.getAxis('left').setLabel('a/g_L')
# w.plotItem.getAxis('left').setScale(0.000000000001)
w.setWindowTitle('Recovery current/voltage')
w.setRange(QtCore.QRectF(0, 0, 4, 1))
w.setLabel('bottom', 'tau_m/tau_w')
w.plotItem.layout.setContentsMargins(10, 10, 10, 10)
self.widgets.append(w)
color = self.kw.get('curve_uv_color', (0, 0, 0))
pen = pg.mkPen(color, width=self.kw.get('curve_uv_width', 5))
c1, c2 = self.get_threshold_oscillation_curves()
x, y = self.get_threshold_oscilltion_point()
color = self.kw.get('curve_uv_color', (255, 0, 0))
brush = pg.mkBrush(color=color)
self.curve_oscillation1 = w.plot(c1[0], c1[1], pen=pen)
self.curve_oscillation2 = w.plot(c2[0], c2[1], pen=pen)
self.curve_oscillation_points1 = w.plot([x[0]], [y[0]],
symbolBrush=brush,
symbol='o',
symbolSize=25.)
color = self.kw.get('curve_uv_color', (0, 0, 255))
brush = pg.mkBrush(color=color)
self.curve_oscillation_points2 = w.plot([x[1]], [y[1]],
symbolBrush=brush,
symbol='o',
symbolSize=15.)
self.draw()
def restore():
global state
add = p['Save/Restore functionality', 'Restore State', 'Add missing items']
rem = p['Save/Restore functionality', 'Restore State',
'Remove extra items']
p.restoreState(state, addChildren=add, removeChildren=rem)
p.param('Save/Restore functionality', 'Save State').sigActivated.connect(save)
p.param('Save/Restore functionality',
'Restore State').sigActivated.connect(restore)
## Create two ParameterTree widgets, both accessing the same data
t = ParameterTree()
t.setParameters(p, showTop=False)
t.setWindowTitle('pyqtgraph example: Parameter Tree')
t2 = ParameterTree()
t2.setParameters(p, showTop=False)
win = QtGui.QWidget()
layout = QtGui.QGridLayout()
win.setLayout(layout)
layout.addWidget(
QtGui.QLabel(
"These are two views of the same data. They should always display the same values."
), 0, 0, 1, 2)
layout.addWidget(t, 1, 0, 1, 1)
layout.addWidget(t2, 1, 1, 1, 1)
win.show()
## test save/restore
class ParameterWidget(QtGui.QWidget):
"""Settings Widget takes a list of dictionaries and provides a widget to edit the values (and key names)
Each dict object must include these keys:
key: The string used to get/set the value, shown to left of value if 'name' not given
value: The value to show next to name, matches 'type' if given else use type of this value
accepts QColor, lambda, list, generic types
Optional keys are:
name: the name which is shown to the left of the value for user readability
type: Specify the type if it is not obvious by the value provided, as a string
suffix: (for float/int values only) added for user readability
children: a list of dicts under a 'group' parameter
removable: bool specifying if this can be removed (set to False)
renamable: bool specifying if this can be renamed (set to False)
appendable: bool specifying if user can add to this group
To pass in a parent parameter with children, pass 'group' to the 'value' key and the list of dicts to a new 'children' parameter
"""
done = QtCore.Signal(dict)
valueChanged = QtCore.Signal(str, object)
def __init__(self, title, paramlist, about="", doneButton=False, appendable=False):
super(ParameterWidget, self).__init__()
self.ParamGroup = ScalableGroup if appendable else pTypes.GroupParameter
self.hasDone = doneButton
self.parameters = self.ParamGroup(name="Parameters", children=ParameterWidget.build_parameter_list(paramlist))
self.parameters.sigTreeStateChanged.connect(self.paramsChanged)
self.info = about
self.tree = ParameterTree()
self.tree.setParameters(self.parameters, showTop=False)
self.tree.setWindowTitle(title)
self.makeLayout()
self.resize(800, 600)
@staticmethod
def type_as_str(var):
if type(var) == tuple and len(var) != 3:
var = list(var)
elif isinstance(var, np.string_):
return "str"
elif isinstance(var, np.generic):
var = float(var)
elif isinstance(var, QtGui.QColor) or (type(var) == tuple and len(var) == 3):
return "color"
elif isinstance(var, dict) or (isinstance(var, list) and all([type(i) == dict for i in var])):
return "group"
elif isinstance(var, (int, float, bool, list, str)):
return type(var).__name__
elif isinstance(var, FunctionType):
return "action"
return "text"
def paramsChanged(self, params, change):
obj, change, val = change[0]
if change == "value":
self.valueChanged.emit(obj.opts["key"], val)
else:
pass
def makeLayout(self):
layout = QtGui.QGridLayout()
self.setLayout(layout)
if len(self.info) > 0:
self.scrollArea = QtGui.QScrollArea(self)
self.scrollArea.setWidgetResizable(True)
self.scrollArea.setWidget(QtGui.QLabel(self.info))
layout.addWidget(self.scrollArea, 0, 0, 1, 2)
layout.addWidget(self.tree, 1, 0, 1, 2)
if self.hasDone:
cancelButton = QtGui.QPushButton("Cancel")
cancelButton.clicked.connect(self.close)
okButton = QtGui.QPushButton("Ok")
okButton.clicked.connect(lambda: self.close(emit=True))
layout.addWidget(cancelButton, 2, 0)
layout.addWidget(okButton, 2, 1)
layout.setRowStretch(1, 4)
@staticmethod
def get_group_dict(groupParam):
d = {}
for c in groupParam.childs:
if isinstance(c, pTypes.GroupParameter):
d[c.opts["name"]] = ParameterWidget.get_group_dict(c)
else:
d[c.opts["key"]] = c.opts["value"]
return d
@staticmethod
def build_parameter_list(params):
return_params = []
for param_dict in params:
assert "key" in param_dict, "Must provide a key for each item"
assert "value" in param_dict, (
"Must provide a value for each item; %s does not have a value" % param_dict["key"]
)
if param_dict["value"] == None:
continue
if "name" not in param_dict:
param_dict["name"] = param_dict["key"]
if param_dict["value"] == "group":
return_params.append(
pTypes.GroupParameter(
name=param_dict["name"], children=ParameterWidget.build_parameter_list(param_dict["children"])
)
)
continue
if "type" not in param_dict:
param_dict["type"] = ParameterWidget.type_as_str(param_dict["value"])
if param_dict["type"] == "list":
param_dict["values"] = param_dict.pop("value")
return_params.append(param_dict)
return return_params
def close(self, emit=False):
super(ParameterWidget, self).close()
if emit == True:
self.done.emit(ParameterWidget.get_group_dict(self.parameters))
class DiffractionGeometry(object):
def __init__(self, parent = None):
self.parent = parent
#############################
## Dock: Diffraction geometry
#############################
self.dock = Dock("Diffraction Geometry", size=(1, 1))
self.win = ParameterTree()
self.win.setWindowTitle('Diffraction geometry')
self.dock.addWidget(self.win)
self.winL = pg.LayoutWidget()
self.deployGeomBtn = QtGui.QPushButton('Deploy manually centred geometry')
self.winL.addWidget(self.deployGeomBtn, row=0, col=0)
self.deployAutoGeomBtn = QtGui.QPushButton('Deploy automatically centred geometry')
self.winL.addWidget(self.deployAutoGeomBtn, row=1, col=0)
self.dock.addWidget(self.winL)
self.resolutionRingList = np.array([100.,300.,500.,700.,900.,1100.])
self.resolutionText = []
self.hasUserDefinedResolution = False
self.geom_grp = 'Diffraction geometry'
self.geom_detectorDistance_str = 'Detector distance'
self.geom_clen_str = 'Home to Detector (clen)'
self.geom_coffset_str = 'Sample to Home (coffset)'
self.geom_photonEnergy_str = 'Photon energy'
self.geom_wavelength_str = "Wavelength"
self.geom_pixelSize_str = 'Pixel size'
self.geom_resolutionRings_str = 'Resolution rings'
self.geom_resolution_str = 'Resolution (pixels)'
self.geom_resolutionUnits_str = 'Units'
self.geom_unitA_crystal_str = 'Crystallography (Angstrom)'
self.geom_unitNm_crystal_str = 'Crystallography (Nanometre)'
self.geom_unitQ_crystal_str = 'Crystallography Reciprocal Space (q)'
self.geom_unitA_physics_str = 'Physics (Angstrom)'
self.geom_unitNm_physics_str = 'Physics (Nanometre)'
self.geom_unitQ_physics_str = 'Physics Reciprocal Space (q)'
self.geom_unitTwoTheta_str = 'Scattering Angle 2Theta'
(self.unitA_c,self.unitNm_c,self.unitQ_c,self.unitA_p,self.unitNm_p,self.unitQ_p,self.unitTwoTheta) = (0,1,2,3,4,5,6)
#######################
# Mandatory parameter #
#######################
self.params = [
{'name': self.geom_grp, 'type': 'group', 'children': [
{'name': self.geom_detectorDistance_str, 'type': 'float', 'value': 0.0, 'precision': 6, 'minVal': 0.0001, 'siFormat': (6,6), 'siPrefix': True, 'suffix': 'mm'},
{'name': self.geom_clen_str, 'type': 'float', 'value': 0.0, 'step': 1e-6, 'siPrefix': True,
'suffix': 'm', 'readonly': True},
{'name': self.geom_coffset_str, 'type': 'float', 'value': 0.0, 'step': 1e-6, 'siPrefix': True,
'suffix': 'm', 'readonly': True},
{'name': self.geom_photonEnergy_str, 'type': 'float', 'value': 0.0, 'step': 1e-6, 'siPrefix': True, 'suffix': 'eV'},
{'name': self.geom_wavelength_str, 'type': 'float', 'value': 0.0, 'step': 1e-6, 'siPrefix': True, 'suffix': 'm', 'readonly': True},
{'name': self.geom_pixelSize_str, 'type': 'float', 'value': 0.0, 'precision': 12, 'minVal': 1e-6, 'siPrefix': True, 'suffix': 'm'},
{'name': self.geom_resolutionRings_str, 'type': 'bool', 'value': False, 'tip': "Display resolution rings", 'children': [
{'name': self.geom_resolution_str, 'type': 'str', 'value': None},
{'name': self.geom_resolutionUnits_str, 'type': 'list', 'values': {self.geom_unitA_crystal_str: self.unitA_c,
self.geom_unitNm_crystal_str: self.unitNm_c,
self.geom_unitQ_crystal_str: self.unitQ_c,
self.geom_unitA_physics_str: self.unitA_p,
self.geom_unitNm_physics_str: self.unitNm_p,
self.geom_unitQ_physics_str: self.unitQ_p,
self.geom_unitTwoTheta_str: self.unitTwoTheta},
'value': self.unitA_c},
]},
]},
]
self.p1 = Parameter.create(name='paramsDiffractionGeometry', type='group', \
children=self.params, expanded=True)
self.p1.sigTreeStateChanged.connect(self.change)
self.win.setParameters(self.p1, showTop=False)
if using_pyqt4:
self.parent.connect(self.deployGeomBtn, QtCore.SIGNAL("clicked()"), self.deploy)
self.parent.connect(self.deployAutoGeomBtn, QtCore.SIGNAL("clicked()"), self.autoDeploy)
else:
self.deployGeomBtn.clicked.connect(self.deploy)
self.deployAutoGeomBtn.clicked.connect(self.autoDeploy)
# If anything changes in the parameter tree, print a message
def change(self, panel, changes):
for param, change, data in changes:
path = panel.childPath(param)
if self.parent.args.v >= 1:
print(' path: %s' % path)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
self.paramUpdate(path, change, data)
##############################
# Mandatory parameter update #
##############################
def paramUpdate(self, path, change, data):
if path[1] == self.geom_detectorDistance_str:
self.updateDetectorDistance(data)
elif path[1] == self.geom_clen_str:
pass
elif path[1] == self.geom_coffset_str:
pass
elif path[1] == self.geom_photonEnergy_str:
self.updatePhotonEnergy(data)
elif path[1] == self.geom_pixelSize_str:
self.updatePixelSize(data)
elif path[1] == self.geom_wavelength_str:
pass
elif path[1] == self.geom_resolutionRings_str and len(path) == 2:
self.updateResolutionRings(data)
elif path[2] == self.geom_resolution_str:
self.updateResolution(data)
elif path[2] == self.geom_resolutionUnits_str:
self.updateResolutionUnits(data)
def findPsanaGeometry(self):
try:
self.source = Detector.PyDetector.map_alias_to_source(self.parent.detInfo,
self.parent.exp.ds.env()) # 'DetInfo(CxiDs2.0:Cspad.0)'
self.calibSource = self.source.split('(')[-1].split(')')[0] # 'CxiDs2.0:Cspad.0'
self.detectorType = gu.det_type_from_source(self.source) # 1
self.calibGroup = gu.dic_det_type_to_calib_group[self.detectorType] # 'CsPad::CalibV1'
self.detectorName = gu.dic_det_type_to_name[self.detectorType].upper() # 'CSPAD'
if self.parent.args.localCalib:
self.calibPath = "./calib/" + self.calibGroup + "/" + self.calibSource + "/geometry"
else:
self.calibPath = self.parent.dir + '/' + self.parent.experimentName[:3] + '/' + \
self.parent.experimentName + "/calib/" + self.calibGroup + '/' + \
self.calibSource + "/geometry"
if self.parent.args.v >= 1: print("### calibPath: ", self.calibPath)
# Determine which calib file to use
geometryFiles = os.listdir(self.calibPath)
if self.parent.args.v >= 1: print("geom: ", geometryFiles)
self.calibFile = None
minDiff = -1e6
for fname in geometryFiles:
if fname.endswith('.data'):
endValid = False
try:
startNum = int(fname.split('-')[0])
except:
continue
endNum = fname.split('-')[-1].split('.data')[0]
diff = startNum - self.parent.runNumber
# Make sure it's end number is valid too
if 'end' in endNum:
endValid = True
else:
try:
if self.parent.runNumber <= int(endNum):
endValid = True
except:
continue
if diff <= 0 and diff > minDiff and endValid is True:
minDiff = diff
self.calibFile = fname
except:
if self.parent.args.v >= 1: print("Couldn't find psana geometry")
self.calibFile = None
def deployCrystfelGeometry(self, arg):
self.findPsanaGeometry()
if self.calibFile is not None and self.parent.writeAccess:
# Convert psana geometry to crystfel geom
if '.temp.geom' in self.parent.index.geom:
self.parent.index.p9.param(self.parent.index.index_grp,
self.parent.index.index_geom_str).setValue(
self.parent.psocakeRunDir + '/.temp.geom')
cmd = ["psana2crystfel", self.calibPath + '/' + self.calibFile,
self.parent.psocakeRunDir + "/.temp.geom", str(self.parent.coffset)]
if self.parent.args.v >= 1: print("cmd: ", cmd)
try:
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
p.communicate()[0]
p.stdout.close()
except:
print(highlight("Warning! deployCrystfelGeometry() failed.", 'r', 1))
# FIXME: Configure crystfel geom file to read in a mask (crystfel 'mask_file=' broken?)
with open(self.parent.psocakeRunDir + '/.temp.geom', 'r') as f: lines = f.readlines()
newGeom = []
for line in lines: # remove commented out lines
if '; mask =' in line:
newGeom.append(line.split('; ')[-1])
elif '; mask_good =' in line:
newGeom.append(line.split('; ')[-1])
elif '; mask_bad =' in line:
newGeom.append(line.split('; ')[-1])
elif '; clen =' in line:
newGeom.append(line.split('; ')[-1])
elif '; photon_energy =' in line:
newGeom.append(line.split('; ')[-1])
elif '; adu_per_eV =' in line:
if 'epix10k' in self.parent.detInfo.lower() or \
'jungfrau4m' in self.parent.detInfo.lower():
newGeom.append(line.split('; ')[-1].split('0.1')[0]+"0.001") # override
else:
newGeom.append(line.split('; ')[-1])
else:
newGeom.append(line)
with open(self.parent.psocakeRunDir + '/.temp.geom', 'w') as f:
f.writelines(newGeom)
if self.parent.args.v >= 1: print("Done deployCrystfelGeometry")
def updateClen(self, arg):
self.p1.param(self.geom_grp, self.geom_clen_str).setValue(self.parent.clen)
self.parent.coffset = self.parent.detectorDistance - self.parent.clen
self.p1.param(self.geom_grp, self.geom_coffset_str).setValue(self.parent.coffset)
if self.parent.args.v >= 1: print("Done updateClen: ", self.parent.coffset, self.parent.detectorDistance, self.parent.clen)
def updateDetectorDistance(self, data):
self.parent.detectorDistance = data / 1000. # mm to metres
self.updateClen(self.parent.facility)
if self.parent.args.v >= 1: print("coffset (m), detectorDistance (m), clen (m): ", self.parent.coffset, self.parent.detectorDistance, self.parent.clen)
self.writeCrystfelGeom(self.parent.facility)
if self.hasGeometryInfo():
if self.parent.args.v >= 1: print("has geometry info")
self.updateGeometry()
self.parent.img.updatePolarizationFactor()
if self.parent.exp.image_property == self.parent.exp.disp_radialCorrection:
self.parent.img.updateImage()
if self.parent.pk.showPeaks: self.parent.pk.updateClassification()
if self.parent.args.v >= 1: print("Done updateDetectorDistance")
def updatePhotonEnergy(self, data):
if data > 0:
self.parent.photonEnergy = data
# E = hc/lambda
h = 6.626070e-34 # J.m
c = 2.99792458e8 # m/s
joulesPerEv = 1.602176621e-19 #J/eV
if self.parent.photonEnergy > 0:
self.parent.wavelength = (h/joulesPerEv*c)/self.parent.photonEnergy
else:
self.parent.wavelength = 0
self.p1.param(self.geom_grp,self.geom_wavelength_str).setValue(self.parent.wavelength)
if self.hasGeometryInfo():
self.updateGeometry()
def updatePixelSize(self, data):
self.parent.pixelSize = data
if self.hasGeometryInfo():
self.updateGeometry()
def hasGeometryInfo(self):
if self.parent.detectorDistance is not None \
and self.parent.photonEnergy is not None \
and self.parent.pixelSize is not None:
return True
else:
return False
def writeCrystfelGeom(self, arg):
if self.parent.index.hiddenCXI is not None:
if os.path.isfile(self.parent.index.hiddenCXI):
f = h5py.File(self.parent.index.hiddenCXI,'r')
encoderVal = f['/LCLS/detector_1/EncoderValue'][0] / 1000. # metres
f.close()
else:
encoderVal = self.parent.clen # metres
coffset = self.parent.detectorDistance - encoderVal
if self.parent.args.v >= 1: print("coffset (m),detectorDistance (m) ,encoderVal (m): ", coffset, self.parent.detectorDistance, encoderVal)
# Replace coffset value in geometry file
if '.temp.geom' in self.parent.index.geom and os.path.exists(self.parent.index.geom):
for line in fileinput.FileInput(self.parent.index.geom, inplace=True):
if 'coffset' in line and line.strip()[0] is not ';':
coffsetStr = line.split('=')[0]+"= "+str(coffset)+"\n"
print(coffsetStr.rstrip()) # FIXME: check whether comma is required
elif 'clen' in line and line.strip()[0] is ';': #FIXME: hack for mfxc00318
_c = line.split('; ')[-1]
print(_c.rstrip()) # comma is required
elif 'photon_energy' in line and line.strip()[0] is ';': #FIXME: hack for mfxc00318
_c = line.split('; ')[-1]
print(_c.rstrip()) # comma is required
elif 'adu_per_eV' in line and line.strip()[0] is ';': #FIXME: hack for mfxc00318
_c = line.split('; ')[-1]
print(_c.rstrip()) # comma is required
else:
print(line.rstrip()) # comma is required
if self.parent.args.v >= 1: print("Done writeCrystfelGeom")
def getClosestGeom(self):
# Search for the correct geom file to use
calibDir = self.parent.rootDir + '/calib/' + self.parent.detInfo + '/geometry'
_geomFiles = glob.glob(calibDir + '/*.geom')
_runWithGeom = np.array([int(a.split('/')[-1].split('-')[0]) for a in _geomFiles])
diff = _runWithGeom - self.parent.runNumber
geomFile = _geomFiles[ int(np.where(diff == np.max(diff[np.where(diff <= 0)[0]]))[0]) ]
if self.parent.args.v >= 1: print("getClosestGeom::Choosing this geom file: ", geomFile)
return geomFile
def updateGeometry(self):
if self.hasUserDefinedResolution:
self.myResolutionRingList = self.parent.resolution
else:
self.myResolutionRingList = self.resolutionRingList
self.thetaMax = np.zeros_like(self.myResolutionRingList)
self.dMin_crystal = np.zeros_like(self.myResolutionRingList)
self.qMax_crystal = np.zeros_like(self.myResolutionRingList)
self.dMin_physics = np.zeros_like(self.myResolutionRingList)
self.qMax_physics = np.zeros_like(self.myResolutionRingList)
for i, pix in enumerate(self.myResolutionRingList):
if self.parent.detectorDistance > 0 and self.parent.wavelength is not None:
self.thetaMax[i] = np.arctan(pix*self.parent.pixelSize/self.parent.detectorDistance)
self.qMax_crystal[i] = 2/self.parent.wavelength*np.sin(self.thetaMax[i]/2)
self.dMin_crystal[i] = 1/self.qMax_crystal[i]
self.qMax_physics[i] = 4*np.pi/self.parent.wavelength*np.sin(self.thetaMax[i]/2)
self.dMin_physics[i] = np.pi/self.qMax_physics[i]
if self.parent.args.v >= 1:
print("updateGeometry: ", i, self.thetaMax[i], self.dMin_crystal[i], self.dMin_physics[i])
if self.parent.resolutionRingsOn:
self.updateRings()
if self.parent.args.v >= 1: print("Done updateGeometry")
def updateDock42(self, data):
a = ['a','b','c','d','e','k','m','n','r','s']
myStr = a[5]+a[8]+a[0]+a[5]+a[4]+a[7]
if myStr in data:
self.d42 = Dock("Console", size=(100,100))
# build an initial namespace for console commands to be executed in (this is optional;
# the user can always import these modules manually)
namespace = {'pg': pg, 'np': np, 'self': self}
# initial text to display in the console
text = "You have awoken the "+myStr+"\nWelcome to psocake IPython: dir(self)\n" \
"Here are some commonly used variables:\n" \
"unassembled detector: self.parent.calib\n" \
"assembled detector: self.parent.data\n" \
"user-defined mask: self.parent.mk.userMask\n" \
"streak mask: self.parent.mk.streakMask\n" \
"psana mask: self.parent.mk.psanaMask"
self.w42 = console.ConsoleWidget(parent=None,namespace=namespace, text=text)
self.d42.addWidget(self.w42)
self.parent.area.addDock(self.d42, 'bottom')
def updateResolutionRings(self, data):
self.parent.resolutionRingsOn = data
if self.parent.exp.hasExpRunDetInfo():
self.updateRings()
if self.parent.args.v >= 1:
print("Done updateResolutionRings")
def updateResolution(self, data):
# convert to array of floats
_resolution = data.split(',')
self.parent.resolution = np.zeros((len(_resolution,)))
self.updateDock42(data)
if data != '':
for i in range(len(_resolution)):
self.parent.resolution[i] = float(_resolution[i])
if data != '':
self.hasUserDefinedResolution = True
else:
self.hasUserDefinedResolution = False
self.myResolutionRingList = self.parent.resolution
self.dMin = np.zeros_like(self.myResolutionRingList)
if self.hasGeometryInfo():
self.updateGeometry()
if self.parent.exp.hasExpRunDetInfo():
self.updateRings()
if self.parent.args.v >= 1:
print("Done updateResolution")
def updateResolutionUnits(self, data):
# convert to array of floats
self.parent.resolutionUnits = data
if self.hasGeometryInfo():
self.updateGeometry()
if self.parent.exp.hasExpRunDetInfo():
self.updateRings()
if self.parent.args.v >= 1:
print("Done updateResolutionUnits")
def updateRings(self):
if self.parent.resolutionRingsOn:
self.clearRings()
cenx = np.ones_like(self.myResolutionRingList)*self.parent.cx
ceny = np.ones_like(self.myResolutionRingList)*self.parent.cy
diameter = 2*self.myResolutionRingList
self.parent.img.ring_feature.setData(cenx, ceny, symbol='o', \
size=diameter, brush=(255,255,255,0), \
pen='r', pxMode=False)
for i,val in enumerate(self.dMin_crystal):
if self.parent.resolutionUnits == self.unitA_c:
self.resolutionText.append(pg.TextItem(text='%s A' % float('%.3g' % (val*1e10)), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitNm_c:
self.resolutionText.append(pg.TextItem(text='%s nm' % float('%.3g' % (val*1e9)), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitQ_c:
self.resolutionText.append(pg.TextItem(text='%s m^-1' % float('%.3g' % (self.qMax_crystal[i])), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitA_p:
self.resolutionText.append(pg.TextItem(text='%s A' % float('%.3g' % (self.dMin_physics[i]*1e10)), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitNm_p:
self.resolutionText.append(pg.TextItem(text='%s nm' % float('%.3g' % (self.dMin_physics[i]*1e9)), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitQ_p:
self.resolutionText.append(pg.TextItem(text='%s m^-1' % float('%.3g' % (self.qMax_physics[i])), border='w', fill=(0, 0, 255, 100)))
elif self.parent.resolutionUnits == self.unitTwoTheta:
self.resolutionText.append(pg.TextItem(text='%s degrees' % float('%.3g' % (self.thetaMax[i]*180/np.pi)), border='w', fill=(0, 0, 255, 100)))
self.parent.img.win.getView().addItem(self.resolutionText[i])
self.resolutionText[i].setPos(self.myResolutionRingList[i]+self.parent.cx, self.parent.cy)
else:
self.clearRings()
if self.parent.args.v >= 1: print("Done updateRings")
def drawCentre(self):
# Always indicate centre of detector
try:
self.parent.img.centre_feature.setData(np.array([self.parent.cx]), np.array([self.parent.cy]), symbol='o', \
size=6, brush=(255, 255, 255, 0), pen='r', pxMode=False)
if self.parent.args.v >= 1: print("Done drawCentre")
except:
pass
def clearRings(self):
if self.resolutionText:
cen = [0,]
self.parent.img.ring_feature.setData(cen, cen, size=0)
for i,val in enumerate(self.resolutionText):
self.parent.img.win.getView().removeItem(self.resolutionText[i])
self.resolutionText = []
def deploy(self):
with pg.BusyCursor():
# Calculate detector translation required in x and y
dx = self.parent.pixelSize * 1e6 * (self.parent.roi.centreX - self.parent.cx) # microns
dy = self.parent.pixelSize * 1e6 * (self.parent.roi.centreY - self.parent.cy) # microns
dz = np.mean(-self.parent.det.coords_z(self.parent.evt)) - self.parent.detectorDistance * 1e6 # microns
geo = self.parent.det.geometry(self.parent.evt)
top = geo.get_top_geo()
children = top.get_list_of_children()[0]
geo.move_geo(children.oname, 0, dx=-dy, dy=-dx, dz=dz)
fname = self.parent.psocakeRunDir + "/"+str(self.parent.runNumber)+'-end.data'
geo.save_pars_in_file(fname)
print("#################################################")
print("Deploying psana detector geometry: ", fname)
print("#################################################")
cmts = {'exp': self.parent.experimentName, 'app': 'psocake', 'comment': 'recentred geometry'}
if self.parent.args.localCalib:
calibDir = './calib'
elif self.parent.args.outDir is None:
calibDir = self.parent.rootDir + '/calib'
else:
calibDir = self.parent.dir + '/' + self.parent.experimentName[:3] + '/' + \
self.parent.experimentName + '/calib'
deploy_calib_file(cdir=calibDir, src=str(self.parent.det.name), type='geometry',
run_start=self.parent.runNumber, run_end=None, ifname=fname, dcmts=cmts, pbits=0)
# Reload new psana geometry
self.parent.exp.setupExperiment()
self.parent.img.getDetImage(self.parent.eventNumber)
self.updateRings()
self.parent.index.updateIndex()
self.drawCentre()
# Show mask
self.parent.mk.updatePsanaMaskOn()
def autoDeploy(self): #FIXME: yet to verify this works correctly on new lab coordinate
with pg.BusyCursor():
powderHits = np.load(self.parent.psocakeRunDir + '/' + self.parent.experimentName + '_' + str(self.parent.runNumber).zfill(4) + '_maxHits.npy')
powderMisses = np.load(self.parent.psocakeRunDir + '/' + self.parent.experimentName + '_' + str(self.parent.runNumber).zfill(4) + '_maxMisses.npy')
powderImg = self.parent.det.image(self.parent.evt, np.maximum(powderHits,powderMisses))
centreRow, centreCol = findDetectorCentre(np.log(abs(powderImg)), self.parent.cx, self.parent.cy, range=200)
print("Current centre along row,centre along column: ", self.parent.cx, self.parent.cy)
print("Optimum centre along row,centre along column: ", centreRow, centreCol)
allowedDeviation = 175 # pixels
if abs(self.parent.cx - centreRow) <= allowedDeviation and \
abs(self.parent.cy - centreCol) <= allowedDeviation:
deploy = True
else:
deploy = False
print("Too far away from current centre. I will not deploy the auto centred geometry.")
if deploy:
# Calculate detector translation in x and y
dx = self.parent.pixelSize * 1e6 * (self.parent.cx - centreRow) # microns
dy = self.parent.pixelSize * 1e6 * (self.parent.cy - centreCol) # microns
dz = np.mean(-self.parent.det.coords_z(self.parent.evt)) - self.parent.detectorDistance * 1e6 # microns
dx = self.parent.pixelSize * 1e6 * (self.parent.roi.centreX - self.parent.cx) # microns
dy = self.parent.pixelSize * 1e6 * (self.parent.roi.centreY - self.parent.cy) # microns
dz = np.mean(-self.parent.det.coords_z(self.parent.evt)) - self.parent.detectorDistance * 1e6 # microns
geo = self.parent.det.geometry(self.parent.evt)
top = geo.get_top_geo()
children = top.get_list_of_children()[0]
geo.move_geo(children.oname, 0, dx=-dy, dy=-dx, dz=dz)
fname = self.parent.psocakeRunDir + "/" + str(self.parent.runNumber) + '-end.data'
geo.save_pars_in_file(fname)
print("#################################################")
print("Deploying psana detector geometry: ", fname)
print("#################################################")
cmts = {'exp': self.parent.experimentName, 'app': 'psocake', 'comment': 'auto recentred geometry'}
if self.parent.args.localCalib:
calibDir = './calib'
elif self.parent.args.outDir is None:
calibDir = self.parent.rootDir + '/calib'
else:
calibDir = self.parent.dir + '/' + self.parent.experimentName[:3] + '/' + self.parent.experimentName + \
'/calib'
deploy_calib_file(cdir=calibDir, src=str(self.parent.det.name), type='geometry',
run_start=self.parent.runNumber, run_end=None, ifname=fname, dcmts=cmts, pbits=0)
# Reload new psana geometry
self.parent.exp.setupExperiment()
self.parent.img.getDetImage(self.parent.eventNumber)
self.updateRings()
self.parent.index.updateIndex()
self.drawCentre()
# Show mask
self.parent.mk.updatePsanaMaskOn()
class Ui_MainWindow(object):
def setupUi(self, MainWindow, params):
#app = QtGui.QApplication([])
#self.win = QtGui.QMainWindow()
self.area = DockArea()
MainWindow.setCentralWidget(self.area)
MainWindow.resize(1200,600)
MainWindow.setWindowTitle('SASE optimization')
## Create docks, place them into the window one at a time.
## Note that size arguments are only a suggestion; docks will still have to
## fill the entire dock area and obey the limits of their internal widgets.
#self.orb_fig = Dock("Orbit", size=(400, 300)) ## give this dock the minimum possible size
#self.orb_fig.float()
#self.sase_fig = Dock("SASE", size=(400,300), closable=True)
self.sase_fig = Dock("SASE", size=(400,300))
self.blm_fig = Dock("BLM", size=(400,200))
self.seq_cntr = Dock("Sequence", size=(150,200))
self.sase_cntr = Dock("Controls", size=(150,200))
#self.orb_cntr = Dock("orb contr.", size=(400,100))
self.cur_fig = Dock("Settings", size=(400,300))
self.logger = Dock("Logger", size=(100,300))
self.area.addDock(self.cur_fig, 'left')
#self.area.addDock(self.orb_fig, 'above', self.cur_fig) ## place d1 at left edge of dock area (it will fill the whole space since there are no other docks yet)
self.area.addDock(self.sase_fig, 'bottom', self.cur_fig) ## place d2 at right edge of dock area
self.area.addDock(self.blm_fig, 'top', self.sase_fig)## place d3 at bottom edge of d1
self.area.addDock(self.sase_cntr, 'right') ## place d5 at left edge of d1
self.area.addDock(self.seq_cntr, 'left', self.sase_cntr) ## place d4 at right edge of dock area
#self.area.addDock(self.orb_cntr, 'bottom', self.orb_fig)
## Test ability to move docks programatically after they have been placed
#self.area.moveDock(self.sase_fig, 'bottom', self.orb_fig) ## move d4 to top edge of d2
#self.area.moveDock(self.blm_fig, 'bottom', self.sase_fig) ## move d6 to stack on top of d4
self.area.addDock(self.logger, 'bottom', self.sase_fig)
self.area.moveDock(self.blm_fig, 'above', self.logger)
## Add widgets into each dock
#add Logger
self.log_lab = QtGui.QTextBrowser()
#self.log_lab.verticalScrollBar().setValue(self.log_lab.verticalScrollBar().maximum())
self.logger.addWidget(self.log_lab)
## first dock gets save/restore buttons
self.t = ParameterTree()
if params != None:
self.p = Parameter.create(name='params', type='group', children=params)
self.t.setParameters(self.p, showTop=False)
self.t.setWindowTitle('SASE optimization')
self.seq_cntr.addWidget(self.t)
self.seq = pg.LayoutWidget()
self.label = QtGui.QLabel("""sequence control""")
self.add_seq_btn = QtGui.QPushButton('Add Action')
self.save_seq_btn = QtGui.QPushButton('Save seqs')
self.load_seq_btn = QtGui.QPushButton('Load seqs')
#self.restoreBtn.setEnabled(False)
self.seq.addWidget(self.label, row=0, col=0)
self.seq.addWidget(self.add_seq_btn, row=1, col=0)
self.seq.addWidget(self.save_seq_btn, row=2, col=0)
self.seq.addWidget(self.load_seq_btn, row=3, col=0)
self.seq_cntr.addWidget(self.seq)
#Currents graphics
self.t_cur_cntr = ParameterTree()
#param = [{'name': 'Devices', 'type': 'list', 'values': {}, 'value': 0}]
param = []
self.p_cur_cntr = Parameter.create(name='control', type='group', children=param)
self.t_cur_cntr.setParameters(self.p_cur_cntr, showTop=False)
self.current = pg.PlotWidget(title="Settings")
self.cur_fig.addWidget(self.current, row=0, col=0)
self.cur_fig.addWidget(self.t_cur_cntr, row=0, col=1)
#BLM graphics
## Hide title bar on dock 3
#d3.hideTitleBar()
self.blm = pg.PlotWidget(title="BLM")
self.blm_fig.addWidget(self.blm)
#SASE graphics
self.sase = pg.PlotWidget(title="SASE")
self.sase_fig.addWidget(self.sase)
#controls
self.w5 = pg.LayoutWidget()
self.start_opt_btm = QtGui.QPushButton('start')
params = [
{'name': 'Basic opt. parameters', 'type': 'group', 'children': [
{'name': 'debug', 'type': 'bool', 'value': False},
{'name': 'logging', 'type': 'bool', 'value': True},
{'name': 'log file', 'type': 'str', 'value': 'test.log'},
{'name': 'timeout', 'type': 'float', 'value': 0.5, 'step': 0.1, 'limits': (0, 10)},
#{'name': 'SASE det.', 'type': 'list', 'values': {'mcp': 'mcp', 'gmd slow':'gmd_fl1_slow', 'bkr':'bkr', 'default':'gmd_default'}, 'value': "default"},
{'name': 'detector', 'type': 'list', 'values': ['gmd_default', 'mcp', 'gmd_fl1_slow', 'bkr'], 'value': "gmd_default"} ]}
]
self.t_cntr = ParameterTree()
self.p_cntr = Parameter.create(name='control', type='group', children=params)
self.t_cntr.setParameters(self.p_cntr, showTop=False)
self.restore_cur_btn = QtGui.QPushButton('Restore')
#self.restore_cur_btn.setEnabled(False)
self.setmax_opt_btn = QtGui.QPushButton('Set currents for max SASE')
#self.setmax_opt_btn.setEnabled(False)
self.stop_opt_btn = QtGui.QPushButton('Stop')
self.clear_disp_btn = QtGui.QPushButton('Clear display')
self.save_machine_btn = QtGui.QPushButton('Save new tuning')
#self.save_machine_btn.setEnabled(False)
#self.stop_btn = QtGui.QPushButton('stop')
#self.w5.addWidget(self.start_opt_btm, row=0, col=0)
self.w5.addWidget(self.stop_opt_btn, row=0, col=0)
self.w5.addWidget(self.restore_cur_btn, row=1, col=0)
#self.w5.addWidget(self.setmax_opt_btn, row=2, col=0)
self.w5.addWidget(self.clear_disp_btn, row=4, col=0)
#self.w5.addWidget(self.debug_opt_chk, row=3, col=0)
#self.w5.addWidget(self.log_opt_chk, row=4, col=0)
self.w5.addWidget(self.t_cntr, row=5, col=0)
#self.w5.addWidget(QtGui.QLabel("""machine settings"""), row=6, col=0)
#self.w5.addWidget(self.save_machine_btn, row=7, col=0)
self.sase_cntr.addWidget(self.w5)
class JsonReader(QWidget):
def __init__(self):
super().__init__()
self.title = 'Json metadata reader'
self.initUI()
def initUI(self):
self.setWindowTitle(self.title)
self.getbtn = QPushButton("Select file")
self.getbtn.clicked.connect(self.get_file)
self.draglbl = DragDropLabel(self)
self.draglbl.setText("... or drop .{} file here".format(
DragDropLabel.acceptedFormat.upper()))
self.draglbl.setAlignment(QtCore.Qt.AlignCenter)
self.draglbl.droppedFile.connect(self.open_file)
self.layout = QGridLayout(self)
self.layout.addWidget(self.getbtn, 0, 0, 1, 2)
self.layout.addWidget(self.draglbl, 1, 0, 1, 2)
self.setLayout(self.layout)
self.show()
def get_file(self):
self.path, _ = QFileDialog.getOpenFileName(
filter="Json files (*.json)")
if not self.path:
pass
else:
self.open_file(self.path)
def open_file(self, filename):
self.filename = filename
with open(filename) as json_file:
self.metadata_dict = json.load(json_file)
self.display_tree_widget(self.metadata_dict)
def display_tree_widget(self, metadata):
"""Display the parameter tree from the experiment metadata.
:param metadata: .json metadata
"""
# Close previous tree widget
self.close_tree()
# Create a variable checking whether changes have been made to the parameter tree values
self.has_changed = False
# Create list with parameters for the tree
self.parameters = self.create_parameters(self.fix_types(metadata))
# Create tree of Parameter objects
self.p = Parameter.create(name='params',
type='group',
children=self.parameters)
# Save original state
self.original_state = self.p.saveState()
# Create ParameterTree widget
self.tree = ParameterTree()
self.tree.setParameters(self.p, showTop=False)
self.tree.setWindowTitle('pyqtgraph example: Parameter Tree')
# Display tree widget
self.layout.addWidget(self.tree, 2, 0, 1, 2)
# And buttons
self.savebtn = QPushButton("Save changes")
self.resetbtn = QPushButton("Reset changes")
self.layout.addWidget(self.savebtn, 3, 0)
self.layout.addWidget(self.resetbtn, 3, 1)
self.savebtn.clicked.connect(self.save_treevals)
self.resetbtn.clicked.connect(self.reset)
# Send signal when any entry is changed
self.p.sigTreeStateChanged.connect(self.change)
def save_treevals(self):
"""Save current values of the parameter tree into a dictionary.
"""
# Recover data from tree and store it in a dict
self.treevals_dict = self.p.getValues()
self.metadata_dict_mod = self.get_mod_dict(self.treevals_dict)
# Nasty way to make new dict (with modified metadata) with same structure as the original one
self.metadata_dict_mod['stimulus']['log'] = self.metadata_dict[
'stimulus']['log']
self.metadata_dict_mod['stimulus']['display_params']['pos'] = \
json.loads(self.metadata_dict_mod['stimulus']['display_params']['pos'])
self.metadata_dict_mod['stimulus']['display_params']['size'] = \
json.loads(self.metadata_dict_mod['stimulus']['display_params']['size'])
self.show_warning()
def show_warning(self):
"""Upon saving, display a warning message
to choose whether to create a new metadata file or replace the existing one.
"""
if self.has_changed:
self.msg = QMessageBox()
self.msg.setIcon(QMessageBox.Warning)
self.setWindowTitle("Saving Warning")
self.msg.setText("Some parameters have changed")
self.msg.setInformativeText(
"Do you want to overwrite the original .json metadata file?")
self.msg.addButton('Create new file', QMessageBox.AcceptRole)
self.msg.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
self.ret = self.msg.exec_()
if self.ret == QMessageBox.Yes:
self.overwrite_metadata_file(self.metadata_dict_mod)
elif self.ret == QMessageBox.AcceptRole:
self.create_metadata_file(self.metadata_dict_mod)
else:
pass
else:
self.msg2 = QMessageBox()
self.msg2.setIcon(QMessageBox.Information)
self.setWindowTitle("Saving Warning")
self.msg2.setText("No changes have been made.")
self.msg2.addButton('OK', QMessageBox.AcceptRole)
self.ret = self.msg2.exec_()
def overwrite_metadata_file(self, metadata_dict_mod):
# Overwritte original metadata file
with open(self.filename, 'w') as file:
json.dump(metadata_dict_mod, file)
def create_metadata_file(self, metadata_dict_mod):
# Overwritte original metadata file
self.name, self.ext = self.filename.split('.')
with open('{}_modified.{}'.format(self.name, self.ext), 'w') as file:
json.dump(metadata_dict_mod, file)
def reset(self):
"""Reset parameter tree values to the original state after loading.
"""
self.p.restoreState(self.original_state, recursive=True)
#self.tree.setParameters(self.p, showTop=False)
def fix_types(self, datadict):
"""Modify metadata dict so only accepted types are found.
"""
param_dict = dict()
for key, value in datadict.items():
if isinstance(value, list):
param_dict[key] = str(value)
elif isinstance(value, dict):
param_dict[key] = self.fix_types(value)
else:
param_dict[key] = value
return param_dict
def create_parameters(self, datadict):
"""Create list with parameters and Children to which the tree will be built from.
"""
parameters = []
for key, value in datadict.items():
if key == 'log':
pass
else:
if isinstance(value, dict):
parameters.append({
'name': '{}'.format(key),
'type': 'group',
'children': self.create_parameters(value)
})
else:
parameters.append({
'name': '{}'.format(key),
'type': '{}'.format(type(value).__name__),
'value': value
})
return parameters
def get_mod_dict(self, treevals_dict):
"""Recursive function to convert into dict output of getValues function.
"""
metadata_dict_mod = dict()
for key, value in treevals_dict.items():
if value[0] is None:
metadata_dict_mod[key] = dict(self.get_mod_dict(value[1]))
else:
metadata_dict_mod[key] = value[0]
return metadata_dict_mod
def change(self, param, changes):
print("tree changes:")
for param, change, data in changes:
path = self.p.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
print(' parameter: %s' % childName)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
if change == 'activated':
pass
else:
self.has_changed = True
def close_tree(self):
try:
self.layout.removeWidget(self.tree)
self.tree.deleteLater()
self.tree = None
except AttributeError:
pass
class ExperimentInfo(object):
def __init__(self, parent = None):
self.parent = parent
#############################
## Dock 2: parameter
#############################
self.d2 = Dock("Experiment Parameters", size=(1, 1))
self.w2 = ParameterTree()
self.w2.setWindowTitle('Parameters')
self.d2.addWidget(self.w2)
self.exp_grp = 'Experiment information'
self.exp_name_str = 'Experiment Name'
self.exp_run_str = 'Run Number'
self.exp_det_str = 'DetInfo'
self.exp_evt_str = 'Event Number'
self.exp_eventID_str = 'EventID'
self.exp_second_str = 'Seconds'
self.exp_nanosecond_str = 'Nanoseconds'
self.exp_fiducial_str = 'Fiducial'
self.exp_numEvents_str = 'Total Events'
self.exp_detInfo_str = 'Detector ID'
self.eventSeconds = 0
self.eventNanoseconds = 0
self.eventFiducial = 0
self.eventTotal = 0
self.run = None
self.times = None
self.disp_grp = 'Display'
self.disp_log_str = 'Logscale'
self.disp_aduPerPhoton_str = 'ADUs per Photon'
self.disp_image_str = 'Image properties'
self.disp_adu_str = 'gain corrected ADU'
self.disp_gain_str = 'gain'
self.disp_gainMask_str = 'gain_mask'
self.disp_coordx_str = 'coord_x'
self.disp_coordy_str = 'coord_y'
self.disp_quad_str = 'quad number'
self.disp_seg_str = 'seg number'
self.disp_row_str = 'row number'
self.disp_col_str = 'col number'
self.disp_raw_str = 'raw ADU'
self.disp_pedestalCorrected_str = 'pedestal corrected ADU'
self.disp_commonModeCorrected_str = 'common mode corrected ADU'
self.disp_photons_str = 'photon counts'
self.disp_rms_str = 'pixel rms'
self.disp_status_str = 'pixel status'
self.disp_pedestal_str = 'pedestal'
self.disp_commonMode_str = 'common mode'
self.disp_friedel_str = 'Apply Friedel symmetry'
self.disp_commonModeOverride_str = 'Common mode (override)'
self.disp_overrideCommonMode_str = 'Apply common mode (override)'
self.disp_commonModeParam0_str = 'parameters 0'
self.disp_commonModeParam1_str = 'parameters 1'
self.disp_commonModeParam2_str = 'parameters 2'
self.disp_commonModeParam3_str = 'parameters 3'
self.disp_medianCorrection_str = 'median background corrected ADU'
self.disp_radialCorrection_str = 'radial background corrected ADU'
self.disp_medianFilterRank_str = 'median filter rank'
self.logscaleOn = False
self.aduPerPhoton = 1.
self.medianFilterRank = 5
# image properties
self.disp_medianCorrection = 19
self.disp_radialCorrection = 18
self.disp_gainMask = 17
self.disp_coordy= 16
self.disp_coordx= 15
self.disp_col= 14
self.disp_row= 13
self.disp_seg= 12
self.disp_quad= 11
self.disp_gain= 10
self.disp_commonMode= 9
self.disp_rms= 8
self.disp_status= 7
self.disp_pedestal= 6
self.disp_photons= 5
self.disp_raw= 4
self.disp_pedestalCorrected= 3
self.disp_commonModeCorrected= 2
self.disp_adu= 1
self.image_property = self.disp_adu
self.applyFriedel = False
self.applyCommonMode = False
self.commonModeParams = np.array([0,0,0,0])
self.commonMode = np.array([0, 0, 0, 0])
self.firstSetupExperiment = True
# e-log
self.logger = False
self.loggerFile = None
self.crawlerRunning = False
self.username = None
self.rt = None
self.table = None
self.params = [
{'name': self.exp_grp, 'type': 'group', 'children': [
{'name': self.exp_name_str, 'type': 'str', 'value': self.parent.experimentName,
'tip': "Experiment name, .e.g. cxic0415"},
{'name': self.exp_run_str, 'type': 'int', 'value': self.parent.runNumber, 'tip': "Run number, e.g. 15"},
{'name': self.exp_detInfo_str, 'type': 'str', 'value': self.parent.detInfo,
'tip': "Detector ID. Look at the terminal for available area detectors, e.g. DscCsPad"},
{'name': self.exp_evt_str, 'type': 'int', 'value': self.parent.eventNumber, 'tip': "Event number, first event is 0",
'children': [
# {'name': exp_eventID_str, 'type': 'str', 'value': self.eventID},#, 'readonly': False},
{'name': self.exp_second_str, 'type': 'str', 'value': self.eventSeconds, 'readonly': True},
{'name': self.exp_nanosecond_str, 'type': 'str', 'value': self.eventNanoseconds, 'readonly': True},
{'name': self.exp_fiducial_str, 'type': 'str', 'value': self.eventFiducial, 'readonly': True},
{'name': self.exp_numEvents_str, 'type': 'str', 'value': self.eventTotal, 'readonly': True},
]},
]},
{'name': self.disp_grp, 'type': 'group', 'children': [
{'name': self.disp_log_str, 'type': 'bool', 'value': self.logscaleOn, 'tip': "Display in log10"},
{'name': self.disp_aduPerPhoton_str, 'type': 'float', 'value': self.aduPerPhoton, 'tip': "ADUs per photon is used for photon conversion"},
{'name': self.disp_medianFilterRank_str, 'type': 'int', 'value': self.medianFilterRank, 'tip': "Window size for median filter"},
{'name': self.disp_image_str, 'type': 'list', 'values': {self.disp_medianCorrection_str: self.disp_medianCorrection,
self.disp_radialCorrection_str: self.disp_radialCorrection,
self.disp_gainMask_str: self.disp_gainMask,
self.disp_coordy_str: self.disp_coordy,
self.disp_coordx_str: self.disp_coordx,
self.disp_col_str: self.disp_col,
self.disp_row_str: self.disp_row,
self.disp_seg_str: self.disp_seg,
self.disp_quad_str: self.disp_quad,
self.disp_gain_str: self.disp_gain,
self.disp_commonMode_str: self.disp_commonMode,
self.disp_rms_str: self.disp_rms,
self.disp_status_str: self.disp_status,
self.disp_pedestal_str: self.disp_pedestal,
self.disp_photons_str: self.disp_photons,
self.disp_raw_str: self.disp_raw,
self.disp_pedestalCorrected_str: self.disp_pedestalCorrected,
self.disp_commonModeCorrected_str: self.disp_commonModeCorrected,
self.disp_adu_str: self.disp_adu},
'value': self.image_property, 'tip': "Choose image property to display"},
{'name': self.disp_friedel_str, 'type': 'bool', 'value': self.applyFriedel,
'tip': "Click to apply Friedel symmetry to the detector image."},
{'name': self.disp_commonModeOverride_str, 'visible': True, 'expanded': False, 'type': 'str', 'value': "",
'readonly': True, 'children': [
{'name': self.disp_overrideCommonMode_str, 'type': 'bool', 'value': self.applyCommonMode,
'tip': "Click to play around with common mode settings.\n This does not change your deployed calib file."},
{'name': self.disp_commonModeParam0_str, 'type': 'int', 'value': self.commonModeParams[0]},
{'name': self.disp_commonModeParam1_str, 'type': 'int', 'value': self.commonModeParams[1]},
{'name': self.disp_commonModeParam2_str, 'type': 'int', 'value': self.commonModeParams[2]},
{'name': self.disp_commonModeParam3_str, 'type': 'int', 'value': self.commonModeParams[3]},
]},
]},
]
self.p = Parameter.create(name='params', type='group', children=self.params, expanded=True)
self.w2.setParameters(self.p, showTop=False)
self.p.sigTreeStateChanged.connect(self.change)
# If anything changes in the parameter tree, print a message
def change(self, panel, changes):
for param, change, data in changes:
path = panel.childPath(param)
if self.parent.args.v >= 1:
print(' path: %s' % path)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
self.paramUpdate(path, change, data)
##############################
# Mandatory parameter update #
##############################
def paramUpdate(self, path, change, data):
if path[0] == self.exp_grp:
if path[1] == self.exp_name_str:
self.updateExpName(data)
if self.parent.pk.showPeaks:
self.parent.pk.updateClassification()
elif path[1] == self.exp_run_str:
self.updateRunNumber(data)
if self.parent.pk.showPeaks:
self.parent.pk.updateClassification()
elif path[1] == self.exp_detInfo_str:
self.updateDetInfo(data)
if self.parent.pk.showPeaks:
self.parent.pk.updateClassification()
elif path[1] == self.exp_evt_str and len(path) == 2 and change is 'value':
self.updateEventNumber(data)
if self.parent.pk.showPeaks: self.parent.pk.updateClassification()
elif path[0] == self.disp_grp:
if path[1] == self.disp_log_str:
self.updateLogscale(data)
elif path[1] == self.disp_aduPerPhoton_str:
self.updateAduPerPhoton(data)
if self.parent.pk.showPeaks: self.parent.pk.updateClassification()
elif path[1] == self.disp_medianFilterRank_str:
self.updateMedianFilter(data)
if self.parent.pk.showPeaks: self.parent.pk.updateClassification()
elif path[1] == self.disp_image_str:
self.updateImageProperty(data)
if self.parent.pk.showPeaks: self.parent.pk.updateClassification()
elif path[1] == self.disp_friedel_str:
self.updateFriedel(data)
elif path[2] == self.disp_commonModeParam0_str:
self.updateCommonModeParam(data, 0)
elif path[2] == self.disp_commonModeParam1_str:
self.updateCommonModeParam(data, 1)
elif path[2] == self.disp_commonModeParam2_str:
self.updateCommonModeParam(data, 2)
elif path[2] == self.disp_commonModeParam3_str:
self.updateCommonModeParam(data, 3)
elif path[2] == self.disp_overrideCommonMode_str:
self.updateCommonMode(data)
if self.parent.pk.showPeaks: self.parent.pk.updateClassification()
###################################
###### Experiment Parameters ######
###################################
def resetVariables(self):
self.secList = None
self.nsecList = None
self.fidList = None
def updateExpName(self, data):
self.parent.experimentName = data
self.parent.hasExperimentName = True
self.parent.detInfoList = None
self.resetVariables()
# Setup elog
if logbook_present:
self.rt = RunTables(**{'web-service-url': 'https://pswww.slac.stanford.edu/ws-kerb'})
try:
self.table = self.rt.findUserTable(exper_name=self.parent.experimentName, table_name='Run summary')
except:
self.table = None
#print "Your experiment may not exist"
#print "Or you need a kerberos ticket. Type: kinit"
#exit()
#exit()
self.setupExperiment()
self.parent.img.updateImage()
if self.parent.args.v >= 1: print "Done updateExperimentName:", self.parent.experimentName
def updateRunNumber(self, data):
if data == 0:
self.parent.runNumber = data
self.parent.hasRunNumber = False
else:
self.parent.runNumber = data
self.parent.hasRunNumber = True
self.parent.detInfoList = None
self.setupExperiment()
self.parent.mk.resetMasks()
self.resetVariables()
self.parent.pk.userUpdate = None
self.parent.img.updateImage()
if self.parent.args.v >= 1: print "Done updateRunNumber: ", self.parent.runNumber
def updateDetInfo(self, data):
if self.parent.hasDetInfo is False or self.parent.detInfo is not data:
self.parent.mk.resetMasks()
self.parent.calib = None
self.parent.data = None
self.parent.firstUpdate = True
self.parent.detInfo = data
if data == 'DscCsPad' or data == 'DsdCsPad' or data == 'DsaCsPad':
self.parent.isCspad = True
self.parent.hasDetInfo = True
self.setupExperiment()
self.parent.img.updateImage()
if self.parent.args.v >= 1: print "Done updateDetInfo: ", self.parent.detInfo
def findEventFromTimestamp(self, secList, nsecList, fidList, sec, nsec, fid):
eventNumber = (np.where(secList == sec)[0] & np.where(nsecList == nsec)[0] & np.where(fidList == fid)[0])[0]
return eventNumber
def convertTimestamp64(self, t):
_sec = int(t) >> 32
_nsec = int(t) & 0xFFFFFFFF
return _sec, _nsec
def convertSecNanosec(self, sec, nsec):
_timestamp64 = int(sec << 32 | nsec)
return _timestamp64
def getEvt(self, evtNumber):
if self.parent.hasRunNumber:
_evt = self.run.event(self.times[evtNumber])
return _evt
else:
return None
def getEventID(self, evt):
if evt is not None:
_evtid = evt.get(psana.EventId)
_seconds = _evtid.time()[0]
_nanoseconds = _evtid.time()[1]
_fiducials = _evtid.fiducials()
return _seconds, _nanoseconds, _fiducials
def updateEventNumber(self, data):
self.parent.eventNumber = data
if self.parent.eventNumber >= self.eventTotal:
self.parent.eventNumber = self.eventTotal - 1
# update timestamps and fiducial
self.parent.evt = self.getEvt(self.parent.eventNumber)
if self.parent.evt is not None:
sec, nanosec, fid = self.getEventID(self.parent.evt)
self.eventSeconds = str(sec)
self.eventNanoseconds = str(nanosec)
self.eventFiducial = str(fid)
self.updateEventID(self.eventSeconds, self.eventNanoseconds, self.eventFiducial)
self.p.param(self.exp_grp, self.exp_evt_str).setValue(self.parent.eventNumber)
self.parent.img.updateImage()
# update labels
if self.parent.args.mode == "all":
if self.parent.evtLabels is not None: self.parent.evtLabels.refresh()
if self.parent.args.v >= 1: print "Done updateEventNumber: ", self.parent.eventNumber
def hasExpRunInfo(self):
if self.parent.hasExperimentName and self.parent.hasRunNumber:
# Check such a run exists
import glob
xtcs = glob.glob('/reg/d/psdm/' + self.parent.experimentName[0:3] + '/' + self.parent.experimentName + '/xtc/*-r' + str(
self.parent.runNumber).zfill(4) + '-*.xtc')
if len(xtcs) > 0:
return True
else:
# reset run number
if self.parent.runNumber > 0:
print "No such run exists in: ", self.parent.experimentName
self.parent.runNumber = 0
self.updateRunNumber(self.parent.runNumber)
self.p.param(self.exp_grp, self.exp_run_str).setValue(self.parent.runNumber)
return False
return False
def hasExpRunDetInfo(self):
if self.parent.args.v >= 1: print "exp,run,det: ", self.parent.hasExperimentName, self.parent.hasRunNumber, self.parent.hasDetInfo
if self.parent.hasExperimentName and self.parent.hasRunNumber and self.parent.hasDetInfo:
if self.parent.args.v >= 1: print "hasExpRunDetInfo: True ", self.parent.runNumber
return True
else:
if self.parent.args.v >= 1: print "hasExpRunDetInfo: False ", self.parent.runNumber
return False
def getUsername(self):
process = subprocess.Popen('whoami', stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
out, err = process.communicate()
self.username = out.strip()
def setupPsocake(self):
self.loggerFile = self.parent.elogDir + '/logger.data'
if os.path.exists(self.parent.elogDir) is False:
try:
os.makedirs(self.parent.elogDir, 0774)
# setup permissions
process = subprocess.Popen('chgrp -R ' + self.parent.experimentName + ' ' + self.parent.elogDir, stdout=subprocess.PIPE,
stderr=subprocess.PIPE, shell=True)
out, err = process.communicate()
process = subprocess.Popen('chmod -R u+rwx,g+rws,o+rx ' + self.parent.elogDir, stdout=subprocess.PIPE,
stderr=subprocess.PIPE, shell=True)
out, err = process.communicate()
# create logger
with open(self.loggerFile, "w") as myfile:
if self.parent.args.outDir is None:
myfile.write(self.username)
else:
myfile.write("NOONE")
except:
print "No write access: ", self.parent.elogDir
else:
# check if I'm a logger
with open(self.loggerFile, "r") as myfile:
content = myfile.readlines()
if content[0].strip() == self.username:
if logbook_present and self.table is not None:
self.logger = True
else:
print "WARNING: logbook not present"
if logbook_present and self.parent.args.v >= 1: print "I'm an elogger"
else:
self.logger = False
if self.parent.args.v >= 1: print "I'm not an elogger"
# Make run folder
try:
if os.path.exists(self.parent.psocakeRunDir) is False:
if self.parent.args.outDir is None:
os.makedirs(self.parent.psocakeRunDir, 0774)
else: # don't let groups and others access to this folder
os.makedirs(self.parent.psocakeRunDir, 0700)
process = subprocess.Popen('chmod -R ' + self.parent.psocakeRunDir,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE, shell=True)
out, err = process.communicate()
self.parent.writeAccess = True
except:
print "No write access: ", self.parent.psocakeRunDir
self.parent.writeAccess = False
# Launch crawler
crawlerThread = []
crawlerThreadCounter = 0
def launchCrawler(self):
self.crawlerThread.append(LogbookCrawler.LogbookCrawler(self.parent)) # send parent parameters with self
self.crawlerThread[self.crawlerThreadCounter].updateLogbook(self.parent.experimentName, self.parent.psocakeDir)
self.crawlerThreadCounter += 1
def getDetectorAlias(self, srcOrAlias):
for i in self.parent.detInfoList:
src, alias, _ = i
if srcOrAlias.lower() == src.lower() or srcOrAlias.lower() == alias.lower():
return alias
def updateHiddenCrystfelFiles(self, arg):
if arg == 'lcls':
if ('cspad' in self.parent.detInfo.lower() and 'cxi' in self.parent.experimentName) or \
('rayonix' in self.parent.detInfo.lower() and 'mfx' in self.parent.experimentName) or \
('rayonix' in self.parent.detInfo.lower() and 'xpp' in self.parent.experimentName):
self.parent.index.hiddenCXI = self.parent.psocakeRunDir + '/.temp.cxi'
self.parent.index.hiddenCrystfelStream = self.parent.psocakeRunDir + '/.temp.stream'
self.parent.index.hiddenCrystfelList = self.parent.psocakeRunDir + '/.temp.lst'
else:
if self.parent.args.v >= 1: print "updateHiddenCrystfelFiles not implemented"
self.parent.index.hiddenCXI = None
def updateDetectorDistance(self, arg):
if arg == 'lcls':
if 'cspad' in self.parent.detInfo.lower() and 'cxi' in self.parent.experimentName:
if self.parent.detectorDistance < 0.01:
self.parent.detectorDistance = np.mean(self.parent.det.coords_z(self.parent.evt)) * 1e-6 # metres
self.parent.geom.p1.param(self.parent.geom.geom_grp, self.parent.geom.geom_detectorDistance_str).setValue(self.parent.detectorDistance*1e3) # mm
self.parent.coffset = self.parent.detectorDistance - self.parent.clen
self.parent.geom.p1.param(self.parent.geom.geom_grp, self.parent.geom.geom_clen_str).setValue(self.parent.clen)
elif 'rayonix' in self.parent.detInfo.lower() and 'mfx' in self.parent.experimentName:
if self.parent.detectorDistance < 0.01:
self.parent.detectorDistance = np.mean(self.parent.det.coords_z(self.parent.evt)) * 1e-6 # metres
self.parent.geom.p1.param(self.parent.geom.geom_grp, self.parent.geom.geom_detectorDistance_str).setValue(self.parent.detectorDistance*1e3) # mm
self.parent.coffset = self.parent.detectorDistance - self.parent.clen
self.parent.geom.p1.param(self.parent.geom.geom_grp, self.parent.geom.geom_clen_str).setValue(self.parent.clen)
elif 'rayonix' in self.parent.detInfo.lower() and 'xpp' in self.parent.experimentName:
if self.parent.detectorDistance < 0.01:
self.parent.detectorDistance = np.mean(self.parent.det.coords_z(self.parent.evt)) * 1e-6 # metres
self.parent.geom.p1.param(self.parent.geom.geom_grp, self.parent.geom.geom_detectorDistance_str).setValue(self.parent.detectorDistance*1e3) # mm
self.parent.coffset = self.parent.detectorDistance - self.parent.clen
self.parent.geom.p1.param(self.parent.geom.geom_grp, self.parent.geom.geom_clen_str).setValue(
self.parent.clen)
else:
if self.parent.args.v >= 1: print "updateDetectorDistance: not implemented for this detector yet"
if self.parent.args.v >= 1:
print "detectorDistance (m), self.clen (m), self.coffset (m): ", self.parent.detectorDistance, self.parent.clen, self.parent.coffset
def updatePixelSize(self, arg):
if arg == 'lcls':
if 'cspad' in self.parent.detInfo.lower(): # TODO: increase pixel size list: epix, rayonix
self.parent.pixelSize = 110e-6 # metres
elif 'pnccd' in self.parent.detInfo.lower():
self.parent.pixelSize = 75e-6 # metres
elif 'rayonix' in self.parent.detInfo.lower():
self.parent.pixelSize = 89e-6 # metres
# Update geometry panel
self.parent.geom.p1.param(self.parent.geom.geom_grp, self.parent.geom.geom_pixelSize_str).setValue(
self.parent.pixelSize) # pixel size
def updatePhotonEnergy(self, arg):
if arg == 'lcls':
self.parent.ebeam = self.parent.evt.get(psana.Bld.BldDataEBeamV7, psana.Source('BldInfo(EBeam)'))
if self.parent.ebeam:
self.parent.photonEnergy = self.parent.ebeam.ebeamPhotonEnergy()
else:
try:
wavelength = self.parent.epics.value('SIOC:SYS0:ML00:AO192') # nanometre
h = 6.626070e-34 # J.m
c = 2.99792458e8 # m/s
joulesPerEv = 1.602176621e-19 # J/eV
self.parent.photonEnergy = (h / joulesPerEv * c) / (wavelength * 1e-9)
except:
self.parent.photonEnergy = 0.0
self.parent.geom.p1.param(self.parent.geom.geom_grp,
self.parent.geom.geom_photonEnergy_str).setValue(self.parent.photonEnergy)
def setClen(self):
if 'cspad' in self.parent.detInfo.lower() and 'cxi' in self.parent.experimentName:
try:
self.parent.clenEpics = str(self.parent.detAlias) + '_z'
self.readEpicsClen()
except:
if 'ds1' in self.parent.detInfo.lower():
self.parent.clenEpics = str('CXI:DS1:MMS:06.RBV')
self.readEpicsClen()
elif 'ds2' in self.parent.detInfo.lower():
self.parent.clenEpics = str('CXI:DS2:MMS:06.RBV')
self.readEpicsClen()
else:
print "Couldn't handle detector clen. Try using the full detector name."
exit()
elif 'rayonix' in self.parent.detInfo.lower() and 'mfx' in self.parent.experimentName:
print "setClen: Not implemented yet"
self.parent.clenEpics = 'MFX:DET:MMS:04' #'Rayonix_z'
try:
self.readEpicsClen()
except:
print "ERROR: No such epics variable, ", self.parent.clenEpics
print "ERROR: setting clen to 0.0 metre"
self.parent.clen = 0.0 # metres
elif 'rayonix' in self.parent.detInfo.lower() and 'xpp' in self.parent.experimentName:
self.parent.clenEpics = 'XPP:ROB:POS:Z'
try:
self.readEpicsClen()
except:
print "ERROR: No such epics variable, ", self.parent.clenEpics
print "ERROR: setting clen to 0.0 metre"
self.parent.clen = 0.0 # metres
else:
if self.parent.args.v >= 1: print "Not implemented yet clen: ", self.parent.detInfo
def readEpicsClen(self):
for i in range(120): # assume at least 1 second run time
evt = self.run.event(self.times[i])
self.parent.clen = self.parent.epics.value(self.parent.clenEpics) / 1000. # metres
if i == 0: _temp = self.parent.clen
if i > 0:
if abs(_temp - self.parent.clen) >= 0.01: break
_temp = self.parent.clen
if self.parent.args.v >= 1: print "Best guess at clen: ", self.parent.clen
def setupExperiment(self):
if self.parent.args.v >= 1: print "Doing setupExperiment"
if self.hasExpRunInfo():
self.getUsername()
# Set up psocake directory in scratch
if self.parent.args.outDir is None:
self.parent.rootDir = '/reg/d/psdm/' + self.parent.experimentName[:3] + '/' + self.parent.experimentName
self.parent.elogDir = self.parent.rootDir + '/scratch/psocake'
self.parent.psocakeDir = self.parent.rootDir + '/scratch/' + self.username + '/psocake'
else:
self.parent.rootDir = self.parent.args.outDir
self.parent.elogDir = self.parent.rootDir + '/psocake'
self.parent.psocakeDir = self.parent.rootDir + '/' + self.username + '/psocake'
self.parent.psocakeRunDir = self.parent.psocakeDir + '/r' + str(self.parent.runNumber).zfill(4)
if self.parent.args.v >= 1: print "psocakeDir: ", self.parent.psocakeDir
# Update peak finder outdir and run number
self.parent.pk.p3.param(self.parent.pk.hitParam_grp, self.parent.pk.hitParam_outDir_str).setValue(self.parent.psocakeDir)
self.parent.pk.p3.param(self.parent.pk.hitParam_grp, self.parent.pk.hitParam_runs_str).setValue(self.parent.runNumber)
# Update powder outdir and run number
self.parent.mk.p6.param(self.parent.mk.powder_grp, self.parent.mk.powder_outDir_str).setValue(self.parent.psocakeDir)
self.parent.mk.p6.param(self.parent.mk.powder_grp, self.parent.mk.powder_runs_str).setValue(self.parent.runNumber)
# Update hit finding outdir, run number
self.parent.hf.p8.param(self.parent.hf.spiParam_grp, self.parent.hf.spiParam_outDir_str).setValue(self.parent.psocakeDir)
self.parent.hf.p8.param(self.parent.hf.spiParam_grp, self.parent.hf.spiParam_runs_str).setValue(self.parent.runNumber)
# Update indexing outdir, run number
self.parent.index.p9.param(self.parent.index.launch_grp, self.parent.index.outDir_str).setValue(self.parent.psocakeDir)
self.parent.index.p9.param(self.parent.index.launch_grp, self.parent.index.runs_str).setValue(self.parent.runNumber)
# Update quantifier filename
fname = self.parent.psocakeRunDir + '/' + self.parent.experimentName + '_' + str(self.parent.runNumber).zfill(4) + '.cxi'
if self.parent.args.mode == 'sfx':
dsetname = '/entry_1/result_1/nPeaksAll'
elif self.parent.args.mode == 'spi':
dsetname = '/entry_1/result_1/nHitsAll'
else:
dsetname = '/entry_1/result_1/'
self.parent.small.pSmall.param(self.parent.small.quantifier_grp, self.parent.small.quantifier_filename_str).setValue(fname)
self.parent.small.pSmall.param(self.parent.small.quantifier_grp, self.parent.small.quantifier_dataset_str).setValue(dsetname)
self.setupPsocake()
# Update hidden CrystFEL files
self.updateHiddenCrystfelFiles('lcls')
if self.parent.args.localCalib:
if self.parent.args.v >= 1: print "Using local calib directory"
psana.setOption('psana.calib-dir', './calib')
try:
self.ds = psana.DataSource('exp=' + str(self.parent.experimentName) + ':run=' + str(
self.parent.runNumber) + ':idx')
except:
print "############# No such datasource exists ###############"
self.run = self.ds.runs().next()
self.times = self.run.times()
self.eventTotal = len(self.times)
self.parent.stack.spinBox.setMaximum(self.eventTotal - self.parent.stack.stackSize)
self.p.param(self.exp_grp, self.exp_evt_str).setLimits((0, self.eventTotal - 1))
self.p.param(self.exp_grp, self.exp_evt_str, self.exp_numEvents_str).setValue(self.eventTotal)
self.env = self.ds.env()
if self.parent.detInfoList is None:
self.parent.evt = self.run.event(self.times[-1])
myAreaDetectors = []
self.parent.detnames = psana.DetNames()
for k in self.parent.detnames:
try:
if Detector.PyDetector.dettype(str(k[0]), self.env) == Detector.AreaDetector.AreaDetector:
myAreaDetectors.append(k)
except ValueError:
continue
self.parent.detInfoList = list(set(myAreaDetectors))
print "#######################################"
print "# Available area detectors: "
for k in self.parent.detInfoList:
print "#", k
print "#######################################"
# Launch e-log crawler
if self.logger and self.crawlerRunning == False:
if self.parent.args.v >= 1: print "Launching crawler"
self.launchCrawler()
self.crawlerRunning = True
if self.hasExpRunDetInfo():
self.parent.det = psana.Detector(str(self.parent.detInfo), self.env)
self.parent.det.do_reshape_2d_to_3d(flag=True)
self.parent.detAlias = self.getDetectorAlias(str(self.parent.detInfo))
self.parent.epics = self.ds.env().epicsStore()
self.setClen()
# detector distance
self.updateDetectorDistance('lcls')
# pixel size
self.updatePixelSize('lcls')
# photon energy
self.updatePhotonEnergy('lcls')
# Some detectors do not read out at 120 Hz. So need to loop over events to guarantee a valid detector image.
if self.parent.evt is None:
self.parent.evt = self.run.event(self.times[0])
self.detGuaranteed = self.parent.det.calib(self.parent.evt)
if self.detGuaranteed is None: # image isn't present for this event
print "No image in this event. Searching for an event..."
for i in np.arange(len(self.times)):
evt = self.run.event(self.times[i])
self.detGuaranteed = self.parent.det.calib(evt)
if self.detGuaranteed is not None:
print "Found an event with image: ", i
break
# Setup pixel indices
if self.detGuaranteed is not None:
self.parent.pixelInd = np.reshape(np.arange(self.detGuaranteed.size) + 1, self.detGuaranteed.shape)
self.parent.pixelIndAssem = self.parent.img.getAssembledImage('lcls', self.parent.pixelInd)
self.parent.pixelIndAssem -= 1 # First pixel is 0
# Get detector shape
self.detGuaranteedData = self.parent.det.image(self.parent.evt, self.detGuaranteed)
# Write a temporary geom file
self.parent.geom.deployCrystfelGeometry('lcls')
self.parent.geom.writeCrystfelGeom('lcls')
self.parent.img.setupRadialBackground()
self.parent.img.updatePolarizationFactor()
if self.parent.args.v >= 1: print "Done setupExperiment"
def updateLogscale(self, data):
self.logscaleOn = data
if self.hasExpRunDetInfo():
self.parent.firstUpdate = True # clicking logscale resets plot colorscale
self.parent.img.updateImage()
if self.parent.args.v >= 1: print "Done updateLogscale: ", self.logscaleOn
def updateAduPerPhoton(self, data):
self.aduPerPhoton = data
if self.hasExpRunDetInfo() is True and self.image_property == self.disp_photons:
#self.parent.firstUpdate = True # clicking logscale resets plot colorscale
self.parent.img.updateImage()
if self.parent.args.v >= 1: print "Done updateAduPerPhoton: ", self.aduPerPhoton
def updateMedianFilter(self, data):
self.medianFilterRank = data
if self.hasExpRunDetInfo() is True and self.image_property == self.disp_medianCorrection:
# self.parent.firstUpdate = True # clicking logscale resets plot colorscale
self.parent.img.updateImage()
if self.parent.args.v >= 1: print "Done updateMedianFilter: ", self.medianFilterRank
def updateImageProperty(self, data):
self.image_property = data
self.parent.img.updateImage()
if self.parent.args.v >= 1: print "Done updateImageProperty: ", self.image_property
def updateFriedel(self, data):
self.applyFriedel = data
self.parent.img.updateImage()
if self.parent.args.v >= 1: print "Done updateFriedel: ", self.applyFriedel
def updateCommonModeParam(self, data, ind):
self.commonModeParams[ind] = data
self.updateCommonMode(self.applyCommonMode)
if self.parent.args.v >= 1: print "Done updateCommonModeParam: ", self.commonModeParams
def updateCommonMode(self, data):
self.applyCommonMode = data
if self.applyCommonMode:
self.commonMode = self.checkCommonMode(self.commonModeParams)
if self.hasExpRunDetInfo():
if self.parent.args.v >= 1: print "%%% Redraw image with new common mode: ", self.commonMode
self.setupExperiment()
self.parent.img.updateImage()
if self.parent.args.v >= 1: print "Done updateCommonMode: ", self.commonMode
def checkCommonMode(self, _commonMode):
# TODO: cspad2x2 can only use algorithms 1 and 5
_alg = int(_commonMode[0])
if _alg >= 1 and _alg <= 4:
_param1 = int(_commonMode[1])
_param2 = int(_commonMode[2])
_param3 = int(_commonMode[3])
return (_alg,_param1,_param2,_param3)
elif _alg == 5:
_param1 = int(_commonMode[1])
return (_alg,_param1)
else:
print "Undefined common mode algorithm"
return None
def updateEventID(self, sec, nanosec, fid):
if self.parent.args.v >= 1: print "eventID: ", sec, nanosec, fid
self.p.param(self.exp_grp, self.exp_evt_str, self.exp_second_str).setValue(self.eventSeconds)
self.p.param(self.exp_grp, self.exp_evt_str, self.exp_nanosecond_str).setValue(self.eventNanoseconds)
self.p.param(self.exp_grp, self.exp_evt_str, self.exp_fiducial_str).setValue(self.eventFiducial)