def addSettings(self, param):
"""Adds a dockwidget designed to store a ParameterTree, also adds to 'Windows' menu"""
parameterTree = ParameterTree()
parameterTree.addParameters(param._PyQtGraphParameter)
dock = self.addDock(parameterTree, name=param.getName(), area=Qt.TopDockWidgetArea)
dock.setMaximumWidth(560)
return dock
def __init__(self):
super(maintest, self).__init__()
self.values = {'module 1': module(1), 'module 2': module(2), 'module 3': module(3)}
self.module = self.values['module 2']
p = [
{'name': 'Module', 'type': 'list',
'values': self.values,
'set': self.setmodule,
'get': self.getmodule,
'childmode': "root",
'help': '%namehdr%Boatload of text is possible here. Can use markup too with external help window.'},
{'name': 'Rocks to Skips', 'type': 'int', 'value': 0, 'help': 'Another help example', 'helpwnd': None, 'linked':['1/Rocks to Skips']},
{'name': '1/Rocks to Skips', 'type': 'float', 'help': 'Another help example', 'helpwnd': None, 'get': self.getLinked}
]
self.params = Parameter(name='Root', type='group', children=p).register()
self.params.init()
self.t = ParameterTree()
self.t.addParameters(self.params.getPyQtGraphParameter())
self.test = Parameter(name='Test', type='group')
self.test.addChildren([
{'name':'baud', 'type':'int', 'key':'baud', 'limits':(500, 2000000), 'value':38400}
])
self.params.append(self.test)
self.test.remove()
self.test.getChild("baud").setValue(500)
self.params.append(self.test)
self.t2 = ParameterTree()
self.params2 = Parameter(name='Root', type='group')
self.params.getChild("Module").stealDynamicParameters(self.params2)
self.t2.addParameters(self.params2._PyQtGraphParameter)
def __init__(self, parent, settings):
super(GeneralTab, self).__init__(parent)
self.settings = settings
self.getParams().addChildren(
[
{
"name": "Project Folder",
"type": "file",
"filter": "dir",
"get": lambda: self.settings.value("project-home-dir"),
"set": lambda v: self.settings.setValue("project-home-dir", v),
"psync": False,
}
]
)
parameterTree = ParameterTree()
parameterTree.addParameters(self.getParams()._PyQtGraphParameter)
defdirLayout = QHBoxLayout()
defdirLayout.addWidget(parameterTree)
mainLayout = QVBoxLayout()
mainLayout.addLayout(defdirLayout)
mainLayout.addStretch(1)
self.setLayout(mainLayout)
def _draw_text_inputs(self, layout):
"""
Generates a GUI that can accept parameter values.
"""
params = [
{'name': 'damage :: Saturation Threshold', 'type': 'int',
'value': 10000, 'suffix': 'ADU'},
{'name': 'damage :: Area Threshold', 'type': 'int',
'value': 20, 'suffix': '%', 'limits': (0, 100)},
{'name': 'xtal :: Saturation Threshold', 'type': 'int',
'value': 5000, 'suffix': 'ADU'},
{'name': 'xtal :: Area Threshold', 'type': 'int',
'value': 1, 'suffix': '%', 'limits': (0, 100)},
{'name': 'diffuse :: Saturation Threshold', 'type': 'int',
'value': 1000, 'suffix': 'ADU'},
{'name': 'diffuse :: Area Threshold', 'type': 'int',
'value': 20, 'suffix': '%', 'limits': (0, 100)}
]
self._params = Parameter.create(name='params', type='group',
children=params)
self._params.sigTreeStateChanged.connect(self._enable_apply)
t = ParameterTree()
t.setParameters(self._params, showTop=False)
layout.addWidget(t, 0, 1)
return
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 LayerControlTree(QtGui.QWidget):
def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
self.basicParam = {'name': 'Layer','expanded':False, 'type': 'group','autoIncrementName':True, 'children': [
{'name': 'LayerType', 'type': 'list', 'values': {"RGB": 0, "LAB": 1, "ChannelWise": 2}, 'value': 0},
{'name': 'Channel', 'type': 'int', 'value': 0,'limits':[0,2]},
{'name': 'Opacity', 'type': 'float', 'value': 0.0, 'step': 0.1,'limits':[0,1]},
{'name': 'Show', 'type': 'bool', 'value': True, 'tip': "Show / Hide this layer"},
{'name': 'HideOthers', 'type': 'action','tip':"Hide all other layers"},
{'name': 'Gradient', 'type': 'colormap'},
#{'name': 'Subgroup', 'type': 'group', 'children': [
# {'name': 'Sub-param 1', 'type': 'int', 'value': 10},
# {'name': 'Sub-param 2', 'type': 'float', 'value': 1.2e6},
#]},
#{'name': 'Text Parameter', 'type': 'text', 'value': 'Some text...'},
#{'name': 'Action Parameter', 'type': 'action'},
]}
params = []
self.paramGroup = Parameter.create(name='params', type='group', children=params)
self.paramGroup.sigTreeStateChanged.connect(self.change)
self.parameterTree = ParameterTree()
self.parameterTree.setParameters(self.paramGroup, showTop=False)
# add view box to graph view layout
self.hbox = QtGui.QHBoxLayout()
self.setLayout(self.hbox)
self.hbox.addWidget(self.parameterTree)
def addLayerControl(self,layer):
layerParam = setupLayerParam(layer.layerName(),layer.baseControlTemplate(),
layer.controlTemplate())
layerParam = self.paramGroup.addChild(layerParam)
# pass parameter to layer itself
layer.setLayerParameter(layerParam)
def removeLayerControl(self,layer):
paramToRemove = layer.layerParameter
self.paramGroup.removeChild(paramToRemove)
## If anything changes in the tree, print a message
def change(self,param, changes):
#print("tree changes:")
for param, change, data in changes:
path = self.paramGroup.childPath(param)
if path is not None:
childName = '.'.join(path)
else:
childName = param.name()
class FringeRemoveNode(Node):
"""Node for removing fringes"""
nodeName = 'FringeRemove'
nodePaths = [('Analysis',)]
def __init__(self, name):
terminals = {
'sig':{'io':'in'},
'ref':{'io':'in'},
'bkg':{'io':'in'},
'sigMask': {'io':'in'},
'ref1':{'io':'out', 'bypass': '******'}
}
super().__init__(name, terminals=terminals)
paras_property = [
{'name': 'rank', 'type': 'int', 'readonly': True},
{'name': 'rankLimit', 'type': 'int', 'value': 100},
{'name': 'trunc', 'type': 'float'},
{'name': 'updateLib', 'type': 'bool'},
{'name': 'reset', 'type': 'action'}
]
self.paras = Parameter.create(name='params', type='group', children=paras_property)
self.paratree = ParameterTree()
self.paratree.setParameters(self.paras, showTop=False)
self.remover = FringeRemove()
self.paras.param('reset').sigActivated.connect(self.remover.reset)
def onReset(self):
self.remover.reset()
self.paras['rank'] = 0
def ctrlWidget(self):
return self.paratree
def process(self, sig, ref, bkg, sigMask, display=True):
self.remover.setTrunc(self.paras['trunc'])
ref = ref - bkg
if self.paras['updateLib'] and self.paras['rank'] <= self.paras['rankLimit']:
self.remover.updateLibrary(ref)
self.paras['rank'] = self.remover.rank
sig = sig - bkg
coef, ref = self.remover.reconstruct(np.ma.array(sig, mask=sigMask))
ref = ref.reshape(512, 512) + bkg
return {'ref1': ref}
def saveState(self):
state = super().saveState()
state['paras'] = self.paras.saveState()
return state
def restoreState(self, state):
super().restoreState(state)
self.paras.restoreState(state['paras'])
class maintest(Parameterized):
def __init__(self):
super(maintest, self).__init__()
self.values = {'module 1': module(1), 'module 2': module(2), 'module 3': module(3)}
self.module = self.values['module 2']
p = [
{'name': 'Module', 'type': 'list',
'values': self.values,
'set': self.setmodule,
'get': self.getmodule,
'childmode': "root",
'help': '%namehdr%Boatload of text is possible here. Can use markup too with external help window.'},
{'name': 'Rocks to Skips', 'type': 'int', 'value': 0, 'help': 'Another help example', 'helpwnd': None,
'linked': ['1/Rocks to Skips']},
{'name': '1/Rocks to Skips', 'type': 'float', 'help': 'Another help example', 'helpwnd': None,
'get': self.getLinked}
]
self.params = Parameter(name='Root', type='group', children=p).register()
self.params.init()
self.t = ParameterTree()
self.t.addParameters(self.params.getPyQtGraphParameter())
self.test = Parameter(name='Test', type='group')
self.test.addChildren([
{'name': 'baud', 'type': 'int', 'key': 'baud', 'limits': (500, 2000000), 'value': 38400}
])
self.params.append(self.test)
self.test.remove()
self.test.getChild("baud").setValue(500)
self.params.append(self.test)
self.t2 = ParameterTree()
self.params2 = Parameter(name='Root', type='group')
self.params.getChild("Module").stealDynamicParameters(self.params2)
self.t2.addParameters(self.params2._PyQtGraphParameter)
self.params.save("abcde.txt")
self.params.load("abcde.txt")
def printhelp(self, msg, obj):
print msg
def getmodule(self):
return self.module
@setupSetParam("Module")
def setmodule(self, module):
print "Changing Module"
self.module = module
def getLinked(self):
try:
return 1.0 / float(self.params.getChild('Rocks to Skips').getValue())
except:
return 0
def setupTree():
params = [
{'name':'Update Time (s)', 'type':'float', 'value':1},
{'name':'std', 'type':'float', 'value':0},
{'name':'Save Figure', 'type':'action', 'visible':True}
]
p = Parameter.create(name = 'params', type = 'group', children = params)
t = ParameterTree()
t.setParameters(p, showTop = False)
return t,p
def setupTree():
params = [
{'name':'Update Time (s)', 'type':'float', 'value':1},
{'name':'Sample Name', 'type':'int', 'value':1},
{'name':'Counter', 'type':'int', 'value':0}
]
p = Parameter.create(name = 'params', type = 'group', children = params)
t = ParameterTree()
t.setParameters(p, showTop = False)
return t,p
def __init__(self,dataSet=None):
self.dataSet=dataSet
ParameterTree.__init__(self)
self.setObjectName("ConfigurationWidget")
self.setWindowTitle("Measurement Configuration")
self.setParams()
self.p.sigTreeStateChanged.connect(self.change)
self.connections=[]
self.p.param("File Configuration","Folder").sigValueChanged.connect(self.folderModeChanged)
class InputCalibrationChannel(SheetForm, SheetBase):
def __init__(self, config, channel, parent=None):
SheetBase.__init__(self, parent)
SheetForm.__init__(self)
self.config = config
self.channel = channel
self.settings = self.config.get("InputCalibration.{0}".format(channel), ChannelSettings())
self.myCalibration = None
self.treeWidget = None
def setupUi(self, callback, MainWindow):
SheetForm.setupUi(self, MainWindow)
self.calibrationsCombo.addItems( list(AnalogInputCalibration.AnalogInputCalibrationMap.keys()) )
self.calibrationsCombo.currentIndexChanged["QString"].connect( self.onCalibrationChanged )
self.callback = callback
if self.settings.calibration:
self.onCalibrationChanged(self.settings.calibration)
self.calibrationsCombo.setCurrentIndex(self.calibrationsCombo.findText(self.settings.calibration))
def onCalibrationChanged(self, calibration):
calibration = str(calibration)
if self.myCalibration:
self.settings.parameters[self.settings.calibration] = self.myCalibration.parameters
self.myCalibration = AnalogInputCalibration.AnalogInputCalibrationMap[calibration]()
if calibration in self.settings.parameters:
self.myCalibration.parameters = self.settings.parameters[calibration]
if not self.treeWidget:
try:
self.param = Parameter.create(name='params', type='group', children=self.myCalibration.paramDef())
self.treeWidget = ParameterTree()
self.treeWidget.setParameters(self.param, showTop=False)
self.verticalLayout.insertWidget(2, self.treeWidget)
self.param.sigTreeStateChanged.connect(self.myCalibration.update, QtCore.Qt.UniqueConnection)
except (TypeError, AttributeError):
pass
else:
self.param = Parameter.create(name='params', type='group', children=self.myCalibration.paramDef())
self.treeWidget.setParameters(self.param, showTop=False)
try:
self.param.sigTreeStateChanged.connect(self.myCalibration.update, QtCore.Qt.UniqueConnection )
except TypeError:
pass # we want the connection to be unique
self.settings.calibration = calibration
self.callback( self.channel, self.myCalibration )
def saveConfig(self):
if self.myCalibration:
self.settings.parameters[self.settings.calibration] = self.myCalibration.parameters
self.config["InputCalibration.{0}".format(self.channel)] = self.settings
def __init__(self):
QtGui.QWidget.__init__(self)
self.neuron_data = None
self.setWindowTitle("Experiment Control - Data Analysis & Visualization")
self.layout = QtGui.QVBoxLayout()
self.layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.layout)
self.splitter = QtGui.QSplitter()
self.splitter.setOrientation(QtCore.Qt.Horizontal)
self.splitter2 = QtGui.QSplitter()
self.splitter2.setOrientation(QtCore.Qt.Vertical)
self.layout.addWidget(self.splitter)
self.splitter.addWidget(self.splitter2)
self.plot_widget = pg.GraphicsLayoutWidget()
self.tree = ParameterTree(showHeader=False)
self.params = Parameter.create(
name="params",
type="group",
children=[
dict(name="Reanalyze", type="bool", value=False),
dict(name="Load", type="action"),
dict(name="GCFR-sigma (ms)", type="float", value=100.0, step=0.1, limits=[1, 5000]),
dict(name="Save", type="action"),
],
)
self.tree.setParameters(self.params, showTop=False)
# self.params.param('Save').sigActivated.connect(self.SavePlot)
self.params.param("Load").sigActivated.connect(self.OpenDataFile)
self.splitter2.addWidget(self.tree)
self.trial_list_tree = pg.TreeWidget(parent=self.splitter2)
self.splitter.addWidget(self.plot_widget)
self.trial_list_tree.setColumnCount(1)
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)
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 __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
self.basicParam = {'name': 'Layer','expanded':False, 'type': 'group','autoIncrementName':True, 'children': [
{'name': 'LayerType', 'type': 'list', 'values': {"RGB": 0, "LAB": 1, "ChannelWise": 2}, 'value': 0},
{'name': 'Channel', 'type': 'int', 'value': 0,'limits':[0,2]},
{'name': 'Opacity', 'type': 'float', 'value': 0.0, 'step': 0.1,'limits':[0,1]},
{'name': 'Show', 'type': 'bool', 'value': True, 'tip': "Show / Hide this layer"},
{'name': 'HideOthers', 'type': 'action','tip':"Hide all other layers"},
{'name': 'Gradient', 'type': 'colormap'},
#{'name': 'Subgroup', 'type': 'group', 'children': [
# {'name': 'Sub-param 1', 'type': 'int', 'value': 10},
# {'name': 'Sub-param 2', 'type': 'float', 'value': 1.2e6},
#]},
#{'name': 'Text Parameter', 'type': 'text', 'value': 'Some text...'},
#{'name': 'Action Parameter', 'type': 'action'},
]}
params = []
self.paramGroup = Parameter.create(name='params', type='group', children=params)
self.paramGroup.sigTreeStateChanged.connect(self.change)
self.parameterTree = ParameterTree()
self.parameterTree.setParameters(self.paramGroup, showTop=False)
# add view box to graph view layout
self.hbox = QtGui.QHBoxLayout()
self.setLayout(self.hbox)
self.hbox.addWidget(self.parameterTree)
def onCalibrationChanged(self, calibration):
calibration = str(calibration)
if self.myCalibration:
self.settings.parameters[self.settings.calibration] = self.myCalibration.parameters
self.myCalibration = AnalogInputCalibration.AnalogInputCalibrationMap[calibration]()
if calibration in self.settings.parameters:
self.myCalibration.parameters = self.settings.parameters[calibration]
if not self.treeWidget:
try:
self.param = Parameter.create(name='params', type='group', children=self.myCalibration.paramDef())
self.treeWidget = ParameterTree()
self.treeWidget.setParameters(self.param, showTop=False)
self.verticalLayout.insertWidget(2, self.treeWidget)
self.param.sigTreeStateChanged.connect(self.myCalibration.update, QtCore.Qt.UniqueConnection)
except (TypeError, AttributeError):
pass
else:
self.param = Parameter.create(name='params', type='group', children=self.myCalibration.paramDef())
self.treeWidget.setParameters(self.param, showTop=False)
try:
self.param.sigTreeStateChanged.connect(self.myCalibration.update, QtCore.Qt.UniqueConnection )
except TypeError:
pass # we want the connection to be unique
self.settings.calibration = calibration
self.callback( self.channel, self.myCalibration )
class SettingsEditorDialog(QtGui.QDialog):
def __init__(self,ndViewer, parent):
super(SettingsEditorDialog, self).__init__(parent)
self.resize(800,600)
self.ndViewer = ndViewer
self.layout = QtGui.QVBoxLayout()
self.setLayout(self.layout)
self.paramTree = ParameterTree()
self.paramTree.setParameters(self.ndViewer.options.p, showTop=False)
self.layout.addWidget(self.paramTree)
def keyPressEvent(self, event):
if event.key() == QtCore.Qt.Key_Escape:
self.hide()
event.accept()
else:
super(QtGui.QDialog, self).keyPressEvent(event)
class InstrumentLoggingSelection( SelectionUi ):
def __init__(self, config, classdict, instancename="ExternalParameterSelection.ParametersSequence", plotNames=None, parent=None, instrumentLoggingHandler=None ):
super(InstrumentLoggingSelection, self).__init__(config, dict(), classdict, instancename, parent)
self.instrumentLoggingHandler = instrumentLoggingHandler
self.current = None
def setupUi(self, MainWindow):
super(InstrumentLoggingSelection, self).setupUi(MainWindow)
self.loggingHandlerTreeWidget = ParameterTree(self.splitter)
self.loggingHandlerTreeWidget.setObjectName("loggingHandlerTreeWidget")
self.loggingHandlerTreeWidget.headerItem().setText(0, "1")
self.loggingHandlerTreeWidget.header().setVisible(False)
def onActiveInstrumentChanged(self, modelIndex, modelIndex2 ):
self.current = self.parameters.at(modelIndex.row()).name
super(InstrumentLoggingSelection, self).onActiveInstrumentChanged( modelIndex, modelIndex2 )
self.loggingHandlerTreeWidget.setParameters( self.instrumentLoggingHandler.parameter(self.current) )
def refreshParamTree(self):
if self.current is not None:
self.loggingHandlerTreeWidget.setParameters( self.instrumentLoggingHandler.parameter(self.current) )
def __init__(self,ndViewer, parent):
super(SettingsEditorDialog, self).__init__(parent)
self.resize(800,600)
self.ndViewer = ndViewer
self.layout = QtGui.QVBoxLayout()
self.setLayout(self.layout)
self.paramTree = ParameterTree()
self.paramTree.setParameters(self.ndViewer.options.p, showTop=False)
self.layout.addWidget(self.paramTree)
def __init__(self, parent = None, with_config = False, **kargs ):
QtGui.QWidget.__init__(self, parent)
self.resize(800,600)
mainlayout = QtGui.QVBoxLayout()
self.setLayout(mainlayout)
self.glview = gl.GLViewWidget()
mainlayout.addWidget(self.glview)
self.glview .setCameraPosition(160,160,15)
if with_config:
h = QtGui.QHBoxLayout()
mainlayout.addLayout(h)
but = QtGui.QPushButton('Config', icon = QtGui.QIcon.fromTheme('configure'))
h.addWidget(but)
but.clicked.connect(self.open_params)
but = QtGui.QPushButton('Save png', icon = QtGui.QIcon.fromTheme('save'))
h.addWidget(but)
but.clicked.connect(self.open_save_dialog)
_params = [
{'name': 'cortical_mesh', 'type': 'list', 'values': cortical_meshes.keys(), 'value' : 'BrainMesh_ICBM152'},
{'name': 'cortical_alpha', 'type': 'float', 'value': .1, 'limits': [0., 1.], 'step' : .01},
{'name': 'cortical_color', 'type': 'color', 'value': 'w'},
{'name': 'background_color', 'type': 'color', 'value': 'k'},
]
self.params = Parameter.create(name='params', type='group', children=_params)
self.tree = ParameterTree(parent = self)
self.tree.setParameters(self.params)
self.tree.setWindowFlags(QtCore.Qt.Dialog)
self.mesh = None
for k,v in kargs.items():
self.params[k] = v
self.change_background_color()
self.plot_mesh()
self.change_color_mesh()
self.params.param('cortical_mesh').sigValueChanged.connect(self.plot_mesh)
self.params.param('cortical_alpha').sigValueChanged.connect(self.change_color_mesh)
self.params.param('cortical_color').sigValueChanged.connect(self.change_color_mesh)
self.params.param('background_color').sigValueChanged.connect(self.change_background_color)
self.glview.resizeGL(self.glview.width(), self.glview.height())
def __init__(self, parent=None):
"""
Constructor
@param parent reference to the parent widget
@type QWidget
"""
super(MainWindow, self).__init__(parent)
self.setupUi(self)
self.plotly_pyqt5 = Plotly_PyQt5()
'''手动调整窗口部件的大小，使之看着更美观'''
self.widget_parameter_tree.setMaximumWidth(300)
self.widget_parameter_tree.setMinimumWidth(200)
self.QWebEngineView_ProductVsHs300.setMinimumHeight(500)
self.tabWidget.setMinimumHeight(400)
'''显示parametertree，这里通过布局管理器来把ParameterTree间接地嵌套进Widget窗口里面'''
from mypyqtgraph import p
from pyqtgraph.parametertree import ParameterTree
t = ParameterTree()
t.setParameters(p, showTop=False)
t.setHeaderLabels(["参数", "数值"])
# t.setWindowTitle('pyqtgraph example: Parameter Tree')
layout = QtGui.QGridLayout()
self.widget_parameter_tree.setLayout(layout)
layout.addWidget(
QtGui.QLabel("千石资本-和聚光明1号资产管理计划基本信息"), 0, 0, 1, 1)
layout.addWidget(t)
'''显示绘图函数'''
self.QWebEngineView_ProductVsHs300.load(
QUrl.fromLocalFile(self.plotly_pyqt5.get_plotly_path_product_vs_hs300()))
self.QWebEngineView_LagestBack.load(QUrl.fromLocalFile(self.plotly_pyqt5.get_plotly_path_lagest_back()))
self.QWebEngineView_PeriodReturn.load(QUrl.fromLocalFile(self.plotly_pyqt5.get_plotly_path_period_return()))
self.QWebEngineview_MonthReturn.load(QUrl.fromLocalFile(self.plotly_pyqt5.get_plotly_path_month_return()))
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)
def setupTree(startup):
params = [
{'name':'ChA', 'type':'int', 'value': startup['ChA']},
{'name':'BiasV_ChA', 'type':'float', 'value': startup['BiasV_ChA']},
{'name':'ChA Singles (cps)', 'type':'float', 'value': startup['ChA Singles (cps)']},
{'name':'ChB', 'type':'int', 'value':startup['ChB']},
{'name':'BiasV_ChB', 'type':'float', 'value':startup['BiasV_ChB']},
{'name':'ChB Singles (cps)', 'type':'float', 'value': startup['ChB Singles (cps)']},
{'name':'Min (s)', 'type':'float', 'value':startup['Min (s)']},
{'name':'Max (s)', 'type':'float', 'value':startup['Max (s)']},
{'name':'binSize', 'type':'int', 'value':startup['binSize']},
{'name':'Update Time (s)', 'type':'float', 'value' :startup['Update Time (s)']},
{'name':'Counter', 'type':'int', 'value':startup['Counter']},
{'name':'algorithm', 'type':'str', 'value':startup['algorithm']},
{'name':'Pause Histogram', 'type':'bool', 'value':startup['Pause Histogram']},
{'name':'Reset Histogram', 'type':'action', 'visible':startup['Reset Histogram']},
{'name':'Save Path', 'type':'str', 'value':startup['Save Path']},
{'name':'Save Figure', 'type':'action', 'visible':startup['Save Figure']},
{'name':'Save Data', 'type':'action', 'visible':startup['Save Data']}
]
p = Parameter.create(name = 'params', type = 'group', children = params)
t = ParameterTree()
t.setParameters(p, showTop = False)
return t,p
def setupParametersTree(self):
"""Setup all parameter trees so they can be reloaded later with changes"""
self.params = Parameter.create(name='Generic Settings', type='group', children=self.cwParams)
ExtendedParameter.setupExtended(self.params, self)
self.paramTree = ParameterTree()
self.paramTree.setParameters(self.params, showTop=False)
self.preprocessingParamTree = ParameterTree()
self.attackParamTree = ParameterTree()
self.postprocessingParamTree = ParameterTree()
self.resultsParamTree = ParameterTree()
self.results.paramListUpdated.connect(self.reloadParamListResults)
self.reloadParamListResults()
def __init__(self):
QtCore.QObject.__init__(self)
self.initParam()
## Create tree of Parameter objects
self.parameter = Parameter.create(name='OCR Parameter', type='group', children=self.params)
def turn2change(param, changes):
self.changeParam(param, changes)
self.parameter.sigTreeStateChanged.connect(turn2change)
self.tree = ParameterTree(None, showHeader=False)
self.tree.setParameters(self.parameter, showTop=True)
#Lazy Mode:
self.textList = None
self.ocrIndex = None
def __init__(self, parent=None):
QMainWindow.__init__(self, parent)
self.setWindowTitle("PyeMovements")
self.modelpicker = QComboBox()
self.modelpicker.addItem("CRISP")
self.modelparams = Parameter.create(name='params', type='group', children=self.params)
self.paramtree = ParameterTree()
self.paramtree.setParameters(self.modelparams, showTop=False)
self.nsaccadelab = QLabel("# Saccades")
self.nsaccadelab.setAlignment(Qt.AlignRight|Qt.AlignVCenter)
self.nsaccades = QSpinBox()
self.nsaccades.setRange(1,1000000)
self.nsaccades.setValue(10000)
self.runbutton = QPushButton("Start simulation")
self.runbutton.clicked.connect(self.handle_runbutton_clicked)
self.resetbutton = QPushButton("Reset simulation")
self.resetbutton.setEnabled(False)
self.resetbutton.clicked.connect(self.handle_resetbutton_clicked)
self.centralwidget = QWidget(self)
self.fixation_plot_widget = pg.PlotWidget(title="Fixation Duration Histogram",labels={"left":"Count","bottom":"Duration (s)"})
self.fixation_plot_data = pg.PlotDataItem()
self.grid = QGridLayout()
self.grid.addWidget(self.modelpicker,0,0,1,2)
self.grid.addWidget(self.paramtree,1,0,1,2)
self.grid.addWidget(self.nsaccadelab,2,0,1,1)
self.grid.addWidget(self.nsaccades,2,1,1,1)
self.grid.addWidget(self.runbutton,3,0,1,1)
self.grid.addWidget(self.resetbutton,3,1,1,1)
self.grid.addWidget(self.fixation_plot_widget,0,2,4,1)
self.setCentralWidget(self.centralwidget)
self.centralwidget.setLayout(self.grid)
self.sim_reset()
self.plots_timer = QTimer()
self.plots_timer.timeout.connect(self.updateFixationPlot)
self.plots_timer.start(50)
def initUI(self):
'''Initializes the main window widgets.'''
self.initToolBar()
self.initMenuBar()
self.parametertree = ParameterTree()
self.viewwidget = gl.GLViewWidget()
widget = QtGui.QWidget()
hbox = QtGui.QHBoxLayout(widget)
hbox.addWidget(self.parametertree)
hbox.addWidget(self.viewwidget, 1)
self.setCentralWidget(widget)
self.resize(1200, 600)
self.setWindowTitle('MolViewer :: Main window')
self.drawgrid()
self.show()
def setupUi(self, Form):
Form.setObjectName(_fromUtf8("Form"))
Form.resize(241, 367)
Form.setWindowTitle(QtGui.QApplication.translate("Form", "Export", None, QtGui.QApplication.UnicodeUTF8))
self.gridLayout = QtGui.QGridLayout(Form)
self.gridLayout.setSpacing(0)
self.gridLayout.setObjectName(_fromUtf8("gridLayout"))
self.label = QtGui.QLabel(Form)
self.label.setText(QtGui.QApplication.translate("Form", "Item to export:", None, QtGui.QApplication.UnicodeUTF8))
self.label.setObjectName(_fromUtf8("label"))
self.gridLayout.addWidget(self.label, 0, 0, 1, 3)
self.itemTree = QtGui.QTreeWidget(Form)
self.itemTree.setObjectName(_fromUtf8("itemTree"))
self.itemTree.headerItem().setText(0, _fromUtf8("1"))
self.itemTree.header().setVisible(False)
self.gridLayout.addWidget(self.itemTree, 1, 0, 1, 3)
self.label_2 = QtGui.QLabel(Form)
self.label_2.setText(QtGui.QApplication.translate("Form", "Export format", None, QtGui.QApplication.UnicodeUTF8))
self.label_2.setObjectName(_fromUtf8("label_2"))
self.gridLayout.addWidget(self.label_2, 2, 0, 1, 3)
self.formatList = QtGui.QListWidget(Form)
self.formatList.setObjectName(_fromUtf8("formatList"))
self.gridLayout.addWidget(self.formatList, 3, 0, 1, 3)
self.exportBtn = QtGui.QPushButton(Form)
self.exportBtn.setText(QtGui.QApplication.translate("Form", "Export", None, QtGui.QApplication.UnicodeUTF8))
self.exportBtn.setObjectName(_fromUtf8("exportBtn"))
self.gridLayout.addWidget(self.exportBtn, 6, 1, 1, 1)
self.closeBtn = QtGui.QPushButton(Form)
self.closeBtn.setText(QtGui.QApplication.translate("Form", "Close", None, QtGui.QApplication.UnicodeUTF8))
self.closeBtn.setObjectName(_fromUtf8("closeBtn"))
self.gridLayout.addWidget(self.closeBtn, 6, 2, 1, 1)
self.paramTree = ParameterTree(Form)
self.paramTree.setObjectName(_fromUtf8("paramTree"))
self.paramTree.headerItem().setText(0, _fromUtf8("1"))
self.paramTree.header().setVisible(False)
self.gridLayout.addWidget(self.paramTree, 5, 0, 1, 3)
self.label_3 = QtGui.QLabel(Form)
self.label_3.setText(QtGui.QApplication.translate("Form", "Export options", None, QtGui.QApplication.UnicodeUTF8))
self.label_3.setObjectName(_fromUtf8("label_3"))
self.gridLayout.addWidget(self.label_3, 4, 0, 1, 3)
self.retranslateUi(Form)
QtCore.QMetaObject.connectSlotsByName(Form)
def __init__(self, parent = None):
self.parent = parent
## Dock 8: Quantifier
self.dSmall = Dock("Small Data", size=(100, 100))
self.w8 = ParameterTree()
self.dSmall.addWidget(self.w8)
self.w11a = pg.LayoutWidget()
self.refreshBtn = QtGui.QPushButton('Refresh')
self.w11a.addWidget(self.refreshBtn, row=0, col=0)
self.dSmall.addWidget(self.w11a)
# Add plot
self.w9 = pg.PlotWidget(title="Metric")
self.dSmall.addWidget(self.w9)
# Quantifier parameter tree
self.quantifier_grp = 'Small data'
self.quantifier_filename_str = 'filename'
self.quantifier_dataset_str = 'dataset'
self.quantifier_sort_str = 'sort'
# Quantifier
self.quantifier_filename = ''
self.quantifier_dataset = '/entry_1/result_1/'
self.quantifier_sort = False
self.quantifierFileOpen = False
self.quantifierHasData = False
self.params = [
{'name': self.quantifier_grp, 'type': 'group', 'children': [
{'name': self.quantifier_filename_str, 'type': 'str', 'value': self.quantifier_filename, 'tip': "Full path Hdf5 filename"},
{'name': self.quantifier_dataset_str, 'type': 'str', 'value': self.quantifier_dataset, 'tip': "Hdf5 dataset metric, nPeaksAll or nHitsAll"},
{'name': self.quantifier_sort_str, 'type': 'bool', 'value': self.quantifier_sort, 'tip': "Ascending sort metric"},
]},
]
self.pSmall = Parameter.create(name='paramsQuantifier', type='group', \
children=self.params, expanded=True)
self.w8.setParameters(self.pSmall, showTop=False)
self.pSmall.sigTreeStateChanged.connect(self.change)
self.refreshBtn.clicked.connect(self.reloadQuantifier)
def set_GUI(self):
"""
Create the graphic interface of the h5 file analyser, including:
* *h5 file dock* : QtreeWidget (custom instance of Tree_layout) showing the contents of the h5 file
* *status bar* : the top_down information bar
* *tree_dock* : The QTree viewer
* *1D viewer dock* : the preview window of 1D data
* *2D viewer dock* : the preview window of 2D data
* *Navigator viewer dock* : the global navigator graphic interface
"""
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# h5 file dock
V_splitter = QtWidgets.QSplitter(Qt.Vertical)
H_splitter = QtWidgets.QSplitter(Qt.Horizontal)
Form = QtWidgets.QWidget()
self.ui.h5file_tree = Tree_layout(Form,
col_counts=2,
labels=["Node", 'Pixmap'])
self.ui.h5file_tree.ui.Tree.setMinimumWidth(250)
self.ui.h5file_tree.ui.Tree.itemClicked.connect(
self.show_h5_attributes)
self.ui.h5file_tree.ui.Tree.itemDoubleClicked.connect(
self.show_h5_data)
V_splitter.addWidget(Form)
self.ui.attributes_table = pymodaq_ptypes.Table_custom()
V_splitter.addWidget(self.ui.attributes_table)
H_splitter.addWidget(V_splitter)
self.ui.settings_tree = ParameterTree()
self.ui.settings_tree.setMinimumWidth(300)
H_splitter.addWidget(self.ui.settings_tree)
self.ui.menubar = self.mainwindow.menuBar()
self.create_menu(self.ui.menubar)
# %%create status bar
self.ui.statusbar = QtWidgets.QStatusBar()
self.ui.statusbar.setMaximumHeight(25)
# %% create tree dock
file_dock = Dock("File data", size=(1, 1), autoOrientation=False)
# give this dock the minimum possible size
file_dock.setOrientation('vertical')
file_dock.addWidget(H_splitter)
file_dock.addWidget(self.ui.statusbar)
self.settings = Parameter.create(name='Param', type='group')
self.ui.settings_tree.setParameters(self.settings, showTop=False)
# #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# #% 1D viewer Dock
viewer1D_widget = QtWidgets.QWidget()
self.ui.viewer1D = Viewer1D(viewer1D_widget)
dock1D = Dock('Viewer1D')
dock1D.addWidget(viewer1D_widget)
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# % 2D viewer Dock
viewer2D_widget = QtWidgets.QWidget()
self.ui.viewer2D = Viewer2D(viewer2D_widget)
dock2D = Dock('Viewer2D')
dock2D.addWidget(viewer2D_widget)
# #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# #% Navigator viewer Dock
navigator1D_widget = QtWidgets.QWidget()
self.ui.navigator1D = Viewer1D(navigator1D_widget)
self.ui.navigator1D.ui.crosshair.crosshair_dragged.connect(
self.update_viewer_data)
self.ui.navigator1D.ui.crosshair_pb.click()
navigator2D_widget = QtWidgets.QWidget()
self.ui.navigator2D = Viewer2D(navigator2D_widget)
self.ui.navigator2D.crosshair_dragged.connect(
self.update_viewer_data
) # export scaled position in conjonction with 2D scaled axes
self.ui.navigator2D.ui.crosshair_pb.click()
dock_nav = Dock('Navigator')
dock_nav.addWidget(navigator1D_widget)
dock_nav.addWidget(navigator2D_widget, 1, 0)
self.dockarea.addDock(file_dock, 'top')
self.dockarea.addDock(dock2D, 'right', file_dock)
self.dockarea.addDock(dock1D, 'bottom', dock2D)
self.dockarea.addDock(dock_nav, 'right', dock2D)
class TreeFromToml(QObject):
def __init__(self, conf_path=None):
super().__init__()
self.config_path = utils.get_set_local_dir().joinpath('config.toml')
config = utils.load_config(self.config_path)
params = [{
'title': 'Config path',
'name': 'config_path',
'type': 'str',
'value': str(self.config_path),
'readonly': True
}]
params.extend(self.dict_to_param(config))
self.settings = Parameter.create(title='settings',
name='settings',
type='group',
children=params)
self.settings_tree = ParameterTree()
self.settings_tree.setParameters(self.settings, showTop=False)
def show_dialog(self):
self.dialog = QtWidgets.QDialog()
self.dialog.setWindowTitle('Please enter new configuration values!')
self.dialog.setLayout(QtWidgets.QVBoxLayout())
buttonBox = QtWidgets.QDialogButtonBox(parent=self.dialog)
buttonBox.addButton('Save', buttonBox.AcceptRole)
buttonBox.accepted.connect(self.dialog.accept)
buttonBox.addButton('Cancel', buttonBox.RejectRole)
buttonBox.rejected.connect(self.dialog.reject)
self.dialog.layout().addWidget(self.settings_tree)
self.dialog.layout().addWidget(buttonBox)
self.dialog.setWindowTitle('Configuration entries')
res = self.dialog.exec()
if res == self.dialog.Accepted:
with open(self.config_path, 'w') as f:
config = self.param_to_dict(self.settings)
config.pop('config_path')
toml.dump(config, f)
@classmethod
def param_to_dict(cls, param):
config = dict()
for child in param.children():
if 'group' in child.opts['type']:
config[child.name()] = cls.param_to_dict(child)
else:
if child.opts['type'] == 'datetime':
config[child.name()] = datetime.fromtimestamp(
child.value().toSecsSinceEpoch()
) # convert QDateTime to python datetime
elif child.opts['type'] == 'date':
qdt = QtCore.QDateTime()
qdt.setDate(child.value())
pdt = datetime.fromtimestamp(qdt.toSecsSinceEpoch())
config[child.name()] = pdt.date()
elif child.opts['type'] == 'list':
config[child.name()] = child.opts['limits']
else:
config[child.name()] = child.value()
return config
@classmethod
def dict_to_param(cls, config):
params = []
for key in config:
if isinstance(config[key], dict):
params.append({
'title':
f'{key.capitalize()}:',
'name':
key,
'type':
'group',
'children':
cls.dict_to_param(config[key]),
'expanded':
'user' in key.lower() or 'general' in key.lower()
})
else:
param = {
'title': f'{key.capitalize()}:',
'name': key,
'value': config[key]
}
if isinstance(config[key], float):
param['type'] = 'float'
elif isinstance(
config[key], bool
): # placed before int because a bool is an instance of int
param['type'] = 'bool'
elif isinstance(config[key], int):
param['type'] = 'int'
elif isinstance(config[key], datetime.datetime):
param['type'] = 'datetime'
elif isinstance(config[key], datetime.date):
param['type'] = 'date'
elif isinstance(config[key], str):
param['type'] = 'str'
elif isinstance(config[key], list):
param['type'] = 'list'
param['values'] = config[key]
param['value'] = config[key][0]
param['show_pb'] = True
params.append(param)
return params
class ScanSelector(QObject):
scan_select_signal = pyqtSignal(ROI)
params = [
{
'title':
'Scan options',
'name':
'scan_options',
'type':
'group',
'children': [
{
'title': 'Sources:',
'name': 'sources',
'type': 'list',
},
{
'title': 'Viewers:',
'name': 'viewers',
'type': 'list',
},
{
'title': 'Scan type:',
'name': 'scan_type',
'type': 'list',
'values': ['Scan1D', 'Scan2D'],
'value': 'Scan2D'
},
]
},
{
'title':
'Scan Area',
'name':
'scan_area',
'type':
'group',
'children': [
{
'title':
'ROI select:',
'name':
'ROIselect',
'type':
'group',
'visible':
True,
'children': [
{
'title': 'x0:',
'name': 'x0',
'type': 'int',
'value': 0,
'min': 0
},
{
'title': 'y0:',
'name': 'y0',
'type': 'int',
'value': 0,
'min': 0
},
{
'title': 'width:',
'name': 'width',
'type': 'int',
'value': 10,
'min': 1
},
{
'title': 'height:',
'name': 'height',
'type': 'int',
'value': 10,
'min': 1
},
]
},
{
'title': 'Coordinates:',
'name': 'coordinates',
'type': 'itemselect',
'visible': True
},
]
},
]
def __init__(self, viewer_items=[], scan_type='Scan2D', positions=[]):
"""
Parameters
----------
viewer_items: dict where the keys are the titles of the sources while the values are dict with keys
viewers: list of plotitems
names: list of viewer titles
scan_type: (str) either 'Scan1D' correspondign to a polyline ROI or 'Scan2D' for a rect Roi
positions: list
in case of 'Scan1D', should be a sequence of 2 floats sequence [(x1,y1),(x2,y2),(x3,y3),...]
in case of 'Scan2D', should be a sequence of 4 floats (x, y , w, h)
"""
super(ScanSelector, self).__init__()
self._viewers_items = viewer_items
self.sources_names = list(viewer_items.keys())
if len(viewer_items) != 0:
self.scan_selector_source = viewer_items[
self.sources_names[0]]['viewers'][0]
else:
self.scan_selector_source = None
self.scan_selector = None
self.setupUI()
self.settings.child('scan_options', 'scan_type').setValue(scan_type)
self.remove_scan_selector()
if self.scan_selector_source is not None:
if len(viewer_items[self.sources_names[0]]['viewers']) == 1:
self.settings.child('scan_options', 'viewers').hide()
else:
self.settings.child('scan_options', 'viewers').hide()
self.update_scan_area_type()
if scan_type == "Scan1D" and positions != []:
self.scan_selector.setPoints(positions)
elif scan_type == 'Scan2D' and positions != []:
self.scan_selector.setPos(positions[:2])
self.scan_selector.setSize(positions[3:])
@property
def viewers_items(self):
return self._viewers_items
@viewers_items.setter
def viewers_items(self, items):
self._viewers_items = items
self.sources_names = list(items.keys())
self.scan_selector_source = items[self.sources_names[0]]['viewers'][0]
self.settings.child('scan_options',
'sources').setOpts(limits=self.sources_names)
viewer_names = self._viewers_items[self.sources_names[0]]['names']
self.settings.child('scan_options',
'viewers').setOpts(limits=viewer_names)
def show(self, visible=True):
self.show_scan_selector(visible)
if visible:
self.widget.show()
else:
self.widget.hide()
def hide(self):
self.show(False)
def setupUI(self):
self.widget = QtWidgets.QWidget()
layout = QtWidgets.QVBoxLayout()
self.settings_tree = ParameterTree()
layout.addWidget(self.settings_tree, 10)
self.settings_tree.setMinimumWidth(300)
self.settings = Parameter.create(name='Settings',
type='group',
children=self.params)
self.settings_tree.setParameters(self.settings, showTop=False)
self.settings.child('scan_options',
'sources').setOpts(limits=self.sources_names)
if len(self.viewers_items):
viewer_names = self._viewers_items[self.sources_names[0]]['names']
else:
viewer_names = []
self.settings.child('scan_options',
'viewers').setOpts(limits=viewer_names)
self.settings.sigTreeStateChanged.connect(self.source_changed)
self.widget.setLayout(layout)
#self.widget.show()
self.widget.setWindowTitle('Scan Selector')
def source_changed(self, param, changes):
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 == 'childAdded':
pass
elif change == 'value':
if param.name() == 'sources' and param.value() is not None:
viewer_names = self._viewers_items[param.value()]['names']
self.settings.child('scan_options',
'viewers').setOpts(limits=viewer_names)
if len(viewer_names) == 1:
self.settings.child('scan_options', 'viewers').hide()
self.remove_scan_selector()
self.scan_selector_source = self._viewers_items[
param.value()]['viewers'][0]
self.update_scan_area_type()
if param.name() == 'scan_type':
if param.value() == 'Scan1D':
self.settings.child('scan_area', 'ROIselect').hide()
self.settings.child('scan_area', 'coordinates').show()
self.remove_scan_selector()
self.update_scan_area_type()
else:
self.settings.child('scan_area', 'ROIselect').show()
self.settings.child('scan_area', 'coordinates').hide()
self.remove_scan_selector()
self.update_scan_area_type()
self.scan_selector.sigRegionChangeFinished.emit(
self.scan_selector)
elif change == 'parent':
pass
def remove_scan_selector(self):
if self.scan_selector_source is not None:
try:
self.scan_selector_source.image_widget.plotitem.removeItem(
self.scan_selector)
except:
pass
pyqtSlot(str)
def update_scan_area_type(self):
if self.settings.child('scan_options',
'scan_type').value() == 'Scan1D':
scan_area_type = 'PolyLines'
else:
scan_area_type = 'Rect'
self.remove_scan_selector()
if scan_area_type == 'Rect':
self.scan_selector = RectROI([0, 0], [10, 10])
elif scan_area_type == 'PolyLines':
self.scan_selector = PolyLineROI_custom([(0, 0), [10, 10]])
if self.scan_selector_source is not None:
self.scan_selector.sigRegionChangeFinished.connect(
self.update_scan)
self.scan_selector_source.image_widget.plotitem.addItem(
self.scan_selector)
self.show_scan_selector()
self.scan_selector.sigRegionChangeFinished.emit(self.scan_selector)
def show_scan_selector(self, visible=True):
self.scan_selector.setVisible(visible)
def update_scan(self, roi):
if self.scan_selector_source is not None:
if isinstance(roi, RectROI):
self.settings.child('scan_area', 'ROIselect',
'x0').setValue(roi.pos().x())
self.settings.child('scan_area', 'ROIselect',
'y0').setValue(roi.pos().y())
self.settings.child('scan_area', 'ROIselect',
'width').setValue(roi.size().x())
self.settings.child('scan_area', 'ROIselect',
'height').setValue(roi.size().y())
elif isinstance(roi, PolyLineROI_custom):
self.settings.child('scan_area', 'coordinates').setValue(
dict(all_items=[
'({:.03f} , {:.03f})'.format(pt.x(), pt.y())
for pt in roi.get_vertex()
],
selected=[]))
self.scan_select_signal.emit(roi)
class Ui_WindowModel(QWidget):
"""
"""
def __init__(self,):
super().__init__()
self.setupUi()
def setupUi(self, ):
"""
"""
self.gridLayout_2 = QtWidgets.QGridLayout(self)
self.gridLayout_2.setObjectName("gridLayout_2")
self.gridGeneral = QtWidgets.QGridLayout()
self.gridGeneral.setObjectName("gridGeneral")
self.toolBox = QtWidgets.QToolBox(self)
self.toolBox.setFrameShadow(QtWidgets.QFrame.Plain)
self.toolBox.setObjectName("toolBox")
self.model = QtWidgets.QWidget()
self.model.setGeometry(QtCore.QRect(0, 0, 558, 451))
self.model.setObjectName("model")
self.gridLayout_4 = QtWidgets.QGridLayout(self.model)
self.gridLayout_4.setContentsMargins(0, 0, 0, 0)
self.gridLayout_4.setObjectName("gridLayout_4")
self.gridModel = QtWidgets.QGridLayout()
self.gridModel.setContentsMargins(5, 5, 5, 5)
self.gridModel.setSpacing(5)
self.gridModel.setObjectName("gridModel")
self.line = QtWidgets.QFrame(self.model)
self.line.setFrameShape(QtWidgets.QFrame.VLine)
self.line.setFrameShadow(QtWidgets.QFrame.Sunken)
self.line.setObjectName("line")
self.gridModel.addWidget(self.line, 0, 1, 1, 1)
self.openGLWidget = QtWidgets.QOpenGLWidget(self.model)
self.openGLWidget.setObjectName("openGLWidget")
self.gridModel.addWidget(self.openGLWidget, 0, 2, 1, 1)
self.ModelDescriptionTree = ParameterTree(self.model)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(
self.ModelDescriptionTree.sizePolicy().hasHeightForWidth())
self.ModelDescriptionTree.setSizePolicy(sizePolicy)
self.ModelDescriptionTree.setObjectName("ModelDescriptionTree")
self.gridModel.addWidget(self.ModelDescriptionTree, 0, 0, 1, 1)
self.gridLayout_4.addLayout(self.gridModel, 0, 1, 1, 1)
self.toolBox.addItem(self.model, "")
self.param = QtWidgets.QWidget()
self.param.setGeometry(QtCore.QRect(0, 0, 558, 451))
self.param.setObjectName("param")
self.gridLayout_6 = QtWidgets.QGridLayout(self.param)
self.gridLayout_6.setContentsMargins(0, 0, 0, 0)
self.gridLayout_6.setObjectName("gridLayout_6")
self.gridParam = QtWidgets.QGridLayout()
self.gridParam.setContentsMargins(5, 5, 5, 5)
self.gridParam.setSpacing(5)
self.gridParam.setObjectName("gridParam")
self.ParametersTree = ParameterTree(self.param)
self.ParametersTree.setObjectName("ParametersTree")
self.gridParam.addWidget(self.ParametersTree, 0, 0, 1, 1)
self.gridLayout_6.addLayout(self.gridParam, 0, 0, 1, 1)
self.toolBox.addItem(self.param, "")
self.result = QtWidgets.QWidget()
self.result.setObjectName("result")
self.gridLayout_8 = QtWidgets.QGridLayout(self.result)
self.gridLayout_8.setContentsMargins(0, 0, 0, 0)
self.gridLayout_8.setObjectName("gridLayout_8")
self.gridRes = QtWidgets.QGridLayout()
self.gridRes.setContentsMargins(5, 5, 5, 5)
self.gridRes.setSpacing(5)
self.gridRes.setObjectName("gridRes")
self.ResTree = ParameterTree(self.result)
self.ResTree.setObjectName("ResTree")
self.gridRes.addWidget(self.ResTree, 0, 0, 1, 1)
self.gridLayout_8.addLayout(self.gridRes, 0, 0, 1, 1)
self.toolBox.addItem(self.result, "")
self.gridGeneral.addWidget(self.toolBox, 0, 0, 1, 1)
self.gridLayout_2.addLayout(self.gridGeneral, 0, 0, 1, 1)
self.retranslateUi(self)
self.toolBox.setCurrentIndex(2)
def retranslateUi(self, WindowModel):
_translate = QtCore.QCoreApplication.translate
self.toolBox.setItemText(self.toolBox.indexOf(self.model),
_translate("WindowModel",
"General information about the subjective model"))
self.toolBox.setItemText(self.toolBox.indexOf(self.param),
_translate("WindowModel",
"Detailed description of the parameters"))
self.toolBox.setItemText(self.toolBox.indexOf(self.result),
_translate("WindowModel",
"Detailed description of the resultes "))
class H5Saver(QObject):
"""QObject containing all methods in order to save datas in a *hdf5 file* with a hierachy compatible with
the H5Browser. The saving parameters are contained within a **Parameter** object: self.settings that can be displayed
on a UI (see :numref:`other_settings`) using the widget self.settings_tree. At the creation of a new file, a node
group named **Raw_datas** and represented by the attribute ``raw_group`` is created and set with a metadata attribute:
* 'type' given by the **save_type** class parameter
The root group of the file is then set with a few metadata:
* 'pymodaq_version' the current pymodaq version, e.g. 1.6.2
* 'file' the file name
* 'date' the current date
* 'time' the current time
All datas will then be saved under this node in various groups
See Also
--------
H5Browser
Parameters
----------
h5_file: pytables hdf5 file
object used to save all datas and metadas
h5_file_path: str or Path
pyqtSignal signal represented by a float. Is emitted each time the hardware reached the target
position within the epsilon precision (see comon_parameters variable)
save_type: str
an element of the list module attribute save_types = ['scan', 'detector', 'custom']
* 'scan' is used for DAQ_Scan module and should be used for similar application
* 'detector' is used for DAQ_Viewer module and should be used for similar application
* 'custom' should be used for customized applications
Attributes
----------
status_sig: pyqtSignal
emits a signal of type Threadcommand in order to senf log information to a main UI
new_file_sig: pyqtSignal
emits a boolean signal to let the program know when the user pressed the new file button on the UI
settings: Parameter
Parameter instance (pyqtgraph) containing all settings (could be represented using the settings_tree widget)
settings_tree: ParameterTree
Widget representing as a Tree structure, all the settings defined in the class preamble variable ``params``
"""
status_sig = pyqtSignal(utils.ThreadCommand)
new_file_sig = pyqtSignal(bool)
params = [
{
'title': 'Save type:',
'name': 'save_type',
'type': 'list',
'values': save_types,
'readonly': True
},
{
'title': 'Save 2D datas:',
'name': 'save_2D',
'type': 'bool',
'value': True
},
{
'title':
'Save raw datas only:',
'name':
'save_raw_only',
'type':
'bool',
'value':
True,
'tooltip':
'if True, will not save extracted ROIs used to do live plotting, only raw datas and the scan \
result will be saved'
},
{
'title': 'Do Save:',
'name': 'do_save',
'type': 'bool',
'default': False,
'value': False
},
{
'title': 'N saved:',
'name': 'N_saved',
'type': 'int',
'default': 0,
'value': 0,
'visible': False
},
{
'title': 'custom_name?:',
'name': 'custom_name',
'type': 'bool',
'default': False,
'value': False
},
{
'title': 'show file content?:',
'name': 'show_file',
'type': 'bool',
'default': False,
'value': False
},
{
'title': 'Base path:',
'name': 'base_path',
'type': 'browsepath',
'value': 'C:\Data',
'filetype': False,
'readonly': True,
},
{
'title': 'Base name:',
'name': 'base_name',
'type': 'str',
'value': 'Scan',
'readonly': True
},
{
'title': 'Current scan:',
'name': 'current_scan_name',
'type': 'str',
'value': '',
'readonly': True
},
{
'title': 'Current path:',
'name': 'current_scan_path',
'type': 'text',
'value': 'C:\Data',
'readonly': True,
'visible': False
},
{
'title': 'h5file:',
'name': 'current_h5_file',
'type': 'text_pb',
'value': '',
'readonly': True
},
{
'title':
'Compression options:',
'name':
'compression_options',
'type':
'group',
'children': [
{
'title': 'Compression library:',
'name': 'h5comp_library',
'type': 'list',
'value': 'zlib',
'values': ['zlib', 'lzo', 'bzip2', 'blosc']
},
{
'title': 'Compression level:',
'name': 'h5comp_level',
'type': 'int',
'value': 5,
'min': 0,
'max': 9
},
]
},
]
def __init__(self, h5_file_path=None, h5_file=None, save_type='scan'):
"""Initialize the H5Saver object
Creates the ``setting`` and ``settings_tree`` object
"""
super(H5Saver, self).__init__()
if save_type not in save_types:
raise Exception('Invalid saving type')
self.h5_file = h5_file
self.h5_file_path = h5_file_path
self.h5_file_name = None
self.logger_array = None
self.current_group = None
self.current_scan_group = None
self.current_scan_name = None
self.raw_group = None
self.settings = Parameter.create(title='Saving settings',
name='save_settings',
type='group',
children=self.params)
self.settings_tree = ParameterTree()
self.settings_tree.setMinimumHeight(310)
self.settings_tree.setParameters(self.settings, showTop=False)
self.settings.child(
('current_h5_file'
)).sigActivated.connect(lambda: self.emit_new_file(True))
self.settings.child(('save_type')).setValue(save_type)
self.filters = tables.Filters(
complevel=self.settings.child('compression_options',
'h5comp_level').value(),
complib=self.settings.child('compression_options',
'h5comp_library').value())
# self.settings.child('saving_options', 'save_independent').show(save_type == 'scan')
# self.settings.child('saving_options', 'do_save').show(not save_type == 'scan')
# self.settings.child('saving_options', 'current_scan_name').show(save_type == 'scan')
self.settings.sigTreeStateChanged.connect(
self.parameter_tree_changed
) # any changes on the settings will update accordingly the detector
def emit_new_file(self, status):
"""Emits the new_file_sig
Parameters
----------
status: bool
emits True if a new file has been asked by the user pressing the new file button on the UI
"""
self.new_file_sig.emit(status)
def init_file(self,
update_h5=False,
custom_naming=False,
addhoc_file_path=None):
"""Initializes a new h5 file.
Could set the h5_file attributes as:
* a file with a name following a template if ``custom_naming`` is ``False`` and ``addhoc_file_path`` is ``None``
* a file within a name set using a file dialog popup if ``custom_naming`` is ``True``
* a file with a custom name if ``addhoc_file_path`` is a ``Path`` object or a path string
Parameters
----------
update_h5: bool
create a new h5 file with name specified by other parameters
if false try to open an existing file and will append new data to it
custom_naming: bool
if True, a selection file dialog opens to set a new file name
addhoc_file_path: Path or str
supplied name by the user for the new file
Returns
-------
update_h5: bool
True if new file has been created, False otherwise
"""
date = datetime.datetime.now()
if addhoc_file_path is None:
if not os.path.isdir(self.settings.child(('base_path')).value()):
os.mkdir(self.settings.child(('base_path')).value())
# set the filename and path
base_name = self.settings.child(('base_name')).value()
if not custom_naming:
custom_naming = self.settings.child(('custom_name')).value()
if not custom_naming:
scan_type = self.settings.child(
('save_type')).value() == 'scan'
scan_path, current_scan_name, save_path = self.update_file_paths(
update_h5)
self.current_scan_name = current_scan_name
self.settings.child(
('current_scan_name')).setValue(current_scan_name)
self.settings.child(
('current_scan_path')).setValue(str(scan_path))
if not scan_type:
self.h5_file_path = save_path #will remove the dataset part used for DAQ_scan datas
self.h5_file_name = base_name + date.strftime(
'_%Y%m%d_%H_%M_%S.h5')
else:
self.h5_file_path = save_path
self.h5_file_name = save_path.name + ".h5"
else:
self.h5_file_name = utils.select_file(start_path=base_name,
save=True,
ext='h5')
self.h5_file_path = self.h5_file_name.parent
else:
if isinstance(addhoc_file_path, str):
addhoc_file_path = Path(addhoc_file_path)
self.h5_file_path = addhoc_file_path.parent
self.h5_file_name = addhoc_file_path.name
fullpathname = str(self.h5_file_path.joinpath(self.h5_file_name))
self.settings.child(('current_h5_file')).setValue(fullpathname)
if update_h5:
self.current_scan_group = None
scan_group = None
if self.current_scan_group is not None:
scan_group = self.current_scan_group._v_name
if update_h5:
self.close_file()
self.h5_file = tables.open_file(fullpathname,
'w',
title='PyMoDAQ file')
self.h5_file.root._v_attrs['pymodaq_version'] = get_version()
else:
self.close_file()
self.h5_file = tables.open_file(fullpathname,
'a',
title='PyMoDAQ file')
self.raw_group = self.get_set_group(self.h5_file.root,
'Raw_datas',
title='Data from PyMoDAQ modules')
self.get_set_logger(self.raw_group)
if scan_group is not None:
self.current_scan_group = self.get_set_group(
self.raw_group, scan_group)
else:
self.current_scan_group = self.get_last_scan()
self.raw_group._v_attrs['type'] = self.settings.child(
('save_type')).value()
self.h5_file.root._v_attrs['file'] = date.strftime(self.h5_file_name)
if update_h5:
self.h5_file.root._v_attrs['date'] = date.strftime('%Y%m%d')
self.h5_file.root._v_attrs['time'] = date.strftime('%H:%M:%S')
return update_h5
def update_file_paths(self, update_h5=False):
"""Apply the template depending on the 'save_type' settings child
Parameters
----------
update_h5: bool
if True, will increment the file name and eventually the current scan index
if False, get the current scan index in the h5 file
Returns
-------
scan_path: Path
current_filename: str
dataset_path: Path
See Also
--------
:py:meth:`pymodaq.daq_utils.daq_utils.set_current_scan_path`
"""
try:
# set the filename and path
base_path = self.settings.child(('base_path')).value()
base_name = self.settings.child(('base_name')).value()
current_scan = self.settings.child(('current_scan_name')).value()
scan_type = self.settings.child(('save_type')).value() == 'scan'
if current_scan == '' or update_h5:
next_scan_index = 0
update_h5 = True #just started the main program so one should create a new h5
else:
next_scan_index = self.get_scan_index()
scan_path, current_filename, dataset_path = utils.set_current_scan_path(
base_path,
base_name,
update_h5,
next_scan_index,
create_dataset_folder=scan_type)
self.settings.child(('current_scan_path')).setValue(str(scan_path))
return scan_path, current_filename, dataset_path
except Exception as e:
print(e)
def get_last_scan(self):
"""Gets the last scan node within the h5_file and under the the **raw_group**
Returns
-------
scan_group: pytables group or None
"""
groups = [
group for group in list(self.raw_group._v_groups)
if 'Scan' in group
]
groups.sort()
if len(groups) != 0:
scan_group = self.h5_file.get_node(self.raw_group, groups[-1])
else:
scan_group = None
return scan_group
def get_scan_index(self):
""" return the scan group index in the "scan templating": Scan000, Scan001 as an integer
"""
try:
if self.current_scan_group is None:
return 0
else:
groups = [
group for group in list(self.raw_group._v_groups)
if 'Scan' in group
]
groups.sort()
flag = False
for child in list(
self.h5_file.get_node(self.raw_group,
groups[-1])._v_groups):
if 'scan' in child:
return len(groups)
return 0
except Exception as e:
return 0
def load_file(self, base_path=None, file_path=None):
"""Opens a file dialog to select a h5file saved on disk to be used
Parameters
----------
base_path
file_path
See Also
--------
:py:meth:`init_file`
:py:meth:`pymodaq.daq_utils.daq_utils.select_file`
"""
if base_path is None:
base_path = self.settings.child('base_path').value()
if not os.path.isdir(base_path):
base_path = None
if file_path is None:
file_path = utils.select_file(base_path, save=False, ext='h5')
if not isinstance(file_path, Path):
file_path = Path(file_path)
if 'h5' not in file_path.suffix:
raise IOError('Invalid file type, should be a h5 file')
self.init_file(addhoc_file_path=file_path)
def close_file(self):
"""Flush data and close the h5file
"""
try:
if self.h5_file is not None:
self.h5_file.flush()
if self.h5_file.isopen:
self.h5_file.close()
except Exception as e:
print(e) #no big deal
def is_node_in_group(self, where, name):
"""
Check if a given node with name is in the group defined by where (comparison on lower case strings)
Parameters
----------
where: (str or node)
path or parent node instance
name: (str)
group node name
Returns
-------
bool
True if node exists, False otherwise
"""
nodes_names = [
node._v_name.lower() for node in self.h5_file.list_nodes(where)
]
return name.lower() in nodes_names
def get_set_logger(self, where):
""" Retrieve or create (if absent) a logger enlargeable array to store logs
Get attributed to the class attribute ``logger_array``
Parameters
----------
where: node
location within the tree where to save or retrieve the array
Returns
-------
logger_array: vlarray
enlargeable array accepting strings as elements
"""
logger = 'Logger'
if not logger in list(self.h5_file.get_node(where)._v_children.keys()):
# check if logger node exist
text_atom = tables.atom.ObjectAtom()
self.logger_array = self.h5_file.create_vlarray(where,
logger,
atom=text_atom)
self.logger_array._v_attrs['type'] = 'log'
else:
self.logger_array = self.h5_file.get_node(where, name=logger)
return self.logger_array
def get_set_group(self, where, name, title=''):
"""Retrieve or create (if absent) a node group
Get attributed to the class attribute ``current_group``
Parameters
----------
where: str or node
path or parent node instance
name: str
group node name
title: str
node title
Returns
-------
group: group node
"""
if not name in list(self.h5_file.get_node(where)._v_children.keys()):
self.current_group = self.h5_file.create_group(where, name, title)
else:
self.current_group = self.h5_file.get_node(where, name)
return self.current_group
def add_data_group(self,
where,
group_data_type,
title='',
settings_as_xml='',
metadata=dict([])):
"""Creates a group node at given location in the tree
Parameters
----------
where: group node
where to create data group
group_data_type: list of str
either ['data0D', 'data1D', 'data2D']
title: str, optional
a title for this node, will be saved as metadata
settings_as_xml: str, optional
XML string created from a Parameter object to be saved as metadata
metadata: dict, optional
will be saved as a new metadata attribute with name: key and value: dict value
Returns
-------
group: group node
See Also
--------
:py:meth:`àdd_group`
"""
if group_data_type not in group_data_types:
raise Exception('Invalid data group type')
group = self.add_group(group_data_type, '', where, title,
settings_as_xml, metadata)
return group
def add_navigation_axis(self,
data,
parent_group,
axis='x_axis',
enlargeable=False,
title='',
metadata=dict([])):
"""
Create carray for navigation axis within a scan
Parameters
----------
data: (ndarray) of dimension 1
parent_group: (str or node) parent node where to save new data
axis: (str) either x_axis or y_axis
"""
if axis not in ['x_axis', 'y_axis', 'z_axis']:
raise Exception('Invalid navigation axis name')
array = self.add_array(parent_group,
'scan_{:s}'.format(axis),
'navigation_axis',
data_shape=data.shape,
data_dimension='1D',
array_to_save=data,
enlargeable=enlargeable,
title=title,
metadata=metadata)
return array
def add_data_live_scan(self,
channel_group,
data_dict,
scan_type='scan1D',
title=''):
shape, dimension, size = utils.get_data_dimension(
data_dict['data'], scan_type=scan_type, remove_scan_dimension=True)
data_array = self.add_array(channel_group,
'Data',
'data',
array_type=np.float,
title=title,
data_shape=shape,
data_dimension=dimension,
scan_type=scan_type,
array_to_save=data_dict['data'])
if 'x_axis' in data_dict:
if not isinstance(data_dict['x_axis'], dict):
array_to_save = data_dict['x_axis']
tmp_dict = dict(label='', units='')
else:
tmp_dict = copy.deepcopy(data_dict['x_axis'])
array_to_save = tmp_dict.pop('data')
if 'x_axis' in data_dict:
array = self.add_array(channel_group,
'x_axis',
'axis',
array_type=np.float,
array_to_save=array_to_save,
enlargeable=False,
data_dimension='1D',
metadata=tmp_dict)
if 'y_axis' in data_dict:
if not isinstance(data_dict['y_axis'], dict):
array_to_save = data_dict['y_axis']
tmp_dict = dict(label='', units='')
else:
tmp_dict = copy.deepcopy(data_dict['y_axis'])
array_to_save = tmp_dict.pop('data')
if 'y_axis' in data_dict:
array = self.add_array(channel_group,
'y_axis',
'axis',
array_type=np.float,
array_to_save=array_to_save,
enlargeable=False,
data_dimension='1D',
metadata=tmp_dict)
return data_array
def add_data(self,
channel_group,
data_dict,
scan_type='scan1D',
scan_shape=[],
title='',
enlargeable=False,
init=False,
add_scan_dim=False):
shape, dimension, size = utils.get_data_dimension(data_dict['data'])
data_array = self.add_array(channel_group,
'Data',
'data',
array_type=np.float,
title=title,
data_shape=shape,
enlargeable=enlargeable,
data_dimension=dimension,
scan_type=scan_type,
scan_shape=scan_shape,
array_to_save=data_dict['data'],
init=init,
add_scan_dim=add_scan_dim)
if 'x_axis' in data_dict:
if not isinstance(data_dict['x_axis'], dict):
array_to_save = data_dict['x_axis']
tmp_dict = dict(label='', units='')
else:
tmp_dict = copy.deepcopy(data_dict['x_axis'])
array_to_save = tmp_dict.pop('data')
array = self.add_array(channel_group,
'x_axis',
'axis',
array_type=np.float,
array_to_save=array_to_save,
enlargeable=False,
data_dimension='1D',
metadata=tmp_dict)
if 'y_axis' in data_dict:
if not isinstance(data_dict['y_axis'], dict):
array_to_save = data_dict['y_axis']
tmp_dict = dict(label='', units='')
else:
tmp_dict = copy.deepcopy(data_dict['y_axis'])
array_to_save = tmp_dict.pop('data')
array = self.add_array(channel_group,
'y_axis',
'axis',
array_type=np.float,
array_to_save=array_to_save,
enlargeable=False,
data_dimension='1D',
metadata=tmp_dict)
self.h5_file.flush()
return data_array
def add_array(self,
where,
name,
data_type,
data_shape=(1, ),
data_dimension='0D',
scan_type='',
scan_shape=[],
title='',
array_to_save=None,
array_type=np.float,
enlargeable=False,
metadata=dict([]),
init=False,
add_scan_dim=False):
if data_dimension not in data_dimensions:
raise Exception('Invalid data dimension')
if data_type not in data_types:
raise Exception('Invalid data type')
if scan_type != '':
scan_type = utils.uncapitalize(scan_type)
if scan_type not in scan_types:
raise Exception('Invalid scan type')
if enlargeable:
shape = [0]
if data_shape != (1, ):
shape.extend(data_shape)
shape = tuple(shape)
array = self.h5_file.create_earray(where,
utils.capitalize(name),
tables.Atom.from_dtype(
np.dtype(array_type)),
shape=shape,
title=title,
filters=self.filters)
array._v_attrs['shape'] = shape
else:
if add_scan_dim: #means it is an array initialization to zero
shape = scan_shape[:]
shape.extend(data_shape)
if init or array_to_save is None:
array_to_save = np.zeros(shape)
array = self.h5_file.create_carray(where,
utils.capitalize(name),
obj=array_to_save,
title=title,
filters=self.filters)
array._v_attrs['shape'] = array_to_save.shape
array._v_attrs['type'] = data_type
array._v_attrs['data_dimension'] = data_dimension
array._v_attrs['scan_type'] = scan_type
for metadat in metadata:
array._v_attrs[metadat] = metadata[metadat]
return array
def append(self, array, data):
if not (isinstance(array, tables.vlarray.VLArray)
or isinstance(array, tables.earray.EArray)):
raise Exception('This array cannot be appended')
if isinstance(data, np.ndarray):
if data.shape != (1, ):
shape = [1]
shape.extend(data.shape)
array.append(data.reshape(shape))
else:
array.append(data)
else:
array.append(data)
sh = list(array._v_attrs['shape'])
sh[0] += 1
array._v_attrs['shape'] = tuple(sh)
def add_group(self,
group_name,
group_type,
where,
title='',
settings_as_xml='',
metadata=dict([])):
"""
Add a node in the h5 file tree of the group type
Parameters
----------
group_name: (str) a custom name for this group
group_type: (str) one of the possible values of **group_types**
where: (str or node) parent node where to create the new group
settings_as_xml: (str) XML string containing Parameters representation (see custom_Tree)
metadata: (dict) extra metadata to be saved with this new group node
Returns
-------
(node): newly created group node
"""
if group_type not in group_types:
raise Exception('Invalid group type')
try:
node = self.h5_file.get_node(where, utils.capitalize(group_name))
except tables.NoSuchNodeError as e:
node = None
if node is None:
node = self.get_set_group(where, utils.capitalize(group_name),
title)
node._v_attrs['settings'] = settings_as_xml
node._v_attrs['type'] = group_type.lower()
for metadat in metadata:
node._v_attrs[metadat] = metadata[metadat]
return node
def add_incremental_group(self,
group_type,
where,
title='',
settings_as_xml='',
metadata=dict([])):
"""
Add a node in the h5 file tree of the group type with an increment in the given name
Parameters
----------
group_type: (str) one of the possible values of **group_types**
where: (str or node) parent node where to create the new group
settings_as_xml: (str) XML string containing Parameters representation (see custom_Tree)
metadata: (dict) extra metadata to be saved with this new group node
Returns
-------
(node): newly created group node
"""
if group_type not in group_types:
raise Exception('Invalid group type')
nodes = list(self.h5_file.get_node(where)._v_children.keys())
nodes_tmp = []
for node in nodes:
if utils.capitalize(group_type) in node:
nodes_tmp.append(node)
nodes_tmp.sort()
if len(nodes_tmp) == 0:
ind_group = -1
else:
ind_group = int(nodes_tmp[-1][-3:])
group = self.get_set_group(
where,
utils.capitalize(group_type) + '{:03d}'.format(ind_group + 1),
title)
group._v_attrs['settings'] = settings_as_xml
if group_type.lower() != 'ch':
group._v_attrs['type'] = group_type.lower()
else:
group._v_attrs['type'] = ''
for metadat in metadata:
group._v_attrs[metadat] = metadata[metadat]
return group
def add_det_group(self,
where,
title='',
settings_as_xml='',
metadata=dict([])):
"""
Add a new group of type detector
See Also
-------
add_incremental_group
"""
group = self.add_incremental_group('detector', where, title,
settings_as_xml, metadata)
return group
def add_CH_group(self,
where,
title='',
settings_as_xml='',
metadata=dict([])):
"""
Add a new group of type channel
See Also
-------
add_incremental_group
"""
group = self.add_incremental_group('ch', where, title, settings_as_xml,
metadata)
return group
def add_live_scan_group(self,
where,
dimensionality,
title='',
settings_as_xml='',
metadata=dict([])):
"""
Add a new group of type live scan
See Also
-------
add_incremental_group
"""
group = self.add_group('Live_scan_{:s}'.format(dimensionality),
'',
where,
title=title,
settings_as_xml=settings_as_xml,
metadata=metadata)
return group
def add_scan_group(self, title='', settings_as_xml='', metadata=dict([])):
"""
Add a new group of type scan
See Also
-------
add_incremental_group
"""
if self.current_scan_group is not None:
if list(self.current_scan_group._v_children) == []:
new_scan = False
else:
new_scan = True
else:
new_scan = True
if new_scan:
self.current_scan_group = self.add_incremental_group(
'scan', self.raw_group, title, settings_as_xml, metadata)
self.current_scan_group._v_attrs['description'] = ''
self.settings.child(('current_scan_name')).setValue(
self.current_scan_group._v_name)
return self.current_scan_group
def add_move_group(self,
where,
title='',
settings_as_xml='',
metadata=dict([])):
"""
Add a new group of type move
See Also
-------
add_incremental_group
"""
group = self.add_incremental_group('move', where, title,
settings_as_xml, metadata)
return group
def parameter_tree_changed(self, param, changes):
for param, change, data in changes:
path = self.settings.childPath(param)
if change == 'childAdded':
pass
elif change == 'value':
if param.name() == 'show_file':
param.setValue(False)
self.show_file_content()
elif param.name() == 'base_path':
try:
if not os.path.isdir(param.value()):
os.mkdir(param.value())
except:
self.update_status(
"The base path couldn't be set, please check your options"
)
elif param.name() in custom_tree.iter_children(
self.settings.child(('compression_options')), []):
self.filters = tables.Filters(
complevel=self.settings.child('compression_options',
'h5comp_level').value(),
complib=self.settings.child('compression_options',
'h5comp_library').value())
elif change == 'parent':
pass
def update_status(self, status):
self.status_sig.emit(
utils.ThreadCommand("Update_Status", [status, 'log']))
def show_file_content(self):
form = QtWidgets.QWidget()
if not self.h5_file.isopen:
if self.h5_file_path.exists():
self.analysis_prog = H5Browser(form, h5file=self.h5_file_path)
else:
raise FileExistsError('no File presents')
else:
self.analysis_prog = H5Browser(form, h5file=self.h5_file)
form.show()
def __init__(self, *args, **kwargs):
super(DefocusParameterTree, self).__init__(*args, **kwargs)
self.setLayout(QVBoxLayout())
self.parameter_tree = ParameterTree()
self.layout().addWidget(self.parameter_tree)
self.layout().setContentsMargins(0, 0, 0, 0)
self.addChild({'name': 'other information', 'type': 'text', 'value': 'Some text...'})
self.addChild({'name': 'save', 'type': 'action'})
##############################################################################
##############################################################################
## Start Qt event loop unless running in interactive mode or using pyside.
if __name__ == '__main__':
## Create tree of Parameter objects
params = [Input(name='Input'),
Generator(name='Generator'),
AllPlotScalableGroup(name='Graph')]
p = Parameter.create(name='params', type='group', children=params)
## Create two ParameterTree widgets, both accessing the same data
t = ParameterTree()
t.setParameters(p, showTop=False)
t.setWindowTitle('pyqtgraph example: Parameter Tree')
win = QtGui.QWidget()
layout = QtGui.QGridLayout()
win.setLayout(layout)
layout.addWidget(t, 1, 0, 1, 1)
win.show()
win.resize(800,800)
import sys
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()
##############################################################################
class BuildGui():
def __init__(self, tree):
"""
Test fixture
"""
self.basename = '/Users/pbmanis/Documents/data/MRK_Pyramidal'
self.filename = None
self.tree = tree
print('tree: ', tree)
self.mainwin = pg.Qt.QtGui.QMainWindow()
self.win = pg.Qt.QtGui.QWidget()
self.main_layout = pg.Qt.QtGui.QGridLayout() # top level layout for the window
self.win.setLayout(self.main_layout)
self.mainwin.setCentralWidget(self.win)
self.mainwin.show()
self.mainwin.setWindowTitle('Data Selection')
self.mainwin.setGeometry( 100 , 100 , 1400 , 900)
# build buttons at top of controls
self.current_DSC = list(self.tree.keys())[0]
self.btn_read = pg.Qt.QtGui.QPushButton("Read")
self.btn_find = pg.Qt.QtGui.QPushButton('Find and Read')
# use a nested grid layout for the buttons
button_layout = pg.Qt.QtGui.QGridLayout()
button_layout.addWidget(self.btn_read, 1, 0, 1, 1)
# button_layout.addWidget(self.btn_analyze, 0, 1, 1, 1)
button_layout.addWidget(self.btn_find, 0, 0, 1, 1)
# build parametertree in left column
#
ptreewidth = 320
self.main_layout.setColumnMinimumWidth(0, ptreewidth)
# analysis # empty in test rig
params = [
{'name': 'Analysis', 'type': 'group', 'children': [],
}]
self.analysis_ptree = ParameterTree()
self.analysis_ptreedata = Parameter.create(name='params', type='group', children=params)
self.analysis_ptree.setParameters(self.analysis_ptreedata)
self.ptree = ParameterTree()
self.ptreedata = Parameter.create(name='dataset', type='group', children=self.setParams(0))
self.ptree.setParameters(self.ptreedata) # add the table with granularity of "cells"
self.prottree = ParameterTree()
self.setProtocols() # add the protocols
# use a grid layout to hold the trees
self.ptree_widget = pg.Qt.QtGui.QWidget()
self.ptree_layout = pg.Qt.QtGui.QGridLayout()
self.ptree_widget.setLayout(self.ptree_layout)
self.ptree_layout.setSpacing(2)
# ptree in row 1 col 0, 4 rows, 2 cols
self.ptree_layout.addWidget(self.analysis_ptree)
self.ptree_layout.addWidget(self.ptree) # Parameter Tree on left
self.ptree_layout.addWidget(self.prottree) # protocol tree just below
# self.ptree_layout.setColumnStretch(0, 5)
self.ptree_layout.setRowStretch(0, 5)
self.ptree_layout.setRowStretch(1, 1)
self.ptree_layout.setRowStretch(2, 1)
# build plot window
self.plots_widget = pg.Qt.QtGui.QWidget()
self.plots_layout = pg.Qt.QtGui.QGridLayout()
self.plots_widget.setLayout(self.plots_layout)
self.plots_layout.setContentsMargins(4, 4, 4, 4)
self.plots_layout.setSpacing(2)
self.plots = {}
for panel in zip(['Wave', 'Average', 'PSTH'], [0, 14, 18], [1, 5, 5],):
self.plots[panel[0]] = pg.PlotWidget()
self.plots_layout.addWidget(self.plots[panel[0]],
panel[1], 0, panel[2], 1)
self.plots[panel[0]].getAxis('left').setLabel('V', color="#ff0000")
self.plots[panel[0]].setTitle(panel[0], color="#ff0000")
self.plots[panel[0]].getAxis('bottom').setLabel('t (sec)', color="#ff0000")
self.main_layout.addWidget(self.plots_widget, 0, 2, 22, 1)
self.main_layout.addLayout(button_layout, 0, 0, 1, 2)
self.main_layout.addWidget(self.ptree_widget, 1, 0, -1, 2)
self.retrieveAllParameters()
# connect buttons and ptrees to actions
self.ptreedata.sigTreeStateChanged.connect(self.update_DSC)
self.prottreedata.sigTreeStateChanged.connect(self.get_current)
self.btn_read.clicked.connect(self.read_run)
# self.btn_analyze.clicked.connect(self.analyze)
self.btn_find.clicked.connect(self.find_run)
# print( self.MParams)
def retrieveAllParameters(self):
pass
def read_run(self):
pass
def find_run(self):
pass
def setParams(self, isel):
self.params = [
{'name': 'Day', 'type': 'group', 'children':
[{'name': 'Slices/Cells', 'type': 'list', 'values': list(self.tree.keys()), 'value': list(self.tree.keys())[isel]}]
}
]
return self.params
def setProtocols(self):
"""
Update the prototocls to correspond to the current parameters, top protocol selected
"""
if self.tree == None:
raise ValueError('setProtocols: Must set up read data before setting up protocols')
self.protocols = [
{'name': 'Protos', 'type': 'group', 'children':
[{'name': 'Protocols', 'type': 'list',
'values': self.tree[self.current_DSC][:], 'value': self.tree[self.current_DSC][0]}]
}
]
self.prottreedata = Parameter.create(name='protocol', type='group', children=self.protocols)
self.prottree.setParameters(self.prottreedata)
self.current_protocol = self.tree[self.current_DSC][0]
self.prottreedata.sigTreeStateChanged.connect(self.get_current)
return self.protocols
def get_current(self, param, changes):
for param, change, data in changes:
# path = self.prottreedata.childPath(param)
# if path is not None:
# childName = '.'.join(path)
# else:
# childName = param.name()
self.current_protocol = data
def update_DSC(self, param, changes):
for param, change, data in changes:
# path = self.ptreedata.childPath(param)
# if path is not None:
# childName = '.'.join(path)
# else:
# childName = param.name()
self.current_DSC = data
self.setProtocols()
def __init__(self, tree):
"""
Test fixture
"""
self.basename = '/Users/pbmanis/Documents/data/MRK_Pyramidal'
self.filename = None
self.tree = tree
print('tree: ', tree)
self.mainwin = pg.Qt.QtGui.QMainWindow()
self.win = pg.Qt.QtGui.QWidget()
self.main_layout = pg.Qt.QtGui.QGridLayout() # top level layout for the window
self.win.setLayout(self.main_layout)
self.mainwin.setCentralWidget(self.win)
self.mainwin.show()
self.mainwin.setWindowTitle('Data Selection')
self.mainwin.setGeometry( 100 , 100 , 1400 , 900)
# build buttons at top of controls
self.current_DSC = list(self.tree.keys())[0]
self.btn_read = pg.Qt.QtGui.QPushButton("Read")
self.btn_find = pg.Qt.QtGui.QPushButton('Find and Read')
# use a nested grid layout for the buttons
button_layout = pg.Qt.QtGui.QGridLayout()
button_layout.addWidget(self.btn_read, 1, 0, 1, 1)
# button_layout.addWidget(self.btn_analyze, 0, 1, 1, 1)
button_layout.addWidget(self.btn_find, 0, 0, 1, 1)
# build parametertree in left column
#
ptreewidth = 320
self.main_layout.setColumnMinimumWidth(0, ptreewidth)
# analysis # empty in test rig
params = [
{'name': 'Analysis', 'type': 'group', 'children': [],
}]
self.analysis_ptree = ParameterTree()
self.analysis_ptreedata = Parameter.create(name='params', type='group', children=params)
self.analysis_ptree.setParameters(self.analysis_ptreedata)
self.ptree = ParameterTree()
self.ptreedata = Parameter.create(name='dataset', type='group', children=self.setParams(0))
self.ptree.setParameters(self.ptreedata) # add the table with granularity of "cells"
self.prottree = ParameterTree()
self.setProtocols() # add the protocols
# use a grid layout to hold the trees
self.ptree_widget = pg.Qt.QtGui.QWidget()
self.ptree_layout = pg.Qt.QtGui.QGridLayout()
self.ptree_widget.setLayout(self.ptree_layout)
self.ptree_layout.setSpacing(2)
# ptree in row 1 col 0, 4 rows, 2 cols
self.ptree_layout.addWidget(self.analysis_ptree)
self.ptree_layout.addWidget(self.ptree) # Parameter Tree on left
self.ptree_layout.addWidget(self.prottree) # protocol tree just below
# self.ptree_layout.setColumnStretch(0, 5)
self.ptree_layout.setRowStretch(0, 5)
self.ptree_layout.setRowStretch(1, 1)
self.ptree_layout.setRowStretch(2, 1)
# build plot window
self.plots_widget = pg.Qt.QtGui.QWidget()
self.plots_layout = pg.Qt.QtGui.QGridLayout()
self.plots_widget.setLayout(self.plots_layout)
self.plots_layout.setContentsMargins(4, 4, 4, 4)
self.plots_layout.setSpacing(2)
self.plots = {}
for panel in zip(['Wave', 'Average', 'PSTH'], [0, 14, 18], [1, 5, 5],):
self.plots[panel[0]] = pg.PlotWidget()
self.plots_layout.addWidget(self.plots[panel[0]],
panel[1], 0, panel[2], 1)
self.plots[panel[0]].getAxis('left').setLabel('V', color="#ff0000")
self.plots[panel[0]].setTitle(panel[0], color="#ff0000")
self.plots[panel[0]].getAxis('bottom').setLabel('t (sec)', color="#ff0000")
self.main_layout.addWidget(self.plots_widget, 0, 2, 22, 1)
self.main_layout.addLayout(button_layout, 0, 0, 1, 2)
self.main_layout.addWidget(self.ptree_widget, 1, 0, -1, 2)
self.retrieveAllParameters()
# connect buttons and ptrees to actions
self.ptreedata.sigTreeStateChanged.connect(self.update_DSC)
self.prottreedata.sigTreeStateChanged.connect(self.get_current)
self.btn_read.clicked.connect(self.read_run)
# self.btn_analyze.clicked.connect(self.analyze)
self.btn_find.clicked.connect(self.find_run)
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"
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)
def __init__(self, parent = None):
self.parent = parent
self.d9 = Dock("Peak Finder", size=(1, 1))
## Dock 9: Peak finder
self.w10 = ParameterTree()
self.d9.addWidget(self.w10)
#self.w11 = pg.LayoutWidget()
#self.generatePowderBtn = QtGui.QPushButton('Generate Powder')
#self.launchBtn = QtGui.QPushButton('Launch peak finder')
#self.w11.addWidget(self.launchBtn, row=0,col=0)
#self.w11.addWidget(self.generatePowderBtn, row=0, col=0)
#self.d9.addWidget(self.w11)
self.userUpdate = None
self.doingUpdate = False
# Peak finding
self.hitParam_grp = 'Peak finder'
self.hitParam_showPeaks_str = 'Show peaks found'
self.hitParam_algorithm_str = 'Algorithm'
# algorithm 0
self.hitParam_algorithm0_str = 'None'
# algorithm 1
self.hitParam_alg1_npix_min_str = 'npix_min'
self.hitParam_alg1_npix_max_str = 'npix_max'
self.hitParam_alg1_amax_thr_str = 'amax_thr'
self.hitParam_alg1_atot_thr_str = 'atot_thr'
self.hitParam_alg1_son_min_str = 'son_min'
self.hitParam_algorithm1_str = 'Droplet'
self.hitParam_alg1_thr_low_str = 'thr_low'
self.hitParam_alg1_thr_high_str = 'thr_high'
self.hitParam_alg1_rank_str = 'rank'
self.hitParam_alg1_radius_str = 'radius'
self.hitParam_alg1_dr_str = 'dr'
# algorithm 2
self.hitParam_alg2_npix_min_str = 'npix_min'
self.hitParam_alg2_npix_max_str = 'npix_max'
self.hitParam_alg2_amax_thr_str = 'amax_thr'
self.hitParam_alg2_atot_thr_str = 'atot_thr'
self.hitParam_alg2_son_min_str = 'son_min'
self.hitParam_algorithm2_str = 'FloodFill'
self.hitParam_alg2_thr_str = 'thr'
self.hitParam_alg2_r0_str = 'r0'
self.hitParam_alg2_dr_str = 'dr'
# algorithm 3
self.hitParam_alg3_npix_min_str = 'npix_min'
self.hitParam_alg3_npix_max_str = 'npix_max'
self.hitParam_alg3_amax_thr_str = 'amax_thr'
self.hitParam_alg3_atot_thr_str = 'atot_thr'
self.hitParam_alg3_son_min_str = 'son_min'
self.hitParam_algorithm3_str = 'Ranker'
self.hitParam_alg3_rank_str = 'rank'
self.hitParam_alg3_r0_str = 'r0'
self.hitParam_alg3_dr_str = 'dr'
# algorithm 4
self.hitParam_alg4_npix_min_str = 'npix_min'
self.hitParam_alg4_npix_max_str = 'npix_max'
self.hitParam_alg4_amax_thr_str = 'amax_thr'
self.hitParam_alg4_atot_thr_str = 'atot_thr'
self.hitParam_alg4_son_min_str = 'son_min'
self.hitParam_algorithm4_str = 'iDroplet'
self.hitParam_alg4_thr_low_str = 'thr_low'
self.hitParam_alg4_thr_high_str = 'thr_high'
self.hitParam_alg4_rank_str = 'rank'
self.hitParam_alg4_r0_str = 'radius'
self.hitParam_alg4_dr_str = 'dr'
self.hitParam_outDir_str = 'Output directory'
self.hitParam_runs_str = 'Run(s)'
self.hitParam_queue_str = 'queue'
self.hitParam_cpu_str = 'CPUs'
self.hitParam_psanaq_str = 'psanaq'
self.hitParam_psnehq_str = 'psnehq'
self.hitParam_psfehq_str = 'psfehq'
self.hitParam_psnehprioq_str = 'psnehprioq'
self.hitParam_psfehprioq_str = 'psfehprioq'
self.hitParam_psnehhiprioq_str = 'psnehhiprioq'
self.hitParam_psfehhiprioq_str = 'psfehhiprioq'
self.hitParam_psdebugq_str = 'psdebugq'
self.hitParam_noe_str = 'Number of events to process'
self.hitParam_threshold_str = 'Indexable number of peaks'
self.hitParam_launch_str = 'Launch peak finder'
self.hitParam_extra_str = 'Extra parameters'
self.save_minPeaks_str = 'Minimum number of peaks'
self.save_maxPeaks_str = 'Maximum number of peaks'
self.save_minRes_str = 'Minimum resolution (pixels)'
self.save_sample_str = 'Sample name'
self.showPeaks = True
self.peaks = None
self.numPeaksFound = 0
self.algorithm = 0
self.algInitDone = False
self.peaksMaxRes = 0
self.classify = False
self.hitParam_alg1_npix_min = 2.
self.hitParam_alg1_npix_max = 20.
self.hitParam_alg1_amax_thr = 0.
self.hitParam_alg1_atot_thr = 1000.
self.hitParam_alg1_son_min = 7.
self.hitParam_alg1_thr_low = 250.
self.hitParam_alg1_thr_high = 600.
self.hitParam_alg1_rank = 2
self.hitParam_alg1_radius = 2
self.hitParam_alg1_dr = 1
# self.hitParam_alg2_npix_min = 1.
# self.hitParam_alg2_npix_max = 5000.
# self.hitParam_alg2_amax_thr = 1.
# self.hitParam_alg2_atot_thr = 1.
# self.hitParam_alg2_son_min = 1.
# self.hitParam_alg2_thr = 10.
# self.hitParam_alg2_r0 = 1.
# self.hitParam_alg2_dr = 0.05
# self.hitParam_alg3_npix_min = 5.
# self.hitParam_alg3_npix_max = 5000.
# self.hitParam_alg3_amax_thr = 0.
# self.hitParam_alg3_atot_thr = 0.
# self.hitParam_alg3_son_min = 4.
# self.hitParam_alg3_rank = 3
# self.hitParam_alg3_r0 = 5.
# self.hitParam_alg3_dr = 0.05
# self.hitParam_alg4_npix_min = 1.
# self.hitParam_alg4_npix_max = 45.
# self.hitParam_alg4_amax_thr = 800.
# self.hitParam_alg4_atot_thr = 0
# self.hitParam_alg4_son_min = 7.
# self.hitParam_alg4_thr_low = 200.
# self.hitParam_alg4_thr_high = self.hitParam_alg1_thr_high
# self.hitParam_alg4_rank = 3
# self.hitParam_alg4_r0 = 2
# self.hitParam_alg4_dr = 1
self.hitParam_outDir = self.parent.psocakeDir
self.hitParam_outDir_overridden = False
self.hitParam_runs = ''
self.hitParam_queue = self.hitParam_psanaq_str
self.hitParam_cpus = 24
self.hitParam_noe = -1
self.hitParam_threshold = 15 # usually crystals with less than 15 peaks are not indexable
self.minPeaks = 15
self.maxPeaks = 2048
self.minRes = -1
self.sample = 'sample'
self.profile = 0
self.hitParam_extra = ''
self.params = [
{'name': self.hitParam_grp, 'type': 'group', 'children': [
{'name': self.hitParam_showPeaks_str, 'type': 'bool', 'value': self.showPeaks,
'tip': "Show peaks found shot-to-shot"},
{'name': self.hitParam_algorithm_str, 'type': 'list', 'values': {self.hitParam_algorithm1_str: 1,
self.hitParam_algorithm0_str: 0},
'value': self.algorithm},
{'name': self.hitParam_algorithm1_str, 'visible': True, 'expanded': False, 'type': 'str', 'value': "",
'readonly': True, 'children': [
{'name': self.hitParam_alg1_npix_min_str, 'type': 'float', 'value': self.hitParam_alg1_npix_min,
'tip': "Only keep the peak if number of pixels above thr_low is above this value"},
{'name': self.hitParam_alg1_npix_max_str, 'type': 'float', 'value': self.hitParam_alg1_npix_max,
'tip': "Only keep the peak if number of pixels above thr_low is below this value"},
{'name': self.hitParam_alg1_amax_thr_str, 'type': 'float', 'value': self.hitParam_alg1_amax_thr,
'tip': "Only keep the peak if max value is above this value"},
{'name': self.hitParam_alg1_atot_thr_str, 'type': 'float', 'value': self.hitParam_alg1_atot_thr,
'tip': "Only keep the peak if integral inside region of interest is above this value"},
{'name': self.hitParam_alg1_son_min_str, 'type': 'float', 'value': self.hitParam_alg1_son_min,
'tip': "Only keep the peak if signal-over-noise is above this value"},
{'name': self.hitParam_alg1_thr_low_str, 'type': 'float', 'value': self.hitParam_alg1_thr_low,
'tip': "Grow a seed peak if above this value"},
{'name': self.hitParam_alg1_thr_high_str, 'type': 'float', 'value': self.hitParam_alg1_thr_high,
'tip': "Start a seed peak if above this value"},
{'name': self.hitParam_alg1_rank_str, 'type': 'int', 'value': self.hitParam_alg1_rank,
'tip': "region of integration is a square, (2r+1)x(2r+1)"},
{'name': self.hitParam_alg1_radius_str, 'type': 'int', 'value': self.hitParam_alg1_radius,
'tip': "region inside the region of interest"},
{'name': self.hitParam_alg1_dr_str, 'type': 'float', 'value': self.hitParam_alg1_dr,
'tip': "background region outside the region of interest"},
]},
{'name': self.save_minPeaks_str, 'type': 'int', 'value': self.minPeaks,
'tip': "Index only if there are more Bragg peaks found"},
{'name': self.save_maxPeaks_str, 'type': 'int', 'value': self.maxPeaks,
'tip': "Index only if there are less Bragg peaks found"},
{'name': self.save_minRes_str, 'type': 'int', 'value': self.minRes,
'tip': "Index only if Bragg peak resolution is at least this"},
{'name': self.save_sample_str, 'type': 'str', 'value': self.sample,
'tip': "Sample name saved inside cxi"},
{'name': self.hitParam_outDir_str, 'type': 'str', 'value': self.hitParam_outDir},
{'name': self.hitParam_runs_str, 'type': 'str', 'value': self.hitParam_runs},
{'name': self.hitParam_queue_str, 'type': 'list', 'values': {self.hitParam_psfehhiprioq_str: 'psfehhiprioq',
self.hitParam_psnehhiprioq_str: 'psnehhiprioq',
self.hitParam_psfehprioq_str: 'psfehprioq',
self.hitParam_psnehprioq_str: 'psnehprioq',
self.hitParam_psfehq_str: 'psfehq',
self.hitParam_psnehq_str: 'psnehq',
self.hitParam_psanaq_str: 'psanaq',
self.hitParam_psdebugq_str: 'psdebugq'},
'value': self.hitParam_queue, 'tip': "Choose queue"},
{'name': self.hitParam_cpu_str, 'type': 'int', 'value': self.hitParam_cpus},
{'name': self.hitParam_noe_str, 'type': 'int', 'value': self.hitParam_noe,
'tip': "number of events to process, default=-1 means process all events"},
{'name': self.hitParam_extra_str, 'type': 'str', 'value': self.hitParam_extra, 'tip': "Extra peak finding flags"},
{'name': self.hitParam_launch_str, 'type': 'action'},
]},
]
self.p3 = Parameter.create(name='paramsPeakFinder', type='group', \
children=self.params, expanded=True)
self.w10.setParameters(self.p3, showTop=False)
self.p3.sigTreeStateChanged.connect(self.change)
class PeakFinding(object):
def __init__(self, parent = None):
self.parent = parent
self.d9 = Dock("Peak Finder", size=(1, 1))
## Dock 9: Peak finder
self.w10 = ParameterTree()
self.d9.addWidget(self.w10)
#self.w11 = pg.LayoutWidget()
#self.generatePowderBtn = QtGui.QPushButton('Generate Powder')
#self.launchBtn = QtGui.QPushButton('Launch peak finder')
#self.w11.addWidget(self.launchBtn, row=0,col=0)
#self.w11.addWidget(self.generatePowderBtn, row=0, col=0)
#self.d9.addWidget(self.w11)
self.userUpdate = None
self.doingUpdate = False
# Peak finding
self.hitParam_grp = 'Peak finder'
self.hitParam_showPeaks_str = 'Show peaks found'
self.hitParam_algorithm_str = 'Algorithm'
# algorithm 0
self.hitParam_algorithm0_str = 'None'
# algorithm 1
self.hitParam_alg1_npix_min_str = 'npix_min'
self.hitParam_alg1_npix_max_str = 'npix_max'
self.hitParam_alg1_amax_thr_str = 'amax_thr'
self.hitParam_alg1_atot_thr_str = 'atot_thr'
self.hitParam_alg1_son_min_str = 'son_min'
self.hitParam_algorithm1_str = 'Droplet'
self.hitParam_alg1_thr_low_str = 'thr_low'
self.hitParam_alg1_thr_high_str = 'thr_high'
self.hitParam_alg1_rank_str = 'rank'
self.hitParam_alg1_radius_str = 'radius'
self.hitParam_alg1_dr_str = 'dr'
# algorithm 2
self.hitParam_alg2_npix_min_str = 'npix_min'
self.hitParam_alg2_npix_max_str = 'npix_max'
self.hitParam_alg2_amax_thr_str = 'amax_thr'
self.hitParam_alg2_atot_thr_str = 'atot_thr'
self.hitParam_alg2_son_min_str = 'son_min'
self.hitParam_algorithm2_str = 'FloodFill'
self.hitParam_alg2_thr_str = 'thr'
self.hitParam_alg2_r0_str = 'r0'
self.hitParam_alg2_dr_str = 'dr'
# algorithm 3
self.hitParam_alg3_npix_min_str = 'npix_min'
self.hitParam_alg3_npix_max_str = 'npix_max'
self.hitParam_alg3_amax_thr_str = 'amax_thr'
self.hitParam_alg3_atot_thr_str = 'atot_thr'
self.hitParam_alg3_son_min_str = 'son_min'
self.hitParam_algorithm3_str = 'Ranker'
self.hitParam_alg3_rank_str = 'rank'
self.hitParam_alg3_r0_str = 'r0'
self.hitParam_alg3_dr_str = 'dr'
# algorithm 4
self.hitParam_alg4_npix_min_str = 'npix_min'
self.hitParam_alg4_npix_max_str = 'npix_max'
self.hitParam_alg4_amax_thr_str = 'amax_thr'
self.hitParam_alg4_atot_thr_str = 'atot_thr'
self.hitParam_alg4_son_min_str = 'son_min'
self.hitParam_algorithm4_str = 'iDroplet'
self.hitParam_alg4_thr_low_str = 'thr_low'
self.hitParam_alg4_thr_high_str = 'thr_high'
self.hitParam_alg4_rank_str = 'rank'
self.hitParam_alg4_r0_str = 'radius'
self.hitParam_alg4_dr_str = 'dr'
self.hitParam_outDir_str = 'Output directory'
self.hitParam_runs_str = 'Run(s)'
self.hitParam_queue_str = 'queue'
self.hitParam_cpu_str = 'CPUs'
self.hitParam_psanaq_str = 'psanaq'
self.hitParam_psnehq_str = 'psnehq'
self.hitParam_psfehq_str = 'psfehq'
self.hitParam_psnehprioq_str = 'psnehprioq'
self.hitParam_psfehprioq_str = 'psfehprioq'
self.hitParam_psnehhiprioq_str = 'psnehhiprioq'
self.hitParam_psfehhiprioq_str = 'psfehhiprioq'
self.hitParam_psdebugq_str = 'psdebugq'
self.hitParam_noe_str = 'Number of events to process'
self.hitParam_threshold_str = 'Indexable number of peaks'
self.hitParam_launch_str = 'Launch peak finder'
self.hitParam_extra_str = 'Extra parameters'
self.save_minPeaks_str = 'Minimum number of peaks'
self.save_maxPeaks_str = 'Maximum number of peaks'
self.save_minRes_str = 'Minimum resolution (pixels)'
self.save_sample_str = 'Sample name'
self.showPeaks = True
self.peaks = None
self.numPeaksFound = 0
self.algorithm = 0
self.algInitDone = False
self.peaksMaxRes = 0
self.classify = False
self.hitParam_alg1_npix_min = 2.
self.hitParam_alg1_npix_max = 20.
self.hitParam_alg1_amax_thr = 0.
self.hitParam_alg1_atot_thr = 1000.
self.hitParam_alg1_son_min = 7.
self.hitParam_alg1_thr_low = 250.
self.hitParam_alg1_thr_high = 600.
self.hitParam_alg1_rank = 2
self.hitParam_alg1_radius = 2
self.hitParam_alg1_dr = 1
# self.hitParam_alg2_npix_min = 1.
# self.hitParam_alg2_npix_max = 5000.
# self.hitParam_alg2_amax_thr = 1.
# self.hitParam_alg2_atot_thr = 1.
# self.hitParam_alg2_son_min = 1.
# self.hitParam_alg2_thr = 10.
# self.hitParam_alg2_r0 = 1.
# self.hitParam_alg2_dr = 0.05
# self.hitParam_alg3_npix_min = 5.
# self.hitParam_alg3_npix_max = 5000.
# self.hitParam_alg3_amax_thr = 0.
# self.hitParam_alg3_atot_thr = 0.
# self.hitParam_alg3_son_min = 4.
# self.hitParam_alg3_rank = 3
# self.hitParam_alg3_r0 = 5.
# self.hitParam_alg3_dr = 0.05
# self.hitParam_alg4_npix_min = 1.
# self.hitParam_alg4_npix_max = 45.
# self.hitParam_alg4_amax_thr = 800.
# self.hitParam_alg4_atot_thr = 0
# self.hitParam_alg4_son_min = 7.
# self.hitParam_alg4_thr_low = 200.
# self.hitParam_alg4_thr_high = self.hitParam_alg1_thr_high
# self.hitParam_alg4_rank = 3
# self.hitParam_alg4_r0 = 2
# self.hitParam_alg4_dr = 1
self.hitParam_outDir = self.parent.psocakeDir
self.hitParam_outDir_overridden = False
self.hitParam_runs = ''
self.hitParam_queue = self.hitParam_psanaq_str
self.hitParam_cpus = 24
self.hitParam_noe = -1
self.hitParam_threshold = 15 # usually crystals with less than 15 peaks are not indexable
self.minPeaks = 15
self.maxPeaks = 2048
self.minRes = -1
self.sample = 'sample'
self.profile = 0
self.hitParam_extra = ''
self.params = [
{'name': self.hitParam_grp, 'type': 'group', 'children': [
{'name': self.hitParam_showPeaks_str, 'type': 'bool', 'value': self.showPeaks,
'tip': "Show peaks found shot-to-shot"},
{'name': self.hitParam_algorithm_str, 'type': 'list', 'values': {self.hitParam_algorithm1_str: 1,
self.hitParam_algorithm0_str: 0},
'value': self.algorithm},
{'name': self.hitParam_algorithm1_str, 'visible': True, 'expanded': False, 'type': 'str', 'value': "",
'readonly': True, 'children': [
{'name': self.hitParam_alg1_npix_min_str, 'type': 'float', 'value': self.hitParam_alg1_npix_min,
'tip': "Only keep the peak if number of pixels above thr_low is above this value"},
{'name': self.hitParam_alg1_npix_max_str, 'type': 'float', 'value': self.hitParam_alg1_npix_max,
'tip': "Only keep the peak if number of pixels above thr_low is below this value"},
{'name': self.hitParam_alg1_amax_thr_str, 'type': 'float', 'value': self.hitParam_alg1_amax_thr,
'tip': "Only keep the peak if max value is above this value"},
{'name': self.hitParam_alg1_atot_thr_str, 'type': 'float', 'value': self.hitParam_alg1_atot_thr,
'tip': "Only keep the peak if integral inside region of interest is above this value"},
{'name': self.hitParam_alg1_son_min_str, 'type': 'float', 'value': self.hitParam_alg1_son_min,
'tip': "Only keep the peak if signal-over-noise is above this value"},
{'name': self.hitParam_alg1_thr_low_str, 'type': 'float', 'value': self.hitParam_alg1_thr_low,
'tip': "Grow a seed peak if above this value"},
{'name': self.hitParam_alg1_thr_high_str, 'type': 'float', 'value': self.hitParam_alg1_thr_high,
'tip': "Start a seed peak if above this value"},
{'name': self.hitParam_alg1_rank_str, 'type': 'int', 'value': self.hitParam_alg1_rank,
'tip': "region of integration is a square, (2r+1)x(2r+1)"},
{'name': self.hitParam_alg1_radius_str, 'type': 'int', 'value': self.hitParam_alg1_radius,
'tip': "region inside the region of interest"},
{'name': self.hitParam_alg1_dr_str, 'type': 'float', 'value': self.hitParam_alg1_dr,
'tip': "background region outside the region of interest"},
]},
{'name': self.save_minPeaks_str, 'type': 'int', 'value': self.minPeaks,
'tip': "Index only if there are more Bragg peaks found"},
{'name': self.save_maxPeaks_str, 'type': 'int', 'value': self.maxPeaks,
'tip': "Index only if there are less Bragg peaks found"},
{'name': self.save_minRes_str, 'type': 'int', 'value': self.minRes,
'tip': "Index only if Bragg peak resolution is at least this"},
{'name': self.save_sample_str, 'type': 'str', 'value': self.sample,
'tip': "Sample name saved inside cxi"},
{'name': self.hitParam_outDir_str, 'type': 'str', 'value': self.hitParam_outDir},
{'name': self.hitParam_runs_str, 'type': 'str', 'value': self.hitParam_runs},
{'name': self.hitParam_queue_str, 'type': 'list', 'values': {self.hitParam_psfehhiprioq_str: 'psfehhiprioq',
self.hitParam_psnehhiprioq_str: 'psnehhiprioq',
self.hitParam_psfehprioq_str: 'psfehprioq',
self.hitParam_psnehprioq_str: 'psnehprioq',
self.hitParam_psfehq_str: 'psfehq',
self.hitParam_psnehq_str: 'psnehq',
self.hitParam_psanaq_str: 'psanaq',
self.hitParam_psdebugq_str: 'psdebugq'},
'value': self.hitParam_queue, 'tip': "Choose queue"},
{'name': self.hitParam_cpu_str, 'type': 'int', 'value': self.hitParam_cpus},
{'name': self.hitParam_noe_str, 'type': 'int', 'value': self.hitParam_noe,
'tip': "number of events to process, default=-1 means process all events"},
{'name': self.hitParam_extra_str, 'type': 'str', 'value': self.hitParam_extra, 'tip': "Extra peak finding flags"},
{'name': self.hitParam_launch_str, 'type': 'action'},
]},
]
self.p3 = Parameter.create(name='paramsPeakFinder', type='group', \
children=self.params, expanded=True)
self.w10.setParameters(self.p3, showTop=False)
self.p3.sigTreeStateChanged.connect(self.change)
#self.parent.connect(self.launchBtn, QtCore.SIGNAL("clicked()"), self.findPeaks)
def digestRunList(self, runList):
runsToDo = []
if not runList:
print "Run(s) is empty. Please type in the run number(s)."
return runsToDo
runLists = str(runList).split(",")
for list in runLists:
temp = list.split(":")
if len(temp) == 2:
for i in np.arange(int(temp[0]),int(temp[1])+1):
runsToDo.append(i)
elif len(temp) == 1:
runsToDo.append(int(temp[0]))
return runsToDo
def updateParam(self):
if self.userUpdate is None:
if self.parent.psocakeRunDir is not None:
peakParamFname = self.parent.psocakeRunDir + '/peakParam.json'
if os.path.exists(peakParamFname):
with open(peakParamFname) as infile:
d = json.load(infile)
if d[self.hitParam_algorithm_str] == 1:
# Update variables
try:
self.hitParam_alg1_npix_min = d[self.hitParam_alg1_npix_min_str]
self.hitParam_alg1_npix_max = d[self.hitParam_alg1_npix_max_str]
self.hitParam_alg1_amax_thr = d[self.hitParam_alg1_amax_thr_str]
self.hitParam_alg1_atot_thr = d[self.hitParam_alg1_atot_thr_str]
self.hitParam_alg1_son_min = d[self.hitParam_alg1_son_min_str]
self.hitParam_alg1_thr_low = d[self.hitParam_alg1_thr_low_str]
self.hitParam_alg1_thr_high = d[self.hitParam_alg1_thr_high_str]
self.hitParam_alg1_rank = int(d[self.hitParam_alg1_rank_str])
self.hitParam_alg1_radius = int(d[self.hitParam_alg1_radius_str])
self.hitParam_alg1_dr = d[self.hitParam_alg1_dr_str]
# Update GUI
self.doingUpdate = True
#self.p3.param(self.hitParam_grp, self.hitParam_algorithm_str).setValue(self.algorithm)
self.p3.param(self.hitParam_grp, self.hitParam_algorithm1_str, self.hitParam_alg1_npix_min_str).setValue(
self.hitParam_alg1_npix_min)
self.p3.param(self.hitParam_grp, self.hitParam_algorithm1_str, self.hitParam_alg1_npix_max_str).setValue(
self.hitParam_alg1_npix_max)
self.p3.param(self.hitParam_grp, self.hitParam_algorithm1_str, self.hitParam_alg1_amax_thr_str).setValue(
self.hitParam_alg1_amax_thr)
self.p3.param(self.hitParam_grp, self.hitParam_algorithm1_str, self.hitParam_alg1_atot_thr_str).setValue(
self.hitParam_alg1_atot_thr)
self.p3.param(self.hitParam_grp, self.hitParam_algorithm1_str, self.hitParam_alg1_son_min_str).setValue(
self.hitParam_alg1_son_min)
self.p3.param(self.hitParam_grp, self.hitParam_algorithm1_str, self.hitParam_alg1_thr_low_str).setValue(
self.hitParam_alg1_thr_low)
self.p3.param(self.hitParam_grp, self.hitParam_algorithm1_str, self.hitParam_alg1_thr_high_str).setValue(
self.hitParam_alg1_thr_high)
self.p3.param(self.hitParam_grp, self.hitParam_algorithm1_str, self.hitParam_alg1_rank_str).setValue(
self.hitParam_alg1_rank)
self.p3.param(self.hitParam_grp, self.hitParam_algorithm1_str, self.hitParam_alg1_radius_str).setValue(
self.hitParam_alg1_radius)
self.doingUpdate = False
self.p3.param(self.hitParam_grp, self.hitParam_algorithm1_str, self.hitParam_alg1_dr_str).setValue(
self.hitParam_alg1_dr)
except:
pass
def writeStatus(self, fname, d):
json.dump(d, open(fname, 'w'))
# Launch peak finding
def findPeaks(self):
self.parent.thread.append(LaunchPeakFinder.LaunchPeakFinder(self.parent)) # send parent parameters with self
self.parent.thread[self.parent.threadCounter].launch(self.parent.experimentName, self.parent.detInfo)
self.parent.threadCounter+=1
# Save peak finding parameters
runsToDo = self.digestRunList(self.hitParam_runs)
for run in runsToDo:
peakParamFname = self.parent.psocakeDir+'/r'+str(run).zfill(4)+'/peakParam.json'
d = {self.hitParam_algorithm_str: self.algorithm,
self.hitParam_alg1_npix_min_str: self.hitParam_alg1_npix_min,
self.hitParam_alg1_npix_max_str: self.hitParam_alg1_npix_max,
self.hitParam_alg1_amax_thr_str: self.hitParam_alg1_amax_thr,
self.hitParam_alg1_atot_thr_str: self.hitParam_alg1_atot_thr,
self.hitParam_alg1_son_min_str: self.hitParam_alg1_son_min,
self.hitParam_alg1_thr_low_str: self.hitParam_alg1_thr_low,
self.hitParam_alg1_thr_high_str: self.hitParam_alg1_thr_high,
self.hitParam_alg1_rank_str: self.hitParam_alg1_rank,
self.hitParam_alg1_radius_str: self.hitParam_alg1_radius,
self.hitParam_alg1_dr_str: self.hitParam_alg1_dr}
self.writeStatus(peakParamFname, d)
# 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.hitParam_grp:
if path[1] == self.hitParam_algorithm_str:
self.algInitDone = False
self.updateAlgorithm(data)
elif path[1] == self.hitParam_showPeaks_str:
self.showPeaks = data
self.drawPeaks()
elif path[1] == self.hitParam_outDir_str:
self.hitParam_outDir = data
self.hitParam_outDir_overridden = True
elif path[1] == self.hitParam_runs_str:
self.hitParam_runs = data
elif path[1] == self.hitParam_queue_str:
self.hitParam_queue = data
elif path[1] == self.hitParam_cpu_str:
self.hitParam_cpus = data
elif path[1] == self.hitParam_noe_str:
self.hitParam_noe = data
elif path[1] == self.hitParam_threshold_str:
self.hitParam_threshold = data
elif path[1] == self.hitParam_launch_str:
self.findPeaks()
elif path[1] == self.save_minPeaks_str:
self.minPeaks = data
elif path[1] == self.save_maxPeaks_str:
self.maxPeaks = data
elif path[1] == self.save_minRes_str:
self.minRes = data
elif path[1] == self.save_sample_str:
self.sample = data
elif path[1] == self.hitParam_extra_str:
self.hitParam_extra = data
elif path[2] == self.hitParam_alg1_npix_min_str and path[1] == self.hitParam_algorithm1_str:
self.hitParam_alg1_npix_min = data
self.algInitDone = False
self.userUpdate = True
if self.showPeaks and self.doingUpdate is False:
self.updateClassification()
elif path[2] == self.hitParam_alg1_npix_max_str and path[1] == self.hitParam_algorithm1_str:
self.hitParam_alg1_npix_max = data
self.algInitDone = False
self.userUpdate = True
if self.showPeaks and self.doingUpdate is False:
self.updateClassification()
elif path[2] == self.hitParam_alg1_amax_thr_str and path[1] == self.hitParam_algorithm1_str:
self.hitParam_alg1_amax_thr = data
self.algInitDone = False
self.userUpdate = True
if self.showPeaks and self.doingUpdate is False:
self.updateClassification()
elif path[2] == self.hitParam_alg1_atot_thr_str and path[1] == self.hitParam_algorithm1_str:
self.hitParam_alg1_atot_thr = data
self.algInitDone = False
self.userUpdate = True
if self.showPeaks and self.doingUpdate is False:
self.updateClassification()
elif path[2] == self.hitParam_alg1_son_min_str and path[1] == self.hitParam_algorithm1_str:
self.hitParam_alg1_son_min = data
self.algInitDone = False
self.userUpdate = True
if self.showPeaks and self.doingUpdate is False:
self.updateClassification()
elif path[2] == self.hitParam_alg1_thr_low_str and path[1] == self.hitParam_algorithm1_str:
self.hitParam_alg1_thr_low = data
self.algInitDone = False
self.userUpdate = True
if self.showPeaks and self.doingUpdate is False:
self.updateClassification()
elif path[2] == self.hitParam_alg1_thr_high_str and path[1] == self.hitParam_algorithm1_str:
self.hitParam_alg1_thr_high = data
self.algInitDone = False
self.userUpdate = True
if self.showPeaks and self.doingUpdate is False:
self.updateClassification()
elif path[2] == self.hitParam_alg1_rank_str and path[1] == self.hitParam_algorithm1_str:
self.hitParam_alg1_rank = data
self.algInitDone = False
self.userUpdate = True
if self.showPeaks and self.doingUpdate is False:
self.updateClassification()
elif path[2] == self.hitParam_alg1_radius_str and path[1] == self.hitParam_algorithm1_str:
self.hitParam_alg1_radius = data
self.algInitDone = False
self.userUpdate = True
if self.showPeaks and self.doingUpdate is False:
self.updateClassification()
elif path[2] == self.hitParam_alg1_dr_str and path[1] == self.hitParam_algorithm1_str:
self.hitParam_alg1_dr = data
self.algInitDone = False
self.userUpdate = True
if self.showPeaks and self.doingUpdate is False:
self.updateClassification()
def updateAlgorithm(self, data):
self.algorithm = data
self.algInitDone = False
self.updateClassification()
if self.parent.args.v >= 1: print "##### Done updateAlgorithm: ", self.algorithm
def saveCheetahFormat(self, arg):
if arg == 'lcls':
if 'cspad' in self.parent.detInfo.lower() and 'cxi' in self.parent.experimentName:
dim0 = 8 * 185
dim1 = 4 * 388
elif 'rayonix' in self.parent.detInfo.lower() and 'mfx' in self.parent.experimentName:
dim0 = 1920 #FIXME: rayonix can be binned
dim1 = 1920
elif 'rayonix' in self.parent.detInfo.lower() and 'xpp' in self.parent.experimentName:
dim0 = 1920 #FIXME: rayonix can be binned
dim1 = 1920
else:
dim0 = 0
dim1 = 0
if dim0 > 0:
maxNumPeaks = 2048
if self.parent.index.hiddenCXI is not None:
myHdf5 = h5py.File(self.parent.index.hiddenCXI, 'w')
grpName = "/entry_1/result_1"
dset_nPeaks = "/nPeaks"
dset_posX = "/peakXPosRaw"
dset_posY = "/peakYPosRaw"
dset_atot = "/peakTotalIntensity"
if grpName in myHdf5:
del myHdf5[grpName]
grp = myHdf5.create_group(grpName)
myHdf5.create_dataset(grpName + dset_nPeaks, (1,), dtype='int')
myHdf5.create_dataset(grpName + dset_posX, (1, maxNumPeaks), dtype='float32', chunks=(1, maxNumPeaks))
myHdf5.create_dataset(grpName + dset_posY, (1, maxNumPeaks), dtype='float32', chunks=(1, maxNumPeaks))
myHdf5.create_dataset(grpName + dset_atot, (1, maxNumPeaks), dtype='float32', chunks=(1, maxNumPeaks))
myHdf5.create_dataset("/LCLS/detector_1/EncoderValue", (1,), dtype=float)
myHdf5.create_dataset("/LCLS/photon_energy_eV", (1,), dtype=float)
dset = myHdf5.create_dataset("/entry_1/data_1/data", (1, dim0, dim1), dtype=float)
# Convert calib image to cheetah image
img = np.zeros((dim0, dim1))
counter = 0
if 'cspad' in self.parent.detInfo.lower() and 'cxi' in self.parent.experimentName:
for quad in range(4):
for seg in range(8):
img[seg * 185:(seg + 1) * 185, quad * 388:(quad + 1) * 388] = self.parent.calib[counter, :, :]
counter += 1
elif 'rayonix' in self.parent.detInfo.lower() and 'mfx' in self.parent.experimentName:
img = self.parent.calib[:, :] # psana format
elif 'rayonix' in self.parent.detInfo.lower() and 'xpp' in self.parent.experimentName:
img = self.parent.calib[:, :] # psana format
else:
print "saveCheetahFormat not implemented"
peaks = self.peaks.copy()
nPeaks = peaks.shape[0]
if nPeaks > maxNumPeaks:
peaks = peaks[:maxNumPeaks]
nPeaks = maxNumPeaks
for i, peak in enumerate(peaks):
seg, row, col, npix, amax, atot, rcent, ccent, rsigma, csigma, rmin, rmax, cmin, cmax, bkgd, rms, son = peak[0:17]
if 'cspad' in self.parent.detInfo.lower() and 'cxi' in self.parent.experimentName:
cheetahRow, cheetahCol = self.convert_peaks_to_cheetah(seg, row, col)
myHdf5[grpName + dset_posX][0, i] = cheetahCol
myHdf5[grpName + dset_posY][0, i] = cheetahRow
myHdf5[grpName + dset_atot][0, i] = atot
elif 'rayonix' in self.parent.detInfo.lower() and 'mfx' in self.parent.experimentName:
myHdf5[grpName + dset_posX][0, i] = col
myHdf5[grpName + dset_posY][0, i] = row
myHdf5[grpName + dset_atot][0, i] = atot
elif 'rayonix' in self.parent.detInfo.lower() and 'xpp' in self.parent.experimentName:
myHdf5[grpName + dset_posX][0, i] = col
myHdf5[grpName + dset_posY][0, i] = row
myHdf5[grpName + dset_atot][0, i] = atot
myHdf5[grpName + dset_nPeaks][0] = nPeaks
if self.parent.args.v >= 1: print "hiddenCXI clen (mm): ", self.parent.clen * 1000.
myHdf5["/LCLS/detector_1/EncoderValue"][0] = self.parent.clen * 1000. # mm
myHdf5["/LCLS/photon_energy_eV"][0] = self.parent.photonEnergy
dset[0, :, :] = img
myHdf5.close()
def updateClassification(self):
if self.parent.calib is not None:
if self.parent.mk.streakMaskOn:
self.parent.mk.initMask()
self.parent.mk.streakMask = self.parent.mk.StreakMask.getStreakMaskCalib(self.parent.evt)
if self.parent.mk.streakMask is None:
self.parent.mk.streakMaskAssem = None
else:
self.parent.mk.streakMaskAssem = self.parent.det.image(self.parent.evt, self.parent.mk.streakMask)
self.algInitDone = False
self.parent.mk.displayMask()
# update combined mask
self.parent.mk.combinedMask = np.ones_like(self.parent.calib)
if self.parent.mk.streakMask is not None and self.parent.mk.streakMaskOn is True:
self.parent.mk.combinedMask *= self.parent.mk.streakMask
if self.parent.mk.userMask is not None and self.parent.mk.userMaskOn is True:
self.parent.mk.combinedMask *= self.parent.mk.userMask
if self.parent.mk.psanaMask is not None and self.parent.mk.psanaMaskOn is True:
self.parent.mk.combinedMask *= self.parent.mk.psanaMask
# Peak output (0-16):
# 0 seg
# 1 row
# 2 col
# 3 npix: no. of pixels in the ROI intensities above threshold
# 4 amp_max: max intensity
# 5 amp_tot: sum of intensities
# 6,7: row_cgrav: center of mass
# 8,9: row_sigma
# 10,11,12,13: minimum bounding box
# 14: background
# 15: noise
# 16: signal over noise
if self.algorithm == 0: # No peak algorithm
self.peaks = None
self.drawPeaks()
else:
# Only initialize the hit finder algorithm once
if self.algInitDone is False:
self.windows = None
self.alg = []
self.alg = PyAlgos(windows=self.windows, mask=self.parent.mk.combinedMask, pbits=0)
# set peak-selector parameters:
if self.algorithm == 1:
self.alg.set_peak_selection_pars(npix_min=self.hitParam_alg1_npix_min, npix_max=self.hitParam_alg1_npix_max, \
amax_thr=self.hitParam_alg1_amax_thr, atot_thr=self.hitParam_alg1_atot_thr, \
son_min=self.hitParam_alg1_son_min)
elif self.algorithm == 2:
self.alg.set_peak_selection_pars(npix_min=self.hitParam_alg2_npix_min, npix_max=self.hitParam_alg2_npix_max, \
amax_thr=self.hitParam_alg2_amax_thr, atot_thr=self.hitParam_alg2_atot_thr, \
son_min=self.hitParam_alg2_son_min)
elif self.algorithm == 3:
self.alg.set_peak_selection_pars(npix_min=self.hitParam_alg3_npix_min, npix_max=self.hitParam_alg3_npix_max, \
amax_thr=self.hitParam_alg3_amax_thr, atot_thr=self.hitParam_alg3_atot_thr, \
son_min=self.hitParam_alg3_son_min)
elif self.algorithm == 4:
self.alg.set_peak_selection_pars(npix_min=self.hitParam_alg4_npix_min, npix_max=self.hitParam_alg4_npix_max, \
amax_thr=self.hitParam_alg4_amax_thr, atot_thr=self.hitParam_alg4_atot_thr, \
son_min=self.hitParam_alg4_son_min)
self.algInitDone = True
self.parent.calib = self.parent.calib * 1.0 # Neccessary when int is returned
if self.algorithm == 1:
# v1 - aka Droplet Finder - two-threshold peak-finding algorithm in restricted region
# around pixel with maximal intensity.
self.peakRadius = int(self.hitParam_alg1_radius)
self.peaks = self.alg.peak_finder_v4r2(self.parent.calib,
thr_low=self.hitParam_alg1_thr_low,
thr_high=self.hitParam_alg1_thr_high,
rank=int(self.hitParam_alg1_rank),
r0=self.peakRadius,
dr=self.hitParam_alg1_dr)
elif self.algorithm == 2:
# v2 - define peaks for regions of connected pixels above threshold
self.peakRadius = int(self.hitParam_alg2_r0)
self.peaks = self.alg.peak_finder_v2(self.parent.calib, thr=self.hitParam_alg2_thr, r0=self.peakRadius, dr=self.hitParam_alg2_dr)
elif self.algorithm == 3:
self.peakRadius = int(self.hitParam_alg3_r0)
self.peaks = self.alg.peak_finder_v3(self.parent.calib, rank=self.hitParam_alg3_rank, r0=self.peakRadius, dr=self.hitParam_alg3_dr)
elif self.algorithm == 4:
# v4 - aka Droplet Finder - the same as v1, but uses rank and r0 parameters in stead of common radius.
self.peakRadius = int(self.hitParam_alg4_r0)
self.peaks = self.alg.peak_finder_v4(self.parent.calib, thr_low=self.hitParam_alg4_thr_low, thr_high=self.hitParam_alg4_thr_high,
rank=self.hitParam_alg4_rank, r0=self.peakRadius, dr=self.hitParam_alg4_dr)
self.numPeaksFound = self.peaks.shape[0]
if self.parent.args.v >= 1: print "Num peaks found: ", self.numPeaksFound, self.peaks.shape
# update clen
self.parent.geom.updateClen('lcls')
self.parent.index.clearIndexedPeaks()
# Save image and peaks in cheetah cxi file
self.saveCheetahFormat('lcls')
if self.parent.index.showIndexedPeaks: self.parent.index.updateIndex()
self.drawPeaks()
if self.parent.args.v >= 1: print "Done updateClassification"
def convert_peaks_to_cheetah(self, s, r, c) :
"""Converts seg, row, col assuming (32,185,388)
to cheetah 2-d table row and col (8*185, 4*388)
"""
segs, rows, cols = (32,185,388)
row2d = (int(s)%8) * rows + int(r) # where s%8 is a segment in quad number [0,7]
col2d = (int(s)/8) * cols + int(c) # where s/8 is a quad number [0,3]
return row2d, col2d
def getMaxRes(self, posX, posY, centerX, centerY):
maxRes = np.max(np.sqrt((posX-centerX)**2 + (posY-centerY)**2))
if self.parent.args.v >= 1: print "maxRes: ", maxRes
return maxRes # in pixels
def drawPeaks(self):
self.parent.img.clearPeakMessage()
if self.showPeaks:
if self.peaks is not None and self.numPeaksFound > 0:
self.ix = self.parent.det.indexes_x(self.parent.evt)
self.iy = self.parent.det.indexes_y(self.parent.evt)
if self.ix is None:
(_, dim0, dim1) = self.parent.calib.shape
self.iy = np.tile(np.arange(dim0),[dim1, 1])
self.ix = np.transpose(self.iy)
self.iX = np.array(self.ix, dtype=np.int64)
self.iY = np.array(self.iy, dtype=np.int64)
if len(self.iX.shape)==2:
self.iX = np.expand_dims(self.iX,axis=0)
self.iY = np.expand_dims(self.iY,axis=0)
cenX = self.iX[np.array(self.peaks[:,0],dtype=np.int64),np.array(self.peaks[:,1],dtype=np.int64),np.array(self.peaks[:,2],dtype=np.int64)] + 0.5
cenY = self.iY[np.array(self.peaks[:,0],dtype=np.int64),np.array(self.peaks[:,1],dtype=np.int64),np.array(self.peaks[:,2],dtype=np.int64)] + 0.5
self.peaksMaxRes = self.getMaxRes(cenX, cenY, self.parent.cx, self.parent.cy)
diameter = self.peakRadius*2+1
self.parent.img.peak_feature.setData(cenX, cenY, symbol='s', \
size=diameter, brush=(255,255,255,0), \
pen=pg.mkPen({'color': "c", 'width': 4}), pxMode=False) #FF0
# Write number of peaks found
xMargin = 5 # pixels
yMargin = 0 # pixels
maxX = np.max(self.ix) + xMargin
maxY = np.max(self.iy) - yMargin
myMessage = '<div style="text-align: center"><span style="color: cyan; font-size: 12pt;">Peaks=' + \
str(self.numPeaksFound) + ' <br>Res=' + str(int(self.peaksMaxRes)) + '<br></span></div>'
self.parent.img.peak_text = pg.TextItem(html=myMessage, anchor=(0, 0))
self.parent.img.w1.getView().addItem(self.parent.img.peak_text)
self.parent.img.peak_text.setPos(maxX, maxY)
else:
self.parent.img.peak_feature.setData([], [], pxMode=False)
self.parent.img.peak_text = pg.TextItem(html='', anchor=(0, 0))
self.parent.img.w1.getView().addItem(self.parent.img.peak_text)
self.parent.img.peak_text.setPos(0,0)
else:
self.parent.img.peak_feature.setData([], [], pxMode=False)
if self.parent.args.v >= 1: print "Done updatePeaks"
class ROIManager(QObject):
ROI_changed = pyqtSignal()
ROI_changed_finished = pyqtSignal()
new_ROI_signal = pyqtSignal(int, str)
remove_ROI_signal = pyqtSignal(str)
roi_settings_changed = pyqtSignal(list)
roi_update_children = pyqtSignal(list)
color_list = np.array(plot_colors)
def __init__(self, viewer_widget=None, ROI_type='1D'):
super().__init__()
self.ROI_type = ROI_type
self.roiwidget = QtWidgets.QWidget()
self.viewer_widget = viewer_widget # either a PlotWidget or a ImageWidget
self.ROIs = OrderedDict([])
self.setupUI()
def setupUI(self):
vlayout = QtWidgets.QVBoxLayout()
self.roiwidget.setLayout(vlayout)
horwidget = QtWidgets.QWidget()
horlayout = QtWidgets.QHBoxLayout()
horwidget.setLayout(horlayout)
self.save_ROI_pb = QtWidgets.QPushButton('Save ROIs')
self.load_ROI_pb = QtWidgets.QPushButton('Load ROIs')
self.clear_ROI_pb = QtWidgets.QPushButton('Clear ROIs')
horlayout.addWidget(self.save_ROI_pb)
horlayout.addWidget(self.load_ROI_pb)
horlayout.addWidget(self.clear_ROI_pb)
vlayout.addWidget(horwidget)
self.roitree = ParameterTree()
vlayout.addWidget(self.roitree)
self.roiwidget.setMinimumWidth(100)
self.roiwidget.setMaximumWidth(300)
params = [{
'title': 'Measurements:',
'name': 'measurements',
'type': 'table',
'value': OrderedDict([]),
'Ncol': 2,
'header': ["LO", "Value"]
},
ROIScalableGroup(roi_type=self.ROI_type, name="ROIs")]
self.settings = Parameter.create(title='ROIs Settings',
name='rois_settings',
type='group',
children=params)
self.roitree.setParameters(self.settings, showTop=False)
self.settings.sigTreeStateChanged.connect(self.roi_tree_changed)
self.save_ROI_pb.clicked.connect(self.save_ROI)
self.load_ROI_pb.clicked.connect(lambda: self.load_ROI(None))
self.clear_ROI_pb.clicked.connect(self.clear_ROI)
def roi_tree_changed(self, param, changes):
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 == 'childAdded': # new roi to create
par = data[0]
newindex = int(par.name()[-2:])
if par.child(('type')).value() == '1D':
roi_type = ''
pos = self.viewer_widget.plotItem.vb.viewRange()[0]
newroi = LinearROI(index=newindex, pos=pos)
newroi.setZValue(-10)
newroi.setBrush(par.child(('Color')).value())
newroi.setOpacity(0.2)
elif par.child(('type')).value() == '2D':
roi_type = par.child(('roi_type')).value()
xrange = self.viewer_widget.plotItem.vb.viewRange()[0]
yrange = self.viewer_widget.plotItem.vb.viewRange()[1]
width = np.max(((xrange[1] - xrange[0]) / 10, 2))
height = np.max(((yrange[1] - yrange[0]) / 10, 2))
pos = [
int(np.mean(xrange) - width / 2),
int(np.mean(yrange) - width / 2)
]
if roi_type == 'RectROI':
newroi = RectROI(index=newindex,
pos=pos,
size=[width, height])
else:
newroi = EllipseROI(index=newindex,
pos=pos,
size=[width, height])
newroi.setPen(par.child(('Color')).value())
newroi.sigRegionChanged.connect(self.ROI_changed.emit)
newroi.sigRegionChangeFinished.connect(
self.ROI_changed_finished.emit)
newroi.index_signal[int].connect(self.update_roi_tree)
try:
self.settings.sigTreeStateChanged.disconnect()
except Exception:
pass
self.settings.sigTreeStateChanged.connect(
self.roi_tree_changed)
self.viewer_widget.plotItem.addItem(newroi)
self.ROIs["ROI_%02.0d" % newindex] = newroi
self.new_ROI_signal.emit(newindex, roi_type)
self.update_roi_tree(newindex)
elif change == 'value':
if param.name() in putils.iter_children(
self.settings.child(('ROIs')), []):
if param.name() == 'Color' or param.name() == 'angle':
parent = param.parent().name()
else:
parent = param.parent().parent().name()
self.update_roi(parent, param)
elif change == 'parent':
if 'ROI' in param.name():
roi = self.ROIs.pop(param.name())
self.viewer_widget.plotItem.removeItem(roi)
self.remove_ROI_signal.emit(param.name())
if param.name() != 'measurements':
self.roi_settings_changed.emit([(param, 'value', param.value())
])
self.ROI_changed_finished.emit()
def update_roi(self, roi_key, param):
if param.name() == 'Color':
self.ROIs[roi_key].setPen(param.value())
elif param.name() == 'left' or param.name() == 'x':
pos = self.ROIs[roi_key].pos()
poss = [param.value(), pos[1]]
poss.sort()
self.ROIs[roi_key].setPos(poss)
elif param.name() == 'right' or param.name() == 'y':
pos = self.ROIs[roi_key].pos()
poss = [pos[0], param.value()]
poss.sort()
self.ROIs[roi_key].setPos(poss)
elif param.name() == 'angle':
self.ROIs[roi_key].setAngle(param.value())
elif param.name() == 'width':
size = self.ROIs[roi_key].size()
self.ROIs[roi_key].setSize((param.value(), size[1]))
elif param.name() == 'height':
size = self.ROIs[roi_key].size()
self.ROIs[roi_key].setSize((size[0], param.value()))
@pyqtSlot(int)
def update_roi_tree(self, index):
roi = self.ROIs['ROI_%02.0d' % index]
par = self.settings.child(*('ROIs', 'ROI_%02.0d' % index))
if isinstance(roi, LinearROI):
pos = roi.getRegion()
else:
pos = roi.pos()
size = roi.size()
angle = roi.angle()
try:
self.settings.sigTreeStateChanged.disconnect()
except Exception:
pass
if isinstance(roi, LinearROI):
par.child(*('position', 'left')).setValue(pos[0])
par.child(*('position', 'right')).setValue(pos[1])
if not isinstance(roi, LinearROI):
par.child(*('position', 'x')).setValue(pos[0])
par.child(*('position', 'y')).setValue(pos[1])
par.child(*('size', 'width')).setValue(size[0])
par.child(*('size', 'height')).setValue(size[1])
par.child('angle').setValue(angle)
self.settings.sigTreeStateChanged.connect(self.roi_tree_changed)
def save_ROI(self):
try:
data = ioxml.parameter_to_xml_string(self.settings.child(('ROIs')))
path = select_file(start_path=Path.home(), ext='xml')
if path != '':
with open(path, 'wb') as f:
f.write(data)
except Exception as e:
print(e)
def clear_ROI(self):
indexes = [roi.index for roi in self.ROIs.values()]
for index in indexes:
self.settings.child(*('ROIs', 'ROI_%02.0d' % index)).remove()
# self.settings.sigTreeStateChanged.connect(self.roi_tree_changed)
def load_ROI(self, path=None, params=None):
try:
if params is None:
if path is None:
path = select_file(start_path=Path.home(),
save=False,
ext='xml')
if path != '':
params = Parameter.create(
title='Settings',
name='settings',
type='group',
children=ioxml.XML_file_to_parameter(path))
if params is not None:
self.clear_ROI()
QtWidgets.QApplication.processEvents()
for param in params:
if 'roi_type' in putils.iter_children(param, []):
self.settings.child(('ROIs')).addNew(
param.child(('roi_type')).value())
else:
self.settings.child(('ROIs')).addNew()
# self.settings.child(('ROIs')).addChildren(params)
QtWidgets.QApplication.processEvents()
# settings = Parameter.create(title='Settings', name='settings', type='group')
#
# for param in params:
# settings.addChildren(custom_tree.XML_string_to_parameter(custom_tree.parameter_to_xml_string(param)))
self.set_roi(self.settings.child(('ROIs')).children(), params)
except Exception as e:
pass
def set_roi(self, roi_params, roi_params_new):
for child, new_child in zip(roi_params, roi_params_new):
if 'group' not in child.opts['type']:
child.setValue(new_child.value())
else:
self.set_roi(child.children(), new_child.children())
class View(QtGui.QWidget):
def __init__(self, parent=None, with_config=False, **kargs):
QtGui.QWidget.__init__(self, parent)
self.resize(800, 600)
mainlayout = QtGui.QVBoxLayout()
self.setLayout(mainlayout)
self.glview = gl.GLViewWidget()
mainlayout.addWidget(self.glview)
self.glview.setCameraPosition(160, 160, 15)
if with_config:
h = QtGui.QHBoxLayout()
mainlayout.addLayout(h)
but = QtGui.QPushButton('Config',
icon=QtGui.QIcon.fromTheme('configure'))
h.addWidget(but)
but.clicked.connect(self.open_params)
but = QtGui.QPushButton('Save png',
icon=QtGui.QIcon.fromTheme('save'))
h.addWidget(but)
but.clicked.connect(self.open_save_dialog)
_params = [
{
'name': 'cortical_mesh',
'type': 'list',
'values': cortical_meshes.keys(),
'value': 'BrainMesh_ICBM152'
},
{
'name': 'cortical_alpha',
'type': 'float',
'value': .1,
'limits': [0., 1.],
'step': .01
},
{
'name': 'cortical_color',
'type': 'color',
'value': 'w'
},
{
'name': 'background_color',
'type': 'color',
'value': 'k'
},
]
self.params = Parameter.create(name='params',
type='group',
children=_params)
self.tree = ParameterTree(parent=self)
self.tree.setParameters(self.params)
self.tree.setWindowFlags(QtCore.Qt.Dialog)
self.mesh = None
for k, v in kargs.items():
self.params[k] = v
self.change_background_color()
self.plot_mesh()
self.change_color_mesh()
self.params.param('cortical_mesh').sigValueChanged.connect(
self.plot_mesh)
self.params.param('cortical_alpha').sigValueChanged.connect(
self.change_color_mesh)
self.params.param('cortical_color').sigValueChanged.connect(
self.change_color_mesh)
self.params.param('background_color').sigValueChanged.connect(
self.change_background_color)
self.glview.resizeGL(self.glview.width(), self.glview.height())
def open_params(self):
self.tree.show()
def change_background_color(self):
background_color = self.params['background_color']
try:
self.glview.setBackgroundColor(background_color)
except:
#~ #FIXME this is buggy in pyqtgrap0.9.8
bgcolor = pg.mkColor(QtGui.QColor(background_color))
glClearColor(bgcolor.red() / 255.,
bgcolor.green() / 255.,
bgcolor.blue() / 255., 1.0)
glClear(GL_DEPTH_BUFFER_BIT | GL_COLOR_BUFFER_BIT)
self.glview.paintGL()
self.glview.update()
def plot_mesh(self):
vertexes, faces = cortical_meshes[self.params['cortical_mesh']]
alpha = self.params['cortical_alpha']
c = self.params['cortical_color']
color = (c.red() / 255., c.green() / 255., c.blue() / 255., alpha)
if self.mesh is None:
self.mesh = gl.GLMeshItem(
vertexes=vertexes,
faces=faces,
smooth=True,
drawFaces=True,
drawEdges=False,
edgeColor=(1., 1., 1., .2),
color=color,
computeNormals=False,
glOptions='translucent',
#~ shader='balloon',
shader='shaded',
)
self.glview.addItem(self.mesh)
else:
self.mesh.setMeshData(vertexes=vertexes, faces=faces)
#~ self.mesh.set
def change_color_mesh(self):
alpha = self.params['cortical_alpha']
c = self.params['cortical_color']
color = (c.red() / 255., c.green() / 255., c.blue() / 255., alpha)
self.mesh.setColor(color)
def add_node(self, coords, color=(1, 1, 1, 0), size=5):
sp1 = gl.GLScatterPlotItem(pos=coords,
size=size,
color=color,
pxMode=False)
self.glview.addItem(sp1)
def add_edge(self, node_coords, connection_with, color=(1, 1, 1, 1)):
for i in range(connection_with.shape[0]):
for j in range(connection_with.shape[1]):
if connection_with[i, j] == 0: continue
plt = gl.GLLinePlotItem(pos=np.vstack(
[node_coords[i], node_coords[j]]),
color=color,
width=connection_with[i, j])
self.glview.addItem(plt)
def open_save_dialog(self):
pathname = unicode(
QtGui.QDesktopServices.storageLocation(
QtGui.QDesktopServices.DesktopLocation))
filename = os.path.join(pathname, 'Il est beau le cerveau.png')
filename = QtGui.QFileDialog.getSaveFileName(self, u'Save png',
filename, 'PNG (*.png)')
if filename:
self.to_file(filename)
def to_file(self, filename):
self.glview.readQImage().save(filename)
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)
def __init__(self, parent=None, with_config=False, **kargs):
QtGui.QWidget.__init__(self, parent)
self.resize(800, 600)
mainlayout = QtGui.QVBoxLayout()
self.setLayout(mainlayout)
self.glview = gl.GLViewWidget()
mainlayout.addWidget(self.glview)
self.glview.setCameraPosition(160, 160, 15)
if with_config:
h = QtGui.QHBoxLayout()
mainlayout.addLayout(h)
but = QtGui.QPushButton('Config',
icon=QtGui.QIcon.fromTheme('configure'))
h.addWidget(but)
but.clicked.connect(self.open_params)
but = QtGui.QPushButton('Save png',
icon=QtGui.QIcon.fromTheme('save'))
h.addWidget(but)
but.clicked.connect(self.open_save_dialog)
_params = [
{
'name': 'cortical_mesh',
'type': 'list',
'values': cortical_meshes.keys(),
'value': 'BrainMesh_ICBM152'
},
{
'name': 'cortical_alpha',
'type': 'float',
'value': .1,
'limits': [0., 1.],
'step': .01
},
{
'name': 'cortical_color',
'type': 'color',
'value': 'w'
},
{
'name': 'background_color',
'type': 'color',
'value': 'k'
},
]
self.params = Parameter.create(name='params',
type='group',
children=_params)
self.tree = ParameterTree(parent=self)
self.tree.setParameters(self.params)
self.tree.setWindowFlags(QtCore.Qt.Dialog)
self.mesh = None
for k, v in kargs.items():
self.params[k] = v
self.change_background_color()
self.plot_mesh()
self.change_color_mesh()
self.params.param('cortical_mesh').sigValueChanged.connect(
self.plot_mesh)
self.params.param('cortical_alpha').sigValueChanged.connect(
self.change_color_mesh)
self.params.param('cortical_color').sigValueChanged.connect(
self.change_color_mesh)
self.params.param('background_color').sigValueChanged.connect(
self.change_background_color)
self.glview.resizeGL(self.glview.width(), self.glview.height())
def __init__(self, parent=None):
self.parent = parent
## Dock: Hit finder
self.dock = Dock("Hit Finder", size=(1, 1))
self.win = ParameterTree()
self.dock.addWidget(self.win)
self.winL = pg.LayoutWidget()
self.dock.addWidget(self.winL)
# Hit finding
self.spiParam_grp = 'Hit finder'
self.spiParam_algorithm_str = 'Algorithm'
# algorithm 0
self.spiParam_algorithm0_str = 'None'
# algorithm 1
self.spiParam_algorithm1_str = 'chiSquared'
self.spiParam_alg1_pruneInterval_str = 'prune interval'
# algorithm 2
self.spiParam_algorithm2_str = 'photonFinder'
self.spiParam_alg2_threshold_str = 'ADUs per photon'
self.spiParam_alg2_hitThreshold_str = 'Number of pixels for a hit'
self.spiParam_outDir_str = 'Output directory'
self.spiParam_runs_str = 'Run(s)'
self.spiParam_queue_str = 'queue'
self.spiParam_cpu_str = 'CPUs'
self.spiParam_psanaq_str = 'psanaq'
self.spiParam_psnehq_str = 'psnehq'
self.spiParam_psfehq_str = 'psfehq'
self.spiParam_psnehprioq_str = 'psnehprioq'
self.spiParam_psfehprioq_str = 'psfehprioq'
self.spiParam_psnehhiprioq_str = 'psnehhiprioq'
self.spiParam_psfehhiprioq_str = 'psfehhiprioq'
self.spiParam_psdebugq_str = 'psdebugq'
self.spiParam_noe_str = 'Number of events to process'
self.spiParam_launch_str = 'Launch hit finder'
self.hitParam_grp = 'Find hits'
self.hitParam_hitThresh_str = 'Hit threshold'
self.hitParam_backgroundThresh_str = 'Background threshold'
self.hitParam_sample_str = 'Sample name'
self.hitParam_save_str = 'Save hits'
# Init hit finding
self.nPixels = 0
self.spiAlgorithm = 2
self.spiParam_alg1_pruneInterval = -1
self.spiParam_alg2_threshold = 30
self.spiParam_outDir = self.parent.psocakeDir
self.spiParam_outDir_overridden = False
self.spiParam_runs = ''
self.spiParam_queue = self.spiParam_psanaq_str
self.spiParam_cpus = 24
self.spiParam_noe = -1
self.hitParam_hitThresh = '-1'
self.hitParam_backgroundThresh = '-1'
self.hitParam_sample = "sample"
self.params = [
{
'name':
self.spiParam_grp,
'type':
'group',
'children': [
{
'name': self.spiParam_algorithm_str,
'type': 'list',
'values': {
self.spiParam_algorithm2_str: 2,
self.spiParam_algorithm0_str: 0
},
'value': self.spiAlgorithm
},
#{'name': self.spiParam_algorithm1_str, 'visible': True, 'expanded': False, 'type': 'str', 'value': "",
# 'readonly': True, 'children': [
# {'name': self.spiParam_alg1_pruneInterval_str, 'type': 'float', 'value': self.spiParam_alg1_pruneInterval,
# 'tip': "update running background"},
#]},
{
'name':
self.spiParam_algorithm2_str,
'visible':
True,
'expanded':
False,
'type':
'str',
'value':
"",
'readonly':
True,
'children': [
{
'name': self.spiParam_alg2_threshold_str,
'type': 'float',
'value': self.spiParam_alg2_threshold,
'tip': "search for pixels above ADU per photon"
},
]
},
{
'name': self.spiParam_outDir_str,
'type': 'str',
'value': self.spiParam_outDir
},
{
'name':
self.spiParam_runs_str,
'type':
'str',
'value':
self.spiParam_runs,
'tip':
"comma separated or use colon for a range, e.g. 1,3,5:7 = runs 1,3,5,6,7"
},
{
'name': self.spiParam_queue_str,
'type': 'list',
'values': {
self.spiParam_psfehhiprioq_str: 'psfehhiprioq',
self.spiParam_psnehhiprioq_str: 'psnehhiprioq',
self.spiParam_psfehprioq_str: 'psfehprioq',
self.spiParam_psnehprioq_str: 'psnehprioq',
self.spiParam_psfehq_str: 'psfehq',
self.spiParam_psnehq_str: 'psnehq',
self.spiParam_psanaq_str: 'psanaq',
self.spiParam_psdebugq_str: 'psdebugq'
},
'value': self.spiParam_queue,
'tip': "Choose queue"
},
{
'name': self.spiParam_cpu_str,
'type': 'int',
'value': self.spiParam_cpus
},
{
'name':
self.spiParam_noe_str,
'type':
'int',
'value':
self.spiParam_noe,
'tip':
"number of events to process, default=0 means process all events"
},
{
'name': self.spiParam_launch_str,
'type': 'action'
},
]
},
{
'name':
self.hitParam_grp,
'type':
'group',
'children': [
{
'name':
self.hitParam_hitThresh_str,
'type':
'str',
'value':
self.hitParam_hitThresh,
'tip':
"Set as hit if number of pixels with photons above this value. Or specify a range using a colon, e.g. 100:10000."
},
{
'name':
self.hitParam_backgroundThresh_str,
'type':
'str',
'value':
self.hitParam_backgroundThresh,
'tip':
"Use as background if number of pixels with photons below this value. Or specify a range using a colon, e.g. 100:10000."
},
{
'name': self.hitParam_sample_str,
'type': 'str',
'value': self.hitParam_sample
},
{
'name': self.hitParam_save_str,
'type': 'action'
},
]
},
]
self.p8 = Parameter.create(name='paramsHitFinder', type='group', \
children=self.params, expanded=True)
self.win.setParameters(self.p8, showTop=False)
self.p8.sigTreeStateChanged.connect(self.change)
class RosBagWidget(QtGui.QWidget):
##
# @brief
#
# @return
def __init__(self):
QtGui.QWidget.__init__(self)
self.file_name = ''
self.bag = None
self.data = {}
self.plot_data = {}
self.gridLayout = None
self.label1 = None
self.loadBtn = None
self.tree = None
self.addBtn = None
self.editBtn = None
self.removeBtn = None
self.plotBtn = None
self.plotTree = None
self.plotData = None
self.plotwin = None
self.plot_num = 1
self.params = [{
'type':
'group',
'name':
u'plot params',
'children': [{
'type': 'str',
'name': 'x axis name',
'value': u'time(s)'
}, {
'type': 'str',
'name': 'y axis name',
'value': u'position(m)'
}, {
'type': 'str',
'name': 'plot name',
'value': u'plot name'
}]
}]
self.line_mark_list = [
'+-', '*-', 'o-', '^-', 's-', 'x-', '.-', 'p-', 'h-', 'd-'
]
self.msg_types = []
self.topics = {}
self.topics_data = {}
self.msg_types_blacklist = [
'sensor_msgs/PointCloud', 'sensor_msgs/Image'
]
self.setup_ui(self)
##
# @brief
#
# @param Form
#
# @return
def setup_ui(self, Form):
self.setObjectName("Form")
self.resize(217, 499)
self.gridLayout = QtGui.QGridLayout(self)
self.gridLayout.setContentsMargins(0, 0, 0, 0)
self.gridLayout.setVerticalSpacing(0)
self.gridLayout.setObjectName("gridLayout")
self.label1 = QtGui.QLabel("")
self.label1.setTextInteractionFlags(QtCore.Qt.TextEditorInteraction)
self.label1.setStyleSheet("border:1px solid black;")
self.gridLayout.addWidget(self.label1, 0, 0)
self.loadBtn = QtGui.QPushButton("...")
self.loadBtn.setFixedWidth(20)
self.gridLayout.addWidget(self.loadBtn, 0, 1)
self.loadBtn.clicked.connect(self.load_file)
self.tree = DataTreeWidget(data=self.data)
self.gridLayout.addWidget(self.tree, 1, 0, 1, 2)
self.addBtn = QtGui.QPushButton("")
add_icon = QtGui.QIcon()
add_icon.addPixmap(QtGui.QPixmap("resources/add.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.addBtn.setIcon(add_icon)
self.addBtn.clicked.connect(self.add_plot)
self.gridLayout.addWidget(self.addBtn, 0, 2)
self.editBtn = QtGui.QPushButton("")
edit_icon = QtGui.QIcon()
edit_icon.addPixmap(QtGui.QPixmap("resources/edit.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.editBtn.setIcon(edit_icon)
self.editBtn.clicked.connect(self.edit_plot)
self.gridLayout.addWidget(self.editBtn, 0, 3)
self.removeBtn = QtGui.QPushButton("")
remove_icon = QtGui.QIcon()
remove_icon.addPixmap(QtGui.QPixmap("resources/remove.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.removeBtn.setIcon(remove_icon)
self.removeBtn.clicked.connect(self.remove_plot)
self.gridLayout.addWidget(self.removeBtn, 0, 4)
self.plotBtn = QtGui.QPushButton("plot")
# plot_icon = QtGui.QIcon()
# plot_icon.addPixmap(QtGui.QPixmap("resources/plot.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
# self.plotBtn.setIcon(plot_icon)
self.plotBtn.clicked.connect(self.plot)
self.gridLayout.addWidget(self.plotBtn, 0, 5)
self.plotTree = ParameterTree()
self.plotData = Parameter.create(name='params',
type='group',
children=self.params)
self.plotTree.setParameters(self.plotData, showTop=False)
self.gridLayout.addWidget(self.plotTree, 1, 2, 1, 4)
# self.tree2.setSizePolicity(self.tree1.width()/2, 499)
# self.tree1.resize(setWidth(150)
# self.tree2.setWidth(50)
self.plotData.sigTreeStateChanged.connect(self.change)
##
# @brief
#
# @param param
# @param changes
#
# @return
def change(self, param, changes): # todo change plot params
print("tree changes:(to do)")
for param, change, data in changes:
path = self.plotData.childPath(param)
print(path)
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(' ----------')
##
# @brief
#
# @param file_name
# @param start_dir
#
# @return
def load_file(self, file_name=None, start_dir=None):
"""Load a rosbag (*.bag) file.
"""
start = time.clock()
if not file_name:
if not start_dir:
start_dir = '.'
self.file_dialog = FileDialog(None, "Load rosbag ..", start_dir,
"rosbag (*.bag)")
# file_dialog.setAcceptMode(QtGui.QFileDialog.AcceptSave)
self.file_dialog.show()
self.file_dialog.fileSelected.connect(self.load_file)
return
file_name = unicode(file_name)
self.file_name = file_name
self.label1.setText(str(file_name))
self.file_info(file_name)
end = time.clock()
print("load file cost %s s" % (end - start))
##
# @brief
#
# @param file_name
#
# @return
def file_info(self, file_name=None):
if not file_name:
self.data = {}
else:
self.bag = rosbag.Bag(file_name)
self.tree.setData(self.bag.get_type_and_topic_info()[1])
# print(self.bag.get_type_and_topic_info()[1])
bag_length = self.get_bag_length(
self.bag.get_type_and_topic_info()[1]) * 10
if len(file_name) * 8 > bag_length:
bag_length = len(file_name) * 8
self.label1.setFixedWidth(bag_length)
# clear data
self.msg_types = []
self.topics = {}
self.topics_data = {}
# print(self.get_bag_length(self.bag.get_type_and_topic_info()[1]))
for m in self.bag.get_type_and_topic_info()[0]:
self.msg_types.append(m)
for t in self.bag.get_type_and_topic_info()[1]:
if self.bag.get_type_and_topic_info(
)[1][t][0] not in self.msg_types_blacklist:
get_topic_params_cmd = "rostopic echo -b " + file_name + " -n 1 -p " + t
topic_parms = os.popen(get_topic_params_cmd).read()
topic_parms_list = self.topic_str2list(topic_parms)
self.topics[t] = topic_parms_list
get_topic_data_cmd = "rostopic echo -b " + self.file_name + " -p " + t
topic_data = os.popen(get_topic_data_cmd).read()
topic_data_list = self.topic_data_str2list(topic_data[:-1])
self.topics_data[t] = topic_data_list
else:
print(t + "is not proper for plot")
# print("topic_data_list", topic_data_list)
# break
@staticmethod
##
# @brief
#
# @param data
#
# @return
def get_bag_length(data):
max_topic_len = 0
max_topic_type_len = 0
for topic in data:
if len(topic) > max_topic_len:
max_topic_len = len(topic)
if len(data[topic][0]) > max_topic_type_len:
max_topic_type_len = len(data[topic][0])
# print(max_topic_len, max_topic_type_len)
return max_topic_len + max_topic_type_len
@staticmethod
##
# @brief
#
# @param topic_str
#
# @return
def topic_str2list(topic_str):
# print(len(topic_str))
# print(topic_str)
topic_list = []
if len(topic_str) > 0:
# print(topic_str[0])
out1 = re.split('\n', topic_str)
params = re.split(',', out1[0])
values = re.split(',', out1[1])
# print(len(params), len(values))
for i in range(len(params)):
if values[i].strip('-').replace(".", '').isdigit():
topic_list.append(params[i])
# print(topic_list)
return topic_list
@staticmethod
##
# @brief
#
# @param topic_data_str
#
# @return
def topic_data_str2list(topic_data_str):
topic_data_list = []
if len(topic_data_str) > 0:
out1 = re.split('\n', topic_data_str)
for o in out1:
data_list = re.split(',', o)
topic_data_list.append(data_list)
return topic_data_list
##
# @brief
#
# @return
def add_plot(self):
if len(self.file_name):
#print("add plot")
self.plotwin = PlotWin(self.topics, self.plot_num)
self.plotwin.setWindowModality(QtCore.Qt.ApplicationModal)
self.plotwin.setGeometry(500, 500, 600, 150)
if self.plotwin.exec_(): # accepted
#print("ok")
self.plot_num = self.plot_num + 1
if len(self.plotwin.plot_name.text()) > 0:
self.plotwin.param['name'] = unicode(
self.plotwin.plot_name.text()) + " " + unicode(
self.plotwin.topic_name.currentText())
self.plotwin.param['type'] = 'group'
x = {
'name': 'x',
'type': 'str',
'value': unicode(self.plotwin.field1.currentText())
}
y = {
'name': 'y',
'type': 'str',
'value': unicode(self.plotwin.field2.currentText())
}
color = self.plotwin.colorBtn.color(mode='byte')
color_str = ''
for i in color[:-1]:
c = str(hex(i)).replace("0x", '')
if len(c) < 2:
c = '0' + c
color_str = color_str + c
# print(color, color_str)
line_color = {
'name': 'line_color',
'type': 'color',
'value': color_str,
'tip': "This is a color button"
}
line_mark = {
'name': 'line_mark',
'type': 'list',
'values': self.line_mark_list,
'value': unicode(self.plotwin.line_mark.currentText())
}
self.plotwin.param['children'] = [
x, y, line_color, line_mark
]
self.params.append(self.plotwin.param)
self.plotData = Parameter.create(
name='params',
type='group',
children=[self.plotwin.param])
self.plotTree.addParameters(self.plotData, showTop=False)
else:
print("Please input the plot name first.")
else:
print("cancel")
else:
print("Please add bag file first!")
##
# @brief
#
# @return
def edit_plot(self):
# print("edit plot", self.plotTree.selectedItems(), self.plotTree.currentItem())
if hasattr(self.plotTree.currentItem(), "param"):
print("edit plot " + re.split(
'\'', str(getattr(self.plotTree.currentItem(), "param")))[1] +
"(to do)")
# if hasattr(getattr(self.plotTree.currentItem(), "param"), "name"):
# print(getattr(getattr(self.plotTree.currentItem(), "param"), "name"))
# print("%x" % id(self.params[0]))
##
# @brief
#
# @return
def remove_plot(self):
if hasattr(self.plotTree.currentItem(), "param"):
print("remove plot " + re.split(
'\'', str(getattr(self.plotTree.currentItem(), "param")))[1] +
"(to do)")
##
# @brief
#
# @return
def plot(self):
print("plot")
plots = []
for p in self.params[1:]:
topic_name = re.split(' ', p['name'])
# print(topic_name[1])
x_name = None
y_name = None
line_color = None
line_mark = None
for c in p['children']:
if c['name'] == 'x':
x_name = c['value']
elif c['name'] == 'y':
y_name = c['value']
elif c['name'] == 'line_color':
line_color = c['value']
elif c['name'] == 'line_mark':
line_mark = c['value']
plots.append([
topic_name[0], topic_name[1], x_name, y_name, line_color,
line_mark
])
# print(plots)
# plt.figure(figsize=(12, 10))
for p in plots:
x, y = self.get_bag_data(p)
plt.plot(x, y, p[5], color=("#" + p[4]), label=p[0])
plt.xlabel(self.params[0]['children'][0]['value'])
plt.ylabel(self.params[0]['children'][1]['value'])
plt.title(self.params[0]['children'][2]['value'])
# plt.ylim(-1.2, 1.2)
plt.legend(loc='upper right')
plt.grid(True)
# plt.savefig(gflags.FLAGS.title + '.svg', format= 'svg')
plt.show()
##
# @brief
#
# @param plot_info
#
# @return
def get_bag_data(self, plot_info):
x = []
y = []
plot_data = self.topics_data[plot_info[1]]
x_index = plot_data[0].index(plot_info[2])
y_index = plot_data[0].index(plot_info[3])
# print(plot_data, x_index, y_index)
for pd in plot_data[1:]:
# print('len(pd)', len(pd))
# print('x_index', x_index)
# print('y_index', y_index)
x.append(pd[x_index])
y.append(pd[y_index])
# break
return x, y
def create_contenu_dock_pg(self):
self.obj_graph['param']['tree'] = ParameterTree()
self.create_parameter()
self.obj_graph['param']['dock'].addWidget(self.obj_graph['param']
['tree'])
def create_widget(self):
self.widget = ParameterTree(showHeader=False)
self.widget.setParameters(self, showTop=True)
size_policy_preferred = QtGui.QSizePolicy.Preferred
self.widget.setSizePolicy(size_policy_preferred, size_policy_preferred)
return self.widget
class JoystickButtonsSelection(QtWidgets.QDialog):
def __init__(self):
super().__init__()
self.setupUI()
self.selection = None
pygame.init()
pygame.joystick.init()
# width, height = 64 * 10, 64 * 8
# self.screen = pygame.display.set_mode((width, height))
joystick_count = pygame.joystick.get_count()
for ind in range(joystick_count):
joystick = pygame.joystick.Joystick(ind)
joystick.init()
self.startTimer(10)
def timerEvent(self, event):
for event in pygame.event.get(): # User did something.
if 'joy' in event.dict:
self.settings.child(('joystickID')).setValue(event.joy)
self.selection = dict(joy=event.joy)
if event.type == pygame.QUIT: # If user clicked close.
self.reject()
elif event.type == pygame.JOYBUTTONDOWN or event.type == pygame.JOYBUTTONUP:
self.settings.child(('buttonID')).show(True)
self.settings.child(('axisID')).show(False)
self.settings.child(('hatID')).show(False)
self.settings.child(('axis_value')).show(False)
self.settings.child(('hat_value1')).show(False)
self.settings.child(('hat_value2')).show(False)
self.settings.child(('buttonID')).setValue(event.button)
self.selection.update(dict(button=event.button))
elif event.type == pygame.JOYAXISMOTION:
self.settings.child(('buttonID')).show(False)
self.settings.child(('axisID')).show(True)
self.settings.child(('hatID')).show(False)
self.settings.child(('axis_value')).show(True)
self.settings.child(('axisID')).setValue(event.axis)
self.settings.child(('axis_value')).setValue(event.value)
self.settings.child(('hat_value1')).show(False)
self.settings.child(('hat_value2')).show(False)
self.selection.update(dict(axis=event.axis, value=event.value))
elif event.type == pygame.JOYHATMOTION:
self.settings.child(('buttonID')).show(False)
self.settings.child(('axisID')).show(False)
self.settings.child(('hatID')).show(True)
self.settings.child(('axis_value')).show(True)
self.settings.child(('hat_value1')).show(True)
self.settings.child(('hat_value2')).show(True)
self.settings.child(('hat_value1')).setValue(event.value[0])
self.settings.child(('hat_value2')).setValue(event.value[1])
self.selection.update(dict(hat=event.hat, value=event.value))
def setupUI(self):
layout = QtWidgets.QVBoxLayout()
self.setLayout(layout)
label = QtWidgets.QLabel('Press a button or move an axis on the Joystick:')
layout.addWidget(label)
params = [{'title': 'Joystick ID', 'name': 'joystickID', 'type': 'int', 'value': -1},
{'title': 'Button ID', 'name': 'buttonID', 'type': 'int', 'value': -1, 'visible': False},
{'title': 'Axis ID', 'name': 'axisID', 'type': 'int', 'value': -1, 'visible': False},
{'title': 'Value:', 'name': 'axis_value', 'type': 'float', 'value': 0., 'visible': False},
{'title': 'Hat ID', 'name': 'hatID', 'type': 'int', 'value': -1, 'visible': False},
{'title': 'Value x:', 'name': 'hat_value1', 'type': 'int', 'value': 0, 'visible': False},
{'title': 'Value y:', 'name': 'hat_value2', 'type': 'int', 'value': 0, 'visible': False}, ]
self.settings = Parameter.create(name='settings', type='group', children=params)
self.settings_tree = ParameterTree()
# tree.setMinimumWidth(400)
# self.settings_tree.setMinimumHeight(500)
self.settings_tree.setParameters(self.settings, showTop=False)
layout.addWidget(self.settings_tree)
buttonBox = QtWidgets.QDialogButtonBox()
buttonBox.addButton(QtWidgets.QDialogButtonBox.Ok)
buttonBox.addButton(QtWidgets.QDialogButtonBox.Cancel)
layout.addWidget(buttonBox)
buttonBox.accepted.connect(self.accept)
buttonBox.rejected.connect(self.reject)
def setupUi(self, ):
"""
"""
self.gridLayout_2 = QtWidgets.QGridLayout(self)
self.gridLayout_2.setObjectName("gridLayout_2")
self.gridGeneral = QtWidgets.QGridLayout()
self.gridGeneral.setObjectName("gridGeneral")
self.toolBox = QtWidgets.QToolBox(self)
self.toolBox.setFrameShadow(QtWidgets.QFrame.Plain)
self.toolBox.setObjectName("toolBox")
self.model = QtWidgets.QWidget()
self.model.setGeometry(QtCore.QRect(0, 0, 558, 451))
self.model.setObjectName("model")
self.gridLayout_4 = QtWidgets.QGridLayout(self.model)
self.gridLayout_4.setContentsMargins(0, 0, 0, 0)
self.gridLayout_4.setObjectName("gridLayout_4")
self.gridModel = QtWidgets.QGridLayout()
self.gridModel.setContentsMargins(5, 5, 5, 5)
self.gridModel.setSpacing(5)
self.gridModel.setObjectName("gridModel")
self.line = QtWidgets.QFrame(self.model)
self.line.setFrameShape(QtWidgets.QFrame.VLine)
self.line.setFrameShadow(QtWidgets.QFrame.Sunken)
self.line.setObjectName("line")
self.gridModel.addWidget(self.line, 0, 1, 1, 1)
self.openGLWidget = QtWidgets.QOpenGLWidget(self.model)
self.openGLWidget.setObjectName("openGLWidget")
self.gridModel.addWidget(self.openGLWidget, 0, 2, 1, 1)
self.ModelDescriptionTree = ParameterTree(self.model)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(
self.ModelDescriptionTree.sizePolicy().hasHeightForWidth())
self.ModelDescriptionTree.setSizePolicy(sizePolicy)
self.ModelDescriptionTree.setObjectName("ModelDescriptionTree")
self.gridModel.addWidget(self.ModelDescriptionTree, 0, 0, 1, 1)
self.gridLayout_4.addLayout(self.gridModel, 0, 1, 1, 1)
self.toolBox.addItem(self.model, "")
self.param = QtWidgets.QWidget()
self.param.setGeometry(QtCore.QRect(0, 0, 558, 451))
self.param.setObjectName("param")
self.gridLayout_6 = QtWidgets.QGridLayout(self.param)
self.gridLayout_6.setContentsMargins(0, 0, 0, 0)
self.gridLayout_6.setObjectName("gridLayout_6")
self.gridParam = QtWidgets.QGridLayout()
self.gridParam.setContentsMargins(5, 5, 5, 5)
self.gridParam.setSpacing(5)
self.gridParam.setObjectName("gridParam")
self.ParametersTree = ParameterTree(self.param)
self.ParametersTree.setObjectName("ParametersTree")
self.gridParam.addWidget(self.ParametersTree, 0, 0, 1, 1)
self.gridLayout_6.addLayout(self.gridParam, 0, 0, 1, 1)
self.toolBox.addItem(self.param, "")
self.result = QtWidgets.QWidget()
self.result.setObjectName("result")
self.gridLayout_8 = QtWidgets.QGridLayout(self.result)
self.gridLayout_8.setContentsMargins(0, 0, 0, 0)
self.gridLayout_8.setObjectName("gridLayout_8")
self.gridRes = QtWidgets.QGridLayout()
self.gridRes.setContentsMargins(5, 5, 5, 5)
self.gridRes.setSpacing(5)
self.gridRes.setObjectName("gridRes")
self.ResTree = ParameterTree(self.result)
self.ResTree.setObjectName("ResTree")
self.gridRes.addWidget(self.ResTree, 0, 0, 1, 1)
self.gridLayout_8.addLayout(self.gridRes, 0, 0, 1, 1)
self.toolBox.addItem(self.result, "")
self.gridGeneral.addWidget(self.toolBox, 0, 0, 1, 1)
self.gridLayout_2.addLayout(self.gridGeneral, 0, 0, 1, 1)
self.retranslateUi(self)
self.toolBox.setCurrentIndex(2)
class RemoteManager(QObject):
remote_changed = pyqtSignal(dict)
def __init__(self, actuators=[], detectors=[], msgbox=False):
super().__init__()
self.actuators = actuators
self.detectors = detectors
if msgbox:
msgBox = QtWidgets.QMessageBox()
msgBox.setText("Preset Manager?")
msgBox.setInformativeText("What do you want to do?")
cancel_button = msgBox.addButton(QtWidgets.QMessageBox.Cancel)
new_button = msgBox.addButton("New", QtWidgets.QMessageBox.ActionRole)
modify_button = msgBox.addButton('Modify', QtWidgets.QMessageBox.AcceptRole)
msgBox.setDefaultButton(QtWidgets.QMessageBox.Cancel)
ret = msgBox.exec()
if msgBox.clickedButton() == new_button:
self.set_new_remote()
elif msgBox.clickedButton() == modify_button:
path = select_file(start_path=remote_path, save=False, ext='xml')
if path != '':
self.set_file_remote(str(path))
else: # cancel
pass
params = [{'title': 'Activate all', 'name': 'activate_all', 'type': 'action'},
{'title': 'Deactivate all', 'name': 'deactivate_all', 'type': 'action'},
{'title:': 'Actions', 'name': 'action_group', 'type': 'group'}]
self.remote_actions = dict(shortcuts=dict([]), joysticks=dict([]))
self.remote_settings = Parameter.create(title='Remote Settings', name='remote', type='group',
children=params)
self.remote_settings.sigTreeStateChanged.connect(self.remote_settings_changed)
self.remote_settings_tree = ParameterTree()
self.remote_settings_tree.setParameters(self.remote_settings, showTop=False)
self.remote_settings.child(('activate_all')).sigActivated.connect(lambda: self.activate_all(True))
self.remote_settings.child(('deactivate_all')).sigActivated.connect(lambda: self.activate_all(False))
def activate_all(self, activate=True):
for child in self.remote_settings.child(('action_group')).children():
child.setValue(activate)
def set_remote_configuration(self):
# remove existing shorcuts
while len(self.remote_actions['shortcuts']):
self.remote_actions['shortcuts'].pop(list(self.remote_actions['shortcuts'].keys())[0])
while len(self.remote_actions['joysticks']):
self.remote_actions['joysticks'].pop(list(self.remote_actions['joysticks'].keys())[0])
all_actions = []
for child in self.remote_params.child('act_actions').children():
module_name = child.opts['title'].split('Actuator ')[1]
module_type = 'act'
for action in child.child(('actions')).children():
all_actions.append((module_name, action, module_type))
for child in self.remote_params.child('det_actions').children():
module_name = child.opts['title'].split('Detector ')[1]
module_type = 'det'
for action in child.child(('actions')).children():
all_actions.append((module_name, action, module_type))
for ind, action_tuple in enumerate(all_actions):
module, action, module_type = action_tuple
if action.child('remote_type').value() == 'Keyboard':
# stc = QtWidgets.QShortcut(QtGui.QKeySequence(action.child(('shortcut')).value()), self.dockarea)
self.remote_settings.child(('action_group')).addChild(
{'title': f"{module}: {action.child(('action')).value()} "
f"{action.child(('shortcut')).value()}:",
'name': f'shortcut{ind:02d}', 'type': 'led_push', 'value': False})
self.remote_actions['shortcuts'][f'shortcut{ind:02d}'] = \
dict(shortcut=action.child(('shortcut')).value(), activated=False, name=f'shortcut{ind:02d}',
action=action.child(('action')).value(), module_name=module, module_type=module_type)
else:
self.remote_settings.child(('action_group')).addChild(
{'title': f"{module}: {action.child(('action')).value()}=>"
f"J{action.child(('joystickID')).value()}/"
f"{action.child(('actionner_type')).value()}"
f"{action.child(('actionnerID')).value()}:",
'name': f'joy{ind:02d}', 'type': 'led_push', 'value': False})
self.remote_actions['joysticks'][f'joy{ind:02d}'] = \
dict(joystickID=action.child(('joystickID')).value(),
actionner_type=action.child(('actionner_type')).value(),
actionnerID=action.child(('actionnerID')).value(),
activated=False, name=f'joy{ind:02d}',
action=action.child(('action')).value(),
module_name=module, module_type=module_type)
self.activate_all()
def set_new_remote(self, file=None):
if file is None:
file = 'remote_default'
param = [
{'title': 'Filename:', 'name': 'filename', 'type': 'str', 'value': file},
]
params_action = [{'title': 'Actuator Actions:', 'name': 'act_actions', 'type': 'groupmodules',
'addList': self.actuators, 'modtype': 'Actuator'},
{'title': 'Detector Actions:', 'name': 'det_actions', 'type': 'groupmodules',
'addList': self.detectors, 'modtype': 'Detector'}
] # PresetScalableGroupMove(name="Moves")]
self.remote_params = Parameter.create(title='Preset', name='Preset', type='group',
children=param + params_action)
self.remote_params.sigTreeStateChanged.connect(self.parameter_tree_changed)
logger.info('Creating a new remote file')
self.show_remote()
def parameter_tree_changed(self, param, changes):
"""
Check for changes in the given (parameter,change,information) tuple list.
In case of value changed, update the DAQscan_settings tree consequently.
=============== ============================================ ==============================
**Parameters** **Type** **Description**
*param* instance of pyqtgraph parameter the parameter to be checked
*changes* (parameter,change,information) tuple list the current changes state
=============== ============================================ ==============================
"""
for param, change, data in changes:
path = self.remote_params.childPath(param)
if change == 'childAdded':
pass
elif change == 'value':
if param.name() == 'remote_type':
status = data == 'Keyboard'
param.parent().child(('set_shortcut')).show(status)
param.parent().child(('shortcut')).show(status)
param.parent().child(('set_joystick')).show(not status)
param.parent().child(('joystickID')).show(not status)
param.parent().child(('actionner_type')).show(not status)
param.parent().child(('actionnerID')).show(not status)
elif param.name() == 'set_shortcut':
msgBox = ShortcutSelection()
ret = msgBox.exec()
if ret:
param.parent().child(('shortcut')).setValue(msgBox.label.text())
elif param.name() == 'set_joystick':
msgBox = JoystickButtonsSelection()
ret = msgBox.exec()
if ret:
param.parent().child(('joystickID')).setValue(msgBox.selection['joy'])
"""
possible cases: ['Axis', 'Button', 'Hat']
"""
if 'axis' in msgBox.selection:
param.parent().child(('actionner_type')).setValue('Axis')
param.parent().child(('actionnerID')).setValue(msgBox.selection['axis'])
elif 'button' in msgBox.selection:
param.parent().child(('actionner_type')).setValue('Button')
param.parent().child(('actionnerID')).setValue(msgBox.selection['button'])
elif 'hat' in msgBox.selection:
param.parent().child(('actionner_type')).setValue('Hat')
param.parent().child(('actionnerID')).setValue(msgBox.selection['hat'])
elif change == 'parent':
pass
def remote_settings_changed(self, param, changes):
for param, change, data in changes:
path = self.remote_params.childPath(param)
if change == 'childAdded':
pass
elif change == 'value':
if 'shortcut' in param.name():
self.remote_actions['shortcuts'][param.name()]['activated'] = data
self.remote_changed.emit(dict(action_type='shortcut',
action_name=param.name(),
action_dict=self.remote_actions['shortcuts'][param.name()]))
elif 'joy' in param.name():
self.remote_actions['joysticks'][param.name()]['activated'] = data
self.remote_changed.emit(dict(action_type='joystick',
action_name=param.name(),
action_dict=self.remote_actions['joysticks'][param.name()]))
def set_file_remote(self, filename, show=True):
"""
"""
children = ioxml.XML_file_to_parameter(filename)
self.remote_params = Parameter.create(title='Shortcuts:', name='shortcuts', type='group', children=children)
if show:
self.show_remote()
def show_remote(self):
"""
"""
dialog = QtWidgets.QDialog()
vlayout = QtWidgets.QVBoxLayout()
tree = ParameterTree()
# tree.setMinimumWidth(400)
tree.setMinimumHeight(500)
tree.setParameters(self.remote_params, showTop=False)
vlayout.addWidget(tree)
dialog.setLayout(vlayout)
buttonBox = QtWidgets.QDialogButtonBox(parent=dialog)
buttonBox.addButton('Save', buttonBox.AcceptRole)
buttonBox.accepted.connect(dialog.accept)
buttonBox.addButton('Cancel', buttonBox.RejectRole)
buttonBox.rejected.connect(dialog.reject)
vlayout.addWidget(buttonBox)
dialog.setWindowTitle('Fill in information about the actions and their shortcuts')
res = dialog.exec()
if res == dialog.Accepted:
# save preset parameters in a xml file
ioxml.parameter_to_xml_file(
self.remote_params, os.path.join(remote_path, self.remote_params.child('filename').value()))
def widget(self):
widget = ParameterTree()
widget.setParameters(self, showTop=False)
return widget
class SmallData(object):
def __init__(self, parent=None):
self.parent = parent
## Dock: Quantifier
self.dock = Dock("Small Data", size=(100, 100))
self.win = ParameterTree()
self.dock.addWidget(self.win)
self.winL = pg.LayoutWidget()
self.refreshBtn = QtGui.QPushButton('Refresh')
self.winL.addWidget(self.refreshBtn, row=0, col=0)
self.peakogramBtn = QtGui.QPushButton('Peakogram')
self.winL.addWidget(self.peakogramBtn, row=0, col=1)
self.dock.addWidget(self.winL)
# Add plot
self.winP = pg.PlotWidget(title="Metric")
self.dock.addWidget(self.winP)
# Quantifier parameter tree
self.quantifier_grp = 'Small data'
self.quantifier_filename_str = 'filename'
self.quantifier_dataset_str = 'dataset'
self.quantifier_sort_str = 'sort'
# Quantifier
self.quantifier_filename = ''
self.quantifier_dataset = '/entry_1/result_1/'
self.quantifier_sort = False
self.quantifierFileOpen = False
self.quantifierHasData = False
self.params = [
{
'name':
self.quantifier_grp,
'type':
'group',
'children': [
{
'name': self.quantifier_filename_str,
'type': 'str',
'value': self.quantifier_filename,
'tip': "Full path Hdf5 filename"
},
{
'name': self.quantifier_dataset_str,
'type': 'str',
'value': self.quantifier_dataset,
'tip': "Hdf5 dataset metric, nPeaksAll or nHitsAll"
},
{
'name': self.quantifier_sort_str,
'type': 'bool',
'value': self.quantifier_sort,
'tip': "Descending sort metric"
},
]
},
]
self.pSmall = Parameter.create(name='paramsQuantifier', type='group', \
children=self.params, expanded=True)
self.win.setParameters(self.pSmall, showTop=False)
self.pSmall.sigTreeStateChanged.connect(self.change)
if using_pyqt4:
self.parent.connect(self.refreshBtn, QtCore.SIGNAL("clicked()"),
self.reloadQuantifier)
self.parent.connect(self.peakogramBtn, QtCore.SIGNAL("clicked()"),
self.showPeakogram)
else:
self.refreshBtn.clicked.connect(self.reloadQuantifier)
self.peakogramBtn.clicked.connect(self.showPeakogram)
# 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.quantifier_grp:
if path[1] == self.quantifier_filename_str:
self.updateQuantifierFilename(data)
elif path[1] == self.quantifier_dataset_str:
self.updateQuantifierDataset(data)
elif path[1] == self.quantifier_sort_str:
self.updateQuantifierSort(data)
##################################
########### Quantifier ###########
##################################
def reloadQuantifier(self):
self.updateQuantifierFilename(self.quantifier_filename)
self.updateQuantifierDataset(self.quantifier_dataset)
def updateQuantifierFilename(self, data):
self.quantifier_filename = data
if self.parent.args.v >= 1: print "Done opening metric"
def updateQuantifierDataset(self, data):
self.quantifier_dataset = data
if os.path.isfile(self.quantifier_filename):
try:
self.quantifierFile = h5py.File(self.quantifier_filename, 'r')
self.quantifierMetric = self.quantifierFile[
self.quantifier_dataset].value
try:
if self.quantifier_dataset[
0] == '/': # dataset starts with "/"
self.quantifier_eventDataset = self.quantifier_dataset.split(
"/")[1] + "/event"
else: # dataset does not start with "/"
self.quantifier_eventDataset = "/" + self.quantifier_dataset.split(
"/")[0] + "/event"
self.quantifierEvent = self.quantifierFile[
self.quantifier_eventDataset].value
except:
if self.parent.args.v >= 1:
print "Couldn't find /event dataset"
self.quantifierEvent = np.arange(len(
self.quantifierMetric))
self.quantifierFile.close()
self.quantifierInd = np.arange(len(self.quantifierMetric))
self.updateQuantifierSort(self.quantifier_sort)
except:
print "Couldn't read metric"
if self.parent.args.v >= 1: print "Done reading metric"
def updateQuantifierSort(self, data):
self.quantifier_sort = data
try:
if self.quantifier_sort is True:
self.quantifierIndSorted = np.argsort(
self.quantifierMetric)[::-1]
self.quantifierMetricSorted = self.quantifierMetric[
self.quantifierIndSorted]
#self.quantifierEventSorted = self.quantifierMetric[self.quantifierInd]
self.updateQuantifierPlot(self.quantifierMetricSorted)
else:
self.updateQuantifierPlot(self.quantifierMetric)
except:
print "Couldn't sort data"
pass
def updateQuantifierPlot(self, metric):
self.winP.getPlotItem().clear()
if len(np.where(metric == -1)[0]) > 0:
self.curve = self.winP.plot(metric,
pen=(200, 200, 200),
symbolBrush=(255, 0, 0),
symbolPen='k') # red
else: # Every event was processed
self.curve = self.winP.plot(metric,
pen=(200, 200, 200),
symbolBrush=(0, 0, 255),
symbolPen='k') # blue
self.winP.setLabel('left', "Small data")
if self.quantifier_sort:
self.winP.setLabel('bottom', "Sorted Event Index")
else:
self.winP.setLabel('bottom', "Event Index")
self.curve.curve.setClickable(True)
self.curve.sigClicked.connect(self.clicked)
def clicked(self, points):
with pg.BusyCursor():
if self.parent.args.v >= 1:
print("curve clicked", points)
from pprint import pprint
pprint(vars(points.scatter))
for i in range(len(points.scatter.data)):
if points.scatter.ptsClicked[0] == points.scatter.data[i][7]:
ind = i
break
indX = points.scatter.data[i][0]
indY = points.scatter.data[i][1]
if self.parent.args.v >= 1: print "x,y: ", indX, indY
if self.quantifier_sort:
ind = self.quantifierIndSorted[ind]
if self.parent.eventNumber != self.quantifierEvent[ind]:
self.parent.eventNumber = self.quantifierEvent[ind]
self.parent.calib, self.parent.data = self.parent.img.getDetImage(
self.parent.eventNumber)
self.parent.img.win.setImage(self.parent.data,
autoRange=False,
autoLevels=False,
autoHistogramRange=False)
self.parent.exp.p.param(self.parent.exp.exp_grp,
self.parent.exp.exp_evt_str).setValue(
self.parent.eventNumber)
def showPeakogram(self):
if os.path.isfile(self.quantifier_filename):
cmd = "peakogram -i " + self.quantifier_filename
subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
def __init__(self):
super(maintest, self).__init__()
self.values = {
'module 1': module(1),
'module 2': module(2),
'module 3': module(3)
}
self.module = self.values['module 2']
p = [{
'name':
'Module',
'type':
'list',
'values':
self.values,
'set':
self.setmodule,
'get':
self.getmodule,
'childmode':
"root",
'help':
'%namehdr%Boatload of text is possible here. Can use markup too with external help window.'
}, {
'name': 'Rocks to Skips',
'type': 'int',
'value': 0,
'help': 'Another help example',
'helpwnd': None,
'linked': ['1/Rocks to Skips']
}, {
'name': '1/Rocks to Skips',
'type': 'float',
'help': 'Another help example',
'helpwnd': None,
'get': self.getLinked
}]
self.params = Parameter(name='Root', type='group',
children=p).register()
self.params.init()
self.t = ParameterTree()
self.t.addParameters(self.params.getPyQtGraphParameter())
self.test = Parameter(name='Test', type='group')
self.test.addChildren([{
'name': 'baud',
'type': 'int',
'key': 'baud',
'limits': (500, 2000000),
'value': 38400
}])
self.params.append(self.test)
self.test.remove()
self.test.getChild("baud").setValue(500)
self.params.append(self.test)
self.t2 = ParameterTree()
self.params2 = Parameter(name='Root', type='group')
self.params.getChild("Module").stealDynamicParameters(self.params2)
self.t2.addParameters(self.params2._PyQtGraphParameter)
self.params.save("abcde.txt")
self.params.load("abcde.txt")
def __init__(self, parent=None):
self.parent = parent
## Dock: Quantifier
self.dock = Dock("Small Data", size=(100, 100))
self.win = ParameterTree()
self.dock.addWidget(self.win)
self.winL = pg.LayoutWidget()
self.refreshBtn = QtGui.QPushButton('Refresh')
self.winL.addWidget(self.refreshBtn, row=0, col=0)
self.peakogramBtn = QtGui.QPushButton('Peakogram')
self.winL.addWidget(self.peakogramBtn, row=0, col=1)
self.dock.addWidget(self.winL)
# Add plot
self.winP = pg.PlotWidget(title="Metric")
self.dock.addWidget(self.winP)
# Quantifier parameter tree
self.quantifier_grp = 'Small data'
self.quantifier_filename_str = 'filename'
self.quantifier_dataset_str = 'dataset'
self.quantifier_sort_str = 'sort'
# Quantifier
self.quantifier_filename = ''
self.quantifier_dataset = '/entry_1/result_1/'
self.quantifier_sort = False
self.quantifierFileOpen = False
self.quantifierHasData = False
self.params = [
{
'name':
self.quantifier_grp,
'type':
'group',
'children': [
{
'name': self.quantifier_filename_str,
'type': 'str',
'value': self.quantifier_filename,
'tip': "Full path Hdf5 filename"
},
{
'name': self.quantifier_dataset_str,
'type': 'str',
'value': self.quantifier_dataset,
'tip': "Hdf5 dataset metric, nPeaksAll or nHitsAll"
},
{
'name': self.quantifier_sort_str,
'type': 'bool',
'value': self.quantifier_sort,
'tip': "Descending sort metric"
},
]
},
]
self.pSmall = Parameter.create(name='paramsQuantifier', type='group', \
children=self.params, expanded=True)
self.win.setParameters(self.pSmall, showTop=False)
self.pSmall.sigTreeStateChanged.connect(self.change)
if using_pyqt4:
self.parent.connect(self.refreshBtn, QtCore.SIGNAL("clicked()"),
self.reloadQuantifier)
self.parent.connect(self.peakogramBtn, QtCore.SIGNAL("clicked()"),
self.showPeakogram)
else:
self.refreshBtn.clicked.connect(self.reloadQuantifier)
self.peakogramBtn.clicked.connect(self.showPeakogram)
class HitFinder(object):
def __init__(self, parent=None):
self.parent = parent
## Dock: Hit finder
self.dock = Dock("Hit Finder", size=(1, 1))
self.win = ParameterTree()
self.dock.addWidget(self.win)
self.winL = pg.LayoutWidget()
self.dock.addWidget(self.winL)
# Hit finding
self.spiParam_grp = 'Hit finder'
self.spiParam_algorithm_str = 'Algorithm'
# algorithm 0
self.spiParam_algorithm0_str = 'None'
# algorithm 1
self.spiParam_algorithm1_str = 'chiSquared'
self.spiParam_alg1_pruneInterval_str = 'prune interval'
# algorithm 2
self.spiParam_algorithm2_str = 'photonFinder'
self.spiParam_alg2_threshold_str = 'ADUs per photon'
self.spiParam_alg2_hitThreshold_str = 'Number of pixels for a hit'
self.spiParam_outDir_str = 'Output directory'
self.spiParam_runs_str = 'Run(s)'
self.spiParam_queue_str = 'queue'
self.spiParam_cpu_str = 'CPUs'
self.spiParam_psanaq_str = 'psanaq'
self.spiParam_psnehq_str = 'psnehq'
self.spiParam_psfehq_str = 'psfehq'
self.spiParam_psnehprioq_str = 'psnehprioq'
self.spiParam_psfehprioq_str = 'psfehprioq'
self.spiParam_psnehhiprioq_str = 'psnehhiprioq'
self.spiParam_psfehhiprioq_str = 'psfehhiprioq'
self.spiParam_psdebugq_str = 'psdebugq'
self.spiParam_noe_str = 'Number of events to process'
self.spiParam_launch_str = 'Launch hit finder'
self.hitParam_grp = 'Find hits'
self.hitParam_hitThresh_str = 'Hit threshold'
self.hitParam_backgroundThresh_str = 'Background threshold'
self.hitParam_sample_str = 'Sample name'
self.hitParam_save_str = 'Save hits'
# Init hit finding
self.nPixels = 0
self.spiAlgorithm = 2
self.spiParam_alg1_pruneInterval = -1
self.spiParam_alg2_threshold = 30
self.spiParam_outDir = self.parent.psocakeDir
self.spiParam_outDir_overridden = False
self.spiParam_runs = ''
self.spiParam_queue = self.spiParam_psanaq_str
self.spiParam_cpus = 24
self.spiParam_noe = -1
self.hitParam_hitThresh = '-1'
self.hitParam_backgroundThresh = '-1'
self.hitParam_sample = "sample"
self.params = [
{
'name':
self.spiParam_grp,
'type':
'group',
'children': [
{
'name': self.spiParam_algorithm_str,
'type': 'list',
'values': {
self.spiParam_algorithm2_str: 2,
self.spiParam_algorithm0_str: 0
},
'value': self.spiAlgorithm
},
#{'name': self.spiParam_algorithm1_str, 'visible': True, 'expanded': False, 'type': 'str', 'value': "",
# 'readonly': True, 'children': [
# {'name': self.spiParam_alg1_pruneInterval_str, 'type': 'float', 'value': self.spiParam_alg1_pruneInterval,
# 'tip': "update running background"},
#]},
{
'name':
self.spiParam_algorithm2_str,
'visible':
True,
'expanded':
False,
'type':
'str',
'value':
"",
'readonly':
True,
'children': [
{
'name': self.spiParam_alg2_threshold_str,
'type': 'float',
'value': self.spiParam_alg2_threshold,
'tip': "search for pixels above ADU per photon"
},
]
},
{
'name': self.spiParam_outDir_str,
'type': 'str',
'value': self.spiParam_outDir
},
{
'name':
self.spiParam_runs_str,
'type':
'str',
'value':
self.spiParam_runs,
'tip':
"comma separated or use colon for a range, e.g. 1,3,5:7 = runs 1,3,5,6,7"
},
{
'name': self.spiParam_queue_str,
'type': 'list',
'values': {
self.spiParam_psfehhiprioq_str: 'psfehhiprioq',
self.spiParam_psnehhiprioq_str: 'psnehhiprioq',
self.spiParam_psfehprioq_str: 'psfehprioq',
self.spiParam_psnehprioq_str: 'psnehprioq',
self.spiParam_psfehq_str: 'psfehq',
self.spiParam_psnehq_str: 'psnehq',
self.spiParam_psanaq_str: 'psanaq',
self.spiParam_psdebugq_str: 'psdebugq'
},
'value': self.spiParam_queue,
'tip': "Choose queue"
},
{
'name': self.spiParam_cpu_str,
'type': 'int',
'value': self.spiParam_cpus
},
{
'name':
self.spiParam_noe_str,
'type':
'int',
'value':
self.spiParam_noe,
'tip':
"number of events to process, default=0 means process all events"
},
{
'name': self.spiParam_launch_str,
'type': 'action'
},
]
},
{
'name':
self.hitParam_grp,
'type':
'group',
'children': [
{
'name':
self.hitParam_hitThresh_str,
'type':
'str',
'value':
self.hitParam_hitThresh,
'tip':
"Set as hit if number of pixels with photons above this value. Or specify a range using a colon, e.g. 100:10000."
},
{
'name':
self.hitParam_backgroundThresh_str,
'type':
'str',
'value':
self.hitParam_backgroundThresh,
'tip':
"Use as background if number of pixels with photons below this value. Or specify a range using a colon, e.g. 100:10000."
},
{
'name': self.hitParam_sample_str,
'type': 'str',
'value': self.hitParam_sample
},
{
'name': self.hitParam_save_str,
'type': 'action'
},
]
},
]
self.p8 = Parameter.create(name='paramsHitFinder', type='group', \
children=self.params, expanded=True)
self.win.setParameters(self.p8, showTop=False)
self.p8.sigTreeStateChanged.connect(self.change)
# Launch hit finding
def findHits(self):
self.parent.thread.append(LaunchHitFinder.HitFinder(
self.parent)) # send parent parameters with self
self.parent.thread[self.parent.threadCounter].findHits(
self.parent.experimentName, self.parent.runNumber,
self.parent.detInfo)
self.parent.threadCounter += 1
def setThreshold(self):
self.parent.thread.append(
LaunchHitConverter.LaunchHitConverter(
self.parent)) # send parent parameters with self
self.parent.thread[self.parent.threadCounter].launch(
self.parent.experimentName, self.parent.detInfo)
self.parent.threadCounter += 1
# 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.spiParam_grp:
if path[1] == self.spiParam_algorithm_str:
self.spiAlgorithm = data
elif path[1] == self.spiParam_outDir_str:
self.spiParam_outDir = data
self.spiParam_outDir_overridden = True
elif path[1] == self.spiParam_runs_str:
self.spiParam_runs = data
elif path[1] == self.spiParam_queue_str:
self.spiParam_queue = data
elif path[1] == self.spiParam_cpu_str:
self.spiParam_cpus = data
elif path[1] == self.spiParam_noe_str:
self.spiParam_noe = data
elif path[1] == self.spiParam_launch_str:
self.findHits()
elif path[2] == self.spiParam_alg1_pruneInterval_str and path[
1] == self.spiParam_algorithm1_str:
self.spiParam_alg1_pruneInterval = data
self.updateHit()
elif path[2] == self.spiParam_alg2_threshold_str and path[
1] == self.spiParam_algorithm2_str:
self.spiParam_alg2_threshold = data
self.updateHit()
elif path[0] == self.hitParam_grp:
if path[1] == self.hitParam_hitThresh_str:
self.hitParam_hitThresh = data
elif path[1] == self.hitParam_backgroundThresh_str:
self.hitParam_backgroundThresh = data
elif path[1] == self.hitParam_sample_str:
self.hitParam_sample = data
elif path[1] == self.hitParam_save_str:
self.setThreshold()
def updateHit(self):
# Save a temporary mask
if self.parent.mk.userMask is None:
userMask = None
else:
userMask = self.parent.psocakeDir + "/r" + str(
self.parent.runNumber).zfill(4) + "/tempUserMask.npy"
np.save(userMask, self.parent.mk.userMask)
worker = alg.HitFinder(
self.parent.experimentName,
self.parent.runNumber,
self.parent.detInfo,
self.parent.evt,
self.parent.det,
self.spiParam_alg2_threshold,
streakMask_on=str(self.parent.mk.streakMaskOn),
streakMask_sigma=self.parent.mk.streak_sigma,
streakMask_width=self.parent.mk.streak_width,
userMask_path=userMask,
psanaMask_on=str(self.parent.mk.psanaMaskOn),
psanaMask_calib=str(self.parent.mk.mask_calibOn),
psanaMask_status=str(self.parent.mk.mask_statusOn),
psanaMask_edges=str(self.parent.mk.mask_edgesOn),
psanaMask_central=str(self.parent.mk.mask_centralOn),
psanaMask_unbond=str(self.parent.mk.mask_unbondOn),
psanaMask_unbondnrs=str(self.parent.mk.mask_unbondnrsOn))
worker.findHits(self.parent.calib, self.parent.evt)
self.nPixels = worker.nPixels
self.indicatePhotons()
if self.parent.args.v >= 1: print "self.nPixels: ", self.nPixels
def indicatePhotons(self):
self.parent.img.clearPeakMessage()
self.parent.mk.displayMask()
# Write number of pixels found containing photons
xMargin = 5 # pixels
yMargin = 0 # pixels
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: cyan; font-size: 12pt;">Pixels=' + \
str(self.nPixels) + ' <br></span></div>'
self.parent.img.peak_text = pg.TextItem(html=myMessage, anchor=(0, 0))
self.parent.img.w1.getView().addItem(self.parent.img.peak_text)
self.parent.img.peak_text.setPos(maxX, maxY)
else:
childName = param.name()
print(' parameter: %s' % childName)
print(' change: %s' % change)
print(' data: %s' % str(data))
print(' ----------')
if childName == 'Tacq':
print "data: ", data
timer.stop()
timer.setInterval(int(data * 1000) + 10)
Tacq = data
timer.start()
p.sigTreeStateChanged.connect(change)
t = ParameterTree()
t.setParameters(p, showTop=False)
###############
if True:
win = QtGui.QMainWindow()
win.resize(1600, 600)
win.setWindowTitle('window title')
glw = QtGui.QWidget()
#glw = pg.GraphicsLayoutWidget()
l = QtGui.QGridLayout()
glw.setLayout(l)
win.setCentralWidget(glw)
