class MainWindow(QMainWindow):
def __init__(self, parent=None):
super(MainWindow, self).__init__(parent)
self.btn1 = QPushButton("Click me", self)
vbox = QVBoxLayout()
vbox.addWidget(QLabel("A1"))
vbox.addWidget(self.btn1)
vbox.addWidget(QLabel("B2"))
self.btn1.clicked.connect(self.doit)
self.my_pop = None
self.main_widget = QWidget(self)
self.main_widget.setLayout(vbox)
self.setCentralWidget(self.main_widget)
def doit(self):
logger.debug("Opening a new popup window")
self.my_pop = MyReindexOpts()
self.my_pop.set_ref(
in_json_path="/tmp/dui2run/dui_files/lin_4_bravais_summary.json",
lin_num=4)
#in_json_path="/tmp/dui_run/dui_files/lin_4_bravais_summary.json"
def opt_picked(self, opt_num):
logger.debug("\n from dynamic_reindex_gui.py MainWindow")
logger.debug("opt_num = %s %s", opt_num, "\n")
def closeEvent(self, event):
logger.debug("<< closeEvent ( from QMainWindow) >>")
if self.my_pop is not None:
self.my_pop.close()
def __init__(self, url, username, password):
KDialog.__init__(self)
decorateWindow(self, i18n('Create User Account'))
self.setButtons(KDialog.ButtonCode(KDialog.Ok | KDialog.Cancel))
vbox = QVBoxLayout()
grid = QFormLayout()
self.lbServer = QLabel()
self.lbServer.setText(url)
grid.addRow(i18n('Game server:'), self.lbServer)
self.lbUser = QLabel()
grid.addRow(i18n('Username:'******'Password:'******'Repeat password:'), self.edPassword2)
vbox.addLayout(grid)
widget = QWidget(self)
widget.setLayout(vbox)
self.setMainWidget(widget)
pol = QSizePolicy()
pol.setHorizontalPolicy(QSizePolicy.Expanding)
self.lbUser.setSizePolicy(pol)
self.edPassword.textChanged.connect(self.passwordChanged)
self.edPassword2.textChanged.connect(self.passwordChanged)
StateSaver(self)
self.username = username
self.password = password
self.passwordChanged()
self.edPassword2.setFocus()
def set_board_widget(self, board_widget):
self.board_widget = board_widget
layout = QHBoxLayout()
layout.addWidget(board_widget, 2)
layout.addWidget(self.create_sidebar_widget())
central_widget = QWidget(self)
central_widget.setLayout(layout)
self.setCentralWidget(central_widget)
self.repaint()
def setupInputFrame(self, parent=None):
if not parent:
parent = self.layout
self.bgMultiVolumeSelector = slicer.qMRMLNodeComboBox()
self.bgMultiVolumeSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.bgMultiVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.bgMultiVolumeSelector.addEnabled = 0
self._bgMultiVolumeSelectorLabel = QLabel('Input multivolume')
inputFrameWidget = QWidget()
self.inputFrameLayout = QFormLayout()
inputFrameWidget.setLayout(self.inputFrameLayout)
self.inputFrameLayout.addRow(self._bgMultiVolumeSelectorLabel, self.bgMultiVolumeSelector)
parent.addWidget(inputFrameWidget)
def create_sidebar_widget(self):
self.lcd_widget = QLCDNumber(self)
self.lcd_widget.setFixedHeight(100)
self.set_score(0, 0)
self.log_widget = QPlainTextEdit(self)
sidebar = QWidget(self)
sidebar_layout = QVBoxLayout()
sidebar_layout.addWidget(self.lcd_widget)
sidebar_layout.addWidget(self.log_widget)
sidebar.setLayout(sidebar_layout)
sidebar.setFixedWidth(250)
return sidebar
def __init__(self, kongs, deferred):
KDialogIgnoringEscape.__init__(self)
decorateWindow(self)
self.setButtons(0)
self.kongs = kongs
self.selectedKong = None
self.deferred = deferred
layout = QVBoxLayout()
label = QLabel(m18n('Which kong do you want to declare?'))
layout.addWidget(label)
layout.setAlignment(label, Qt.AlignHCenter)
self.buttons = []
for kong in kongs:
button = QRadioButton((kong[0].name()), self)
self.buttons.append(button)
layout.addWidget(button)
button.toggled.connect(self.toggled)
widget = QWidget(self)
widget.setLayout(layout)
self.setMainWidget(widget)
def __init__(self, kongs, deferred):
KDialogIgnoringEscape.__init__(self)
decorateWindow(self)
self.setButtons(0)
self.kongs = kongs
self.selectedKong = None
self.deferred = deferred
layout = QVBoxLayout()
label = QLabel(i18n('Which kong do you want to declare?'))
layout.addWidget(label)
layout.setAlignment(label, Qt.AlignHCenter)
self.buttons = []
for kong in kongs:
button = QRadioButton((kong[0].name()), self)
self.buttons.append(button)
layout.addWidget(button)
button.toggled.connect(self.toggled)
widget = QWidget(self)
widget.setLayout(layout)
self.setMainWidget(widget)
def __init__(self, chows, propose, deferred):
KDialogIgnoringEscape.__init__(self)
decorateWindow(self)
self.setButtons(KDialog.NoButton)
self.chows = chows
self.selectedChow = None
self.deferred = deferred
layout = QVBoxLayout()
label = QLabel(m18n('Which chow do you want to expose?'))
layout.addWidget(label)
layout.setAlignment(label, Qt.AlignHCenter)
self.buttons = []
for chow in chows:
button = QRadioButton('{}-{}-{}'.format(*(x.value for x in chow)))
self.buttons.append(button)
layout.addWidget(button)
layout.setAlignment(button, Qt.AlignHCenter)
button.toggled.connect(self.toggled)
widget = QWidget(self)
widget.setLayout(layout)
self.setMainWidget(widget)
for idx, chow in enumerate(chows):
if chow == propose:
self.buttons[idx].setFocus()
def __init__(self, chows, propose, deferred):
KDialogIgnoringEscape.__init__(self)
decorateWindow(self)
self.setButtons(KDialog.NoButton)
self.chows = chows
self.selectedChow = None
self.deferred = deferred
layout = QVBoxLayout()
label = QLabel(i18n('Which chow do you want to expose?'))
layout.addWidget(label)
layout.setAlignment(label, Qt.AlignHCenter)
self.buttons = []
for chow in chows:
button = QRadioButton('{}-{}-{}'.format(*(x.value for x in chow)))
self.buttons.append(button)
layout.addWidget(button)
layout.setAlignment(button, Qt.AlignHCenter)
button.toggled.connect(self.toggled)
widget = QWidget(self)
widget.setLayout(layout)
self.setMainWidget(widget)
for idx, chow in enumerate(chows):
if chow == propose:
self.buttons[idx].setFocus()
class qSlicerMultiVolumeExplorerSimplifiedModuleWidget:
def __init__(self, parent=None):
logging.debug(
"qSlicerMultiVolumeExplorerSimplifiedModuleWidget:init() called")
if not parent or not hasattr(parent, "layout"):
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(QVBoxLayout())
else:
self.parent = parent
self.layout = self.parent.layout()
self._bgMultiVolumeNode = None
self._fgMultiVolumeNode = None
self.styleObserverTags = []
self.sliceWidgetsPerStyle = {}
self.chartPopupWindow = None
self.chartPopupSize = QSize(600, 300)
self.chartPopupPosition = QPoint(0, 0)
def hide(self):
self.widget.hide()
def show(self):
self.widget.show()
def setup(self):
self.widget = QWidget()
layout = QGridLayout()
self.widget.setLayout(layout)
self.layout.addWidget(self.widget)
self.widget.show()
self.layout = layout
self.setupInputFrame()
self.setupFrameControlFrame()
self.setupAdditionalFrames()
self.setupPlottingFrame()
self.setFramesEnabled(False)
self.timer = QTimer()
self.timer.setInterval(50)
self.setupConnections()
# initialize slice observers (from DataProbe.py)
# keep list of pairs: [observee,tag] so they can be removed easily
self.styleObserverTags = []
# keep a map of interactor styles to sliceWidgets so we can easily get sliceLogic
self.sliceWidgetsPerStyle = {}
self.refreshObservers()
def setupInputFrame(self, parent=None):
if not parent:
parent = self.layout
self.bgMultiVolumeSelector = slicer.qMRMLNodeComboBox()
self.bgMultiVolumeSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.bgMultiVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.bgMultiVolumeSelector.addEnabled = 0
self._bgMultiVolumeSelectorLabel = QLabel('Input multivolume')
inputFrameWidget = QWidget()
self.inputFrameLayout = QFormLayout()
inputFrameWidget.setLayout(self.inputFrameLayout)
self.inputFrameLayout.addRow(self._bgMultiVolumeSelectorLabel,
self.bgMultiVolumeSelector)
parent.addWidget(inputFrameWidget)
def setupFrameControlFrame(self):
# TODO: initialize the slider based on the contents of the labels array
self.frameSlider = ctk.ctkSliderWidget()
self.frameSlider.setSizePolicy(QSizePolicy.Ignored,
QSizePolicy.Preferred)
self.frameLabel = QLabel('Current frame number')
self.playButton = QPushButton('Play')
self.playButton.toolTip = 'Iterate over multivolume frames'
self.playButton.checkable = True
frameControlHBox = QHBoxLayout()
frameControlHBox.addWidget(self.frameLabel)
frameControlHBox.addWidget(self.frameSlider)
frameControlHBox.addWidget(self.playButton)
self.inputFrameLayout.addRow(frameControlHBox)
def setupAdditionalFrames(self):
pass
def setupPlottingFrame(self, parent=None):
if not parent:
parent = self.layout
self.plottingFrameWidget = QWidget()
self.plottingFrameLayout = QGridLayout()
self.plottingFrameWidget.setLayout(self.plottingFrameLayout)
self._multiVolumeIntensityChart = MultiVolumeIntensityChartView()
self.popupChartButton = QPushButton("Undock chart")
self.popupChartButton.setCheckable(True)
self.plottingFrameLayout.addWidget(
self._multiVolumeIntensityChart.chartView)
self.plottingFrameLayout.addWidget(self.popupChartButton)
parent.addWidget(self.plottingFrameWidget)
def setupConnections(self):
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVCMRMLSceneChanged)
self.bgMultiVolumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onBackgroundInputChanged)
self.playButton.connect('toggled(bool)', self.onPlayButtonToggled)
self.frameSlider.connect('valueChanged(double)', self.onSliderChanged)
self.timer.connect('timeout()', self.goToNext)
self.popupChartButton.connect('toggled(bool)',
self.onDockChartViewToggled)
def onDockChartViewToggled(self, checked):
if checked:
self.chartPopupWindow = QDialog()
self.chartPopupWindow.setWindowFlags(
PythonQt.QtCore.Qt.WindowStaysOnTopHint)
layout = QGridLayout()
self.chartPopupWindow.setLayout(layout)
layout.addWidget(self._multiVolumeIntensityChart.chartView)
layout.addWidget(self.popupChartButton)
self.chartPopupWindow.finished.connect(self.dockChartView)
self.chartPopupWindow.resize(self.chartPopupSize)
self.chartPopupWindow.move(self.chartPopupPosition)
self.chartPopupWindow.show()
self.popupChartButton.setText("Dock chart")
self._multiVolumeIntensityChart.chartView.show()
else:
self.chartPopupWindow.close()
def dockChartView(self):
self.chartPopupSize = self.chartPopupWindow.size
self.chartPopupPosition = self.chartPopupWindow.pos
self.plottingFrameLayout.addWidget(
self._multiVolumeIntensityChart.chartView)
self.plottingFrameLayout.addWidget(self.popupChartButton)
self.popupChartButton.setText("Undock chart")
self.popupChartButton.disconnect('toggled(bool)',
self.onDockChartViewToggled)
self.popupChartButton.checked = False
self.popupChartButton.connect('toggled(bool)',
self.onDockChartViewToggled)
def onSliderChanged(self, frameId):
if self._bgMultiVolumeNode is None:
return
newValue = int(frameId)
self.setCurrentFrameNumber(newValue)
def onVCMRMLSceneChanged(self, mrmlScene):
logging.debug(
"qSlicerMultiVolumeExplorerSimplifiedModuleWidget:onVCMRMLSceneChanged"
)
self.bgMultiVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.onBackgroundInputChanged()
def refreshGUIForNewBackgroundImage(self):
self._multiVolumeIntensityChart.reset()
self.setFramesEnabled(True)
if self._fgMultiVolumeNode and self._bgMultiVolumeNode:
Helper.SetBgFgVolumes(self._bgMultiVolumeNode.GetID(),
self._fgMultiVolumeNode.GetID())
else:
Helper.SetBgVolume(self._bgMultiVolumeNode.GetID())
self.refreshFrameSlider()
self._multiVolumeIntensityChart.bgMultiVolumeNode = self._bgMultiVolumeNode
self.refreshObservers()
def getBackgroundMultiVolumeNode(self):
return self.bgMultiVolumeSelector.currentNode()
def onBackgroundInputChanged(self):
self._bgMultiVolumeNode = self.getBackgroundMultiVolumeNode()
if self._bgMultiVolumeNode is not None:
self.refreshGUIForNewBackgroundImage()
else:
self.setFramesEnabled(False)
def onPlayButtonToggled(self, checked):
if self._bgMultiVolumeNode is None:
return
if checked:
self.timer.start()
self.playButton.text = 'Stop'
else:
self.timer.stop()
self.playButton.text = 'Play'
def processEvent(self, observee, event):
# logging.debug("processing event %s" % event)
if self._bgMultiVolumeNode is None:
return
# TODO: use a timer to delay calculation and compress events
if event == 'LeaveEvent':
# reset all the readouts
# TODO: reset the label text
return
if not self.sliceWidgetsPerStyle.has_key(observee):
return
interactor = observee.GetInteractor()
self.createChart(self.sliceWidgetsPerStyle[observee],
interactor.GetEventPosition())
def createChart(self, sliceWidget, position):
self._multiVolumeIntensityChart.createChart(sliceWidget, position)
def setCurrentFrameNumber(self, frameNumber):
mvDisplayNode = self._bgMultiVolumeNode.GetDisplayNode()
mvDisplayNode.SetFrameComponent(frameNumber)
def setFramesEnabled(self, enabled):
pass
def refreshObservers(self):
""" When the layout changes, drop the observers from
all the old widgets and create new observers for the
newly created widgets"""
self.removeObservers()
# get new slice nodes
layoutManager = slicer.app.layoutManager()
sliceNodeCount = slicer.mrmlScene.GetNumberOfNodesByClass(
'vtkMRMLSliceNode')
for nodeIndex in xrange(sliceNodeCount):
# find the widget for each node in scene
sliceNode = slicer.mrmlScene.GetNthNodeByClass(
nodeIndex, 'vtkMRMLSliceNode')
sliceWidget = layoutManager.sliceWidget(sliceNode.GetLayoutName())
if sliceWidget:
# add observers and keep track of tags
style = sliceWidget.sliceView().interactorStyle()
self.sliceWidgetsPerStyle[style] = sliceWidget
events = ("MouseMoveEvent", "EnterEvent", "LeaveEvent")
for event in events:
tag = style.AddObserver(event, self.processEvent)
self.styleObserverTags.append([style, tag])
def removeObservers(self):
for observee, tag in self.styleObserverTags:
observee.RemoveObserver(tag)
self.styleObserverTags = []
self.sliceWidgetsPerStyle = {}
def refreshFrameSlider(self):
self.frameSlider.minimum = 0
if not self._bgMultiVolumeNode:
self.frameSlider.maximum = 0
return
nFrames = self._bgMultiVolumeNode.GetNumberOfFrames()
self.frameSlider.maximum = nFrames - 1
def goToNext(self):
currentElement = self.frameSlider.value
currentElement += 1
if currentElement > self.frameSlider.maximum:
currentElement = 0
self.frameSlider.value = currentElement
def __init__(self, parent=None):
super(InfoWidget, self).__init__()
empty_str = "__________"
beam_group = QGroupBox(" Beam ")
bm_v_layout = QVBoxLayout()
bm_v_layout.addLayout(get_spacebox(130))
xb_label = QLabel(" X (mm) ")
yb_label = QLabel(" Y (mm) ")
bm_label_a_layout = QHBoxLayout()
bm_label_a_layout.addWidget(xb_label)
bm_label_a_layout.addWidget(yb_label)
bm_v_layout.addLayout(bm_label_a_layout)
self.xb_data = QLabel(empty_str)
self.yb_data = QLabel(empty_str)
bm_data_layout = QHBoxLayout()
bm_data_layout.addWidget(self.xb_data)
bm_data_layout.addWidget(self.yb_data)
bm_v_layout.addLayout(bm_data_layout)
bm_v_layout.addWidget(QLabel(" "))
tmp_str = " Wavelength (" + u"\u212B" + ") "
w_lambda_label = QLabel(tmp_str)
bm_v_layout.addWidget(w_lambda_label)
self.w_lambda_data = QLabel(empty_str)
bm_v_layout.addWidget(self.w_lambda_data)
# bm_v_layout.addWidget(QLabel(" "))
# bm_v_layout.addStretch()
beam_group.setLayout(bm_v_layout)
cell_group = QGroupBox(" Crystal ")
cell_v_layout = QVBoxLayout()
cell_v_layout.addLayout(get_spacebox(160))
a_label = QLabel(" a ")
b_label = QLabel(" b ")
c_label = QLabel(" c ")
cell_label_d_layout = QHBoxLayout()
cell_label_d_layout.addWidget(a_label)
cell_label_d_layout.addWidget(b_label)
cell_label_d_layout.addWidget(c_label)
cell_v_layout.addLayout(cell_label_d_layout)
self.a_data = QLabel(empty_str)
self.b_data = QLabel(empty_str)
self.c_data = QLabel(empty_str)
cell_data_layout = QHBoxLayout()
cell_data_layout.addWidget(self.a_data)
cell_data_layout.addWidget(self.b_data)
cell_data_layout.addWidget(self.c_data)
cell_v_layout.addLayout(cell_data_layout)
cell_v_layout.addWidget(QLabel(" "))
left_margin_str = " "
alpha_str = left_margin_str + u"\u03B1"
beta_str = left_margin_str + u"\u03B2"
gamma_str = left_margin_str + u"\u03B3"
alpha_label = QLabel(alpha_str)
beta_label = QLabel(beta_str)
gamma_label = QLabel(gamma_str)
cell_label_a_layout = QHBoxLayout()
cell_label_a_layout.addWidget(alpha_label)
cell_label_a_layout.addWidget(beta_label)
cell_label_a_layout.addWidget(gamma_label)
cell_v_layout.addLayout(cell_label_a_layout)
self.alpha_data = QLabel(empty_str)
self.beta_data = QLabel(empty_str)
self.gamma_data = QLabel(empty_str)
cell_data_layout = QHBoxLayout()
cell_data_layout.addWidget(self.alpha_data)
cell_data_layout.addWidget(self.beta_data)
cell_data_layout.addWidget(self.gamma_data)
cell_v_layout.addLayout(cell_data_layout)
cell_v_layout.addWidget(QLabel(" "))
spgrp_label = QLabel(" Space Group")
self.spgrp_data = QLabel(empty_str)
spgrp_hbox = QHBoxLayout()
spgrp_hbox.addWidget(spgrp_label)
spgrp_hbox.addWidget(self.spgrp_data)
cell_v_layout.addLayout(spgrp_hbox)
r_layout = QVBoxLayout()
r_layout.addWidget(QLabel(" "))
r_layout.addWidget(QLabel(" Orientation (deg) "))
r_label_layout = QHBoxLayout()
r1_label = QLabel(" rot X")
r2_label = QLabel(" rot Y")
r3_label = QLabel(" rot Z")
r_label_layout.addWidget(r1_label)
r_label_layout.addWidget(r2_label)
r_label_layout.addWidget(r3_label)
r_data_layout = QHBoxLayout()
self.r1_data = QLabel(empty_str)
self.r2_data = QLabel(empty_str)
self.r3_data = QLabel(empty_str)
r_data_layout.addWidget(self.r1_data)
r_data_layout.addWidget(self.r2_data)
r_data_layout.addWidget(self.r3_data)
r_layout.addLayout(r_label_layout)
r_layout.addLayout(r_data_layout)
crys_v_layout = QVBoxLayout()
crys_v_layout.addLayout(cell_v_layout)
crys_v_layout.addLayout(r_layout)
# crys_v_layout.addStretch()
cell_group.setLayout(crys_v_layout)
scan_group = QGroupBox(" Scan ")
scan_v_layout = QVBoxLayout()
scan_v_layout.addLayout(get_spacebox(180))
scan_v_layout.addWidget(QLabel(" Image Range "))
img_ran_h_layout = QHBoxLayout()
img_ran1_v_layout = QVBoxLayout()
# img_ran1_label = QLabel(" from")
self.img_ran1_data = QLabel(empty_str)
# img_ran1_v_layout.addWidget(img_ran1_label)
img_ran1_v_layout.addWidget(self.img_ran1_data)
img_ran2_v_layout = QVBoxLayout()
# img_ran2_label = QLabel(" to")
self.img_ran2_data = QLabel(empty_str)
# img_ran2_v_layout.addWidget(img_ran2_label)
img_ran2_v_layout.addWidget(self.img_ran2_data)
img_ran_h_layout.addLayout(img_ran1_v_layout)
img_ran_h_layout.addLayout(img_ran2_v_layout)
scan_v_layout.addLayout(img_ran_h_layout)
scan_v_layout.addWidget(QLabel(" "))
oscil_h_layout = QHBoxLayout()
oscil1_v_layout = QVBoxLayout()
oscil_h_layout.addWidget(QLabel("Oscillation "))
oscil2_v_layout = QVBoxLayout()
# oscil2_label = QLabel(" to ")
self.oscil2_data = QLabel(empty_str)
# oscil2_v_layout.addWidget(oscil2_label)
oscil2_v_layout.addWidget(self.oscil2_data)
oscil_h_layout.addLayout(oscil1_v_layout)
oscil_h_layout.addLayout(oscil2_v_layout)
scan_v_layout.addLayout(oscil_h_layout)
e_time_label = QLabel("Exposure Time")
self.e_time_data = QLabel(empty_str)
e_time_hbox = QHBoxLayout()
e_time_hbox.addWidget(e_time_label)
e_time_hbox.addWidget(self.e_time_data)
scan_v_layout.addLayout(e_time_hbox)
scan_v_layout.addWidget(QLabel(" "))
strn_sp_label = QLabel("Strong Spots")
self.strn_sp_data = QLabel(empty_str)
strn_hbox = QHBoxLayout()
strn_hbox.addWidget(strn_sp_label)
strn_hbox.addWidget(self.strn_sp_data)
scan_v_layout.addLayout(strn_hbox)
# scan_v_layout.addWidget(QLabel(" "))
indx_sp_label = QLabel("Indexed Spots")
self.indx_sp_data = QLabel(empty_str)
indx_hbox = QHBoxLayout()
indx_hbox.addWidget(indx_sp_label)
indx_hbox.addWidget(self.indx_sp_data)
scan_v_layout.addLayout(indx_hbox)
# scan_v_layout.addWidget(QLabel(" "))
refn_sp_label = QLabel("Refined Spots")
self.refn_sp_data = QLabel(empty_str)
refn_hbox = QHBoxLayout()
refn_hbox.addWidget(refn_sp_label)
refn_hbox.addWidget(self.refn_sp_data)
scan_v_layout.addLayout(refn_hbox)
# scan_v_layout.addWidget(QLabel(" "))
itgr_prf_label = QLabel("Prof int Spots")
self.itgr_prf_data = QLabel(empty_str)
itgr_prf_hbox = QHBoxLayout()
itgr_prf_hbox.addWidget(itgr_prf_label)
itgr_prf_hbox.addWidget(self.itgr_prf_data)
scan_v_layout.addLayout(itgr_prf_hbox)
# scan_v_layout.addWidget(QLabel(" "))
itgr_sum_label = QLabel("Sum int Spots")
self.itgr_sum_data = QLabel(empty_str)
itgr_sum_hbox = QHBoxLayout()
itgr_sum_hbox.addWidget(itgr_sum_label)
itgr_sum_hbox.addWidget(self.itgr_sum_data)
scan_v_layout.addLayout(itgr_sum_hbox)
scan_v_layout.addStretch()
scan_group.setLayout(scan_v_layout)
detec_group = QGroupBox(" Detector ")
detec_v_layout = QVBoxLayout()
detec_v_layout.addLayout(get_spacebox(160))
# detec_v_layout.addWidget(QLabel(" "))
d_dist_label = QLabel(" Distance (mm)")
self.d_dist_data = QLabel(empty_str)
d_dist_hbox = QHBoxLayout()
d_dist_hbox.addWidget(d_dist_label)
d_dist_hbox.addWidget(self.d_dist_data)
detec_v_layout.addLayout(d_dist_hbox)
# detec_v_layout.addWidget(QLabel(" "))
n_pans_label = QLabel(" Number of Panels ")
self.n_pans_data = QLabel(empty_str)
n_pans_hbox = QHBoxLayout()
n_pans_hbox.addWidget(n_pans_label)
n_pans_hbox.addWidget(self.n_pans_data)
detec_v_layout.addLayout(n_pans_hbox)
# detec_v_layout.addWidget(QLabel(" "))
gain_label = QLabel(" Gain ")
self.gain_data = QLabel(empty_str)
gain_hbox = QHBoxLayout()
gain_hbox.addWidget(gain_label)
gain_hbox.addWidget(self.gain_data)
detec_v_layout.addLayout(gain_hbox)
# detec_v_layout.addWidget(QLabel(" "))
max_res_label = QLabel(" Max res (" + u"\u212B" + ")")
self.max_res_data = QLabel(empty_str)
max_res_hbox = QHBoxLayout()
max_res_hbox.addWidget(max_res_label)
max_res_hbox.addWidget(self.max_res_data)
detec_v_layout.addLayout(max_res_hbox)
detec_v_layout.addWidget(QLabel(" "))
pix_size_label = QLabel(" Pixel Size ")
detec_v_layout.addWidget(pix_size_label)
px_h_layout = QHBoxLayout()
px_x_v_layout = QVBoxLayout()
x_px_size_label = QLabel(" X (mm)")
self.x_px_size_data = QLabel(empty_str)
px_x_v_layout.addWidget(x_px_size_label)
px_x_v_layout.addWidget(self.x_px_size_data)
px_y_v_layout = QVBoxLayout()
y_px_size_label = QLabel(" Y (mm)")
self.y_px_size_data = QLabel(empty_str)
px_y_v_layout.addWidget(y_px_size_label)
px_y_v_layout.addWidget(self.y_px_size_data)
px_h_layout.addLayout(px_x_v_layout)
px_h_layout.addLayout(px_y_v_layout)
detec_v_layout.addLayout(px_h_layout)
# detec_v_layout.addWidget(QLabel(" "))
# detec_v_layout.addStretch()
detec_group.setLayout(detec_v_layout)
left_big_box = QHBoxLayout()
left_big_box.addWidget(beam_group)
left_big_box.addWidget(cell_group)
left_big_box.addStretch()
right_big_box = QHBoxLayout()
right_big_box.addWidget(detec_group)
right_big_box.addWidget(scan_group)
right_big_box.addStretch()
inner_main_h_box = QVBoxLayout()
inner_main_h_box.addLayout(left_big_box)
inner_main_h_box.addLayout(right_big_box)
self.my_json_path = None
self.my_pikl_path = None
self.update_data(exp_json_path=self.my_json_path,
refl_pikl_path=self.my_pikl_path)
self.my_scrollable = QScrollArea()
tmp_widget = QWidget()
tmp_widget.setLayout(inner_main_h_box)
self.my_scrollable.setWidget(tmp_widget)
main_v_box = QVBoxLayout()
main_v_box.addWidget(self.my_scrollable)
self.setLayout(main_v_box)
def __init__(self):
super(MainWidget, self).__init__()
self.my_pop = None # Any child popup windows. Only bravais_table ATM
self.storage_path = sys_arg.directory
refresh_gui = False
# Load the previous state of DUI, if present
dui_files_path = os.path.join(self.storage_path, "dui_files")
if os.path.isfile(os.path.join(dui_files_path, "bkp.pickle")):
try:
self.idials_runner = load_previous_state(dui_files_path)
except Exception as e:
# Something went wrong - tell the user then close
msg = traceback.format_exc()
logger.error("ERROR LOADING PREVIOUS DATA:\n%s", msg)
raise_from(DUIDataLoadingError(msg), e)
refresh_gui = True
else:
# No dui_files path - start with a fresh state
if not os.path.isdir(dui_files_path):
os.mkdir(dui_files_path)
self.idials_runner = Runner()
self.gui2_log = {"pairs_list": []}
self.cli_tree_output = TreeShow()
self.cli_tree_output(self.idials_runner)
self.cur_html = None
self.cur_pick = None
self.cur_json = None
self.cur_log = None
self.cur_cmd_name = "None"
main_box = QVBoxLayout()
self.centre_par_widget = ControlWidget()
self.centre_par_widget.pass_sys_arg_object_to_import(sys_arg)
self.stop_run_retry = StopRunRetry()
self.tree_out = TreeNavWidget()
left_control_box = QHBoxLayout()
left_top_control_box = QVBoxLayout()
left_top_control_box.addWidget(self.centre_par_widget)
left_top_control_box.addStretch()
left_control_box.addLayout(left_top_control_box)
centre_control_box = QVBoxLayout()
v_control_splitter = QSplitter()
v_control_splitter.setOrientation(Qt.Vertical)
v_control_splitter.addWidget(self.tree_out)
v_control_splitter.addWidget(self.centre_par_widget.step_param_widg)
centre_control_box.addWidget(v_control_splitter)
centre_control_box.addWidget(self.stop_run_retry)
left_control_box.addLayout(centre_control_box)
dummy_left_widget = QWidget()
dummy_h_layout = QHBoxLayout()
dummy_h_layout.addLayout(left_control_box)
dummy_left_widget.setLayout(dummy_h_layout)
dummy_left_widget.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
h_main_splitter = QSplitter()
h_main_splitter.setOrientation(Qt.Horizontal)
h_main_splitter.addWidget(dummy_left_widget)
self.cli_out = CliOutView()
self.web_view = WebTab()
self.img_view = MyImgWin()
self.ext_view = OuterCaller()
self.info_widget = InfoWidget()
self.output_info_tabs = QTabWidget()
self.output_info_tabs.addTab(self.img_view, "Image")
self.output_info_tabs.addTab(self.cli_out, "Log")
self.output_info_tabs.addTab(self.web_view, "Report")
self.output_info_tabs.addTab(self.ext_view, "Tools")
self.output_info_tabs.addTab(self.info_widget, "Experiment")
self.view_tab_num = 0
self.output_info_tabs.currentChanged.connect(self.tab_changed)
self.img_view.mask_applied.connect(self.pop_mask_list)
self.img_view.predic_changed.connect(self.tab_changed)
self.img_view.bc_applied.connect(self.pop_b_centr_coord)
self.img_view.new_pars_applied.connect(self.pass_parmams)
# self.ext_view.pass_parmam_lst.connect(self.pass_parmams)
self.centre_par_widget.finished_masking.connect(self.img_view.unchec_my_mask)
self.centre_par_widget.click_mask.connect(self.img_view.chec_my_mask)
self.centre_par_widget.finished_b_centr.connect(self.img_view.unchec_b_centr)
self.centre_par_widget.click_b_centr.connect(self.img_view.chec_b_centr)
v_info_splitter = QSplitter()
v_info_splitter.setOrientation(Qt.Vertical)
v_info_splitter.addWidget(self.output_info_tabs)
h_main_splitter.addWidget(v_info_splitter)
main_box.addWidget(h_main_splitter)
self.txt_bar = Text_w_Bar()
main_box.addWidget(self.txt_bar)
self.connect_all()
self.custom_thread = CommandThread()
self.custom_thread.finished.connect(self.update_after_finished)
self.custom_thread.str_fail_signal.connect(self.after_failed)
self.custom_thread.str_print_signal.connect(self.cli_out.add_txt)
self.custom_thread.str_print_signal.connect(self.txt_bar.setText)
self.custom_thread.busy_box_on.connect(self.pop_busy_box)
self.custom_thread.busy_box_off.connect(self.close_busy_box)
self.main_widget = QWidget()
self.main_widget.setLayout(main_box)
self.setCentralWidget(self.main_widget)
self.setWindowTitle("CCP4 DUI - {}: {}".format(__version__,
dui_files_path))
self.setWindowIcon(QIcon(self.stop_run_retry.dials_logo_path))
self.just_reindexed = False
self.user_stoped = False
self.reconnect_when_ready()
self.my_pop = None
if refresh_gui:
self.refresh_my_gui()
class MainWidget(QMainWindow):
def __init__(self):
super(MainWidget, self).__init__()
self.my_pop = None # Any child popup windows. Only bravais_table ATM
self.storage_path = sys_arg.directory
refresh_gui = False
# Load the previous state of DUI, if present
dui_files_path = os.path.join(self.storage_path, "dui_files")
if os.path.isfile(os.path.join(dui_files_path, "bkp.pickle")):
try:
self.idials_runner = load_previous_state(dui_files_path)
except Exception as e:
# Something went wrong - tell the user then close
msg = traceback.format_exc()
logger.error("ERROR LOADING PREVIOUS DATA:\n%s", msg)
raise_from(DUIDataLoadingError(msg), e)
refresh_gui = True
else:
# No dui_files path - start with a fresh state
if not os.path.isdir(dui_files_path):
os.mkdir(dui_files_path)
self.idials_runner = Runner()
self.gui2_log = {"pairs_list": []}
self.cli_tree_output = TreeShow()
self.cli_tree_output(self.idials_runner)
self.cur_html = None
self.cur_pick = None
self.cur_json = None
self.cur_log = None
self.cur_cmd_name = "None"
main_box = QVBoxLayout()
self.centre_par_widget = ControlWidget()
self.centre_par_widget.pass_sys_arg_object_to_import(sys_arg)
self.stop_run_retry = StopRunRetry()
self.tree_out = TreeNavWidget()
left_control_box = QHBoxLayout()
left_top_control_box = QVBoxLayout()
left_top_control_box.addWidget(self.centre_par_widget)
left_top_control_box.addStretch()
left_control_box.addLayout(left_top_control_box)
centre_control_box = QVBoxLayout()
v_control_splitter = QSplitter()
v_control_splitter.setOrientation(Qt.Vertical)
v_control_splitter.addWidget(self.tree_out)
v_control_splitter.addWidget(self.centre_par_widget.step_param_widg)
centre_control_box.addWidget(v_control_splitter)
centre_control_box.addWidget(self.stop_run_retry)
left_control_box.addLayout(centre_control_box)
dummy_left_widget = QWidget()
dummy_h_layout = QHBoxLayout()
dummy_h_layout.addLayout(left_control_box)
dummy_left_widget.setLayout(dummy_h_layout)
dummy_left_widget.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
h_main_splitter = QSplitter()
h_main_splitter.setOrientation(Qt.Horizontal)
h_main_splitter.addWidget(dummy_left_widget)
self.cli_out = CliOutView()
self.web_view = WebTab()
self.img_view = MyImgWin()
self.ext_view = OuterCaller()
self.info_widget = InfoWidget()
self.output_info_tabs = QTabWidget()
self.output_info_tabs.addTab(self.img_view, "Image")
self.output_info_tabs.addTab(self.cli_out, "Log")
self.output_info_tabs.addTab(self.web_view, "Report")
self.output_info_tabs.addTab(self.ext_view, "Tools")
self.output_info_tabs.addTab(self.info_widget, "Experiment")
self.view_tab_num = 0
self.output_info_tabs.currentChanged.connect(self.tab_changed)
self.img_view.mask_applied.connect(self.pop_mask_list)
self.img_view.predic_changed.connect(self.tab_changed)
self.img_view.bc_applied.connect(self.pop_b_centr_coord)
self.img_view.new_pars_applied.connect(self.pass_parmams)
# self.ext_view.pass_parmam_lst.connect(self.pass_parmams)
self.centre_par_widget.finished_masking.connect(self.img_view.unchec_my_mask)
self.centre_par_widget.click_mask.connect(self.img_view.chec_my_mask)
self.centre_par_widget.finished_b_centr.connect(self.img_view.unchec_b_centr)
self.centre_par_widget.click_b_centr.connect(self.img_view.chec_b_centr)
v_info_splitter = QSplitter()
v_info_splitter.setOrientation(Qt.Vertical)
v_info_splitter.addWidget(self.output_info_tabs)
h_main_splitter.addWidget(v_info_splitter)
main_box.addWidget(h_main_splitter)
self.txt_bar = Text_w_Bar()
main_box.addWidget(self.txt_bar)
self.connect_all()
self.custom_thread = CommandThread()
self.custom_thread.finished.connect(self.update_after_finished)
self.custom_thread.str_fail_signal.connect(self.after_failed)
self.custom_thread.str_print_signal.connect(self.cli_out.add_txt)
self.custom_thread.str_print_signal.connect(self.txt_bar.setText)
self.custom_thread.busy_box_on.connect(self.pop_busy_box)
self.custom_thread.busy_box_off.connect(self.close_busy_box)
self.main_widget = QWidget()
self.main_widget.setLayout(main_box)
self.setCentralWidget(self.main_widget)
self.setWindowTitle("CCP4 DUI - {}: {}".format(__version__,
dui_files_path))
self.setWindowIcon(QIcon(self.stop_run_retry.dials_logo_path))
self.just_reindexed = False
self.user_stoped = False
self.reconnect_when_ready()
self.my_pop = None
if refresh_gui:
self.refresh_my_gui()
def pop_mask_list(self, mask_itm_lst):
tmp_cmd_lst = build_mask_command_lst(mask_itm_lst)
self.centre_par_widget.mask_page.set_par(tmp_cmd_lst)
self.centre_par_widget.step_param_widg.setCurrentWidget(
self.centre_par_widget.mask_page
)
def pop_b_centr_coord(self, new_b_centr):
logger.info("New b_centr =", new_b_centr)
self.centre_par_widget.b_centr_page.set_par(new_b_centr)
self.centre_par_widget.step_param_widg.setCurrentWidget(
self.centre_par_widget.b_centr_page
)
def connect_all(self):
self.setCursor(Qt.ArrowCursor)
self.tree_clickable = True
self.tree_out.clicked[QModelIndex].connect(self.node_clicked)
self.stop_run_retry.repeat_btn.clicked.connect(self.rep_clicked)
self.stop_run_retry.run_btn.clicked.connect(self.run_clicked)
self.stop_run_retry.stop_btn.clicked.connect(self.stop_clicked)
self.centre_par_widget.user_changed.connect(self.cmd_changed_by_user)
self.centre_par_widget.update_command_lst_high_level.connect(
self.update_low_level_command_lst
)
self.centre_par_widget.step_param_widg.currentChanged.connect(
self.cmd_changed_by_any
)
self.check_gray_outs()
def disconnect_while_running(self):
self.setCursor(Qt.BusyCursor)
self.tree_clickable = False
self.stop_run_retry.repeat_btn.setEnabled(False)
self.stop_run_retry.run_btn.setEnabled(False)
self.stop_run_retry.stop_btn.setEnabled(True)
self.centre_par_widget.gray_outs_all()
self.centre_par_widget.step_param_widg.currentWidget().my_widget.gray_me_out()
self.user_stoped = False
def reconnect_when_ready(self):
self.setCursor(Qt.ArrowCursor)
self.tree_clickable = True
self.stop_run_retry.repeat_btn.setEnabled(False)
self.stop_run_retry.stop_btn.setEnabled(False)
self.stop_run_retry.run_btn.setEnabled(False)
if self.user_stoped:
self.idials_runner.current_node.success = None
my_widget = self.centre_par_widget.step_param_widg.currentWidget().my_widget
if self.idials_runner.current_node.success is None:
self.stop_run_retry.run_btn.setEnabled(True)
my_widget.activate_me(cur_nod=self.idials_runner.current_node)
else:
if self.idials_runner.current_node.ll_command_lst[0][0] != "export":
self.stop_run_retry.repeat_btn.setEnabled(True)
my_widget.gray_me_out()
if self.idials_runner.current_node.ll_command_lst[0][0] == "reindex":
self.stop_run_retry.run_btn.setEnabled(False)
self.stop_run_retry.repeat_btn.setEnabled(False)
self.check_gray_outs()
self.user_stoped = False
self.update_nav_tree()
def chouse_if_predict_or_report(self):
if (
self.idials_runner.current_node.ll_command_lst[0][0]
!= "refine_bravais_settings"
):
if self.view_tab_num == 0 and self.img_view.rad_but_pre_hkl.checkState():
self.pop_busy_box(text_in_bar="Generating Predictions")
self.idials_runner.current_node.gen_repr_n_pred(to_run="predict")
self.close_busy_box()
elif self.view_tab_num == 2:
"""
##########################################################################
tmp_bar = ProgBarBox(min_val=0, max_val=10, text=text_in_bar)
tmp_bar(5)
tmp_bar.ended()
################################################################################
"""
tmp_bar = ProgBarBox(min_val=0, max_val=10, text="Generating Report")
tmp_bar(5)
self.idials_runner.current_node.gen_repr_n_pred(to_run="report")
tmp_bar.ended()
def tab_changed(self, num=0):
self.view_tab_num = num
self.chouse_if_predict_or_report()
update_info(self)
def pass_parmams(self, cmd_lst):
"""(We've been passed a parameter by the external tool signal)"""
current_parameter_widget = (
self.centre_par_widget.step_param_widg.currentWidget()
)
action_name = current_parameter_widget.my_widget.command_lst[0][0]
to_remove = """
if (
action_name in ["find_spots", "integrate"]
and self.idials_runner.current_node.success is None
):
"""
if (
action_name == "find_spots"
and self.idials_runner.current_node.success is None
):
gain = cmd_lst[0]
size = cmd_lst[1]
nsig_b = cmd_lst[2]
nsig_s = cmd_lst[3]
global_threshold = cmd_lst[4]
min_count = cmd_lst[5]
full_command = [
"find_spots",
"spotfinder.threshold.dispersion.gain=" + str(gain),
"spotfinder.threshold.dispersion.kernel_size="
+ str(size[0])
+ ","
+ str(size[1]),
"spotfinder.threshold.dispersion.sigma_background=" + str(nsig_b),
"spotfinder.threshold.dispersion.sigma_strong=" + str(nsig_s),
"spotfinder.threshold.dispersion.min_local=" + str(min_count),
"spotfinder.threshold.dispersion.global_threshold="
+ str(global_threshold),
]
current_parameter_widget.my_widget.update_param_w_lst(full_command)
else:
logger.debug("No need to feed back params")
"""
logger.info(
"my_widget_now.my_widget.command_lst = %s",
current_parameter_widget.my_widget.command_lst,
)
"""
def update_low_level_command_lst(self, command_lst):
self.idials_runner.current_node.ll_command_lst = command_lst
self.reconnect_when_ready()
def cmd_changed_by_user(self, my_label):
logger.debug("cmd_changed_by_user()")
tmp_curr = self.idials_runner.current_node
if tmp_curr.success is True:
self.cmd_exe(["mkchi"])
self.idials_runner.current_node.ll_command_lst = [[str(my_label)]]
self.centre_par_widget.step_param_widg.currentWidget().my_widget.reset_par()
path_to_mask_pickle = None
if self.idials_runner.current_node.ll_command_lst[0][0] == "integrate":
logger.debug("Running: try_find_prev_mask_pickle")
path_to_mask_pickle = try_find_prev_mask_pickle(
self.idials_runner.current_node
)
if path_to_mask_pickle is not None:
self.pass_parmams(["lookup.mask=" + path_to_mask_pickle])
self.cmd_exe(["clean"])
elif tmp_curr.success is None:
self.idials_runner.current_node.ll_command_lst[0] = [str(my_label)]
self.reconnect_when_ready()
def cmd_changed_by_any(self):
tmp_curr_widg = self.centre_par_widget.step_param_widg.currentWidget()
self.cur_cmd_name = tmp_curr_widg.my_widget.command_lst[0][0]
self.reconnect_when_ready()
def rep_clicked(self):
logger.debug("rep_clicked")
self.cmd_exe(["mksib"])
self.cmd_exe(["clean"])
self.check_gray_outs()
def stop_clicked(self):
logger.debug("\n\n <<< Stop clicked >>> \n\n")
# TODO fix spelling on << dials_command >>
pr_to_kill = self.idials_runner.current_node.dials_command.my_pid
logger.debug(
"self.idials_runner.current_node.dials_command.my_pid = %s", pr_to_kill
)
self.user_stoped = True
kill_w_child(pr_to_kill)
def run_clicked(self):
logger.debug("run_clicked")
logger.debug(
"...currentWidget(ref) = %s",
self.centre_par_widget.step_param_widg.currentWidget(),
)
self.img_view.draw_img_img()
cmd_tmp = (
self.centre_par_widget.step_param_widg.currentWidget().my_widget.command_lst
)
self.cmd_launch(cmd_tmp)
def cmd_exe(self, new_cmd):
# Running NOT in parallel
update_info(self)
self.idials_runner.run(command=new_cmd, ref_to_class=None)
self.check_reindex_pop()
self.reconnect_when_ready()
def cmd_launch(self, new_cmd):
# Running WITH threading
self.cli_out.clear()
self.cli_out.make_green()
self.txt_bar.start_motion()
self.txt_bar.setText("Running")
self.disconnect_while_running()
self.custom_thread(new_cmd, self.idials_runner)
def update_after_finished(self):
self.chouse_if_predict_or_report()
update_info(self)
self.txt_bar.end_motion()
self.just_reindexed = False
tmp_curr = self.idials_runner.current_node
prn_lst_lst_cmd(tmp_curr)
if (
tmp_curr.ll_command_lst[0][0] == "refine_bravais_settings"
and tmp_curr.success is True
):
self.idials_runner.run(command=["mkchi"], ref_to_class=None)
self.idials_runner.current_node.ll_command_lst = [["reindex"]]
elif tmp_curr.ll_command_lst[0][0] == "reindex" and tmp_curr.success is True:
self.just_reindexed = True
try:
self.my_pop.close()
except BaseException as e:
# We don't want to catch bare exceptions but don't know
# what this was supposed to catch. Log it.
logger.debug(
"Caught unknown exception type %s: %s", type(e).__name__, e
)
logger.debug("no need to close reindex table")
elif tmp_curr.ll_command_lst[0][0] == "export" and tmp_curr.success is True:
self.gui2_log = try_move_last_info(tmp_curr, self.gui2_log)
self.check_reindex_pop()
self.check_gray_outs()
self.reconnect_when_ready()
if (
tmp_curr.ll_command_lst[0][0] == "generate_mask"
and tmp_curr.success is True
):
self.img_view.my_painter.reset_mask_tool(None)
elif (
tmp_curr.ll_command_lst[0][0] == "modify_geometry"
and tmp_curr.success is True
):
self.img_view.my_painter.reset_bc_tool(None)
with open(self.storage_path + "/dui_files/bkp.pickle", "wb") as bkp_out:
pickle.dump(self.idials_runner, bkp_out)
def pop_busy_box(self, text_in_bar):
#logger.info("OPENING busy pop bar with the text: ", text_in_bar)
if (
self.idials_runner.current_node.ll_command_lst[0][0]
!= "refine_bravais_settings"
):
self.my_bar = ProgBarBox(min_val=0, max_val=10, text=text_in_bar)
self.my_bar(5)
def close_busy_box(self):
logger.info("trying to close busy pop bar")
try:
self.my_bar.ended()
except AttributeError:
logger.info("no need to close busy pop bar")
def check_gray_outs(self):
tmp_curr = self.idials_runner.current_node
if tmp_curr.success is not True:
tmp_curr = tmp_curr.prev_step
# TODO fix "generate_mask" and "modify_geometry" : it should be the same as the previous step
# This dictionary defines which tasks can be performed at each step and
# which should be grayed out
cmd_connects = {
"Root": ["import"],
"import": ["find_spots"],
"find_spots": ["index"],
"index": ["refine_bravais_settings", "refine", "integrate"],
"refine_bravais_settings": [None],
"reindex": ["refine", "integrate", "index"],
"refine": [
"refine_bravais_settings",
"refine",
"integrate",
"index",
],
"integrate": ["symmetry", "scale", "export", "index", "export"],
"symmetry": ["refine_bravais_settings", "scale", "export"],
"scale": ["refine_bravais_settings", "symmetry", "export"],
"export": [None],
"generate_mask": ["find_spots"],
"modify_geometry": ["find_spots"],
"None": [None],
}
more_conservative = """
cmd_connects = {
"Root": ["import"],
"import": ["find_spots"],
"find_spots": ["index"],
"index": ["refine_bravais_settings", "refine", "integrate"],
"refine_bravais_settings": [None],
"reindex": ["refine", "integrate"],
"refine": ["refine_bravais_settings", "refine", "integrate"],
"integrate": ["symmetry", "scale", "export"],
"symmetry": ["scale", "export"],
"scale": ["symmetry", "export"],
"export": [None],
"generate_mask": ["find_spots"],
"modify_geometry":["find_spots"],
"None": [None],
}
"""
lst_nxt = cmd_connects[str(tmp_curr.ll_command_lst[0][0])]
self.centre_par_widget.gray_outs_from_lst(lst_nxt)
def check_reindex_pop(self):
tmp_curr = self.idials_runner.current_node
#logger.info("\n_________________________ check_reindex_pop 01 \n")
if tmp_curr.ll_command_lst[0][0] == "reindex" and not self.just_reindexed:
#logger.info("\n_________________________ check_reindex_pop 02 \n")
try:
self.my_pop = MyReindexOpts()
self.my_pop.set_ref(
in_json_path=tmp_curr.prev_step.json_file_out,
lin_num=tmp_curr.prev_step.lin_num,
)
self.my_pop.my_inner_table.opt_signal.connect(self.opt_dobl_clicked)
except Exception as my_err:
logger.info("ERROR in check_reindex_pop(m_idials_gui) \n")
logger.info("str(my_err) = ", str(my_err))
logger.info("my_err.__doc__ = ", my_err.__doc__)
logger.info("my_err.message = ", my_err.message)
# TODO find an elegant way to interrupt and remove nodes
else:
try:
self.my_pop.close()
except BaseException as e:
# We don't want to catch bare exceptions but don't know
# what this was supposed to catch. Log it.
logger.debug(
"Caught unknown exception type %s: %s", type(e).__name__, e
)
logger.debug("no need to close reindex table")
self.just_reindexed = False
def update_nav_tree(self):
self.tree_out.update_me(
self.idials_runner.step_list[0], self.idials_runner.current_line
)
update_pbar_msg(self)
self.img_view.my_painter.repaint()
def after_failed(self):
logger.info("\n FAILED STEP:")
self.update_nav_tree()
self.txt_bar.end_motion()
curr_step = self.idials_runner.current_node
for err_lin in curr_step.dials_command.tmp_std_all:
logger.debug(err_lin)
err_log_file_out = (
self.storage_path
+ "/dui_files"
+ os.sep
+ str(curr_step.lin_num)
+ "_err_out.log"
)
logger.info("\n ERROR \n err_log_file_out = %s %s", err_log_file_out, "\n")
fil_obj = open(err_log_file_out, "w")
for err_lin in curr_step.dials_command.tmp_std_all:
fil_obj.write(err_lin)
fil_obj.write("\n")
fil_obj.close()
self.idials_runner.current_node.err_file_out = err_log_file_out
def opt_dobl_clicked(self, row):
re_idx = row + 1
logger.debug("Solution clicked = %s", re_idx)
cmd_tmp = ["reindex", "solution=" + str(re_idx)]
self.cmd_launch([cmd_tmp])
def node_clicked(self, it_index):
logger.debug("\n it_index = %s", it_index)
logger.debug(" type(it_index) = %s", type(it_index))
if self.tree_clickable:
# TODO Think of a more robust way to "disconnect" ... next line
try:
self.centre_par_widget.update_command_lst_high_level.disconnect(
self.update_low_level_command_lst
)
except BaseException as e:
# We don't want to catch bare exceptions but don't know
# what this was supposed to catch. Log it.
logger.info(" Caught unknown exception type %s: %s", type(e).__name__, e)
logger.info("\n Tst A1 \n")
item = self.tree_out.std_mod.itemFromIndex(it_index)
prn_lst_lst_cmd(item.idials_node)
lin_num = item.idials_node.lin_num
cmd_ovr = "goto " + str(lin_num)
self.cmd_exe(cmd_ovr)
self.centre_par_widget.set_widget(
nxt_cmd=item.idials_node.ll_command_lst[0][0],
curr_step=self.idials_runner.current_node,
)
self.check_reindex_pop()
self.chouse_if_predict_or_report()
update_info(self)
self.check_gray_outs()
self.reconnect_when_ready()
self.centre_par_widget.update_command_lst_high_level.connect(
self.update_low_level_command_lst
)
def refresh_my_gui(self):
lin_num = self.idials_runner.current_node.lin_num
logger.debug("doing goto: %s", lin_num)
cmd_ovr = "goto " + str(lin_num)
self.cmd_exe(cmd_ovr)
self.centre_par_widget.set_widget(
nxt_cmd=self.idials_runner.current_node.ll_command_lst[0][0],
curr_step=self.idials_runner.current_node,
)
self.check_reindex_pop()
self.chouse_if_predict_or_report()
update_info(self)
self.check_gray_outs()
self.reconnect_when_ready()
logger.info("\n ... recovering from previous run of GUI \n")
def closeEvent(self, event):
if self.my_pop:
self.my_pop.close()
class qSlicerMultiVolumeExplorerSimplifiedModuleWidget:
def __init__(self, parent=None):
logging.debug("qSlicerMultiVolumeExplorerSimplifiedModuleWidget:init() called")
if not parent or not hasattr(parent, "layout"):
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(QVBoxLayout())
else:
self.parent = parent
self.layout = self.parent.layout()
self._bgMultiVolumeNode = None
self._fgMultiVolumeNode = None
self.styleObserverTags = []
self.sliceWidgetsPerStyle = {}
self.chartPopupWindow = None
self.chartPopupSize = QSize(600, 300)
self.chartPopupPosition = QPoint(0,0)
def hide(self):
self.widget.hide()
def show(self):
self.widget.show()
def setup(self):
self.widget = QWidget()
layout = QGridLayout()
self.widget.setLayout(layout)
self.layout.addWidget(self.widget)
self.widget.show()
self.layout = layout
self.setupInputFrame()
self.setupFrameControlFrame()
self.setupAdditionalFrames()
self.setupPlottingFrame()
self.setFramesEnabled(False)
self.timer = QTimer()
self.timer.setInterval(50)
self.setupConnections()
# initialize slice observers (from DataProbe.py)
# keep list of pairs: [observee,tag] so they can be removed easily
self.styleObserverTags = []
# keep a map of interactor styles to sliceWidgets so we can easily get sliceLogic
self.sliceWidgetsPerStyle = {}
self.refreshObservers()
def setupInputFrame(self, parent=None):
if not parent:
parent = self.layout
self.bgMultiVolumeSelector = slicer.qMRMLNodeComboBox()
self.bgMultiVolumeSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.bgMultiVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.bgMultiVolumeSelector.addEnabled = 0
self._bgMultiVolumeSelectorLabel = QLabel('Input multivolume')
inputFrameWidget = QWidget()
self.inputFrameLayout = QFormLayout()
inputFrameWidget.setLayout(self.inputFrameLayout)
self.inputFrameLayout.addRow(self._bgMultiVolumeSelectorLabel, self.bgMultiVolumeSelector)
parent.addWidget(inputFrameWidget)
def setupFrameControlFrame(self):
# TODO: initialize the slider based on the contents of the labels array
self.frameSlider = ctk.ctkSliderWidget()
self.frameLabel = QLabel('Current frame number')
self.playButton = QPushButton('Play')
self.playButton.toolTip = 'Iterate over multivolume frames'
self.playButton.checkable = True
frameControlHBox = QHBoxLayout()
frameControlHBox.addWidget(self.frameLabel)
frameControlHBox.addWidget(self.frameSlider)
frameControlHBox.addWidget(self.playButton)
self.inputFrameLayout.addRow(frameControlHBox)
def setupAdditionalFrames(self):
pass
def setupPlottingFrame(self, parent=None):
if not parent:
parent = self.layout
self.plottingFrameWidget = QWidget()
self.plottingFrameLayout = QGridLayout()
self.plottingFrameWidget.setLayout(self.plottingFrameLayout)
self._multiVolumeIntensityChart = MultiVolumeIntensityChartView()
self.popupChartButton = QPushButton("Undock chart")
self.popupChartButton.setCheckable(True)
self.plottingFrameLayout.addWidget(self._multiVolumeIntensityChart.chartView)
self.plottingFrameLayout.addWidget(self.popupChartButton)
parent.addWidget(self.plottingFrameWidget)
def setupConnections(self):
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)', self.onVCMRMLSceneChanged)
self.bgMultiVolumeSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onBackgroundInputChanged)
self.playButton.connect('toggled(bool)', self.onPlayButtonToggled)
self.frameSlider.connect('valueChanged(double)', self.onSliderChanged)
self.timer.connect('timeout()', self.goToNext)
self.popupChartButton.connect('toggled(bool)', self.onDockChartViewToggled)
def onDockChartViewToggled(self, checked):
if checked:
self.chartPopupWindow = QDialog()
self.chartPopupWindow.setWindowFlags(PythonQt.QtCore.Qt.WindowStaysOnTopHint)
layout = QGridLayout()
self.chartPopupWindow.setLayout(layout)
layout.addWidget(self._multiVolumeIntensityChart.chartView)
layout.addWidget(self.popupChartButton)
self.chartPopupWindow.finished.connect(self.dockChartView)
self.chartPopupWindow.resize(self.chartPopupSize)
self.chartPopupWindow.move(self.chartPopupPosition)
self.chartPopupWindow.show()
self.popupChartButton.setText("Dock chart")
self._multiVolumeIntensityChart.chartView.show()
else:
self.chartPopupWindow.close()
def dockChartView(self):
self.chartPopupSize = self.chartPopupWindow.size
self.chartPopupPosition = self.chartPopupWindow.pos
self.plottingFrameLayout.addWidget(self._multiVolumeIntensityChart.chartView)
self.plottingFrameLayout.addWidget(self.popupChartButton)
self.popupChartButton.setText("Undock chart")
self.popupChartButton.disconnect('toggled(bool)', self.onDockChartViewToggled)
self.popupChartButton.checked = False
self.popupChartButton.connect('toggled(bool)', self.onDockChartViewToggled)
def onSliderChanged(self, frameId):
if self._bgMultiVolumeNode is None:
return
newValue = int(frameId)
self.setCurrentFrameNumber(newValue)
def onVCMRMLSceneChanged(self, mrmlScene):
logging.debug("qSlicerMultiVolumeExplorerSimplifiedModuleWidget:onVCMRMLSceneChanged")
self.bgMultiVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.onBackgroundInputChanged()
def refreshGUIForNewBackgroundImage(self):
self._multiVolumeIntensityChart.reset()
self.setFramesEnabled(True)
if self._fgMultiVolumeNode and self._bgMultiVolumeNode:
Helper.SetBgFgVolumes(self._bgMultiVolumeNode.GetID(), self._fgMultiVolumeNode.GetID())
else:
Helper.SetBgVolume(self._bgMultiVolumeNode.GetID())
self.refreshFrameSlider()
self._multiVolumeIntensityChart.bgMultiVolumeNode = self._bgMultiVolumeNode
self.refreshObservers()
def getBackgroundMultiVolumeNode(self):
return self.bgMultiVolumeSelector.currentNode()
def onBackgroundInputChanged(self):
self._bgMultiVolumeNode = self.getBackgroundMultiVolumeNode()
if self._bgMultiVolumeNode is not None:
self.refreshGUIForNewBackgroundImage()
else:
self.setFramesEnabled(False)
def onPlayButtonToggled(self, checked):
if self._bgMultiVolumeNode is None:
return
if checked:
self.timer.start()
self.playButton.text = 'Stop'
else:
self.timer.stop()
self.playButton.text = 'Play'
def processEvent(self, observee, event):
# logging.debug("processing event %s" % event)
if self._bgMultiVolumeNode is None:
return
# TODO: use a timer to delay calculation and compress events
if event == 'LeaveEvent':
# reset all the readouts
# TODO: reset the label text
return
if not self.sliceWidgetsPerStyle.has_key(observee):
return
interactor = observee.GetInteractor()
self.createChart(self.sliceWidgetsPerStyle[observee], interactor.GetEventPosition())
def createChart(self, sliceWidget, position):
self._multiVolumeIntensityChart.createChart(sliceWidget, position)
def setCurrentFrameNumber(self, frameNumber):
mvDisplayNode = self._bgMultiVolumeNode.GetDisplayNode()
mvDisplayNode.SetFrameComponent(frameNumber)
def setFramesEnabled(self, enabled):
pass
def refreshObservers(self):
""" When the layout changes, drop the observers from
all the old widgets and create new observers for the
newly created widgets"""
self.removeObservers()
# get new slice nodes
layoutManager = slicer.app.layoutManager()
sliceNodeCount = slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLSliceNode')
for nodeIndex in xrange(sliceNodeCount):
# find the widget for each node in scene
sliceNode = slicer.mrmlScene.GetNthNodeByClass(nodeIndex, 'vtkMRMLSliceNode')
sliceWidget = layoutManager.sliceWidget(sliceNode.GetLayoutName())
if sliceWidget:
# add observers and keep track of tags
style = sliceWidget.sliceView().interactorStyle()
self.sliceWidgetsPerStyle[style] = sliceWidget
events = ("MouseMoveEvent", "EnterEvent", "LeaveEvent")
for event in events:
tag = style.AddObserver(event, self.processEvent)
self.styleObserverTags.append([style,tag])
def removeObservers(self):
for observee,tag in self.styleObserverTags:
observee.RemoveObserver(tag)
self.styleObserverTags = []
self.sliceWidgetsPerStyle = {}
def refreshFrameSlider(self):
self.frameSlider.minimum = 0
if not self._bgMultiVolumeNode:
self.frameSlider.maximum = 0
return
nFrames = self._bgMultiVolumeNode.GetNumberOfFrames()
self.frameSlider.maximum = nFrames - 1
def goToNext(self):
currentElement = self.frameSlider.value
currentElement += 1
if currentElement > self.frameSlider.maximum:
currentElement = 0
self.frameSlider.value = currentElement
