def on_loadImagesPushButton_clicked(self):
''' Load the current batch of images into the list
'''
selmodel = self.ui.imageListView.selectionModel()
self.disconnect(
selmodel,
QtCore.SIGNAL(
"selectionChanged(const QItemSelection &, const QItemSelection &)"
), self.onSelectionChanged)
ImageViewerWindow.on_loadImagesPushButton_clicked(self)
selmodel = self.ui.imageListView.selectionModel()
self.connect(
selmodel,
QtCore.SIGNAL(
"selectionChanged(const QItemSelection &, const QItemSelection &)"
), self.onSelectionChanged)
def registerPage(self, wizardPage):
'''
'''
wizardPage.registerField(
wizardPage.wizard().param("raw_reference_file*"),
self.ui.referenceLineEdit)
wizardPage.registerField(wizardPage.wizard().param("curr_apix*"),
self.ui.referencePixelSizeDoubleSpinBox,
"value",
QtCore.SIGNAL('valueChanged(double)'))
def setup(self):
''' Display specific setup
'''
selmodel = self.ui.imageListView.selectionModel()
self.connect(
selmodel,
QtCore.SIGNAL(
"selectionChanged(const QItemSelection &, const QItemSelection &)"
), self.onSelectionChanged)
self.ui.imageListView.setStyleSheet(
'QListView::item:selected{ color: #008000; border: 3px solid #6FFF00; }'
)
def registerPage(self, wizardPage):
'''
'''
wizardPage.registerField("sessions*", self, "selected",
QtCore.SIGNAL('selectionChanged()'))
def __init__(self, parent=None):
"Initialize a image display window"
QtGui.QMainWindow.__init__(self, parent)
# Setup logging
root = logging.getLogger()
while len(root.handlers) > 0:
root.removeHandler(root.handlers[0])
h = logging.StreamHandler()
h.setFormatter(logging.Formatter('%(message)s'))
root.addHandler(h)
# Build window
_logger.info("\rBuilding main window ...")
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
# Setup variables
self.lastpath = str(QtCore.QDir.currentPath())
self.coordinates_files = []
self.stack_file = ""
self.inifile = "" #'ara_view.ini'
self.data = None
self.header = None
self.group_indices = None
self.label_cols = []
self.rtsq_cols = []
self.select_col = -1
self.markers = ['s', 'o', '^', '>', 'v', 'd', 'p', 'h', '8', '+', 'x']
self.selectedImage = None
# Setup Plotting View
self.fig = Figure((6.0, 4.0)) #, dpi=self.ui.dpiSpinBox.value())
self.ui.canvas = FigureCanvas(self.fig)
self.ui.canvas.setParent(self.ui.centralwidget)
self.axes = self.fig.add_subplot(111)
self.ui.centralHLayout.addWidget(self.ui.canvas)
self.ui.centralHLayout.setStretchFactor(self.ui.canvas, 4)
#self.ui.canvas.mpl_connect('motion_notify_event', self.onHover)
self.ui.canvas.mpl_connect('pick_event', self.displayLabel)
self.annotation = None
# Setup Navigation Tool Bar
self.ui.mpl_toolbar = NavigationToolbar(self.ui.canvas, self)
self.ui.mpl_toolbar.hide()
self.addToolBar(QtCore.Qt.TopToolBarArea, self.ui.mpl_toolbar)
if not hasattr(self.ui.mpl_toolbar, 'edit_parameters'):
self.ui.toolBar.removeAction(self.ui.actionShow_Options)
# Custom Actions
self.ui.toggleImageDockAction = self.ui.imageDockWidget.toggleViewAction(
)
icon8 = QtGui.QIcon()
icon8.addPixmap(QtGui.QPixmap(":/mini/mini/image.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.toggleImageDockAction.setIcon(icon8)
self.ui.toolBar.insertAction(self.ui.actionShow_Options,
self.ui.toggleImageDockAction)
self.ui.imageDockWidget.hide()
self.ui.toggleImageDockAction.setEnabled(False)
action = self.ui.plotDockWidget.toggleViewAction()
icon8 = QtGui.QIcon()
icon8.addPixmap(QtGui.QPixmap(":/mini/mini/chart_line.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
action.setIcon(icon8)
self.ui.toolBar.insertAction(self.ui.actionShow_Options, action)
self.ui.toggleAdvancedDockAction = self.ui.advancedDockWidget.toggleViewAction(
)
icon8 = QtGui.QIcon()
icon8.addPixmap(QtGui.QPixmap(":/mini/mini/cog_edit.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.toggleAdvancedDockAction.setIcon(icon8)
self.ui.toolBar.insertAction(self.ui.actionShow_Options,
self.ui.toggleAdvancedDockAction)
self.ui.advancedDockWidget.hide()
action = self.ui.fileDockWidget.toggleViewAction()
icon8 = QtGui.QIcon()
icon8.addPixmap(QtGui.QPixmap(":/mini/mini/folder_explore.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
action.setIcon(icon8)
self.ui.toolBar.insertAction(self.ui.actionShow_Options, action)
# Create advanced settings
property.setView(self.ui.advancedSettingsTreeView)
self.advanced_settings, self.advanced_names = self.ui.advancedSettingsTreeView.model(
).addOptionList(self.advancedSettings())
self.ui.advancedSettingsTreeView.setStyleSheet(
'QTreeView::item[readOnly="true"]{ color: #000000; }')
for i in xrange(
self.ui.advancedSettingsTreeView.model().rowCount() - 1, 0,
-1):
if self.ui.advancedSettingsTreeView.model().index(
i, 0).internalPointer().isReadOnly(
): # Hide widget items (read only)
self.ui.advancedSettingsTreeView.setRowHidden(
i, QtCore.QModelIndex(), True)
# Subset List
self.subsetListModel = QtGui.QStandardItemModel()
self.ui.subsetListView.setModel(self.subsetListModel)
# File List
self.fileListModel = QtGui.QStandardItemModel()
self.ui.fileTableView.setModel(self.fileListModel)
self.fileListModel.setHorizontalHeaderLabels(['file', 'items'])
self.connect(
self.ui.fileTableView.selectionModel(),
QtCore.SIGNAL(
"selectionChanged(const QItemSelection &, const QItemSelection &)"
), self.openSelectedFile)
# Plot
# Create advanced settings
#property.setView(self.ui.advancedSettingsTreeView)
#self.advanced_settings, self.advanced_names = self.ui.advancedSettingsTreeView.model().addOptionList(self.advancedSettings())
#self.ui.advancedSettingsTreeView.setStyleSheet('QTreeView::item[readOnly="true"]{ color: #000000; }')
#for i in xrange(self.ui.advancedSettingsTreeView.model().rowCount()-1, 0, -1):
# if self.ui.advancedSettingsTreeView.model().index(i, 0).internalPointer().isReadOnly(): # Hide widget items (read only)
# self.ui.advancedSettingsTreeView.setRowHidden(i, QtCore.QModelIndex(), True)
# Load the settings
_logger.info("\rLoading settings ...")
self.loadSettings()
def __init__(self, screen_shot_file=None, parent=None):
'''
'''
QtGui.QWizard.__init__(self, parent)
self.ui = Ui_ProjectWizard()
self.ui.setupUi(self)
#self.subPages={}
self.lastmicpath = str(QtCore.QDir.currentPath())
self.lastgainpath = str(QtCore.QDir.currentPath())
self.micrograph_files = []
self.gain_files = []
self.parameters = []
self.screen_shot_file = screen_shot_file
self.helpDialog = HelpDialog(self)
self.default_spider_path = '/guam.raid.cluster.software/spider.21.00/'
version = arachnid.__version__
n = version.find('_')
if n != -1: version = version[:n]
self.setWindowTitle("Arachnid - Workflow Creation Wizard - v%s" %
version)
self.docs_url = ""
self.setPixmap(
QtGui.QWizard.WatermarkPixmap,
QtGui.QPixmap(':/icons/logo/ArachnidLogoWindow_small.png'
)) #:/icons/icons/icon256x256.png'))
self.setPixmap(
QtGui.QWizard.BackgroundPixmap,
QtGui.QPixmap(':/icons/logo/ArachnidLogoWindow_small.png'
)) #:/icons/icons/icon256x256.png'))
########################################################################################################################################
###### Introduction Page
########################################################################################################################################
self.ui.introductionPage.setTitle('Welcome to Arachnid - v%s' %
version)
if screen_shot_file:
self.ui.screenShotCheckBox.setCheckState(QtCore.Qt.Checked)
self.ui.screenShotCheckBox.setEnabled(False)
########################################################################################################################################
###### Question Page
########################################################################################################################################
self.currentIdChanged.connect(self.onCurrentIDChanged)
self.ui.yesLeginonPushButton.clicked.connect(self.next)
self.ui.noLeginonPushButton.clicked.connect(self.next)
self.ui.yesReferencePushButton.clicked.connect(self.next)
self.ui.noReferencePushButton.clicked.connect(self.next)
########################################################################################################################################
###### Leginon Page
########################################################################################################################################
self.ui.leginonWidget = LeginonUI(self, self.helpDialog)
self.ui.leginonDBLayout.addWidget(self.ui.leginonWidget)
#self.subPages[self.idOf(self.ui.leginonDBPage)]=self.ui.leginonWidget
self.ui.leginonWidget.registerPage(self.ui.leginonDBPage)
#self.ui.leginonWidget.loadFinished.connect(self.next)
self.ui.leginonWidget.loadFinished.connect(self.onLeginonLoadFinished)
self.ui.leginonWidget.captureScreen.connect(self.captureScreen)
########################################################################################################################################
###### Reference Page
########################################################################################################################################
self.ui.referenceWidget = ReferenceUI(self, self.helpDialog)
self.ui.referenceLayout.addWidget(self.ui.referenceWidget)
#self.subPages[self.idOf(self.ui.referencePage)]=self.ui.referenceWidget
self.ui.referenceWidget.registerPage(self.ui.referencePage)
#self.ui.referencePage.registerField("referenceEdit*", self.ui.referenceWidget.ui.referenceLineEdit)
self.ui.referenceWidget.captureScreen.connect(self.captureScreen)
self.ui.referenceWidget.updateParticleDiameter.connect(
self.ui.particleSizeDoubleSpinBox.setValue)
########################################################################################################################################
###### Monitor Page
########################################################################################################################################
self.ui.monitorWidget = MonitorUI(self, self.helpDialog)
self.ui.monitorLayout.insertWidget(0, self.ui.monitorWidget)
self.ui.monitorWidget.programStarted.connect(self.onProgramStarted)
self.ui.monitorWidget.programCompleted.connect(self.onProgramCompleted)
########################################################################################################################################
###### Fine Settings Page
########################################################################################################################################
self.ui.settingsTabWidget = SettingsUI(self)
sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
sizePolicy.setHorizontalStretch(2)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(
self.ui.settingsTabWidget.sizePolicy().hasHeightForWidth())
self.ui.settingsTabWidget.setSizePolicy(sizePolicy)
self.ui.settingsHorizontalLayout.addWidget(self.ui.settingsTabWidget)
self.ui.workflowListView.setModel(self.ui.monitorWidget.model())
selmodel = self.ui.workflowListView.selectionModel()
selmodel.currentChanged.connect(
self.ui.settingsTabWidget.settingsChanged)
########################################################################################################################################
###### Manual Settings Page
########################################################################################################################################
self.ui.manualSettingsPage.registerField(
self.param("apix*"), self.ui.pixelSizeDoubleSpinBox, "value",
QtCore.SIGNAL('valueChanged(double)'))
self.ui.manualSettingsPage.registerField(
self.param("voltage*"), self.ui.voltageDoubleSpinBox, "value",
QtCore.SIGNAL('valueChanged(double)'))
self.ui.manualSettingsPage.registerField(
self.param("cs*"), self.ui.csDoubleSpinBox, "value",
QtCore.SIGNAL('valueChanged(double)'))
self.ui.manualSettingsPage.registerField(
self.param("input_files*"), self, 'micrographFiles',
QtCore.SIGNAL('micrographFilesUpdated()'))
self.ui.manualSettingsPage.registerField(
self.param("gain_files"), self, 'gainFiles',
QtCore.SIGNAL('gainFilesUpdated()'))
self.ui.manualSettingsPage.registerField(self.param("gain_file"), self,
'gainFile')
self.ui.manualSettingsPage.registerField(self.param("invert"),
self.ui.invertCheckBox)
self.ui.imageStatTableView.setModel(
ListTableModel([], ['Exposure', 'Gain'],
['Width', 'Height', 'Frames', 'Total'], self))
self.ui.importMessageLabel.setVisible(False)
########################################################################################################################################
###### Additional Settings Page
########################################################################################################################################
if os.path.exists(self.default_spider_path):
self.updateSpiderExe(self.default_spider_path, True)
self.updateParticleSizeSpinBox = lambda x: self.ui.particleSizeSpinBox.setValue(
int(x / self.ui.pixelSizeDoubleSpinBox.value())
if self.ui.pixelSizeDoubleSpinBox.value() > 0 else 0)
self.updateWindowSizeSpinBox = lambda x: self.ui.windowSizeSpinBox.setValue(
int(x / self.ui.pixelSizeDoubleSpinBox.value())
if self.ui.pixelSizeDoubleSpinBox.value() > 0 else 0)
self.updateMaskDiameterSpinBox = lambda x: self.ui.maskDiameterSpinBox.setValue(
int(x / self.ui.pixelSizeDoubleSpinBox.value())
if self.ui.pixelSizeDoubleSpinBox.value() > 0 else 0)
self.updateParticleSizeDoubleSpinBox = lambda x: self.ui.particleSizeDoubleSpinBox.setValue(
float(x * self.ui.pixelSizeDoubleSpinBox.value())
if self.ui.pixelSizeDoubleSpinBox.value() > 0 else 0.0)
self.updateWindowSizeDoubleSpinBox = lambda x: self.ui.windowSizeDoubleSpinBox.setValue(
float(x * self.ui.pixelSizeDoubleSpinBox.value())
if self.ui.pixelSizeDoubleSpinBox.value() > 0 else 0.0)
self.updateMaskDiameterDoubleSpinBox = lambda x: self.ui.maskDiameterDoubleSpinBox.setValue(
float(x * self.ui.pixelSizeDoubleSpinBox.value())
if self.ui.pixelSizeDoubleSpinBox.value() > 0 else 0.0)
self.ui.particleSizeDoubleSpinBox.valueChanged.connect(
self.updateParticleSizeSpinBox)
self.ui.windowSizeDoubleSpinBox.valueChanged.connect(
self.updateWindowSizeSpinBox)
self.ui.maskDiameterDoubleSpinBox.valueChanged.connect(
self.updateMaskDiameterSpinBox)
self.ui.particleSizeUnitComboBox.currentIndexChanged.connect(
self.ui.particleDiameterStackedWidget.setCurrentIndex)
self.ui.windowSizeUnitComboBox.currentIndexChanged.connect(
self.ui.windowSizeStackedWidget.setCurrentIndex)
self.ui.maskDiameterUnitComboBox.currentIndexChanged.connect(
self.ui.maskDiameterStackedWidget.setCurrentIndex)
self.ui.particleSizeUnitComboBox.currentIndexChanged.connect(
functools.partial(
connect_visible_spin_box,
signals=(self.ui.particleSizeDoubleSpinBox.valueChanged,
self.ui.particleSizeSpinBox.valueChanged),
slots=(self.updateParticleSizeSpinBox,
self.updateParticleSizeDoubleSpinBox)))
self.ui.windowSizeUnitComboBox.currentIndexChanged.connect(
functools.partial(
connect_visible_spin_box,
signals=(self.ui.windowSizeDoubleSpinBox.valueChanged,
self.ui.windowSizeSpinBox.valueChanged),
slots=(self.updateWindowSizeSpinBox,
self.updateWindowSizeDoubleSpinBox)))
self.ui.maskDiameterUnitComboBox.currentIndexChanged.connect(
functools.partial(
connect_visible_spin_box,
signals=(self.ui.maskDiameterDoubleSpinBox.valueChanged,
self.ui.maskDiameterSpinBox.valueChanged),
slots=(self.updateMaskDiameterSpinBox,
self.updateMaskDiameterDoubleSpinBox)))
self.ui.particleSizeDoubleSpinBox.valueChanged.connect(
lambda x: self.ui.windowSizeDoubleSpinBox.setValue(
ensure_even_window(x * 1.4,
self.ui.pixelSizeDoubleSpinBox.value())))
self.ui.particleSizeDoubleSpinBox.valueChanged.connect(
lambda x: self.ui.maskDiameterDoubleSpinBox.setValue(x * 1.2))
self.ui.additionalSettingsPage.registerField(
self.param("spider_path"), self.ui.spiderExecutableLineEdit)
self.ui.particleSizeDoubleSpinBox.valueChanged.connect(
self.diameterChanged)
self.ui.additionalSettingsPage.registerField(
self.param("particle_diameter*"),
self.ui.particleSizeDoubleSpinBox, "value",
QtCore.SIGNAL('valueChanged(double)'))
#self.ui.additionalSettingsPage.registerField(self.param("particle_diameter*"), self, "particleDiameter", QtCore.SIGNAL('diameterChanged(double)'))
self.ui.additionalSettingsPage.registerField(
self.param("window_actual*"), self.ui.windowSizeDoubleSpinBox,
"value", QtCore.SIGNAL('valueChanged(double)'))
self.ui.additionalSettingsPage.registerField(
self.param("mask_diameter*"), self.ui.maskDiameterDoubleSpinBox,
"value", QtCore.SIGNAL('valueChanged(double)'))
self.ui.additionalSettingsPage.registerField(
self.param('worker_count'), self.ui.workerCountSpinBox)
self.ui.additionalSettingsPage.registerField(
self.param('thread_count'), self.ui.threadCountSpinBox)
self.ui.additionalSettingsPage.registerField(self.param("window"),
self, "window")
self.ui.additionalSettingsPage.registerField(
self.param('enable_stderr'), self.ui.enableStderrCheckBox)
self.ui.additionalSettingsPage.registerField(self.param("disk_mult"),
self, 'sampleShape')
self.ui.additionalSettingsPage.registerField(
self.param("overlap_mult"), self, 'sampleDensity')
self.ui.additionalSettingsPage.registerField(
self.param("threshold_minimum"), self, 'sampleDensityMin')
self.ui.sampleShapeComboBox.setItemData(0, 0.6)
self.ui.sampleShapeComboBox.setItemData(1, 0.35)
self.ui.sampleDensityComboBox.setItemData(0, 1.0)
self.ui.sampleDensityComboBox.setItemData(1, 1.2)
self.ui.sampleDensityComboBox.setItemData(2, 0.8)
thread_count = 1
if openmp.is_openmp_enabled():
thread_count = openmp.get_num_procs()
else:
try:
thread_count = multiprocessing.cpu_count()
except:
pass
# Hack to determine whether CPU supports hyperthreading
frac = 1.0
if sys.platform == 'darwin':
try:
info = dict([
line.strip().split(':')
for line in os.popen('sysctl hw').readlines()[1:20]
if line.find(':') != -1
])
frac = float(info['hw.activecpu'].strip()) / float(
info['hw.physicalcpu'].strip())
except:
pass
else:
if os.path.exists('/proc/cpuinfo'):
info = dict([
(line.strip().split(':')[0].strip(),
line.strip().split(':')[1].strip())
for line in open('/proc/cpuinfo', 'r').readlines()
if line.find(':') != -1
])
frac = float(info['siblings'].strip()) / float(
info['cpu cores'].strip())
thread_count = int(thread_count / frac)
self.ui.workerCountSpinBox.setValue(thread_count)
self.ui.selectLeginonInformationLabel.setVisible(False)
self.ui.selectReferenceInformationLabel.setVisible(False)
_logger.info("\rLoading project settings ...")
self.readSettings()
self.loadProject()