def readSettings(self):
'''
'''
settings = QtCore.QSettings()
settings.beginGroup("LeginonUI")
val = settings.value('leginonDB')
if val: self.ui.leginonHostnameLineEdit.setText(val)
val = settings.value('leginonPath')
if val: self.ui.leginonDBNameLineEdit.setText(val)
val = settings.value('projectDB')
if val: self.ui.projectHostnameLineEdit.setText(val)
val = settings.value('projectPath')
if val: self.ui.projectDBNameLineEdit.setText(val)
self.ui.usernameLineEdit.setText(settings.value('targetuser'))
self.ui.passwordLineEdit.setText(settings.value('targetpass'))
val = settings.value('username')
if val: self.ui.dbUsernameLineEdit.setText(val)
val = settings.value('password')
if val: self.ui.dbPasswordLineEdit.setText(base64.b64decode(val))
#self.ui.alternateUserLineEdit.setText(settings.value('alternate-user'))
settings.endGroup()
if self.ui.usernameLineEdit.text() == "":
self.ui.usernameLineEdit.setText(getpass.getuser())
def __init__(self, parent=None, helpDialog=None):
'''
'''
QtGui.QWidget.__init__(self, parent)
self.ui = Ui_Form()
self.timer_interval=500
self.ui.jobUpdateTimer = QtCore.QTimer(self)
self.ui.jobUpdateTimer.setInterval(self.timer_interval)
self.ui.jobUpdateTimer.setSingleShot(False)
self.helpDialog=helpDialog
self.last_offset=0
self.total_running=0
self.ui.setupUi(self)
#self.ui.pushButton.clicked.connect(self.runProgram)
self.ui.jobUpdateTimer.timeout.connect(self.on_jobUpdateTimer_timeout)
self.ui.jobProgressBar.setMinimum(0)
self.ui.jobListView.setModel(QtGui.QStandardItemModel(self))
self.job_status_icons=[QtGui.QIcon(f) for f in [':/mini/mini/clock.png', ':/mini/mini/arrow_refresh.png', ':/mini/mini/tick.png', ':/mini/mini/cross.png']]
self.ui.crashReportToolButton.setEnabled(False)
#self.text_cursor = QtGui.QTextCursor(self.ui.logTextEdit.document())
self.current_pid = None
self.fin = None
self.log_file = None
self.created = None
self.log_text=""
self.workflowProcess=None
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 on_monitorInformationToolButton_clicked(self):
'''
'''
if self.helpDialog is not None:
self.helpDialog.setHTML(self.ui.pushButton.toolTip())
self.helpDialog.show()
else:
QtGui.QToolTip.showText(self.ui.pushButton.mapToGlobal(QtCore.QPoint(0,0)), self.ui.pushButton.toolTip())
def getSettings(self):
''' Get the settings object
'''
'''
return QtCore.QSettings(QtCore.QSettings.IniFormat, QtCore.QSettings.UserScope, "Arachnid", "ImageScreen")
'''
if self.inifile == "": return None
return QtCore.QSettings(self.inifile, QtCore.QSettings.IniFormat)
def writeSettings(self):
'''
'''
settings = QtCore.QSettings()
settings.beginGroup("ProjectUI")
settings.setValue('spiderExecutable',
self.ui.spiderExecutableLineEdit.text())
settings.endGroup()
def readSettings(self):
'''
'''
settings = QtCore.QSettings()
settings.beginGroup("ProjectUI")
val = settings.value('spiderExecutable')
if val: self.ui.spiderExecutableLineEdit.setText(val)
settings.endGroup()
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 on_imageZoomDoubleSpinBox_valueChanged(self, zoom=None):
''' Called when the user wants to plot only a subset of the data
:Parameters:
index : int
New index in the subset combobox
'''
if zoom is None: zoom = self.ui.imageZoomDoubleSpinBox.value()
self.ui.zoomSlider.blockSignals(True)
self.ui.zoomSlider.setValue(int(self.ui.zoomSlider.maximum() * zoom))
self.ui.zoomSlider.blockSignals(False)
if self.imagesize > 0:
n = max(5, int(self.imagesize * zoom))
self.ui.imageListView.setIconSize(QtCore.QSize(n, n))
def writeSettings(self):
'''
'''
settings = QtCore.QSettings()
settings.beginGroup("LeginonUI")
settings.setValue('leginonDB', self.ui.leginonHostnameLineEdit.text())
settings.setValue('leginonPath', self.ui.leginonDBNameLineEdit.text())
settings.setValue('projectDB', self.ui.projectHostnameLineEdit.text())
settings.setValue('projectPath', self.ui.projectDBNameLineEdit.text())
settings.setValue('targetuser', self.ui.usernameLineEdit.text())
settings.setValue('targetpass', self.ui.passwordLineEdit.text())
settings.setValue('username', self.ui.dbUsernameLineEdit.text())
settings.setValue('password',
base64.b64encode(self.ui.dbPasswordLineEdit.text()))
#settings.setValue('alternate-user', self.ui.alternateUserLineEdit.text())
settings.endGroup()
def on_loadImagesPushButton_clicked(self):
''' Load the current batch of images into the list
'''
if len(self.files) == 0: return
self.imageListModel.clear()
index, start = self.imageSubset(self.ui.pageSpinBox.value() - 1,
self.ui.imageCountSpinBox.value())
if len(index) == 0:
self.ui.pageSpinBox.blockSignals(True)
self.ui.pageSpinBox.setValue(0)
self.ui.pageSpinBox.blockSignals(False)
self.ui.imageCountSpinBox.blockSignals(True)
self.ui.imageCountSpinBox.setValue(1)
self.ui.imageCountSpinBox.blockSignals(False)
index, start = self.imageSubset(0, 1)
bin_factor = self.ui.decimateSpinBox.value()
nstd = self.ui.clampDoubleSpinBox.value()
img = None
self.loaded_images = []
self.base_level = None
zoom = self.ui.imageZoomDoubleSpinBox.value()
masks = {}
template = self.get_template()
progressDialog = QtGui.QProgressDialog('Opening...', "Cancel", 0,
len(index), self)
progressDialog.setWindowModality(QtCore.Qt.WindowModal)
progressDialog.show()
self.ui.imageListView.setModel(None)
if not drawing.is_available():
_logger.info("No PIL loaded")
self.advanced_settings.mark_image = False
if not plotting.is_available():
_logger.info("No matplotlib loaded")
self.advanced_settings.mark_image = False
current_powerspec = self.advanced_settings.current_powerspec
if current_powerspec:
if self.advanced_settings.invert:
_logger.info("Cannot invert a power spectra")
else:
if self.advanced_settings.center_mask > 0:
_logger.info("Cannot mask micrograph")
added_items = []
for i, (imgname, img, pixel_size) in enumerate(
iter_images(self.files, index, template)):
selimg = None
progressDialog.setValue(i + 1)
if hasattr(img, 'ndim'):
if current_powerspec and self.advanced_settings.center_mask > 0 and img.shape not in masks:
masks[img.shape] = ndimage_utility.model_disk(
self.advanced_settings.center_mask, img.shape) * -1 + 1
if self.advanced_settings.invert and not current_powerspec:
if img.max() != img.min(): ndimage_utility.invert(img, img)
img = ndimage_utility.replace_outlier(img,
nstd,
nstd,
replace='mean')
if self.advanced_settings.gaussian_high_pass > 0.0:
img = ndimage_filter.filter_gaussian_highpass(
img,
pixel_size / self.advanced_settings.gaussian_high_pass)
if self.advanced_settings.gaussian_low_pass > 0.0:
img = ndimage_filter.filter_gaussian_lowpass(
img,
pixel_size / self.advanced_settings.gaussian_low_pass)
if current_powerspec and self.advanced_settings.center_mask > 0:
#img[numpy.logical_not(masks[img.shape])] = numpy.mean(img[masks[img.shape]])
img *= masks[img.shape]
if bin_factor > 1.0:
img = ndimage_interpolate.interpolate(
img, bin_factor,
self.advanced_settings.downsample_type)
pixel_size *= bin_factor
img = self.display_powerspectra_1D(img, imgname, pixel_size)
img = self.display_resolution(img, imgname, pixel_size)
img = self.box_particles(img, imgname)
if self.advanced_settings.mark_image:
imgm = self.imageMarker(img)
selimg = qimage_utility.numpy_to_qimage(imgm)
qimg = qimage_utility.numpy_to_qimage(img)
if img.ndim == 2:
if self.base_level is not None:
qimg.setColorTable(self.color_level)
else:
self.base_level = qimg.colorTable()
self.color_level = qimage_utility.adjust_level(
qimage_utility.change_contrast, self.base_level,
self.ui.contrastSlider.value())
qimg.setColorTable(self.color_level)
else:
if self.base_level is None: self.base_level = []
self.base_level.append(qimg.colorTable())
self.color_level = qimage_utility.adjust_level(
qimage_utility.change_contrast, self.base_level[-1],
self.ui.contrastSlider.value())
qimg.setColorTable(self.color_level)
else:
qimg = img.convertToFormat(QtGui.QImage.Format_Indexed8)
if self.base_level is None: self.base_level = []
self.base_level.append(qimg.colorTable())
self.color_level = qimage_utility.adjust_level(
qimage_utility.change_contrast, self.base_level[-1],
self.ui.contrastSlider.value())
qimg.setColorTable(self.color_level)
self.loaded_images.append(qimg)
pix = QtGui.QPixmap.fromImage(qimg)
icon = QtGui.QIcon()
icon.addPixmap(pix, QtGui.QIcon.Normal)
if selimg is not None:
pix = QtGui.QPixmap.fromImage(selimg)
icon.addPixmap(pix, QtGui.QIcon.Selected)
if self.advanced_settings.show_label:
item = QtGui.QStandardItem(
icon,
"%s/%d" % (os.path.basename(imgname[0]), imgname[1] + 1))
else:
item = QtGui.QStandardItem(icon, "")
if hasattr(start, '__iter__'):
item.setData(start[i], QtCore.Qt.UserRole)
else:
item.setData(i + start, QtCore.Qt.UserRole)
self.addToolTipImage(imgname, item, pixel_size)
self.imageListModel.appendRow(item)
added_items.append(item)
self.ui.imageListView.setModel(self.imageListModel)
progressDialog.hide()
for item in added_items:
self.notify_added_item(item)
self.imagesize = img.shape[0] if hasattr(img, 'shape') else img.width()
n = max(5, int(self.imagesize * zoom))
self.ui.imageListView.setIconSize(QtCore.QSize(n, n))
batch_count = numpy.ceil(
float(self.imageTotal()) / self.ui.imageCountSpinBox.value())
self.ui.pageSpinBox.setSuffix(" of %d" % batch_count)
self.ui.pageSpinBox.setMaximum(batch_count)
self.ui.actionForward.setEnabled(
self.ui.pageSpinBox.value() < batch_count)
self.ui.actionBackward.setEnabled(self.ui.pageSpinBox.value() > 0)
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.loaded_images = []
self.files = []
self.file_index = []
self.color_level = None
self.base_level = None
self.inifile = '' #'ara_view.ini'
self.settings_group = 'ImageViewer'
self.imagesize = 0
# Image View
self.imageListModel = QtGui.QStandardItemModel(self)
self.ui.imageListView.setModel(self.imageListModel)
#self.templateListModel = QtGui.QStandardItemModel(self)
#self.ui.templateListView.setModel(self.templateListModel)
# Empty init
self.ui.actionForward.setEnabled(False)
self.ui.actionBackward.setEnabled(False)
self.setup()
self.ui.autopickWidget = AutoPickWidget(self)
self.ui.tabWidget.addTab(self.ui.autopickWidget, "AutoPick")
self.ui.tabWidget.currentChanged.connect(self.tabValid)
# Custom Actions
self.ui.dockWidgetAction = self.ui.dockWidget.toggleViewAction()
self.ui.whatsThisAction = QtGui.QWhatsThis.createAction(self)
icon8 = QtGui.QIcon()
icon8.addPixmap(QtGui.QPixmap(":/mini/mini/application_side_list.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.dockWidgetAction.setIcon(icon8)
self.ui.dockWidgetAction.setToolTip("Show or hide the controls widget")
self.ui.dockWidgetAction.setWhatsThis(
QtGui.QApplication.translate(
"MainWindow",
'<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">\n<html><head><meta name="qrichtext" content="1" /><style type="text/css">\np, li { white-space: pre-wrap; }\n</style></head><body style=" font-family:\'Lucida Grande\'; font-size:13pt; font-weight:400; font-style:normal;">\n<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><img src=":/mini/mini/application_side_list.png" /> Display/Hide the controls widget</p>\n<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"></p>\n<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">This widget can be hidden to increase the number of images that can be shown.</p></body></html>',
None, QtGui.QApplication.UnicodeUTF8))
self.ui.toolBar.addAction(self.ui.dockWidgetAction)
self.ui.toolBar.addAction(self.ui.whatsThisAction)
# 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)
# Help system
self.helpDialog = HelpDialog(self)
_logger.info("\rLoading settings ...")
self.loadSettings()
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()