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 addSettings(self, option_list, group_list, values):
'''
'''
for group in group_list:
if group.is_child(): continue
treeView = self.copyTreeView()
property.setView(treeView)
self.tree_views[group.title] = treeView
treeView.model().addOptions(group.get_config_options(),
group.option_groups, values)
icon = QtGui.QIcon()
if treeView.model().totalInvalid() > 0:
icon.addPixmap(QtGui.QPixmap(":/mini/mini/exclamation.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.invalid_count += 1
else:
icon.addPixmap(QtGui.QPixmap(":/mini/mini/accept.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.model_tab[treeView.model()] = self.count() - 1
self.addTab(treeView, icon, group.title)
#if treeView.model().totalInvalid() > 0:
treeView.model().propertyValidity.connect(self.updateValid)
width = treeView.model().maximumTextWidth(self.fontMetrics(),
treeView.indentation())
treeView.setColumnWidth(0, width)
#self.ui.propertyTreeView.model().addOptions(option_list, [], values)
self.controlValidity.emit(self, self.isValid())
def copyTreeView(self):
'''Copy the properties from the original tree view
:Returns:
treeView : QTreeView
Copy of current tree view
'''
treeView = QtGui.QTreeView(self)
metaObjectFrom = self.ui.propertyTreeView.metaObject()
metaObjectTo = treeView.metaObject()
while metaObjectFrom is not None:
_logger.debug("Class: %s" % metaObjectFrom.className())
if metaObjectFrom.className() == 'QWidget': break
for i in xrange(metaObjectFrom.propertyOffset(),
metaObjectFrom.propertyCount()):
name = metaObjectFrom.property(i).name()
if name == 'editTriggers': continue
_logger.debug("Copy tree view: " + str(name))
treeView.setProperty(name,
self.ui.propertyTreeView.property(name))
metaObjectFrom = metaObjectFrom.superClass()
metaObjectTo = metaObjectTo.superClass()
treeView.setEditTriggers(self.ui.propertyTreeView.editTriggers())
treeView.setStyleSheet(self.treeViewStyle)
return treeView
def read_image(filename, index=None):
'''
'''
qimg = QtGui.QImage()
if qimg.load(filename): return qimg
return ndimage_utility.normalize_min_max(
ndimage_file.read_image(filename, index))
def updateValid(self, model, prop, valid):
'''
'''
invalid = model.totalInvalid()
if self.invalid_count != invalid:
if valid:
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(":/mini/mini/accept.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.setTabIcon(self.model_tab[model], icon)
self.invalid_count = invalid
else:
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(":/mini/mini/exclamation.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.setTabIcon(self.model_tab[model], icon)
self.invalid_count = invalid
self.controlValidity.emit(self, self.isValid())
def openFiles(self, files):
''' Open a collection of files, sort by content type
:Parameters:
files : list
List of input files
'''
coordfile = None
for filename in files:
filename = str(filename)
if not ndimage_file.spider.is_readable(
filename) and not ndimage_file.mrc.is_readable(
filename) and format.is_readable(filename):
nameItem = QtGui.QStandardItem(os.path.basename(filename))
nameItem.setData(filename)
nameItem.setToolTip(filename)
countItem = QtGui.QStandardItem(str(len(
format.read(filename))))
countItem.setData(filename)
countItem.setToolTip(filename)
self.fileListModel.appendRow([nameItem, countItem])
self.coordinates_files.append(filename)
if coordfile is None: coordfile = nameItem #coordfile=filename
else:
self.stack_file = filename
self.coordinates_files = list(set(self.coordinates_files))
if coordfile is not None:
self.ui.fileTableView.selectionModel().setCurrentIndex(
coordfile.index(), QtGui.QItemSelectionModel.Select
| QtGui.QItemSelectionModel.Rows)
#self.openFile(coordfile)
if self.stack_file != "":
self.ui.toggleImageDockAction.setEnabled(True)
self.ui.imageDockWidget.show()
self.ui.canvas.mpl_connect('pick_event', self.displayImage)
def on_contrastSlider_valueChanged(self, value):
''' Called when the user uses the contrast slider
'''
if self.color_level is None: return
if self.base_level is not None and len(
self.base_level) > 0 and not isinstance(
self.base_level[0], list):
if value != 200:
self.color_level = qimage_utility.adjust_level(
qimage_utility.change_contrast, self.base_level, value)
else:
self.color_level = self.base_level
for i in xrange(len(self.loaded_images)):
self.loaded_images[i].setColorTable(self.color_level)
pix = QtGui.QPixmap.fromImage(self.loaded_images[i])
icon = QtGui.QIcon(pix)
icon.addPixmap(pix, QtGui.QIcon.Normal)
icon.addPixmap(pix, QtGui.QIcon.Selected)
self.imageListModel.item(i).setIcon(icon)
else:
for i in xrange(len(self.loaded_images)):
if value != 200:
self.color_level = qimage_utility.adjust_level(
qimage_utility.change_contrast, self.base_level[i],
value)
else:
self.color_level = self.base_level[i]
self.loaded_images[i].setColorTable(self.color_level)
pix = QtGui.QPixmap.fromImage(self.loaded_images[i])
icon = QtGui.QIcon(pix)
icon.addPixmap(pix, QtGui.QIcon.Normal)
icon.addPixmap(pix, QtGui.QIcon.Selected)
self.imageListModel.item(i).setIcon(icon)
def __init__(self, program, parent=None):
"Initialize screener window"
QtGui.QDialog.__init__(self, parent)
# Build window
_logger.info("Building main window ...")
self.ui = Ui_Dialog()
self.ui.setupUi(self)
self.ui.settingsTabWidget = TabWidget(self)
self.ui.configTabLayout = QtGui.QHBoxLayout(self.ui.configTab)
self.ui.configTabLayout.addWidget(self.ui.settingsTabWidget)
self.ui.settingsTabWidget.controlValidity.connect(self.setValid)
self.ui.monitorWidget = MonitorWidget(self)
self.ui.runTabLayout = QtGui.QHBoxLayout(self.ui.runTab)
self.ui.runTabLayout.addWidget(self.ui.monitorWidget)
#self.ui.monitorWidget.runProgram.connect(self.runProgram)
#self.ui.monitorWidget.monitorProgram.connect(self.monitorProgram)
self.program = program
self.ui.settingsTabWidget.addSettings(*program.settings())
self.ui.monitorWidget.setWorkflow(program)
self.ui.monitorWidget.setLogFile(program.values.log_file)
def setWorkflow(self, workflow):
'''
'''
if not hasattr(workflow, '__iter__'): workflow=[workflow]
model = self.ui.jobListView.model()
model.clear()
mode='w'
for mod in workflow:
if self.log_file:
mod.values.log_file = self.log_file
mod.values.log_mode = mode
item = QtGui.QStandardItem(self.job_status_icons[0], mod.name())
item.setData(mod, QtCore.Qt.UserRole)
model.appendRow(item)
if mode != 'a': mode='a'
def __init__(self, parent=None, helpDialog=None):
"Initialize LeginonUI widget"
QtGui.QWidget.__init__(self, parent)
# Build window
_logger.info("\rBuilding main window ...")
self.ui = Ui_Form()
self.ui.setupUi(self)
self.login = {}
self.helpDialog = helpDialog
self.startTabIndex = 0
self.ui.progressDialog = QtGui.QProgressDialog('Loading...', "", 0, 5,
self)
self.ui.progressDialog.setWindowModality(QtCore.Qt.ApplicationModal)
self.ui.progressDialog.findChildren(QtGui.QPushButton)[0].hide()
#self.ui.progressDialog.setCancelButton(0) # might work
#self.ui.progressDialog.setWindowFlags(self.ui.progressDialog.windowFlags() & ~QtCore.Qt.WindowCloseButtonHint) #v5s
self.ui.progressDialog.setWindowFlags(QtCore.Qt.Window
| QtCore.Qt.WindowTitleHint
| QtCore.Qt.CustomizeWindowHint)
self.ui.reloadTableToolButton.clicked.connect(
self.queryDatabaseForProjects)
self.taskUpdated.connect(self.updateProgress)
self.ui.leginonHostnameLineEdit.editingFinished.connect(
lambda: self.ui.projectHostnameLineEdit.setText(
self.ui.leginonHostnameLineEdit.text())
if self.ui.projectHostnameLineEdit.text() == "" else None)
header = [('Session', None), ('Project', None), ('Images', None),
('Voltage', 'voltage'), ('Pixel Size', 'apix'),
('Magnification', None), ('CS', 'cs'), ('Image Name', None),
('Image Path', None), ('Frame Path', None)]
self.header = [h[0] for h in header]
self.headermap = dict([h for h in header if h[1] is not None])
self.images = []
self.ui.projectTableView.setModel(
ListTableModel([], self.header, None, self))
selmodel = self.ui.projectTableView.selectionModel()
selmodel.selectionChanged.connect(self.selectionChanged)
_logger.info("\rLoading settings ...")
self.readSettings()
self.on_loginPushButton_clicked()
def __init__(self, parent=None):
"Initialize screener window"
QtGui.QWidget.__init__(self, parent)
self.parent_control = parent
# Build window
_logger.info("Building main window ...")
self.ui = Ui_Form()
self.ui.setupUi(self)
self.header = ['# Mics', '# Particles', 'Disk', 'Mask', 'Overlap']
self.options = [
self.ui.diskDoubleSpinBox.statusTip(),
self.ui.diskDoubleSpinBox.statusTip(),
self.ui.diskDoubleSpinBox.statusTip()
]
self.data = []
self.micrograph_files = []
self.output = None
self.output_base = None
self.ui.autopickHistoryTableView.setModel(
ListTableModel([], self.header, None, self))
#selmodel=self.ui.autopickHistoryTableView.selectionModel()
self.ui.autopickHistoryTableView.doubleClicked.connect(
self.on_runPushButton_clicked)
#doubleClicked ( const QModelIndex & index )
self.ui.progressDialog = QtGui.QProgressDialog('Running...', "Close",
0, 1, self)
self.ui.progressDialog.setWindowModality(QtCore.Qt.ApplicationModal)
#self.ui.progressDialog.findChildren(QtGui.QPushButton)[0].hide()
self.ui.progressDialog.setWindowFlags(QtCore.Qt.Window
| QtCore.Qt.WindowTitleHint
| QtCore.Qt.CustomizeWindowHint)
self.task = None
self.output = None
self.taskUpdated.connect(self.updateProgress)
self.option_control_map = self._collect_options_controls()
self._add_controls()
def on_subsetComboBox_currentIndexChanged(self, index):
''' Called when the user wants to plot only a subset of the data
:Parameters:
index : int
New index in the subset combobox
'''
if index > 0:
index = self.ui.subsetComboBox.itemData(index)
vals = [str(v) for v in numpy.unique(self.data[:, index])]
else:
vals = []
self.subsetListModel.clear()
for name in vals:
item = QtGui.QStandardItem(name)
item.setCheckState(QtCore.Qt.Checked)
item.setCheckable(True)
self.subsetListModel.appendRow(item)
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()
def saveSelection(self, invert=False, filename=None, prefix=None):
'''
'''
if filename is None: filename = self.selection_file
self.setEnabled(False)
try:
progressDialog = QtGui.QProgressDialog('Saving...', "", 0, 5, self)
progressDialog.setWindowModality(QtCore.Qt.WindowModal)
progressDialog.show()
if isinstance(filename, tuple): filename = filename[0]
if not filename: return
file_index = self.file_index.copy()
if invert:
sel = file_index[:, 2] > -1
file_index[sel, 2] = numpy.logical_not(file_index[sel, 2] > 0)
if filename != "":
if self.advanced_settings.relion != "" and os.path.splitext(
filename)[1] == '.star':
if not (len(self.files) == 1
or len(self.files) == len(file_index)):
progressDialog.hide()
QtGui.QMessageBox.critical(
self, "Saving Relion Selection File",
"You have opened more than one class stack. Cannot save a Relion Selection file!",
QtGui.QMessageBox.Ok | QtGui.QMessageBox.Default
| QtGui.QMessageBox.NoButton)
self.setEnabled(True)
return
progressDialog.setValue(1)
_logger.info("Saving Relion selection file to %s" %
filename)
class_column_name = 'rlnClassNumber'
vals = format.read(self.advanced_settings.relion,
numeric=True)
progressDialog.setValue(2)
subset = []
selected = set([v[1] + 1 for v in file_index if v[2] > 0])
progressDialog.setValue(3)
for v in vals:
id = int(getattr(v, class_column_name))
if id in selected: subset.append(v)
progressDialog.setValue(4)
format.write(filename, subset, prefix=prefix)
progressDialog.setValue(5)
#relion_selection.select_class_subset(vals, select, filename)
elif len(self.files) == 1 or len(
self.files) == len(file_index):
progressDialog.setValue(3)
_logger.info("Saving single selection file to %s" %
filename)
if not spider_utility.is_spider_filename(
self.files) and len(self.files) > 1:
_logger.info(
"File names do not conform to SPIDER, writing as star file"
)
filename = os.path.splitext(filename)[0] + '.star'
vals = [(self.files[v[0]], 1) for v in file_index
if v[2] > 0]
elif len(self.files) > 1:
vals = [(spider_utility.spider_id(self.files[v[0]]), 1)
for v in file_index if v[2] > 0]
else:
vals = [(v[1] + 1, 1) for v in file_index if v[2] > 0]
progressDialog.setValue(4)
format.write(filename,
vals,
header='id,select'.split(','),
default_format=format.spidersel,
prefix=prefix)
progressDialog.setValue(5)
else:
progressDialog.setValue(3)
_logger.info(
"Saving multiple selection files by stack to %s" %
filename)
if not spider_utility.is_spider_filename(self.files):
_logger.info(
"File names do not conform to SPIDER, writing as star file"
)
filename = os.path.splitext(filename)[0] + '.star'
vals = [(relion_utility.relion_identifier(
self.files[v[0]], v[1] + 1), 1) for v in file_index
if v[2] > 0]
format.write(filename,
vals,
header='id,select'.split(','))
else:
micselect = {}
for v in file_index:
if v[2] > 0:
mic = spider_utility.spider_id(
self.files[v[0]])
if mic not in micselect: micselect[mic] = []
micselect[mic].append((v[1] + 1, 1))
for mic, vals in micselect.iteritems():
format.write(filename,
numpy.asarray(vals),
spiderid=mic,
header="id,select".split(','),
default_format=format.spidersel,
prefix=prefix)
progressDialog.setValue(5)
finally:
self.setEnabled(True)
#progressDialog.hide()
print 'done'
def iter_images(files, index, template=None, average=False):
''' Wrapper for iterate images that support color PNG files
:Parameters:
filename : str
Input filename
:Returns:
img : array
Image array
'''
qimg = QtGui.QImage()
if template is not None:
filename = spider_utility.spider_filename(template, files[0])
else:
filename = files[0]
header = {}
if qimg.load(filename):
if isinstance(index[0], str): files = index
else: files = [files[i[0]] for i in index]
for filename in files:
qimg = QtGui.QImage()
if template is not None:
filename = spider_utility.spider_filename(template, filename)
if not qimg.load(filename):
qimg = QtGui.QPixmap(":/mini/mini/cross.png").toImage()
_logger.warn("Unable to read image - %s" % filename)
#raise IOError, "Unable to read image - %s"%filename
yield (filename, 0), qimg, 1.0
else:
# todo reorganize with
'''
for img in itertools.imap(ndimage_utility.normalize_min_max, ndimage_file.iter_images(filename, index)):
'''
if isinstance(index[0], str):
for f in index:
avg = None
if template is not None:
f1 = spider_utility.spider_filename(template, f)
if os.path.exists(f1): f = f1
else:
_logger.warn("Unabled to find alternate image: %s" %
f1)
for img in ndimage_file.iter_images(f, header=header):
if avg is None: avg = img
else: avg += img
try:
img = ndimage_utility.normalize_min_max(avg)
except:
img = avg
yield (f, 0), img, header.get('apix', 1.0)
else:
for idx in index:
f, i = idx[:2]
filename = files[f]
if template is not None:
filename = spider_utility.spider_filename(
template, filename)
try:
img = ndimage_file.read_image(filename, i, header=header)
except:
_logger.exception("Error while reading!")
img = ndimage_file.read_image(filename, header=header)
#print f, i, len(files), files[f], template, filename
#raise
try:
img = ndimage_utility.normalize_min_max(img)
except:
pass
yield (filename, i), img, header.get('apix', 1.0)
'''
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 __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, parent=None, helpDialog=None):
"Initialize ReferenceUI widget"
QtGui.QWidget.__init__(self, parent)
# Build window
_logger.info("\rBuilding main window ...")
self.ui = Ui_Form()
self.ui.setupUi(self)
self.task = None
self.lastpath = str(QtCore.QDir.currentPath())
self.helpDialog = helpDialog
self.ui.referenceTabWidget.currentChanged.connect(
lambda x: self.captureScreen.emit(x + 1))
self.emdbCannedModel = QtGui.QStandardItemModel(self)
canned = [
('Ribosome-40S', '1346',
':/references/reference/1346/emdb_1346_pix32.png',
"""The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome.
Passmore LA, Schmeing TM, Maag D, Applefield DJ, Acker MG, Algire MA, Lorsch JR, Ramakrishnan V
MOLECULAR CELL (2007) 26, pp. 41-50"""),
('Ribosome-60S', '1705',
':/references/reference/1705/emdb_1705_pix32.png',
"""Mechanism of eIF6-mediated inhibition of ribosomal subunit joining.
Gartmann M, Blau M, Armache JP, Mielke T, Topf M, Beckmann R
J.BIOL.CHEM. (2010) 285, pp. 14848-14851"""),
('Ribosome-80S', '2275',
':/references/reference/2275/emdb_2275_pix32.png',
"""Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles.
Bai XC, Fernandez IS, McMullan G, Scheres SH
ELIFE (2013) 2, pp. e00461-e00461"""),
('ATP synthase', '5335',
':/references/reference/5335/emd_5335_pix32.png',
"""Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase.
Lau WC, Rubinstein JL
NATURE (2012) 481, pp. 214-218"""),
('Ribosome-70S', '5360',
':/references/reference/5360/emdb_5360_pix32.png',
"""Structural characterization of mRNA-tRNA translocation intermediates.
Agirrezabala X, Liao HY, Schreiner E, Fu J, Ortiz-Meoz RF, Schulten K, Green R, Frank J
PROC.NAT.ACAD.SCI.USA (2012) 109, pp. 6094-6099"""),
('Ribosome-30S', '5503',
':/references/reference/5503/emdb_5503_pix512.png',
"""Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM and general features of the assembly process.
Guo Q, Goto S, Chen Y, Feng B, Xu Y, Muto A, Himeno H, Deng H, Lei J, Gao N
NUCLEIC ACIDS RES. (2013) 41, pp. 2609-2620"""),
('Ribosome-50S', '5787',
':/references/reference/5787/emdb_5787_pix32.png',
"""Functional domains of the 50S subunit mature late in the assembly process.
Jomaa A, Jain N, Davis JH, Williamson JR, Britton RA, Ortega J
NUCLEIC ACIDS RES. (2013)"""),
]
for entry in canned:
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(entry[2]), QtGui.QIcon.Normal,
QtGui.QIcon.Off)
item = QtGui.QStandardItem(icon, entry[0])
item.setData(entry[1], QtCore.Qt.UserRole)
item.setData(entry[3], QtCore.Qt.UserRole + 1)
self.emdbCannedModel.appendRow(item)
self.ui.emdbCannedListView.setModel(self.emdbCannedModel)
self.taskFinished.connect(self.onDownloadFromEMDBComplete)
self.ui.referenceLineEdit.editingFinished.connect(
self.onReferenceEditChanged)
self.ui.referenceTabWidget.setCurrentIndex(0)
self.ui.referenceTabWidget.setCurrentIndex(1)