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 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 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 __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, 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 __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)