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 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 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 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)