def _qfiledialog_wrapper(attr,
parent=None,
caption='',
basedir='',
filters='',
selectedfilter='',
options=None):
if options is None:
options = QFileDialog.Options(0)
# PySide or PyQt >=v4.6
QString = None # analysis:ignore
tuple_returned = True
try:
# PyQt >=v4.6
func = getattr(QFileDialog, attr + 'AndFilter')
except AttributeError:
# PySide or PyQt <v4.6
func = getattr(QFileDialog, attr)
if QString is not None:
selectedfilter = QString()
tuple_returned = False
# Calling QFileDialog static method
if sys.platform == "win32":
# On Windows platforms: redirect standard outputs
_temp1, _temp2 = sys.stdout, sys.stderr
sys.stdout, sys.stderr = None, None
try:
result = func(parent, caption, basedir, filters, selectedfilter,
options)
except TypeError:
# The selectedfilter option (`initialFilter` in Qt) has only been
# introduced in Jan. 2010 for PyQt v4.7, that's why we handle here
# the TypeError exception which will be raised with PyQt v4.6
# (see Issue 960 for more details)
result = func(parent, caption, basedir, filters, options)
finally:
if sys.platform == "win32":
# On Windows platforms: restore standard outputs
sys.stdout, sys.stderr = _temp1, _temp2
# Processing output
if tuple_returned:
# PySide or PyQt >=v4.6
output, selectedfilter = result
else:
# PyQt <v4.6 (API #1)
output = result
if QString is not None:
# PyQt API #1: conversions needed from QString/QStringList
selectedfilter = to_text_string(selectedfilter)
if isinstance(output, QString):
# Single filename
output = to_text_string(output)
else:
# List of filenames
output = [to_text_string(fname) for fname in output]
# Always returns the tuple (output, selectedfilter)
return output, selectedfilter
def _chooseDirectory(self):
# Find the directory of the most recently opened image file
mostRecentStackDirectory = PreferencesManager().get(
'DataSelection', 'recent stack directory')
if mostRecentStackDirectory is not None:
defaultDirectory = os.path.split(mostRecentStackDirectory)[0]
else:
defaultDirectory = os.path.expanduser('~')
options = QFileDialog.Options(QFileDialog.ShowDirsOnly)
if ilastik.config.cfg.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
# Launch the "Open File" dialog
directory = QFileDialog.getExistingDirectory(self,
"Image Stack Directory",
defaultDirectory,
options=options)
if directory.isNull():
# User cancelled
return
directory = encode_from_qstring(directory)
PreferencesManager().set('DataSelection', 'recent stack directory',
directory)
self.directoryEdit.setText(decode_to_qstring(directory))
try:
globstring = self._getGlobString(directory)
except StackFileSelectionWidget.DetermineStackError, e:
QMessageBox.warning(self, "Invalid selection", str(e))
def repairFile(self, path, filt=None):
"""get new path to lost file"""
from PyQt4.QtGui import QFileDialog, QMessageBox
text = "The file at {} could not be found any more. Do you want to search for it at another directory?".format(
path)
c = QMessageBox.critical(None, "update external data", text,
QMessageBox.Ok | QMessageBox.Cancel)
if c == QMessageBox.Cancel:
raise RuntimeError("Could not find external data: " + path)
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
fileName = QFileDialog.getOpenFileName(None,
"repair files",
path,
filt,
options=options)
if fileName.isEmpty():
raise RuntimeError("Could not find external data: " + path)
else:
return str(fileName)
def exportRelabeling(self):
# Ask for the export path
exportPath = QFileDialog.getSaveFileName(
self,
"Save supervoxel relabeling",
"",
"Hdf5 Files (*.h5 *.hdf5)",
options=QFileDialog.Options(QFileDialog.DontUseNativeDialog))
if exportPath.isNull():
return
def handleProgress(progress):
# TODO: Hook this up to the progress bar
logger.info("Export progress: {}%".format(progress))
op = self.topLevelOperatorView
req = op.exportFinalSupervoxels(encode_from_qstring(exportPath), "zyx",
handleProgress)
self._drawer.exportButton.setEnabled(False)
def handleFinish(*args):
self._drawer.exportButton.setEnabled(True)
req.notify_finished(handleFinish)
req.notify_failed(handleFinish)
def save(self):
options = QFileDialog.Options()
fileName = QFileDialog.getSaveFileName(
self,
"QFileDialog.getSaveFileName()",
"",
"All Files (*);;Text Files (*.txt)",
options=options)
#except:
# fileName, _= QFileDialog.getSaveFileName(self,"QFileDialog.getSaveFileName()","","All Files (*);;Text Files (*.txt)", options=options)
if PYQT == 5:
fileName = fileName[0]
else:
pass
if fileName:
file1 = open(fileName, 'w')
#print ('open',fileName)
file1.write(
'name, F_0,V_0,K_0,Kprime_0 Debye_0,grueneisen-0,q_0,G_0,Gprime_0, eta_s0 '
)
file1.write('\n')
for i in self.Solidsolution:
for j in i.parameters(self.Pressure, self.Temperature):
file1.write('{:8.8}'.format(j))
file1.write(' ')
file1.write('\n')
file1.close()
def _chooseDirectory(self):
# Find the directory of the most recently opened image file
mostRecentStackDirectory = PreferencesManager().get(
'DataSelection', 'recent stack directory')
if mostRecentStackDirectory is not None:
defaultDirectory = os.path.split(mostRecentStackDirectory)[0]
else:
defaultDirectory = os.path.expanduser('~')
options = QFileDialog.Options(QFileDialog.ShowDirsOnly)
if ilastik.config.cfg.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
# Launch the "Open File" dialog
directory = QFileDialog.getExistingDirectory(self,
"Image Stack Directory",
defaultDirectory,
options=options)
if directory.isNull():
# User cancelled
return
directory = encode_from_qstring(directory)
PreferencesManager().set('DataSelection', 'recent stack directory',
directory)
self.directoryEdit.setText(decode_to_qstring(directory))
globstring = self._getGlobString(directory)
if globstring:
filenames = OpStackLoader.expandGlobStrings(globstring)
self._updateFileList(sorted(filenames))
# As a convenience, also show the glob string in the pattern field
self.patternEdit.setText(decode_to_qstring(globstring))
def getOpenFileNames(parent=None,
caption='',
directory='',
filter='',
selectedFilter='',
options=QFileDialogQt4.Options()):
return QFileDialogQt4.getOpenFileNamesAndFilter(
parent, caption, directory, filter, selectedFilter, options)
def getSaveFileName(parent=None,
caption='',
directory='',
filter='',
selectedFilter='',
options=OldFileDialog.Options()):
return OldFileDialog.getSaveFileNameAndFilter(
parent, caption, directory, filter, selectedFilter, options)
def _onSave(self):
# If we are actually playing a recording right now, then the "Stop Recording" action gets triggered as the last step.
# Ignore it.
if self._recorder is None:
return
self.commentsDisplayEdit.setFocus(True)
self._autopaused = False
if not self._recorder.paused:
self._onPause(False)
settings = QSettings("eventcapture", "gui")
# Author name is required
author_name = str(self.authorEdit.text())
if author_name == '':
QMessageBox.critical(
self, "Author name required",
"Please enter your name as the author of this test case.")
return
else:
# Save as default for next recording.
settings.setValue("author_name", author_name)
default_dir = self._default_save_dir
variant = settings.value("recordings_directory")
if not variant.isNull():
default_dir = str(variant.toString())
if default_dir is None:
default_dir = ''
now = datetime.datetime.now()
timestr = "{:04d}{:02d}{:02d}-{:02d}{:02d}".format(
now.year, now.month, now.day, now.hour, now.minute)
default_script_path = os.path.join(
default_dir, "recording-{timestr}.py".format(timestr=timestr))
dlg = QFileDialog(self, "Save Playback Script", default_script_path,
"eventcapture scripts (*.py)")
dlg.setObjectName("event_recorder_save_dlg")
dlg.setAcceptMode(QFileDialog.AcceptSave)
dlg.setOptions(QFileDialog.Options(QFileDialog.DontUseNativeDialog))
dlg.exec_()
# If the user cancelled, stop now
if dlg.result() == QFileDialog.Rejected:
return
script_path = encode_from_qstring(dlg.selectedFiles()[0])
# Remember the directory as our new default
default_dir = os.path.split(script_path)[0]
settings.setValue("recordings_directory", default_dir)
with open(script_path, 'w') as f:
self._recorder.writeScript(f, author_name)
self._saved = True
def saveFileLocation(self):
"""Prompts user where to save the file"""
options = QFileDialog.Options()
fileName = QFileDialog.getSaveFileName(self,
"Save as",
"",
"CSV(*.csv)",
options=options)
return str(fileName)
def handleDirectoryButtonClicked(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directoryName = QFileDialog.getExistingDirectory(self,
"Base Directory",
self.defaultDirectory,
options=options)
self.ui.directoryInput.setText(directoryName)
def openChooserDialog(categories="Image files (*.jpg);;Video files (*.mp4)"):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
filename = QFileDialog.getOpenFileName(None,
"Choose File..",
"",
categories,
options=options)
return filename
def _onLineageFileNameButton(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
fn = QFileDialog.getSaveFileName(self, 'Save Lineage Trees', os.getenv('HOME'), options=options)
if fn is None:
logger.info( "cancelled." )
return
self._drawer.lineageFileNameEdit.setText(str(fn))
def openMultipleVideoChooserDialog(categories="Video files (*.mp4)"):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
filelist = QFileDialog.getOpenFileNames(None,
"Choose File..",
"",
categories,
options=options)
return filelist
def openFileLocation(self):
"""Prompts user to upload a file"""
options = QFileDialog.Options()
fileName = QFileDialog.getOpenFileName(self,
"Open File",
"",
"All Files (*)",
options=options)
return str(fileName)
def __selectDirClicked(self):
" Selects the script working dir "
dirName = QFileDialog.getExistingDirectory(
self, "Select the script working directory", self.__dirEdit.text(),
QFileDialog.Options(QFileDialog.ShowDirsOnly))
if dirName:
self.__dirEdit.setText(os.path.normpath(dirName))
return
def _selectFiles(self):
# Find the directory of the most recently opened image file
mostRecentStackDirectory = PreferencesManager().get(
'DataSelection', 'recent stack directory')
if mostRecentStackDirectory is not None:
defaultDirectory = os.path.split(mostRecentStackDirectory)[0]
else:
defaultDirectory = os.path.expanduser('~')
options = QFileDialog.Options(QFileDialog.ShowDirsOnly)
if ilastik.config.cfg.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
# Launch the "Open File" dialog
extensions = vigra.impex.listExtensions().split()
filt = "Image files (" + ' '.join('*.' + x for x in extensions) + ')'
options = QFileDialog.Options()
if ilastik.config.cfg.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
fileNames = QFileDialog.getOpenFileNames(self,
"Select Images for Stack",
defaultDirectory,
filt,
options=options)
fileNames = map(encode_from_qstring, fileNames)
if len(fileNames) == 0:
return
if len(fileNames) == 1:
msg = 'Cannot create stack: You only chose a single file. '
msg += 'If your stack is contained in a single file (e.g. a multi-page tiff or hdf5 volume),'
msg += ' please use the "Add File" button.'
QMessageBox.warning(self, "Invalid selection", msg)
return None
directory = os.path.split(fileNames[0])[0]
PreferencesManager().set('DataSelection', 'recent stack directory',
directory)
self._updateFileList(fileNames)
def __selectDirClicked(self):
" The user selects a directory "
dirName = QFileDialog.getExistingDirectory(
self, "Select directory to search in",
self.dirEditCombo.currentText(),
QFileDialog.Options(QFileDialog.ShowDirsOnly))
if dirName:
self.dirEditCombo.setEditText(os.path.normpath(dirName))
self.__testSearchability()
return
def onDirButton( self ):
" Displays a directory selection dialog "
dirName = QFileDialog.getExistingDirectory( self,
"Select project directory",
self.dirEdit.text(),
QFileDialog.Options( QFileDialog.ShowDirsOnly ) )
if dirName:
self.dirEdit.setText( os.path.normpath( dirName ) )
return
def __init__(self, path="", name="", parent=None, confirm_overwrite=False):
super(FileWidget, self).__init__(name, parent)
layout = QFormLayout(self)
browse_button = QPushButton("File Path")
self.filename_edit = QLineEdit(path)
layout.addRow(browse_button, self.filename_edit)
browse_button.clicked.connect(self.set_path)
self.dialog_options = QFileDialog.Options()
if not confirm_overwrite:
self.dialog_options |= QFileDialog.DontConfirmOverwrite
self.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Fixed)
def _onExportTifButtonPressed(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
directory = encode_from_qstring(QFileDialog.getExistingDirectory(self, 'Select Directory',os.path.expanduser("~"), options=options))
if directory is None or len(str(directory)) == 0:
logger.info( "cancelled." )
return
logger.info( 'Saving results as tiffs...' )
label2color = self.mainOperator.label2color
lshape = list(self.mainOperator.LabelImage.meta.shape)
def _handle_progress(x):
self.applet.progressSignal.emit(x)
def _export():
num_files = float(len(label2color))
for t, label2color_at in enumerate(label2color):
if len(label2color_at) == 0:
continue
logger.info( 'exporting tiffs for t = ' + str(t) )
roi = SubRegion(self.mainOperator.LabelImage, start=[t,] + 4*[0,], stop=[t+1,] + list(lshape[1:]))
labelImage = self.mainOperator.LabelImage.get(roi).wait()
relabeled = relabel(labelImage[0,...,0],label2color_at)
for i in range(relabeled.shape[2]):
out_im = relabeled[:,:,i]
out_fn = str(directory) + '/vis_t' + str(t).zfill(4) + '_z' + str(i).zfill(4) + '.tif'
vigra.impex.writeImage(np.asarray(out_im,dtype=np.uint32), out_fn)
_handle_progress(t/num_files * 100)
logger.info( 'Tiffs exported.' )
def _handle_finished(*args):
self._drawer.exportTifButton.setEnabled(True)
self.applet.progressSignal.emit(100)
def _handle_failure( exc, exc_info ):
msg = "Exception raised during export. See traceback above.\n"
log_exception( logger, msg, exc_info )
self.applet.progressSignal.emit(100)
self._drawer.exportTifButton.setEnabled(True)
self._drawer.exportTifButton.setEnabled(False)
self.applet.progressSignal.emit(0)
req = Request( _export )
req.notify_failed( _handle_failure )
req.notify_finished( _handle_finished )
req.submit()
def onUsePrecomputedFeaturesButtonClicked(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
filename = QFileDialog.getOpenFileName(self,
'Open Feature List',
'.',
options=options)
filename = encode_from_qstring(filename)
#sanity checks on the given file
if not filename:
return
if not os.path.exists(filename):
QMessageBox.critical(self, "Open Feature List",
"File '%s' does not exist" % filename)
return
f = open(filename, 'r')
with f:
for line in f:
line = line.strip()
if len(line) == 0:
continue
if not os.path.exists(line):
QMessageBox.critical(
self, "Open Feature List",
"File '%s', referenced in '%s', does not exist" %
(line, filename))
return
try:
h = h5py.File(line, 'r')
with h:
assert len(h["data"].shape) == 3
except:
QMessageBox.critical(
self, "Open Feature List",
"File '%s', referenced in '%s', could not be opened as an HDF5 file or does not contain a 3D dataset called 'data'"
% (line, filename))
return
self.topLevelOperatorView.FeatureListFilename.setValue(filename)
self.topLevelOperatorView._setupOutputs()
self.onFeaturesSelectionsChanged()
# Notify the workflow that some applets may have changed state now.
# (For example, the downstream pixel classification applet can
# be used now that there are features selected)
self.parentApplet.appletStateUpdateRequested.emit()
def _select_file_with_dialog(self,
caption = 'Select file',
initialDir = None,
filetype_filter = None):
'''Show a modal select file dialog to select a file.'''
filename = QFileDialog.getOpenFileName(self,
caption,
initialDir or '',
filetype_filter or '',
# The remaining attributes are currently unused
None, # selectedFilter
QFileDialog.Options()) #options
return filename
def getProjectPathToOpen(self, defaultDirectory):
"""
Return the path of the project the user wants to open (or None if he cancels).
"""
projectFilePath = QFileDialog.getOpenFileName(
self,
"Open Ilastik Project",
defaultDirectory,
"Ilastik project files (*.ilp)",
options=QFileDialog.Options(QFileDialog.DontUseNativeDialog))
# If the user canceled, stop now
if projectFilePath.isNull():
return None
return str(projectFilePath)
def onUsePrecomputedFeaturesButtonClicked(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
filenames = QFileDialog.getOpenFileNames(self,
'Open Feature Files',
'.',
options=options)
filenames = map(encode_from_qstring, filenames)
# Check if file exists
if not filenames:
return
for filename in filenames:
if not os.path.exists(filename):
QMessageBox.critical(self, "Open Feature List",
"File '%s' does not exist" % filename)
return
num_lanes = len(self.parentApplet.topLevelOperator.FeatureListFilename)
if num_lanes != len(filenames):
QMessageBox.critical(
self, "Wrong number of feature files",
"You must select all pre-computed feature files at once (shift-click).\n"
"You selected {} file(s), but there are {} image(s) loaded".
format(len(filenames), num_lanes))
return
for filename, slot in zip(
filenames,
self.parentApplet.topLevelOperator.FeatureListFilename):
slot.setValue(filename)
# Create a dummy SelectionMatrix, just so the operator knows it is configured
# This is a little hacky. We should really make SelectionMatrix optional,
# and then handle the choice correctly in setupOutputs, probably involving
# the Output.meta.NOTREADY flag
dummy_matrix = numpy.zeros((6, 7), dtype=bool)
dummy_matrix[0, 0] = True
self.parentApplet.topLevelOperator.SelectionMatrix.setValue(True)
# Notify the workflow that some applets may have changed state now.
# (For example, the downstream pixel classification applet can
# be used now that there are features selected)
self.parentApplet.appletStateUpdateRequested.emit()
def _onSave(self):
# If we are actually playing a recording right now, then the "Stop Recording" action gets triggered as the last step.
# Ignore it.
if self._recorder is None:
return
self.commentsDisplayEdit.setFocus(True)
self._autopaused = False
if not self._recorder.paused:
self._onPause(False)
self.startButton.setEnabled(True)
settings = QSettings("Ilastik", "Event Recorder")
variant = settings.value("recordings_directory")
if not variant.isNull():
default_dir = str( variant.toString() )
else:
import ilastik
ilastik_module_root = os.path.split(ilastik.__file__)[0]
ilastik_repo_root = os.path.split( ilastik_module_root )[0]
default_dir = os.path.join( ilastik_repo_root, "tests" )
now = datetime.datetime.now()
timestr = "{:04d}{:02d}{:02d}-{:02d}{:02d}".format( now.year, now.month, now.day, now.hour, now.minute )
default_script_path = os.path.join( default_dir, "recording-{timestr}.py".format( timestr=timestr ) )
dlg = QFileDialog(self, "Save Playback Script", default_script_path, "Ilastik event playback scripts (*.py)")
dlg.setObjectName("event_recorder_save_dlg")
dlg.setAcceptMode(QFileDialog.AcceptSave)
dlg.setOptions( QFileDialog.Options(QFileDialog.DontUseNativeDialog) )
dlg.exec_()
# If the user cancelled, stop now
if dlg.result() == QFileDialog.Rejected:
return
script_path = str(dlg.selectedFiles()[0])
# Remember the directory as our new default
default_dir = os.path.split(script_path)[0]
settings.setValue( "recordings_directory", default_dir )
with open(script_path, 'w') as f:
self._recorder.writeScript(f)
self._saved = True
def getImageFileNamesToOpen(self, defaultDirectory):
"""
Launch an "Open File" dialog to ask the user for one or more image files.
"""
extensions = OpDataSelection.SupportedExtensions
filt = "Image files (" + ' '.join('*.' + x for x in extensions) + ')'
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
fileNames = QFileDialog.getOpenFileNames(self,
"Select Images",
defaultDirectory,
filt,
options=options)
# Convert from QtString to python str
fileNames = [str(s) for s in fileNames]
return fileNames
def getProjectPathToCreate(self,
defaultPath=None,
caption="Create Ilastik Project"):
"""
Ask the user where he would like to create a project file.
"""
if defaultPath is None:
defaultPath = os.path.expanduser("~/MyProject.ilp")
fileSelected = False
while not fileSelected:
projectFilePath = QFileDialog.getSaveFileName(
self,
caption,
defaultPath,
"Ilastik project files (*.ilp)",
options=QFileDialog.Options(QFileDialog.DontUseNativeDialog))
# If the user cancelled, stop now
if projectFilePath.isNull():
return None
projectFilePath = str(projectFilePath)
fileSelected = True
# Add extension if necessary
fileExtension = os.path.splitext(projectFilePath)[1].lower()
if fileExtension != '.ilp':
projectFilePath += ".ilp"
if os.path.exists(projectFilePath):
# Since we changed the file path, we need to re-check if we're overwriting an existing file.
message = "A file named '" + projectFilePath + "' already exists in this location.\n"
message += "Are you sure you want to overwrite it?"
buttons = QMessageBox.Yes | QMessageBox.Cancel
response = QMessageBox.warning(
self,
"Overwrite existing project?",
message,
buttons,
defaultButton=QMessageBox.Cancel)
if response == QMessageBox.Cancel:
# Try again...
fileSelected = False
return projectFilePath
def onUsePrecomputedFeaturesButtonClicked(self):
options = QFileDialog.Options()
if ilastik_config.getboolean("ilastik", "debug"):
options |= QFileDialog.DontUseNativeDialog
filename = QFileDialog.getOpenFileName(self,
'Open Feature List',
'.',
options=options)
#sanity checks on the given file
if not filename:
return
if not os.path.exists(filename):
QMessageBox.critical(self, "Open Feature List",
"File '%s' does not exist" % filename)
return
f = open(filename, 'r')
with f:
for line in f:
line = line.strip()
if len(line) == 0:
continue
if not os.path.exists(line):
QMessageBox.critical(
self, "Open Feature List",
"File '%s', referenced in '%s', does not exist" %
(line, filename))
return
try:
h = h5py.File(line, 'r')
with h:
assert len(h["data"].shape) == 3
except:
QMessageBox.critical(
self, "Open Feature List",
"File '%s', referenced in '%s', could not be opened as an HDF5 file or does not contain a 3D dataset called 'data'"
% (line, filename))
return
self.topLevelOperatorView.FeatureListFilename.setValue(filename)
self.topLevelOperatorView._setupOutputs()
self.onFeaturesSelectionsChanged()
def exportFinalSegmentation(self):
# Ask for the export path
exportPath = QFileDialog.getSaveFileName( self,
"Save final segmentation",
"",
"Hdf5 Files (*.h5 *.hdf5)",
options=QFileDialog.Options(QFileDialog.DontUseNativeDialog) )
if exportPath.isNull():
return
def handleProgress(progress):
# TODO: Hook this up to the progress bar
print "Export progress: {}%".format( progress )
op = self.topLevelOperatorView
req = op.exportFinalSegmentation( str(exportPath),
"zyx",
handleProgress )
self._drawer.exportButton.setEnabled(False)
def handleFinish(*args):
self._drawer.exportButton.setEnabled(True)
req.notify_finished( handleFinish )
req.notify_failed( handleFinish )
