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 initAppletDrawerUi(self):
        # Load the ui file (find it in our own directory)
        localDir = os.path.split(__file__)[0]
        self._drawer = uic.loadUi(localDir + "/drawer.ui")
        self._drawer.selectFeaturesButton.pressed.connect(
            self._selectFeaturesButtonPressed)
        if not ilastik_config.getboolean("ilastik", "debug"):
            self._drawer.exportButton.setVisible(False)

        self._drawer.exportButton.pressed.connect(
            self._exportFeaturesButtonPressed)

        slot = self.topLevelOperatorView.Features
        if slot.ready():
            selectedFeatures = self.topLevelOperatorView.Features([]).wait()
        else:
            selectedFeatures = None

        nfeatures = 0
        if selectedFeatures is not None:
            for plugin_features in selectedFeatures.values():
                nfeatures += len(plugin_features)

        self._drawer.featuresSelected.setText(
            "{} features computed, \nsome may have multiple channels".format(
                nfeatures))

        # get the applet reference from the workflow (needed for the progressSignal)
        self.applet = self.topLevelOperatorView.parent.parent.objectExtractionApplet
Exemplo n.º 3
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    def getImageFileNamesToOpen(self, defaultDirectory):
        """
        Launch an "Open File" dialog to ask the user for one or more image files.
        """
        file_dialog = QFileDialog(self, "Select Images")

        extensions = OpDataSelection.SupportedExtensions
        filter_strs = ["*." + x for x in extensions]
        filters = ["{filt} ({filt})".format(filt=x) for x in filter_strs]
        filt_all_str = "Image files (" + ' '.join(filter_strs) + ')'
        file_dialog.setFilters([filt_all_str] + filters)

        # do not display file types associated with a filter
        # the line for "Image files" is too long otherwise
        file_dialog.setNameFilterDetailsVisible(False)
        # select multiple files
        file_dialog.setFileMode(QFileDialog.ExistingFiles)
        if ilastik_config.getboolean("ilastik", "debug"):
            file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)

        if file_dialog.exec_():
            fileNames = file_dialog.selectedFiles()
            # Convert from QtString to python str
            fileNames = map(encode_from_qstring, fileNames)
            return fileNames

        return []
Exemplo n.º 4
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    def initAppletDrawerUi(self):
        # Load the ui file (find it in our own directory)
        localDir = os.path.split(__file__)[0]
        self._drawer = uic.loadUi(localDir+"/drawer.ui")
        self._drawer.selectFeaturesButton.pressed.connect(self._selectFeaturesButtonPressed)
        if not ilastik_config.getboolean("ilastik", "debug"):
            self._drawer.exportButton.setVisible(False)
            
        self._drawer.exportButton.pressed.connect(self._exportFeaturesButtonPressed)
        
        slot = self.topLevelOperatorView.Features
        if slot.ready():
            selectedFeatures = self.topLevelOperatorView.Features([]).wait()
        else:
            selectedFeatures = None
        
        nfeatures = 0
        if selectedFeatures is not None:
            for plugin_features in selectedFeatures.itervalues():
                nfeatures += len(plugin_features)

        self._drawer.featuresSelected.setText("{} features computed, \nsome may have multiple channels".format(nfeatures))
        
        # get the applet reference from the workflow (needed for the progressSignal)
        self.applet = self.topLevelOperatorView.parent.parent.objectExtractionApplet
Exemplo n.º 5
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    def getImageFileNamesToOpen(cls, parent_window, defaultDirectory):
        """
        Launch an "Open File" dialog to ask the user for one or more image files.
        """
        extensions = OpDataSelection.SupportedExtensions
        filter_strs = ["*." + x for x in extensions]
        filters = ["{filt} ({filt})".format(filt=x) for x in filter_strs]
        filt_all_str = "Image files (" + " ".join(filter_strs) + ")"

        fileNames = []

        if ilastik_config.getboolean("ilastik", "debug"):
            # use Qt dialog in debug mode (more portable?)
            file_dialog = QFileDialog(parent_window, "Select Images")
            file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
            # do not display file types associated with a filter
            # the line for "Image files" is too long otherwise
            file_dialog.setFilters([filt_all_str] + filters)
            file_dialog.setNameFilterDetailsVisible(False)
            # select multiple files
            file_dialog.setFileMode(QFileDialog.ExistingFiles)
            file_dialog.setDirectory(defaultDirectory)

            if file_dialog.exec_():
                fileNames = file_dialog.selectedFiles()
        else:
            # otherwise, use native dialog of the present platform
            fileNames = QFileDialog.getOpenFileNames(parent_window, "Select Images", defaultDirectory, filt_all_str)
        # Convert from QtString to python str
        fileNames = map(encode_from_qstring, fileNames)
        return fileNames
Exemplo n.º 6
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    def chooseNewExportDirectory(self):
        """
        The user wants to choose a new export directory.
        """
        # Launch the "Open File" dialog
        options = QFileDialog.Options()
        if ilastik_config.getboolean("ilastik", "debug"):
            options |= QFileDialog.DontUseNativeDialog

        defaultpath = self.topLevelOperator.WorkingDirectory.value
        directoryName = QFileDialog.getExistingDirectory(self,
                                                         "Export Directory",
                                                         defaultpath,
                                                         options=options)

        # Stop now if the user canceled
        if directoryName.isNull():
            return

        self.chosenExportDirectory = str(directoryName)
        self.drawer.outputDirEdit.setText(directoryName)

        # Auto-check the radio button for this option if necessary
        if not self.drawer.saveToDirButton.isChecked():
            self.drawer.saveToDirButton.setChecked(True)
        else:
            self.handleExportLocationOptionChanged()
Exemplo n.º 7
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def _update_debug_mode(parsed_args):
    # Force debug mode if any of these flags are active.
    if parsed_args.debug or ilastik_config.getboolean("ilastik", "debug"):
        # There are two places that debug mode can be checked.
        # Make sure both are set.
        ilastik_config.set("ilastik", "debug", "true")
        parsed_args.debug = True
Exemplo n.º 8
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    def handleAddStackButtonClicked(self):
        """
        The user clicked the "Import Stack Directory" button.
        """
        # 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.getboolean("ilastik", "debug"):
            options |= QFileDialog.DontUseNativeDialog

        # Launch the "Open File" dialog
        directoryName = QFileDialog.getExistingDirectory(self,
                                                         "Image Stack Directory",
                                                         defaultDirectory,
                                                         options=options)

        # If the user didn't cancel
        if not directoryName.isNull():
            PreferencesManager().set('DataSelection', 'recent stack directory', str(directoryName))
            globString = self.getGlobString( str(directoryName).replace("\\","/" ) )        
            if globString is not None:
                self.importStackFromGlobString( globString )
Exemplo n.º 9
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    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) + ')'
        dlg = QFileDialog( self, "Select Images", defaultDirectory, filt )
        dlg.setOption( QFileDialog.HideNameFilterDetails, False )
        if ilastik_config.getboolean("ilastik", "debug"):
            dlg.setOption( QFileDialog.DontUseNativeDialog, True )
        dlg.setViewMode( QFileDialog.Detail )
        dlg.setFileMode( QFileDialog.ExistingFiles )

        if True: # FIXME: Test scripts can't allow modal dialogs
            dlg.show()
            if dlg.result() == QDialog.Accepted:
                fileNames = dlg.selectedFiles()
            else:
                fileNames = []
        if dlg.exec_():
            fileNames = dlg.selectedFiles()
        else:
            fileNames = []

        # Convert from QtString to python str
        fileNames = [str(s) for s in fileNames]
        return fileNames
Exemplo n.º 10
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def _update_debug_mode(parsed_args):
    # Force debug mode if any of these flags are active.
    if parsed_args.debug or ilastik_config.getboolean('ilastik', 'debug'):
        # There are two places that debug mode can be checked.
        # Make sure both are set.
        ilastik_config.set('ilastik', 'debug', 'true')
        parsed_args.debug = True
Exemplo n.º 11
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    def connectLane(self, laneIndex):
        # Get a handle to each operator
        opData = self.dataSelectionApplet.topLevelOperator.getLane(laneIndex)
        opTrainingFeatures = self.featureSelectionApplet.topLevelOperator.getLane(laneIndex)
        opClassify = self.pcApplet.topLevelOperator.getLane(laneIndex)
        opDataExport = self.dataExportApplet.topLevelOperator.getLane(laneIndex)
        
        # Input Image -> Feature Op
        #         and -> Classification Op (for display)
        opTrainingFeatures.InputImage.connect( opData.Image )
        opClassify.InputImages.connect( opData.Image )
        
        if ilastik_config.getboolean('ilastik', 'debug'):
            opClassify.PredictionMasks.connect( opData.ImageGroup[self.DATA_ROLE_PREDICTION_MASK] )
        
        # Feature Images -> Classification Op (for training, prediction)
        opClassify.FeatureImages.connect( opTrainingFeatures.OutputImage )
        opClassify.CachedFeatureImages.connect( opTrainingFeatures.CachedOutputImage )
        
        # Training flags -> Classification Op (for GUI restrictions)
        opClassify.LabelsAllowedFlags.connect( opData.AllowLabels )

        # Data Export connections
        opDataExport.RawData.connect( opData.ImageGroup[self.DATA_ROLE_RAW] )
        opDataExport.RawDatasetInfo.connect( opData.DatasetGroup[self.DATA_ROLE_RAW] )
        opDataExport.ConstraintDataset.connect( opData.ImageGroup[self.DATA_ROLE_RAW] )
        opDataExport.Inputs.resize( len(self.EXPORT_NAMES) )
        opDataExport.Inputs[0].connect( opClassify.HeadlessPredictionProbabilities )
        opDataExport.Inputs[1].connect( opClassify.SimpleSegmentation )
        opDataExport.Inputs[2].connect( opClassify.HeadlessUncertaintyEstimate )
        opDataExport.Inputs[3].connect( opClassify.FeatureImages )
        for slot in opDataExport.Inputs:
            assert slot.partner is not None
Exemplo n.º 12
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    def _onExportTifButtonPressed(self):
        options = QFileDialog.Options()
        if ilastik_config.getboolean("ilastik", "debug"):
            options |= QFileDialog.DontUseNativeDialog

        directory = QFileDialog.getExistingDirectory(self, 'Select Directory',os.getenv('HOME'), options=options)      
        
        if directory is None:
            print "cancelled."
            return
        
        print 'Saving results as tiffs...'
        
        label2color = self.mainOperator.label2color
        lshape = list(self.mainOperator.LabelImage.meta.shape)
    
        for t, label2color_at in enumerate(label2color):
            if len(label2color_at) == 0:                
                continue
            print '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)
        
        print 'Tiffs exported.'
Exemplo n.º 13
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    def connectLane(self, laneIndex):
        # Get a handle to each operator
        opData = self.dataSelectionApplet.topLevelOperator.getLane(laneIndex)
        opTrainingFeatures = self.featureSelectionApplet.topLevelOperator.getLane(laneIndex)
        opClassify = self.pcApplet.topLevelOperator.getLane(laneIndex)
        opDataExport = self.dataExportApplet.topLevelOperator.getLane(laneIndex)
        
        # Input Image -> Feature Op
        #         and -> Classification Op (for display)
        opTrainingFeatures.InputImage.connect( opData.Image )
        opClassify.InputImages.connect( opData.Image )
        
        if ilastik_config.getboolean('ilastik', 'debug'):
            opClassify.PredictionMasks.connect( opData.ImageGroup[self.DATA_ROLE_PREDICTION_MASK] )
        
        # Feature Images -> Classification Op (for training, prediction)
        opClassify.FeatureImages.connect( opTrainingFeatures.OutputImage )
        opClassify.CachedFeatureImages.connect( opTrainingFeatures.CachedOutputImage )
        
        # Training flags -> Classification Op (for GUI restrictions)
        opClassify.LabelsAllowedFlags.connect( opData.AllowLabels )

        # Data Export connections
        opDataExport.RawData.connect( opData.ImageGroup[self.DATA_ROLE_RAW] )
        opDataExport.RawDatasetInfo.connect( opData.DatasetGroup[self.DATA_ROLE_RAW] )
        opDataExport.ConstraintDataset.connect( opData.ImageGroup[self.DATA_ROLE_RAW] )
        opDataExport.Inputs.resize( len(self.EXPORT_NAMES) )
        opDataExport.Inputs[0].connect( opClassify.HeadlessPredictionProbabilities )
        opDataExport.Inputs[1].connect( opClassify.SimpleSegmentation )
        opDataExport.Inputs[2].connect( opClassify.HeadlessUncertaintyEstimate )
        opDataExport.Inputs[3].connect( opClassify.FeatureImages )
        for slot in opDataExport.Inputs:
            assert slot.partner is not None
Exemplo n.º 14
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    def initAppletDrawerUi(self):
        super(ConservationTrackingGui, self).initAppletDrawerUi()        

        self._allowedTimeoutInputRegEx = re.compile('^[0-9]*$')
        self._drawer.timeoutBox.textChanged.connect(self._onTimeoutBoxChanged)

        if not ilastik_config.getboolean("ilastik", "debug"):
            assert self._drawer.trackletsBox.isChecked()
            self._drawer.trackletsBox.hide()
            
            assert not self._drawer.hardPriorBox.isChecked()
            self._drawer.hardPriorBox.hide()

            assert not self._drawer.opticalBox.isChecked()
            self._drawer.opticalBox.hide()

            self._drawer.maxDistBox.hide() # hide the maximal distance box
            self._drawer.label_2.hide() # hie the maximal distance label
            self._drawer.label_5.hide() # hide division threshold label
            self._drawer.divThreshBox.hide()
            self._drawer.label_25.hide() # hide avg. obj size label
            self._drawer.avgSizeBox.hide()
          
        self.mergerLabels = [self._drawer.merg1,
                             self._drawer.merg2,
                             self._drawer.merg3,
                             self._drawer.merg4,
                             self._drawer.merg5,
                             self._drawer.merg6,
                             self._drawer.merg7]
        for i in range(len(self.mergerLabels)):
            self._labelSetStyleSheet(self.mergerLabels[i], self.mergerColors[i+1])
        
        self._onMaxObjectsBoxChanged()
        self._drawer.maxObjectsBox.valueChanged.connect(self._onMaxObjectsBoxChanged)                
Exemplo n.º 15
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 def menus(self):
     m = QMenu("&Export", self.volumeEditorWidget)
     #m.addAction("Export Object Information").triggered.connect(self.show_export_dialog)
     if ilastik_config.getboolean("ilastik", "debug"):
         m.addAction("Export All Label Info").triggered.connect( self.exportLabelInfo )
         m.addAction("Import New Label Info").triggered.connect( self.importLabelInfo )
     return [m]
Exemplo n.º 16
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    def chooseNewExportDirectory(self):
        """
        The user wants to choose a new export directory.
        """
        with Tracer(traceLogger):
            # Launch the "Open File" dialog
            options = QFileDialog.Options()
            if ilastik_config.getboolean("ilastik", "debug"):
                options |= QFileDialog.DontUseNativeDialog

            defaultpath = self.topLevelOperator.WorkingDirectory.value
            directoryName = QFileDialog.getExistingDirectory(
                self, "Export Directory", defaultpath, options=options)

            # Stop now if the user canceled
            if directoryName.isNull():
                return

            self.chosenExportDirectory = str(directoryName)
            self.drawer.outputDirEdit.setText(directoryName)

            # Auto-check the radio button for this option if necessary
            if not self.drawer.saveToDirButton.isChecked():
                self.drawer.saveToDirButton.setChecked(True)
            else:
                self.handleExportLocationOptionChanged()
Exemplo n.º 17
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    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)
Exemplo n.º 18
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def _init_logging( parsed_args ):
    from ilastik.ilastik_logging import default_config, startUpdateInterval
    if ilastik_config.getboolean('ilastik', 'debug') or parsed_args.headless:
        default_config.init(output_mode=default_config.OutputMode.BOTH)
    else:
        default_config.init(output_mode=default_config.OutputMode.LOGFILE_WITH_CONSOLE_ERRORS)
        startUpdateInterval(10) # 10 second periodic refresh
Exemplo n.º 19
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    def initAppletDrawerUi(self):
        super(ConservationTrackingGui, self).initAppletDrawerUi()

        self._allowedTimeoutInputRegEx = re.compile('^[0-9]*$')
        self._drawer.timeoutBox.textChanged.connect(self._onTimeoutBoxChanged)

        if not ilastik_config.getboolean("ilastik", "debug"):
            assert self._drawer.trackletsBox.isChecked()
            self._drawer.trackletsBox.hide()

            assert not self._drawer.hardPriorBox.isChecked()
            self._drawer.hardPriorBox.hide()

            assert not self._drawer.opticalBox.isChecked()
            self._drawer.opticalBox.hide()

            self._drawer.maxDistBox.hide()  # hide the maximal distance box
            self._drawer.label_2.hide()  # hie the maximal distance label
            self._drawer.label_5.hide()  # hide division threshold label
            self._drawer.divThreshBox.hide()
            self._drawer.label_25.hide()  # hide avg. obj size label
            self._drawer.avgSizeBox.hide()

        self.mergerLabels = [
            self._drawer.merg1, self._drawer.merg2, self._drawer.merg3,
            self._drawer.merg4, self._drawer.merg5, self._drawer.merg6,
            self._drawer.merg7
        ]
        for i in range(len(self.mergerLabels)):
            self._labelSetStyleSheet(self.mergerLabels[i],
                                     self.mergerColors[i + 1])

        self._onMaxObjectsBoxChanged()
        self._drawer.maxObjectsBox.valueChanged.connect(
            self._onMaxObjectsBoxChanged)
Exemplo n.º 20
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 def menus(self):
     m = QMenu("&Export", self.volumeEditorWidget)
     #m.addAction("Export Object Information").triggered.connect(self.show_export_dialog)
     if ilastik_config.getboolean("ilastik", "debug"):
         m.addAction("Export All Label Info").triggered.connect( self.exportLabelInfo )
         m.addAction("Import New Label Info").triggered.connect( self.importLabelInfo )
     return [m]
    def testBasic(self):
        # NOTE: In this test, cmd-line args to nosetests will also end up getting "parsed" by ilastik.
        #       That shouldn't be an issue, since the pixel classification workflow ignores unrecognized options.
        #       See if __name__ == __main__ section, below.
        args = "--project=" + self.PROJECT_FILE
        args += " --headless"
        
        #args += " --sys_tmp_dir=/tmp"

        # Batch export options
        args += " --output_format=hdf5"
        args += " --output_filename_format={dataset_dir}/{nickname}_prediction.h5"
        args += " --output_internal_path=volume/pred_volume"
        args += " --raw_data" # (Specifying the role name like this is optional for pixel classification, unless we are also using a mask...)
        args += " " + self.SAMPLE_DATA
        if ilastik_config.getboolean('ilastik', 'debug'):
            args += " --prediction_mask" # (Specifying the role name like this is optional for pixel classification)
            args += " " + self.SAMPLE_MASK

        sys.argv = ['ilastik.py'] # Clear the existing commandline args so it looks like we're starting fresh.
        sys.argv += args.split()

        # Start up the ilastik.py entry script as if we had launched it from the command line
        self.ilastik_startup.main()
        
        # Examine the output for basic attributes
        output_path = self.SAMPLE_DATA[:-4] + "_prediction.h5"
        with h5py.File(output_path, 'r') as f:
            assert "/volume/pred_volume" in f
            pred_shape = f["/volume/pred_volume"].shape
            # Assume channel is last axis
            assert pred_shape[:-1] == self.data.shape[:-1], "Prediction volume has wrong shape: {}".format( pred_shape )
            assert pred_shape[-1] == 2, "Prediction volume has wrong shape: {}".format( pred_shape )
Exemplo n.º 22
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    def getImageFileNamesToOpen(cls, parent_window, defaultDirectory):
        """
        opens a QFileDialog for importing files
        """
        extensions = ['nn']
        filter_strs = ["*." + x for x in extensions]
        filters = ["{filt} ({filt})".format(filt=x) for x in filter_strs]
        filt_all_str = "Image files (" + ' '.join(filter_strs) + ')'

        fileNames = []

        if ilastik_config.getboolean("ilastik", "debug"):
            # use Qt dialog in debug mode (more portable?)
            file_dialog = QFileDialog(parent_window, "Select Model")
            file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
            # do not display file types associated with a filter
            # the line for "Image files" is too long otherwise
            file_dialog.setNameFilters([filt_all_str] + filters)
            #file_dialog.setNameFilterDetailsVisible(False)
            # select multiple files
            file_dialog.setFileMode(QFileDialog.ExistingFiles)
            file_dialog.setDirectory(defaultDirectory)

            if file_dialog.exec_():
                fileNames = file_dialog.selectedFiles()
        else:
            # otherwise, use native dialog of the present platform
            fileNames, _ = QFileDialog.getOpenFileNames(parent_window, "Select Model", defaultDirectory, filt_all_str)

        return fileNames
Exemplo n.º 23
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    def getModelFileNameToOpen(cls, parent_window, defaultDirectory):
        """
        opens a QFileDialog for importing files
        """
        extensions = ["pytorch"]
        filter_strs = ["*." + x for x in extensions]
        filters = ["{filt} ({filt})".format(filt=x) for x in filter_strs]
        filt_all_str = "Neural nets (" + " ".join(filter_strs) + ")"

        fileName = None

        if ilastik_config.getboolean("ilastik", "debug"):
            # use Qt dialog in debug mode (more portable?)
            file_dialog = QFileDialog(parent_window, "Select Model")
            file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
            # do not display file types associated with a filter
            # the line for "Image files" is too long otherwise
            file_dialog.setNameFilters([filt_all_str] + filters)
            # file_dialog.setNameFilterDetailsVisible(False)
            file_dialog.setFileMode(QFileDialog.ExistingFile)
            file_dialog.setDirectory(defaultDirectory)

            if file_dialog.exec_():
                fileName = file_dialog.selectedFiles()[0]
        else:
            # otherwise, use native dialog of the present platform
            fileName, _ = QFileDialog.getOpenFileName(parent_window,
                                                      "Select Model",
                                                      defaultDirectory,
                                                      filt_all_str)

        return fileName
Exemplo n.º 24
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    def getImageFileNamesToOpen(cls, parent_window, defaultDirectory):
        """
        Launch an "Open File" dialog to ask the user for one or more image files.
        """
        extensions = OpDataSelection.SupportedExtensions
        filter_strs = ["*." + x for x in extensions]
        filters = ["{filt} ({filt})".format(filt=x) for x in filter_strs]
        filt_all_str = "Image files (" + ' '.join(filter_strs) + ')'

        fileNames = []
        
        if ilastik_config.getboolean("ilastik", "debug"):
            # use Qt dialog in debug mode (more portable?)
            file_dialog = QFileDialog(parent_window, "Select Images")
            file_dialog.setOption(QFileDialog.DontUseNativeDialog, True)
            # do not display file types associated with a filter
            # the line for "Image files" is too long otherwise
            file_dialog.setNameFilters([filt_all_str] + filters)
            #file_dialog.setNameFilterDetailsVisible(False)
            # select multiple files
            file_dialog.setFileMode(QFileDialog.ExistingFiles)
            file_dialog.setDirectory( defaultDirectory )

            if file_dialog.exec_():
                fileNames = file_dialog.selectedFiles()
        else:
            # otherwise, use native dialog of the present platform
            fileNames, _filter = QFileDialog.getOpenFileNames(parent_window, "Select Images", defaultDirectory, filt_all_str)
        return fileNames
Exemplo n.º 25
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 def menus(self):
     if ilastik_config.getboolean('ilastik', 'debug'):
         m = QMenu("Special Stuff", self.volumeEditorWidget)
         m.addAction( "Export to Knime" ).triggered.connect(self.exportObjectInfo)
         mlist = [m]
     else:
         mlist = []
     return mlist
Exemplo n.º 26
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    def initAppletDrawerUi(self):
        super(ConservationTrackingGui, self).initAppletDrawerUi()

        self._allowedTimeoutInputRegEx = re.compile("^[0-9]*$")
        self._drawer.timeoutBox.textChanged.connect(self._onTimeoutBoxChanged)

        if not ilastik_config.getboolean("ilastik", "debug"):

            def checkboxAssertHandler(checkbox, assertEnabled=True):
                if checkbox.isChecked() == assertEnabled:
                    checkbox.hide()
                else:
                    checkbox.setEnabled(False)

            checkboxAssertHandler(self._drawer.trackletsBox, True)

            if self._drawer.classifierPriorBox.isChecked():
                self._drawer.hardPriorBox.hide()
                self._drawer.classifierPriorBox.hide()
                self._drawer.sizeDepBox.hide()
            else:
                self._drawer.hardPriorBox.setEnabled(False)
                self._drawer.classifierPriorBox.setEnabled(False)
                self._drawer.sizeDepBox.setEnabled(False)

            checkboxAssertHandler(self._drawer.opticalBox, False)
            checkboxAssertHandler(self._drawer.mergerResolutionBox, True)

            self._drawer.maxDistBox.hide()  # hide the maximal distance box
            self._drawer.label_2.hide()  # hie the maximal distance label
            self._drawer.label_5.hide()  # hide division threshold label
            self._drawer.divThreshBox.hide()
            self._drawer.label_25.hide()  # hide avg. obj size label
            self._drawer.avgSizeBox.hide()
            self._drawer.label_24.hide()  # hide motion model weight label
            self._drawer.motionModelWeightBox.hide()

        self.mergerLabels = [
            self._drawer.merg1,
            self._drawer.merg2,
            self._drawer.merg3,
            self._drawer.merg4,
            self._drawer.merg5,
            self._drawer.merg6,
            self._drawer.merg7,
        ]
        for i in range(len(self.mergerLabels)):
            self._labelSetStyleSheet(self.mergerLabels[i],
                                     QColor(self.mergerColors[i + 1]))

        self._onMaxObjectsBoxChanged()
        self._drawer.maxObjectsBox.valueChanged.connect(
            self._onMaxObjectsBoxChanged)
        self._drawer.mergerResolutionBox.stateChanged.connect(
            self._onMaxObjectsBoxChanged)

        self._drawer.exportButton.hide()
Exemplo n.º 27
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 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)
Exemplo n.º 28
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 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)
Exemplo n.º 29
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 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))
Exemplo n.º 30
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 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))
Exemplo n.º 31
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 def menus(self):
     if ilastik_config.getboolean('ilastik', 'debug'):
         m = QMenu("Special Stuff", self.volumeEditorWidget)
         m.addAction("Export to Knime").triggered.connect(
             self.exportObjectInfo)
         mlist = [m]
     else:
         mlist = []
     return mlist
Exemplo n.º 32
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def _update_debug_mode( parsed_args ):
    # Force debug mode if any of these flags are active.
    if parsed_args.debug \
    or parsed_args.start_recording \
    or parsed_args.playback_script \
    or ilastik_config.getboolean('ilastik', 'debug'):
        # There are two places that debug mode can be checked.
        # Make sure both are set.
        ilastik_config.set('ilastik', 'debug', 'true')
        parsed_args.debug = True
Exemplo n.º 33
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def _init_logging( parsed_args ):
    from ilastik.ilastik_logging import default_config, startUpdateInterval
    if ilastik_config.getboolean('ilastik', 'debug') or parsed_args.headless:
        default_config.init(output_mode=default_config.OutputMode.BOTH)
    else:
        default_config.init(output_mode=default_config.OutputMode.LOGFILE_WITH_CONSOLE_ERRORS)
        startUpdateInterval(10) # 10 second periodic refresh
    
    if parsed_args.redirect_output:
        logger.info( "All console output is being redirected to: {}"
                     .format( parsed_args.redirect_output ) )
Exemplo n.º 34
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    def _onExportTifButtonPressed(self):
        options = QFileDialog.Options()
        if ilastik_config.getboolean("ilastik", "debug"):
            options |= QFileDialog.DontUseNativeDialog

        directory = QFileDialog.getExistingDirectory(self, 'Select Directory',os.getenv('HOME'), options=options)      
                
        if directory is None or len(str(directory)) == 0:
            print "cancelled."
            return
        
        print '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
                print '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)
            print 'Tiffs exported.'
            
        def _handle_finished(*args):
            self._drawer.exportTifButton.setEnabled(True)
            self.applet.progressSignal.emit(100)
               
        def _handle_failure( exc, exc_info ):
            import traceback, sys
            traceback.print_exception(*exc_info)
            sys.stderr.write("Exception raised during export.  See traceback above.\n")
            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()
Exemplo n.º 35
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def main( parsed_args, workflow_cmdline_args=[] ):
    this_path = os.path.dirname(__file__)
    ilastik_dir = os.path.abspath(os.path.join(this_path, "..%s.." % os.path.sep))
    
    # If necessary, redirect stdout BEFORE logging is initialized
    _redirect_output( parsed_args )
    _init_logging( parsed_args ) # Initialize logging before anything else

    _init_configfile( parsed_args )
    
    _clean_paths( parsed_args, ilastik_dir )
    _update_debug_mode( parsed_args )
    _init_threading_monkeypatch()
    _validate_arg_compatibility( parsed_args )

    # Extra initialization functions.
    # Called during app startup.
    init_funcs = []
    lazyflow_config_fn = _prepare_lazyflow_config( parsed_args )
    if lazyflow_config_fn:
        init_funcs.append( lazyflow_config_fn )    

    load_fn = _prepare_auto_open_project( parsed_args )
    if load_fn:
        init_funcs.append( load_fn )    
    
    create_fn = _prepare_auto_create_new_project( parsed_args )
    if create_fn:
        init_funcs.append( create_fn )

    _enable_faulthandler()
    _init_excepthooks( parsed_args )
    eventcapture_mode, playback_args = _prepare_test_recording_and_playback( parsed_args )    

    if ilastik_config.getboolean("ilastik", "debug"):
        message = 'Starting ilastik in debug mode from "%s".' % ilastik_dir
        logger.info(message)
        print message     # always print the startup message
    else:
        message = 'Starting ilastik from "%s".' % ilastik_dir
        logger.info(message)
        print message     # always print the startup message
    
    # Headless launch
    if parsed_args.headless:
        from ilastik.shell.headless.headlessShell import HeadlessShell
        shell = HeadlessShell( workflow_cmdline_args )
        for f in init_funcs:
            f(shell)
        return shell
    # Normal launch
    else:
        from ilastik.shell.gui.startShellGui import startShellGui
        sys.exit(startShellGui(workflow_cmdline_args, eventcapture_mode, playback_args, *init_funcs))
Exemplo n.º 36
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def _init_excepthooks( parsed_args ):
    # Initialize global exception handling behavior
    import ilastik.excepthooks
    if parsed_args.exit_on_failure:
        # Auto-exit on uncaught exceptions (useful for testing)
        ilastik.excepthooks.init_early_exit_excepthook()
    elif not ilastik_config.getboolean('ilastik', 'debug') and not parsed_args.headless:
        # Show most uncaught exceptions to the user (default behavior)
        ilastik.excepthooks.init_user_mode_excepthook()
    else:
        # Log all exceptions as errors
        ilastik.excepthooks.init_developer_mode_excepthook()
Exemplo n.º 37
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    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()
Exemplo n.º 38
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def _init_excepthooks( parsed_args ):
    # Initialize global exception handling behavior
    import ilastik.excepthooks
    if parsed_args.exit_on_failure:
        # Auto-exit on uncaught exceptions (useful for testing)
        ilastik.excepthooks.init_early_exit_excepthook()
    elif not ilastik_config.getboolean('ilastik', 'debug') and not parsed_args.headless:
        # Show most uncaught exceptions to the user (default behavior)
        ilastik.excepthooks.init_user_mode_excepthook()
    else:
        # Log all exceptions as errors
        ilastik.excepthooks.init_developer_mode_excepthook()
Exemplo n.º 39
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def _update_debug_mode(parsed_args):
    # Force debug mode if any of these flags are active.
    if (
        parsed_args.debug
        or parsed_args.start_recording
        or parsed_args.playback_script
        or ilastik_config.getboolean("ilastik", "debug")
    ):
        # There are two places that debug mode can be checked.
        # Make sure both are set.
        ilastik_config.set("ilastik", "debug", "true")
        parsed_args.debug = True
Exemplo n.º 40
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 def initAppletDrawerUi(self):
     """
     Load the ui file for the applet drawer, which we own.
     """
     localDir = os.path.split(__file__)[0]
     # (We don't pass self here because we keep the drawer ui in a separate object.)
     self.drawer = uic.loadUi(localDir + "/featureSelectionDrawer.ui")
     self.drawer.SelectFeaturesButton.clicked.connect(self.onFeatureButtonClicked)
     self.drawer.UsePrecomputedFeaturesButton.clicked.connect(self.onUsePrecomputedFeaturesButtonClicked)
     dbg = ilastik_config.getboolean("ilastik", "debug")
     if not dbg:
         self.drawer.UsePrecomputedFeaturesButton.setHidden(True)
Exemplo n.º 41
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def init(format_prefix="",
         output_mode=OutputMode.LOGFILE_WITH_CONSOLE_ERRORS,
         logfile_path=DEFAULT_LOGFILE_PATH):
    if logfile_path == "/dev/null":
        assert output_mode != OutputMode.LOGFILE, "Must enable a logging mode."
        output_mode = OutputMode.CONSOLE

    # Preserve pre-existing handlers
    original_root_handlers = list(logging.getLogger().handlers)

    # Start with the default
    default_config = get_default_config(format_prefix, output_mode,
                                        logfile_path)
    logging.config.dictConfig(default_config)

    # Preserve pre-existing handlers
    for handler in original_root_handlers:
        logging.getLogger().addHandler(handler)

    # Update from the user's customizations
    loggingHelpers.updateFromConfigFile()

    # Capture warnings from the warnings module
    logging.captureWarnings(True)

    # Warnings module warnings are shown only once
    warnings.filterwarnings("once")

    # Don't warn about pending deprecations (PyQt generates some of these)
    warnings.filterwarnings("ignore", category=PendingDeprecationWarning)

    # Don't warn about duplicate python bindings for opengm
    # (We import opengm twice, as 'opengm' 'opengm_with_cplex'.)
    warnings.filterwarnings("ignore",
                            message='.*to-Python converter for .*opengm.*',
                            category=RuntimeWarning)

    # Hide all other python converter warnings unless we're in debug mode.
    if not ilastik_config.getboolean("ilastik", "debug"):
        warnings.filterwarnings(
            "ignore",
            message=
            '.*to-Python converter for .*second conversion method ignored.*',
            category=RuntimeWarning)

    # Custom format for warnings
    def simple_warning_format(message, category, filename, lineno, line=None):
        filename = os.path.split(filename)[1]
        return filename + "(" + str(
            lineno) + "): " + category.__name__ + ": " + message[0]

    warnings.formatwarning = simple_warning_format
Exemplo n.º 42
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 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
Exemplo n.º 43
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    def initAppletDrawerUi(self):
        super(ConservationTrackingGui, self).initAppletDrawerUi()

        self._allowedTimeoutInputRegEx = re.compile('^[0-9]*$')
        self._drawer.timeoutBox.textChanged.connect(self._onTimeoutBoxChanged)

        if not ilastik_config.getboolean("ilastik", "debug"):
            def checkboxAssertHandler(checkbox, assertEnabled=True):
                if checkbox.isChecked() == assertEnabled:
                    checkbox.hide()
                else:
                    checkbox.setEnabled(False)

            checkboxAssertHandler(self._drawer.trackletsBox, True)

            if self._drawer.classifierPriorBox.isChecked():
                self._drawer.hardPriorBox.hide()
                self._drawer.classifierPriorBox.hide()
                self._drawer.sizeDepBox.hide()
            else:
                self._drawer.hardPriorBox.setEnabled(False)
                self._drawer.classifierPriorBox.setEnabled(False)
                self._drawer.sizeDepBox.setEnabled(False)

            checkboxAssertHandler(self._drawer.opticalBox, False)
            checkboxAssertHandler(self._drawer.mergerResolutionBox, True)

            self._drawer.maxDistBox.hide() # hide the maximal distance box
            self._drawer.label_2.hide() # hie the maximal distance label
            self._drawer.label_5.hide() # hide division threshold label
            self._drawer.divThreshBox.hide()
            self._drawer.label_25.hide() # hide avg. obj size label
            self._drawer.avgSizeBox.hide()
            self._drawer.label_24.hide() # hide motion model weight label
            self._drawer.motionModelWeightBox.hide()
            self._drawer.maxNearestNeighborsSpinBox.hide()
            self._drawer.MaxNearestNeighbourLabel.hide()
          
        self.mergerLabels = [self._drawer.merg1,
                             self._drawer.merg2,
                             self._drawer.merg3,
                             self._drawer.merg4,
                             self._drawer.merg5,
                             self._drawer.merg6,
                             self._drawer.merg7]
        for i in range(len(self.mergerLabels)):
            self._labelSetStyleSheet(self.mergerLabels[i], self.mergerColors[i+1])
        
        self._onMaxObjectsBoxChanged()
        self._drawer.maxObjectsBox.valueChanged.connect(self._onMaxObjectsBoxChanged)
        self._drawer.mergerResolutionBox.stateChanged.connect(self._onMaxObjectsBoxChanged)
Exemplo n.º 44
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    def add_peer(self, name, address):
        host, port = address
        key = (host, name)
        if key not in self.peers:
            self.peers[key] = {
                "enabled": ilastik_config.getboolean("ipc raw tcp", "autoaccept"),
                "address": [host, port]
            }

        elif self.peers[key]["address"][1] != port:
            self.peers[key]["address"][1] = port
        else:
            return
        self.info.update_connections(self.peers)
Exemplo n.º 45
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 def initAppletDrawerUi(self):
     """
     Load the ui file for the applet drawer, which we own.
     """
     localDir = os.path.split(__file__)[0]
     # (We don't pass self here because we keep the drawer ui in a separate object.)
     self.drawer = uic.loadUi(localDir + "/featureSelectionDrawer.ui")
     self.drawer.SelectFeaturesButton.clicked.connect(
         self.onFeatureButtonClicked)
     self.drawer.UsePrecomputedFeaturesButton.clicked.connect(
         self.onUsePrecomputedFeaturesButtonClicked)
     dbg = ilastik_config.getboolean("ilastik", "debug")
     if not dbg:
         self.drawer.UsePrecomputedFeaturesButton.setHidden(True)
Exemplo n.º 46
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    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()
Exemplo n.º 47
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    def add_peer(self, name, address):
        host, port = address
        key = (host, name)
        if key not in self.peers:
            self.peers[key] = {
                "enabled": ilastik_config.getboolean("ipc raw tcp",
                                                     "autoaccept"),
                "address": [host, port],
            }

        elif self.peers[key]["address"][1] != port:
            self.peers[key]["address"][1] = port
        else:
            return
        self.info.update_connections(self.peers)
Exemplo n.º 48
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    def menus( self ):
        menus = super( PixelClassificationGui, self ).menus()

        # For now classifier selection is only available in debug mode
        if ilastik_config.getboolean('ilastik', 'debug'):
            def handleClassifierAction():
                dlg = ClassifierSelectionDlg(self.topLevelOperatorView, parent=self)
                dlg.exec_()
            
            advanced_menu = QMenu("Advanced", parent=self)
            classifier_action = advanced_menu.addAction("Classifier...")
            classifier_action.triggered.connect( handleClassifierAction )
            menus += [advanced_menu]

        return menus
Exemplo n.º 49
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    def _onExportButtonPressed(self):
        options = QFileDialog.Options()
        if ilastik_config.getboolean("ilastik", "debug"):
            options |= QFileDialog.DontUseNativeDialog

        directory = QFileDialog.getExistingDirectory(self, 'Select Directory',os.getenv('HOME'), options=options)      
        
        if directory is None:
            print "cancelled."
            return
        
        # determine from_time (it could has been changed in the GUI meanwhile)
        for t_from, label2color_at in enumerate(self.mainOperator.label2color):
            if len(label2color_at) == 0:                
                continue
            else:
                break
            
        print "Saving first label image..."
        key = []
        for idx, flag in enumerate(axisTagsToString(self.mainOperator.LabelImage.meta.axistags)):
            if flag is 't':
                key.append(slice(t_from,t_from+1))
            elif flag is 'c':
                key.append(slice(0,1))                
            else:
                key.append(slice(0,self.mainOperator.LabelImage.meta.shape[idx]))                        
        
        roi = SubRegion(self.mainOperator.LabelImage, key)
        labelImage = self.mainOperator.LabelImage.get(roi).wait()
        labelImage = labelImage[0,...,0]
        
        write_events([], str(directory), t_from, labelImage)
        
        events = self.mainOperator.events
        print "Saving events..."
        print "Length of events " + str(len(events))
        
        for i, events_at in enumerate(events):
            t = t_from + i            
            key[0] = slice(t+1,t+2)
            roi = SubRegion(self.mainOperator.LabelImage, key)
            labelImage = self.mainOperator.LabelImage.get(roi).wait()
            labelImage = labelImage[0,...,0]
            if self.withMergers:                
                write_events(events_at, str(directory), t+1, labelImage, self.mainOperator.mergers)
            else:
                write_events(events_at, str(directory), t+1, labelImage)
Exemplo n.º 50
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    def populate(self):
        self.ui.treeWidget.setColumnCount(1)
        for pluginName, features in self.featureDict.iteritems():
            if pluginName == "TestFeatures" and not ilastik_config.getboolean(
                    "ilastik", "debug"):
                continue
            parent = QTreeWidgetItem(self.ui.treeWidget)
            parent.setText(0, pluginName)
            parent.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
            # hack to ensure checkboxes visible
            parent.setCheckState(0, Qt.Checked)
            parent.setCheckState(0, Qt.Unchecked)
            parent.setExpanded(False)
            self.countChecked[pluginName] = 0
            self.countAll[pluginName] = len(self.featureDict[pluginName])
            advanced_names = []
            simple_names = []
            for name in sorted(features.keys()):
                parameters = features[name]
                if 'advanced' in parameters:
                    advanced_names.append(name)
                else:
                    simple_names.append(name)

            for name in simple_names + advanced_names:
                parameters = features[name]

                item = QTreeWidgetItem(parent)
                item.setText(0, name)
                item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
                if 'tooltip' in parameters:
                    item.setToolTip(0, parameters['tooltip'])
                # hack to ensure checkboxes visible
                item.setCheckState(0, Qt.Checked)
                item.setCheckState(0, Qt.Unchecked)
                if pluginName in self.selectedFeatures:
                    if name in self.selectedFeatures[pluginName]:
                        item.setCheckState(0, Qt.Checked)
                        self.countChecked[pluginName] += 1
            if self.countChecked[pluginName] == 0:
                parent.setCheckState(0, Qt.Unchecked)
            elif self.countChecked[pluginName] == self.countAll[pluginName]:
                parent.setCheckState(0, Qt.Checked)
            else:
                parent.setCheckState(0, Qt.PartiallyChecked)
            self.updateToolTip(parent)
        # facilitates switching of the CheckBox when clicking on the Text of a QTreeWidgetItem
        self.ui.treeWidget.setCurrentItem(None)
Exemplo n.º 51
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    def onUsePrecomputedFeaturesButtonClicked(self):
        options = QFileDialog.Options()
        if ilastik_config.getboolean("ilastik", "debug"):
            options |= QFileDialog.DontUseNativeDialog

        filenames, _filter = QFileDialog.getOpenFileNames(self,
                                                          "Open Feature Files",
                                                          ".",
                                                          options=options)

        # 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()
Exemplo n.º 52
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def _init_logging(parsed_args):
    from ilastik.ilastik_logging import default_config, startUpdateInterval, DEFAULT_LOGFILE_PATH

    logfile_path = parsed_args.logfile or DEFAULT_LOGFILE_PATH
    process_name = ""
    if parsed_args.process_name:
        process_name = parsed_args.process_name + " "

    if ilastik_config.getboolean("ilastik", "debug") or parsed_args.headless:
        default_config.init(process_name, default_config.OutputMode.BOTH, logfile_path)
    else:
        default_config.init(process_name, default_config.OutputMode.LOGFILE_WITH_CONSOLE_ERRORS, logfile_path)
        startUpdateInterval(10)  # 10 second periodic refresh

    if parsed_args.redirect_output:
        logger.info("All console output is being redirected to: {}".format(parsed_args.redirect_output))
Exemplo n.º 53
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    def menus(self):
        menus = super(PixelClassificationGui, self).menus()

        # For now classifier selection is only available in debug mode
        if ilastik_config.getboolean('ilastik', 'debug'):

            def handleClassifierAction():
                dlg = ClassifierSelectionDlg(self.topLevelOperatorView,
                                             parent=self)
                dlg.exec_()

            advanced_menu = QMenu("Advanced", parent=self)
            classifier_action = advanced_menu.addAction("Classifier...")
            classifier_action.triggered.connect(handleClassifierAction)
            menus += [advanced_menu]

        return menus
Exemplo n.º 54
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 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
Exemplo n.º 55
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def _init_logging( parsed_args ):
    from ilastik.ilastik_logging import default_config, startUpdateInterval, DEFAULT_LOGFILE_PATH

    logfile_path = parsed_args.logfile or DEFAULT_LOGFILE_PATH
    process_name = ""
    if parsed_args.process_name:
        process_name = parsed_args.process_name + " "

    if ilastik_config.getboolean('ilastik', 'debug') or parsed_args.headless:
        default_config.init(process_name, default_config.OutputMode.BOTH, logfile_path)
    else:
        default_config.init(process_name, default_config.OutputMode.LOGFILE_WITH_CONSOLE_ERRORS, logfile_path)
        startUpdateInterval(10) # 10 second periodic refresh
    
    if parsed_args.redirect_output:
        logger.info( "All console output is being redirected to: {}"
                     .format( parsed_args.redirect_output ) )
Exemplo n.º 56
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    def initAppletDrawerUi(self):
        self._drawer = self._loadUiFile()

        if not ilastik_config.getboolean("ilastik", "debug"):
            self._drawer.exportLabel.hide()
            self._drawer.exportTifButton.hide()

        self._drawer.TrackButton.pressed.connect(self._onTrackButtonPressed)
        self._drawer.exportButton.pressed.connect(self._onExportButtonPressed)
        self._drawer.exportTifButton.pressed.connect(self._onExportTifButtonPressed)

        self._drawer.from_time.valueChanged.connect(self._setRanges)
        self._drawer.from_x.valueChanged.connect(self._setRanges)
        self._drawer.from_y.valueChanged.connect(self._setRanges)
        self._drawer.from_z.valueChanged.connect(self._setRanges)
        self._drawer.to_time.valueChanged.connect(self._setRanges)
        self._drawer.to_x.valueChanged.connect(self._setRanges)
        self._drawer.to_y.valueChanged.connect(self._setRanges)
        self._drawer.to_z.valueChanged.connect(self._setRanges)
Exemplo n.º 57
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    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()
Exemplo n.º 58
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    def populate(self):
        self.ui.treeWidget.setColumnCount(1)
        for pluginName, features in self.featureDict.iteritems():
            if pluginName == "TestFeatures" and not ilastik_config.getboolean(
                    "ilastik", "debug"):
                continue

            parent = QTreeWidgetItem(self.ui.treeWidget)
            if pluginName == "Standard Object Features":
                parent.setText(0, pluginName)
                parent.setToolTip(
                    0,
                    'http://hci.iwr.uni-heidelberg.de/vigra/doc/vigra/group__FeatureAccumulators.html'
                )
            else:
                parent.setText(0, pluginName)
            parent.setExpanded(True)
            advanced_names = []
            simple_names = []
            for name in sorted(features.keys()):
                parameters = features[name]
                if 'advanced' in parameters:
                    advanced_names.append(name)
                else:
                    simple_names.append(name)

            for name in simple_names + advanced_names:
                parameters = features[name]

                item = QTreeWidgetItem(parent)
                item.setText(0, name)
                item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
                if 'tooltip' in parameters:
                    item.setToolTip(0, parameters['tooltip'])
                # hack to ensure checkboxes visible
                item.setCheckState(0, Qt.Checked)
                item.setCheckState(0, Qt.Unchecked)

                if pluginName in self.selectedFeatures:
                    if name in self.selectedFeatures[pluginName]:
                        item.setCheckState(0, Qt.Checked)