Python DatasetInfo.axistags方法代码示例

# 需要导入模块: from ilastik.applets.dataSelection.opDataSelection import DatasetInfo [as 别名]
# 或者: from ilastik.applets.dataSelection.opDataSelection.DatasetInfo import axistags [as 别名]
    def _get_template_dataset_infos(self, input_axes=None):
        """
        Sometimes the default settings for an input file are not suitable (e.g. the axistags need to be changed).
        We assume the LAST non-batch input in the workflow has settings that will work for all batch processing inputs.
        Here, we get the DatasetInfo objects from that lane and store them as 'templates' to modify for all batch-processing files.
        """
        template_infos = {}

        # If there isn't an available dataset to use as a template
        if len(self.dataSelectionApplet.topLevelOperator.DatasetGroup) == 0:
            num_roles = len(self.dataSelectionApplet.topLevelOperator.DatasetRoles.value)
            for role_index in range(num_roles):
                template_infos[role_index] = DatasetInfo()
                template_infos[role_index].axistags = vigra.defaultAxistags(input_axes)
            return template_infos

        # Use the LAST non-batch input file as our 'template' for DatasetInfo settings (e.g. axistags)
        template_lane = len(self.dataSelectionApplet.topLevelOperator.DatasetGroup) - 1
        opDataSelectionTemplateView = self.dataSelectionApplet.topLevelOperator.getLane(template_lane)

        for role_index, info_slot in enumerate(opDataSelectionTemplateView.DatasetGroup):
            if info_slot.ready():
                template_infos[role_index] = info_slot.value
            else:
                template_infos[role_index] = DatasetInfo()
            if input_axes:
                # Support the --input_axes arg to override input axis order, same as DataSelection applet.
                template_infos[role_index].axistags = vigra.defaultAxistags(input_axes)
        return template_infos

# 需要导入模块: from ilastik.applets.dataSelection.opDataSelection import DatasetInfo [as 别名]
# 或者: from ilastik.applets.dataSelection.opDataSelection.DatasetInfo import axistags [as 别名]
        def impl():
            projFilePath = self.PROJECT_FILE
            shell = self.shell

            # New project
            shell.createAndLoadNewProject(projFilePath, self.workflowClass())
            workflow = shell.projectManager.workflow

            from ilastik.applets.dataSelection.opDataSelection import DatasetInfo
            opDataSelection = workflow.dataSelectionApplet.topLevelOperator
            for i, dataFile in enumerate(self.SAMPLE_DATA):
                # Add a file
                info = DatasetInfo()

                info.filePath = dataFile
                info.axistags = vigra.defaultAxistags('xyc')

                opDataSelection.DatasetGroup.resize(i+1)
                opDataSelection.DatasetGroup[i][0].setValue(info)

            # Set some features
            opFeatures = workflow.featureSelectionApplet.topLevelOperator
            #                    sigma:   0.3    0.7    1.0    1.6    3.5    5.0   10.0
            selections = numpy.array( [[True, False, False, False, False, False, False],
                                       [True, False, False, False, False, False, False],
                                       [True, False, False, False, False, False, False],
                                       [False, False, False, False, False, False, False],
                                       [False, False, False, False, False, False, False],
                                       [False, False, False, False, False, False, False]] )
            opFeatures.SelectionMatrix.setValue(selections)

            # Save and close
            shell.projectManager.saveProject()
            shell.ensureNoCurrentProject(assertClean=True)

# 需要导入模块: from ilastik.applets.dataSelection.opDataSelection import DatasetInfo [as 别名]
# 或者: from ilastik.applets.dataSelection.opDataSelection.DatasetInfo import axistags [as 别名]
    def testWeirdAxisInfos(self):
        """
        If we add a dataset that has the channel axis in the wrong place, 
        the operator should automatically transpose it to be last.
        """
        weirdAxisFilename = os.path.join(self.workingDir, 'WeirdAxes.npy')
        expected_data = numpy.random.random( (3,100,100) )
        numpy.save(weirdAxisFilename, expected_data)

        info = DatasetInfo()
        info.filePath = weirdAxisFilename
        info.axistags = vigra.defaultAxistags('cxy')
        
        graph = Graph()
        op = OpDataSelectionGroup(graph=graph, forceAxisOrder=False)
        op.WorkingDirectory.setValue( self.workingDir )
        op.DatasetRoles.setValue( ['RoleA'] )

        op.DatasetGroup.resize( 1 )
        op.DatasetGroup[0].setValue( info )

        assert op.ImageGroup[0].ready()
        
        data_from_op = op.ImageGroup[0][:].wait()
        
        assert data_from_op.dtype == expected_data.dtype 
        assert data_from_op.shape == expected_data.shape, (data_from_op.shape, expected_data.shape)
        assert (data_from_op == expected_data).all()

        # op.Image is a synonym for op.ImageGroup[0]
        assert op.Image.ready()
        assert (op.Image[:].wait() == expected_data).all()
        
        # Ensure that files opened by the inner operators are closed before we exit.
        op.DatasetGroup.resize(0)

# 需要导入模块: from ilastik.applets.dataSelection.opDataSelection import DatasetInfo [as 别名]
# 或者: from ilastik.applets.dataSelection.opDataSelection.DatasetInfo import axistags [as 别名]
    def test_fake_data_source(self):
        graph = lazyflow.graph.Graph()
        reader = OperatorWrapper(OpDataSelection, graph=graph,
                                 operator_kwargs={'forceAxisOrder': False})
        reader.ProjectFile.setValue(self.projectFile)
        reader.WorkingDirectory.setValue(os.getcwd())
        reader.ProjectDataGroup.setValue('DataSelection/local_data')

        info = DatasetInfo()
        # Will be read from the filesystem since the data won't be found in the project file.
        info.location = DatasetInfo.Location.ProjectInternal
        info.filePath = self.testRawDataFileName
        info.internalPath = ""
        info.invertColors = False
        info.convertToGrayscale = False
        # Use *fake* data source
        info.realDataSource = False
        info.axistags = vigra.defaultAxistags('tczyx')
        info.laneShape = self.imgData.shape
        info.laneDtype = self.imgData.dtype

        reader.Dataset.setValues([info])

        # Verify that now data selection operator returns fake data
        # with expected shape and type
        imgData = reader.Image[0][...].wait()

        assert imgData.shape == self.imgData.shape
        assert imgData.dtype == self.imgData.dtype
        expected_fake_data = numpy.zeros(info.laneShape, dtype=info.laneDtype)
        numpy.testing.assert_array_equal(imgData, expected_fake_data)

# 需要导入模块: from ilastik.applets.dataSelection.opDataSelection import DatasetInfo [as 别名]
# 或者: from ilastik.applets.dataSelection.opDataSelection.DatasetInfo import axistags [as 别名]
    def testBasic3DWrongAxes(self):
        """Test if 3D file with intentionally wrong axes is rejected """
        for fileName in self.imgFileNames3D:
            graph = lazyflow.graph.Graph()
            reader = OperatorWrapper(OpDataSelection, graph=graph, operator_kwargs={'forceAxisOrder': False})
            reader.ProjectFile.setValue(self.projectFile)
            reader.WorkingDirectory.setValue(os.getcwd())
            reader.ProjectDataGroup.setValue('DataSelection/local_data')

            info = DatasetInfo()
            # Will be read from the filesystem since the data won't be found in the project file.
            info.location = DatasetInfo.Location.ProjectInternal
            info.filePath = fileName
            info.internalPath = ""
            info.invertColors = False
            info.convertToGrayscale = False
            info.axistags = vigra.defaultAxistags('tzyc')

            try:
                reader.Dataset.setValues([info])
                assert False, "Should have thrown an exception!"
            except DatasetConstraintError:
                pass
            except:
                assert False, "Should have thrown a DatasetConstraintError!"

# 需要导入模块: from ilastik.applets.dataSelection.opDataSelection import DatasetInfo [as 别名]
# 或者: from ilastik.applets.dataSelection.opDataSelection.DatasetInfo import axistags [as 别名]
def append_lane(workflow, input_filepath, axisorder=None):
    # Sanity checks
    assert isinstance(workflow, PixelClassificationWorkflow)
    opPixelClassification = workflow.pcApplet.topLevelOperator
    assert opPixelClassification.Classifier.ready()

    # If the filepath is a globstring, convert the stack to h5
    input_filepath = DataSelectionApplet.convertStacksToH5( [input_filepath], TMP_DIR )[0]

    info = DatasetInfo()
    info.location = DatasetInfo.Location.FileSystem
    info.filePath = input_filepath

    comp = PathComponents(input_filepath)

    # Convert all (non-url) paths to absolute 
    # (otherwise they are relative to the project file, which probably isn't what the user meant)        
    if not isUrl(input_filepath):
        comp.externalPath = os.path.abspath(comp.externalPath)
        info.filePath = comp.totalPath()
    info.nickname = comp.filenameBase
    if axisorder:
        info.axistags = vigra.defaultAxistags(axisorder)

    logger.debug( "adding lane: {}".format( info ) )

    opDataSelection = workflow.dataSelectionApplet.topLevelOperator

    # Add a lane
    num_lanes = len( opDataSelection.DatasetGroup )+1
    logger.debug( "num_lanes: {}".format( num_lanes ) )
    opDataSelection.DatasetGroup.resize( num_lanes )
    
    # Configure it.
    role_index = 0 # raw data
    opDataSelection.DatasetGroup[-1][role_index].setValue( info )

    # Sanity check
    assert len(opPixelClassification.InputImages) == num_lanes
    
    return opPixelClassification

# 需要导入模块: from ilastik.applets.dataSelection.opDataSelection import DatasetInfo [as 别名]
# 或者: from ilastik.applets.dataSelection.opDataSelection.DatasetInfo import axistags [as 别名]
def append_lane(workflow, input_filepath, axisorder=None):
    """
    Add a lane to the project file for the given input file.

    If axisorder is given, override the default axisorder for
    the file and force the project to use the given one.
    
    Globstrings are supported, in which case the files are converted to HDF5 first.
    """
    # If the filepath is a globstring, convert the stack to h5
    input_filepath = DataSelectionApplet.convertStacksToH5( [input_filepath], tempfile.mkdtemp() )[0]

    info = DatasetInfo()
    info.location = DatasetInfo.Location.FileSystem
    info.filePath = input_filepath

    comp = PathComponents(input_filepath)

    # Convert all (non-url) paths to absolute 
    # (otherwise they are relative to the project file, which probably isn't what the user meant)        
    if not isUrl(input_filepath):
        comp.externalPath = os.path.abspath(comp.externalPath)
        info.filePath = comp.totalPath()
    info.nickname = comp.filenameBase
    if axisorder:
        info.axistags = vigra.defaultAxistags(axisorder)

    logger.debug( "adding lane: {}".format( info ) )

    opDataSelection = workflow.dataSelectionApplet.topLevelOperator

    # Add a lane
    num_lanes = len( opDataSelection.DatasetGroup )+1
    logger.debug( "num_lanes: {}".format( num_lanes ) )
    opDataSelection.DatasetGroup.resize( num_lanes )
    
    # Configure it.
    role_index = 0 # raw data
    opDataSelection.DatasetGroup[-1][role_index].setValue( info )

# 需要导入模块: from ilastik.applets.dataSelection.opDataSelection import DatasetInfo [as 别名]
# 或者: from ilastik.applets.dataSelection.opDataSelection.DatasetInfo import axistags [as 别名]
    def testNoChannelAxis(self):
        """
        If we add a dataset that is missing a channel axis altogether, 
        the operator should automatically append a channel axis.
        """
        noChannelFilename = os.path.join(self.workingDir, 'NoChannelAxis.npy')
        noChannelData = numpy.random.random( (100,100) )
        numpy.save(noChannelFilename, noChannelData)

        info = DatasetInfo()
        info.filePath = noChannelFilename
        info.axistags = vigra.defaultAxistags('xy')
        
        graph = Graph()
        op = OpDataSelectionGroup( graph=graph )
        op.WorkingDirectory.setValue( self.workingDir )
        op.DatasetRoles.setValue( ['RoleA'] )

        op.DatasetGroup.resize( 1 )
        op.DatasetGroup[0].setValue( info )

        assert op.ImageGroup[0].ready()
        
        # Note that we expect a channel axis to be appended to the data.
        expected_data = noChannelData[:,:,numpy.newaxis]
        data_from_op = op.ImageGroup[0][:].wait()
        
        assert data_from_op.dtype == expected_data.dtype 
        assert data_from_op.shape == expected_data.shape
        assert (data_from_op == expected_data).all()

        # op.Image is a synonym for op.ImageGroup[0]
        assert op.Image.ready()
        assert (op.Image[:].wait() == expected_data).all()
        
        # Ensure that files opened by the inner operators are closed before we exit.
        op.DatasetGroup.resize(0)