Python vigra.defaultAxistags函数代码示例

    def setupOutputs(self):
        self.fileNameList = []
        globStrings = self.globstring.value

        # Parse list into separate globstrings and combine them
        for globString in sorted(globStrings.split("//")):
            self.fileNameList += sorted(glob.glob(globString))

        num_files = len(self.fileNameList)
        if len(self.fileNameList) == 0:
            self.stack.meta.NOTREADY = True
            return
        try:
            self.info = vigra.impex.ImageInfo(self.fileNameList[0])
            self.slices_per_file = vigra.impex.numberImages(self.fileNameList[0])
        except RuntimeError:
            raise OpStackLoader.FileOpenError(self.fileNameList[0])

        slice_shape = self.info.getShape()
        X, Y, C = slice_shape
        if self.slices_per_file == 1:
            # If this is a stack of 2D images, we assume xy slices stacked along z
            Z = num_files
            shape = (Z, Y, X, C)
            axistags = vigra.defaultAxistags('zyxc')
        else:
            # If it's a stack of 3D volumes, we assume xyz blocks stacked along t
            T = num_files
            Z = self.slices_per_file
            shape = (T, Z, Y, X, C)
            axistags = vigra.defaultAxistags('tzyxc')
            
        self.stack.meta.shape = shape
        self.stack.meta.axistags = axistags
        self.stack.meta.dtype = self.info.getDtype()

 def setUp(self):
     self.data2d = numpy.zeros((3, 3, 3))
     self.data2d[:, :, 0] = 1
     self.data2d[:, :, 1] = 2
     self.data2d[:, :, 2] = 3
     
     self.data2d = self.data2d.view(vigra.VigraArray)
     self.data2d.axistags = vigra.defaultAxistags("xyc")
     
     
     self.data3d = numpy.zeros((3, 3, 3, 3))
     self.data3d[:, :, :, 0] = 1
     self.data3d[:, :, :, 1] = 2
     self.data3d[:, :, :, 2] = 3
     
     self.data3d = self.data3d.view(vigra.VigraArray)
     self.data3d.axistags = vigra.defaultAxistags("xyzc")
     
     self.data_bad_channel = numpy.zeros((3, 3, 3, 3))
     self.data_bad_channel[:, :, 0, :] = 1
     self.data_bad_channel[:, :, 1, :] = 2
     self.data_bad_channel[:, :, 2, :] = 3
     
     self.data_bad_channel = self.data_bad_channel.view(vigra.VigraArray)
     self.data_bad_channel.axistags = vigra.defaultAxistags("xycz")

    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

    def setupOutputs(self):
        self.fileNameList = self.expandGlobStrings(self.globstring.value)

        num_files = len(self.fileNameList)
        if len(self.fileNameList) == 0:
            self.stack.meta.NOTREADY = True
            return
        try:
            self.info = vigra.impex.ImageInfo(self.fileNameList[0])
            self.slices_per_file = vigra.impex.numberImages(self.fileNameList[0])
        except RuntimeError as e:
            logger.error(str(e))
            raise OpStackLoader.FileOpenError(self.fileNameList[0])

        slice_shape = self.info.getShape()
        X, Y, C = slice_shape
        if self.slices_per_file == 1:
            # If this is a stack of 2D images, we assume xy slices stacked along z
            Z = num_files
            shape = (Z, Y, X, C)
            axistags = vigra.defaultAxistags('zyxc')
        else:
            # If it's a stack of 3D volumes, we assume xyz blocks stacked along t
            T = num_files
            Z = self.slices_per_file
            shape = (T, Z, Y, X, C)
            axistags = vigra.defaultAxistags('tzyxc')
            
        self.stack.meta.shape = shape
        self.stack.meta.axistags = axistags
        self.stack.meta.dtype = self.info.getDtype()

    def testChangeBlockshape_masked(self):
        logger.info("Generating sample data...")
        sampleData = numpy.indices((100, 200, 150), dtype=numpy.float32).sum(0)
        sampleData = sampleData.view(numpy.ma.masked_array)
        sampleData.set_fill_value(numpy.float32(numpy.nan))
        sampleData[0] = numpy.ma.masked

        graph = Graph()
        opData = OpArrayPiper(graph=graph)
        opData.Input.meta.has_mask = True
        opData.Input.meta.axistags = vigra.defaultAxistags("xyz")
        opData.Input.setValue(sampleData)

        op = OpCompressedCache(parent=None, graph=graph)
        # logger.debug("Setting block shape...")
        op.BlockShape.setValue([100, 75, 50])
        op.Input.connect(opData.Output)

        assert op.Output.ready()

        slicing = numpy.s_[0:100, 50:150, 75:150]
        expectedData = sampleData[slicing]

        # logger.debug("Requesting data...")
        readData = op.Output[slicing].wait()

        # logger.debug("Checking data...")
        assert (
            (readData == expectedData).all()
            and (readData.mask == expectedData.mask).all()
            and (
                (readData.fill_value == expectedData.fill_value)
                | (numpy.isnan(readData.fill_value) & numpy.isnan(expectedData.fill_value))
            ).all()
        ), "Incorrect output!"

        # Now change the blockshape and the input and try again...
        sampleDataWithChannel = sampleData[..., None]
        opData.Input.meta.axistags = vigra.defaultAxistags("xyzc")
        opData.Input.setValue(sampleDataWithChannel)
        op.BlockShape.setValue([45, 33, 40, 1])

        assert op.Output.ready()

        slicing = numpy.s_[60:70, 50:110, 60:120, 0:1]
        expectedData = sampleDataWithChannel[slicing]

        # logger.debug("Requesting data...")
        readData = op.Output[slicing].wait()

        # logger.debug("Checking data...")
        assert (
            (readData == expectedData).all()
            and (readData.mask == expectedData.mask).all()
            and (
                (readData.fill_value == expectedData.fill_value)
                | (numpy.isnan(readData.fill_value) & numpy.isnan(expectedData.fill_value))
            ).all()
        ), "Incorrect output!"

 def setupOutputs(self):
     # assert len(self.Input.meta.shape) == 1
     self.Output.meta.shape = (self.Input.meta.shape[0], 1)
     self.Output.meta.dtype = np.float32
     self.Output.meta.axistags = vigra.defaultAxistags('tc')
     self.Valid.meta.shape = self.Output.meta.shape[:1]
     self.Valid.meta.axistags = vigra.defaultAxistags('t')
     self.Valid.meta.dtype = np.uint8

    def setUp(self):
        if 'TRAVIS' in os.environ:
            # This test takes a long time, so skip it on Travis-CI.
            import nose
            raise nose.SkipTest

        self.scaleZ = 2
        self.scales = [0.3, 0.7, 1, 1.6, 3.5, 5.0, 10.0]
        self.featureIds = [ 'GaussianSmoothing', 'LaplacianOfGaussian',\
                   'GaussianGradientMagnitude',
                   'DifferenceOfGaussians',
                   'StructureTensorEigenvalues',
                   'HessianOfGaussianEigenvalues' ]
        
        #setup the data
        self.nx = 50
        self.ny = 50
        self.nz = 50
        self.data3d = numpy.zeros((self.nx, self.ny, self.nz, 1), dtype=numpy.float32)
        for i in range(self.data3d.shape[2]):
            self.data3d[:, :, i, 0]=i
        
        newRangeZ = self.scaleZ*(self.nz-1)+1
        self.data3dInterp = vigra.sampling.resizeVolumeSplineInterpolation(self.data3d.squeeze(), \
                                                       shape=(self.nx, self.ny, newRangeZ))
        
        self.data3dInterp = self.data3dInterp.reshape(self.data3dInterp.shape + (1,))

        self.data3d = self.data3d.view(vigra.VigraArray)
        self.data3d.axistags =  vigra.VigraArray.defaultAxistags(4)
        self.data3dInterp = self.data3dInterp.view(vigra.VigraArray)
        self.data3dInterp.axistags =  vigra.VigraArray.defaultAxistags(4)
        
        self.randomData = (numpy.random.random((self.nx, self.ny, self.nz, 1))).astype(numpy.float32)
        self.randomDataInterp = vigra.sampling.resizeVolumeSplineInterpolation(self.randomData.squeeze(), \
                                                                               shape = (self.nx, self.ny, newRangeZ))
        self.randomDataInterp = self.randomDataInterp.reshape(self.randomDataInterp.shape+(1,))
        
        self.randomData = self.randomData.view(vigra.VigraArray).astype(numpy.float32)
        self.randomData.axistags = vigra.defaultAxistags(4)
        self.randomDataInterp = self.randomDataInterp.view(vigra.VigraArray)
        self.randomDataInterp.axistags = vigra.defaultAxistags(4)
        
        #data without channels
        self.dataNoChannels = self.randomData.squeeze()
        self.dataNoChannels = self.dataNoChannels.view(vigra.VigraArray)
        self.dataNoChannels.axistags = vigra.defaultAxistags(3, noChannels=True)
        
        #setup the feature selection
        rows = 6
        cols = 7
        self.selectedFeatures = []
        #only test 1 feature 1 sigma setup for now
        for i in range(rows):
            for j in range(cols):
                features = numpy.zeros((rows,cols), dtype=bool)
                features[i, j]=True
                self.selectedFeatures.append(features)

    def setupOutputs(self):
        window = self.WindowSize.value
        self.Output.meta.shape = (self.Input.meta.shape[0], window)
        self.Output.meta.axistags = vigra.defaultAxistags('tc')
        self.Output.meta.dtype = self.Input.meta.dtype

        self.Valid.meta.shape = (self.Input.meta.shape[0],)
        self.Valid.meta.axistags = vigra.defaultAxistags('t')
        self.Valid.dtype = np.uint8

    def setupOutputs(self):
        assert (len(self.Input.meta.shape) <= 2 or
                np.prod(self.Input.meta.shape[1:]) == 1)
        self.Output.meta.shape = (self.Input.meta.shape[0], 1)
        self.Output.meta.axistags = vigra.defaultAxistags('tc')
        self.Output.meta.dtype = np.float32

        self.Valid.meta.shape = (self.Input.meta.shape[0],)
        self.Valid.meta.axistags = vigra.defaultAxistags('t')
        self.Valid.meta.dtype = np.uint8

    def test_2d_vigra_along_z(self):
        """Test if 2d files generated through vigra are recognized correctly"""
        # Prepare some data set for this case
        data = numpy.random.randint(0, 255, (20, 100, 200, 3)).astype(numpy.uint8)
        axistags = vigra.defaultAxistags("yxc")
        expected_axistags = vigra.defaultAxistags("zyxc")

        h5_op = OpStreamingH5N5SequenceReaderM(graph=self.graph)
        n5_op = OpStreamingH5N5SequenceReaderM(graph=self.graph)

        tempdir = tempfile.TemporaryDirectory()
        try:
            for sliceIndex, zSlice in enumerate(data):
                testDataH5FileName = f"{tempdir.name}/test-{sliceIndex:02d}.h5"
                testDataN5FileName = f"{tempdir.name}/test-{sliceIndex:02d}.n5"
                # Write the dataset to an hdf5 and a n5 file
                # (Note: Don't use vigra to do this, which may reorder the axes)
                h5File = h5py.File(testDataH5FileName)
                n5File = z5py.N5File(testDataN5FileName)
                try:
                    h5File.create_group("volume")
                    n5File.create_group("volume")

                    h5File["volume"].create_dataset("subvolume", data=zSlice)
                    n5File["volume"].create_dataset("subvolume", data=zSlice)
                    # Write the axistags attribute
                    current_path = "volume/subvolume"
                    h5File[current_path].attrs["axistags"] = axistags.toJSON()
                    n5File[current_path].attrs["axistags"] = axistags.toJSON()
                finally:
                    h5File.close()
                    n5File.close()

            # Read the data with an operator
            hdf5GlobString = f"{tempdir.name}/test-*.h5/volume/subvolume"
            n5GlobString = f"{tempdir.name}/test-*.n5/volume/subvolume"
            h5_op.SequenceAxis.setValue("z")
            n5_op.SequenceAxis.setValue("z")
            h5_op.GlobString.setValue(hdf5GlobString)
            n5_op.GlobString.setValue(n5GlobString)

            assert h5_op.OutputImage.ready()
            assert n5_op.OutputImage.ready()
            assert h5_op.OutputImage.meta.axistags == expected_axistags
            assert n5_op.OutputImage.meta.axistags == expected_axistags
            numpy.testing.assert_array_equal(
                h5_op.OutputImage.value[5:10, 50:100, 100:150], data[5:10, 50:100, 100:150]
            )
            numpy.testing.assert_array_equal(
                n5_op.OutputImage.value[5:10, 50:100, 100:150], data[5:10, 50:100, 100:150]
            )
        finally:
            h5_op.cleanUp()
            n5_op.cleanUp()

    def setupOutputs(self):
        self.fileNameList = self.expandGlobStrings(self.globstring.value)

        num_files = len(self.fileNameList)
        if len(self.fileNameList) == 0:
            self.stack.meta.NOTREADY = True
            return
        try:
            self.info = vigra.impex.ImageInfo(self.fileNameList[0])
            self.slices_per_file = vigra.impex.numberImages(self.fileNameList[0])
        except RuntimeError as e:
            logger.error(str(e))
            raise OpStackLoader.FileOpenError(self.fileNameList[0]) from e

        slice_shape = self.info.getShape()
        X, Y, C = slice_shape
        if self.slices_per_file == 1:
            if self.SequenceAxis.ready():
                sequence_axis = str(self.SequenceAxis.value)
                assert sequence_axis in "tzc"
            else:
                sequence_axis = "z"
            # For stacks of 2D images, we assume xy slices
            if sequence_axis == "c":
                shape = (X, Y, C * num_files)
                axistags = vigra.defaultAxistags("xyc")
            else:
                shape = (num_files, Y, X, C)
                axistags = vigra.defaultAxistags(sequence_axis + "yxc")
        else:
            if self.SequenceAxis.ready():
                sequence_axis = self.SequenceAxis.value
                assert sequence_axis in "tzc"
            else:
                sequence_axis = "t"

            if sequence_axis == "z":
                axistags = vigra.defaultAxistags("ztyxc")
            elif sequence_axis == "t":
                axistags = vigra.defaultAxistags("tzyxc")
            else:
                axistags = vigra.defaultAxistags("czyx")

            # For stacks of 3D volumes, we assume xyz blocks stacked along
            # sequence_axis
            if sequence_axis == "c":
                shape = (num_files * C, self.slices_per_file, Y, X)
            else:
                shape = (num_files, self.slices_per_file, Y, X, C)

        self.stack.meta.shape = shape
        self.stack.meta.axistags = axistags
        self.stack.meta.dtype = self.info.getDtype()

    def test_3d_vigra_along_t(self):
        """Test if 3d volumes generated through vigra are recognized correctly"""
        # Prepare some data set for this case
        data = numpy.random.randint(0, 255, (10, 15, 50, 100, 3)).astype(numpy.uint8)

        axistags = vigra.defaultAxistags("zyxc")
        expected_axistags = vigra.defaultAxistags("tzyxc")

        h5_op = OpStreamingH5N5SequenceReaderS(graph=self.graph)
        n5_op = OpStreamingH5N5SequenceReaderS(graph=self.graph)

        try:
            testDataH5FileName = f"{self.tempdir_normalized_name}/test.h5"
            testDataN5FileName = f"{self.tempdir_normalized_name}/test.n5"
            # Write the dataset to an hdf5 file
            # (Note: Don't use vigra to do this, which may reorder the axes)
            h5File = h5py.File(testDataH5FileName)
            n5File = z5py.N5File(testDataN5FileName)

            try:
                h5File.create_group("volumes")
                n5File.create_group("volumes")

                internalPathString = "subvolume-{sliceIndex:02d}"
                for sliceIndex, tSlice in enumerate(data):
                    subpath = internalPathString.format(sliceIndex=sliceIndex)
                    h5File["volumes"].create_dataset(subpath, data=tSlice)
                    n5File["volumes"].create_dataset(subpath, data=tSlice)
                    # Write the axistags attribute
                    current_path = "volumes/{}".format(subpath)
                    h5File[current_path].attrs["axistags"] = axistags.toJSON()
                    n5File[current_path].attrs["axistags"] = axistags.toJSON()
            finally:
                h5File.close()
                n5File.close()

            # Read the data with an operator
            hdf5GlobString = f"{testDataH5FileName}/volumes/subvolume-*"
            n5GlobString = f"{testDataN5FileName}/volumes/subvolume-*"
            h5_op.SequenceAxis.setValue("t")
            n5_op.SequenceAxis.setValue("t")
            h5_op.GlobString.setValue(hdf5GlobString)
            n5_op.GlobString.setValue(n5GlobString)

            assert h5_op.OutputImage.ready()
            assert n5_op.OutputImage.ready()
            assert h5_op.OutputImage.meta.axistags == expected_axistags
            assert n5_op.OutputImage.meta.axistags == expected_axistags
            numpy.testing.assert_array_equal(h5_op.OutputImage.value, data)
            numpy.testing.assert_array_equal(n5_op.OutputImage.value, data)
        finally:
            h5_op.cleanUp()
            n5_op.cleanUp()

 def setUp(self):
     self.delta = numpy.zeros((19, 19, 19, 1), dtype=numpy.float32)
     self.delta[9, 9, 9, 0]=1
     self.delta = self.delta.view(vigra.VigraArray)
     self.delta.axistags = vigra.defaultAxistags(4)
     
     self.dataShape = ((100, 100, 100, 1))
     self.randomData = (numpy.random.random(self.dataShape) * 100).astype(int)
     self.randomData = self.randomData.view(vigra.VigraArray)
     self.randomData.axistags = vigra.defaultAxistags(4)
     
     self.anisotropicSigmas = [(3, 3, 1), (1.6, 1.6, 1)]
     self.isotropicSigmasTuple = [(3, 3, 3), (1, 1, 1)]
     self.isotropicSigmas = [3, 1]

    def test1(self):
        superpixels = generate_random_voronoi((100,200), 200)
        superpixels.axistags = vigra.defaultAxistags('yx')

        feature_names = ['edgeregion_edge_regionradii']

        rag = Rag( superpixels )
        acc = EdgeRegionEdgeAccumulator(rag, feature_names)
        features_df = rag.compute_features(None, feature_names, accumulator_set=[acc])
        radii = features_df[features_df.columns.values[2:]].values
        assert (radii[:,0] >= radii[:,1]).all()
 
        # Transpose superpixels and check again
        # Should match (radii are sorted by magnitude).
        superpixels.axistags = vigra.defaultAxistags('xy')
        rag = Rag( superpixels )
        acc = EdgeRegionEdgeAccumulator(rag, feature_names)

        transposed_features_df = rag.compute_features(None, feature_names, accumulator_set=[acc])
        transposed_radii = transposed_features_df[transposed_features_df.columns.values[2:]].values

        assert (transposed_features_df[['sp1', 'sp1']].values == features_df[['sp1', 'sp1']].values).all()
        
        DEBUG = False
        if DEBUG:
            count_features = rag.compute_features(None, ['standard_edge_count', 'standard_sp_count'])
    
            import pandas as pd
            combined_features_df = pd.merge(features_df, transposed_features_df, how='left', on=['sp1', 'sp2'], suffixes=('_orig', '_transposed'))
            combined_features_df = pd.merge(combined_features_df, count_features, how='left', on=['sp1', 'sp2'])
            
            problem_rows = np.logical_or(np.isclose(radii[:, 0], transposed_radii[:, 0]) != 1,
                                         np.isclose(radii[:, 1], transposed_radii[:, 1]) != 1)
            problem_df = combined_features_df.loc[problem_rows][sorted(list(combined_features_df.columns))]
            print(problem_df.transpose())
            
            debug_sp = np.zeros_like(superpixels, dtype=np.uint8)
            for sp1 in problem_df['sp1'].values:
                debug_sp[superpixels == sp1] = 128
            for sp2 in problem_df['sp2'].values:
                debug_sp[superpixels == sp2] = 255
    
            vigra.impex.writeImage(debug_sp, '/tmp/debug_sp.png', dtype='NATIVE')
                
        # The first axes should all be close.
        # The second axes may differ somewhat in the case of purely linear edges,
        # so we allow a higher tolerance.
        assert np.isclose(radii[:,0], transposed_radii[:,0]).all()
        assert np.isclose(radii[:,1], transposed_radii[:,1], atol=0.001).all()

    def setup(self):
        graph = Graph()
        op = OpCompressedUserLabelArray(graph=graph)
        arrayshape = (1,100,100,10,1)
        op.inputs["shape"].setValue( arrayshape )
        blockshape = (1,10,10,10,1) # Why doesn't this work if blockshape is an ndarray?
        op.inputs["blockShape"].setValue( blockshape )
        op.eraser.setValue(100)

        op.Input.meta.axistags = vigra.defaultAxistags('txyzc')
        op.Input.meta.has_mask = True
        dummyData = numpy.zeros(arrayshape, dtype=numpy.uint8)
        dummyData = numpy.ma.masked_array(dummyData, mask=numpy.ma.getmaskarray(dummyData), fill_value=numpy.uint8(0), shrink=False)
        op.Input.setValue( dummyData )

        slicing = sl[0:1, 1:15, 2:36, 3:7, 0:1]
        inDataShape = slicing2shape(slicing)
        inputData = ( 3*numpy.random.random(inDataShape) ).astype(numpy.uint8)
        inputData = numpy.ma.masked_array(inputData, mask=numpy.ma.getmaskarray(inputData), fill_value=numpy.uint8(0), shrink=False)
        inputData[:, 0] = numpy.ma.masked
        op.Input[slicing] = inputData
        data = numpy.ma.zeros(arrayshape, dtype=numpy.uint8, fill_value=numpy.uint8(0))
        data[slicing] = inputData

        self.op = op
        self.slicing = slicing
        self.inData = inputData
        self.data = data