def testBasic(self):
graph = lazyflow.graph.Graph()
reader = OperatorWrapper(OpDataSelection, graph=graph)
reader.ProjectFile.setValue(self.projectFile)
reader.WorkingDirectory.setValue(os.getcwd())
reader.ProjectDataGroup.setValue('DataSelection/local_data')
# Create a list of dataset infos . . .
datasetInfos = []
# npy
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.testNpyFileName
info.internalPath = ""
info.invertColors = False
info.convertToGrayscale = False
datasetInfos.append(info)
# png
info = DatasetInfo()
info.location = DatasetInfo.Location.FileSystem
info.filePath = self.testPngFileName
info.internalPath = ""
info.invertColors = False
info.convertToGrayscale = False
datasetInfos.append(info)
reader.Dataset.setValues(datasetInfos)
# Read the test files using the data selection operator and verify the contents
npyData = reader.Image[0][...].wait()
pngData = reader.Image[1][...].wait()
# Check the file name output
print reader.ImageName[0].value
assert reader.ImageName[0].value == self.testNpyFileName
assert reader.ImageName[1].value == self.testPngFileName
# Check raw images
assert npyData.shape == (10, 11, 1)
for x in range(npyData.shape[0]):
for y in range(npyData.shape[1]):
assert npyData[x, y, 0] == x + y
assert pngData.shape == (100, 200, 3)
for x in range(pngData.shape[0]):
for y in range(pngData.shape[1]):
for c in range(pngData.shape[2]):
assert pngData[x, y, c] == (x + y) % 256
def testBasic(self):
graph = lazyflow.graph.Graph()
reader = OperatorWrapper( OpDataSelection, graph=graph )
reader.ProjectFile.setValue(self.projectFile)
reader.WorkingDirectory.setValue( os.getcwd() )
reader.ProjectDataGroup.setValue( 'DataSelection/local_data' )
# Create a list of dataset infos . . .
datasetInfos = []
# npy
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.testNpyFileName
info.internalPath = ""
info.invertColors = False
info.convertToGrayscale = False
datasetInfos.append(info)
# png
info = DatasetInfo()
info.location = DatasetInfo.Location.FileSystem
info.filePath = self.testPngFileName
info.internalPath = ""
info.invertColors = False
info.convertToGrayscale = False
datasetInfos.append(info)
reader.Dataset.setValues(datasetInfos)
# Read the test files using the data selection operator and verify the contents
npyData = reader.Image[0][...].wait()
pngData = reader.Image[1][...].wait()
# Check the file name output
print reader.ImageName[0].value
assert reader.ImageName[0].value == self.testNpyFileName
assert reader.ImageName[1].value == self.testPngFileName
# Check raw images
assert npyData.shape == (10,11,1)
for x in range(npyData.shape[0]):
for y in range(npyData.shape[1]):
assert npyData[x,y,0] == x+y
assert pngData.shape == (100, 200, 3)
for x in range(pngData.shape[0]):
for y in range(pngData.shape[1]):
for c in range(pngData.shape[2]):
assert pngData[x,y,c] == (x+y) % 256
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)
def test_real_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 real data source
info.realDataSource = True
reader.Dataset.setValues([info])
# Read the test file using the data selection operator and verify the contents
imgData = reader.Image[0][...].wait()
assert imgData.shape == self.imgData.shape
numpy.testing.assert_array_equal(imgData, self.imgData)
def test_load_single_file_with_list(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')
fileNameString = os.path.pathsep.join(self.file_names)
info = DatasetInfo(filepath=fileNameString)
# Will be read from the filesystem since the data won't be found in the project file.
info.location = DatasetInfo.Location.ProjectInternal
info.internalPath = ""
info.invertColors = False
info.convertToGrayscale = False
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData = reader.Image[0][...].wait()
print('imgData', reader.Image.meta.axistags, reader.Image.meta.original_axistags)
# Check raw images
assert imgData.shape == self.imgData3Dct.shape, (imgData.shape, self.imgData3Dct.shape)
numpy.testing.assert_array_equal(imgData, self.imgData3Dct)
def testBasic3DcStackFromGlobString(self):
"""Test if stacked 2d 3-channel files are loaded correctly"""
# For some reason vigra saves 2D+c data compressed in gifs, so skip!
self.compressedExtensions.append('.gif')
for fileName in self.imgFileNameGlobs2Dc:
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
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData3Dc = reader.Image[0][...].wait()
# Check the file name output
assert reader.ImageName[0].value == fileName
# Check raw images
assert imgData3Dc.shape == self.imgData3Dc.shape, (imgData3Dc.shape, self.imgData3Dc.shape)
# skip this if image was saved compressed:
if any(x in fileName.lower() for x in self.compressedExtensions):
print("Skipping raw comparison for compressed data: {}".format(fileName))
continue
numpy.testing.assert_array_equal(imgData3Dc, self.imgData3Dc)
def testBasic3DstacksFromFileList(self):
for ext, fileNames in list(self.imgFileLists2D.items()):
fileNameString = os.path.pathsep.join(fileNames)
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(filepath=fileNameString)
# Will be read from the filesystem since the data won't be found in the project file.
info.location = DatasetInfo.Location.ProjectInternal
info.internalPath = ""
info.invertColors = False
info.convertToGrayscale = False
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData3D = reader.Image[0][...].wait()
# Check raw images
assert imgData3D.shape == self.imgData3D.shape, (imgData3D.shape, self.imgData3D.shape)
# skip this if image was saved compressed:
if any(x.strip('.') in ext.lower() for x in self.compressedExtensions):
print("Skipping raw comparison for compressed data: {}".format(ext))
continue
numpy.testing.assert_array_equal(imgData3D, self.imgData3D)
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!"
def testBasic3D(self):
"""Test if plane 2d files are loaded correctly"""
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
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData3D = reader.Image[0][...].wait()
# Check the file name output
assert reader.ImageName[0].value == fileName
# Check raw images
assert imgData3D.shape == self.imgData3D.shape, (imgData3D.shape, self.imgData3D.shape)
# skip this if image was saved compressed:
numpy.testing.assert_array_equal(imgData3D, self.imgData3D)
def testProjectLocalData(self):
graph = lazyflow.graph.Graph()
reader = OperatorWrapper( OpDataSelection, graph=graph )
reader.ProjectFile.setValue(self.projectFile)
reader.WorkingDirectory.setValue( os.getcwd() )
reader.ProjectDataGroup.setValue( 'DataSelection/local_data' )
# Create a list of dataset infos . . .
datasetInfos = []
# From project
info = DatasetInfo()
info.location = DatasetInfo.Location.ProjectInternal
info.filePath = "This string should be ignored..."
info._datasetId = 'dataset1' # (Cheating a bit here...)
info.invertColors = False
info.convertToGrayscale = False
datasetInfos.append(info)
reader.Dataset.setValues(datasetInfos)
projectInternalData = reader.Image[0][...].wait()
assert projectInternalData.shape == self.pngData.shape
assert (projectInternalData == self.pngData).all()
def testBasic3DcStackFromGlobString(self):
"""Test if stacked 2d 3-channel files are loaded correctly"""
# For some reason vigra saves 2D+c data compressed in gifs, so skip!
self.compressedExtensions.append('.gif')
for fileName in self.imgFileNameGlobs2Dc:
graph = lazyflow.graph.Graph()
reader = OperatorWrapper(OpDataSelection, graph=graph)
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
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData3Dc = reader.Image[0][...].wait()
# Check the file name output
assert reader.ImageName[0].value == fileName
# Check raw images
assert imgData3Dc.shape == self.imgData3Dc.shape
# skip this if image was saved compressed:
if any(x in fileName.lower() for x in self.compressedExtensions):
print("Skipping raw comparison for compressed data: {}".format(
fileName))
continue
numpy.testing.assert_array_equal(imgData3Dc, self.imgData3Dc)
def testBasic3DstacksFromFileList(self):
for ext, fileNames in self.imgFileLists2D.items():
fileNameString = os.path.pathsep.join(fileNames)
graph = lazyflow.graph.Graph()
reader = OperatorWrapper(OpDataSelection, graph=graph)
reader.ProjectFile.setValue(self.projectFile)
reader.WorkingDirectory.setValue(os.getcwd())
reader.ProjectDataGroup.setValue('DataSelection/local_data')
info = DatasetInfo(filepath=fileNameString)
# Will be read from the filesystem since the data won't be found in the project file.
info.location = DatasetInfo.Location.ProjectInternal
info.internalPath = ""
info.invertColors = False
info.convertToGrayscale = False
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData3D = reader.Image[0][...].wait()
# Check raw images
assert imgData3D.shape == self.imgData3D.shape
# skip this if image was saved compressed:
if any(
x.strip('.') in ext.lower()
for x in self.compressedExtensions):
print("Skipping raw comparison for compressed data: {}".format(
ext))
continue
numpy.testing.assert_array_equal(imgData3D, self.imgData3D)
def testBasic2D(self):
"""Test if plane 2d files are loaded correctly"""
for fileName in self.imgFileNames2D:
graph = lazyflow.graph.Graph()
reader = OperatorWrapper(OpDataSelection, graph=graph)
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
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData2D = reader.Image[0][...].wait()
# Check the file name output
assert reader.ImageName[0].value == fileName
# Check raw images
assert imgData2D.shape == self.imgData2D.shape
# skip this if image was saved compressed:
if any(x in fileName.lower() for x in self.compressedExtensions):
print("Skipping raw comparison for compressed data: {}".format(fileName))
continue
numpy.testing.assert_array_equal(imgData2D, self.imgData2D)
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)
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!"
def testProjectLocalData(self):
graph = lazyflow.graph.Graph()
reader = OperatorWrapper(OpDataSelection, graph=graph)
reader.ProjectFile.setValue(self.projectFile)
reader.WorkingDirectory.setValue(os.getcwd())
reader.ProjectDataGroup.setValue('DataSelection/local_data')
# Create a list of dataset infos . . .
datasetInfos = []
# From project
info = DatasetInfo()
info.location = DatasetInfo.Location.ProjectInternal
info.filePath = "This string should be ignored..."
info._datasetId = 'dataset1' # (Cheating a bit here...)
info.invertColors = False
info.convertToGrayscale = False
datasetInfos.append(info)
reader.Dataset.setValues(datasetInfos)
projectInternalData = reader.Image[0][...].wait()
assert projectInternalData.shape == self.imgData3Dc.shape
assert (projectInternalData == self.imgData3Dc).all()
def testBasic3D(self):
"""Test if plane 2d files are loaded correctly"""
for fileName in self.imgFileNames3D:
graph = lazyflow.graph.Graph()
reader = OperatorWrapper(OpDataSelection, graph=graph)
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
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData3D = reader.Image[0][...].wait()
# Check the file name output
assert reader.ImageName[0].value == fileName
# Check raw images
assert imgData3D.shape == self.imgData3D.shape
# skip this if image was saved compressed:
numpy.testing.assert_array_equal(imgData3D, self.imgData3D)
def test_load_single_file_with_list(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')
fileNameString = os.path.pathsep.join(self.file_names)
info = DatasetInfo(filepath=fileNameString)
# Will be read from the filesystem since the data won't be found in the project file.
info.location = DatasetInfo.Location.ProjectInternal
info.internalPath = ""
info.invertColors = False
info.convertToGrayscale = False
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData = reader.Image[0][...].wait()
print('imgData', reader.Image.meta.axistags,
reader.Image.meta.original_axistags)
# Check raw images
assert imgData.shape == self.imgData3Dct.shape, (
imgData.shape, self.imgData3Dct.shape)
numpy.testing.assert_array_equal(imgData, self.imgData3Dct)
def testBasic2D(self):
"""Test if plane 2d files are loaded correctly"""
for fileName in self.imgFileNames2D:
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
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData2D = reader.Image[0][...].wait()
# Check the file name output
assert reader.ImageName[0].value == fileName
# Check raw images
assert imgData2D.shape == self.imgData2D.shape
# skip this if image was saved compressed:
if any(x in fileName.lower() for x in self.compressedExtensions):
print("Skipping raw comparison for compressed data: {}".format(
fileName))
continue
numpy.testing.assert_array_equal(imgData2D, self.imgData2D)
def test_load_single_file_with_glob(self):
graph = lazyflow.graph.Graph()
reader = OperatorWrapper(OpDataSelection, graph=graph)
reader.ProjectFile.setValue(self.projectFile)
reader.WorkingDirectory.setValue(os.getcwd())
reader.ProjectDataGroup.setValue('DataSelection/local_data')
info = DatasetInfo(filepath=self.glob_string)
# Will be read from the filesystem since the data won't be found in the project file.
info.location = DatasetInfo.Location.ProjectInternal
info.internalPath = ""
info.invertColors = False
info.convertToGrayscale = False
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData = reader.Image[0][...].wait()
# Check raw images
assert imgData.shape == self.imgData3Dct.shape
numpy.testing.assert_array_equal(imgData, self.imgData3Dct)
def test_load_single_file_with_glob(self):
graph = lazyflow.graph.Graph()
reader = OperatorWrapper(OpDataSelection, graph=graph)
reader.ProjectFile.setValue(self.projectFile)
reader.WorkingDirectory.setValue(os.getcwd())
reader.ProjectDataGroup.setValue('DataSelection/local_data')
info = DatasetInfo(filepath=self.glob_string)
# Will be read from the filesystem since the data won't be found in the project file.
info.location = DatasetInfo.Location.ProjectInternal
info.internalPath = ""
info.invertColors = False
info.convertToGrayscale = False
reader.Dataset.setValues([info])
# Read the test files using the data selection operator and verify the contents
imgData = reader.Image[0][...].wait()
# Check raw images
assert imgData.shape == self.imgData3Dct.shape
numpy.testing.assert_array_equal(imgData, self.imgData3Dct)