def test_9_TestView(self):
"""
Load some of the dataset again; this time with an offset view.
Note: The original blockwise fileset must be closed before this test starts.
"""
# Create a copy of the original description, but specify a translated (and smaller) view
desc = BlockwiseFileset.readDescription(self.description_path)
desc.view_origin = [0, 300, 200, 100, 0]
desc.view_shape = [1, 50, 50, 50, 1]
offsetConfigPath = self.description_path + "_offset"
BlockwiseFileset.writeDescription(offsetConfigPath, desc)
# Open the fileset using the special description file
bfs = BlockwiseFileset(offsetConfigPath, "r")
try:
assert (bfs.description.view_origin == desc.view_origin).all()
assert (bfs.description.view_shape == desc.view_shape).all()
# Read some data
logger.debug("Reading data...")
disk_slicing = numpy.s_[:, 300:350, 200:250, 100:150, :]
view_slicing = numpy.s_[:, 0:50, 0:50, 0:50, :]
roi = sliceToRoi(view_slicing, self.dataShape)
roiShape = roi[1] - roi[0]
read_data = numpy.zeros(tuple(roiShape), dtype=numpy.uint8)
bfs.readData(roi, read_data)
# The data we read should match the correct part of the original dataset.
logger.debug("Checking data...")
assert self.data[disk_slicing].shape == read_data.shape
assert (self.data[disk_slicing] == read_data).all(), "Data didn't match."
finally:
bfs.close()
class OpBlockwiseFilesetReader(Operator):
"""
Adapter that provides an operator interface to the BlockwiseFileset class for reading ONLY.
"""
name = "OpBlockwiseFilesetReader"
DescriptionFilePath = InputSlot(stype="filestring")
Output = OutputSlot()
class MissingDatasetError(Exception):
pass
def __init__(self, *args, **kwargs):
super(OpBlockwiseFilesetReader, self).__init__(*args, **kwargs)
self._blockwiseFileset = None
self._opDummyData = OpDummyData(parent=self)
def setupOutputs(self):
if not os.path.exists(self.DescriptionFilePath.value):
raise OpBlockwiseFilesetReader.MissingDatasetError(
"Dataset description not found: {}".format(
self.DescriptionFilePath.value))
# Load up the class that does the real work
self._blockwiseFileset = BlockwiseFileset(
self.DescriptionFilePath.value)
# Check for errors in the description file
descriptionFields = self._blockwiseFileset.description
axes = descriptionFields.axes
assert False not in [
a in "txyzc" for a in axes
], "Unknown axis type. Known axes: txyzc Your axes:".format(axes)
self.Output.meta.shape = tuple(descriptionFields.view_shape)
self.Output.meta.dtype = descriptionFields.dtype
self.Output.meta.axistags = vigra.defaultAxistags(
str(descriptionFields.axes))
drange = descriptionFields.drange
if drange is not None:
self.Output.meta.drange = drange
def execute(self, slot, subindex, roi, result):
assert slot == self.Output, "Unknown output slot"
try:
self._blockwiseFileset.readData((roi.start, roi.stop), result)
except BlockwiseFileset.BlockNotReadyError:
result[:] = self._opDummyData.execute(slot, subindex, roi, result)
return result
def propagateDirty(self, slot, subindex, roi):
assert slot == self.DescriptionFilePath, "Unknown input slot."
self.Output.setDirty(slice(None))
def cleanUp(self):
if self._blockwiseFileset is not None:
self._blockwiseFileset.close()
super(OpBlockwiseFilesetReader, self).cleanUp()
class OpBlockwiseFilesetReader(Operator):
"""
Adapter that provides an operator interface to the BlockwiseFileset class for reading ONLY.
"""
name = "OpBlockwiseFilesetReader"
DescriptionFilePath = InputSlot(stype="filestring")
Output = OutputSlot()
class MissingDatasetError(Exception):
pass
def __init__(self, *args, **kwargs):
super(OpBlockwiseFilesetReader, self).__init__(*args, **kwargs)
self._blockwiseFileset = None
self._opDummyData = OpDummyData(parent=self)
def setupOutputs(self):
if not os.path.exists(self.DescriptionFilePath.value):
raise OpBlockwiseFilesetReader.MissingDatasetError(
"Dataset description not found: {}".format(self.DescriptionFilePath.value)
)
# Load up the class that does the real work
self._blockwiseFileset = BlockwiseFileset(self.DescriptionFilePath.value)
# Check for errors in the description file
descriptionFields = self._blockwiseFileset.description
axes = descriptionFields.axes
assert False not in [a in "txyzc" for a in axes], "Unknown axis type. Known axes: txyzc Your axes:".format(
axes
)
self.Output.meta.shape = tuple(descriptionFields.view_shape)
self.Output.meta.dtype = descriptionFields.dtype
self.Output.meta.axistags = vigra.defaultAxistags(str(descriptionFields.axes))
drange = descriptionFields.drange
if drange is not None:
self.Output.meta.drange = drange
def execute(self, slot, subindex, roi, result):
assert slot == self.Output, "Unknown output slot"
try:
self._blockwiseFileset.readData((roi.start, roi.stop), result)
except BlockwiseFileset.BlockNotReadyError:
result[:] = self._opDummyData.execute(slot, subindex, roi, result)
return result
def propagateDirty(self, slot, subindex, roi):
assert slot == self.DescriptionFilePath, "Unknown input slot."
self.Output.setDirty(slice(None))
def cleanUp(self):
if self._blockwiseFileset is not None:
self._blockwiseFileset.close()
super(OpBlockwiseFilesetReader, self).cleanUp()
def test_9_TestView(self):
"""
Load some of the dataset again; this time with an offset view.
Note: The original blockwise fileset must be closed before this test starts.
"""
# Create a copy of the original description, but specify a translated (and smaller) view
desc = BlockwiseFileset.readDescription(self.description_path)
desc.view_origin = [0, 300, 200, 100, 0]
desc.view_shape = [1, 50, 50, 50, 1]
offsetConfigPath = self.description_path + "_offset"
BlockwiseFileset.writeDescription(offsetConfigPath, desc)
# Open the fileset using the special description file
bfs = BlockwiseFileset(offsetConfigPath, "r")
try:
assert (bfs.description.view_origin == desc.view_origin).all()
assert (bfs.description.view_shape == desc.view_shape).all()
# Read some data
logger.debug("Reading data...")
disk_slicing = numpy.s_[:, 300:350, 200:250, 100:150, :]
view_slicing = numpy.s_[:, 0:50, 0:50, 0:50, :]
roi = sliceToRoi(view_slicing, self.dataShape)
roiShape = roi[1] - roi[0]
read_data = numpy.zeros(tuple(roiShape), dtype=numpy.uint8)
bfs.readData(roi, read_data)
# The data we read should match the correct part of the original dataset.
logger.debug("Checking data...")
assert self.data[disk_slicing].shape == read_data.shape
assert (self.data[disk_slicing] == read_data
).all(), "Data didn't match."
finally:
bfs.close()
def test_6_TestExportSubset(self):
roi = ((0, 0, 50, 100, 0), (1, 100, 200, 200, 1))
exportDir = tempfile.mkdtemp()
self.bfs.close()
self.bfs.reopen("r")
exported_description_path = self.bfs.exportSubset(roi, exportDir)
try:
exported_bfs = BlockwiseFileset(exported_description_path, "r")
assert os.path.exists(exported_description_path), "Couldn't even find the exported description file."
read_data = exported_bfs.readData(roi)
expected_data = self.data[roiToSlice(*roi)]
assert read_data.shape == expected_data.shape, "Exported data had wrong shape"
assert read_data.dtype == expected_data.dtype, "Exported data had wrong dtype"
assert (read_data == expected_data).all(), "Exported data did not match expected data"
finally:
shutil.rmtree(exportDir)
def test_6_TestExportSubset(self):
roi = ((0, 0, 50, 100, 0), (1, 100, 200, 200, 1))
exportDir = tempfile.mkdtemp()
self.bfs.close()
self.bfs.reopen("r")
exported_description_path = self.bfs.exportSubset(roi, exportDir)
try:
exported_bfs = BlockwiseFileset(exported_description_path, "r")
assert os.path.exists(
exported_description_path
), "Couldn't even find the exported description file."
read_data = exported_bfs.readData(roi)
expected_data = self.data[roiToSlice(*roi)]
assert read_data.shape == expected_data.shape, "Exported data had wrong shape"
assert read_data.dtype == expected_data.dtype, "Exported data had wrong dtype"
assert (read_data == expected_data
).all(), "Exported data did not match expected data"
finally:
shutil.rmtree(exportDir)