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_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 _prepareDestination(self):
"""
- If the result file doesn't exist yet, create it (and the dataset)
- If the result file already exists, return a list of the rois that
are NOT needed (their data already exists in the final output)
"""
originalDescription = BlockwiseFileset.readDescription(self.OutputDatasetDescription.value)
datasetDescription = copy.deepcopy(originalDescription)
# Modify description fields as needed
# -- axes
datasetDescription.axes = "".join(list(self.Input.meta.getTaggedShape().keys()))
assert set(originalDescription.axes) == set(datasetDescription.axes), (
"Can't prepare destination dataset: original dataset description listed "
"axes as {}, but actual output axes are {}".format(originalDescription.axes, datasetDescription.axes)
)
# -- shape
datasetDescription.view_shape = list(self.Input.meta.shape)
# -- block_shape
assert originalDescription.block_shape is not None
originalBlockDims = collections.OrderedDict(
list(zip(originalDescription.axes, originalDescription.block_shape))
)
datasetDescription.block_shape = [originalBlockDims[a] for a in datasetDescription.axes]
datasetDescription.block_shape = list(
map(min, list(zip(datasetDescription.block_shape, self.Input.meta.shape)))
)
# -- chunks
if originalDescription.chunks is not None:
originalChunkDims = collections.OrderedDict(list(zip(originalDescription.axes, originalDescription.chunks)))
datasetDescription.chunks = [originalChunkDims[a] for a in datasetDescription.axes]
datasetDescription.chunks = list(map(min, list(zip(datasetDescription.chunks, self.Input.meta.shape))))
# -- dtype
if datasetDescription.dtype != self.Input.meta.dtype:
dtype = self.Input.meta.dtype
if type(dtype) is numpy.dtype:
dtype = dtype.type
datasetDescription.dtype = dtype().__class__.__name__
# Create a unique hash for this blocking scheme.
# If it changes, we can't use any previous data.
sha = hashlib.sha1()
sha.update(str(tuple(datasetDescription.block_shape)))
sha.update(datasetDescription.axes)
sha.update(datasetDescription.block_file_name_format)
datasetDescription.hash_id = sha.hexdigest()
if datasetDescription != originalDescription:
descriptionFilePath = self.OutputDatasetDescription.value
logger.info("Overwriting dataset description: {}".format(descriptionFilePath))
BlockwiseFileset.writeDescription(descriptionFilePath, datasetDescription)
with open(descriptionFilePath, "r") as f:
logger.info(f.read())
# Now open the dataset
blockwiseFileset = BlockwiseFileset(self.OutputDatasetDescription.value)
taskInfos = self._prepareTaskInfos(blockwiseFileset.getAllBlockRois())
if blockwiseFileset.description.hash_id != originalDescription.hash_id:
# Something about our blocking scheme changed.
# Make sure all blocks are marked as NOT available.
# (Just in case some were left over from a previous run.)
for roi in list(taskInfos.keys()):
blockwiseFileset.setBlockStatus(roi[0], BlockwiseFileset.BLOCK_NOT_AVAILABLE)
return blockwiseFileset, taskInfos
def _prepareDestination(self):
"""
- If the result file doesn't exist yet, create it (and the dataset)
- If the result file already exists, return a list of the rois that
are NOT needed (their data already exists in the final output)
"""
originalDescription = BlockwiseFileset.readDescription(self.OutputDatasetDescription.value)
datasetDescription = copy.deepcopy(originalDescription)
# Modify description fields as needed
# -- axes
datasetDescription.axes = "".join( list(self.Input.meta.getTaggedShape().keys()) )
assert set(originalDescription.axes) == set( datasetDescription.axes ), \
"Can't prepare destination dataset: original dataset description listed " \
"axes as {}, but actual output axes are {}".format( originalDescription.axes, datasetDescription.axes )
# -- shape
datasetDescription.view_shape = list(self.Input.meta.shape)
# -- block_shape
assert originalDescription.block_shape is not None
originalBlockDims = collections.OrderedDict( list(zip( originalDescription.axes, originalDescription.block_shape )) )
datasetDescription.block_shape = [originalBlockDims[a] for a in datasetDescription.axes]
datasetDescription.block_shape = list(map( min, list(zip( datasetDescription.block_shape, self.Input.meta.shape )) ))
# -- chunks
if originalDescription.chunks is not None:
originalChunkDims = collections.OrderedDict( list(zip( originalDescription.axes, originalDescription.chunks )) )
datasetDescription.chunks = [originalChunkDims[a] for a in datasetDescription.axes]
datasetDescription.chunks = list(map( min, list(zip( datasetDescription.chunks, self.Input.meta.shape )) ))
# -- dtype
if datasetDescription.dtype != self.Input.meta.dtype:
dtype = self.Input.meta.dtype
if type(dtype) is numpy.dtype:
dtype = dtype.type
datasetDescription.dtype = dtype().__class__.__name__
# Create a unique hash for this blocking scheme.
# If it changes, we can't use any previous data.
sha = hashlib.sha1()
sha.update( str( tuple( datasetDescription.block_shape) ) )
sha.update( datasetDescription.axes )
sha.update( datasetDescription.block_file_name_format )
datasetDescription.hash_id = sha.hexdigest()
if datasetDescription != originalDescription:
descriptionFilePath = self.OutputDatasetDescription.value
logger.info( "Overwriting dataset description: {}".format( descriptionFilePath ) )
BlockwiseFileset.writeDescription(descriptionFilePath, datasetDescription)
with open( descriptionFilePath, 'r' ) as f:
logger.info( f.read() )
# Now open the dataset
blockwiseFileset = BlockwiseFileset( self.OutputDatasetDescription.value )
taskInfos = self._prepareTaskInfos( blockwiseFileset.getAllBlockRois() )
if blockwiseFileset.description.hash_id != originalDescription.hash_id:
# Something about our blocking scheme changed.
# Make sure all blocks are marked as NOT available.
# (Just in case some were left over from a previous run.)
for roi in list(taskInfos.keys()):
blockwiseFileset.setBlockStatus( roi[0], BlockwiseFileset.BLOCK_NOT_AVAILABLE )
return blockwiseFileset, taskInfos
