def setUp(self):
"""
Create a blockwise fileset to test with.
"""
if platform.system() == 'Windows':
# On windows, there are errors, and we make no attempt to solve them (at the moment).
raise nose.SkipTest
try:
BlockwiseFileset._prepare_system()
except ValueError:
# If the system isn't configured to allow lots of open files, we can't run this test.
raise nose.SkipTest
testConfig = \
"""
{
"_schema_name" : "blockwise-fileset-description",
"_schema_version" : 1.0,
"name" : "synapse_small",
"format" : "hdf5",
"axes" : "txyzc",
"shape" : [1,400,400,100,1],
"dtype" : "numpy.uint8",
"block_shape" : [1, 50, 50, 50, 100],
"block_file_name_format" : "cube{roiString}.h5/volume/data"
}
"""
self.tempDir = tempfile.mkdtemp()
self.configpath = os.path.join(self.tempDir, "config.json")
logger.debug("Loading config file...")
with open(self.configpath, 'w') as f:
f.write(testConfig)
logger.debug("Creating random test data...")
bfs = BlockwiseFileset(self.configpath, 'a')
dataShape = tuple(bfs.description.shape)
self.data = numpy.random.randint(255,
size=dataShape).astype(numpy.uint8)
logger.debug("Writing test data...")
datasetRoi = ([0, 0, 0, 0, 0], dataShape)
bfs.writeData(datasetRoi, self.data)
block_starts = getIntersectingBlocks(bfs.description.block_shape,
datasetRoi)
for block_start in block_starts:
bfs.setBlockStatus(block_start, BlockwiseFileset.BLOCK_AVAILABLE)
bfs.close()
def setUp(self):
"""
Create a blockwise fileset to test with.
"""
if platform.system() == 'Windows':
# On windows, there are errors, and we make no attempt to solve them (at the moment).
raise nose.SkipTest
try:
BlockwiseFileset._prepare_system()
except ValueError:
# If the system isn't configured to allow lots of open files, we can't run this test.
raise nose.SkipTest
testConfig = \
"""
{
"_schema_name" : "blockwise-fileset-description",
"_schema_version" : 1.0,
"name" : "synapse_small",
"format" : "hdf5",
"axes" : "txyzc",
"shape" : [1,400,400,100,1],
"dtype" : "numpy.uint8",
"block_shape" : [1, 50, 50, 50, 100],
"block_file_name_format" : "cube{roiString}.h5/volume/data"
}
"""
self.tempDir = tempfile.mkdtemp()
self.configpath = os.path.join(self.tempDir, "config.json")
logger.debug( "Loading config file..." )
with open(self.configpath, 'w') as f:
f.write(testConfig)
logger.debug( "Creating random test data..." )
bfs = BlockwiseFileset( self.configpath, 'a' )
dataShape = tuple(bfs.description.shape)
self.data = numpy.random.randint( 255, size=dataShape ).astype(numpy.uint8)
logger.debug( "Writing test data..." )
datasetRoi = ([0,0,0,0,0], dataShape)
bfs.writeData( datasetRoi, self.data )
block_starts = getIntersectingBlocks(bfs.description.block_shape, datasetRoi)
for block_start in block_starts:
bfs.setBlockStatus(block_start, BlockwiseFileset.BLOCK_AVAILABLE)
bfs.close()
class OpTaskWorker(Operator):
Input = InputSlot()
RoiString = InputSlot(stype="string")
TaskName = InputSlot(stype="string")
ConfigFilePath = InputSlot(stype="filestring")
OutputFilesetDescription = InputSlot(stype="filestring")
ReturnCode = OutputSlot()
def __init__(self, *args, **kwargs):
super(OpTaskWorker, self).__init__(*args, **kwargs)
self.progressSignal = OrderedSignal()
self._primaryBlockwiseFileset = None
def setupOutputs(self):
self.ReturnCode.meta.dtype = bool
self.ReturnCode.meta.shape = (1,)
self._closeFiles()
self._primaryBlockwiseFileset = BlockwiseFileset(self.OutputFilesetDescription.value, "a")
def cleanUp(self):
self._closeFiles()
super(OpTaskWorker, self).cleanUp()
def _closeFiles(self):
if self._primaryBlockwiseFileset is not None:
self._primaryBlockwiseFileset.close()
self._primaryBlockwiseFileset = None
def execute(self, slot, subindex, ignored_roi, result):
configFilePath = self.ConfigFilePath.value
config = parseClusterConfigFile(configFilePath)
blockwiseFileset = self._primaryBlockwiseFileset
# Check axis compatibility
inputAxes = list(self.Input.meta.getTaggedShape().keys())
outputAxes = list(blockwiseFileset.description.axes)
assert set(inputAxes) == set(
outputAxes
), "Output dataset has the wrong set of axes. Input axes: {}, Output axes: {}".format(
"".join(inputAxes), "".join(outputAxes)
)
roiString = self.RoiString.value
roi = Roi.loads(roiString)
if len(roi.start) != len(self.Input.meta.shape):
assert (
False
), "Task roi: {} is not valid for this input. Did the master launch this task correctly?".format(roiString)
logger.info("Executing for roi: {}".format(roi))
if config.use_node_local_scratch:
assert False, "FIXME."
assert (
blockwiseFileset.getEntireBlockRoi(roi.start)[1] == roi.stop
).all(), "Each task must execute exactly one full block. ({},{}) is not a valid block roi.".format(
roi.start, roi.stop
)
assert self.Input.ready()
with Timer() as computeTimer:
# Stream the data out to disk.
request_blockshape = (
self._primaryBlockwiseFileset.description.sub_block_shape
) # Could be None. That's okay.
streamer = BigRequestStreamer(self.Input, (roi.start, roi.stop), request_blockshape)
streamer.progressSignal.subscribe(self.progressSignal)
streamer.resultSignal.subscribe(self._handlePrimaryResultBlock)
streamer.execute()
# Now the block is ready. Update the status.
blockwiseFileset.setBlockStatus(roi.start, BlockwiseFileset.BLOCK_AVAILABLE)
logger.info("Finished task in {} seconds".format(computeTimer.seconds()))
result[0] = True
return result
def propagateDirty(self, slot, subindex, roi):
self.ReturnCode.setDirty(slice(None))
def _handlePrimaryResultBlock(self, roi, result):
# First write the primary
self._primaryBlockwiseFileset.writeData(roi, result)
# Ask the workflow if there is any special post-processing to do...
self.get_workflow().postprocessClusterSubResult(roi, result, self._primaryBlockwiseFileset)
def get_workflow(self):
op = self
while not isinstance(op, Workflow):
op = op.parent
return op
class OpTaskWorker(Operator):
Input = InputSlot()
RoiString = InputSlot(stype='string')
TaskName = InputSlot(stype='string')
ConfigFilePath = InputSlot(stype='filestring')
OutputFilesetDescription = InputSlot(stype='filestring')
ReturnCode = OutputSlot()
def __init__(self, *args, **kwargs):
super( OpTaskWorker, self ).__init__( *args, **kwargs )
self.progressSignal = OrderedSignal()
self._primaryBlockwiseFileset = None
def setupOutputs(self):
self.ReturnCode.meta.dtype = bool
self.ReturnCode.meta.shape = (1,)
self._closeFiles()
self._primaryBlockwiseFileset = BlockwiseFileset( self.OutputFilesetDescription.value, 'a' )
def cleanUp(self):
self._closeFiles()
super( OpTaskWorker, self ).cleanUp()
def _closeFiles(self):
if self._primaryBlockwiseFileset is not None:
self._primaryBlockwiseFileset.close()
self._primaryBlockwiseFileset = None
def execute(self, slot, subindex, ignored_roi, result):
configFilePath = self.ConfigFilePath.value
config = parseClusterConfigFile( configFilePath )
blockwiseFileset = self._primaryBlockwiseFileset
# Check axis compatibility
inputAxes = list(self.Input.meta.getTaggedShape().keys())
outputAxes = list(blockwiseFileset.description.axes)
assert set(inputAxes) == set(outputAxes), \
"Output dataset has the wrong set of axes. Input axes: {}, Output axes: {}".format( "".join(inputAxes), "".join(outputAxes) )
roiString = self.RoiString.value
roi = Roi.loads(roiString)
if len( roi.start ) != len( self.Input.meta.shape ):
assert False, "Task roi: {} is not valid for this input. Did the master launch this task correctly?".format( roiString )
logger.info( "Executing for roi: {}".format(roi) )
if config.use_node_local_scratch:
assert False, "FIXME."
assert (blockwiseFileset.getEntireBlockRoi( roi.start )[1] == roi.stop).all(), "Each task must execute exactly one full block. ({},{}) is not a valid block roi.".format( roi.start, roi.stop )
assert self.Input.ready()
with Timer() as computeTimer:
# Stream the data out to disk.
request_blockshape = self._primaryBlockwiseFileset.description.sub_block_shape # Could be None. That's okay.
streamer = BigRequestStreamer(self.Input, (roi.start, roi.stop), request_blockshape )
streamer.progressSignal.subscribe( self.progressSignal )
streamer.resultSignal.subscribe( self._handlePrimaryResultBlock )
streamer.execute()
# Now the block is ready. Update the status.
blockwiseFileset.setBlockStatus( roi.start, BlockwiseFileset.BLOCK_AVAILABLE )
logger.info( "Finished task in {} seconds".format( computeTimer.seconds() ) )
result[0] = True
return result
def propagateDirty(self, slot, subindex, roi):
self.ReturnCode.setDirty( slice(None) )
def _handlePrimaryResultBlock(self, roi, result):
# First write the primary
self._primaryBlockwiseFileset.writeData(roi, result)
# Ask the workflow if there is any special post-processing to do...
self.get_workflow().postprocessClusterSubResult(roi, result, self._primaryBlockwiseFileset)
def get_workflow(self):
op = self
while not isinstance(op, Workflow):
op = op.parent
return op
