class OpRESTfulBlockwiseFilesetReader(Operator):
"""
Adapter that provides an operator interface to the BlockwiseFileset class for reading ONLY.
"""
name = "OpRESTfulBlockwiseFilesetReader"
DescriptionFilePath = InputSlot(stype='filestring')
Output = OutputSlot()
class MissingDatasetError(Exception):
pass
def __init__(self, *args, **kwargs):
super(OpRESTfulBlockwiseFilesetReader, self).__init__(*args, **kwargs)
self._blockwiseFileset = None
def setupOutputs(self):
if not os.path.exists(self.DescriptionFilePath.value):
raise OpRESTfulBlockwiseFilesetReader.MissingDatasetError(
"Dataset description not found: {}".format(
self.DescriptionFilePath.value))
# Load up the class that does the real work
self._blockwiseFileset = RESTfulBlockwiseFileset(
self.DescriptionFilePath.value)
# Check for errors in the description file
localDescription = self._blockwiseFileset.compositeDescription.local_description
axes = localDescription.axes
assert False not in map(
lambda a: a in 'txyzc',
axes), "Unknown axis type. Known axes: txyzc Your axes:".format(
axes)
self.Output.meta.shape = tuple(localDescription.view_shape)
self.Output.meta.dtype = localDescription.dtype
self.Output.meta.axistags = vigra.defaultAxistags(
localDescription.axes)
drange = localDescription.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"
self._blockwiseFileset.readData((roi.start, roi.stop), result)
return result
def propagateDirty(self, slot, subindex, roi):
assert slot == self.DescriptionFilePath, "Unknown input slot."
self.Output.setDirty(slice(None))
def cleanUp(self):
import sys
if self._blockwiseFileset is not None:
self._blockwiseFileset.close()
super(OpRESTfulBlockwiseFilesetReader, self).cleanUp()
class OpRESTfulBlockwiseFilesetReader(Operator):
"""
Adapter that provides an operator interface to the BlockwiseFileset class for reading ONLY.
"""
name = "OpRESTfulBlockwiseFilesetReader"
DescriptionFilePath = InputSlot(stype='filestring')
Output = OutputSlot()
class MissingDatasetError(Exception):
pass
def __init__(self, *args, **kwargs):
super(OpRESTfulBlockwiseFilesetReader, self).__init__(*args, **kwargs)
self._blockwiseFileset = None
def setupOutputs(self):
if not os.path.exists(self.DescriptionFilePath.value):
raise OpRESTfulBlockwiseFilesetReader.MissingDatasetError("Dataset description not found: {}".format( self.DescriptionFilePath.value ) )
# Load up the class that does the real work
self._blockwiseFileset = RESTfulBlockwiseFileset( self.DescriptionFilePath.value )
# Check for errors in the description file
localDescription = self._blockwiseFileset.compositeDescription.local_description
axes = localDescription.axes
assert False not in map(lambda a: a in 'txyzc', axes), "Unknown axis type. Known axes: txyzc Your axes:".format(axes)
self.Output.meta.shape = tuple(localDescription.view_shape)
self.Output.meta.dtype = localDescription.dtype
self.Output.meta.axistags = vigra.defaultAxistags(localDescription.axes)
drange = localDescription.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"
self._blockwiseFileset.readData( (roi.start, roi.stop), result )
return result
def propagateDirty(self, slot, subindex, roi):
assert slot == self.DescriptionFilePath, "Unknown input slot."
self.Output.setDirty( slice(None) )
def cleanUp(self):
import sys
if self._blockwiseFileset is not None:
self._blockwiseFileset.close()
super(OpRESTfulBlockwiseFilesetReader, self).cleanUp()
def test_4_OffsetDownload(self):
volume = RESTfulBlockwiseFileset( self.descriptionFilePath )
slicing = numpy.s_[20:40, 20:40, 20:40]
roi = sliceToRoi(slicing, volume.description.shape)
data = volume.readData( roi )
assert data.shape == (20,20,20)
assert volume.getBlockStatus( ([20,20,20]) ) == BlockwiseFileset.BLOCK_AVAILABLE
offsetVolume = RESTfulBlockwiseFileset( self.descriptionFilePath_offset )
offsetSlicing = numpy.s_[20:40, 0:20, 20:40] # Note middle slice is offset (see view_origin in setupClass)
offsetRoi = sliceToRoi(offsetSlicing, offsetVolume.description.shape)
offsetData = offsetVolume.readData( offsetRoi )
assert offsetData.shape == (20,20,20)
assert offsetVolume.getBlockStatus( ([20,0,20]) ) == BlockwiseFileset.BLOCK_AVAILABLE
# Data should be the same
assert (offsetData == data).all()
def test_1_SingleDownload(self):
volume = RESTfulBlockwiseFileset( self.descriptionFilePath )
slicing = numpy.s_[0:20, 0:20, 0:20]
roi = sliceToRoi(slicing, volume.description.shape)
data = volume.readData( roi )
assert data.shape == (20,20,20)
assert volume.getBlockStatus( ([0,0,0]) ) == BlockwiseFileset.BLOCK_AVAILABLE
def test_4_OffsetDownload(self):
volume = RESTfulBlockwiseFileset( self.descriptionFilePath )
slicing = numpy.s_[20:40, 20:40, 20:40]
roi = sliceToRoi(slicing, volume.description.shape)
data = volume.readData( roi )
assert data.shape == (20,20,20)
assert volume.getBlockStatus( ([20,20,20]) ) == BlockwiseFileset.BLOCK_AVAILABLE
offsetVolume = RESTfulBlockwiseFileset( self.descriptionFilePath_offset )
offsetSlicing = numpy.s_[20:40, 0:20, 20:40] # Note middle slice is offset (see view_origin in setupClass)
offsetRoi = sliceToRoi(offsetSlicing, offsetVolume.description.shape)
offsetData = offsetVolume.readData( offsetRoi )
assert offsetData.shape == (20,20,20)
assert offsetVolume.getBlockStatus( ([20,0,20]) ) == BlockwiseFileset.BLOCK_AVAILABLE
# Data should be the same
assert (offsetData == data).all()
def test_1_SingleDownload(self):
volume = RESTfulBlockwiseFileset( self.descriptionFilePath )
slicing = numpy.s_[0:20, 0:20, 0:20]
roi = sliceToRoi(slicing, volume.description.shape)
data = volume.readData( roi )
assert data.shape == (20,20,20)
assert volume.getBlockStatus( ([0,0,0]) ) == BlockwiseFileset.BLOCK_AVAILABLE
