def test_special_z_translation(self):
"""
This tests the special
"""
tiled_volume = TiledVolume(
self.data_setup.SPECIAL_Z_VOLUME_DESCRIPTION_FILE)
tiled_volume.TEST_MODE = True
reference_roi = numpy.array([(20, 150, 100), (40, 550, 550)])
result_out = numpy.zeros(reference_roi[1] - reference_roi[0],
dtype=tiled_volume.description.dtype)
roi_translated = reference_roi - [11, 0, 0]
tiled_volume.read(roi_translated, result_out)
ref_path_comp = PathComponents(self.data_setup.REFERENCE_VOL_PATH)
with h5py.File(ref_path_comp.externalPath, 'r') as f:
ref_data = f[ref_path_comp.internalPath][:]
expected = ref_data[roiToSlice(*reference_roi)]
#numpy.save('/tmp/expected.npy', expected)
#numpy.save('/tmp/result_out.npy', result_out)
assert (expected == result_out).all()
def testBasic(self):
tiled_volume = TiledVolume( self.data_setup.VOLUME_DESCRIPTION_FILE )
tiled_volume.TEST_MODE = True
roi = numpy.array( [(10, 150, 100), (30, 550, 550)] )
result_out = numpy.zeros( roi[1] - roi[0], dtype=tiled_volume.description.dtype )
tiled_volume.read( roi, result_out )
ref_path_comp = PathComponents(self.data_setup.REFERENCE_VOL_PATH)
with h5py.File(ref_path_comp.externalPath, 'r') as f:
ref_data = f[ref_path_comp.internalPath][:]
expected = ref_data[roiToSlice(*roi)]
#numpy.save('/tmp/expected.npy', expected)
#numpy.save('/tmp/result_out.npy', result_out)
assert (expected == result_out).all()
def testBasic(self):
tiled_volume = TiledVolume( self.data_setup.LOCAL_VOLUME_DESCRIPTION_FILE )
tiled_volume.TEST_MODE = True
roi = numpy.array( [(10, 150, 100), (30, 550, 550)] )
result_out = numpy.zeros( roi[1] - roi[0], dtype=tiled_volume.description.dtype )
tiled_volume.read( roi, result_out )
ref_path_comp = PathComponents(self.data_setup.REFERENCE_VOL_PATH)
with h5py.File(ref_path_comp.externalPath, 'r') as f:
ref_data = f[ref_path_comp.internalPath][:]
expected = ref_data[roiToSlice(*roi)]
#numpy.save('/tmp/expected.npy', expected)
#numpy.save('/tmp/result_out.npy', result_out)
assert (expected == result_out).all()
def testMissingTiles(self):
tiled_volume = TiledVolume( self.data_setup.VOLUME_DESCRIPTION_FILE )
tiled_volume.TEST_MODE = True
# The test data should be missing slice 2, and the config doesn't remap the data.
roi = numpy.array( [(0, 150, 100), (10, 550, 550)] )
result_out = numpy.zeros( roi[1] - roi[0], dtype=tiled_volume.description.dtype )
tiled_volume.read( roi, result_out )
ref_path_comp = PathComponents(self.data_setup.REFERENCE_VOL_PATH)
with h5py.File(ref_path_comp.externalPath, 'r') as f:
ref_data = f[ref_path_comp.internalPath][:]
# Slice 2 is missing from the server data
expected = ref_data[roiToSlice(*roi)]
expected[2] = 0
#numpy.save('/tmp/expected.npy', expected)
#numpy.save('/tmp/result_out.npy', result_out)
assert (expected == result_out).all()
def testMissingTiles(self):
tiled_volume = TiledVolume( self.data_setup.VOLUME_DESCRIPTION_FILE )
tiled_volume.TEST_MODE = True
# The test data should be missing slice 2, and the config doesn't remap the data.
roi = numpy.array( [(0, 150, 100), (10, 550, 550)] )
result_out = numpy.zeros( roi[1] - roi[0], dtype=tiled_volume.description.dtype )
tiled_volume.read( roi, result_out )
ref_path_comp = PathComponents(self.data_setup.REFERENCE_VOL_PATH)
with h5py.File(ref_path_comp.externalPath, 'r') as f:
ref_data = f[ref_path_comp.internalPath][:]
# Slice 2 is missing from the server data
expected = ref_data[roiToSlice(*roi)]
expected[2] = 0
#numpy.save('/tmp/expected.npy', expected)
#numpy.save('/tmp/result_out.npy', result_out)
assert (expected == result_out).all()
class OpTiledVolumeReader(Operator):
"""
An operator to retrieve volumes from a remote server that provides volumes via image tiles.
The operator requires a LOCAL json config file that describes the remote dataset and interface.
(See tiledVolume.py)
"""
DescriptionFilePath = InputSlot(stype="filestring")
Output = OutputSlot()
def __init__(self, *args, **kwargs):
super(OpTiledVolumeReader, self).__init__(*args, **kwargs)
self.tiled_volume = None
def setupOutputs(self):
if self.tiled_volume:
self.tiled_volume.close()
# Create a TiledVolume object to read the description file and do the downloads.
self.tiled_volume = TiledVolume(self.DescriptionFilePath.value)
self.Output.meta.shape = tuple(self.tiled_volume.output_shape)
self.Output.meta.dtype = self.tiled_volume.description.dtype
self.Output.meta.axistags = vigra.defaultAxistags(self.tiled_volume.description.output_axes)
self.Output.meta.prefer_2d = True
self.Output.meta.nickname = self.tiled_volume.description.name
def execute(self, slot, subindex, roi, result):
self.tiled_volume.read((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):
if self.tiled_volume:
self.tiled_volume.close()
super(OpTiledVolumeReader, self).cleanUp()
class OpTiledVolumeReader(Operator):
"""
An operator to retrieve volumes from a remote server that provides volumes via image tiles.
The operator requires a LOCAL json config file that describes the remote dataset and interface.
(See tiledVolume.py)
"""
DescriptionFilePath = InputSlot(stype='filestring')
Output = OutputSlot()
def __init__(self, *args, **kwargs):
super(OpTiledVolumeReader, self).__init__(*args, **kwargs)
self.tiled_volume = None
def setupOutputs(self):
if self.tiled_volume:
self.tiled_volume.close()
# Create a TiledVolume object to read the description file and do the downloads.
self.tiled_volume = TiledVolume(self.DescriptionFilePath.value)
self.Output.meta.shape = tuple(self.tiled_volume.output_shape)
self.Output.meta.dtype = self.tiled_volume.description.dtype
self.Output.meta.axistags = vigra.defaultAxistags(
self.tiled_volume.description.output_axes)
self.Output.meta.prefer_2d = True
self.Output.meta.nickname = self.tiled_volume.description.name
def execute(self, slot, subindex, roi, result):
self.tiled_volume.read((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):
if self.tiled_volume:
self.tiled_volume.close()
super(OpTiledVolumeReader, self).cleanUp()
def testRemappedTiles(self):
# The config above specifies that slices 45:47 get their data from slice 44,
# and slice 41 is the same as 40
tiled_volume = TiledVolume( self.data_setup.VOLUME_DESCRIPTION_FILE )
tiled_volume.TEST_MODE = True
roi = numpy.array( [(40, 150, 100), (50, 550, 550)] )
result_out = numpy.zeros( roi[1] - roi[0], dtype=tiled_volume.description.dtype )
tiled_volume.read( roi, result_out )
ref_path_comp = PathComponents(self.data_setup.REFERENCE_VOL_PATH)
with h5py.File(ref_path_comp.externalPath, 'r') as f:
ref_data = f[ref_path_comp.internalPath][:]
# Slices 5,6,7 are missing from the server data, and 'filled in' with slice 4
# Similarly, slice 1 is missing and filled in with slice 0.
expected = ref_data[roiToSlice(*roi)]
expected[5:8] = expected[4]
expected[1] = expected[0]
#numpy.save('/tmp/expected.npy', expected)
#numpy.save('/tmp/result_out.npy', result_out)
assert (expected == result_out).all()
def testRemappedTiles(self):
# The config above specifies that slices 45:47 get their data from slice 44,
# and slice 41 is the same as 40
tiled_volume = TiledVolume( self.data_setup.VOLUME_DESCRIPTION_FILE )
tiled_volume.TEST_MODE = True
roi = numpy.array( [(40, 150, 100), (50, 550, 550)] )
result_out = numpy.zeros( roi[1] - roi[0], dtype=tiled_volume.description.dtype )
tiled_volume.read( roi, result_out )
ref_path_comp = PathComponents(self.data_setup.REFERENCE_VOL_PATH)
with h5py.File(ref_path_comp.externalPath, 'r') as f:
ref_data = f[ref_path_comp.internalPath][:]
# Slices 5,6,7 are missing from the server data, and 'filled in' with slice 4
# Similarly, slice 1 is missing and filled in with slice 0.
expected = ref_data[roiToSlice(*roi)]
expected[5:8] = expected[4]
expected[1] = expected[0]
#numpy.save('/tmp/expected.npy', expected)
#numpy.save('/tmp/result_out.npy', result_out)
assert (expected == result_out).all()
def test_special_z_translation(self):
"""
This tests the special
"""
tiled_volume = TiledVolume( self.data_setup.SPECIAL_Z_VOLUME_DESCRIPTION_FILE )
tiled_volume.TEST_MODE = True
reference_roi = numpy.array( [(20, 150, 100), (40, 550, 550)] )
result_out = numpy.zeros( reference_roi[1] - reference_roi[0], dtype=tiled_volume.description.dtype )
roi_translated = reference_roi - [11,0,0]
tiled_volume.read( roi_translated, result_out )
ref_path_comp = PathComponents(self.data_setup.REFERENCE_VOL_PATH)
with h5py.File(ref_path_comp.externalPath, 'r') as f:
ref_data = f[ref_path_comp.internalPath][:]
expected = ref_data[roiToSlice(*reference_roi)]
#numpy.save('/tmp/expected.npy', expected)
#numpy.save('/tmp/result_out.npy', result_out)
assert (expected == result_out).all()
