class OpRESTfulBlockwiseFilesetReader(Operator):
"""
Adapter that provides an operator interface to the BlockwiseFileset class for reading ONLY.
"""
name = "OpRESTfulBlockwiseFilesetReader"
DescriptionFilePath = InputSlot(stype='filestring')
Output = OutputSlot()
def __init__(self, *args, **kwargs):
super(OpRESTfulBlockwiseFilesetReader, self).__init__(*args, **kwargs)
self._blockwiseFileset = None
def setupOutputs(self):
# 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 = localDescription.view_shape
self.Output.meta.dtype = localDescription.dtype
self.Output.meta.axistags = vigra.defaultAxistags(localDescription.axes)
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 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 setupOutputs(self):
# 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 = localDescription.view_shape
self.Output.meta.dtype = localDescription.dtype
self.Output.meta.axistags = vigra.defaultAxistags(localDescription.axes)
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 setupClass(cls):
cls.tempDir = tempfile.mkdtemp()
logger.debug("Working in {}".format( cls.tempDir ))
# Create the two sub-descriptions
Bock11VolumeDescription = """
{
"_schema_name" : "RESTful-volume-description",
"_schema_version" : 1.0,
"name" : "Bock11-level0",
"format" : "hdf5",
"axes" : "zyx",
"##NOTE":"The first z-slice of the bock dataset is 2917, so the origin_offset must be at least 2917",
"origin_offset" : [2917, 50000, 50000],
"bounds" : [4156, 135424, 119808],
"dtype" : "numpy.uint8",
"url_format" : "http://openconnecto.me/emca/bock11/hdf5/0/{x_start},{x_stop}/{y_start},{y_stop}/{z_start},{z_stop}/",
"hdf5_dataset" : "cube"
}
"""
blockwiseFilesetDescription = \
"""
{
"_schema_name" : "blockwise-fileset-description",
"_schema_version" : 1.0,
"name" : "bock11-blocks",
"format" : "hdf5",
"axes" : "zyx",
"shape" : [40,40,40],
"dtype" : "numpy.uint8",
"block_shape" : [20, 20, 20],
"block_file_name_format" : "block-{roiString}.h5/cube",
"dataset_root_dir" : "blocks"
}
"""
# Combine them into the composite description (see RESTfulBlockwiseFileset.DescriptionFields)
compositeDescription = \
"""
{{
"_schema_name" : "RESTful-blockwise-fileset-description",
"_schema_version" : 1.0,
"remote_description" : {remote_description},
"local_description" : {local_description}
}}
""".format( remote_description=Bock11VolumeDescription, local_description=blockwiseFilesetDescription )
# Create the description file
cls.descriptionFilePath = os.path.join(cls.tempDir, "description.json")
with open(cls.descriptionFilePath, 'w') as f:
f.write(compositeDescription)
# Create a new fileset that views the same data and stores it the
# same way locally, but this time we'll use an offset 'view'
# Start with a copy of the non-offset description
offsetDescription = RESTfulBlockwiseFileset.readDescription(cls.descriptionFilePath)
offsetDescription.local_description.view_origin = numpy.array([0,20,0])
offsetDescription.local_description.dataset_root_dir = "offset_blocks"
cls.descriptionFilePath_offset = os.path.join(cls.tempDir, "description_offset.json")
RESTfulBlockwiseFileset.writeDescription(cls.descriptionFilePath_offset, offsetDescription)