class OpBlockwiseFilesetReader(Operator):
"""
Adapter that provides an operator interface to the BlockwiseFileset class for reading ONLY.
"""
name = "OpBlockwiseFilesetReader"
DescriptionFilePath = InputSlot(stype='filestring')
Output = OutputSlot()
def __init__(self, *args, **kwargs):
super(OpBlockwiseFilesetReader, self).__init__(*args, **kwargs)
self._blockwiseFileset = None
def setupOutputs(self):
# Load up the class that does the real work
self._blockwiseFileset = BlockwiseFileset( self.DescriptionFilePath.value )
# Check for errors in the description file
descriptionFields = self._blockwiseFileset.description
axes = descriptionFields.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 = descriptionFields.view_shape
self.Output.meta.dtype = descriptionFields.dtype
self.Output.meta.axistags = vigra.defaultAxistags(descriptionFields.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_6_TestView(self):
"""
Load some of the dataset again; this time with an offset view
"""
# Create a copy of the original description, but specify a translated (and smaller) view
desc = BlockwiseFileset.readDescription(self.configpath)
desc.view_origin = [0, 300, 200, 100, 0]
desc.view_shape = [1, 50, 50, 50, 1]
offsetConfigPath = self.configpath + '_offset'
BlockwiseFileset.writeDescription(offsetConfigPath, desc)
# Open the fileset using the special description file
bfs = BlockwiseFileset( offsetConfigPath, 'r' )
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."
