testOpBlockwiseFilesetReader.py

from builtins import object
###############################################################################
#   lazyflow: data flow based lazy parallel computation framework
#
#       Copyright (C) 2011-2014, the ilastik developers
#                                <team@ilastik.org>
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the Lesser GNU General Public License
# as published by the Free Software Foundation; either version 2.1
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# See the files LICENSE.lgpl2 and LICENSE.lgpl3 for full text of the
# GNU Lesser General Public License version 2.1 and 3 respectively.
# This information is also available on the ilastik web site at:
#		   http://ilastik.org/license/
###############################################################################
import os
import sys
import shutil
import tempfile
import platform

import numpy
import nose

from lazyflow.graph import Graph
from lazyflow.roi import getIntersectingBlocks
from lazyflow.utility.io_util.blockwiseFileset import BlockwiseFileset
from lazyflow.operators.ioOperators import OpBlockwiseFilesetReader

import logging
logger = logging.getLogger(__name__)
logger.addHandler(logging.StreamHandler(sys.stdout))

logger.setLevel(logging.INFO)
#logger.setLevel(logging.DEBUG)

class TestOpBlockwiseFilesetReader(object):
    
    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 tearDown(self):
        shutil.rmtree(self.tempDir)

    def testRead(self):
        graph = Graph()
        op = OpBlockwiseFilesetReader(graph=graph)
        op.DescriptionFilePath.setValue( self.configpath )
        
        slice1 = numpy.s_[ :, 20:150, 20:150, 20:100, : ]
        readData = op.Output[ slice1 ].wait()
        assert (readData == self.data[slice1]).all()
        op.cleanUp()

if __name__ == "__main__":
    import sys
    import nose
    sys.argv.append("--nocapture")    # Don't steal stdout.  Show it on the console as usual.
    sys.argv.append("--nologcapture") # Don't set the logging level to DEBUG.  Leave it alone.
    ret = nose.run(defaultTest=__file__)


    if not ret: sys.exit(1)