testOpRESTfulVolumeReader.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 nose
import os
import sys
import tempfile
import h5py
from lazyflow.operators.ioOperators.opRESTfulVolumeReader import OpRESTfulVolumeReader
from lazyflow.graph import Graph

import logging
logger = logging.getLogger(__name__)
logger.addHandler( logging.StreamHandler( sys.stdout ) )
logger.setLevel(logging.INFO)
#logger.setLevel(logging.DEBUG)

class TestRESTfulVolume(object):

    def testBasic(self):
        # The openconnectome site appears to be down at the moment.
        # This test fails when that happens...
        raise nose.SkipTest

        if 'TRAVIS' in os.environ:
            raise nose.SkipTest
        testConfig0 = """
        {
            "_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/ocp/ca/bock11/hdf5/0/{x_start},{x_stop}/{y_start},{y_stop}/{z_start},{z_stop}/",
            "hdf5_dataset" : "CUTOUT"
        }
        """
    
        testConfig4 = """
        {
            "_schema_name" : "RESTful-volume-description",
            "_schema_version" : 1.0,
        
            "name" : "Bock11-level4",
            "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, 0, 0],
            "bounds" : [4156, 8704, 7680],
            "dtype" : "numpy.uint8",
            "url_format" : "http://openconnecto.me/ocp/ca/bock11/hdf5/4/{x_start},{x_stop}/{y_start},{y_stop}/{z_start},{z_stop}/",
            "hdf5_dataset" : "CUTOUT"
        }
        """
        descriptionFilePath = os.path.join(tempfile.mkdtemp(), 'desc.json')
        with open(descriptionFilePath, 'w') as descFile:
            descFile.write( testConfig4 )
        
        graph = Graph()
        op = OpRESTfulVolumeReader(graph=graph)
        op.DescriptionFilePath.setValue( descriptionFilePath )
        
        #data = op.Output[0:100, 50000:50200, 50000:50200].wait()
        data = op.Output[0:10, 4000:4100, 4000:4100, 0:1].wait()
        
        # We expect a channel dimension to be added automatically...
        assert data.shape == ( 10, 100, 100, 1 )
    
        outputDataFilePath = os.path.join(tempfile.mkdtemp(), 'testOutput.h5')
        with h5py.File( outputDataFilePath, 'w' ) as outputDataFile:
            outputDataFile.create_dataset('volume', data=data)
    
        logger.debug( "Wrote data to {}".format(outputDataFilePath) )

            
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)