def setup(self):
"""
Generate a directory with all the files needed for this test.
We use the same temporary directory every time, so we don't
waste time regenerating the data if the test has already been run recently.
The directory consists of the following files:
- reference_volume.h5
- volume_description.json
- transposed_volume_description.json
- [lots of png tiles..]
"""
tmp = tempfile.gettempdir()
self.TILE_DIRECTORY = os.path.join( tmp, 'testTiledVolume_data' )
logger.debug("Using test directory: {}".format( self.TILE_DIRECTORY ))
self.REFERENCE_VOL_PATH = os.path.join( self.TILE_DIRECTORY, 'reference_volume.h5/data' )
ref_vol_path_comp = PathComponents(self.REFERENCE_VOL_PATH)
self.REFERENCE_VOL_FILE = ref_vol_path_comp.externalPath
self.VOLUME_DESCRIPTION_FILE = os.path.join( self.TILE_DIRECTORY, 'volume_description.json' )
self.TRANSPOSED_VOLUME_DESCRIPTION_FILE = os.path.join( self.TILE_DIRECTORY, 'transposed_volume_description.json' )
if not os.path.exists(self.TILE_DIRECTORY):
print "Creating new tile directory: {}".format( self.TILE_DIRECTORY )
os.mkdir(self.TILE_DIRECTORY)
if not os.path.exists(self.REFERENCE_VOL_FILE):
ref_vol = numpy.random.randint(0,255, (100,600,600) ).astype(numpy.uint8)
with h5py.File(self.REFERENCE_VOL_FILE, 'w') as ref_file:
ref_file[ref_vol_path_comp.internalPath] = ref_vol
else:
with h5py.File(self.REFERENCE_VOL_FILE, 'r') as ref_file:
ref_vol = ref_file[ref_vol_path_comp.internalPath][:]
need_rewrite = False
if not os.path.exists( self.VOLUME_DESCRIPTION_FILE ):
need_rewrite = True
else:
with open(self.VOLUME_DESCRIPTION_FILE, 'r') as f:
if f.read() != volume_description_text:
need_rewrite = True
if need_rewrite:
with open(self.VOLUME_DESCRIPTION_FILE, 'w') as f:
f.write(volume_description_text)
# Read the volume description as a JsonConfig Namespace
volume_description = TiledVolume.readDescription(self.VOLUME_DESCRIPTION_FILE)
# Write out a copy of the description, but with custom output axes
config_helper = JsonConfigParser( TiledVolume.DescriptionFields )
transposed_description = copy.copy(volume_description)
transposed_description.output_axes = "xyz"
config_helper.writeConfigFile(self.TRANSPOSED_VOLUME_DESCRIPTION_FILE, transposed_description)
# Remove all old image tiles in the tile directory
files = os.listdir(self.TILE_DIRECTORY)
for name in files:
if os.path.splitext(name)[1] == '.' + volume_description.format:
os.remove( os.path.join(self.TILE_DIRECTORY, name) )
# Write the new tiles
export_to_tiles( ref_vol, volume_description.tile_shape_2d_yx[0], self.TILE_DIRECTORY, print_progress=False )
# To support testMissingTiles (below), remove slice 2
files = os.listdir(self.TILE_DIRECTORY)
for name in files:
if name.startswith("tile_z00002"):
p = os.path.join(self.TILE_DIRECTORY, name)
print "removing:", p
os.remove( p )
# lastly, start the server
self._start_server()
def setup(self):
"""
Generate a directory with all the files needed for this test.
We use the same temporary directory every time, so we don't
waste time regenerating the data if the test has already been run recently.
The directory consists of the following files:
- reference_volume.h5
- volume_description.json
- transposed_volume_description.json
- [lots of png tiles..]
"""
tmp = tempfile.gettempdir()
self.TILE_DIRECTORY = os.path.join(tmp, 'testTiledVolume_data')
logger.debug("Using test directory: {}".format(self.TILE_DIRECTORY))
self.REFERENCE_VOL_PATH = os.path.join(self.TILE_DIRECTORY,
'reference_volume.h5/data')
ref_vol_path_comp = PathComponents(self.REFERENCE_VOL_PATH)
self.REFERENCE_VOL_FILE = ref_vol_path_comp.externalPath
self.VOLUME_DESCRIPTION_FILE = os.path.join(self.TILE_DIRECTORY,
'volume_description.json')
self.TRANSPOSED_VOLUME_DESCRIPTION_FILE = os.path.join(
self.TILE_DIRECTORY, 'transposed_volume_description.json')
if not os.path.exists(self.TILE_DIRECTORY):
print "Creating new tile directory: {}".format(self.TILE_DIRECTORY)
os.mkdir(self.TILE_DIRECTORY)
if not os.path.exists(self.REFERENCE_VOL_FILE):
ref_vol = numpy.random.randint(0, 255,
(100, 600, 600)).astype(numpy.uint8)
with h5py.File(self.REFERENCE_VOL_FILE, 'w') as ref_file:
ref_file[ref_vol_path_comp.internalPath] = ref_vol
else:
with h5py.File(self.REFERENCE_VOL_FILE, 'r') as ref_file:
ref_vol = ref_file[ref_vol_path_comp.internalPath][:]
need_rewrite = False
if not os.path.exists(self.VOLUME_DESCRIPTION_FILE):
need_rewrite = True
else:
with open(self.VOLUME_DESCRIPTION_FILE, 'r') as f:
if f.read() != volume_description_text:
need_rewrite = True
if need_rewrite:
with open(self.VOLUME_DESCRIPTION_FILE, 'w') as f:
f.write(volume_description_text)
# Read the volume description as a JsonConfig Namespace
volume_description = TiledVolume.readDescription(
self.VOLUME_DESCRIPTION_FILE)
# Write out a copy of the description, but with custom output axes
config_helper = JsonConfigParser(TiledVolume.DescriptionFields)
transposed_description = copy.copy(volume_description)
transposed_description.output_axes = "xyz"
config_helper.writeConfigFile(
self.TRANSPOSED_VOLUME_DESCRIPTION_FILE,
transposed_description)
# Remove all old image tiles in the tile directory
files = os.listdir(self.TILE_DIRECTORY)
for name in files:
if os.path.splitext(
name)[1] == '.' + volume_description.format:
os.remove(os.path.join(self.TILE_DIRECTORY, name))
# Write the new tiles
export_to_tiles(ref_vol,
volume_description.tile_shape_2d_yx[0],
self.TILE_DIRECTORY,
print_progress=False)
# To support testMissingTiles (below), remove slice 2
files = os.listdir(self.TILE_DIRECTORY)
for name in files:
if name.startswith("tile_z00002"):
p = os.path.join(self.TILE_DIRECTORY, name)
print "removing:", p
os.remove(p)
# lastly, start the server
self._start_server()
