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..]
"""
global volume_description_text
global port
try:
with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as sock:
# allow the socket port to be reused if in TIME_WAIT state
sock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
sock.bind(('localhost', port)) # try default/previous port
except Exception as e:
with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as sock:
# allow the socket port to be reused if in TIME_WAIT state
sock.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
sock.bind(('localhost', 0)) # find free port
port = sock.getsockname()[1]
volume_description_text = volume_description_text.replace(
'{port}', str(port))
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.LOCAL_VOLUME_DESCRIPTION_FILE = os.path.join(
self.TILE_DIRECTORY, 'local_volume_description.json')
self.TRANSPOSED_VOLUME_DESCRIPTION_FILE = os.path.join(
self.TILE_DIRECTORY, 'transposed_volume_description.json')
self.TRANSLATED_VOLUME_DESCRIPTION_FILE = os.path.join(
self.TILE_DIRECTORY, 'translated_volume_description.json')
self.SPECIAL_Z_VOLUME_DESCRIPTION_FILE = os.path.join(
self.TILE_DIRECTORY, 'special_z_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 a local tile path instead of a URL
config_helper = JsonConfigParser(TiledVolume.DescriptionFields)
local_description = copy.copy(volume_description)
local_description.tile_url_format = self.TILE_DIRECTORY + "/tile_z{z_start:05}_y{y_start:05}_x{x_start:05}.png"
config_helper.writeConfigFile(self.LOCAL_VOLUME_DESCRIPTION_FILE,
local_description)
# 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)
# Write out another copy of the description, but with an origin translation
config_helper = JsonConfigParser(TiledVolume.DescriptionFields)
translated_description = copy.copy(volume_description)
translated_description.view_origin_zyx = [10, 20, 30]
translated_description.shape_zyx = None
config_helper.writeConfigFile(
self.TRANSLATED_VOLUME_DESCRIPTION_FILE,
translated_description)
# Write out another copy of the description, but with a special function for translating z-coordinates.
config_helper = JsonConfigParser(TiledVolume.DescriptionFields)
special_z_description = copy.copy(volume_description)
special_z_description.z_translation_function = "lambda z: z+11"
config_helper.writeConfigFile(
self.SPECIAL_Z_VOLUME_DESCRIPTION_FILE, special_z_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()
"""
(This script is not generally useful for most ilastik users or developers.)
Input: hdf5 volume
Output: directory of .png tiles representing the volume.
"""
if __name__ == "__main__":
import sys
import h5py
import logging
import argparse
from lazyflow.utility import PathComponents, export_to_tiles
logger = logging.getLogger()
logger.addHandler(logging.StreamHandler(sys.stdout))
logger.setLevel(logging.INFO)
# Usage: python make_tiles.py --tile_size=250 /path/to/my_vol.h5/some/dataset /path/to/output_dir
parser = argparse.ArgumentParser()
parser.add_argument("--tile_size", type=int)
parser.add_argument("hdf5_dataset_path")
parser.add_argument("output_dir")
parsed_args = parser.parse_args(sys.argv[1:])
path_comp = PathComponents(parsed_args.hdf5_dataset_path)
with h5py.File(path_comp.externalPath) as input_file:
vol_dset = input_file[path_comp.internalPath]
export_to_tiles(vol_dset, parsed_args.tile_size, parsed_args.output_dir)
(This script is not generally useful for most ilastik users or developers.)
Input: hdf5 volume
Output: directory of .png tiles representing the volume.
"""
if __name__ == "__main__":
import sys
import h5py
import logging
import argparse
from lazyflow.utility import PathComponents, export_to_tiles
logger = logging.getLogger()
logger.addHandler(logging.StreamHandler(sys.stdout))
logger.setLevel(logging.INFO)
# Usage: python make_tiles.py --tile_size=250 /path/to/my_vol.h5/some/dataset /path/to/output_dir
parser = argparse.ArgumentParser()
parser.add_argument("--tile_size", type=int)
parser.add_argument("hdf5_dataset_path")
parser.add_argument("output_dir")
parsed_args = parser.parse_args(sys.argv[1:])
path_comp = PathComponents(parsed_args.hdf5_dataset_path)
with h5py.File(path_comp.externalPath) as input_file:
vol_dset = input_file[path_comp.internalPath]
export_to_tiles(vol_dset, parsed_args.tile_size,
parsed_args.output_dir)
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.LOCAL_VOLUME_DESCRIPTION_FILE = os.path.join(self.TILE_DIRECTORY, "local_volume_description.json")
self.TRANSPOSED_VOLUME_DESCRIPTION_FILE = os.path.join(
self.TILE_DIRECTORY, "transposed_volume_description.json"
)
self.TRANSLATED_VOLUME_DESCRIPTION_FILE = os.path.join(
self.TILE_DIRECTORY, "translated_volume_description.json"
)
self.SPECIAL_Z_VOLUME_DESCRIPTION_FILE = os.path.join(self.TILE_DIRECTORY, "special_z_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 a local tile path instead of a URL
config_helper = JsonConfigParser(TiledVolume.DescriptionFields)
local_description = copy.copy(volume_description)
local_description.tile_url_format = (
self.TILE_DIRECTORY + "/tile_z{z_start:05}_y{y_start:05}_x{x_start:05}.png"
)
config_helper.writeConfigFile(self.LOCAL_VOLUME_DESCRIPTION_FILE, local_description)
# 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)
# Write out another copy of the description, but with an origin translation
config_helper = JsonConfigParser(TiledVolume.DescriptionFields)
translated_description = copy.copy(volume_description)
translated_description.view_origin_zyx = [10, 20, 30]
translated_description.shape_zyx = None
config_helper.writeConfigFile(self.TRANSLATED_VOLUME_DESCRIPTION_FILE, translated_description)
# Write out another copy of the description, but with a special function for translating z-coordinates.
config_helper = JsonConfigParser(TiledVolume.DescriptionFields)
special_z_description = copy.copy(volume_description)
special_z_description.z_translation_function = "lambda z: z+11"
config_helper.writeConfigFile(self.SPECIAL_Z_VOLUME_DESCRIPTION_FILE, special_z_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()
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()
