def transform(source, sink = [], transform_parameter_file = None, transform_directory = None, result_directory = None):
"""Transform a raw data set to reference using the elastix alignment results.
Arguments
---------
source : str or array
Image source to be transformed.
sink : str, [] or None
Image sink to save transformed image to. If [] return the default name
of the data file generated by transformix.
transform_parameter_file : str or None
Parameter file for the primary transformation.
If None, the file is determined from the transform_directory.
transform_directory : str or None
Result directory of elastix alignment.
If None the transform_parameter_file has to be given.
result_directory : str or None
The directorty for the transformix results.
Returns
-------
transformed : array or st
Array or file name of the transformed data.
Note
----
If the map determined by elastix is
:math:`T: \\mathrm{fixed} \\rightarrow \\mathrm{moving}`,
transformix on data works as :math:`T^{-1}(\\mathrm{data})`.
"""
check_elastix_initialized();
# image
source = io.as_source(source);
if isinstance(source, io.tif.Source):
imgname = source.location;
delete_image = None;
else:
imgname = os.path.join(tempfile.gettempdir(), 'elastix_input.tif');
io.write(source, imgname);
delete_image = imgname;
# result directory
delete_result_directory = None;
if result_directory == None:
resultdirname = os.path.join(tempfile.gettempdir(), 'elastix_output');
delete_result_directory = resultdirname;
else:
resultdirname = result_directory;
if not os.path.exists(resultdirname):
os.makedirs(resultdirname);
# tranformation parameter
transform_parameter_dir, transform_parameter_file = transform_directory_and_file(transform_parameter_file = transform_parameter_file, transform_directory = transform_directory);
set_path_transform_files(transform_parameter_dir);
#transformix -in inputImage.ext -out outputDirectory -tp TransformParameters.txx
cmd = '%s -in %s -out %s -tp %s' % (transformix_binary, imgname, resultdirname, transform_parameter_file);
res = os.system(cmd);
if res != 0:
raise RuntimeError('transform_data: failed executing: ' + cmd);
# read data and clean up
if delete_image is not None:
os.remove(delete_image);
if sink == []:
return result_data_file(resultdirname);
elif sink is None:
resultfile = result_data_file(resultdirname);
result = io.read(resultfile);
elif isinstance(sink, str):
resultfile = result_data_file(resultdirname);
result = io.convert(resultfile, sink);
else:
raise RuntimeError('transform_data: sink not valid!');
if delete_result_directory is not None:
shutil.rmtree(delete_result_directory);
return result;
def deformation_field(sink = [], transform_parameter_file = None, transform_directory = None, result_directory = None):
"""Create the deformation field T(x) - x.
Arguments
---------
sink : str, [] or None
Image sink to save the transformation field; if [] return the default name
of the data file generated by transformix.
transform_parameter_file : str or None
Parameter file for the primary transformation, if None, the file is
determined from the transform_directory.
transform_directory : str or None
Result directory of elastix alignment, if None the
transform_parameter_file has to be given.
result_directory : str or None
The directorty for the transformix results.
Returns
-------
deformation_field : array or str
Array or file name of the deformation field data.
Note
----
The map determined by elastix is
:math:`T \\mathrm{fixed} \\rightarrow \\mathrm{moving}`.
"""
check_elastix_initialized();
# result directory
delete_result_directory = None;
if result_directory == None:
resultdirname = os.path.join(tempfile.gettempdir(), 'elastix_output');
delete_result_directory = resultdirname;
else:
resultdirname = result_directory;
if not os.path.exists(resultdirname):
os.makedirs(resultdirname);
# setup transformation
transform_parameter_dir, transform_parameter_file = transform_directory_and_file(transform_parameter_file = transform_parameter_file, transform_directory = transform_directory);
set_path_transform_files(transform_parameter_dir);
#transformix -in inputImage.ext -out outputDirectory -tp TransformParameters.txt
cmd = '%s -def all -out %s -tp %s' % (transformix_binary, resultdirname, transform_parameter_file)
res = os.system(cmd);
if res != 0:
raise RuntimeError('deformation_field: failed executing: ' + cmd);
# read result and clean up
if sink == []:
return result_data_file(resultdirname);
elif sink is None:
resultfile = result_data_file(resultdirname);
result = io.read(resultfile);
elif isinstance(sink, str):
resultfile = result_data_file(resultdirname);
result = io.convert(resultfile, sink);
else:
raise RuntimeError('deformation_field: sink not valid!');
if delete_result_directory is not None:
shutil.rmtree(delete_result_directory);
return result;
ws.update(raw=expression_raw)
#ws.debug = 'medchunk'
print(ws.info())
# convert raw to stitched npy file
source = ws.source('raw')
sink = ws.filename('stitched')
if not os.path.exists(os.path.join(directory, "final_blocks")):
os.mkdir(os.path.join(directory, "final_blocks"))
if step == 0:
print("++++++++++ STEP 0 +++++++++++++")
# convert single z planes to stitched
io.delete_file(sink)
io.convert(source, sink, processes=None, verbose=True)
elif step == 1:
# Split into blocks
print("splitting into blocks")
blocks = bp.split_into_blocks(
ws.source('stitched'),
processes=12,
axes=[2], # chunks along z
size_min=5,
size_max=20,
overlap=2,
verbose=True)
print("Done splitting into blocks of len {} for array {}".format(
len(blocks), arrayid))
if arrayid <= len(blocks):
