def run(self, prefix=None):
"""
Parameters
----------
prefix: str
A prefix that is added to the stats volumes. To locate correct transform inversion files, look for files
with this prefix missing
"""
# inverting_names = os.listdir(self.inverted_tform_stage_dirs[ # 0])
# for i, vol_name in enumerate(inverting_names):
# if self.batch_invert:
# invertable = self.invertables
# else:
# invertable = self.invertables[vol_name]
volname, ext = splitext(basename(self.invertables))
if prefix and volname.startswith(prefix):
original_vol_name = volname[len(prefix):] # remove the prfix to get the original vol name to find the tf
else:
original_vol_name = volname
invertable = self.invertables
for inversion_stage in self.inverted_tform_stage_dirs:
invert_stage_out = join(self.out_dir, basename(inversion_stage))
common.mkdir_if_not_exists(invert_stage_out)
inv_tform_dir = join(inversion_stage, original_vol_name)
transform_file = join(inv_tform_dir, IMAGE_INVERTED_TRANSFORM)
invert_vol_out_dir = join(invert_stage_out, volname)
common.mkdir_if_not_exists(invert_vol_out_dir)
invertable = self._invert(invertable, transform_file, invert_vol_out_dir, self.threads)
def run(self):
"""
"""
done_file = self.out_dir / 'invert.done'
common.touch(done_file)
vol_ids = os.listdir(self._transform_dirs()[0])
logging.info('inverting volumes')
for i, id_ in enumerate(vol_ids):
invertable = self.invertables
for inversion_stage in self._transform_dirs():
invert_stage_out = self.out_dir / inversion_stage.name
common.mkdir_if_not_exists(invert_stage_out)
invert_vol_out_dir = invert_stage_out / id_
common.mkdir_if_not_exists(invert_vol_out_dir)
transform_file = inversion_stage / id_ / self.invert_transform_name
# logging.info('inverting {}'.format(transform_file))
invertable = self._invert(invertable, transform_file, invert_vol_out_dir, self.threads)
if not invertable: # If inversion failed or there is nocobber, will get None
continue
self.last_invert_dir = invert_stage_out
def __init__(self, config_path: Path, invertable, outdir, threads=None, noclobber=False):
"""
Inverts a series of volumes. A yaml config file specifies the order of inverted transform parameters
to use. This config file should be in the root of the directory containing these inverted tform dirs.
Also need to input a directory containing volumes/label maps etc to invert. These need to be in directories
named with the same name as the corresponding inverted tform file directories
Parameters
----------
config_path
path to yaml config containing the oder of the inverted directories to use. The directories containing
propagation tfransfrom files should be in the same diretory
threads: str/ None
number of threas to use. If None, use all available threads
invertable: str
path to object to invert (raw image, mask, label map etc)
outdir
where to store inverted volumes
invertable: str
dir or path. If dir, invert all objects within the subdirectories.
If path to object (eg. labelmap) invert that instead
noclobber: bool
if True do not overwrite already inverted labels
"""
self.noclobber = noclobber
common.test_installation('transformix')
self.config = cfg_load(config_path)
self.invertables = invertable
self.config_dir = config_path.parent # The dir containing the inverted elx param files
self.threads = threads
self.out_dir = outdir
common.mkdir_if_not_exists(self.out_dir)
self.elx_param_prefix = ELX_PARAM_PREFIX
self.PROPAGATION_TFORM_NAME = None # Set in subclasses
self.last_invert_dir = None # I thik this is used as a way to find volumes to do organ vol calculation on