def _write_thresholded_label_map(self, label_map: np.ndarray, hits, out: Path):
"""
Write a label map with only the 'hit' organs in it
"""
if len(hits) > 0:
# Make a copy as it may be being used elsewhere
l = np.copy(label_map)
# Clear any non-hits
l[~np.isin(l, hits)] = 0
write_array(l, out, ras=True)
def _write(self, t_stats, pvals, qvals, outdir, name):
filtered_tstats = result_cutoff_filter(t_stats, qvals)
filtered_result = self.rebuild_array(filtered_tstats, self.shape, self.mask)
unfiltered_result = self.rebuild_array(t_stats, self.shape, self.mask)
heatmap_path = outdir / f'{name}_{self.stats_name}_t_fdr5.nrrd'
heatmap_path_unfiltered = outdir / f'{name}_{self.stats_name}_t.nrrd'
# Write qval-filtered t-stats
write_array(filtered_result, heatmap_path, ras=True)
# Write raw t-stats
write_array(unfiltered_result, heatmap_path_unfiltered, ras=True)
return heatmap_path
def _write(self, t_stats, pvals, qvals, outdir, name):
if self.two_way:
pvals = np.array_split(pvals, 3)
f_stats = np.array_split(t_stats, 3)
qvals = np.array_split(qvals, 3)
groups = ['geno', 'treat', 'int']
for i, f_stat in enumerate(f_stats):
filtered_fstats = result_cutoff_filter(f_stat, qvals[i])
filtered_result = self.rebuild_array(filtered_fstats,
self.shape, self.mask)
unfiltered_result = self.rebuild_array(f_stat, self.shape,
self.mask)
heatmap_path = outdir / f'{name}_{self.stats_name}_{groups[i]}_f_fdr5.nrrd'
heatmap_path_unfiltered = outdir / f'{name}_{self.stats_name}_{groups[i]}_f.nrrd'
# Write qval-filtered t-stats
write_array(filtered_result, heatmap_path, ras=True)
# Write raw t-stats
write_array(unfiltered_result,
heatmap_path_unfiltered,
ras=True)
else:
filtered_tstats = result_cutoff_filter(t_stats, qvals)
filtered_result = self.rebuild_array(filtered_tstats, self.shape,
self.mask)
unfiltered_result = self.rebuild_array(t_stats, self.shape,
self.mask)
heatmap_path = outdir / f'{name}_{self.stats_name}_t_fdr5.nrrd'
heatmap_path_unfiltered = outdir / f'{name}_{self.stats_name}_t.nrrd'
# Write qval-filtered t-stats
write_array(filtered_result, heatmap_path, ras=True)
# Write raw t-stats
write_array(unfiltered_result, heatmap_path_unfiltered, ras=True)
return heatmap_path
def _get_deformations(tform: Path,
deformation_dir: Path,
jacobian_dir: Path,
log_jacobians_dir: Path,
filetype: str,
specimen_id: str,
threads: int,
make_jacmat: bool,
write_vectors: bool = False,
write_raw_jacobians: bool = False,
write_log_jacobians: bool = True) -> Union[None, np.array]:
"""
Generate spatial jacobians and optionally deformation files.
Returns
-------
the jacobian array if there are any values < 0
"""
cmd = ['transformix',
'-out', str(deformation_dir),
'-tp', str(tform),
'-jac', 'all'
]
if write_vectors:
cmd.extend(['-def', 'all'])
if make_jacmat:
cmd.extend(['-jacmat', 'all'])
if threads:
cmd.extend(['-threads', str(threads)])
try:
subprocess.check_output(cmd)
except subprocess.CalledProcessError as e:
logging.exception('transformix failed')
logging.exception(e)
# raise subprocess.CalledProcessError(f'### Transformix failed ###\nError message: {e}\nelastix command:{cmd}')
raise ValueError
else:
deformation_out = deformation_dir / f'deformationField.{filetype}'
jacobian_out = deformation_dir / f'spatialJacobian.{filetype}'
# rename and move output
if write_vectors:
new_def = deformation_dir / (specimen_id + '.' + filetype)
shutil.move(deformation_out, new_def)
new_jac = jacobian_dir / (specimen_id + '.' + filetype)
try:
shutil.move(jacobian_out, new_jac)
except IOError:
# Bit of a hack. If trasforms conatain subtransforms from pairwise, elastix is unable to generate
# deformation fields. So try with itk
def_img = sitk.ReadImage(new_def)
jac_img = sitk.DisplacementFieldJacobianDeterminant(def_img)
sitk.WriteImage(jac_img, new_jac)
# if we have full jacobian matrix, rename and remove that
if make_jacmat:
make_jacmat.mkdir()
jacmat_file = deformation_dir / f'fullSpatialJacobian.{filetype}' # The name given by elastix
jacmat_new = make_jacmat / (specimen_id + '.' + filetype) # New informative name
shutil.move(jacmat_file, jacmat_new)
# test if there has been any folding in the jacobians
jac_img = sitk.ReadImage(str(new_jac))
jac_arr = sitk.GetArrayFromImage(jac_img)
jac_min = jac_arr.min()
jac_max = jac_arr.max()
logging.info("{} spatial jacobian, min:{}, max:{}".format(specimen_id, jac_min, jac_max))
if jac_min <= 0:
logging.warning(
"The jacobian determinant for {} has negative values. You may need to add a penalty term to the later registration stages".format(
specimen_id))
# Highlight the regions folding
jac_arr[jac_arr > 0] = 0
log_jac_path = log_jacobians_dir / ('ERROR_NEGATIVE_JACOBIANS_' + specimen_id + '.' + filetype)
common.write_array(jac_arr, log_jac_path)
elif write_log_jacobians:
# Spit out the log transformed jacobians
log_jac = np.log(jac_arr)
log_jac_path = log_jacobians_dir / ( 'log_jac_' + specimen_id + '.' + filetype)
if not write_raw_jacobians:
new_jac.unlink()
common.write_array(log_jac, log_jac_path)
logging.info('Finished generating deformation fields')
if jac_min <=0:
return jac_arr
def secondary_segmentation(config: LamaConfig):
"""
Use user-added scripts to segment/cleanup organs
Parameters
----------
config
Returns
-------
"""
plugin_dir = config.config_dir / config['seg_plugin_dir']
if not plugin_dir.is_dir():
logging.error(f'Cannot find plugin director: {plugin_dir}')
return
# Find the directories containing the segmentations
# Get the final inversion stage
invert_config = config['inverted_transforms'] / PROPAGATE_CONFIG
segmentation_dir = cfg_load(invert_config)['label_propagation_order'][
-1] # rename to segmentation stage
inverted_label_dir = config['inverted_labels'] / segmentation_dir
initial_segmentation_path = next(inverted_label_dir.glob('**/*.nrrd'))
first_reg_dir = config['root_reg_dir'] / config[
'registration_stage_params'][0]['stage_id'] # usually rigid
image_to_segment = next(first_reg_dir.glob('**/*.nrrd'))
segmentations = []
for plugin_src in [
x for x in plugin_dir.iterdir()
if str(x).endswith('.py') and x.name != 'plugin_interface.py'
]:
# catch all exceptions as we don't want plugin crashing the pipeline
try:
spec = importlib.util.spec_from_file_location(
plugin_src.stem, str(plugin_src))
plugin = importlib.util.module_from_spec(spec)
spec.loader.exec_module(plugin)
new_segmetation = plugin.run(image_to_segment,
initial_segmentation_path)
except Exception as e:
logging.error(f'Plugin {plugin_src} failed\n{e}')
else:
segmentations.append(new_segmetation)
if not segmentations:
logging.error(f'No segmentations returned from {plugin_src.name}')
# Merge all the segmentations into a single label map. If there are any overlaps, the plugin called last will have
# priority
seg = None
for s in segmentations:
if not seg:
seg = s
continue
seg[s != 0] = s[s != 0]
additional_seg_dir = config.mkdir('additional_seg_dir')
write_array(seg, additional_seg_dir /
f'{config.config_dir.name}_additonal_seg.nrrd'
) # TODO include specimen name