diff --git a/chimera/chimera.py b/chimera/chimera.py index 0ee7763..355d5a7 100644 --- a/chimera/chimera.py +++ b/chimera/chimera.py @@ -153,7 +153,7 @@ def __init__(self, parc_code, parcel_names = cltmisc._filter_by_substring(parcel_names, seg_tmp, boolcase=False) # Saving the new parcels names - meth_dict['Parcels'] = parcel_names + meth_dict['parcels'] = parcel_names # Adding the dictionary to the temp_dict temp_dict[supra_names[i]] = meth_dict @@ -188,8 +188,8 @@ def _prepare_templates(self, fssubj_dir:str = None): cltfree.FreeSurferSubject._set_freesurfer_directory(fssubj_dir) # Create the simlink to the FreeSurfer directory - - cltfree._create_fsaverage_links(fssubj_dir, fsavg_dir=None, refsubj_name=self.parc_dict["Cortical"]["reference"]) + if "Cortical" in self.parc_dict.keys(): + cltfree._create_fsaverage_links(fssubj_dir, fsavg_dir=None, refsubj_name=self.parc_dict["Cortical"]["reference"]) # Detecting the base directory @@ -280,8 +280,7 @@ def _prepare_templates(self, fssubj_dir:str = None): atlas_ext = '.gcs' method = 'gcs2indiv' - - + ctx_parc_lh = glob(os.path.join(atlas_dir, '*-L_*' + atlas_ext)) ctx_parc_rh = glob(os.path.join(atlas_dir, '*-R_*' + atlas_ext)) @@ -682,6 +681,48 @@ def _export_table(self, out_basename:str = None, format:Union[list, str] = 'tsv' colors = tab_df['color'].tolist() cltparc.Parcellation.write_luttable(codes=codes, names=names, colors=colors, out_file=out_file_lut, headerlines=parc_desc, force=True) + def _build_lut_header(self): + """ + This method builds the header of the LUT file. + + """ + + # Detecting the base directory + chim_dir = os.path.dirname(os.path.abspath(__file__)) + + # Get the absolute of this file + parc_json = os.path.join(chim_dir, 'config', 'supraregions_dictionary.json') + + # Reading the parcellation dictionary + with open(parc_json) as f: + parc_dict = json.load(f) + + # Reading the names of the supra-regions + supra_names = list(parc_dict.keys()) + + # Reading the parcellation code + chim_code = self.parc_code + + # Creating the header lines + headerlines = [" # Chimera parcellation code: {}".format(self.parc_code)] + for i, supra in enumerate(supra_names): + tmp_dict = parc_dict[supra] + + # Check if the parcellation code is in the dictionary + if chim_code[i] in tmp_dict.keys(): + tmp_dict = tmp_dict[chim_code[i]] + + if tmp_dict["description"].endswith('.'): + tmp_dict["description"] = tmp_dict["description"][:-1] + + cite = "{} {}.". format (tmp_dict["atlas"], tmp_dict["citation"]) + glob_desc = tmp_dict["description"] + ". Name: " + cite + headerlines.append(" " + glob_desc) + else: + headerlines.append(" # {}. The parcellation code {} is not present in the dictionary for the supra-region {}.".format(i+1, chim_code[i], supra)) + + return headerlines + def _build_parcellation1(self, t1:str, bids_dir:str, deriv_dir:str = None, fssubj_dir:str = None, @@ -764,12 +805,12 @@ def _build_parcellation1(self, t1:str, bids_dir:str, sub2proc._launch_freesurfer(force=force, cont_tech=cont_tech_freesurfer, cont_image=cont_image_freesurfer) - bool_ctx = False - - # This is done to avoid the cortical parcellation in the first step. - # We are going to create parcellations Right, Left and Middle parcellations - # that will be added to the different cortical configurations + # Building the main header information for the LUT file + glob_header_info = self._build_lut_header() + + # Detecting if Cortical is on the list of supra-regions + bool_ctx = False if 'Cortical' in supra_names: # Remove it from the list supra_names.remove('Cortical') @@ -1123,17 +1164,20 @@ def _build_parcellation1(self, t1:str, bids_dir:str, lh_supra_parc._rearange_parc() lh_parc._add_parcellation(lh_supra_parc, append=True) nlh_subc = len(lh_parc.index) + del lh_supra_parc # lh_parc._save_parcellation(out_file= '/home/yaleman/lh_test.nii.gz', save_lut=True) if "rh_supra_parc" in locals(): rh_supra_parc._rearange_parc() rh_parc._add_parcellation(rh_supra_parc, append=True) nrh_subc = len(rh_parc.index) + del rh_supra_parc # rh_parc._save_parcellation(out_file= '/home/yaleman/rh_test.nii.gz', save_lut=True) if 'mid_supra_parc' in locals(): mid_supra_parc._rearange_parc() mid_parc._add_parcellation(mid_supra_parc, append=True) + del mid_supra_parc # mid_parc._save_parcellation(out_file= '/home/yaleman/mid_test.nii.gz', save_lut=True) # Detecting the number of regions @@ -1146,13 +1190,10 @@ def _build_parcellation1(self, t1:str, bids_dir:str, if 'mid_parc' in locals(): nmid_subc = len(mid_parc.index) - # if "WhiteMatter" in supra_names: #self.supra_dict[supra][supra][atlas_code]["none"]["index"] - - - + date_time = datetime.now().strftime("%d/%m/%Y %H:%M:%S") if bool_ctx: # Atributes for the cortical parcellation @@ -1164,6 +1205,9 @@ def _build_parcellation1(self, t1:str, bids_dir:str, nctx_parc = len(self.parc_dict["Cortical"]["processing"]["labels"]["lh"]) for c in np.arange(nctx_parc): + # Temporal header lines + glob_header_info_tmp = copy.deepcopy(glob_header_info) + ## -------- Cortical parcellation for the left hemisphere --------------- # Creating the name for the output file lh_in_parc = self.parc_dict["Cortical"]["processing"]["labels"]["lh"][c] @@ -1220,7 +1264,7 @@ def _build_parcellation1(self, t1:str, bids_dir:str, # Copying to the labels folder temp_lh = os.path.join(sub2proc.subjs_dir, sub2proc.subj_id, 'label', 'lh.' + at_name + '.annot') shutil.copyfile(lh_out_annot, temp_lh) - + # Copying to the labels folder temp_rh = os.path.join(sub2proc.subjs_dir, sub2proc.subj_id, 'label', 'rh.' + at_name + '.annot') shutil.copyfile(rh_out_annot, temp_rh) @@ -1229,7 +1273,31 @@ def _build_parcellation1(self, t1:str, bids_dir:str, out_vol_dir = os.path.join(deriv_dir, self.parc_dict["Cortical"]["deriv_volfold"], path_cad) if growwm is None: growwm = ['0'] + + ent_dict = cltbids._str2entity(at_name) + if "scale" in ent_dict.keys(): + scale_cad = 'Scale: {}'.format(ent_dict["scale"]) + else: + scale_cad = None + if "seg" in ent_dict.keys(): + seg_cad = 'Segmentation: {}'.format(ent_dict["seg"]) + else: + seg_cad = None + + if scale_cad is not None or seg_cad is not None: + if scale_cad is not None and seg_cad is not None: + cad2add = '. ' + scale_cad + ' - ' + seg_cad + + elif scale_cad is not None and seg_cad is None: + cad2add = '. ' + scale_cad + + elif scale_cad is None and seg_cad is not None: + cad2add = '. ' + seg_cad + + glob_header_info_tmp[0] = glob_header_info_tmp[0] + cad2add + + for ngrow in np.arange(len(growwm)): if growwm[ngrow] == '0': out_vol_name = fullid + '_' + at_name + '_dseg.nii.gz' @@ -1261,6 +1329,15 @@ def _build_parcellation1(self, t1:str, bids_dir:str, chim_parc_lut = os.path.join(str(chim_dir), cltbids._replace_entity_value(chim_parc_name, {"extension": "lut"})) chim_parc_tsv = os.path.join(str(chim_dir), cltbids._replace_entity_value(chim_parc_name, {"extension": "tsv"})) + # Creating the first part of the headers + part_header = ['# $Id: {} {} \n'.format(chim_parc_lut, date_time)] + + part_header.append('# Corresponding parcellation: {} \n'.format(chim_parc_file)) + + lut_header = part_header + glob_header_info_tmp + lut_header = lut_header + ['\n'] + lut_header.append('{:<4} {:<50} {:>3} {:>3} {:>3} {:>3}'.format("#No.", "Label Name:", "R", "G", "B", "A")) + if not os.path.isfile(chim_parc_file) or not os.path.isfile(chim_parc_lut) or not os.path.isfile(chim_parc_tsv) or force: # Creating the joined parcellation ref_image = np.zeros_like(t1_image.get_fdata(), dtype=np.int32) @@ -1307,27 +1384,81 @@ def _build_parcellation1(self, t1:str, bids_dir:str, lh_wm_parc._rearange_parc(offset=3000 + nrh_ctx + nrh_subc) else: bool_wm = False - + + # Adding the right cortical parcellation to the final image rh_ctx_parc._rearange_parc() chim_parc._add_parcellation(rh_ctx_parc, append=True) + del rh_ctx_parc + + # Adding the right non-cortical parcellation to the final image if "rh_parc" in locals(): chim_parc._add_parcellation(rh_parc, append=True) + # Adding the left cortical parcellation to the final image lh_ctx_parc._rearange_parc() chim_parc._add_parcellation(lh_ctx_parc, append=True) + del lh_ctx_parc + + # Adding the left non-cortical parcellation to the final image if "lh_parc" in locals(): chim_parc._add_parcellation(lh_parc, append=True) - + + # Adding the regions that do not belong to any hemisphere to the final image if "mid_parc" in locals(): chim_parc._add_parcellation(mid_parc, append=True) + # Adding the white matter to the final image if bool_wm: chim_parc._add_parcellation(brain_wm_parc, append=False) + del brain_wm_parc + chim_parc._add_parcellation(rh_wm_parc, append=False) + del rh_wm_parc + chim_parc._add_parcellation(lh_wm_parc, append=False) + del lh_wm_parc - chim_parc._save_parcellation(out_file=chim_parc_file, affine=affine, save_lut=True, save_tsv=True) + # Saving the FINAL parcellation + chim_parc._save_parcellation(out_file=chim_parc_file, affine=affine, headerlines=lut_header, save_lut=True, save_tsv=True) + del chim_parc + else: + out_vol_name = fullid + '_dseg.nii.gz' + chim_parc_name = cltbids._insert_entity(out_vol_name, {"atlas": "chimera" + chim_code} ) + chim_parc_file = os.path.join(str(chim_dir), chim_parc_name) + chim_parc_lut = os.path.join(str(chim_dir), cltbids._replace_entity_value(chim_parc_name, {"extension": "lut"})) + chim_parc_tsv = os.path.join(str(chim_dir), cltbids._replace_entity_value(chim_parc_name, {"extension": "tsv"})) + + if not os.path.isfile(chim_parc_file) or not os.path.isfile(chim_parc_lut) or not os.path.isfile(chim_parc_tsv) or force: + part_header = ['# $Id: {} {} \n'.format(chim_parc_lut, date_time)] + part_header.append('# Corresponding parcellation: {} \n'.format(chim_parc_file)) + + lut_header = part_header + glob_header_info + lut_header = lut_header + ['\n'] + lut_header.append('{:<4} {:<50} {:>3} {:>3} {:>3} {:>3}'.format("#No.", "Label Name:", "R", "G", "B", "A")) + + # Creating the joined parcellation + ref_image = np.zeros_like(t1_image.get_fdata(), dtype=np.int32) + chim_parc = cltparc.Parcellation(parc_file=ref_image, affine=affine) + + # Adding the right non-cortical parcellation to the final image + if "rh_parc" in locals(): + rh_parc._rearange_parc() + chim_parc._add_parcellation(rh_parc, append=True) + + # Adding the left non-cortical parcellation to the final image + if "lh_parc" in locals(): + lh_parc._rearange_parc() + chim_parc._add_parcellation(lh_parc, append=True) + + # Adding the regions that do not belong to any hemisphere to the final image + if "mid_parc" in locals(): + mid_parc._rearange_parc() + chim_parc._add_parcellation(mid_parc, append=True) + + # Saving the FINAL parcellation + chim_parc._save_parcellation(out_file=chim_parc_file, affine=affine, headerlines=lut_header, save_lut=True, save_tsv=True) + del chim_parc # Loading the JSON file containing the available parcellations def _pipeline_info(pipe_json:str=None): @@ -1532,10 +1663,10 @@ def _build_args_parser(): requiredNamed.add_argument('--growwm', '-g', action='store', required=False, metavar='GROWWM', type=str, nargs=1, help="R| Grow of GM labels inside the white matter in mm. \n", default=None) - requiredNamed.add_argument('--txt2filter', '-x', action='store', required=False, metavar='FILE', type=str, nargs=1, - help="R| File containing the basename of the NIFTI images that will be ran. \n" - " This file is useful to tun Chimera, only, on certain T1s in case of multiple T1s \n" - " for the same session.\n" + requiredNamed.add_argument('--subjids', '-ids', action='store', required=False, metavar='FILE', type=str, nargs=1, + help="R| Subject IDs. Multiple subject ids can be specified separating them by a comma. \n" + " The ID should be the basename of the T1-weighted image that will be ran. \n" + " A txt file containing the IDs can be also used. \n" " Example of this file: \n" " sub-00001_ses-0001_run-2 \n" " sub-00001_ses-0003_run-1\n" @@ -2308,8 +2439,8 @@ def main(): code_dict = {"code": parcodes, "scale": scale_id, "seg": seg_id} - if args.txt2filter is not None: - t1s2run_file = args.txt2filter[0] + if args.subjids is not None: + t1s2run_file = args.subjids[0] else: t1s2run_file = ''