pyAFQ 2.0__tar.gz → 2.1__tar.gz

{pyafq-2.0 → pyafq-2.1}/AFQ/api/bundle_dict.py

@@ -451,7 +451,7 @@ def baby_bd():
                            'mahal': {'distance_threshold': 4}},
         'Forceps Minor': {'cross_midline': True,
                           'include': [templates['FA_R'],
-                                      templates['mid-saggital'],
+                                      templates['mid-sagittal'],
                                       templates['FA_L']],
                           'exclude': [],
                           'space': 'template',
@@ -459,7 +459,7 @@ def baby_bd():
                           'mahal': {'distance_threshold': 4}},
         'Forceps Major': {'cross_midline': True,
                           'include': [templates['FP_R'],
-                                      templates['mid-saggital'],
+                                      templates['mid-sagittal'],
                                       templates['FP_L']],
                           'exclude': [],
                           'space': 'template',
@@ -722,8 +722,10 @@ class BundleDict(MutableMapping):
         If there are bundles in bundle_info with the 'space' attribute
         set to 'subject', their images (all ROIs and probability maps)
         will be resampled to the affine and shape of this image.
+        If None, resamples to DWI. Be careful if you use this,
+        that this is the correct choice.
         If False, no resampling will be done.
-        Default: None
+        Default: False
 
     keep_in_memory : bool, optional
         Whether, once loaded, all ROIs and probability maps will stay
@@ -1017,9 +1019,9 @@ class BundleDict(MutableMapping):
         new_affine : array
             Affine of space transformed into.
         base_fname : str, optional
-            Base file path to save ROIs too. Additional BIDS
+            Base file path to construct file path from. Additional BIDS
             descriptors will be added to this file path. If None,
-            do not save the ROIs.
+            no file paths returned.
         to_space : str, optional
             Name for space for exported ROIs. Only used if base_fname
             is not None.
@@ -1033,8 +1035,8 @@ class BundleDict(MutableMapping):
         -------
         If base_fname is None, a dictionary where keys are
         the roi type and values are the transformed ROIs.
-        Otherwise, a list of file names where the transformed
-        ROIs are saved.
+        Otherwise, a list of file names and a list of transformed ROIs
+        are returned.
         """
         if self.is_bundle_in_template(bundle_name):
             transformed_rois = self.apply_to_rois(
@@ -1055,6 +1057,7 @@ class BundleDict(MutableMapping):
 
         if base_fname is not None:
             fnames = []
+            list_of_rois_to_save = []
             for roi_type, rois in transformed_rois.items():
                 if roi_type == "prob_map":
                     suffix = "probseg"
@@ -1079,12 +1082,9 @@ class BundleDict(MutableMapping):
                         f"{desc}"
                         f"_{suffix}.nii.gz",
                         "ROIs")
-                    nib.save(
-                        nib.Nifti1Image(
-                            roi.get_fdata().astype(np.float32),
-                            roi.affine), fname)
                     fnames.append(fname)
-            return fnames
+                    list_of_rois_to_save.append(roi)
+            return list_of_rois_to_save, fnames
         else:
             return transformed_rois
 

{pyafq-2.0 → pyafq-2.1}/AFQ/api/group.py

@@ -127,7 +127,7 @@ class GroupAFQ(object):
 
         Examples
         --------
-        api.GroupAFQ(my_path, csd_sh_order=4)
+        api.GroupAFQ(my_path, csd_sh_order_max=4)
         api.GroupAFQ(
             my_path,
             reg_template_spec="mni_t2", reg_subject_spec="b0")
@@ -208,8 +208,9 @@ class GroupAFQ(object):
 
         pl_desc_file = op.join(self.afq_path, 'dataset_description.json')
 
-        with open(pl_desc_file, 'w') as outfile:
-            json.dump(pipeline_description, outfile)
+        if not op.exists(pl_desc_file):
+            with open(pl_desc_file, 'w') as outfile:
+                json.dump(pipeline_description, outfile)
 
         self.subjects = bids_layout.get(return_type='id', target='subject')
         if not len(self.subjects):
@@ -410,7 +411,12 @@ class GroupAFQ(object):
             self.afq_path, "tract_profiles.csv"))
         os.makedirs(op.dirname(out_file), exist_ok=True)
         _df = clean_pandas_df(_df)
-        _df.to_csv(out_file, index=False)
+        try:
+            _df.to_csv(out_file, index=False)
+        except:
+            logger.warning((
+                "Unable to update combined tract profile. "
+                "This is likely due to file permissions."))
         return _df
 
     def get_streamlines_json(self):
@@ -502,6 +508,8 @@ class GroupAFQ(object):
             None if called without arguments.
         """
         section = check_attribute(attr_name)
+        if section == False:
+            return None
 
         # iterate over subjects / sessions,
         # decide if they need to be calculated or not
@@ -554,6 +562,9 @@ class GroupAFQ(object):
             Name of the output to export up to. Default: "help"
         """
         section = check_attribute(attr_name)
+        if section == False:
+            return None
+
         wf_dict = self.wf_dict[
             self.valid_sub_list[0]][self.valid_ses_list[0]]
         if section is not None:
@@ -772,7 +783,13 @@ class GroupAFQ(object):
                 self.afq_path,
                 (f"bundle-{bundle_name}_view-{view}"
                     f"_idx-{curr_file_num}_montage.png")))
-            curr_img.save(save_path)
+            try:
+                curr_img.save(save_path)
+            except:
+                if op.exists(save_path):
+                    logger.info("Montage file already exists, skipping.")
+                else:
+                    logger.warning("Unable to save montage file, skipping.")
             all_fnames.append(save_path)
 
         this_img_trimmed = {}
@@ -865,12 +882,23 @@ class GroupAFQ(object):
             sls_mni,
             reg_template,
             Space.VOX)
-        save_tractogram(
-            moved_sft,
-            op.abspath(op.join(
-                self.afq_path,
-                f"bundle-{bundle_name}_subjects-all_MNI.trk")),
-            bbox_valid_check=False)
+
+        save_path = op.abspath(op.join(
+            self.afq_path,
+            f"bundle-{bundle_name}_subjects-all_MNI.trk"))
+        try:
+            save_tractogram(
+                moved_sft,
+                save_path,
+                bbox_valid_check=False)
+        except:
+            if op.exists(save_path):
+                logger.info(("Combined bundles file "
+                             "already exists, skipping."))
+            else:
+                logger.warning((
+                    "Unable to save combined "
+                    "bundles file, skipping."))
 
     def upload_to_s3(self, s3fs, remote_path):
         """ Upload entire AFQ derivatives folder to S3"""

{pyafq-2.0 → pyafq-2.1}/AFQ/api/participant.py

@@ -56,7 +56,7 @@ class ParticipantAFQ(object):
         --------
         api.ParticipantAFQ(
             dwi_data_file, bval_file, bvec_file, output_dir,
-            csd_sh_order=4)
+            csd_sh_order_max=4)
         api.ParticipantAFQ(
             dwi_data_file, bval_file, bvec_file, output_dir,
             reg_template_spec="mni_t2", reg_subject_spec="b0")
@@ -149,6 +149,8 @@ class ParticipantAFQ(object):
             The specific output, or None if called without arguments.
         """
         section = check_attribute(attr_name)
+        if section == False:
+            return None
 
         if section is None:
             return self.wf_dict[attr_name]
@@ -156,7 +158,7 @@ class ParticipantAFQ(object):
 
     def export_up_to(self, attr_name="help"):
         f"""
-        Export all derivatives necessary for a specific output.
+        Export all derivatives up to, but not including, the specified output.
         To print a list of available outputs,
         call export_up_to without arguments.
         {valid_exports_string}
@@ -167,6 +169,9 @@ class ParticipantAFQ(object):
             Name of the output to export up to. Default: "help"
         """
         section = check_attribute(attr_name)
+        if section == False:
+            return None
+
         wf_dict = self.wf_dict
         if section is not None:
             wf_dict = wf_dict[section]

{pyafq-2.0 → pyafq-2.1}/AFQ/api/utils.py

@@ -1,8 +1,8 @@
 import contextlib
 from importlib import import_module
 from AFQ.viz.utils import viz_import_msg_error
+from AFQ.utils.docstring_parser import parse_numpy_docstring
 import pimms
-from funcargparse import FuncArgParser
 import logging
 import warnings
 
@@ -23,18 +23,31 @@ set_sft_logger_level(logging.CRITICAL)
 
 task_modules = ["data", "mapping", "segmentation", "tractography", "viz"]
 
-methods_descriptors = {}
-methods_sections = {}
+methods_descriptors = {
+    "dwi_data_file": "Path to DWI data file",
+    "bval_file": "Path to bval file",
+    "bvec_file": "Path to bvec file",
+    "output_dir": "Path to output directory",
+    "best_scalar": "Go-to scalar for visualizations",
+    "base_fname": "Base file name for outputs",
+}
+methods_sections = {
+    "dwi_data_file": "data",
+    "bval_file": "data",
+    "bvec_file": "data",
+    "output_dir": "data",
+    "best_scalar": "tractography",
+    "base_fname": "data",
+}
 kwargs_descriptors = {}
 for task_module in task_modules:
     kwargs_descriptors[task_module] = {}
     for calc_obj in import_module(
             f"AFQ.tasks.{task_module}").__dict__.values():
         if isinstance(calc_obj, pimms.calculation.Calc):
-            docstr_parser = FuncArgParser()
-            docstr_parser.setup_args(calc_obj.function)
+            docstr_parsed = parse_numpy_docstring(calc_obj.function)
             if len(calc_obj.efferents) > 1:
-                eff_descs = docstr_parser.description.split(",")
+                eff_descs = docstr_parsed["description"].split(",")
                 if len(eff_descs) != len(calc_obj.efferents):
                     raise NotImplementedError((
                         "If calc method has mutliple outputs, "
@@ -56,10 +69,10 @@ for task_module in task_modules:
             else:
                 methods_descriptors[
                     calc_obj.efferents[0]] =\
-                    docstr_parser.description
+                    docstr_parsed["description"]
                 methods_sections[calc_obj.efferents[0]] =\
                     task_module
-            for arg, info in docstr_parser.unfinished_arguments.items():
+            for arg, info in docstr_parsed["arguments"].items():
                 if "help" in info:
                     default = info["default"] if "default" in info else None
                     kwargs_descriptors[task_module][arg] = dict(
@@ -97,6 +110,9 @@ valid_exports_string = (
 def check_attribute(attr_name):
     if attr_name == "help":
         print(valid_exports_string)
+        return False
+
+    if attr_name[:-5] in task_modules:
         return None
 
     if attr_name in methods_sections:

{pyafq-2.0 → pyafq-2.1}/AFQ/data/fetch.py

@@ -238,7 +238,7 @@ pediatric_fnames = [
     "VOF_box_L.nii.gz", "VOF_box_R.nii.gz",
     "UNCNeo-withCerebellum-for-babyAFQ.nii.gz",
     "UNCNeo_JHU_tracts_prob-for-babyAFQ.nii.gz",
-    "mid-saggital.nii.gz",
+    "mid-sagittal.nii.gz",
     "OR_rightV1.nii.gz",
     "OR_rightThal.nii.gz",
     "OR_right_roi3.nii.gz",
@@ -308,7 +308,7 @@ pediatric_remote_fnames = [
     "24880739", "24880742", "24880754", "24880757", "24880760", "24880763",
     "24880769", "24880772", "24880775", "24880778", "24880781", "24880787",
     "24880790", "24880793", "24880796", "24880802", "24880805", "24880808",
-    "24880616", "24880613", "24986396",
+    "24880616", "24880613", "54869903",
     "42120480",
     "42120483",
     "42120486",
@@ -405,6 +405,8 @@ def read_resample_roi(roi, resample_to=None, threshold=False):
     nibabel image class instance that contains the binary ROI resampled into
     the requested space.
     """
+    logger = logging.getLogger('AFQ')
+
     if isinstance(roi, str):
         roi = nib.load(roi)
 
@@ -414,7 +416,11 @@ def read_resample_roi(roi, resample_to=None, threshold=False):
     if isinstance(resample_to, str):
         resample_to = nib.load(resample_to)
 
-    if resample_to is False or np.allclose(resample_to.affine, roi.affine):
+    if resample_to is False:
+        return roi
+
+    if np.allclose(resample_to.affine, roi.affine):
+        logger.info("Resampling skipped as affines already match.")
         return roi
 
     as_array = resample(
@@ -1049,8 +1055,9 @@ def to_bids_description(path, fname='dataset_description.json',
     """Dumps a dict into a bids description at the given location"""
     kwargs.update({"BIDSVersion": BIDSVersion})
     desc_file = op.join(path, fname)
-    with open(desc_file, 'w') as outfile:
-        json.dump(kwargs, outfile)
+    if not op.exists(desc_file):
+        with open(desc_file, 'w') as outfile:
+            json.dump(kwargs, outfile)
 
 
 def organize_cfin_data(path=None):

{pyafq-2.0 → pyafq-2.1}/AFQ/models/QBallTP.py

@@ -7,7 +7,7 @@ from dipy.reconst.shm import anisotropic_power, sh_to_sf_matrix
 __all__ = ["extract_odf", "anisotropic_index", "anisotropic_power"]
 
 
-def extract_odf(odf, sphere=default_sphere, sh_order=8):
+def extract_odf(odf, sphere=default_sphere, sh_order_max=8):
     """
     Calculates spherical harmonics coefficients and
     isotropic and anisotropic diffusion components
@@ -18,7 +18,7 @@ def extract_odf(odf, sphere=default_sphere, sh_order=8):
     ISO = odf_norm.min(axis=-1)
 
     _, invB = sh_to_sf_matrix(
-        sphere, sh_order=sh_order, basis_type=None, return_inv=True)
+        sphere, sh_order_max=sh_order_max, basis_type=None, return_inv=True)
     shm = blas.dgemm(
         alpha=1.,
         a=odf.reshape(-1, invB.shape[0]), b=invB).reshape(

{pyafq-2.0 → pyafq-2.1}/AFQ/models/csd.py

@@ -23,19 +23,19 @@ class CsdNanResponseError(Exception):
     pass
 
 
-def _model(gtab, data, response=None, sh_order=None, csd_fa_thr=0.7):
+def _model(gtab, data, response=None, sh_order_max=None, csd_fa_thr=0.7):
     """
     Helper function that defines a CSD model.
     """
-    if sh_order is None:
+    if sh_order_max is None:
         ndata = np.sum(~gtab.b0s_mask)
         # See dipy.reconst.shm.calculate_max_order
         L1 = (-3 + np.sqrt(1 + 8 * ndata)) / 2.0
-        sh_order = int(L1)
-        if np.mod(sh_order, 2) != 0:
-            sh_order = sh_order - 1
-        if sh_order > 8:
-            sh_order = 8
+        sh_order_max = int(L1)
+        if np.mod(sh_order_max, 2) != 0:
+            sh_order_max = sh_order_max - 1
+        if sh_order_max > 8:
+            sh_order_max = 8
 
     my_model = csd.ConstrainedSphericalDeconvModel
     if response is None:
@@ -55,21 +55,21 @@ def _model(gtab, data, response=None, sh_order=None, csd_fa_thr=0.7):
     if np.all(np.isnan(response[0])):
         raise CsdNanResponseError
 
-    csdmodel = my_model(gtab, response, sh_order=sh_order)
+    csdmodel = my_model(gtab, response, sh_order_max=sh_order_max)
     return csdmodel
 
 
-def _fit(gtab, data, mask, response=None, sh_order=None,
+def _fit(gtab, data, mask, response=None, sh_order_max=None,
          lambda_=1, tau=0.1, csd_fa_thr=0.7):
     """
     Helper function that does the core of fitting a model to data.
     """
-    return _model(gtab, data, response, sh_order, csd_fa_thr).fit(
+    return _model(gtab, data, response, sh_order_max, csd_fa_thr).fit(
         data, mask=mask)
 
 
 def fit_csd(data_files, bval_files, bvec_files, mask=None, response=None,
-            b0_threshold=50, sh_order=None, lambda_=1, tau=0.1, out_dir=None):
+            b0_threshold=50, sh_order_max=None, lambda_=1, tau=0.1, out_dir=None):
     """
     Fit the CSD model and save file with SH coefficients.
 
@@ -94,7 +94,7 @@ def fit_csd(data_files, bval_files, bvec_files, mask=None, response=None,
     b0_threshold : float,optional.
       The value of diffusion-weighting under which we consider it to be
       equivalent to 0. Default:50
-    sh_order : int, optional.
+    sh_order_max : int, optional.
         default: infer the number of parameters from the number of data
         volumes, but no larger than 8.
     lambda_ : float, optional.
@@ -126,7 +126,7 @@ def fit_csd(data_files, bval_files, bvec_files, mask=None, response=None,
                                             b0_threshold=b0_threshold,
                                             mask=mask)
 
-    csdfit = _fit(gtab, data, mask, response=response, sh_order=sh_order,
+    csdfit = _fit(gtab, data, mask, response=response, sh_order_max=sh_order_max,
                   lambda_=lambda_, tau=tau)
 
     if out_dir is None:

{pyafq-2.0 → pyafq-2.1}/AFQ/recognition/criteria.py

@@ -334,6 +334,21 @@ def run_bundle_rec_plan(
         mapping,
         img.affine,
         apply_to_recobundles=True))
+
+    def check_space(roi):
+        if not np.allclose(img.affine, roi.affine):
+            logger.warning(
+                "Resampling set to False in case where affines "
+                "do not match. This is likely due to subject space ROIs"
+                " not being in the right space. This found for bundle "
+                f"{bundle_name}")
+
+    apply_to_roi_dict(
+        bundle_def,
+        check_space,
+        dry_run=True,
+        apply_to_prob_map=True)
+
     apply_to_roi_dict(
         bundle_def,
         lambda roi_img: nib.Nifti1Image(

{pyafq-2.0 → pyafq-2.1}/AFQ/recognition/recognize.py

@@ -122,16 +122,18 @@ def recognize(
     References
     ----------
     .. [Hua2008] Hua K, Zhang J, Wakana S, Jiang H, Li X, et al. (2008)
-    Tract probability maps in stereotaxic spaces: analyses of white
-    matter anatomy and tract-specific quantification. Neuroimage 39:
-    336-347
+        Tract probability maps in stereotaxic spaces: analyses of white
+        matter anatomy and tract-specific quantification. Neuroimage 39:
+        336-347
+
     .. [Yeatman2012] Yeatman, Jason D., Robert F. Dougherty, Nathaniel J.
-    Myall, Brian A. Wandell, and Heidi M. Feldman. 2012. "Tract Profiles of
-    White Matter Properties: Automating Fiber-Tract Quantification"
-    PloS One 7 (11): e49790.
-    .. [Garyfallidis17] Garyfallidis et al. Recognition of white matter
-    bundles using local and global streamline-based registration and
-    clustering, Neuroimage, 2017.
+        Myall, Brian A. Wandell, and Heidi M. Feldman. 2012. "Tract Profiles
+        of White Matter Properties: Automating Fiber-Tract Quantification"
+        PloS One 7 (11): e49790.
+
+    .. [Garyfallidis2018] Garyfallidis et al. Recognition of white matter
+        bundles using local and global streamline-based registration and
+        clustering, Neuroimage, 2017.
     """
     if rng is None:
         rng = np.random.RandomState()

{pyafq-2.0 → pyafq-2.1}/AFQ/tasks/data.py

@@ -86,7 +86,7 @@ def get_data_gtab(dwi_data_file, bval_file, bvec_file, min_bval=None,
         bvals = bvals[valid_b]
         bvecs = bvecs[valid_b]
     gtab = dpg.gradient_table(
-        bvals, bvecs,
+        bvals=bvals, bvecs=bvecs,
         b0_threshold=b0_threshold)
     img = nib.Nifti1Image(data, img.affine)
     return data, gtab, img, img.affine
@@ -293,7 +293,7 @@ def msdki_msk(msdki_tf):
          subfolder="models")
 @as_img
 def csd_params(dwi, brain_mask, gtab, data,
-               csd_response=None, csd_sh_order=None,
+               csd_response=None, csd_sh_order_max=None,
                csd_lambda_=1, csd_tau=0.1,
                csd_fa_thr=0.7):
     """
@@ -309,7 +309,7 @@ def csd_params(dwi, brain_mask, gtab, data,
         (i.e. S0). If not provided, auto_response will be used to calculate
         these values.
         Default: None
-    csd_sh_order : int or None, optional.
+    csd_sh_order_max : int or None, optional.
         default: infer the number of parameters from the number of data
         volumes, but no larger than 8.
         Default: None
@@ -340,7 +340,7 @@ def csd_params(dwi, brain_mask, gtab, data,
         csdf = csd_fit_model(
             gtab, data,
             mask=mask,
-            response=csd_response, sh_order=csd_sh_order,
+            response=csd_response, sh_order_max=csd_sh_order_max,
             lambda_=csd_lambda_, tau=csd_tau,
             csd_fa_thr=csd_fa_thr)
     except CsdNanResponseError as e:
@@ -349,7 +349,7 @@ def csd_params(dwi, brain_mask, gtab, data,
             f'{dwi}.') from e
 
     meta = dict(
-        SphericalHarmonicDegree=csd_sh_order,
+        SphericalHarmonicDegree=csd_sh_order_max,
         ResponseFunctionTensor=csd_response,
         lambda_=csd_lambda_,
         tau=csd_tau,
@@ -579,7 +579,7 @@ def rumba_f_wm(rumba_fit):
 @pimms.calc("opdt_params", "opdt_gfa")
 def opdt_params(base_fname, data, gtab,
                 dwi_affine, brain_mask,
-                opdt_sh_order=8):
+                opdt_sh_order_max=8):
     """
     full path to a nifti file containing
     parameters for the Orientation Probability Density Transform
@@ -592,7 +592,7 @@ def opdt_params(base_fname, data, gtab,
         Spherical harmonics order for OPDT model. Must be even.
         Default: 8
     """
-    opdt_model = shm.OpdtModel(gtab, opdt_sh_order)
+    opdt_model = shm.OpdtModel(gtab, opdt_sh_order_max)
     opdt_fit = opdt_model.fit(data, mask=brain_mask)
 
     params_suffix = "_model-OPDT_param-fod_dwimap.nii.gz"
@@ -602,7 +602,7 @@ def opdt_params(base_fname, data, gtab,
         get_fname(base_fname,
                   f"{drop_extension(params_suffix)}.json",
                   "models"),
-        dict(sh_order=opdt_sh_order)
+        dict(sh_order_max=opdt_sh_order_max)
     )
 
     GFA_suffix = "_model-OPDT_param-GFA_dwimap.nii.gz"
@@ -610,7 +610,7 @@ def opdt_params(base_fname, data, gtab,
     nib.save(nib.Nifti1Image(opdt_fit.gfa, dwi_affine), GFA_fname)
     write_json(
         get_fname(base_fname, f"{drop_extension(GFA_suffix)}.json", "models"),
-        dict(sh_order=opdt_sh_order)
+        dict(sh_order_max=opdt_sh_order_max)
     )
 
     return params_fname, GFA_fname
@@ -647,7 +647,7 @@ def opdt_ai(opdt_params):
 @pimms.calc("csa_params", "csa_gfa")
 def csa_params(base_fname, data, gtab,
                dwi_affine, brain_mask,
-               csa_sh_order=8):
+               csa_sh_order_max=8):
     """
     full path to a nifti file containing
     parameters for the Constant Solid Angle
@@ -660,7 +660,7 @@ def csa_params(base_fname, data, gtab,
         Spherical harmonics order for CSA model. Must be even.
         Default: 8
     """
-    csa_model = shm.CsaOdfModel(gtab, csa_sh_order)
+    csa_model = shm.CsaOdfModel(gtab, csa_sh_order_max)
     csa_fit = csa_model.fit(data, mask=brain_mask)
 
     params_suffix = "_model-csa_param-fod_dwimap.nii.gz"
@@ -670,7 +670,7 @@ def csa_params(base_fname, data, gtab,
         get_fname(base_fname,
                   f"{drop_extension(params_suffix)}.json",
                   "models"),
-        dict(sh_order=csa_sh_order)
+        dict(sh_order_max=csa_sh_order_max)
     )
 
     GFA_suffix = "_model-csa_param-gfa_dwimap.nii.gz"
@@ -681,7 +681,7 @@ def csa_params(base_fname, data, gtab,
             base_fname,
             f"{drop_extension(GFA_suffix)}.json",
             "models"),
-        dict(sh_order=csa_sh_order)
+        dict(sh_order_max=csa_sh_order_max)
     )
 
     return params_fname, GFA_fname
@@ -1081,8 +1081,7 @@ def brain_mask(b0, brain_mask_definition=None):
 
 
 @pimms.calc("bundle_dict", "reg_template", "tmpl_name")
-def get_bundle_dict(segmentation_params,
-                    brain_mask, b0,
+def get_bundle_dict(brain_mask, b0,
                     bundle_info=None, reg_template_spec="mni_T1",
                     reg_template_space_name="mni"):
     """
@@ -1157,6 +1156,9 @@ def get_bundle_dict(segmentation_params,
             bundle_info,
             resample_to=reg_template)
 
+    if bundle_dict.resample_subject_to is None:
+        bundle_dict.resample_subject_to = b0
+
     return bundle_dict, reg_template, reg_template_space_name
 
 

{pyafq-2.0 → pyafq-2.1}/AFQ/tasks/decorators.py

@@ -143,9 +143,11 @@ def as_file(suffix, include_track=False, include_seg=False, subfolder=None):
                     this_file = this_file + ".trk"
 
             if not op.exists(this_file):
+                logger.info(f"Calculating {suffix}")
+
                 gen, meta = func(*args[:og_arg_count], **kwargs)
 
-                logger.info(f"Saving {this_file}")
+                logger.info(f"{suffix} completed. Saving to {this_file}")
                 if isinstance(gen, nib.Nifti1Image):
                     nib.save(gen, this_file)
                 elif isinstance(gen, StatefulTractogram):

{pyafq-2.0 → pyafq-2.1}/AFQ/tasks/mapping.py

@@ -1,4 +1,5 @@
 import nibabel as nib
+import numpy as np
 import os.path as op
 import logging
 
@@ -84,16 +85,21 @@ def export_rois(base_fname, output_dir, dwi_data_file, data_imap, mapping):
     to_space = space_from_fname(dwi_data_file)
     for bundle_name in bundle_dict:
         roi_files[bundle_name] = []
-        for roi_fname in bundle_dict.transform_rois(
+        for roi, roi_fname in zip(*bundle_dict.transform_rois(
                 bundle_name, mapping, data_imap["dwi_affine"],
                 base_fname=base_roi_fname,
-                to_space=to_space):
-            logger.info(f"Saving {roi_fname}")
+                to_space=to_space)):
             roi_files[bundle_name].append(roi_fname)
-            meta = {
-                "Bundle Definition": bundle_dict.get_b_info(bundle_name)}
-            meta_fname = f'{drop_extension(roi_fname)}.json'
-            write_json(meta_fname, meta)
+            if not op.exists(roi_fname):
+                logger.info(f"Saving {roi_fname}")
+                nib.save(
+                    nib.Nifti1Image(
+                        roi.get_fdata().astype(np.float32),
+                        roi.affine), roi_fname)
+                meta = {
+                    "Bundle Definition": bundle_dict.get_b_info(bundle_name)}
+                meta_fname = f'{drop_extension(roi_fname)}.json'
+                write_json(meta_fname, meta)
     return {'rois': roi_files}