more tweaks

AFQ/api/bundle_dict.py

@@ -1050,14 +1050,25 @@ def transform_rois(self, bundle_name, mapping, new_affine,
         if base_fname is not None:
             fnames = []
             for roi_type, rois in transformed_rois.items():
+                if roi_type == "prob_map":
+                    suffix = "probseg"
+                else:
+                    suffix = "mask"
+                roi_type_name = roi_type.lower().replace(
+                    " ", "").replace(
+                        "_", "").replace(
+                            "-", "")
                 if not isinstance(rois, list):
                     rois = [rois]
                 for ii, roi in enumerate(rois):
+                    suffix = f"{str_to_desc(bundle_name)}{roi_type_name}"
+                    if roi_type in ["include", "exclude"]:
+                        suffix = f"{suffix}{ii}"
                     fname = get_fname(
                         base_fname,
                         "_space-subject_desc-"
-                        f"{str_to_desc(bundle_name)}{roi_type}{ii}"
-                        "_mask.nii.gz",
+                        f"{suffix}"
+                        f"_{suffix}.nii.gz",
                         "ROIs")
                     nib.save(
                         nib.Nifti1Image(

AFQ/tasks/data.py

@@ -93,7 +93,7 @@ def get_data_gtab(dwi_data_file, bval_file, bvec_file, min_bval=None,
 
 
 @pimms.calc("b0")
-@as_file('_desc-b0_dwimap.nii.gz')
+@as_file('_b0ref.nii.gz')
 def b0(dwi, gtab):
     """
     full path to a nifti file containing the mean b0
@@ -105,7 +105,7 @@ def b0(dwi, gtab):
 
 
 @pimms.calc("masked_b0")
-@as_file('_desc-maskedb0_dwimap.nii.gz')
+@as_file('_desc-masked_b0ref.nii.gz')
 def b0_mask(b0, brain_mask):
     """
     full path to a nifti file containing the

AFQ/tasks/mapping.py

@@ -28,7 +28,7 @@ def export_registered_b0(base_fname, data_imap, mapping):
     """
     warped_b0_fname = get_fname(
         base_fname,
-        f'_space-{data_imap["tmpl_name"]}_desc-b0_dwimap.nii.gz')
+        f'_space-{data_imap["tmpl_name"]}_b0ref.nii.gz')
     if not op.exists(warped_b0_fname):
         mean_b0 = nib.load(data_imap["b0"]).get_fdata()
         warped_b0 = mapping.transform(mean_b0)
@@ -40,7 +40,7 @@ def export_registered_b0(base_fname, data_imap, mapping):
             dependent="dwi")
         meta_fname = get_fname(
             base_fname,
-            f'_space-{data_imap["tmpl_name"]}_desc-b0_dwimap.json')
+            f'_space-{data_imap["tmpl_name"]}_b0ref.json')
         write_json(meta_fname, meta)
 
     return warped_b0_fname

AFQ/tasks/segmentation.py

@@ -39,7 +39,7 @@
 
 
 @pimms.calc("bundles")
-@as_file('desc-bundles_tractography',
+@as_file('_desc-bundles_tractography',
          include_track=True,
          include_seg=True)
 def segment(data_imap, mapping_imap,
@@ -69,18 +69,18 @@ def segment(data_imap, mapping_imap,
         tg = trx.to_sft()
     elif streamlines.endswith(".tck.gz"):
         # uncompress tck.gz to a temporary tck:
-        temp_tck = op.join(mkdtemp(), op.split(streamlines.replace(".gz", ""))[1])
+        temp_tck = op.join(mkdtemp(), op.split(
+            streamlines.replace(".gz", ""))[1])
         logger.info(f"Temporary tck file created at: {temp_tck}")
         with gzip.open(streamlines, 'rb') as f_in:
             with open(temp_tck, 'wb') as f_out:
                 shutil.copyfileobj(f_in, f_out)
         # initialize stateful tractogram from tck file:
         tg = load_tractogram(
-            temp_tck, data_imap["dwi"], Space.VOX, 
+            temp_tck, data_imap["dwi"], Space.VOX,
             bbox_valid_check=False)
         is_trx = False
 
-
     indices_to_remove, _ = tg.remove_invalid_streamlines()
     if len(indices_to_remove) > 0:
         logger.warning(f"{len(indices_to_remove)} invalid streamlines removed")
@@ -335,7 +335,14 @@ def _median_weight(bundle):
                     this_prof_weights = _median_weight
             else:
                 this_prof_weights = profile_weights
-            this_prof_weights[np.isnan(this_prof_weights)] = 0
+            if np.any(np.isnan(this_prof_weights)):  # fit failed
+                logger.warning((
+                    f"Even weighting used for "
+                    f"bundle {bundle_name}, scalar {scalar} "
+                    f"in profiling due inability to estimate weights. "
+                    "This is often caused by low streamline count or "
+                    "low variance in the scalar data."))
+                this_prof_weights = np.ones_like(this_prof_weights)
             this_profile[ii] = afq_profile(
                 scalar_data,
                 this_sl,

AFQ/tasks/tractography.py

@@ -92,8 +92,8 @@ def export_seed_mask_thresholded(data_imap, seed, tracking_params):
     tractography seed mask thresholded
     """
     thresh = tracking_params['seed_threshold']
-    threshed_data = seed.get_fdata() > thresh
-    seed_mask_desc = dict(source=tracking_params['seed_mask'], thresh=thresh)
+    threshed_data = nib.load(seed).get_fdata() > thresh
+    seed_mask_desc = dict(source=seed, thresh=thresh)
     return nib.Nifti1Image(
         threshed_data.astype(np.float32),
         data_imap["dwi_affine"]), seed_mask_desc
@@ -130,8 +130,8 @@ def export_stop_mask_thresholded(data_imap, stop, tracking_params):
     tractography stop mask thresholded
     """
     thresh = tracking_params['stop_threshold']
-    threshed_data = stop.get_fdata() > thresh
-    stop_mask_desc = dict(source=tracking_params['stop_mask'], thresh=thresh)
+    threshed_data = nib.load(stop).get_fdata() > thresh
+    stop_mask_desc = dict(source=stop, thresh=thresh)
     return nib.Nifti1Image(
         threshed_data.astype(np.float32),
         data_imap["dwi_affine"]), stop_mask_desc

AFQ/tasks/utils.py

@@ -46,10 +46,7 @@ def get_fname(base_fname, suffix, subfolder=None):
         if folders[-1] == "dwi":
             if len(folders) > 1 and "sub-" in folders[-2] or \
                     "ses-" in folders[-2]:
-                if "sub-" in folders[-2] or len(folders) == 2:
-                    return op.join(*folders[:-2], base_fname + suffix)
-                else:
-                    return op.join(*folders[:-3], base_fname + suffix)
+                return op.join(*folders[:-2], folders[-2] + suffix)
             else:
                 return op.join(*folders[:-1], base_fname + suffix)
         else:

AFQ/tasks/viz.py

@@ -336,7 +336,7 @@ def plot_tract_profiles(base_fname, output_dir, scalars, segmentation_imap):
         this_scalar = scalar if isinstance(scalar, str) else scalar.get_name()
         fname = get_fname(
             base_fname,
-            f'_param-{str_to_desc(this_scalar)}_desc-vizprofile_dwimap.png',
+            f'_param-{str_to_desc(this_scalar)}_desc-vizprofile_tractography.png',
             'tract_profile_plots')
 
         visualize_tract_profiles(

AFQ/utils/path.py

@@ -98,3 +98,6 @@ def apply_cmd_to_afq_derivs(
                 if filename == "viz_core_bundles" and \
                         "prof" in dependent_on_list:
                     os.system(f"{cmd} -r {full_path} {suffix}")
+                if filename == "tract_profile_plots" and \
+                        "prof" in dependent_on_list:
+                    os.system(f"{cmd} -r {full_path} {suffix}")