From 187decfd2cd9fd3f128aeb5870067a8a8d0bfa78 Mon Sep 17 00:00:00 2001
From: 36000 <jk6.28@outlook.com>
Date: Thu, 19 Dec 2024 18:03:05 -0800
Subject: [PATCH] more tweaks

---
 AFQ/api/bundle_dict.py | 17 ++++++++++-------
 AFQ/tasks/viz.py       |  4 ++--
 AFQ/viz/plot.py        | 13 ++++++++++++-
 3 files changed, 24 insertions(+), 10 deletions(-)

diff --git a/AFQ/api/bundle_dict.py b/AFQ/api/bundle_dict.py
index 25064476..e2c11478 100644
--- a/AFQ/api/bundle_dict.py
+++ b/AFQ/api/bundle_dict.py
@@ -1052,22 +1052,25 @@ def transform_rois(self, bundle_name, mapping, new_affine,
             for roi_type, rois in transformed_rois.items():
                 if roi_type == "prob_map":
                     suffix = "probseg"
+                    roi_type_name = ""
                 else:
                     suffix = "mask"
-                roi_type_name = roi_type.lower().replace(
-                    " ", "").replace(
-                        "_", "").replace(
-                            "-", "")
+                    roi_type_name = roi_type.lower().replace(
+                        " ", "").replace(
+                            "_", "").replace(
+                                "-", "")
+                    roi_type_name = roi_type_name[0].upper() \
+                        + roi_type_name[1:]
                 if not isinstance(rois, list):
                     rois = [rois]
                 for ii, roi in enumerate(rois):
-                    suffix = f"{str_to_desc(bundle_name)}{roi_type_name}"
+                    desc = f"{str_to_desc(bundle_name)}{roi_type_name}"
                     if roi_type in ["include", "exclude"]:
-                        suffix = f"{suffix}{ii}"
+                        desc = f"{suffix}{ii}"
                     fname = get_fname(
                         base_fname,
                         "_space-subject_desc-"
-                        f"{suffix}"
+                        f"{desc}"
                         f"_{suffix}.nii.gz",
                         "ROIs")
                     nib.save(
diff --git a/AFQ/tasks/viz.py b/AFQ/tasks/viz.py
index 1c8f2623..a4c0550a 100644
--- a/AFQ/tasks/viz.py
+++ b/AFQ/tasks/viz.py
@@ -283,7 +283,7 @@ def viz_indivBundle(base_fname,
             if len(indiv_profile) > 1:
                 fname = get_fname(
                     base_fname,
-                    f'_desc-{str_to_desc(bundle_name)}'
+                    f'_desc-{str_to_desc(bundle_name)}Core'
                     f'_tractography.html',
                     "viz_core_bundles")
                 core_fig = make_subplots(
@@ -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_tractography.png',
+            f'_param-{str_to_desc(this_scalar)}_desc-vizprofile_tractography',
             'tract_profile_plots')
 
         visualize_tract_profiles(
diff --git a/AFQ/viz/plot.py b/AFQ/viz/plot.py
index bb8ca815..f4dd359f 100644
--- a/AFQ/viz/plot.py
+++ b/AFQ/viz/plot.py
@@ -12,6 +12,7 @@
 from AFQ.viz.utils import display_string
 from AFQ.utils.stats import contrast_index as calc_contrast_index
 from AFQ.data.utils import BUNDLE_RECO_2_AFQ, BUNDLE_MAT_2_PYTHON
+from AFQ.utils.path import drop_extension
 
 try:
     from pingouin import intraclass_corr, corr
@@ -659,8 +660,18 @@ def tract_profiles(self, names=None, scalar="FA",
             if ba.is_using_temp_axis():
                 ba.temp_fig.legend(
                     labels_temp, names, fontsize=vut.medium_font)
+                if "_desc" in o_file:  # Use BIDS naming convention
+                    o_file_pre = o_file.split("_desc-")[0]
+                    o_file_post = o_file.split("_desc-")[1]
+                    bids_bname = bundle.lower().replace(
+                        " ", "").replace(
+                            "-", "").replace(
+                                "_", "")
+                    bf_name = o_file_pre + "_desc-" + bids_bname + o_file_post
+                else:
+                    bf_name = f"{o_file}_{bundle}"
                 ba.save_temp_fig(
-                    o_folder, f"{o_file}_{bundle}", self._save_fig)
+                    o_folder, bf_name, self._save_fig)
         if len(names) > 1:
             ba.fig.legend(
                 labels, names, loc='center',