changes done at the relaunch

rlink7 · Oct 10, 2024 · f03d56d · f03d56d
1 parent 05ba1ef
commit f03d56d
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 11 deletions.
diff --git a/li2mni/make_mni_snapshot.py b/li2mni/make_mni_snapshot.py
@@ -56,19 +56,23 @@ def cohorte(li2mni_path, output_path, norm=False, site=False,
         dot per inch of the png created.
     """
     list_sub = [i for i in os.listdir(li2mni_path) if i.startswith('sub')]
-    print(list_sub, len(list_sub))
+    print(list_sub)
+    print(len(list_sub))
     for sub in list_sub:
-        template = f"{li2mni_path}/{sub}/ses-M03Li/li2mnianat.nii.gz"
+        template = f"{li2mni_path}/{sub}/ses-M03Li/lianat2mni.nii.gz"
+        assert os.path.isfile(template), f"file not found : {template}"
         if norm is False:
             overlay = f"{li2mni_path}/{sub}/ses-M03Li/li2mni.nii.gz"
             output = os.path.join(output_path, f"{sub}_overlay_mni")
+            assert os.path.isfile(template), f"file not found : {overlay}"
         else:
             overlay = f"{li2mni_path}/{sub}/ses-M03Li/li2mninorm.nii.gz"
+            assert os.path.isfile(template), f"file not found : {overlay}"
             output = os.path.join(output_path, f"{sub}_overlay_mni_norm")
 
         if os.path.isfile(template) and os.path.isfile(overlay)\
            and os.path.isfile(output + ".png") is False:
-            print("la")
+            print(f"Making {sub}")
             print(os.path.isfile(output))
             print(output)
             overlay_nifti(template, overlay, output, dpi=dpi)
@@ -91,8 +95,9 @@ def cohorte(li2mni_path, output_path, norm=False, site=False,
                                                      f"_site-{site}_over"))
             if os.path.isfile(file_to_check) is False:
                 shutil.copy2(os.path.join(path, png), file_to_check)
+                print('copy done')
             liste_site.append(site)
-        print('cp done')
+
         if pdf:
             for site in set(liste_site):
                 images = []

diff --git a/li2mni/runtime1.py b/li2mni/runtime1.py
@@ -125,10 +125,9 @@ def run(datadir, outdir, name="li2mni", process=False, njobs=10,
             lianat_file=lianat_files,
             hanat_file=hanat_files,
             outdir=sub_outdirs,
-            hopla_name_replace=True,
-            hopla_iterative_kwargs=["li-file", "lianat-file", "hanat-file",
+            hopla_iterative_kwargs=["li_file", "lianat_file", "hanat_file",
                                     "outdir"],
-            hopla_optional=["li-file", "lianat-file", "hanat-file",
+            hopla_optional=["li_file", "lianat_file", "hanat_file",
                             "outdir"],
             hopla_cpus=njobs,
             hopla_logfile=logfile,

diff --git a/li2mni/runtime2.py b/li2mni/runtime2.py
@@ -26,7 +26,7 @@ def run(datadir, outdir, phdir, participant_file, name="li2mninorm",
     Parameters
     ----------
     datadir: str
-        path to the BIDS derivatives directory.
+        path to the li2mni derivatives directory.
     outdir: str
         path to the BIDS derivatives directory.
     phdir: str
@@ -111,9 +111,8 @@ def run(datadir, outdir, phdir, participant_file, name="li2mninorm",
             outdir=sub_outdirs,
             norm="norm",
             ref_value=ph_vals,
-            hopla_name_replace=True,
-            hopla_iterative_kwargs=["li2mni-file", "ref-value", "outdir"],
-            hopla_optional=["li2mni-file", "ref_value", "mask_file",
+            hopla_iterative_kwargs=["li2mni_file", "ref_value", "outdir"],
+            hopla_optional=["li2mni_file", "ref_value", "mask_file",
                             "outdir", "norm"],
             hopla_cpus=njobs,
             hopla_logfile=logfile,