🔊 Improve dropped variant logging

Author: shnizzedy

CPAC/anat_preproc/anat_preproc.py

@@ -695,13 +695,15 @@ def afni_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
 
     wf.connect(anat_skullstrip, "out_file", anat_brain_mask, "in_file_a")
 
+    outputs = {}
+
     if strat_pool.check_rpool("desc-preproc_T1w"):
         outputs = {"space-T1w_desc-brain_mask": (anat_brain_mask, "out_file")}
 
     elif strat_pool.check_rpool("desc-preproc_T2w"):
         outputs = {"space-T2w_desc-brain_mask": (anat_brain_mask, "out_file")}
 
-    return (wf, outputs)
+    return wf, outputs
 
 
 def fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
@@ -1392,9 +1394,8 @@ def mask_T2(wf_name="mask_T2"):
 )
 def anatomical_init(wf, cfg, strat_pool, pipe_num, opt=None):
     if opt not in anatomical_init.option_val:
-        raise ValueError(
-            f"\n[!] Error: Invalid option for deoblique: {opt}. \nExpected one of {anatomical_init.option_val}"
-        )
+        msg = f"\n[!] Error: Invalid option for deoblique: {opt}. \nExpected one of {anatomical_init.option_val}"
+        raise ValueError(msg)
 
     if opt == "warp":
         anat_deoblique = pe.Node(
@@ -2004,6 +2005,7 @@ def brain_mask_acpc_freesurfer(wf, cfg, strat_pool, pipe_num, opt=None):
     functions = {
         "FreeSurfer-ABCD": freesurfer_abcd_brain_connector,
         "FreeSurfer-Brainmask": freesurfer_brain_connector,
+        "FreeSurfer-BET-Loose": freesurfer_fsl_brain_connector,
         "FreeSurfer-BET-Tight": freesurfer_fsl_brain_connector,
     }
     if opt in ["FreeSurfer-BET-Loose", "FreeSurfer-BET-Tight"]:

CPAC/anat_preproc/tests/test_anat_preproc.py

@@ -289,7 +289,7 @@ def test_anat_brain(self):
 
 @pytest.mark.parametrize("opt", ["FreeSurfer-BET-Loose", "FreeSurfer-BET-Tight"])
 @pytest.mark.parametrize("t1w", ["desc-restore_T1w", "desc-preproc_T1w"])
-def test_brain_mask_freesurfer_fsl_real(opt: str, t1w: str):
+def test_brain_mask_freesurfer_fsl(opt: str, t1w: str):
     """Test that brain_mask_freesurfer_fsl correctly generates output key using real code."""
     # Create minimal mocks for required workflow/config/strat_pool, but do not patch freesurfer_fsl_brain_connector
 

CPAC/pipeline/engine.py

@@ -43,6 +43,7 @@
 from CPAC.pipeline.nodeblock import NodeBlockFunction
 from CPAC.pipeline.utils import (
     CrossedVariantsError,
+    find_variants,
     MOVEMENT_FILTER_KEYS,
     name_fork,
     short_circuit_crossed_variants,
@@ -860,7 +861,10 @@ def get_strats(self, resources, debug: bool | str = False):
             except CrossedVariantsError:
                 if debug:
                     verbose_logger = getLogger("CPAC.engine")
-                    verbose_logger.debug("Dropped crossed variants strat: %s", pipe_idx)
+                    verbose_logger.debug(
+                        "Dropped crossed variants strat: %s",
+                        find_variants(strat_pool, resources),
+                    )
                 continue
         if debug:
             verbose_logger = getLogger("CPAC.engine")
@@ -1634,6 +1638,11 @@ def connect_block(self, wf, cfg, rpool):
                         opts.append(option_val)
             else:  # AND, if there are multiple option-val's (in a list) in the docstring, it gets iterated below in 'for opt in option' etc. AND THAT'S WHEN YOU HAVE TO DELINEATE WITHIN THE NODE BLOCK CODE!!!
                 opts = [None]
+            if debug:
+                verbose_logger = getLogger("CPAC.engine")
+                verbose_logger.debug(
+                    f"[connect_block] opts resolved for {name}: {opts}"
+                )
             all_opts += opts
 
         sidecar_additions = {

CPAC/registration/registration.py

@@ -3311,7 +3311,7 @@ def coregistration_prep_fmriprep(wf, cfg, strat_pool, pipe_num, opt=None):
         ),
         (
             "desc-preproc_T1w",
-            ["desc-restore-brain_T1w", "desc-preproc_T1w"],
+            "desc-restore-brain_T1w",
             "desc-preproc_T2w",
             "desc-preproc_T2w",
             "T2w",