From c9ac98b971c4179e585c021e178dececf0a6635f Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Fri, 10 Jan 2025 09:15:41 -0500
Subject: [PATCH] use updated structure and secondary types

---
 hippunfold/workflow/rules/gifti.smk       | 27 +++++++++++++++++++----
 hippunfold/workflow/rules/native_surf.smk |  8 +++----
 2 files changed, 27 insertions(+), 8 deletions(-)

diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk
index 8d3637e4..c28907ab 100644
--- a/hippunfold/workflow/rules/gifti.smk
+++ b/hippunfold/workflow/rules/gifti.smk
@@ -1,9 +1,24 @@
 # lookup tables for structure:
 hemi_to_structure = {"L": "CORTEX_LEFT", "R": "CORTEX_RIGHT"}
+
+
+def get_structure(hemi, label):
+    if label == "hipp":
+        if hemi == "L":
+            return "HIPPOCAMPUS_LEFT"
+        elif hemi == "R":
+            return "HIPPOCAMPUS_RIGHT"
+    elif label == "dentate":
+        if hemi == "L":
+            return "HIPPOCAMPUS_DENTATE_LEFT"
+        elif hemi == "R":
+            return "HIPPOCAMPUS_DENTATE_RIGHT"
+
+
 surf_to_secondary_type = {
     "midthickness": "MIDTHICKNESS",
-    "inner": "PIAL",
-    "outer": "GRAY_WHITE",
+    "inner": "INNER",
+    "outer": "OUTER",
 }
 
 
@@ -18,7 +33,9 @@ rule cp_template_to_unfold:
             "tpl-avg_space-unfold_den-{density}_{surfname}.surf.gii",
         ),
     params:
-        structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
+        structure_type=lambda wildcards: get_structure(
+            wildcards.hemi, wildcards.autotop
+        ),
         secondary_type=lambda wildcards: surf_to_secondary_type[wildcards.surfname],
         surface_type="FLAT",
     output:
@@ -59,7 +76,9 @@ rule calc_unfold_template_coords:
         coord_IO="coord-IO.shape.gii",
         origin=lambda wildcards: config["{autotop}"]["origin"],
         extent=lambda wildcards: config["{autotop}"]["extent"],
-        structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
+        structure_type=lambda wildcards: get_structure(
+            wildcards.hemi, wildcards.autotop
+        ),
     output:
         coords_gii=bids(
             root=work,
diff --git a/hippunfold/workflow/rules/native_surf.smk b/hippunfold/workflow/rules/native_surf.smk
index cc8e2883..aa886450 100644
--- a/hippunfold/workflow/rules/native_surf.smk
+++ b/hippunfold/workflow/rules/native_surf.smk
@@ -238,7 +238,7 @@ rule update_native_mesh_structure:
             **inputs.subj_wildcards
         ),
     params:
-        structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
+        structure_type=lambda wildcards: get_structure(wildcards.hemi, wildcards.label),
         secondary_type=lambda wildcards: surf_to_secondary_type[wildcards.surfname],
         surface_type="ANATOMICAL",
     output:
@@ -320,7 +320,7 @@ rule warp_native_mesh_to_unfold:
             mode="surface"
         ),
     params:
-        structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
+        structure_type=lambda wildcards: get_structure(wildcards.hemi, wildcards.label),
         secondary_type=lambda wildcards: surf_to_secondary_type[wildcards.surfname],
         surface_type="FLAT",
     output:
@@ -699,7 +699,7 @@ rule warp_midthickness_to_inout:
             **inputs.subj_wildcards
         ),
     params:
-        structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
+        structure_type=lambda wildcards: get_structure(wildcards.hemi, wildcards.label),
         secondary_type=lambda wildcards: surf_to_secondary_type[wildcards.surfname],
         surface_type="ANATOMICAL",
     output:
@@ -1414,7 +1414,7 @@ rule warp_unfold_native_to_unfoldreg:
             **inputs.subj_wildcards,
         ),
     params:
-        structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
+        structure_type=lambda wildcards: get_structure(wildcards.hemi, wildcards.label),
         secondary_type=lambda wildcards: surf_to_secondary_type[wildcards.surfname],
         surface_type="FLAT",
     output: