Merge branch 'dev-v2.0.0' into hires-inject

khanlab · Feb 12, 2025 · 37bd22c · 37bd22c
2 parents ef9c6f5 + 3b6f5db
commit 37bd22c
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Showing 3 changed files with 21 additions and 10 deletions.
diff --git a/.github/workflows/python-testing.yml b/.github/workflows/python-testing.yml
@@ -96,11 +96,11 @@ jobs:
 
       - name: Test manualseg bids, with path override
         run: |
-          poetry run hippunfold test_data/bids_manualseg test_out participant -np --modality manualseg --path_manualseg test_data/bids_manualseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
+          poetry run hippunfold test_data/bids_dsegtissue test_out participant -np --modality dsegtissue --path_dsegtissue test_data/bids_dsegtissue/sub-{subject}_hemi-{hemi}_dseg.nii.gz
 
       - name: Test manualseg bids, one hemisphere hemi
         run: |
-          poetry run hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality manualseg --hemi L
+          poetry run hippunfold test_data/bids_dsegtissue_1hemi test_out participant -np --modality dsegtissue --hemi L
 
       - name: Test T2w with T1w template registration
         run: |

diff --git a/hippunfold/workflow/rules/coords.smk b/hippunfold/workflow/rules/coords.smk
@@ -108,7 +108,7 @@ rule get_nan_mask:
             suffix="mask.nii.gz",
             space="corobl",
             dir="{dir}",
-            desc="nan",
+            desc="{srcsink,src|sink}",
             hemi="{hemi}",
             label="{label}",
             **inputs.subj_wildcards,
@@ -123,19 +123,28 @@ rule get_nan_mask:
         "c3d {input} -background -1 -retain-labels {params} -binarize {output}"
 
 
-rule get_src_sink_mask:
+rule get_src_sink_sdt:
+    """calculate signed distance transform (negative inside, positive outside)"""
     input:
-        labelmap=get_labels_for_laplace,
-    params:
-        labels=get_src_sink_labels,
-    output:
         mask=bids(
             root=work,
             datatype="coords",
             suffix="mask.nii.gz",
             space="corobl",
             dir="{dir}",
-            desc="{srcsink,src|sink}",
+            desc="{srcsink}",
+            hemi="{hemi}",
+            label="{label}",
+            **inputs.subj_wildcards,
+        ),
+    output:
+        sdt=bids(
+            root=work,
+            datatype="coords",
+            suffix="sdt.nii.gz",
+            space="corobl",
+            dir="{dir}",
+            desc="{srcsink}",
             hemi="{hemi}",
             label="{label}",
             **inputs.subj_wildcards,
@@ -147,7 +156,7 @@ rule get_src_sink_mask:
     group:
         "subj"
     shell:
-        "c3d {input} -background -1 -retain-labels {params} -binarize {output}"
+        "c3d {input} -sdt -o {output}"
 
 
 rule get_src_sink_sdt:

diff --git a/hippunfold/workflow/scripts/laplace_beltrami.py b/hippunfold/workflow/scripts/laplace_beltrami.py
@@ -107,6 +107,7 @@ def get_terminal_indices_percentile(
 def get_terminal_indices_threshold(
     sdt, min_dist, max_dist, min_vertices, boundary_mask
 ):
+
     """
     Gets the terminal (src/sink) vertex indices based on distance to the src/sink mask,
     a boundary mask, and a minumum number of vertices. The distance from the mask is
@@ -248,6 +249,7 @@ def solve_laplace_beltrami_open_mesh(vertices, faces, boundary_conditions=None):
 logger.info(f"# of src boundary vertices: {len(src_indices)}")
 logger.info(f"# of sink boundary vertices: {len(sink_indices)}")
 
+
 src_vals = [0 for i in range(len(src_indices))]
 sink_vals = [1 for i in range(len(sink_indices))]