Merge pull request #280 from khanlab/fix-download

fixes bugs introduced in download-osf PR
khanlab · Feb 16, 2024 · 203a039 · 203a039
2 parents 480627f + 7a6d33d
commit 203a039
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Showing 6 changed files with 38 additions and 29 deletions.
diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk
@@ -466,7 +466,7 @@ rule metric_to_nii:
     params:
         interp="-nearest-vertex 1",
         refflatnii=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"]["multihist7"]["label_nii"],
+        / config["atlas_files"]["multihist7"]["label_nii"].format(**wildcards),
     output:
         metric_nii=bids(
             root=work,
@@ -531,11 +531,11 @@ rule unfolded_registration:
         warpfn="tmp1Warp.nii.gz",
         invwarpfn="tmp1InverseWarp.nii.gz",
         refthickness=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"][wildcards.atlas]["thickness"],
+        / config["atlas_files"][wildcards.atlas]["thickness"].format(**wildcards),
         refcurvature=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"][wildcards.atlas]["curvature"],
+        / config["atlas_files"][wildcards.atlas]["curvature"].format(**wildcards),
         refgyrification=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"][wildcards.atlas]["gyrification"],
+        / config["atlas_files"][wildcards.atlas]["gyrification"].format(**wildcards),
     output:
         warp=bids(
             root=work,
@@ -1058,7 +1058,7 @@ rule resample_atlas_to_refvol:
         atlas_dir=lambda wildcards: Path(download_dir) / "atlas" / wildcards.atlas,
     params:
         atlas=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"][wildcards.atlas]["label_nii"],
+        / config["atlas_files"][wildcards.atlas]["label_nii"].format(**wildcards),
     output:
         label_nii=bids(
             root=work,
@@ -1110,7 +1110,7 @@ rule nii_to_label_gii:
         atlas_dir=lambda wildcards: Path(download_dir) / "atlas" / wildcards.atlas,
     params:
         label_list=lambda wildcards, input: Path(input.atlas_dir)
-        / config["atlas_files"][wildcards.atlas]["label_list"],
+        / config["atlas_files"][wildcards.atlas]["label_list"].format(**wildcards),
         structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
     output:
         label_gii=bids(
@@ -1131,7 +1131,7 @@ rule nii_to_label_gii:
     shadow:
         "minimal"
     shell:
-        "wb_command -volume-to-surface-mapping {params.label_list} {input.surf} temp.shape.gii -enclosing  && "
+        "wb_command -volume-to-surface-mapping {input.label_nii} {input.surf} temp.shape.gii -enclosing  && "
         "wb_command -metric-label-import temp.shape.gii {params.label_list} {output.label_gii} && "
         "wb_command -set-structure {output.label_gii} {params.structure_type}"
 

diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk
@@ -203,15 +203,13 @@ rule unflip_nnunet_nii:
 def get_f3d_ref(wildcards, input):
 
     if config["modality"] == "T2w":
-        nii = (
-            Path(input.template_dir)
-            / config["template_files"][config["template"]]["crop_ref"]
-        )
+        nii = Path(input.template_dir) / config["template_files"][config["template"]][
+            "crop_ref"
+        ].format(**wildcards)
     elif config["modality"] == "T1w":
-        nii = (
-            Path(input.template_dir)
-            / config["template_files"][config["template"]]["crop_refT1w"]
-        )
+        nii = Path(input.template_dir) / config["template_files"][config["template"]][
+            "crop_refT1w"
+        ].format(**wildcards)
     else:
         raise ValueError("modality not supported for nnunet!")
     return nii
@@ -302,8 +300,12 @@ rule qc_nnunet_dice:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         hipp_lbls=[1, 2, 7, 8],
-        ref=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["Mask_crop"],
+        ref=lambda wildcards, input: (
+            Path(input.template_dir)
+            / config["template_files"][config["template"]]["Mask_crop"].format(
+                **wildcards
+            )
+        ),
     output:
         dice=report(
             bids(

diff --git a/hippunfold/workflow/rules/preproc_seg.smk b/hippunfold/workflow/rules/preproc_seg.smk
@@ -42,7 +42,7 @@ rule warp_seg_to_corobl_crop:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         ref=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["crop_ref"],
+        / config["template_files"][config["template"]]["crop_ref"].format(**wildcards),
     output:
         nii=bids(
             root=work,

diff --git a/hippunfold/workflow/rules/preproc_t1.smk b/hippunfold/workflow/rules/preproc_t1.smk
@@ -72,9 +72,11 @@ else:
 
 def reg_to_template_cmd(wildcards, input, output):
 
-    ref = (
+    ref = str(
         Path(input.template_dir)
-        / config["template_files"][config["template"]][wildcards.modality],
+        / config["template_files"][config["template"]][wildcards.modality].format(
+            **wildcards
+        ),
     )
     if config["no_reg_template"]:
         cmd = f"reg_resample -flo {input.flo} -ref {ref} -res {output.warped_subj} -aff {input.xfm_identity}; cp {input.xfm_identity} {output.xfm_ras}"
@@ -183,7 +185,9 @@ rule compose_template_xfm_corobl:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         std_to_cor=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["xfm_corobl"],
+        / config["template_files"][config["template"]]["xfm_corobl"].format(
+            **wildcards
+        ),
     output:
         sub_to_cor=bids(
             root=work,
@@ -288,7 +292,7 @@ rule warp_t1_to_corobl_crop:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         ref=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["crop_ref"],
+        / config["template_files"][config["template"]]["crop_ref"].format(**wildcards),
     output:
         t1=bids(
             root=work,

diff --git a/hippunfold/workflow/rules/preproc_t2.smk b/hippunfold/workflow/rules/preproc_t2.smk
@@ -308,10 +308,9 @@ def get_cmd_compose_t2_xfm_corobl(wildcards, input):
         # xfm0: t2 to template
         xfm0 = input.t2_to_std
         # xfm1: template to corobl
-        xfm1 = (
-            Path(input.template_dir)
-            / config["template_files"][config["template"]]["xfm_corobl"]
-        )
+        xfm1 = Path(input.template_dir) / config["template_files"][config["template"]][
+            "xfm_corobl"
+        ].format(**wildcards)
 
     return "c3d_affine_tool -itk {xfm0} -itk {xfm1} -mult -oitk {output}"
 
@@ -394,7 +393,7 @@ rule warp_t2_to_corobl_crop:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         ref=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["crop_ref"],
+        / config["template_files"][config["template"]]["crop_ref"].format(**wildcards),
     output:
         nii=bids(
             root=work,

diff --git a/hippunfold/workflow/rules/qc.smk b/hippunfold/workflow/rules/qc.smk
@@ -10,8 +10,12 @@ rule qc_reg_to_template:
         ),
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
-        ref=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]][wildcards.native_modality],
+        ref=lambda wildcards, input: str(
+            Path(input.template_dir)
+            / config["template_files"][config["template"]][
+                wildcards.native_modality
+            ].format(**wildcards)
+        ),
     output:
         png=report(
             bids(