cleaned out unused scripts, rules

also renamed laplace-beltrami.py to laplace_beltrami.py for consistency

hippunfold/workflow/rules/native_surf.smk

@@ -339,7 +339,7 @@ rule laplace_beltrami:
     container:
         config["singularity"]["autotop"]
     script:
-        "../scripts/laplace-beltrami.py"
+        "../scripts/laplace_beltrami.py"
 
 
 def get_unfold_z_level(wildcards):
@@ -1371,55 +1371,6 @@ def get_unfold_ref(wildcards):
     )
 
 
-rule warp_unfold_native_to_unfoldreg_NOTWORKING:
-    """this seems to give bounding box errors for no good reason.."""
-    input:
-        surf_gii=bids(
-            root=root,
-            datatype="surf",
-            suffix="{surfname}.surf.gii",
-            space="unfold",
-            hemi="{hemi}",
-            label="{label}",
-            **inputs.subj_wildcards
-        ),
-        warp=bids(
-            root=work,
-            suffix="xfm.nii.gz",
-            datatype="warps",
-            desc=unfoldreg_method,
-            from_="native",
-            to=config["atlas"],
-            space="unfold",
-            type_="surface",
-            hemi="{hemi}",
-            label="{label}",
-            **inputs.subj_wildcards,
-        ),
-    params:
-        structure_type=lambda wildcards: get_structure(wildcards.hemi, wildcards.label),
-        secondary_type=lambda wildcards: surf_to_secondary_type[wildcards.surfname],
-        surface_type="FLAT",
-    output:
-        surf_gii=bids(
-            root=work,
-            datatype="surf",
-            suffix="{surfname}.surf.gii",
-            space="unfoldregNOTWORKING",
-            hemi="{hemi}",
-            label="{label}",
-            **inputs.subj_wildcards
-        ),
-    container:
-        config["singularity"]["autotop"]
-    group:
-        "subj"
-    shell:
-        "wb_command -surface-apply-warpfield {input.surf_gii} {input.warp} {output.surf_gii} && "
-        "wb_command -set-structure {output.surf_gii} {params.structure_type} -surface-type {params.surface_type}"
-        " -surface-secondary-type {params.secondary_type}"
-
-
 rule warp_unfold_native_to_unfoldreg:
     input:
         surf_gii=bids(
@@ -1444,10 +1395,6 @@ rule warp_unfold_native_to_unfoldreg:
             label="{label}",
             **inputs.subj_wildcards,
         ),
-    params:
-        structure_type=lambda wildcards: get_structure(wildcards.hemi, wildcards.label),
-        secondary_type=lambda wildcards: surf_to_secondary_type[wildcards.surfname],
-        surface_type="FLAT",
     output:
         surf_gii=bids(
             root=work,