lint

hippunfold/workflow/rules/nnunet.smk

@@ -171,7 +171,6 @@ rule run_inference:
         "cp {params.temp_lbl} {output.nnunet_seg}"
 
 
-
 def get_f3d_ref(wildcards, input):
     if config["modality"] == "T2w":
         nii = Path(input.template_dir) / config["template_files"][config["template"]][

hippunfold/workflow/rules/preproc_hippb500.smk

@@ -35,7 +35,6 @@ rule resample_hippdwi_to_template:
         " -trim 0vox -o {output}"
 
 
-
 rule cp_b500_to_anat_dir:
     input:
         nii=bids(

hippunfold/workflow/rules/preproc_t1.smk

@@ -102,4 +102,3 @@ rule warp_t1_to_corobl_crop:
     shell:
         "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} "
         "antsApplyTransforms -d 3 --interpolation Linear -i {input.t1} -o {output.t1} -r {params.ref}  -t {input.xfm}"
-

hippunfold/workflow/rules/preproc_t2.smk

@@ -412,4 +412,3 @@ rule warp_t2_to_corobl_crop:
     shell:
         "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} "
         "antsApplyTransforms -d 3 --interpolation Linear -i {input.nii} -o {output.nii} -r {params.ref}  -t {input.xfm}"
-

hippunfold/workflow/rules/shape_inject.smk

@@ -17,7 +17,9 @@ rule import_template_shape:
             space="template",
             **inputs.subj_wildcards,
             desc="hipptissue",
-            hemi=config["template_based_segmentation"][config["inject_template"]]["hemi"],
+            hemi=config["template_based_segmentation"][config["inject_template"]][
+                "hemi"
+            ],
             suffix="dseg.nii.gz"
         ),
     group:
@@ -36,7 +38,9 @@ rule flip_template_dseg:
             space="template",
             **inputs.subj_wildcards,
             desc="hipptissue",
-            hemi=config["template_based_segmentation"][config["inject_template"]]["hemi"],
+            hemi=config["template_based_segmentation"][config["inject_template"]][
+                "hemi"
+            ],
             suffix="dseg.nii.gz"
         ),
     output:
@@ -120,7 +124,6 @@ rule prep_segs_for_greedy:
         "c3d {input} -retain-labels {params.labels} -split -foreach -smooth {params.smoothing_stdev} -endfor -oo {output}/label_%02d.nii.gz"
 
 
-
 def get_image_pairs(wildcards, input):
     """This rule requires snakemake 6.4.0, since it uses the new feature to execute if input files are not found"""
 
@@ -352,7 +355,6 @@ rule inject_init_laplace_coords:
         "greedy -d 3 -threads {threads} {params.interp_opt} -rf {input.subject_seg} -rm {params.coords} {output.init_coords}  -r {input.warp} {input.matrix} &> {log}"
 
 
-
 rule reinsert_subject_labels:
     input:
         inject_seg=bids(
@@ -385,4 +387,3 @@ rule reinsert_subject_labels:
         config["singularity"]["autotop"]
     shell:
         "c3d {input.subject_seg} -retain-labels {params.labels} -popas LBL -push LBL -threshold 0 0 1 0 {input.inject_seg} -multiply -push LBL -add -o {output.postproc_seg}"
-

hippunfold/workflow/rules/templateseg.smk

@@ -26,7 +26,9 @@ rule import_template_shape:
             space="template",
             **inputs.subj_wildcards,
             desc="hipptissue",
-            hemi=config["template_based_segmentation"][config["inject_template"]]["hemi"],
+            hemi=config["template_based_segmentation"][config["inject_template"]][
+                "hemi"
+            ],
             suffix="dseg.nii.gz"
         ),
     group:
@@ -45,7 +47,9 @@ rule flip_template_dseg:
             space="template",
             **inputs.subj_wildcards,
             desc="hipptissue",
-            hemi=config["template_based_segmentation"][config["inject_template"]]["hemi"],
+            hemi=config["template_based_segmentation"][config["inject_template"]][
+                "hemi"
+            ],
             suffix="dseg.nii.gz"
         ),
     output:
@@ -71,9 +75,9 @@ rule import_template_anat:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         template_anat=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]][get_modality_suffix(config["modality"])].format(
-            **wildcards
-        ),
+        / config["template_files"][config["template"]][
+            get_modality_suffix(config["modality"])
+        ].format(**wildcards),
     output:
         template_anat=bids(
             root=work,
@@ -129,9 +133,7 @@ rule import_template_coords:
         template_dir=Path(download_dir) / "template" / config["template"],
     params:
         template_coords=lambda wildcards, input: Path(input.template_dir)
-        / config["template_files"][config["template"]]["coords"].format(
-            **wildcards
-        ),
+        / config["template_files"][config["template"]]["coords"].format(**wildcards),
     output:
         template_coords=bids(
             root=work,
@@ -143,7 +145,7 @@ rule import_template_coords:
             desc="init",
             space="template",
             hemi="{hemi}"
-        )
+        ),
     group:
         "subj"
     container:
@@ -163,8 +165,10 @@ rule flip_template_coords:
             suffix="coords.nii.gz",
             desc="init",
             space="template",
-            hemi=config["template_based_segmentation"][config["inject_template"]]["hemi"],
-        )
+            hemi=config["template_based_segmentation"][config["inject_template"]][
+                "hemi"
+            ],
+        ),
     output:
         template_coords=bids(
             root=work,
@@ -394,7 +398,7 @@ rule warp_template_anat:
             suffix=f"{config['modality']}.nii.gz",
             desc="warpedtemplate",
             space="corobl",
-            hemi="{hemi}"
+            hemi="{hemi}",
         ),
     group:
         "subj"
@@ -403,4 +407,3 @@ rule warp_template_anat:
     threads: 8
     shell:
         "greedy -d 3 -threads {threads} -rf {input.ref} -rm {params.template_anat} {output.warped}  -r  {input.warp} {params.xfm_corobl}"
-