stringing rules together

khanlab · Oct 31, 2023 · 2366360 · 2366360
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diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
@@ -363,43 +363,43 @@ template: CITI168
 
 template_files:
   CITI168:
-    T1w: templates-3d/CITI168/T1w_head_700um.nii.gz
-    T2w: templates-3d/CITI168/T2w_head_700um.nii.gz
-    xfm_corobl: templates-3d/CITI168/CoronalOblique_rigid.txt
-    crop_ref: templates-3d/CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    crop_refT1w: templates-3d/CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    Mask_crop: templates-3d/CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
+    T1w: CITI168/T1w_head_700um.nii.gz
+    T2w: CITI168/T2w_head_700um.nii.gz
+    xfm_corobl: CITI168/CoronalOblique_rigid.txt
+    crop_ref: CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    crop_refT1w: CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    Mask_crop: CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
   dHCP:
-    T1w: templates-3d/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_res-1_T1w.nii.gz
-    xfm_corobl: templates-3d/tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_to-corobl_affine.txt
-    crop_ref: templates-3d/CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    crop_refT1w: templates-3d/CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
-    Mask_crop: templates-3d/CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
+    T1w: tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_res-1_T1w.nii.gz
+    xfm_corobl: tpl-dHCP/cohort-1/tpl-dHCP_cohort-1_to-corobl_affine.txt
+    crop_ref: CITI168/T2w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    crop_refT1w: CITI168/T1w_300umCoronalOblique_hemi-{hemi}.nii.gz
+    Mask_crop: CITI168/Mask_300umCoronalOblique_hemi-{hemi}.nii.gz
     upenn:
-    dseg: templates-3d/tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
-    coords: templates-3d/tpl-upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
+    dseg: tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
+    coords: tpl-upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
   MBMv2:
-    T1w: templates-3d/tpl-MBMv2/Template_sym_MTR_80um.nii.gz
-    T2w: templates-3d/tpl-MBMv2/Template_sym_T2_80um.nii.gz
-    xfm_corobl: templates-3d/tpl-MBMv2/tpl-MBMv2_from-native_to-corobl_type-itk_affine.txt
-    crop_ref: templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_T2w.nii.gz
-    crop_refT1w: templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_MTR.nii.gz
-    Mask_crop: templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
-    dseg: templates-3d/tpl-MBMv2/tpl-MBMv2_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
-    coords: templates-3d/tpl-MBMv2/tpl-MBMv2_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
+    T1w: tpl-MBMv2/Template_sym_MTR_80um.nii.gz
+    T2w: tpl-MBMv2/Template_sym_T2_80um.nii.gz
+    xfm_corobl: tpl-MBMv2/tpl-MBMv2_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_T2w.nii.gz
+    crop_refT1w: tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_MTR.nii.gz
+    Mask_crop: tpl-MBMv2/tpl-MBMv2_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
+    dseg: tpl-MBMv2/tpl-MBMv2_hemi-R_space-corobl_desc-tissuemanual_dseg.nii.gz
+    coords: tpl-MBMv2/tpl-MBMv2_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
   MBMv3:
-    T1w: templates-3d/tpl-MBMv3/tpl-MBMv3_T1w.nii.gz
-    T2w: templates-3d/tpl-MBMv3/tpl-MBMv3_T2w.nii.gz
-    xfm_corobl: templates-3d/tpl-MBMv3/tpl-MBMv3_from-native_to-corobl_type-itk_affine.txt
-    crop_ref: templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T2w.nii.gz
-    crop_refT1w: templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T1w.nii.gz
-    Mask_crop: templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
-    dseg: templates-3d/tpl-MBMv3/tpl-MBMv3_hemi-R_space-corobl_desc-tissue_dseg.nii.gz
-    coords: templates-3d/tpl-MBMv3/tpl-MBMv3_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
+    T1w: tpl-MBMv3/tpl-MBMv3_T1w.nii.gz
+    T2w: tpl-MBMv3/tpl-MBMv3_T2w.nii.gz
+    xfm_corobl: tpl-MBMv3/tpl-MBMv3_from-native_to-corobl_type-itk_affine.txt
+    crop_ref: tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T2w.nii.gz
+    crop_refT1w: tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_T1w.nii.gz
+    Mask_crop: tpl-MBMv3/tpl-MBMv3_hemi-{hemi}_space-corobl_desc-hipp_mask.nii.gz
+    dseg: tpl-MBMv3/tpl-MBMv3_hemi-R_space-corobl_desc-tissue_dseg.nii.gz
+    coords: tpl-MBMv3/tpl-MBMv3_dir-{dir}_hemi-R_space-corobl_label-{autotop}_desc-laplace_coords.nii.gz 
   upenn:
-    T1w: templates-3d/tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
-    dseg: templates-3d/tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
-    coords: templates-3d/tpl-upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
+    T1w: tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
+    dseg: tpl-upenn/tpl-upenn_desc-hipptissue_dseg.nii.gz
+    coords: tpl-upenn/tpl-upenn_dir-{dir}_label-{autotop}_coords.nii.gz
 
 
 
@@ -408,20 +408,20 @@ atlas:
 
 atlas_files:
   multihist7:
-    label_nii: atlases-unfolded/multihist7/sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz
-    label_list: atlases-unfolded/multihist7/labellist.txt
-    thick: atlases-unfolded/multihist7/thickness.nii.gz
-    curv: atlases-unfolded/multihist7/curvature.nii.gz
-    gyr: atlases-unfolded/multihist7/gyrification.nii.gz
+    label_nii: multihist7/sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz
+    label_list: multihist7/labellist.txt
+    thick: multihist7/thickness.nii.gz
+    curv: multihist7/curvature.nii.gz
+    gyr: multihist7/gyrification.nii.gz
   bigbrain:
-    label_nii: atlases-unfolded/bigbrain/sub-bigbrain_hemi-{hemi}_label-hipp_desc-manualsubfields_dseg.nii.gz
-    label_list: atlases-unfolded/bigbrain/sub-bigbrain_labellist.txt
+    label_nii: bigbrain/sub-bigbrain_hemi-{hemi}_label-hipp_desc-manualsubfields_dseg.nii.gz
+    label_list: bigbrain/sub-bigbrain_labellist.txt
   magdeburg:
-    label_nii: atlases-unfolded/magdeburg/sub-all_hemi-{hemi}_label-hipp_desc-manualsubfields_maxprob.nii.gz
-    label_list: atlases-unfolded/magdeburg/magdeburg_labellist.txt
+    label_nii: magdeburg/sub-all_hemi-{hemi}_label-hipp_desc-manualsubfields_maxprob.nii.gz
+    label_list: magdeburg/magdeburg_labellist.txt
   freesurfer:
-    label_nii: atlases-unfolded/freesurfer/sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
-    label_list: atlases-unfolded/freesurfer/freesurfer_labellist.txt
+    label_nii: freesurfer/sub-all_hemi-{hemi}_space-unfold_label-hipp_desc-freesurfersubfields_dseg.nii.gz
+    label_list: freesurfer/freesurfer_labellist.txt
 
 
 inject_template: upenn

diff --git a/hippunfold/workflow/rules/downloads.smk b/hippunfold/workflow/rules/downloads.smk
@@ -10,7 +10,6 @@ def get_model_tar():
 
     return os.path.abspath(os.path.join(download_dir, local_tar.split("/")[-1]))
 
-
 rule download_model:
     params:
         url=config["nnunet_model"][config["force_nnunet_model"]]
@@ -34,6 +33,16 @@ rule download_atlas:
     shell:
         "wget https://{params.url} -O {output.model_zip}"
 
+rule download_template:
+    params:
+        url=lambda wildcards: config["template_files_osf"][wildcards.atlas],
+    output:
+        model_zip=os.path.join(download_dir,"{template}"+'.zip')
+    container:
+        config["singularity"]["autotop"]
+    shell:
+        "wget https://{params.url} -O {output.model_zip}"
+
 
 def atlas_outs():
     outs = []
@@ -42,35 +51,44 @@ def atlas_outs():
             outs.append(os.path.join(download_dir,config["atlas_files"][a][fn]))
     return outs
 
-rule unzip_atlas:
+def template_outs():
+    outs = []
+    for fn in config["template_files"][config["template"]]:
+        outs.append(os.path.join(download_dir,config["template_files"][config["template"]][fn]))
+    return outs
+
+
+rule unzip_template:
     input:
-        model_zip=lambda wildcards: os.path.join(download_dir,"{wildcards.atlas}"+'.zip'),
-        atlas=config["atlas"],
+        model_zip=os.path.join(download_dir,"{template}"+'.zip'),
     params:
         dir=download_dir,
     output:
-        atlas_outs(),
+        template_outs(),
     shell:
         "unzip {input.model_zip} -d {params.dir}"
 
-
-rule download_template:
+rule unzip_atlas:
+    input:
+        model_zip=os.path.join(download_dir,"{atlas}"+'.zip'),
     params:
-        url=config["template_files_osf"][config["template"]],
+        dir=download_dir,
     output:
-        model_zip=os.path.join(download_dir,config["template"]+'.zip')
-    container:
-        config["singularity"]["autotop"]
+        atlas_outs()
     shell:
-        "wget https://{params.url} -O {output.model_zip}"
+        "unzip {input.model_zip} -d {params.dir}"
 
 
-rule unzip_template:
+rule unzip_template_shape:
     input:
-        model_zip=os.path.join(download_dir,config["template"]+'.zip'),
+        model_zip=os.path.join(download_dir,config["inject_template"]+'.zip'),
     params:
         dir=download_dir,
     output:
-        os.path.join(download_dir,config["template_files"][config["template"]]["T1w"])
+        template_seg=os.path.join(
+            download_dir,
+            config["template_files"][config["inject_template"]]["dseg"],
+        )
     shell:
         "unzip {input.model_zip} -d {params.dir}"
+
diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk
@@ -176,7 +176,7 @@ def get_f3d_ref(wildcards):
     if config["modality"] == "T2w":
         nii = (
             os.path.join(
-                download_dir
+                download_dir,
                 config["template_files"][config["template"]]["crop_ref"],
             ),
         )

diff --git a/hippunfold/workflow/rules/shape_inject.smk b/hippunfold/workflow/rules/shape_inject.smk
@@ -89,8 +89,7 @@ rule prep_segs_for_greedy:
 rule import_template_shape:
     input:
         template_seg=os.path.join(
-            workflow.basedir,
-            "..",
+            download_dir,
             config["template_files"][config["inject_template"]]["dseg"],
         ),
     output:
@@ -278,8 +277,7 @@ rule template_shape_inject:
 rule inject_init_laplace_coords:
     input:
         coords=os.path.join(
-            workflow.basedir,
-            "..",
+            download_dir,
             config["template_files"][config["inject_template"]]["coords"],
         ),
         subject_seg=get_input_for_shape_inject,