moved nnunet_urls to resource_urls

TODO: use other urls too
khanlab · Feb 14, 2024 · e7ca2b2 · e7ca2b2
1 parent bf4ca6b
commit e7ca2b2
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diff --git a/hippunfold/config/nnunet_model_urls.yml b/hippunfold/config/nnunet_model_urls.yml
diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
@@ -410,15 +410,31 @@ modality: T2w
 
 
 #these will be downloaded to ~/.cache/hippunfold
-nnunet_model:
-  T1w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task101_hcp1200_T1w.nnUNetTrainerV2.model_best.tar'
-  T2w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task102_hcp1200_T2w.nnUNetTrainerV2.model_best.tar'
-  hippb500: 'zenodo.org/record/5732291/files/trained_model.3d_fullres.Task110_hcp1200_b1000crop.nnUNetTrainerV2.model_best.tar'
-  neonateT1w: 'zenodo.org/record/5733556/files/trained_model.3d_fullres.Task205_hcp1200_b1000_finetuneround2_dhcp_T1w.nnUNetTrainerV2.model_best.tar'
-  neonateT1w_v2: 'zenodo.org/record/8209029/files/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar'
-  T1T2w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task103_hcp1200_T1T2w.nnUNetTrainerV2.model_best.tar'
-  synthseg_v0.1: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task102_synsegGenDetailed.nnUNetTrainerV2.model_best.tar'
-  synthseg_v0.2: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task203_synthseg.nnUNetTrainerV2.model_best.tar'
+resource_urls:
+  nnunet_model:
+    T1w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task101_hcp1200_T1w.nnUNetTrainerV2.model_best.tar'
+    T2w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task102_hcp1200_T2w.nnUNetTrainerV2.model_best.tar'
+    hippb500: 'zenodo.org/record/5732291/files/trained_model.3d_fullres.Task110_hcp1200_b1000crop.nnUNetTrainerV2.model_best.tar'
+    neonateT1w: 'zenodo.org/record/5733556/files/trained_model.3d_fullres.Task205_hcp1200_b1000_finetuneround2_dhcp_T1w.nnUNetTrainerV2.model_best.tar'
+    neonateT1w_v2: 'zenodo.org/record/8209029/files/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar'
+    T1T2w: 'zenodo.org/record/4508747/files/trained_model.3d_fullres.Task103_hcp1200_T1T2w.nnUNetTrainerV2.model_best.tar'
+    synthseg_v0.1: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task102_synsegGenDetailed.nnUNetTrainerV2.model_best.tar'
+    synthseg_v0.2: 'zenodo.org/record/8184230/files/trained_model.3d_fullres.Task203_synthseg.nnUNetTrainerV2.model_best.tar'
+  atlas:
+    multihist7: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b782827451220b86dd8/?zip='
+    bigbrain: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8b13d27b123094c96f/?zip='
+    magdeburg: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8013d27b122f94c938/?zip='
+    freesurfer: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395b8513d27b123094c96a/?zip='
+  template:
+    CITI168: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bf0282745121fb86a93/?zip='
+    dHCP: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395bff13d27b123094c9b4/?zip='
+    MBMv2: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0887852d133ca597dd/?zip='
+    MBMv3: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c0e8a28b11240ffc6e9/?zip='
+    upenn: 'files.ca-1.osf.io/v1/resources/v8acf/providers/osfstorage/65395c1613d27b122a94ca09/?zip='
+#to get hash, see https://github.com/CenterForOpenScience/osf.io/issues/8256#issuecomment-379833911
+
+
+
 
 crop_native_box: '256x256x256vox'
 crop_native_res: '0.2x0.2x0.2mm'

diff --git a/hippunfold/workflow/rules/common.smk b/hippunfold/workflow/rules/common.smk
@@ -397,6 +397,16 @@ def get_work_dir(wildcards):
     return folder_without_file
 
 
+def get_download_dir():
+    if "HIPPUNFOLD_CACHE_DIR" in os.environ.keys():
+        download_dir = os.environ["HIPPUNFOLD_CACHE_DIR"]
+    else:
+        # create local download dir if it doesn't exist
+        dirs = AppDirs("hippunfold", "khanlab")
+        download_dir = dirs.user_cache_dir
+    return download_dir
+
+
 rule archive_work_after_final:
     input:
         get_final_subj_output(),

diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk
@@ -43,19 +43,14 @@ def get_nnunet_input(wildcards):
 
 def get_model_tar():
 
-    if "HIPPUNFOLD_CACHE_DIR" in os.environ.keys():
-        download_dir = os.environ["HIPPUNFOLD_CACHE_DIR"]
-    else:
-        # create local download dir if it doesn't exist
-        dirs = AppDirs("hippunfold", "khanlab")
-        download_dir = dirs.user_cache_dir
+    download_dir=get_download_dir()
 
     if config["force_nnunet_model"]:
         model_name = config["force_nnunet_model"]
     else:
         model_name = config["modality"]
 
-    local_tar = config["nnunet_model"].get(model_name, None)
+    local_tar = config["resource_urls"]["nnunet_model"].get(model_name, None)
     if local_tar == None:
         print(f"ERROR: {model_name} does not exist in nnunet_model in the config file")
 
@@ -91,9 +86,9 @@ def parse_trainer_from_tar(wildcards, input):
 
 rule download_model:
     params:
-        url=config["nnunet_model"][config["force_nnunet_model"]]
+        url=config["resource_urls"]["nnunet_model"][config["force_nnunet_model"]]
         if config["force_nnunet_model"]
-        else config["nnunet_model"][config["modality"]],
+        else config["resource_urls"]["nnunet_model"][config["modality"]],
     output:
         model_tar=get_model_tar(),
     container: