Save all seeds into common /assets/seeds/ rather than dataset specifi…

…c folders
VemundFredriksen · Oct 29, 2023 · 82f459c · 82f459c
1 parent 1ac1b94
commit 82f459c
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Showing 3 changed files with 7 additions and 8 deletions.
diff --git a/synthlung/__main__.py b/synthlung/__main__.py
@@ -6,14 +6,14 @@
 from lungmask import LMInferer
 import json
 
-def seed_msd():
-    json_file_path = "./assets/source/msd/dataset.json"
+def seed():
+    json_file_path = "./assets/source/dataset.json"
 
     with open(json_file_path, 'r') as json_file:
         image_dict = json.load(json_file)
     crop_pipeline = TumorCropPipeline()
     crop_pipeline(image_dict)
-    formatter = MSDGenerateJSONFormatter("./assets/seeds/msd/")
+    formatter = MSDGenerateJSONFormatter("./assets/seeds/")
     formatter.generate_json()
 
 def format_msd():
@@ -55,8 +55,7 @@ def main():
         if(args.dataset == "msd"):
             format_msd()
     elif args.action == "seed":
-        if(args.dataset == "msd"):
-            seed_msd()
+        seed()
     elif args.action == "generate":
         if(args.dataset == "msd"):
             generate_randomized_tumors()

diff --git a/synthlung/utils/dataset_formatter.py b/synthlung/utils/dataset_formatter.py
@@ -9,7 +9,7 @@
 LABEL_NII_GZ = 'label.nii.gz'
 
 class MSDImageSourceFormatter(ImageSourceFormatter, JSONGenerator):
-    def __init__(self, source_directory: str = "./assets/Task06_Lung/", target_directory: str = "./assets/source/msd/") -> None:
+    def __init__(self, source_directory: str = "./assets/Task06_Lung/", target_directory: str = "./assets/source/") -> None:
         self.target_directory = target_directory
         self.source_directory = source_directory
 

diff --git a/synthlung/utils/tumor_isolation_pipeline.py b/synthlung/utils/tumor_isolation_pipeline.py
@@ -70,8 +70,8 @@ def __init__(self) -> None:
             LoadImaged(keys=['image', 'label'], image_only = False),
             TumorSeedIsolationd(image_key='image', label_key='label', image_output_key='seed_image', label_output_key='seed_label'),
             RenameSourceToSeed(meta_dict_keys=['seed_image_meta_dict', 'seed_label_meta_dict']),
-            SaveImaged(keys=['seed_image'], output_dir='./assets/seeds/msd/', output_postfix='', separate_folder=False),
-            SaveImaged(keys=['seed_label'], output_dir='./assets/seeds/msd/', output_postfix='', separate_folder=False)
+            SaveImaged(keys=['seed_image'], output_dir='./assets/seeds/', output_postfix='', separate_folder=False),
+            SaveImaged(keys=['seed_label'], output_dir='./assets/seeds/', output_postfix='', separate_folder=False)
         ])
 
     def __call__(self, image_dict) -> None: