correction in predict test

tests/test_predict.py

@@ -1,14 +1,14 @@
 # coding: utf8
 import json
-import os
 import shutil
 from os.path import exists
 from pathlib import Path
 
 import pytest
 
 from clinicadl import MapsManager
-from tests.testing_tools import clean_folder, compare_folders
+
+from .testing_tools import compare_folders, modify_maps
 
 
 @pytest.fixture(
@@ -33,46 +33,71 @@ def test_predict(cmdopt, tmp_path, test_name):
     tmp_out_dir.mkdir(parents=True)
 
     if test_name == "predict_image_classification":
-        model_folder = input_dir / "maps_image_cnn"
+        maps_name = "maps_image_cnn"
         modes = ["image"]
         use_labels = True
     elif test_name == "predict_slice_classification":
-        model_folder = input_dir / "maps_slice_cnn"
+        maps_name = "maps_slice_cnn"
         modes = ["image", "slice"]
         use_labels = True
     elif test_name == "predict_patch_regression":
-        model_folder = input_dir / "maps_patch_cnn"
+        maps_name = "maps_patch_cnn"
         modes = ["image", "patch"]
         use_labels = False
     elif test_name == "predict_roi_regression":
-        model_folder = input_dir / "maps_roi_cnn"
+        maps_name = "maps_roi_cnn"
         modes = ["image", "roi"]
         use_labels = False
     elif test_name == "predict_patch_multi_classification":
-        model_folder = input_dir / "maps_patch_multi_cnn"
+        maps_name = "maps_patch_multi_cnn"
         modes = ["image", "patch"]
         use_labels = False
     elif test_name == "predict_roi_reconstruction":
-        model_folder = input_dir / "maps_roi_ae"
+        maps_name = "maps_roi_ae"
         modes = ["roi"]
         use_labels = False
     else:
         raise NotImplementedError(f"Test {test_name} is not implemented.")
 
-    out_dir = str(model_folder / "split-0/best-loss/test-RANDOM")
+    shutil.copytree(input_dir / maps_name, tmp_out_dir / maps_name)
+    model_folder = tmp_out_dir / maps_name
+
+    if cmdopt["adapt-base-dir"]:
+        with open(model_folder / "maps.json", "r") as f:
+            config = json.load(f)
+        config = modify_maps(
+            maps=config,
+            base_dir=base_dir,
+            no_gpu=cmdopt["no-gpu"],
+            adapt_base_dir=cmdopt["adapt-base-dir"],
+        )
+        with open(model_folder / "maps.json", "w") as f:
+            json.dump(config, f, skipkeys=True, indent=4)
+
+        with open(model_folder / "groups/test-RANDOM/maps.json", "r") as f:
+            config = json.load(f)
+        config = modify_maps(
+            maps=config,
+            base_dir=base_dir,
+            no_gpu=False,
+            adapt_base_dir=cmdopt["adapt-base-dir"],
+        )
+        with open(model_folder / "groups/test-RANDOM/maps.json", "w") as f:
+            json.dump(config, f, skipkeys=True, indent=4)
 
-    if exists(out_dir):
-        shutil.rmtree(out_dir)
+    tmp_out_subdir = str(model_folder / "split-0/best-loss/test-RANDOM")
+    if exists(tmp_out_subdir):
+        shutil.rmtree(tmp_out_subdir)
 
-    # Correction of JSON file for ROI
-    if "roi" in modes:
-        json_path = model_folder / "maps.json"
-        with open(json_path, "r") as f:
-            parameters = json.load(f)
-        parameters["roi_list"] = ["leftHippocampusBox", "rightHippocampusBox"]
-        json_data = json.dumps(parameters, skipkeys=True, indent=4)
-        with open(json_path, "w") as f:
-            f.write(json_data)
+    # # Correction of JSON file for ROI
+    # if "roi" in modes:
+    #     json_path = model_folder / "maps.json"
+    #     with open(json_path, "r") as f:
+    #         parameters = json.load(f)
+    #     parameters["roi_list"] = ["leftHippocampusBox", "rightHippocampusBox"]
+    #     json_data = json.dumps(parameters, skipkeys=True, indent=4)
+    #     with open(json_path, "w") as f:
+    #         f.write(json_data)
 
     maps_manager = MapsManager(model_folder, verbose="debug")
     maps_manager.predict(
@@ -91,7 +116,7 @@ def test_predict(cmdopt, tmp_path, test_name):
             maps_manager.get_metrics(data_group="test-RANDOM", mode=mode)
 
     assert compare_folders(
-        tmp_out_dir / test_name,
-        ref_dir / test_name,
+        tmp_out_dir / maps_name,
+        ref_dir / maps_name,
         tmp_out_dir,
     )