Flag for local tests

tests/test_interpret.py

@@ -61,6 +61,9 @@ def test_interpret(cmdopt, tmp_path, test_name):
     else:
         raise NotImplementedError(f"Test {test_name} is not implemented.")
 
+    if cmdopt["no-gpu"]:
+        cnn_input.append("--no-gpu")
+
     run_interpret(cnn_input, tmp_out_dir, ref_dir)
 
 

tests/test_random_search.py

@@ -1,14 +1,13 @@
 # coding: utf8
 
-import json
 import os
 import shutil
 from os.path import join
 from pathlib import Path
 
 import pytest
 
-from tests.testing_tools import compare_folders
+from .testing_tools import change_gpu_in_toml, compare_folders
 
 
 # random searxh for ROI with CNN
@@ -34,17 +33,22 @@ def test_random_search(cmdopt, tmp_path, test_name):
     else:
         raise NotImplementedError(f"Test {test_name} is not implemented.")
 
-    run_test_random_search(toml_path, generate_input, tmp_out_dir, ref_dir)
+    run_test_random_search(
+        toml_path, generate_input, tmp_out_dir, ref_dir, cmdopt["no-gpu"]
+    )
 
 
-def run_test_random_search(toml_path, generate_input, tmp_out_dir, ref_dir):
+def run_test_random_search(toml_path, generate_input, tmp_out_dir, ref_dir, no_gpu):
     if os.path.exists(tmp_out_dir):
         shutil.rmtree(tmp_out_dir)
 
     # Write random_search.toml file
     os.makedirs(tmp_out_dir, exist_ok=True)
     shutil.copy(toml_path, tmp_out_dir)
 
+    if no_gpu:
+        change_gpu_in_toml(tmp_out_dir / "random_search.toml")
+
     flag_error_generate = not os.system("clinicadl " + " ".join(generate_input))
     performances_flag = os.path.exists(
         tmp_out_dir / "job-1" / "split-0" / "best-loss" / "train"

tests/test_resume.py

@@ -1,15 +1,14 @@
 # coding: utf8
 import json
-import os
 import shutil
 from os import system
-from os.path import join
 from pathlib import Path
 
 import pytest
 
 from clinicadl import MapsManager
-from tests.testing_tools import compare_folders
+
+from .testing_tools import modify_maps
 
 
 @pytest.fixture(
@@ -33,6 +32,18 @@ def test_resume(cmdopt, tmp_path, test_name):
     shutil.copytree(input_dir / test_name, tmp_out_dir / test_name)
     maps_stopped = tmp_out_dir / test_name
 
+    if cmdopt["no-gpu"] or cmdopt["adapt-base-dir"]:  # modify the input MAPS
+        with open(maps_stopped / "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(maps_stopped / "maps.json", "w") as f:
+            json.dump(config, f)
+
     flag_error = not system(f"clinicadl -vv train resume {maps_stopped}")
     assert flag_error
 
@@ -48,4 +59,13 @@ def test_resume(cmdopt, tmp_path, test_name):
             json_data_out = json.load(out)
         with open(ref_dir / "maps_image_cnn" / "maps.json", "r") as ref:
             json_data_ref = json.load(ref)
+
+        if cmdopt["no-gpu"] or cmdopt["adapt-base-dir"]:
+            json_data_ref = modify_maps(
+                maps=json_data_ref,
+                base_dir=base_dir,
+                no_gpu=cmdopt["no-gpu"],
+                adapt_base_dir=cmdopt["adapt-base-dir"],
+            )
+
         assert json_data_ref == json_data_out

tests/test_train_ae.py

@@ -3,12 +3,11 @@
 import json
 import os
 import shutil
-from os.path import join
 from pathlib import Path
 
 import pytest
 
-from tests.testing_tools import clean_folder, compare_folders
+from .testing_tools import clean_folder, compare_folders, modify_maps
 
 
 @pytest.fixture(
@@ -27,8 +26,8 @@ def test_train_ae(cmdopt, tmp_path, test_name):
     base_dir = Path(cmdopt["input"])
     input_dir = base_dir / "train" / "in"
     ref_dir = base_dir / "train" / "ref"
-    tmp_out_dir = base_dir / "train" / "out"
-    # tmp_out_dir.mkdir(parents=True)
+    tmp_out_dir = tmp_path / "train" / "out"
+    tmp_out_dir.mkdir(parents=True)
 
     clean_folder(tmp_out_dir, recreate=True)
 
@@ -102,18 +101,12 @@ def test_train_ae(cmdopt, tmp_path, test_name):
     with open(ref_dir / ("maps_" + test_name) / "maps.json", "r") as ref:
         json_data_ref = json.load(ref)
 
-    if test_name == "patch_multi_ae":
-        json_data_out["multi_network"] = True
-    if cmdopt["no-gpu"]:
-        json_data_ref["gpu"] = False
-    if cmdopt["adapt-base-dir"]:
-        base_dir = base_dir.resolve()
-        ref_base_dir = Path(json_data_ref["caps_directory"]).parents[2]
-        json_data_ref["caps_directory"] = str(
-            base_dir / Path(json_data_ref["caps_directory"]).relative_to(ref_base_dir)
-        )
-        json_data_ref["tsv_path"] = str(
-            base_dir / Path(json_data_ref["tsv_path"]).relative_to(ref_base_dir)
+    if cmdopt["no-gpu"] or cmdopt["adapt-base-dir"]:
+        json_data_ref = modify_maps(
+            maps=json_data_ref,
+            base_dir=base_dir,
+            no_gpu=cmdopt["no-gpu"],
+            adapt_base_dir=cmdopt["adapt-base-dir"],
         )
     assert json_data_out == json_data_ref  # ["mode"] == mode
 

tests/test_train_cnn.py

@@ -3,12 +3,11 @@
 import json
 import os
 import shutil
-from os.path import join
 from pathlib import Path
 
 import pytest
 
-from tests.testing_tools import compare_folders
+from .testing_tools import compare_folders, modify_maps
 
 
 @pytest.fixture(
@@ -101,6 +100,9 @@ def test_train_cnn(cmdopt, tmp_path, test_name):
     else:
         raise NotImplementedError(f"Test {test_name} is not implemented.")
 
+    if cmdopt["no-gpu"]:
+        test_input.append("--no-gpu")
+
     if tmp_out_dir.is_dir():
         shutil.rmtree(tmp_out_dir)
 
@@ -117,6 +119,13 @@ def test_train_cnn(cmdopt, tmp_path, test_name):
     with open(ref_dir / ("maps_" + test_name) / "maps.json", "r") as ref:
         json_data_ref = json.load(ref)
 
+    if cmdopt["no-gpu"] or cmdopt["adapt-base-dir"]:
+        json_data_ref = modify_maps(
+            maps=json_data_ref,
+            base_dir=base_dir,
+            no_gpu=cmdopt["no-gpu"],
+            adapt_base_dir=cmdopt["adapt-base-dir"],
+        )
     assert json_data_out == json_data_ref  # ["mode"] == mode
 
     assert compare_folders(

tests/test_train_from_json.py

@@ -1,17 +1,14 @@
-import os
-import pathlib
+import json
 import shutil
-from os import path, system
-from os.path import join
+from os import system
 from pathlib import Path
 
-from .testing_tools import compare_folders_with_hashes, create_hashes_dict, models_equal
+from .testing_tools import compare_folders_with_hashes, create_hashes_dict, modify_maps
 
 
 def test_json_compatibility(cmdopt, tmp_path):
     base_dir = Path(cmdopt["input"])
     input_dir = base_dir / "train_from_json" / "in"
-    ref_dir = base_dir / "train_from_json" / "ref"
     tmp_out_dir = tmp_path / "train_from_json" / "out"
     tmp_out_dir.mkdir(parents=True)
 
@@ -22,6 +19,19 @@ def test_json_compatibility(cmdopt, tmp_path):
     if reproduced_maps_dir.exists():
         shutil.rmtree(reproduced_maps_dir)
 
+    if cmdopt["no-gpu"] or cmdopt["adapt-base-dir"]:  # virtually modify the input MAPS
+        with open(config_json, "r") as f:
+            config = json.load(f)
+        config_json = tmp_out_dir / "modified_maps.json"
+        config = modify_maps(
+            maps=config,
+            base_dir=base_dir,
+            no_gpu=cmdopt["no-gpu"],
+            adapt_base_dir=cmdopt["adapt-base-dir"],
+        )
+        with open(config_json, "w+") as f:
+            json.dump(config, f)
+
     flag_error = not system(
         f"clinicadl train from_json {str(config_json)} {str(reproduced_maps_dir)} -s {split}"
     )
@@ -31,7 +41,6 @@ def test_json_compatibility(cmdopt, tmp_path):
 def test_determinism(cmdopt, tmp_path):
     base_dir = Path(cmdopt["input"])
     input_dir = base_dir / "train_from_json" / "in"
-    ref_dir = base_dir / "train_from_json" / "ref"
     tmp_out_dir = tmp_path / "train_from_json" / "out"
     tmp_out_dir.mkdir(parents=True)
 
@@ -50,8 +59,11 @@ def test_determinism(cmdopt, tmp_path):
         str(maps_dir),
         "-c",
         str(input_dir / "reproducibility_config.toml"),
-        "--no-gpu",
     ]
+
+    if cmdopt["no-gpu"]:
+        test_input.append("--no-gpu")
+
     # Run first experiment
     flag_error = not system("clinicadl " + " ".join(test_input))
     assert flag_error

tests/test_transfer_learning.py

@@ -1,12 +1,11 @@
 import json
 import os
 import shutil
-from os.path import join
 from pathlib import Path
 
 import pytest
 
-from tests.testing_tools import compare_folders
+from .testing_tools import compare_folders, modify_maps
 
 
 # Everything is tested on roi except for cnn --> multicnn (patch) as multicnn is not implemented for roi.
@@ -41,7 +40,7 @@ def test_transfer_learning(cmdopt, tmp_path, test_name):
             str(caps_roi_path),
             extract_roi_str,
             str(labels_path),
-            str(tmp_out_dir),
+            str(tmp_out_dir / "maps_roi_ae"),
             "-c",
             str(config_path),
         ]
@@ -55,7 +54,7 @@ def test_transfer_learning(cmdopt, tmp_path, test_name):
             "-c",
             str(config_path),
             "--transfer_path",
-            str(tmp_out_dir),
+            str(tmp_out_dir / "maps_roi_ae"),
         ]
         name = "aeTOae"
     elif test_name == "transfer_ae_cnn":
@@ -65,7 +64,7 @@ def test_transfer_learning(cmdopt, tmp_path, test_name):
             str(caps_roi_path),
             extract_roi_str,
             str(labels_path),
-            str(tmp_out_dir),
+            str(tmp_out_dir / "maps_roi_ae"),
             "-c",
             str(config_path),
         ]
@@ -79,7 +78,7 @@ def test_transfer_learning(cmdopt, tmp_path, test_name):
             "-c",
             str(config_path),
             "--transfer_path",
-            str(tmp_out_dir),
+            str(tmp_out_dir / "maps_roi_ae"),
         ]
         name = "aeTOcnn"
     elif test_name == "transfer_cnn_cnn":
@@ -89,7 +88,7 @@ def test_transfer_learning(cmdopt, tmp_path, test_name):
             str(caps_roi_path),
             extract_roi_str,
             str(labels_path),
-            str(tmp_out_dir),
+            str(tmp_out_dir / "maps_roi_cnn"),
             "-c",
             str(config_path),
         ]
@@ -103,7 +102,7 @@ def test_transfer_learning(cmdopt, tmp_path, test_name):
             "-c",
             str(config_path),
             "--transfer_path",
-            str(tmp_out_dir),
+            str(tmp_out_dir / "maps_roi_cnn"),
         ]
         name = "cnnTOcnn"
     elif test_name == "transfer_cnn_multicnn":
@@ -113,7 +112,7 @@ def test_transfer_learning(cmdopt, tmp_path, test_name):
             str(caps_roi_path),
             extract_roi_str,
             str(labels_path),
-            str(tmp_out_dir),
+            str(tmp_out_dir / "maps_roi_cnn"),
             "-c",
             str(config_path),
         ]
@@ -127,12 +126,17 @@ def test_transfer_learning(cmdopt, tmp_path, test_name):
             "-c",
             str(config_path),
             "--transfer_path",
-            str(tmp_out_dir),
+            str(tmp_out_dir / "maps_roi_cnn"),
+            "--multi_network",
         ]
-        name = "cnnTOcnn"
+        name = "cnnTOmulticnn"
     else:
         raise NotImplementedError(f"Test {test_name} is not implemented.")
 
+    if cmdopt["no-gpu"]:
+        source_task.append("--no-gpu")
+        target_task.append("--no-gpu")
+
     if tmp_out_dir.exists():
         shutil.rmtree(tmp_out_dir)
     if tmp_target_dir.exists():
@@ -148,9 +152,21 @@ def test_transfer_learning(cmdopt, tmp_path, test_name):
     with open(ref_dir / ("maps_roi_" + name) / "maps.json", "r") as ref:
         json_data_ref = json.load(ref)
 
-    json_data_ref["transfer_path"] = json_data_out["transfer_path"]
-    json_data_ref["gpu"] = json_data_out["gpu"]
+    ref_source_dir = Path(json_data_ref["transfer_path"]).parent
+    json_data_ref["transfer_path"] = str(
+        tmp_out_dir / Path(json_data_ref["transfer_path"]).relative_to(ref_source_dir)
+    )
+    if cmdopt["no-gpu"] or cmdopt["adapt-base-dir"]:
+        json_data_ref = modify_maps(
+            maps=json_data_ref,
+            base_dir=base_dir,
+            no_gpu=cmdopt["no-gpu"],
+            adapt_base_dir=cmdopt["adapt-base-dir"],
+        )
+    # TODO: remove and update data
     json_data_ref["caps_directory"] = json_data_out["caps_directory"]
+    json_data_ref["gpu"] = json_data_out["gpu"]
+    ###
     assert json_data_out == json_data_ref  # ["mode"] == mode
 
     assert compare_folders(