Move all test data into test_data folder

.gitignore

@@ -1,4 +1,6 @@
 __pycache__/
 .ipynb_checkpoints/
 *.out
-experiments/
+experiments/
+checkpoints/
+.pytest_cache

models/tests/test_cut.py

@@ -15,9 +15,9 @@
 @pytest.fixture()
 def config():
     config_path = os.path.join(
-        '/home/vincentwu',
-        'URUST_exp',
-        'config_lung_lesion_for_test_cut.yaml'
+        "./test_data",
+        "configs",
+        "config_lung_lesion_for_test_cut.yaml"
     )
     config = read_yaml_config(config_path)
 
@@ -29,7 +29,7 @@ def in_model(config):
     model = get_model(
         config=config,
         model_name=config["MODEL_NAME"],
-        normalization='in',
+        normalization="in",
         isTrain=False,
     )
     model.load_networks(config["INFERENCE_SETTING"]["MODEL_VERSION"])
@@ -42,7 +42,7 @@ def kin_model(config):
     model = get_model(
         config=config,
         model_name=config["MODEL_NAME"],
-        normalization='kin',
+        normalization="kin",
         isTrain=False,
     )
     model.load_networks(config["INFERENCE_SETTING"]["MODEL_VERSION"])
@@ -71,11 +71,10 @@ def dataloader(dataset):
 @pytest.fixture()
 def in_expected_outputs(config):
     expected_output_dir = os.path.join(
-        config["EXPERIMENT_ROOT_PATH"],
+        config["INFERENCE_SETTING"]["TEST_DIR_Y"],
         config["EXPERIMENT_NAME"],
-        "test",
         "in",
-        f"{config['INFERENCE_SETTING']['MODEL_VERSION']}_pytest",
+        f"{config['INFERENCE_SETTING']['MODEL_VERSION']}",
 
     )
     expected_output_files = sorted(
@@ -97,14 +96,12 @@ def in_expected_outputs(config):
 @pytest.fixture()
 def kin_expected_outputs(config):
     expected_output_dir = os.path.join(
-        config["EXPERIMENT_ROOT_PATH"],
+        config["INFERENCE_SETTING"]["TEST_DIR_Y"],
         config["EXPERIMENT_NAME"],
-        "test",
         "kin",
         config["INFERENCE_SETTING"]["MODEL_VERSION"],
         f"{config['INFERENCE_SETTING']['KIN_KERNEL']}_"
-        f"{config['INFERENCE_SETTING']['KIN_PADDING']}_pytest",
-
+        f"{config['INFERENCE_SETTING']['KIN_PADDING']}"
     )
     expected_output_files = sorted(
         os.listdir(expected_output_dir)

models/tests/test_cyclegan.py

@@ -15,9 +15,9 @@
 @pytest.fixture()
 def config():
     config_path = os.path.join(
-        '/home/vincentwu',
-        'URUST_exp',
-        'config_lung_lesion_for_test_cyclegan.yaml'
+        "./test_data",
+        "configs",
+        "config_lung_lesion_for_test_cyclegan.yaml"
     )
     config = read_yaml_config(config_path)
 
@@ -29,7 +29,7 @@ def in_model(config):
     model = get_model(
         config=config,
         model_name=config["MODEL_NAME"],
-        normalization='in',
+        normalization="in",
         isTrain=False,
     )
     model.load_networks(config["INFERENCE_SETTING"]["MODEL_VERSION"])
@@ -42,7 +42,7 @@ def kin_model(config):
     model = get_model(
         config=config,
         model_name=config["MODEL_NAME"],
-        normalization='kin',
+        normalization="kin",
         isTrain=False,
     )
     model.load_networks(config["INFERENCE_SETTING"]["MODEL_VERSION"])
@@ -71,11 +71,10 @@ def dataloader(dataset):
 @pytest.fixture()
 def in_expected_outputs(config):
     expected_output_dir = os.path.join(
-        config["EXPERIMENT_ROOT_PATH"],
+        config["INFERENCE_SETTING"]["TEST_DIR_Y"],
         config["EXPERIMENT_NAME"],
-        "test",
         "in",
-        f"{config['INFERENCE_SETTING']['MODEL_VERSION']}_pytest",
+        f"{config['INFERENCE_SETTING']['MODEL_VERSION']}",
 
     )
     expected_output_files = sorted(
@@ -97,13 +96,12 @@ def in_expected_outputs(config):
 @pytest.fixture()
 def kin_expected_outputs(config):
     expected_output_dir = os.path.join(
-        config["EXPERIMENT_ROOT_PATH"],
+        config["INFERENCE_SETTING"]["TEST_DIR_Y"],
         config["EXPERIMENT_NAME"],
-        "test",
         "kin",
         config["INFERENCE_SETTING"]["MODEL_VERSION"],
         f"{config['INFERENCE_SETTING']['KIN_KERNEL']}_"
-        f"{config['INFERENCE_SETTING']['KIN_PADDING']}_pytest",
+        f"{config['INFERENCE_SETTING']['KIN_PADDING']}",
 
     )
     expected_output_files = sorted(

models/tests/test_data/configs/config_lung_lesion_for_test_cut.yaml

@@ -0,0 +1,27 @@
+EXPERIMENT_ROOT_PATH: "./test_data/checkpoints/lung_lesion"
+EXPERIMENT_NAME: "lung_lesion_CUT"
+MODEL_NAME: "CUT" # currently only CUT and cycleGAN are support
+DEVICE: "cuda"
+
+TRAINING_SETTING:
+  PAIRED_TRAINING: False
+  NUM_EPOCHS: 100
+  LAMBDA_Y: 1
+  LEARNING_RATE: 0.0002
+  BATCH_SIZE: 1
+  NUM_WORKERS: 4
+  SAVE_MODEL: true
+  SAVE_MODEL_EPOCH_STEP: 10
+  VISUALIZATION_STEP: 250
+  LOAD_MODEL: false
+  LOAD_EPOCH: 0
+
+INFERENCE_SETTING:
+  TEST_DIR_X: "./test_data/test_dir_x/lung_lesion/"
+  TEST_DIR_Y: "./test_data/test_dir_y/lung_lesion"
+  MODEL_VERSION: "latest"
+  SAVE_ORIGINAL_IMAGE: False
+  NORMALIZATION: "kin"
+  THUMBNAIL: "None" # set to "None" if it's not required
+  KIN_PADDING: 1 # for kin
+  KIN_KERNEL: "gaussian" #constant or gaussian

models/tests/test_data/configs/config_lung_lesion_for_test_cyclegan.yaml

@@ -0,0 +1,27 @@
+EXPERIMENT_ROOT_PATH: "./test_data/checkpoints/lung_lesion"
+EXPERIMENT_NAME: "lung_lesion_cycleGAN"
+MODEL_NAME: "cycleGAN" # currently only CUT and cycleGAN are support
+DEVICE: "cuda"
+
+TRAINING_SETTING:
+  PAIRED_TRAINING: False
+  NUM_EPOCHS: 100
+  LAMBDA_Y: 1
+  LEARNING_RATE: 0.0002
+  BATCH_SIZE: 1
+  NUM_WORKERS: 4
+  SAVE_MODEL: true
+  SAVE_MODEL_EPOCH_STEP: 10
+  VISUALIZATION_STEP: 250
+  LOAD_MODEL: false
+  LOAD_EPOCH: 0
+
+INFERENCE_SETTING:
+  TEST_DIR_X: "./test_data/test_dir_x/lung_lesion/"
+  TEST_DIR_Y: "./test_data/test_dir_y/lung_lesion"
+  MODEL_VERSION: "60"
+  SAVE_ORIGINAL_IMAGE: False
+  NORMALIZATION: "kin"
+  THUMBNAIL: "None" # set to "None" if it's not required
+  KIN_PADDING: 1 # for kin
+  KIN_KERNEL: "gaussian" #constant or gaussian

models/tests/test_data/test_dir_x/lung_lesion/blank_patches_list.csv

@@ -0,0 +1,64 @@
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