pytest fixes:

fixing directory issues

test/quick_test/common.py

@@ -5,7 +5,7 @@
 logger = getLogger(__name__)
 
 
-def load_test_files():
+def load_test_subjects():
     """
     Load the test files from the given file path.
 
@@ -14,19 +14,19 @@ def load_test_files():
     """
 
     subjects_dir = os.environ["SUBJECTS_DIR"]
-    subject_id = os.environ["SUBJECTS_LIST"]
+    subjects_list = os.environ["SUBJECTS_LIST"]
 
-    test_files = []
+    test_subjects = []
 
     # Load the reference and test files
-    with open(os.path.join(subjects_dir, subject_id), 'r') as file:
+    with open(os.path.join(subjects_dir, subjects_list), 'r') as file:
         for line in file:
             filename = line.strip()
             logger.debug(filename)
             # test_file = os.path.join(subjects_dir, filename)
-            test_files.append(filename)
+            test_subjects.append(filename)
 
-    return test_files
+    return test_subjects
 
 
 def load_reference_file():

test/quick_test/test_errors_in_logfiles.py

@@ -34,7 +34,7 @@ def load_errors():
     return errors, whitelist
 
 
-def load_log_files(test_dir: str):
+def load_log_files(test_subject: str):
     """
     Retrieve the log files in the given log directory.
 
@@ -51,14 +51,14 @@ def load_log_files(test_dir: str):
 
     # Retrieve the log files in given log directory
 
-    log_directory = os.path.join(test_dir, "scripts")
+    log_directory = os.path.join(test_subject, "scripts")
     log_files = [file for file in Path(log_directory).iterdir() if file.suffix == '.log']
 
     return log_files
 
 
-@pytest.mark.parametrize("test_file", load_test_files())
-def test_errors(subjects_dir, test_file: str):
+@pytest.mark.parametrize("test_subject", load_test_subjects())
+def test_errors(subjects_dir, test_subject: str):
     """
     Test if there are any errors in the log files.
 
@@ -75,8 +75,8 @@ def test_errors(subjects_dir, test_file: str):
         If any of the keywords are in the log files.
     """
 
-    test_file = os.path.join(subjects_dir, test_file)
-    log_files = load_log_files(test_file)
+    test_subject = os.path.join(subjects_dir, test_subject)
+    log_files = load_log_files(test_subject)
 
     error_flag = False
 

test/quick_test/test_file_existence.py

@@ -56,8 +56,8 @@ def get_files_from_folder(folder_path: str):
     return filenames
 
 
-@pytest.mark.parametrize("test_file", load_test_files())
-def test_file_existence(subjects_dir, test_file: str,
+@pytest.mark.parametrize("test_subject", load_test_subjects())
+def test_file_existence(subjects_dir, test_subject: str,
                         reference_file: str):
     """
     Test the existence of files in the folder.
@@ -78,10 +78,10 @@ def test_file_existence(subjects_dir, test_file: str,
     """
 
     # Get reference files from the reference subject directory
-    reference_files = get_files_from_folder(test_file)
+    reference_files = get_files_from_folder(test_subject)
 
     # Get test list of files in the test subject directory
-    test_file = os.path.join(subjects_dir, test_file)
+    test_file = os.path.join(subjects_dir, test_subject)
     test_files = get_files_from_folder(reference_file)
 
     # Check if each file in the reference list exists in the test list

test/quick_test/test_images.py

@@ -121,8 +121,8 @@ def compute_mean_square_error(test_data: np.ndarray,
     return mse
 
 
-@pytest.mark.parametrize("test_file", load_test_files())
-def test_image_headers(subjects_dir, test_file, reference_file):
+@pytest.mark.parametrize("test_subject", load_test_subjects())
+def test_image_headers(subjects_dir, test_subject, reference_file):
     """
     Test image headers using nibabel.
 
@@ -142,7 +142,7 @@ def test_image_headers(subjects_dir, test_file, reference_file):
     """
 
     # Load images
-    test_file = os.path.join(subjects_dir, test_file)
+    test_file = os.path.join(subjects_dir, test_subject)
     test_image = load_image(test_file, "brain.mgz")
     reference_image = load_image(reference_file, "brain.mgz")
 
@@ -155,8 +155,8 @@ def test_image_headers(subjects_dir, test_file, reference_file):
     logger.debug("Image headers are correct")
 
 
-@pytest.mark.parametrize("test_file", load_test_files())
-def test_seg_data(subjects_dir, test_file: str,
+@pytest.mark.parametrize("test_subject", load_test_subjects())
+def test_seg_data(subjects_dir, test_subject: str,
                   reference_file: str):
     """
     Test the segmentation data by calculating and comparing dice scores.
@@ -178,7 +178,7 @@ def test_seg_data(subjects_dir, test_file: str,
 
     labels = load_labels()
 
-    test_file = os.path.join(subjects_dir, test_file)
+    test_file = os.path.join(subjects_dir, test_subject)
     test_image = load_image(test_file, "brain.mgz")
     reference_image = load_image(reference_file, "brain.mgz")
 
@@ -197,8 +197,8 @@ def test_seg_data(subjects_dir, test_file: str,
     logger.debug("Dice scores are within range for all classes")
 
 
-@pytest.mark.parametrize("test_file", load_test_files())
-def test_int_data(subjects_dir, test_file: str,
+@pytest.mark.parametrize("test_subject", load_test_subjects())
+def test_int_data(subjects_dir, test_subject: str,
                   reference_file: str):
     """
     Test the intensity data by calculating and comparing mean square errors.
@@ -218,7 +218,7 @@ def test_int_data(subjects_dir, test_file: str,
         If the mean square error is not 0
     """
 
-    test_file = os.path.join(subjects_dir, test_file)
+    test_file = os.path.join(subjects_dir, test_subject)
     test_image = load_image(test_file, "brain.mgz")
     reference_image = load_image(reference_file, "brain.mgz")
 

test/quick_test/test_stats.py

@@ -39,6 +39,18 @@ def thresholds():
     return default_threshold, thresholds
 
 
+def load_stats_file(test_subject: str):
+
+    files = os.listdir(os.path.join(test_subject, "stats"))
+
+    if "aseg.stats" in files:
+        return os.path.join(test_subject, "stats", "aseg.stats")
+    elif "aparc+DKT.stats" in files:
+        return os.path.join(test_subject, "stats", "aparc+DKT.stats")
+    else:
+        raise ValueError("Unknown stats file")
+
+
 # def load_structs():
 #     """
 #     Load the structs from the given file path.
@@ -103,8 +115,6 @@ def read_measure_stats(file_path: str):
     measure = []
     measurements = {}
 
-    file_path = os.path.join(file_path, "stats", "aseg.stats")
-
     # Retrieve lines starting with "# Measure" from the stats file
     with open(file_path, 'r') as file:
         # Read each line in the file
@@ -164,10 +174,10 @@ def read_table(file_path: str):
     return table
 
 
-@pytest.mark.parametrize("test_file", load_test_files())
+@pytest.mark.parametrize("test_subject", load_test_subjects())
 def test_measure_exists(
         subjects_dir: str,
-        test_file: str,
+        test_subject: str,
 ):
     """
     Test if the measure exists in the stats file.
@@ -185,7 +195,8 @@ def test_measure_exists(
         If the measure does not exist in the stats file.
     """
 
-    test_file = os.path.join(subjects_dir, test_file)
+    test_subject = os.path.join(subjects_dir, test_subject)
+    test_file = load_stats_file(test_subject)
     data = read_measure_stats(test_file)
     ref_data = read_measure_stats(test_file)
     errors = []
@@ -237,8 +248,8 @@ def test_measure_exists(
 #     if threshold := thresholds.get(struct):
 #         assert variation <= threshold, f"Variation of {struct} is greater than threshold."
 
-@pytest.mark.parametrize("test_file", load_test_files())
-def test_tables(subjects_dir, test_file, reference_file, thresholds):
+@pytest.mark.parametrize("test_subject", load_test_subjects())
+def test_tables(subjects_dir, test_subject, reference_file, thresholds):
     """
     Test if the table values are within the threshold.
 
@@ -261,7 +272,7 @@ def test_tables(subjects_dir, test_file, reference_file, thresholds):
 
     # Read the reference and test files
 
-    test_file = os.path.join(subjects_dir, test_file)
+    test_file = os.path.join(subjects_dir, test_subject)
     test_table = read_table(test_file)
     ref_table = read_table(reference_file)