Address bug with T2w-only processing (PennLINC#1060)

tsalo · Feb 26, 2024 · 1edc27f · 1edc27f
1 parent fcda9f9
commit 1edc27f
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Showing 3 changed files with 26 additions and 22 deletions.
diff --git a/xcp_d/tests/test_cli.py b/xcp_d/tests/test_cli.py
@@ -1,7 +1,7 @@
 """Command-line interface tests."""
 
 import os
-import shutil
+from glob import glob
 
 import numpy as np
 import pandas as pd
@@ -16,6 +16,7 @@
     check_generated_files,
     download_test_data,
     get_test_data_path,
+    list_files,
     run_command,
 )
 
@@ -282,28 +283,17 @@ def test_pnc_cifti_t2wonly(data_dir, output_dir, working_dir):
     out_dir = os.path.join(output_dir, test_name)
     work_dir = os.path.join(working_dir, test_name)
 
-    # Simulate a T2w image
+    # Rename all T1w-related files in anat folder to T2w.
+    # T1w-related files in func folder should not impact XCP-D.
     anat_dir = os.path.join(dataset_dir, "sub-1648798153/ses-PNC1/anat")
-    files_to_copy = [
-        "sub-1648798153_ses-PNC1_acq-refaced_desc-preproc_T1w.nii.gz",
-        "sub-1648798153_ses-PNC1_acq-refaced_desc-preproc_T1w.json",
-        (
-            "sub-1648798153_ses-PNC1_acq-refaced_space-MNI152NLin6Asym_res-2_desc-preproc_"
-            "T1w.nii.gz"
-        ),
-        (
-            "sub-1648798153_ses-PNC1_acq-refaced_space-MNI152NLin6Asym_res-2_desc-preproc_"
-            "T1w.json"
-        ),
-        "sub-1648798153_ses-PNC1_acq-refaced_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5",
-        "sub-1648798153_ses-PNC1_acq-refaced_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5",
-        "sub-1648798153_ses-PNC1_acq-refaced_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5",
-        "sub-1648798153_ses-PNC1_acq-refaced_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5",
-    ]
+    files_to_copy = sorted(glob(os.path.join(anat_dir, "*T1w*")))
     for file_to_copy in files_to_copy:
-        t2w_file = os.path.join(anat_dir, file_to_copy.replace("T1w", "T2w"))
+        t2w_file = file_to_copy.replace("T1w", "T2w")
         if not os.path.isfile(t2w_file):
-            shutil.copyfile(os.path.join(anat_dir, file_to_copy), t2w_file)
+            os.rename(os.path.join(anat_dir, file_to_copy), t2w_file)
+
+    tree = list_files(dataset_dir)
+    LOGGER.info(f"Tree after adding T2w:\n{tree}")
 
     test_data_dir = get_test_data_path()
     filter_file = os.path.join(test_data_dir, "pnc_cifti_t2wonly_filter.json")

diff --git a/xcp_d/tests/utils.py b/xcp_d/tests/utils.py
@@ -226,3 +226,17 @@ def reorder_expected_outputs():
 
         with open(expected_output_file, "w") as fo:
             fo.writelines(file_contents)
+
+
+def list_files(startpath):
+    """List files in a directory."""
+    tree = ""
+    for root, _, files in os.walk(startpath):
+        level = root.replace(startpath, "").count(os.sep)
+        indent = " " * 4 * (level)
+        tree += f"{indent}{os.path.basename(root)}/\n"
+        subindent = " " * 4 * (level + 1)
+        for f in files:
+            tree += f"{subindent}{f}\n"
+
+    return tree
diff --git a/xcp_d/utils/bids.py b/xcp_d/utils/bids.py
@@ -216,7 +216,7 @@ def collect_data(
         # "from" entity will be set later
         "template_to_anat_xfm": {
             "datatype": "anat",
-            "to": "T1w",
+            "to": ["T1w", "T2w"],
             "suffix": "xfm",
         },
         # native T1w-space brain mask
@@ -231,7 +231,7 @@ def collect_data(
         # "to" entity will be set later
         "anat_to_template_xfm": {
             "datatype": "anat",
-            "from": "T1w",
+            "from": ["T1w", "T2w"],
             "suffix": "xfm",
         },
     }