fix missing repetition time (#218)

bidsmreye/bids_utils.py

@@ -4,8 +4,8 @@
 from pathlib import Path
 from typing import Any
 
-import nibabel as nib
 from bids import BIDSLayout  # type: ignore
+from bids.layout import BIDSFile
 
 from bidsmreye._version import __version__
 from bidsmreye.configuration import (
@@ -143,15 +143,16 @@ def create_sidecar(
 
 
 def save_sampling_frequency_to_json(
-    layout_out: BIDSLayout, img: str, source: str
+    layout_out: BIDSLayout, img: BIDSFile, source: str
 ) -> None:
-    func_img = nib.load(img)
-    header = func_img.header
-    sampling_frequency = header.get_zooms()[3]
-    if sampling_frequency <= 1:
-        log.warning(f"Found a repetition time of {sampling_frequency} seconds.")
+    metadata = img.get_metadata()
+    repetition_time = metadata["RepetitionTime"]
+    # TODO handle rare edge case where preprocessed data
+    # does not contain RepetitionTime metadata
+    if repetition_time <= 1:
+        log.warning(f"Found a repetition time of {repetition_time} seconds.")
     create_sidecar(
-        layout_out, img, SamplingFrequency=1 / float(sampling_frequency), source=source
+        layout_out, img.path, SamplingFrequency=1 / float(repetition_time), source=source
     )
 
 

bidsmreye/generalize.py

@@ -158,19 +158,18 @@ def process_subject(cfg: Config, layout_out: BIDSLayout, subject_label: str) ->
     this_filter = set_this_filter(cfg, subject_label, "no_label")
 
     bf = layout_out.get(
-        return_type="filename",
         regex_search=True,
         **this_filter,
     )
 
     check_if_file_found(bf, this_filter, layout_out)
 
     for file in bf:
-        log.info(f"Processing file: {Path(file).name}")
+        log.info(f"Processing file: {Path(file.path).name}")
 
         print("\n")
-        generators = data_generator.create_generators([file], [file])
-        generators = (*generators, [file], [file])
+        generators = data_generator.create_generators([file.path], [file.path])
+        generators = (*generators, [file.path], [file.path])
         print("\n")
 
         opts = model_opts.get_opts()
@@ -200,7 +199,7 @@ def process_subject(cfg: Config, layout_out: BIDSLayout, subject_label: str) ->
             percentile_cut=80,
         )
 
-        create_confounds_tsv(layout_out, file, subject_label)
+        create_confounds_tsv(layout_out, file.path, subject_label)
 
 
 def generalize(cfg: Config) -> None:

bidsmreye/prepare_data.py

@@ -8,6 +8,7 @@
 
 import numpy as np
 from bids import BIDSLayout  # type: ignore
+from bids.layout import BIDSFile
 from deepmreye import preprocess
 
 from bidsmreye.bids_utils import (
@@ -131,7 +132,6 @@ def process_subject(
     this_filter = set_this_filter(cfg, subject_label, "bold")
 
     bf = layout_in.get(
-        return_type="filename",
         regex_search=True,
         **this_filter,
     )
@@ -143,12 +143,14 @@ def process_subject(
 
 
 def prepapre_image(
-    cfg: Config, layout_in: BIDSLayout, layout_out: BIDSLayout, img: str
+    cfg: Config, layout_in: BIDSLayout, layout_out: BIDSLayout, img: BIDSFile
 ) -> None:
     """Preprocess a single functional image."""
-    report_name = create_bidsname(layout_out, filename=img, filetype="report")
-    mask_name = create_bidsname(layout_out, filename=img, filetype="mask")
-    output_file = create_bidsname(layout_out, Path(img), "no_label")
+    img_path = img.path
+
+    report_name = create_bidsname(layout_out, filename=img_path, filetype="report")
+    mask_name = create_bidsname(layout_out, filename=img_path, filetype="mask")
+    output_file = create_bidsname(layout_out, Path(img_path), "no_label")
 
     if (
         not cfg.force
@@ -159,21 +161,23 @@ def prepapre_image(
         log.debug(
             "Output for the following file already exists. "
             "Use the '--force' option to overwrite. "
-            f"\n '{Path(img).name}'"
+            f"\n '{Path(img_path).name}'"
         )
         return
 
-    log.info(f"Processing file: {Path(img).name}")
+    log.info(f"Processing file: {Path(img_path).name}")
 
-    coregister_and_extract_data(img, non_linear_coreg=cfg.non_linear_coreg)
+    coregister_and_extract_data(img_path, non_linear_coreg=cfg.non_linear_coreg)
 
-    deepmreye_mask_report = get_deepmreye_filename(layout_in, img=img, filetype="report")
+    deepmreye_mask_report = get_deepmreye_filename(
+        layout_in, img=img_path, filetype="report"
+    )
     move_file(deepmreye_mask_report, report_name)
 
-    deepmreye_mask_name = get_deepmreye_filename(layout_in, img=img, filetype="mask")
+    deepmreye_mask_name = get_deepmreye_filename(layout_in, img=img_path, filetype="mask")
     move_file(deepmreye_mask_name, mask_name)
 
-    source = str(Path(img).relative_to(layout_in.root))
+    source = str(Path(img_path).relative_to(layout_in.root))
     save_sampling_frequency_to_json(layout_out, img=img, source=source)
 
     combine_data_with_empty_labels(layout_out, mask_name)

bidsmreye/quality_control.py

@@ -218,15 +218,14 @@ def qc_subject(
     this_filter = set_this_filter(cfg, subject_label, "eyetrack")
 
     bf = layout_in.get(
-        return_type="filename",
         regex_search=True,
         **this_filter,
     )
 
     check_if_file_found(bf, this_filter, layout_in)
 
     for file in bf:
-        perform_quality_control(cfg, layout_in, file, layout_out)
+        perform_quality_control(cfg, layout_in, file.path, layout_out)
 
 
 def compute_robust_outliers(

bidsmreye/utils.py

@@ -7,6 +7,7 @@
 from typing import Any
 
 from bids import BIDSLayout  # type: ignore
+from bids.layout import BIDSFile
 from rich.progress import (
     BarColumn,
     MofNCompleteColumn,
@@ -63,11 +64,13 @@ def add_sidecar_in_root(layout_out: BIDSLayout) -> None:
     json.dump(content, open(sidecar_name, "w"), indent=4)
 
 
-def check_if_file_found(bf: Any, this_filter: dict[str, Any], layout: BIDSLayout) -> None:
-    if len(bf) == 0:
+def check_if_file_found(
+    bf: list[BIDSFile], this_filter: dict[str, Any], layout: BIDSLayout
+) -> None:
+    if not bf:
         log.warning(f"No file found for filter {this_filter}")
     else:
-        to_print = [str(Path(x).relative_to(layout.root)) for x in bf]
+        to_print = [str(Path(x.path).relative_to(layout.root)) for x in bf]
         log.debug(f"Found files\n{to_print}")
 
 

bidsmreye/visualize.py

@@ -54,7 +54,6 @@ def collect_group_qc_data(cfg: Config) -> pd.DataFrame | None:
     this_filter = set_this_filter(cfg, subjects, "eyetrack_qc")
 
     bf = layout.get(
-        return_type="filename",
         regex_search=True,
         **this_filter,
     )
@@ -63,17 +62,17 @@ def collect_group_qc_data(cfg: Config) -> pd.DataFrame | None:
 
     qc_data = None
     for i, file in enumerate(bf):
-        log.info(f"Processing file: {file}")
+        log.info(f"Processing file: {file.path}")
 
-        entities = layout.parse_file_entities(file)
+        entities = layout.parse_file_entities(file.path)
 
-        with open(file) as f:
+        with open(file.path) as f:
             data = json.loads(f.read())
 
         print(data)
 
         df = pd.json_normalize(data)
-        df["filename"] = Path(file).name
+        df["filename"] = Path(file.path).name
         df["subject"] = entities["subject"]
         qc_data = df if i == 0 else pd.concat([qc_data, df], sort=False)
 

pyproject.toml

@@ -156,6 +156,7 @@ module = [
 ignore_missing_imports = true
 module = [
     'attrs.*',
+    'bids.layout.*',
     "bidsmreye._version",
     'chevron.*',
     'deepmreye.*',

tests/test_bids_utils.py

@@ -82,13 +82,12 @@ def test_save_sampling_frequency_to_json(data_dir, pybids_test_dataset):
     this_filter = set_this_filter(cfg, "01", "bold")
 
     bf = layout_in.get(
-        return_type="filename",
         regex_search=True,
         **this_filter,
     )
     source = "foo"
     save_sampling_frequency_to_json(layout_in, bf[0], source)
-    sidecar_name = create_bidsname(layout_in, bf[0], "confounds_json")
+    sidecar_name = create_bidsname(layout_in, bf[0].path, "confounds_json")
     with open(sidecar_name) as f:
         content = json.load(f)
     assert content["Sources"][0] == "foo"