Merge pull request #68 from Remi-Gau/templates

[ENH] use bids metadata directly and adapt to new templates

bids/ext/reports/cli.py

@@ -127,5 +127,6 @@ def cli(args: Sequence[str] = None, namespace=None) -> None:
     if not common_patterns:
         LOGGER.warning("No common patterns found.")
     else:
+        output_dir.mkdir(parents=True, exist_ok=True)
         with open(output_dir / "report.txt", "w") as f:
             f.write(str(counter.most_common()[0][0]))

bids/ext/reports/parameters.py

@@ -88,15 +88,6 @@ def duration(all_imgs: list[Nifti1Image], metadata: dict[str, Any]) -> str:
     return f"{min_dur}-{max_dur}"
 
 
-def multiband_factor(metadata: dict[str, Any]) -> str:
-    """Generate description of the multi-band acceleration applied, if used."""
-    return (
-        f'MB factor={metadata["MultibandAccelerationFactor"]}'
-        if metadata.get("MultibandAccelerationFactor", 1) > 1
-        else ""
-    )
-
-
 def echo_time_ms(files: list[BIDSFile]) -> str:
     """Generate description of echo times from metadata field.
 
@@ -168,15 +159,6 @@ def echo_times_fmap(files: list[BIDSFile]) -> tuple[float, float]:
     return te1, te2
 
 
-def inplane_accel(metadata: dict[str, Any]) -> str:
-    """Generate description of in-plane acceleration factor, if any."""
-    return (
-        f'in-plane acceleration factor={metadata["ParallelReductionFactorInPlane"]}'
-        if metadata.get("ParallelReductionFactorInPlane", 1) > 1
-        else ""
-    )
-
-
 def bvals(bval_file: str | Path) -> str:
     """Generate description of dMRI b-values."""
     # Parse bval file
@@ -291,7 +273,7 @@ def variants(metadata: dict[str, Any], config: dict[str, dict[str, str]]) -> str
     variants = metadata.get("SequenceVariant", "")
     if isinstance(variants, str):
         variants = [
-            config["seqvar"].get(var, "UNKNOwN SEQUENCE VARIANT") for var in variants.split("_")
+            config["seqvar"].get(var, "UNKNOWN SEQUENCE VARIANT") for var in variants.split("_")
         ]
     return list_to_str(variants)
 
@@ -321,7 +303,7 @@ def sequence(metadata: dict[str, Any], config: dict[str, dict[str, str]]) -> str
     if seq_abbrs[0] and seqs_as_str:
         seqs_as_str += f" ({'/'.join(seq_abbrs)})"
     else:
-        seqs_as_str = "UNKNOwN SEQUENCE"
+        seqs_as_str = "UNKNOWN SEQUENCE"
 
     return seqs_as_str
 

bids/ext/reports/parsing.py

@@ -16,6 +16,21 @@
 LOGGER = pybids_reports_logger()
 
 
+def institution_info(files: list[BIDSFile]):
+    first_file = files[0]
+    metadata = first_file.get_metadata()
+    if metadata.get("InstitutionName"):
+        return templates.institution_info(metadata)
+    else:
+        return ""
+
+
+def mri_scanner_info(files: list[BIDSFile]):
+    first_file = files[0]
+    metadata = first_file.get_metadata()
+    return templates.mri_scanner_info(metadata)
+
+
 def common_mri_desc(
     img: None | nib.Nifti1Image,
     metadata: dict[str, Any],
@@ -34,9 +49,7 @@ def common_mri_desc(
 
     return {
         **metadata,
-        "field_strength": metadata.get("MagneticFieldStrength", "UNKNOWN"),
         "tr": tr,
-        "flip_angle": metadata.get("FlipAngle", "UNKNOWN"),
         "fov": parameters.field_of_view(img),
         "matrix_size": parameters.matrix_size(img),
         "voxel_size": parameters.voxel_size(img),
@@ -93,11 +106,8 @@ def func_info(files: list[BIDSFile], config: dict[str, dict[str, str]], layout:
 
     desc_data = {
         **common_mri_desc(img, metadata, config),
-        **device_info(metadata),
         "echo_time": parameters.echo_time_ms(files),
         "slice_order": parameters.slice_order(metadata),
-        "multiband_factor": parameters.multiband_factor(metadata),
-        "inplane_accel": parameters.inplane_accel(metadata),
         "nb_runs": parameters.nb_runs(all_runs),
         "task_name": metadata.get("TaskName", task_name),
         "multi_echo": parameters.multi_echo(files),
@@ -181,7 +191,6 @@ def dwi_info(files: list[BIDSFile], config: dict[str, dict[str, str]], layout: B
         "nb_runs": parameters.nb_runs(all_runs),
         "bvals": parameters.bvals(bval_file),
         "dmri_dir": dmri_dir,
-        "multiband_factor": parameters.multiband_factor(metadata),
     }
 
     return templates.dwi_info(desc_data)
@@ -213,17 +222,16 @@ def fmap_info(layout: BIDSLayout, files: list[BIDSFile], config: dict[str, dict[
     if img is None:
         files_not_found_warning(Path(first_file.path).relative_to(layout.root))
 
-    dir = "UNKNOWN PHASE ENCODING"
+    direction = "UNKNOWN PHASE ENCODING"
     if PhaseEncodingDirection := metadata.get("PhaseEncodingDirection"):
-        dir = config["dir"].get(PhaseEncodingDirection, "UNKNOWN PHASE ENCODING")
+        direction = config["dir"].get(PhaseEncodingDirection, "UNKNOWN PHASE ENCODING")
 
     desc_data = {
         **common_mri_desc(img, metadata, config),
         "te_1": parameters.echo_times_fmap(files)[0],
         "te_2": parameters.echo_times_fmap(files)[1],
         "slice_order": parameters.slice_order(metadata),
-        "dir": dir,
-        "multiband_factor": parameters.multiband_factor(metadata),
+        "dir": direction,
         "intended_for": parameters.intendedfor_targets(metadata, layout),
     }
 
@@ -250,17 +258,7 @@ def meg_info(files: list[BIDSFile]) -> str:
     first_file = files[0]
     metadata = first_file.get_metadata()
 
-    desc_data = {**device_info(metadata), **metadata}
-
-    return templates.meg_info(desc_data)
-
-
-def device_info(metadata: dict[str, Any]) -> dict[str, Any]:
-    """Extract device information from metadata."""
-    return {
-        "manufacturer": metadata.get("Manufacturer", "MANUFACTURER"),
-        "model_name": metadata.get("ManufacturersModelName", "MODEL"),
-    }
+    return templates.meg_info(metadata)
 
 
 def final_paragraph(metadata: dict[str, Any]) -> str:
@@ -306,11 +304,26 @@ def parse_files(
     # Group files into individual runs
     data_files = collect_associated_files(layout, data_files, extra_entities=["run"])
 
-    # print(data_files)
+    # Will only get institution from the first file.
+    # This assumes that ALL files from ALL datatypes
+    # were acquired in the same institution.
+    description_list = [institution_info(data_files[0])]
 
-    # description_list = [general_acquisition_info(data_files[0][0].get_metadata())]
-    description_list = []
+    # %% MRI
+    mri_datatypes = ["anat", "func", "fmap", "perf", "dwi"]
+    mri_scanner_info_done = False
     for group in data_files:
+
+        if group[0].entities["datatype"] not in mri_datatypes:
+            continue
+
+        # assume all MRI data was acquires on the same scanner
+        if not mri_scanner_info_done:
+            description_list.append(mri_scanner_info(group))
+            mri_scanner_info_done = True
+
+        group_description = ""
+
         if group[0].entities["datatype"] == "func":
             group_description = func_info(group, config, layout)
 
@@ -335,7 +348,17 @@ def parse_files(
         ] == "phasediff":
             group_description = fmap_info(layout, group, config)
 
-        elif group[0].entities["datatype"] in [
+        description_list.append(group_description)
+
+    # %% other
+    for group in data_files:
+
+        if group[0].entities["datatype"] in mri_datatypes:
+            continue
+
+        group_description = ""
+
+        if group[0].entities["datatype"] in [
             "eeg",
             "meg",
             "pet",
@@ -346,11 +369,9 @@ def parse_files(
             "microscopy",
         ]:
             LOGGER.warning(f" '{group[0].entities['datatype']}' not yet supported.")
-            group_description = ""
 
         else:
             LOGGER.warning(f" '{group[0].filename}' not yet supported.")
-            group_description = ""
 
         description_list.append(group_description)
 

bids/ext/reports/report.py

@@ -237,7 +237,7 @@ def _report_subject(self, subject: str, **kwargs: Any) -> str:
 
         # Assume all data were converted the same way and use the first nifti
         # file's json for conversion information.
-        description = "\n\t".join(description_list)
+        description = "\n".join(description_list)
         if metadata:
             description += f"\n\n{parsing.final_paragraph(metadata)}"
         return description

bids/ext/reports/templates.py

@@ -24,11 +24,13 @@ def render(template_name: str, data: dict[str, Any] | None = None) -> str:
         return tmp
 
 
-def highlight_missing_tags(foo: str) -> str:
+def highlight_missing_tags(foo: str, color="cyan") -> str:
     """Highlight missing tags in a rendered template."""
-    foo = f"[blue]{foo}[/blue]"
-    foo = foo.replace("{{", "[/blue][red]{{")
-    foo = foo.replace("}}", "}}[/red][blue]")
+    foo = f"[{color}]{foo}[/{color}]"
+    open_del = "{{"
+    foo = foo.replace("{{", f"[/{color}][red]{open_del}")
+    close_del = "}}"
+    foo = foo.replace("}}", f"{close_del}[/red][{color}]")
     return foo
 
 
@@ -40,6 +42,16 @@ def footer() -> str:
     return f"This section was (in part) generated automatically using pybids {__version__}."
 
 
+def mri_scanner_info(desc_data: dict[str, Any]) -> str:
+    """Generate mri scanner info report."""
+    return render(template_name="mri_scanner_info.mustache", data=desc_data)
+
+
+def institution_info(desc_data: dict[str, Any]) -> str:
+    """Generate institution report."""
+    return render(template_name="institution.mustache", data=desc_data)
+
+
 def anat_info(desc_data: dict[str, Any]) -> str:
     """Generate anatomical report."""
     return render(template_name="anat.mustache", data=desc_data)

bids/ext/reports/tests/test_parameters.py

@@ -16,7 +16,7 @@
         ("RM", "research mode (RM)"),
         ("SE", "spin echo (SE)"),
         ("SE_EP", "spin echo and echo planar (SE/EP)"),
-        ("spam egg", "UNKNOwN SEQUENCE"),
+        ("spam egg", "UNKNOWN SEQUENCE"),
     ],
 )
 def test_sequence(ScanningSequence, expected_seq, testconfig):
@@ -39,7 +39,7 @@ def test_sequence(ScanningSequence, expected_seq, testconfig):
         ("SS", "steady state"),
         ("TRSS", "time reversed steady state"),
         ("MP_SS", "MAG prepared and steady state"),
-        ("spam", "UNKNOwN SEQUENCE VARIANT"),
+        ("spam", "UNKNOWN SEQUENCE VARIANT"),
     ],
 )
 def test_variants(SequenceVariant, expected_var, testconfig):
@@ -94,34 +94,6 @@ def test_describe_func_duration_smoke():
     assert duration == expected
 
 
-def test_multiband_factor_smoke(testmeta, testmeta_light):
-    # when
-    multiband_factor = parameters.multiband_factor(testmeta)
-    # then
-    expected = "MB factor=2"
-    assert multiband_factor == expected
-
-    # when
-    multiband_factor = parameters.multiband_factor(testmeta_light)
-    # then
-    expected = ""
-    assert multiband_factor == expected
-
-
-def test_inplane_accel_smoke(testmeta, testmeta_light):
-    # when
-    multiband_factor = parameters.inplane_accel(testmeta)
-    # then
-    expected = "in-plane acceleration factor=2"
-    assert multiband_factor == expected
-
-    # when
-    multiband_factor = parameters.inplane_accel(testmeta_light)
-    # then
-    expected = ""
-    assert multiband_factor == expected
-
-
 @pytest.mark.parametrize(
     "slice_times, expected",
     [

bids/ext/reports/tests/test_parsing.py

@@ -10,6 +10,16 @@
 from bids.ext.reports import parsing
 
 
+def test_institution_info(testlayout):
+    files = testlayout.get(
+        subject="01",
+        session="01",
+        extension=[".nii.gz"],
+    )
+    desc = parsing.institution_info(files)
+    assert desc == ""
+
+
 def test_anat_info_smoke(testlayout, testconfig):
     """Smoke test for parsing.anat_info.
 

bids/ext/reports/tests/test_templates.py

@@ -5,12 +5,11 @@
 import json
 from pathlib import Path
 
-from bids.ext.reports import parsing, templates
+from bids.ext.reports import templates
 
 
 def test_pet():
     with open(Path(__file__).parent / "data" / "sub-01_ses-01_pet.json") as f:
         metadata = json.load(f)
 
-    desc_data = {**parsing.device_info(metadata), **metadata}
-    templates.pet_info(desc_data)
+    templates.pet_info(metadata)

docs/source/conf.py

@@ -17,9 +17,9 @@
 sys.path.insert(0, os.path.abspath(os.path.pardir))
 sys.path.insert(0, os.path.abspath("sphinxext"))
 
-from github_link import make_linkcode_resolve
+from github_link import make_linkcode_resolve  # noqa
 
-import bids.ext.reports
+import bids.ext.reports  # noqa
 
 __version__ = bids.ext.reports.__version__