[Bug Fixes] Metadata Import Error and Better Handling of Missing Dicom Images (#349)

Fixed bugs and added better handling for missing dicoms.

* update how metadata import works
* raise error if missing images detected by dcm2niix
* bump version

Author: bendhouseart

pypet2bids/poetry.lock

@@ -176,6 +176,7 @@ def __init__(
         silent=False,
         tempdir_location=None,
         ezbids=False,
+        ignore_dcm2niix_errors=False,
     ):
         """
         This class is a simple wrapper for dcm2niix and contains methods to do the following in order:
@@ -223,7 +224,7 @@ def __init__(
                 "dcm2niix not found, this module depends on it for conversions, exiting."
             )
             sys.exit(1)
-
+        self.ignore_dcm2niix_errors = ignore_dcm2niix_errors
         # check for the version of dcm2niix
         minimum_version = "v1.0.20220720"
         version_string = subprocess.run([self.dcm2niix_path, "-v"], capture_output=True)
@@ -486,15 +487,23 @@ def run_dcm2niix(self):
             }
             self.telemetry_data.update(count_output_files(self.tempdir_location))
 
-            if convert.returncode != 0:
+            if (
+                convert.returncode != 0
+                or "error" in convert.stderr.decode("utf-8").lower()
+            ) and not self.ignore_dcm2niix_errors:
                 print(
                     "Check output .nii files, dcm2iix returned these errors during conversion:"
                 )
+                # raise error if missing images is found
+                if "missing images" in convert.stderr.decode("utf8").lower():
+                    error_message = convert.stderr.decode("utf8").replace("Error:", "")
+                    error_message = f"{error_message}for dicoms in {image_folder}"
+                    raise FileNotFoundError(error_message)
                 if (
                     bytes("Skipping existing file name", "utf-8") not in convert.stdout
                     or convert.stderr
                 ):
-                    print(convert.stderr)
+                    print(convert.stderr.decode("utf-8"))
                 elif (
                     convert.returncode != 0
                     and bytes("Error: Check sorted order", "utf-8") in convert.stdout
@@ -1174,6 +1183,13 @@ def cli():
         help="Add fields to json output that are useful for ezBIDS or other conversion software. This will de-anonymize"
         " pet2bids output and add AcquisitionDate an AcquisitionTime into the output json.",
     )
+    parser.add_argument(
+        "--ignore-dcm2niix-errors",
+        action="store_true",
+        default=False,
+        help="Accept any NifTi produced by dcm2niix even if it contains errors. This flag should only be used for "
+        "batch processing and only if you're performing robust QC after the fact.",
+    )
     return parser
 
 
@@ -1341,6 +1357,7 @@ def main():
             tempdir_location=cli_args.tempdir,
             silent=cli_args.silent,
             ezbids=cli_args.ezbids,
+            ignore_dcm2niix_errors=cli_args.ignore_dcm2niix_errors,
         )
 
         if cli_args.trc:

pypet2bids/pypet2bids/dcm2niix4pet.py

@@ -42,15 +42,14 @@
 import importlib
 
 try:
-    import metadata
+    from importlib import metadata
 except ImportError:
-    from pypet2bids import metadata
-
-parent_dir = pathlib.Path(__file__).parent.resolve()
-project_dir = parent_dir.parent.parent
-if "PET2BIDS" not in project_dir.parts:
-    project_dir = parent_dir
+    import importlib_metadata as metadata
 
+try:
+    import pet_metadata as metadata
+except ImportError:
+    import pypet2bids.pet_metadata as metadata
 
 # load bids schema
 schema = metadata.schema
@@ -287,14 +286,13 @@ def get_version():
     """
     # this scripts directory path
     scripts_dir = pathlib.Path(os.path.dirname(__file__))
-
-    # first try using importlib.metadata.version to determine version
-
-    version = importlib.metadata.version("pypet2bids")
+    try:
+        version = metadata.version("pypet2bids")
+    except Exception:
+        version = None
 
     if not version:
         tomlfile = {}
-
         try:
             # if this is bundled as a package look next to this file for the pyproject.toml
             toml_path = os.path.join(scripts_dir, "pyproject.toml")

pypet2bids/pypet2bids/helper_functions.py

@@ -15,20 +15,20 @@
     import helper_functions
     import ecat
     import dcm2niix4pet
-    import metadata
+    import pet_metadata
 except ModuleNotFoundError:
     import pypet2bids.helper_functions as helper_functions
     import pypet2bids.ecat as ecat
     import pypet2bids.dcm2niix4pet as dcm2niix4pet
-    import pypet2bids.metadata
+    import pypet2bids.pet_metadata as pet_metadata
 
 
 def spread_sheet_check_for_pet(sourcefile: Union[str, Path], **kwargs):
     # load data from spreadsheet
     data = helper_functions.open_meta_data(sourcefile)
 
     try:
-        pet_field_requirements = metadata.PET_metadata
+        pet_field_requirements = pet_metadata.PET_metadata
     except:
         pet_field_requirements = {}
 

pypet2bids/pypet2bids/is_pet.py

@@ -5,10 +5,10 @@
 
 try:
     import helper_functions
-    import metadata
+    import pet_metadata
 except ModuleNotFoundError:
     import pypet2bids.helper_functions as helper_functions
-    import pypet2bids.metadata as metadata
+    import pypet2bids.pet_metadata as pet_metadata
 
 
 parent_dir = pathlib.Path(__file__).parent.resolve()

pypet2bids/pypet2bids/metadata_spreadsheet_example_reader.py

@@ -9,10 +9,10 @@
 
 try:
     import pypet2bids.helper_functions as helper_functions
-    import pypet2bids.metadata as metadata
+    import pypet2bids.pet_metadata as pet_metadata
 except ModuleNotFoundError:
     import helper_functions
-    import metadata
+    import pet_metadata
 
 
 def read_multi_subject_spreadsheets(
@@ -43,7 +43,7 @@ def read_multi_subject_spreadsheets(
 
     """
 
-    required_fields = metadata.PET_metadata
+    required_fields = pet_metadata.PET_metadata
 
     if (
         general_metadata_spreadsheet.is_file()

pypet2bids/pypet2bids/multiple_spreadsheets.py

@@ -1,3 +1,6 @@
+import sys
+from types import SimpleNamespace
+
 blood_metadata = {
     "mandatory": [
         "PlasmaAvail",
@@ -10708,3 +10711,13 @@
         "whole_blood_radioactivity",
     ],
 }
+
+sys.modules[__name__] = SimpleNamespace(
+    blood_metadata=blood_metadata,
+    dicom2bids=dicom2bids,
+    PET_reconstruction_filters=PET_reconstruction_filters,
+    definitions=definitions,
+    PET_reconstruction_methods=PET_reconstruction_methods,
+    schema=schema,
+    PET_metadata=PET_metadata,
+)

pypet2bids/pypet2bids/metadata.py renamed to pypet2bids/pypet2bids/pet_metadata.py

@@ -7,10 +7,10 @@
 
 try:
     import helper_functions
-    import metadata
+    import pet_metadata as metadata
 except ModuleNotFoundError:
     import pypet2bids.helper_functions as helper_functions
-    import pypet2bids.metadata as metadata
+    import pypet2bids.pet_metadata as metadata
 
 # from pypet2bids.helper_functions import single_spreadsheet_reader, \
 #    collect_bids_part, open_meta_data, load_pet_bids_requirements_json, ParseKwargs

pypet2bids/pypet2bids/single_spreadsheet.py

@@ -14,11 +14,11 @@
 try:
     import helper_functions
     import is_pet
-    import metadata
+    import pet_metadata as metadata
 except ModuleNotFoundError:
     import pypet2bids.helper_functions as helper_functions
     import pypet2bids.is_pet as is_pet
-    import pypet2bids.metadata as metadata
+    import pypet2bids.pet_metadata as metadata
 
 # import logging
 logger = helper_functions.logger("pypet2bids")
@@ -51,7 +51,7 @@ def check_json(
     :type spreadsheet_metadata:
     :param path_to_json: path to a json file e.g. a BIDS sidecar file created after running dcm2niix
     :param items_to_check: a dictionary with items to check for within that json. If None is supplied defaults to the
-           PET_metadata imported from metadata.PET_metadata
+           PET_metadata imported from pet_metadata.PET_metadata
     :param silent: Raises warnings or errors to stdout if this flag is set to True
     :return: dictionary of items existence and value state, if key is True/False there exists/(does not exist) a
             corresponding entry in the json the same can be said of value
@@ -181,7 +181,7 @@ def update_json_with_dicom_value(
     # purely to clean up the generated read the docs page from sphinx, otherwise the entire json appears in the
     # read the docs page.
     if dicom2bids_json is None:
-        dicom2bids_json = metadata_dictionaries["dicom2bids.json"]
+        dicom2bids_json = metadata_dictionaries["dicom2bids"]
 
     # Units gets written as Unit in older versions of dcm2niix here we check for missing Units and present Unit entity
     units = missing_values.get("Units", None)

pypet2bids/pypet2bids/update_json_pet_file.py

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pypet2bids"
-version = "1.4.2"
+version = "1.4.3"
 description = "A python library for converting PET imaging and blood data to BIDS."
 authors = ["anthony galassi <[email protected]>"]
 license = "MIT"