Merge branch 'main' into patch-1

Author: bendhouseart

.github/workflows/python.yaml

@@ -53,7 +53,7 @@ jobs:
         run: |
           cd pypet2bids
           python -m pip install --upgrade pip
-          pip install poetry
+          pip install poetry==1.6.1
           poetry install --with dev
 
       - name: Collect ECAT and other phantoms

.readthedocs.yaml

@@ -21,7 +21,7 @@ build:
     post_create_environment:
       - cp -r metadata pypet2bids/pypet2bids/
       # install poetry
-      - pip install poetry
+      - pip install poetry==1.6.1
       - poetry config virtualenvs.create false
       # just use poetry to export a requirements.txt as that worked much better than the previous attempts
       - cd pypet2bids && poetry lock && poetry export --without-hashes --with dev --format=requirements.txt > requirements.txt

Makefile

@@ -26,7 +26,6 @@ add:
 
 # copies metadata to path included in pypet2bids project to enable packaging of those files w/ poetry
 buildpackage:
-	@cp -R metadata/ pypet2bids/pypet2bids/metadata
 	@cp pypet2bids/pyproject.toml pypet2bids/pypet2bids/pyproject.toml
 	@rm -rf pypet2bids/dist
 	@cd pypet2bids && poetry lock && poetry build

contributors.md

@@ -12,6 +12,7 @@ Granville Matheson 📝 🐛 ✅
 Martin Norgaard 💻 💬 🤔 ⚠️ 👀  
 Cyril Pernet 💻 📖 💬 🎨 💡 📋 🤔 ⚠️  
 Chris Rorden 💻 🐛 📖  
+Maximilian Cosmo Sitter 💻
 Claus Svarer 💻 💡⚠️   
 Adam G Thomas  🔍 🤔  
 Robert Innis 💡⚠️💵   

matlab/ecat2nii.m

@@ -211,12 +211,16 @@
                 Sca      = Sca*MinImg/(-32768);
             end
 
-            % save scaling factor to file located at ecat_save_steps_dir/8.5_sca_matlab.txt
-            % fid = fopen([ecat_save_steps_dir filesep '8.5_sca_matlab.txt'],'w');
+            if (ecat_save_steps == '1')
+              save scaling factor to file located at ecat_save_steps_dir/8.5_sca_matlab.txt
+              fid = fopen([ecat_save_steps_dir filesep '8.5_sca_matlab.txt'],'w');
+              fclose(fid);
+            end
+            
             fprintf(fid,'Scaling factor: %10e\n',Sca);
             x = mh.ecat_calibration_factor * Sca;
-            fprintf(fid,'Scaling factor * ECAT Cal Factor: %10.10f\n',x);
-            % fclose(fid);
+            fprintf(fid,'Scaling factor * ECAT Cal Factor: %10.10f\n',x);   
+            
         end
 
         % save debugging step 8 - rescale to 16 bits

pypet2bids/poetry.lock

@@ -175,6 +175,7 @@ def __init__(
         file_format="%p_%i_%t_%s",
         silent=False,
         tempdir_location=None,
+        ezbids=False
     ):
         """
         This class is a simple wrapper for dcm2niix and contains methods to do the following in order:
@@ -215,6 +216,7 @@ def __init__(
         self.blood_json = None
         self.blood_tsv = None
         self.telemetry_data = {}
+        self.ezbids=ezbids
         self.dcm2niix_path = self.check_for_dcm2niix()
         if not self.dcm2niix_path:
             logger.error(
@@ -588,7 +590,8 @@ def run_dcm2niix(self):
                             created_path,
                             check_for_missing,
                             dicom_header,
-                            dicom2bids_json=metadata_dictionaries["dicom2bids.json"],
+                            dicom2bids_json=metadata_dictionaries["dicom2bids"],
+                            ezbids=self.ezbids,
                             **self.additional_arguments,
                         )
 
@@ -1162,6 +1165,13 @@ def cli():
         "This information helps to improve PET2BIDS and provides an indicator of real world "
         "usage crucial for obtaining funding.",
     )
+    parser.add_argument(
+        "--ezbids",
+        action="store_true",
+        default=False,
+        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."
+    )
     return parser
 
 
@@ -1328,6 +1338,7 @@ def main():
             additional_arguments=cli_args.kwargs,
             tempdir_location=cli_args.tempdir,
             silent=cli_args.silent,
+            ezbids=cli_args.ezbids,
         )
 
         if cli_args.trc:

pypet2bids/pypet2bids/dcm2niix4pet.py

@@ -244,7 +244,7 @@ def make_nifti(self, output_path=None):
         self.telemetry_data["NiftiFiles"] = 1
         self.telemetry_data["NiftiFilesSize"] = pathlib.Path(output).stat().st_size
 
-        if "nii.gz" not in output:
+        if "nii.gz" not in pathlib.Path(output).name:
             output = helper_functions.compress(output)
 
         return output

pypet2bids/pypet2bids/ecat.py

@@ -39,30 +39,26 @@
 import argparse
 from typing import Union
 from platform import system
+import importlib
+
+try:
+    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
 
-metadata_dir = os.path.join(project_dir, "metadata")
-
-# check to see where the schema is at
-pet_metadata_json = os.path.join(metadata_dir, "PET_metadata.json")
-permalink_pet_metadata_json = "https://github.com/openneuropet/PET2BIDS/blob/76d95cf65fa8a14f55a4405df3fdec705e2147cf/metadata/PET_metadata.json"
-pet_reconstruction_metadata_json = os.path.join(
-    metadata_dir, "PET_reconstruction_methods.json"
-)
 
 # load bids schema
-bids_schema_path = os.path.join(metadata_dir, "schema.json")
-schema = json.load(open(bids_schema_path, "r"))
-
+schema = metadata.schema
+pet_metadata = metadata.PET_metadata
 # putting these paths here as they are reused in dcm2niix4pet.py, update_json_pet_file.py, and ecat.py
 module_folder = Path(__file__).parent.resolve()
 python_folder = module_folder.parent
 pet2bids_folder = python_folder.parent
-metadata_folder = os.path.join(pet2bids_folder, "metadata")
 
 loggers = {}
 
@@ -91,19 +87,6 @@ def logger(name):
         return logger
 
 
-def load_pet_bids_requirements_json(
-    pet_bids_req_json: Union[str, pathlib.Path] = pet_metadata_json
-) -> dict:
-    if type(pet_bids_req_json) is str:
-        pet_bids_req_json = pathlib.Path(pet_bids_req_json)
-    if pet_bids_req_json.is_file():
-        with open(pet_bids_req_json, "r") as infile:
-            reqs = json.load(infile)
-        return reqs
-    else:
-        raise FileNotFoundError(pet_bids_req_json)
-
-
 def flatten_series(series):
     """
     This function retrieves either a list or a single value from a pandas series object thus converting a complex
@@ -146,12 +129,13 @@ def collect_spreadsheets(folder_path: pathlib.Path):
 
 def single_spreadsheet_reader(
     path_to_spreadsheet: Union[str, pathlib.Path],
-    pet2bids_metadata_json: Union[str, pathlib.Path] = pet_metadata_json,
+    pet2bids_metadata: dict = metadata.PET_metadata,
     dicom_metadata={},
     **kwargs,
 ) -> dict:
 
-    metadata = {}
+    spreadsheet_metadata = {}
+    metadata_fields = pet2bids_metadata
 
     if type(path_to_spreadsheet) is str:
         path_to_spreadsheet = pathlib.Path(path_to_spreadsheet)
@@ -161,24 +145,6 @@ def single_spreadsheet_reader(
     else:
         raise FileNotFoundError(f"{path_to_spreadsheet} does not exist.")
 
-    if pet2bids_metadata_json:
-        if type(pet_metadata_json) is str:
-            pet2bids_metadata_json = pathlib.Path(pet2bids_metadata_json)
-
-        if pet2bids_metadata_json.is_file():
-            with open(pet_metadata_json, "r") as infile:
-                metadata_fields = json.load(infile)
-        else:
-            raise FileNotFoundError(
-                f"Required metadata file not found at {pet_metadata_json}, check to see if this file exists;"
-                f"\nelse pass path to file formatted to this {permalink_pet_metadata_json} via "
-                f"pet2bids_metadata_json argument in simplest_spreadsheet_reader call."
-            )
-    else:
-        raise FileNotFoundError(
-            f"pet2bids_metadata_json input required for function call, you provided {pet2bids_metadata_json}"
-        )
-
     spreadsheet_dataframe = open_meta_data(path_to_spreadsheet)
 
     log = logging.getLogger("pypet2bids")
@@ -188,7 +154,7 @@ def single_spreadsheet_reader(
         for field in metadata_fields[field_level]:
             series = spreadsheet_dataframe.get(field, Series(dtype=numpy.float64))
             if not series.empty:
-                metadata[field] = flatten_series(series)
+                spreadsheet_metadata[field] = flatten_series(series)
             elif (
                 series.empty
                 and field_level == "mandatory"
@@ -200,10 +166,10 @@ def single_spreadsheet_reader(
                 )
 
     # lastly apply any kwargs to the metadata
-    metadata.update(**kwargs)
+    spreadsheet_metadata.update(**kwargs)
 
     # more lastly, check to see if values are of the correct datatype (e.g. string, number, boolean)
-    for field, value in metadata.items():
+    for field, value in spreadsheet_metadata.items():
         # check schema for field
         field_schema_properties = schema["objects"]["metadata"].get(field, None)
         if field_schema_properties:
@@ -216,7 +182,7 @@ def single_spreadsheet_reader(
                     try:
                         check_bool = int(value) / 1
                         if check_bool == 0 or check_bool == 1:
-                            metadata[field] = bool(value)
+                            spreadsheet_metadata[field] = bool(value)
                         else:
                             log.warning(
                                 f"{field} is not boolean, it's value is {value}"
@@ -228,7 +194,7 @@ def single_spreadsheet_reader(
                     log.warning(f"{field} is not string, it's value is {value}")
             else:
                 pass
-    return metadata
+    return spreadsheet_metadata
 
 
 def compress(file_like_object, output_path: str = None):
@@ -316,27 +282,37 @@ def load_vars_from_config(
 
 def get_version():
     """
-    Gets the version of this software from the toml file
-    :return: version number from pyproject.toml
+    Gets the version of this software
+    :return: version number
     """
     # this scripts directory path
     scripts_dir = pathlib.Path(os.path.dirname(__file__))
 
-    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")
-        with open(toml_path, "r") as infile:
-            tomlfile = toml.load(infile)
-    except FileNotFoundError:
-        # when in development the toml file with the version is 2 directories above (e.g. where it should actually live)
-        toml_dir = scripts_dir.parent
-        toml_path = os.path.join(toml_dir, "pyproject.toml")
-        with open(toml_path, "r") as infile:
-            tomlfile = toml.load(infile)
-
-    attrs = tomlfile.get("tool", {})
-    poetry = attrs.get("poetry", {})
-    version = poetry.get("version", "")
+    # first try using importlib.metadata.version to determine version
+
+    version = importlib.metadata.version("pypet2bids")
+
+    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")
+            with open(toml_path, "r") as infile:
+                tomlfile = toml.load(infile)
+        except FileNotFoundError:
+            # when in development the toml file with the version is 2 directories above (e.g. where it should actually live)
+            try:
+                toml_dir = scripts_dir.parent
+                toml_path = os.path.join(toml_dir, "pyproject.toml")
+                with open(toml_path, "r") as infile:
+                    tomlfile = toml.load(infile)
+            except FileNotFoundError:
+                pass
+
+        attrs = tomlfile.get("tool", {})
+        poetry = attrs.get("poetry", {})
+        version = poetry.get("version", "")
 
     return version
 
@@ -820,9 +796,7 @@ def get_recon_method(ReconstructionMethodString: str) -> dict:
         dimension = re.search(search_criteria, ReconMethodName)[0]
 
     # doing some more manipulation of the recon method name to expand it from not so helpful acronyms
-    possible_names = load_pet_bids_requirements_json(pet_reconstruction_metadata_json)[
-        "reconstruction_names"
-    ]
+    possible_names =  metadata.PET_reconstruction_methods.get("reconstruction_names", [])
 
     # we want to sort the possible names by longest first that we don't break up an acronym prematurely
     sorted_df = pandas.DataFrame(possible_names).sort_values(

pypet2bids/pypet2bids/helper_functions.py

@@ -15,28 +15,21 @@
     import helper_functions
     import ecat
     import dcm2niix4pet
+    import metadata
 except ModuleNotFoundError:
     import pypet2bids.helper_functions as helper_functions
     import pypet2bids.ecat as ecat
     import pypet2bids.dcm2niix4pet as dcm2niix4pet
+    import pypet2bids.metadata
 
 
 def spread_sheet_check_for_pet(sourcefile: Union[str, Path], **kwargs):
     # load data from spreadsheet
     data = helper_functions.open_meta_data(sourcefile)
 
-    # load BIDS PET requirements
     try:
-        with open(
-            helper_functions.pet_metadata_json, "r"
-        ) as pet_field_requirements_json:
-            pet_field_requirements = json.load(pet_field_requirements_json)
-    except (FileNotFoundError, json.JSONDecodeError) as error:
-        print(
-            f"Unable to load list of required, recommended, and optional PET BIDS fields from"
-            f" {helper_functions.pet_metadata_json}, will not be able to determine if sourcefile contains"
-            f" PET BIDS specific metadata"
-        )
+        pet_field_requirements = metadata.PET_metadata
+    except:
         pet_field_requirements = {}
 
     mandatory_fields = pet_field_requirements.get("mandatory", [])