Merge branch 'main' of github.com:openneuropet/PET2BIDS into development

Author: bendhouseart

.blackignore

@@ -0,0 +1,111 @@
+# Virtual environments
+.venv/
+venv/
+env/
+ENV/
+env.bak/
+venv.bak/
+
+# Python cache
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+.pytest_cache/
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Project specific
+__MACOSX/
+*.zip
+*.mat
+*.v
+*.v.gz
+*.avi
+*.jpg
+*.bytes 

Makefile

@@ -87,6 +87,4 @@ pythongithubworkflow: installdependencies collectphantoms decompressphantoms tes
 	@echo finished running python tests
 
 black:
-	@for file in `find pypet2bids/ -name "*.py"`; do \
-		black $$file; \
-	done
+	@black pypet2bids/

pypet2bids/pypet2bids/dcm2niix4pet.py

@@ -172,6 +172,7 @@ def __init__(
         metadata_path=None,
         metadata_translation_script=None,
         additional_arguments={},
+        dcm2niix_options="",
         file_format="%p_%i_%t_%s",
         silent=False,
         tempdir_location=None,
@@ -364,6 +365,42 @@ def __init__(
                 load_spreadsheet_data["blood_json"]
             )
 
+            # we default to these options, a user may supply their own combination, this will allow full customization of all
+        # but the file arguments for dcm2niix
+        if dcm2niix_options:
+            # Filter out -f flag and its value from custom options since file format is handled separately
+            options_list = dcm2niix_options.split()
+            filtered_options = []
+            i = 0
+            while i < len(options_list):
+                if options_list[i] == "-f" and i + 1 < len(options_list):
+                    # Skip -f and its value
+                    i += 2
+                else:
+                    filtered_options.append(options_list[i])
+                    i += 1
+            self.dcm2niix_options = " ".join(filtered_options)
+        else:
+            # Check for dcm2niix options in config file and environment variable
+            config_options = helper_functions.check_pet2bids_config(
+                "PET2BIDS_DCM2NIIX_OPTIONS"
+            )
+            env_options = environ.get("PET2BIDS_DCM2NIIX_OPTIONS")
+
+            # Priority: command line > environment variable > config file > default
+            if env_options:
+                self.dcm2niix_options = env_options
+                logger.info(
+                    f"Using dcm2niix options from environment variable: {env_options}"
+                )
+            elif config_options:
+                self.dcm2niix_options = config_options
+                logger.info(
+                    f"Using dcm2niix options from config file: {config_options}"
+                )
+            else:
+                self.dcm2niix_options = "-b y -w 1 -z y"
+                logger.debug("Using default dcm2niix options: -b y -w 1 -z y")
         self.file_format = file_format
         # we may want to include additional information to the sidecar, tsv, or json files generated after conversion
         # this variable stores the mapping between output files and a single dicom header used to generate those files
@@ -480,7 +517,7 @@ def run_dcm2niix(self):
             self.tempdir_location = tempdir_pathlike
             # people use screwy paths, we do this before running dcm2niix to account for that
             image_folder = helper_functions.sanitize_bad_path(self.image_folder)
-            cmd = f"{self.dcm2niix_path} -b y -w 1 -z y {file_format_args} -o {tempdir_pathlike} {image_folder}"
+            cmd = f"{self.dcm2niix_path} {self.dcm2niix_options} {file_format_args} -o {tempdir_pathlike} {image_folder}"
             convert = subprocess.run(cmd, shell=True, capture_output=True)
             self.telemetry_data["dcm2niix"] = {
                 "returncode": convert.returncode,
@@ -674,10 +711,19 @@ def run_dcm2niix(self):
                             if re.search(
                                 r"\d+.\d+", sidecar_json.get("ConvolutionKernel")
                             ):
-                                recon_filter_size = re.search(
-                                    r"\d+.\d*", sidecar_json.get("ConvolutionKernel")
-                                )[0]
-                                recon_filter_size = float(recon_filter_size)
+                                try:
+                                    recon_filter_size = re.search(
+                                        r"\d+.\d*",
+                                        sidecar_json.get("ConvolutionKernel"),
+                                    )[0]
+                                    recon_filter_size = float(recon_filter_size)
+                                except ValueError:
+                                    # If float conversion fails, try splitting and take first part
+                                    match_str = re.search(
+                                        r"\d+.\d*",
+                                        sidecar_json.get("ConvolutionKernel"),
+                                    )[0]
+                                    recon_filter_size = float(match_str.split()[0])
                                 sidecar_json.update(
                                     {"ReconFilterSize": float(recon_filter_size)}
                                 )
@@ -1037,9 +1083,13 @@ def load_spread_sheet_data(self):
     
     example usage:
     
-    dcm2niix4pet folder_with_pet_dicoms/ --destinationp-path sub-ValidBidSSubject/pet # the simplest conversion
+    dcm2niix4pet folder_with_pet_dicoms/ --destination-path sub-ValidBidSSubject/pet # the simplest conversion
     dcm2niix4pet folder_with_pet_dicoms/ --destination-path sub-ValidBidsSubject/pet --metadata-path metadata.xlsx \
     # use with an input spreadsheet
+    dcm2niix4pet folder_with_pet_dicoms/ --destination-path sub-ValidBidsSubject/pet --dcm2niix-options -v y -w 1 -z y \
+    # use with custom dcm2niix options
+    dcm2niix4pet --set-dcm2niix-options '-v y -w 1 -z y' \
+    # set default dcm2niix options in config file
     
 """
 )
@@ -1135,6 +1185,13 @@ def cli():
         f"DCM2NIIX_PATH",
         type=pathlib.Path,
     )
+    parser.add_argument(
+        "--set-dcm2niix-options",
+        help="Provide dcm2niix options to be used as defaults, writes to config "
+        f"file {Path.home()}/.pet2bidsconfig under the variable "
+        f"PET2BIDS_DCM2NIIX_OPTIONS. Example: --set-dcm2niix-options '-v y -w 1 -z y'",
+        type=str,
+    )
     parser.add_argument(
         "--set-default-metadata-json",
         help="Provide a path to a default metadata file json file."
@@ -1190,6 +1247,15 @@ def cli():
         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.",
     )
+    parser.add_argument(
+        "--dcm2niix-options",
+        nargs="*",
+        default=[],
+        help="Additional dcm2niix options to pass through. Use the same format as dcm2niix command line. "
+        "Note: -f flag and its value will be filtered out as file format is handled separately. "
+        "You can also set default options using --set-dcm2niix-options or the PET2BIDS_DCM2NIIX_OPTIONS environment variable. "
+        "Example: --dcm2niix-options -v y -w 1 -z y",
+    )
     return parser
 
 
@@ -1336,6 +1402,12 @@ def main():
         helper_functions.modify_config_file("DCM2NIIX_PATH", cli_args.set_dcm2niix_path)
         sys.exit(0)
 
+    if cli_args.set_dcm2niix_options:
+        helper_functions.modify_config_file(
+            "PET2BIDS_DCM2NIIX_OPTIONS", cli_args.set_dcm2niix_options
+        )
+        sys.exit(0)
+
     if cli_args.set_default_metadata_json:
         helper_functions.modify_config_file(
             "DEFAULT_METADATA_JSON", cli_args.set_default_metadata_json
@@ -1354,6 +1426,9 @@ def main():
                 cli_args.translation_script_path
             ),
             additional_arguments=cli_args.kwargs,
+            dcm2niix_options=(
+                " ".join(cli_args.dcm2niix_options) if cli_args.dcm2niix_options else ""
+            ),
             tempdir_location=cli_args.tempdir,
             silent=cli_args.silent,
             ezbids=cli_args.ezbids,

pypet2bids/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "pypet2bids"
 version = "1.4.3"
-version = "1.4.3"
+version = "1.4.4"
 description = "A python library for converting PET imaging and blood data to BIDS."
 authors = [
     {name = "anthony galassi", email = "[email protected]"}
@@ -53,6 +53,7 @@ dev = [
     "pyinstaller>=5.4.1",
     "build>=0.10.0",
     "briefcase>=0.3.23; python_version>='3.9'",
+    "black>=23.0.0",
 ]
 
 [project.scripts]
@@ -79,3 +80,21 @@ include = [
     "/pypet2bids",
     "/README.md",
 ]
+
+[tool.black]
+line-length = 88
+target-version = ['py38']
+include = '\.pyi?$'
+extend-exclude = '''
+/(
+  # directories
+  \.eggs
+  | \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | build
+  | dist
+)/
+'''