add dcm2niix binaries

Author: bendhouseart

.github/workflows/test-included-binaries.yaml

@@ -0,0 +1,59 @@
+name: Test Included Binaries
+on:
+  push:
+    branches:
+      - main
+      - add-dcm2niix-binaries
+  pull_request:
+    branches:
+      - main
+      - add-dcm2niix-binaries
+  workflow_dispatch:
+    inputs:
+      debug_enabled:
+        type: boolean
+        description: 'Run with tmate debugging enabled'
+        required: false
+        default: false
+
+jobs:
+  test-included-binaries:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python: ['3.12']
+      fail-fast: false
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+          cache: 'pip'
+          cache-dependency-path: 'pypet2bids/pyproject.toml'
+
+      - name: Install UV
+        if: matrix.os != 'windows-latest'
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh && echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      - name: Install UV (Windows)
+        if: matrix.os == 'windows-latest'
+        run: |
+          powershell -c "irm https://astral.sh/uv/install.ps1 | iex"
+          echo "$env:USERPROFILE\.cargo\bin" >> $env:GITHUB_PATH
+
+      - name: Debug Session
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+        timeout-minutes: 15
+        with:
+          limit-access-to-actor: true
+
+      - name: Run Tests
+        run: |
+          cd pypet2bids
+          uv run pytest tests/test_included_binaries.py -v

.gitignore

@@ -67,3 +67,5 @@ ecat_testing/**/*.nii*
 
 matlab/SiemensHRRTparameters.txt
 
+dcm2niix
+dcm2niix.exe

pypet2bids/pypet2bids/dcm2niix4pet.py

@@ -20,6 +20,7 @@
 import subprocess
 import pandas as pd
 from os.path import join
+from os import chmod
 from os import listdir, walk, environ
 from pathlib import Path
 import json
@@ -29,6 +30,8 @@
 import shutil
 import argparse
 import importlib
+import zipfile
+import stat
 
 try:
     import helper_functions
@@ -172,6 +175,50 @@ def collect_date_time_from_file_name(file_name):
     return date, time
 
 
+def use_included_binary():
+    # get system platform
+    systems_system = system().lower()
+    module_folder = Path(__file__).parent.resolve()
+    binary_folder = module_folder / "dcm2niix_binaries"
+    dcm2niix_zip = "dcm2niix_{}.zip"
+    if "darwin" in systems_system:
+        zipped = binary_folder / dcm2niix_zip.format("mac")
+    elif "linux" in systems_system:
+        zipped = binary_folder / dcm2niix_zip.format("lnx")
+    elif "windows" in systems_system:
+        zipped = binary_folder / dcm2niix_zip.format("win")
+    else:
+        raise ValueError(
+            f"System must be Darwin, Linux, or Windows to use included binaries, got {system()}"
+        )
+
+    # Check if binary already exists
+    if systems_system == "windows":
+        dcm2niix_binary = binary_folder / "dcm2niix.exe"
+    else:
+        dcm2niix_binary = binary_folder / "dcm2niix"
+
+    # Only extract if binary doesn't exist
+    if not dcm2niix_binary.exists() and zipped.exists():
+        try:
+            with zipfile.ZipFile(zipped, "r") as ref:
+                ref.extractall(zipped.parent)
+        except zipfile.BadZipFile as e:
+            logger.error(
+                f"Unable to extract {zipped}, try manually setting DCM2NIIX_PATH in env or .pypet2bids_config"
+            )
+            raise e
+
+    # Check to make sure binary is there and set permissions
+    if dcm2niix_binary.exists():
+        if systems_system != "windows":
+            chmod(dcm2niix_binary, stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH)
+        helper_functions.modify_config_file("DCM2NIIX_PATH", dcm2niix_binary)
+        return dcm2niix_binary
+    else:
+        return None
+
+
 class Dcm2niix4PET:
     def __init__(
         self,
@@ -445,17 +492,21 @@ def check_posix():
             dcm2niix_path = helper_functions.check_pet2bids_config()
 
         if not dcm2niix_path:
-            pkged = "https://github.com/rordenlab/dcm2niix/releases"
-            instructions = "https://github.com/rordenlab/dcm2niix#install"
-            no_dcm2niix = f"""Unable to locate Dcm2niix on your system $PATH or using the path specified in 
-                        $HOME/.pypet2bidsconfig. Installation instructions for dcm2niix can be found here 
-                        {instructions} 
-                        and packaged versions can be found at 
-                        {pkged}
-                        Alternatively, you can set the path to dcm2niix in the config file at $HOME/.pet2bidsconfig
-                        using the command dcm2niix4pet --set-dcm2niix-path."""
-            logger.error(no_dcm2niix)
-            dcm2niix_path = None
+            # determine if osx or linux
+            dcm2niix_path = use_included_binary()
+
+            if not dcm2niix_path:
+                pkged = "https://github.com/rordenlab/dcm2niix/releases"
+                instructions = "https://github.com/rordenlab/dcm2niix#install"
+                no_dcm2niix = f"""Unable to locate Dcm2niix on your system $PATH or using the path specified in 
+                            $HOME/.pypet2bidsconfig. Installation instructions for dcm2niix can be found here 
+                            {instructions} 
+                            and packaged versions can be found at 
+                            {pkged}
+                            Alternatively, you can set the path to dcm2niix in the config file at $HOME/.pet2bidsconfig
+                            using the command dcm2niix4pet --set-dcm2niix-path."""
+                logger.error(no_dcm2niix)
+                dcm2niix_path = None
 
         return dcm2niix_path
 
@@ -465,8 +516,8 @@ def check_for_dcm2niix(self):
 
         :return: status code of the command dcm2niix -h
         """
-
-        if system().lower() != "windows":
+        operating_system = system().lower()
+        if operating_system != "windows":
             dcm2niix_path = self.check_posix()
             # fall back and check the config file if it's not on the path
             if not dcm2niix_path:

pypet2bids/pypet2bids/dcm2niix_binaries/dcm2niix_lnx.zip

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pypet2bids"
-version = "1.4.4"
+version = "1.4.5"
 description = "A python library for converting PET imaging and blood data to BIDS."
 authors = [
     {name = "anthony galassi", email = "[email protected]"}
@@ -78,6 +78,7 @@ packages = ["pypet2bids"]
 include = [
     "/pypet2bids",
     "/README.md",
+    "/pypet2bids/dcm2niix_binaries/*.zip"
 ]
 
 [tool.black]