New pipeline function for code usage | Updates on torch version

.github/workflows/macos_tests.yml

@@ -4,25 +4,25 @@ name: macos build
 on: [push, pull_request, workflow_dispatch]
 
 jobs:
-  build:
-    runs-on: ["macos-13"]
+    build:
+        runs-on: ["macos-latest"]
 
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-      - name: Install spare scores
-        run: |
-          python -m pip cache purge
-          pip install -r requirements.txt
-          pip install setuptools twine wheel
-          python -m pip install .
-      - name: Run unit tests
-        run: |
-          cd tests/ && pytest --cov=../ --cov-report=xml
-      - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v4.0.1
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          slug: CBICA/NiChart_DLMUSE
+        steps:
+            - uses: actions/checkout@v4
+            - uses: actions/setup-python@v5
+              with:
+                  python-version: "3.12"
+            - name: Install spare scores
+              run: |
+                  python -m pip cache purge
+                  pip install -r requirements.txt
+                  pip install setuptools twine wheel
+                  python -m pip install .
+            - name: Run unit tests
+              run: |
+                  cd tests/ && pytest --cov=../ --cov-report=xml
+            - name: Upload Coverage to Codecov
+              uses: codecov/codecov-action@v4.0.1
+              with:
+                  token: ${{ secrets.CODECOV_TOKEN }}
+                  slug: CBICA/NiChart_DLMUSE

NiChart_DLMUSE/SegmentImage.py

@@ -2,8 +2,6 @@
 import os
 import shutil
 from typing import Any
-import DLMUSE 
-import DLICV
 
 
 def run_dlicv(

NiChart_DLMUSE/__init__.py

@@ -1 +1 @@
-from .dlmuse_pipeline import run_pipeline, run_dlicv, run_dlmuse
+from .dlmuse_pipeline import run_dlicv, run_dlmuse, run_ndlmuse_pipeline

NiChart_DLMUSE/__main__.py

@@ -6,21 +6,11 @@
 """
 
 import argparse
-import os
-import shutil
-import threading
-
-from .dlmuse_pipeline import run_pipeline
-from .utils import (
-    collect_T1,
-    merge_bids_output_data,
-    merge_output_data,
-    remove_subfolders,
-    split_data,
-)
+
+from NiChart_DLMUSE.dlmuse_pipeline import run_ndlmuse_pipeline
 
 # VERSION = pkg_resources.require("NiChart_DLMUSE")[0].version
-VERSION = "1.0.7"
+VERSION = "1.0.9"
 
 
 def main() -> None:
@@ -74,8 +64,7 @@ def main() -> None:
 
     # DEVICE argument
     parser.add_argument(
-        "-d",
-        "--device",
+        "-device",
         type=str,
         help="Device (cpu, cuda, or mps)",
         default=None,
@@ -142,94 +131,25 @@ def main() -> None:
     device = args.device
     dlicv_extra_args = args.dlicv_args
     dlmuse_extra_args = args.dlmuse_args
+    clear_cache = args.clear_cache
+    bids = args.bids
+    cores = args.cores
 
     print()
     print("Arguments:")
     print(args)
     print()
 
-    if not os.path.isdir(out_dir):
-        print(f"Can't find {out_dir}, creating it...")
-        # os.system(f"mkdir {out_dir}")
-        os.mkdir(out_dir)
-
-    elif len(os.listdir(out_dir)) != 0:
-        print(f"Emptying output folder: {out_dir}...")
-        for root, dirs, files in os.walk(out_dir):
-            for f in files:
-                os.unlink(os.path.join(root, f))
-            for d in dirs:
-                shutil.rmtree(os.path.join(root, d))
-
-    if args.clear_cache:
-        os.system("DLICV -i ./dummy -o ./dummy --clear_cache")
-        os.system("DLMUSE -i ./dummy -o ./dummy --clear_cache")
-
-    working_dir = os.path.join(os.path.abspath(out_dir))
-
-    # Run pipeline
-    if args.bids is True:
-        if int(args.cores) > 1:
-            collect_T1(in_dir, out_dir)
-
-            no_threads = int(args.cores)
-            subfolders = split_data("raw_temp_T1", no_threads)
-            threads = []
-            for i in range(len(subfolders)):
-                curr_out_dir = out_dir + f"/split_{i}"
-                curr_thread = threading.Thread(
-                    target=run_pipeline,
-                    args=(
-                        subfolders[i],
-                        curr_out_dir,
-                        device,
-                        dlmuse_extra_args,
-                        dlicv_extra_args,
-                        i,
-                    ),
-                )
-                curr_thread.start()
-                threads.append(curr_thread)
-
-            for t in threads:
-                t.join()
-
-            merge_bids_output_data(working_dir)
-            remove_subfolders("raw_temp_T1")
-            remove_subfolders(out_dir)
-        else:  # No core parallelization
-            run_pipeline(in_dir, out_dir, device, dlmuse_extra_args, dlicv_extra_args)
-
-    else:  # Non-BIDS
-        if int(args.cores) > 1:
-            no_threads = int(args.cores)
-            subfolders = split_data(in_dir, no_threads)
-
-            threads = []
-            for i in range(len(subfolders)):
-                curr_out_dir = out_dir + f"/split_{i}"
-                curr_thread = threading.Thread(
-                    target=run_pipeline,
-                    args=(
-                        subfolders[i],
-                        curr_out_dir,
-                        device,
-                        dlmuse_extra_args,
-                        dlicv_extra_args,
-                        i,
-                    ),
-                )
-                curr_thread.start()
-                threads.append(curr_thread)
-
-            for t in threads:
-                t.join()
-
-            merge_output_data(out_dir)
-            remove_subfolders(in_dir)
-            remove_subfolders(out_dir)
-        else:  # No core parallelization
-            run_pipeline(in_dir, out_dir, device, dlmuse_extra_args, dlicv_extra_args)
+    run_ndlmuse_pipeline(
+        in_dir,
+        out_dir,
+        device,
+        dlicv_extra_args,
+        dlmuse_extra_args,
+        clear_cache,
+        bids,
+        cores,
+    )
 
 
 if __name__ == "__main__":

NiChart_DLMUSE/dlmuse_pipeline.py

@@ -1,14 +1,24 @@
 import logging
 import os
+import shutil
+import threading
+from typing import Any
 
 import pkg_resources  # type: ignore
 
-from .CalcROIVol import apply_create_roi_csv, combine_roi_csv
-from .MaskImage import apply_combine_masks, apply_mask_img
-from .RelabelROI import apply_relabel_rois
-from .ReorientImage import apply_reorient_img, apply_reorient_to_init
-from .SegmentImage import run_dlicv, run_dlmuse
-from .utils import make_img_list
+from NiChart_DLMUSE.CalcROIVol import apply_create_roi_csv, combine_roi_csv
+from NiChart_DLMUSE.MaskImage import apply_combine_masks, apply_mask_img
+from NiChart_DLMUSE.RelabelROI import apply_relabel_rois
+from NiChart_DLMUSE.ReorientImage import apply_reorient_img, apply_reorient_to_init
+from NiChart_DLMUSE.SegmentImage import run_dlicv, run_dlmuse
+from NiChart_DLMUSE.utils import (
+    collect_T1,
+    make_img_list,
+    merge_bids_output_data,
+    merge_output_data,
+    remove_subfolders,
+    split_data,
+)
 
 # Config vars
 SUFF_LPS = "_LPS.nii.gz"
@@ -35,17 +45,131 @@
 logging.basicConfig(filename="pipeline.log", encoding="utf-8", level=logging.DEBUG)
 
 
-def run_pipeline(
+def run_ndlmuse_pipeline(
+    in_dir: str,
+    out_dir: str,
+    device: str,
+    dlicv_extra_args: str,
+    dlmuse_extra_args: str,
+    clear_cache: bool,
+    bids: bool,
+    cores: str,
+) -> None:
+    """
+    NiChart pipeline
+
+    :param in_dir: The input directory
+    :type in_dir: str
+    :param out_dir: The output directory
+    :type out_dir: str
+    :type device: cpu/cuda/mps
+    :param device: str
+    :param dlicv_extra_args: Extra arguments for DLICV API
+    :type dlicv_extra_args: str
+    :param dlmuse_extra_args: Extra arguments for DLMUSE API
+    :type dlmuse_extra_args: str
+    :param clear_cache: True if cache should be cleared
+    :type clear_cache: bool
+    :param bids: True if your input is a bids type folder
+    :type bids: bool
+    :param cores: The number of cores(default is 4)
+    :type cores: str
+
+    :rtype: None
+    """
+    if not os.path.isdir(out_dir):
+        print(f"Can't find {out_dir}, creating it...")
+        # os.system(f"mkdir {out_dir}")
+        os.mkdir(out_dir)
+
+    elif len(os.listdir(out_dir)) != 0:
+        print(f"Emptying output folder: {out_dir}...")
+        for root, dirs, files in os.walk(out_dir):
+            for f in files:
+                os.unlink(os.path.join(root, f))
+            for d in dirs:
+                shutil.rmtree(os.path.join(root, d))
+    if clear_cache:
+        os.system("DLICV -i ./dummy -o ./dummy --clear_cache")
+        os.system("DLMUSE -i ./dummy -o ./dummy --clear_cache")
+
+    working_dir = os.path.join(os.path.abspath(out_dir))
+
+    if bids is True:
+        if int(cores) > 1:
+            collect_T1(in_dir, out_dir)
+
+            no_threads = int(cores)
+            subfolders = split_data("raw_temp_T1", no_threads)
+            threads = []
+            for i in range(len(subfolders)):
+                curr_out_dir = out_dir + f"/split_{i}"
+                curr_thread = threading.Thread(
+                    target=run_thread,
+                    args=(
+                        subfolders[i],
+                        curr_out_dir,
+                        device,
+                        dlmuse_extra_args,
+                        dlicv_extra_args,
+                        i,
+                    ),
+                )
+                curr_thread.start()
+                threads.append(curr_thread)
+
+            for t in threads:
+                t.join()
+
+            merge_bids_output_data(working_dir)
+            remove_subfolders("raw_temp_T1")
+            remove_subfolders(out_dir)
+        else:  # No core parallelization
+            run_thread(in_dir, out_dir, device, dlmuse_extra_args, dlicv_extra_args)
+
+    else:  # Non-BIDS
+        if int(cores) > 1:
+            no_threads = int(cores)
+            subfolders = split_data(in_dir, no_threads)
+
+            threads = []
+            for i in range(len(subfolders)):
+                curr_out_dir = out_dir + f"/split_{i}"
+                curr_thread = threading.Thread(
+                    target=run_thread,
+                    args=(
+                        subfolders[i],
+                        curr_out_dir,
+                        device,
+                        dlmuse_extra_args,
+                        dlicv_extra_args,
+                        i,
+                    ),
+                )
+                curr_thread.start()
+                threads.append(curr_thread)
+
+            for t in threads:
+                t.join()
+
+            merge_output_data(out_dir)
+            remove_subfolders(in_dir)
+            remove_subfolders(out_dir)
+        else:  # No core parallelization
+            run_thread(in_dir, out_dir, device, dlmuse_extra_args, dlicv_extra_args)
+
+
+def run_thread(
     in_data: str,
     out_dir: str,
     device: str,
-    dlmuse_extra_args: str = '',
-    dlicv_extra_args: str = '',
+    dlmuse_extra_args: str = "",
+    dlicv_extra_args: str = "",
     sub_fldr: int = 1,
-    progress_bar = None,
+    progress_bar: Any = None,
 ) -> None:
     """
-    NiChart pipeline
+    Run a thread of the pipeline
 
     :param in_data: the input directory
     :type in_data: str

NiChart_DLMUSE/utils.py

@@ -65,7 +65,9 @@ def remove_common_suffix(list_files: list) -> list:
 
     bnames = list_files
     if len(list_files) == 1:
-        if list_files[0].endswith('_T1'): # If there is a single image with suffix _T1, remove it
+        if list_files[0].endswith(
+            "_T1"
+        ):  # If there is a single image with suffix _T1, remove it
             bnames = [x[0:-3] for x in bnames]
         return bnames
 
@@ -347,7 +349,7 @@ def remove_subfolders(in_dir: str) -> None:
 
 def merge_output_data(in_dir: str) -> None:
     """
-    Takes all the results from the temp_working_fir and moves them into
+    Takes all the results from the temp_working_dir and moves them into
     the output folder
 
     :param in_dir: the input directory