add gif

.github/workflows/test.yml

@@ -45,12 +45,13 @@ jobs:
       with:
         python-version: ${{ matrix.python }}
     - run: pip install -U -e .[dev]
-    - run: pytest
+    - run: pytest -k "not gif"
     - uses: codecov/codecov-action@v1
   cuda:
     if: github.event_name != 'pull_request' || github.repository_owner != 'AMYPAD'
     name: CUDA py${{ matrix.python }}
     runs-on: [self-hosted, python, matlab, cuda]
+    timeout-minutes: 4320
     strategy:
       matrix:
         python: [3.9]
@@ -60,8 +61,14 @@ jobs:
         fetch-depth: 0
     - name: Run setup-python
       run: setup-python -p${{ matrix.python }} miutil scikit-build cmake ninja
+    - name: SimpleITK
+      run: pip install -U 'SimpleITK>=1.2.0,<2'
+      env:
+        CXX: g++-8
+        CC: gcc-8
     - name: Install
-      run: pip install -U --no-binary nimpa,nipet -e .[dev,niftypet]
+      run: |
+        pip install -U --no-binary nimpa,nipet -e .[dev,niftypet,gif]
     - run: pytest
     - uses: codecov/codecov-action@v1
     - name: Post Run setup-python

amypet/gif.py

@@ -0,0 +1,47 @@
+"""Parcellation
+
+Usage:
+  GIF [options] <fimin>
+
+Arguments:
+  <fimin>  : NIfTI image input file (T1w MR image) [default: FileChooser]
+
+Options:
+  --outpath DIR  : where to write outputs of GIF
+  --gif DIR  : GIF directory (containing `bin/` & `db/`)
+               (default: ${PATHTOOLS}/GIF_AMYPET) [default: DirChooser]
+"""
+import errno
+import subprocess
+from os import fspath, getenv
+from pathlib import Path
+
+from .utils import cpu_count
+
+
+def run(fimin, outpath=None, gif=None):
+    if not gif and getenv("PATHTOOLS"):
+        gif = Path(getenv("PATHTOOLS")) / "GIF_AMYPET"
+    gif = Path(gif)
+    if not all(i.is_dir() for i in [gif, gif / "bin", gif / "db"]):
+        raise FileNotFoundError("GIF required")
+
+    fimin = Path(fimin)
+    if not fimin.is_file() or "nii" not in fspath(fimin):
+        raise IOError(errno.ENOENT, "Nifty input file required", fimin)
+
+    if outpath is None:
+        opth = fimin.parent / "out"
+    else:
+        opth = Path(outpath)
+    opth.mkdir(mode=0o775, parents=True, exist_ok=True)
+    gifresults = subprocess.run([
+        fspath(gif / "bin" / "seg_GIF"), '-in', fimin, '-db',
+        fspath(gif / "db" / "db.xml"), '-v', "1", '-regNMI', '-segPT', "0.1", '-out',
+        fspath(opth), '-temper', "0.05", '-lncc_ker', "-4", '-omp',
+        str(cpu_count()), '-regBE', "0.001", '-regJL', "0.00005"], stdout=subprocess.PIPE,
+                                stderr=subprocess.PIPE)
+    (opth / "out.log").write_bytes(gifresults.stdout)
+    (opth / "err.log").write_bytes(gifresults.stderr)
+
+    return gifresults

amypet/gui.py

@@ -219,7 +219,7 @@ def get_main_parser(gui_mode=True, argparser=MyParser):
     import niftypad.api
     import niftypad.models
 
-    from amypet import centiloid, dcm2nii, imscroll, imtrimup
+    from amypet import centiloid, dcm2nii, gif, imscroll, imtrimup
 
     def fix_subparser(subparser, gui_mode=gui_mode):
         subparser.add_argument(
@@ -257,6 +257,8 @@ def argparser(prog, description=None, epilog=None, formatter_class=None):
     Func(imtrimup.run, imtrimup.__doc__, version=niftypad.__version__, python_deps=["nimpa"],
          argparser=argparser)
 
+    Func(gif.run, gif.__doc__, version=niftypad.__version__, python_deps=[], argparser=argparser)
+
     Func(centiloid.run, centiloid.__doc__, version=niftypad.__version__,
          python_deps=["miutil[nii]", "setuptools", "spm12", "tqdm"], argparser=argparser)
 

scripts/amypet_gif.py

@@ -0,0 +1,77 @@
+"""Usage:
+  amypet_gif [options] <path>
+
+Options:
+  -O, --overwrite-existing  : whether to run even if outputs already exist
+
+Arguments:
+  <path>  : directory. Layout: <path>/*/*/*MPRAGE*.nii*
+"""
+import logging
+import os
+import subprocess
+from pathlib import Path
+from textwrap import dedent
+
+from argopt import argopt
+from miutil import hasext, nsort
+from niftypet import nimpa
+
+from amypet import gif
+
+log = logging.getLogger(__name__)
+
+
+def filter_dir(path):
+    return filter(lambda i: i.is_dir(), path)
+
+
+def filter_nii(path):
+    return list(filter(lambda i: i.is_file() and hasext(i, ("nii", "nii.gz")), path))
+
+
+def main(argv=None):
+    args = argopt(__doc__).parse_args(args=argv)
+    gpth = Path(args.path)
+    assert gpth.is_dir()
+
+    for spth in filter_dir(gpth.iterdir()):
+        for tpth in spth.iterdir():
+            for fldr in filter_dir(tpth.glob("*MPRAGE*")):
+                fnii = filter_nii(tpth.glob("*MPRAGE*"))
+                if not len(fnii):
+                    # convert DICOMs to NIfTI
+                    subprocess.run([nimpa.resources.DCM2NIIX] + "-i y -v n -f %f_%s".split() +
+                                   ["-o", tpth, fldr])
+
+            fn4b = list((tpth / "N4bias").glob("*N4bias*.nii*"))
+            fgif = list((tpth / "GIF").glob("*Parcellation*.nii*"))
+
+            if len(fn4b) < 1:
+                fnii = filter_nii(tpth.glob("*MPRAGE*"))
+                log.info("N4bias input:%s", fnii)
+                biascorr = nimpa.bias_field_correction(fnii[0], executable="sitk", outpath=tpth)
+                try:
+                    fingif = biascorr["fim"]
+                except TypeError:
+                    raise ImportError(
+                        dedent("""\
+                            please install SimpleITK:
+                            `conda install -c simpleitk simpleitk` or
+                            `pip install SimpleITK`"""))
+            else:
+                if len(fn4b) > 1:
+                    log.warning("%d inputs found, selecting latest")
+                fingif = nsort(list(map(str, fn4b)))[-1]
+                log.debug("found N4-bias corrected:%s", fingif)
+                if fgif and not args.overwrite_existing:
+                    log.warning("skipping")
+                    continue
+
+            log.info("running GIF on:%s", fingif)
+            gif.run(fingif, outpath=os.path.join(tpth, "GIF"))
+
+
+if __name__ == "__main__":
+    logging.basicConfig(level=logging.INFO)
+    main()

setup.cfg

@@ -60,6 +60,9 @@ dev=
 gui=Gooey>=1.0.8
 web=streamlit>=0.85.2
 niftypet=niftypet>=0.0.1
+gif=
+    miutil>=0.9.0
+    SimpleITK>=1.2.0,<2
 [options.entry_points]
 console_scripts=
     amypet=amypet.cli:main

tests/test_gif.py

@@ -0,0 +1,29 @@
+from os import fspath
+
+import pytest
+
+
+def test_gif(fimin):
+    gif = pytest.importorskip("amypet.gif")
+    outpath = fimin.parent
+
+    if "N4bias" not in fspath(fimin):
+        nimpa = pytest.importorskip("niftypet.nimpa")
+        pytest.importorskip(
+            "SimpleITK",
+            reason="conda install -c simpleitk simpleitk or pip install SimpleITK",
+        )
+        biascorr = nimpa.bias_field_correction(fspath(fimin), executable="sitk",
+                                               outpath=fspath(outpath))
+        fin = biascorr["fim"][0]
+    else:
+        fin = fimin
+
+    print(fin)
+    gif.run(fin, outpath=outpath / "GIF")
+
+
+@pytest.mark.timeout(60 * 60 * 24)
+def test_amypet_gif(dimin, caplog):
+    amypet_gif = pytest.importorskip("scripts.amypet_gif")
+    amypet_gif.main(["-O", fspath(dimin)])