Merge pull request #11 from AMYPAD/imtrimup

Author: casperdcl

.github/workflows/test.yml

@@ -47,8 +47,28 @@ jobs:
     - run: pip install -U -e .[dev]
     - run: pytest
     - uses: codecov/codecov-action@v1
+  cuda:
+    if: github.event_name != 'pull_request' || github.repository_owner != 'AMYPAD'
+    name: CUDA py${{ matrix.python }}
+    runs-on: [self-hosted, python, matlab, cuda]
+    strategy:
+      matrix:
+        python: [3.9]
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - name: Run setup-python
+      run: setup-python -p${{ matrix.python }} miutil scikit-build cmake ninja
+    - name: Install
+      run: pip install -U --no-binary nimpa,nipet -e .[dev,niftypet]
+    - run: pytest
+    - uses: codecov/codecov-action@v1
+    - name: Post Run setup-python
+      run: setup-python -p${{ matrix.python }} -Dr
+      if: ${{ always() }}
   deploy:
-    needs: [check, test]
+    needs: [check, test, cuda]
     name: PyPI Deploy
     runs-on: ubuntu-latest
     steps:

amypad/gui.py

@@ -249,7 +249,7 @@ def main(args=None, gui_mode=True):
     import niftypad.api
     import niftypad.models
 
-    from amypad import centiloid, imscroll
+    from amypad import centiloid, imscroll, imtrimup
 
     parser = fix_subparser(MyParser(prog=None if gui_mode else "amypad"), gui_mode=gui_mode)
     sub_kwargs = {}
@@ -273,6 +273,9 @@ def argparser(prog, description=None, epilog=None, formatter_class=None):
     Func(imscroll.run, imscroll.__doc__, version=niftypad.__version__,
          python_deps=["miutil[nii,plot]", "tqdm"], argparser=argparser)
 
+    Func(imtrimup.run, imtrimup.__doc__, version=niftypad.__version__, python_deps=["nimpa"],
+         argparser=argparser)
+
     Func(centiloid.run, centiloid.__doc__, version=niftypad.__version__,
          python_deps=["miutil[nii]", "setuptools", "spm12", "tqdm"], argparser=argparser)
 

amypad/imtrimup.py

@@ -0,0 +1,48 @@
+"""Trimming and upscaling
+
+Usage:
+  imtrimup [options] <dyndir>
+
+Arguments:
+  <dyndir>  : Input folder containing dynamic scans [default: DirChooser]
+
+Options:
+  --glob PATTERN  : File matching pattern [default: *.nii*]
+  --scale FACTOR  : Sampling scale factor [default: 2:int]
+  --refim PATH  : Reference image [default: FileChooser]
+  --fcomment COMMENT  : Prefix to add to outputs
+  --no-memlim  : Whether to use more memory (faster)
+  --store-img-intrmd  : Whether to write output image files
+  --store-img  : Whether to write output image sum file
+"""
+import logging
+from pathlib import Path
+
+from niftypet import nimpa
+
+log = logging.getLogger(__name__)
+
+
+def run(
+    dyndir,
+    glob="*.nii*",
+    scale=2,
+    refim="",
+    fcomment="",
+    no_memlim=False,
+    store_img_intrmd=False,
+    store_img=False,
+):
+    dyndir = Path(dyndir)
+    assert dyndir.is_dir()
+    # get the file data
+    fdyns = list(map(str, dyndir.glob(glob)))
+    log.info("found %d files", len(fdyns))
+    log.info("sort the dynamic images and output the sorted file names and numpy array")
+    imdyn = nimpa.niisort(fdyns)
+    log.info("trim & upscale")
+    res = nimpa.imtrimup(imdyn["files"], scale=scale, memlim=not no_memlim, refim=refim or "",
+                         fcomment=fcomment or "", store_img_intrmd=store_img_intrmd,
+                         store_img=store_img)
+    log.debug("trimmed and scaled images, shape %r", res['im'].shape)
+    return res

amypad/utils.py

@@ -0,0 +1,9 @@
+try:
+    from os import cpu_count
+except ImportError:
+    try:
+        from multiprocessing import cpu_count
+    except ImportError:
+
+        def cpu_count():
+            return 4

scripts/__init__.py

@@ -38,11 +38,12 @@ classifiers=
     Topic :: Utilities
 [options]
 zip_safe=False
-setup_requires=setuptools>=42; setuptools_scm[toml]>=3.4
+setup_requires=setuptools>=42; wheel; setuptools_scm[toml]>=3.4
 install_requires=
     argopt
     miutil[cuda,nii]>=0.8.0
     niftypad>=1.1.1
+    nimpa
     setuptools
     shtab>1.3.2
     spm12
@@ -93,3 +94,5 @@ timeout=10
 log_level=INFO
 python_files=tests/test_*.py
 addopts=-v --tb=short -rxs -W=error -n=auto --durations=0 --durations-min=1 --cov=amypad --cov-report=term-missing --cov-report=xml
+filterwarnings=
+    ignore:numpy.ufunc size changed.*:RuntimeWarning

setup.cfg

@@ -1,5 +1,11 @@
+import logging
+from os import getenv
+from pathlib import Path
+
 import pytest
 
+HOME = Path(getenv("DATA_ROOT", "~")).expanduser()
+
 
 @pytest.fixture(scope="session")
 def nvml():
@@ -10,3 +16,42 @@ def nvml():
     except pynvml.NVMLError as exc:
         pytest.skip(str(exc))
     return pynvml
+
+
+@pytest.fixture(scope="session")
+def mMRpars():
+    nipet = pytest.importorskip("niftypet.nipet")
+    params = nipet.get_mmrparams()
+    # params["Cnt"]["VERBOSE"] = True
+    params["Cnt"]["LOG"] = logging.INFO
+    return params
+
+
+@pytest.fixture(scope="session")
+def datain(mMRpars):
+    nipet = pytest.importorskip("niftypet.nipet")
+    folder_in = HOME / "Ab_PET_mMR_test"
+    if not folder_in.is_dir():
+        pytest.skip(f"""Cannot find Ab_PET_mMR_test in
+${{DATA_ROOT:-~}} ({HOME}).
+""")
+    return nipet.classify_input(folder_in, mMRpars)
+
+
+@pytest.fixture(scope="session")
+def dimin():
+    trt = HOME / "DPUK" / "TRT"
+    if not trt.is_dir():
+        pytest.skip(f"""Cannot find DPUK/TRT in
+${{DATA_ROOT:-~}} ({HOME}).
+""")
+    return trt
+
+
+@pytest.fixture(scope="session")
+def fimin(dimin):
+    mprage = (dimin / "NEW002_ODE_S02442" / "TP0" /
+              "NEW002_PETMR_V1_00015_MR_images_MPRAGE_q-_MPRAGE_20200212145346_15.nii")
+    if not mprage.is_file():
+        pytest.skip("fimin not found")
+    return mprage

tests/conftest.py

@@ -0,0 +1,61 @@
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture
+def dyndir(datain, mMRpars):
+    # definition of dynamic frames for kinetic analysis
+    frmdef = ["def", [4, 15], [8, 30], [9, 60], [2, 180], [8, 300]]
+    # output path
+    opth = str(Path(datain["corepath"]).parent / "amypad" / "dyndir")
+
+    res = Path(opth) / "PET" / "multiple-frames"
+    if res.is_dir():
+        return res
+
+    nipet = pytest.importorskip("niftypet.nipet")
+    hst = nipet.mmrhist(datain, mMRpars)
+    # offset for the time from which meaningful events are detected
+    toff = nipet.lm.get_time_offset(hst)
+    # dynamic frame timings
+    frm_timings = nipet.lm.dynamic_timings(frmdef, offset=toff)
+    nipet.lm.draw_frames(hst, frm_timings["timings"])
+    # hardware mu-map
+    muhdct = nipet.hdw_mumap(datain, [1, 2, 4], mMRpars, outpath=opth, use_stored=True)
+
+    # object mu-map with alignment
+    mupdct = nipet.align_mumap(
+        datain,
+        mMRpars,
+        outpath=opth,
+        store=True,
+        hst=hst,
+        itr=2,
+        petopt="ac",
+        fcomment="_mu",
+        musrc="pct",
+    )
+    # object mu-map without alignment--straight from DICOM resampled to PET
+    # muodct = nipet.obj_mumap(datain, mMRpars, outpath=opth, store=True)
+
+    nipet.mmrchain(
+        datain,
+        mMRpars,
+        frames=frm_timings["timings"],
+        mu_h=muhdct,
+        mu_o=mupdct,                   # muodct,
+        itr=5,
+        fwhm=0.0,
+        outpath=opth,
+        fcomment="_dyn",
+        store_img=True,
+        store_img_intrmd=True,
+    )
+    return Path(opth) / "PET" / "multiple-frames"
+
+
+@pytest.mark.timeout(2 * 60 * 60) # 2h
+def test_rectrim(dyndir):
+    rectrim = pytest.importorskip("amypad.rectrim")
+    rectrim.run(dyndir)