bump version, merge pull request #5 from AMYPAD/cuda

.github/workflows/comment-bot.yml

@@ -4,7 +4,6 @@ on:
     types: [created]
   pull_request_review_comment:
     types: [created]
-
 jobs:
   tag:  # /tag <tagname> <commit>
     if: startsWith(github.event.comment.body, '/tag ')
@@ -33,13 +32,10 @@ jobs:
             comment_id: context.payload.comment.id, content: "eyes"})
     - name: Tag Commit
       run: |
-        git clone https://${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY} repo
-        git -C repo tag $(echo "$BODY" | awk '{print $2" "$3}')
-        git -C repo push --tags
-        rm -rf repo
+        git tag $(echo "$BODY" | awk '{print $2" "$3}')
+        git push --tags
       env:
         BODY: ${{ github.event.comment.body }}
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     - name: React Success
       uses: actions/github-script@v2
       with:

.github/workflows/test.yml

@@ -39,15 +39,21 @@ jobs:
         python-version: ${{ matrix.python }}
     - run: pip install -U .[dev]
     - run: python -m tests --cov-report=term-missing --cov-report=xml
+    - run: codecov
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   matlab:
     runs-on: [self-hosted, matlab]
-    name: Test matlab
+    name: Test matlab & cuda
     steps:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
-    - run: pip install -U .[dev]
+    - run: pip install -U .[dev,cuda]
     - run: python -m tests --cov-report=term-missing --cov-report=xml
+    - run: codecov
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   deploy:
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
     needs: [check, matlab, test]
@@ -57,5 +63,6 @@ jobs:
       - uses: actions/checkout@v2
       - uses: casperdcl/deploy-pypi@v1
         with:
-           password: ${{ secrets.pypi_token }}
+           password: ${{ secrets.PYPI_TOKEN }}
            build: true
+           gpg_key: ${{ secrets.GPG_KEY }}

README.rst

@@ -3,7 +3,7 @@ miutil
 
 Medical imaging utilities.
 
-|Versions| |Py-Versions| |Tests| |LICENCE|
+|Versions| |Py-Versions| |Tests| |Coverage| |LICENCE|
 
 Basic functionality needed for `AMYPAD <https://github.com/AMYPAD/AMYPAD>`_
 and `NiftyPET <https://github.com/NiftyPET/NiftyPET>`_.
@@ -13,17 +13,31 @@ Install
 -------
 
 Intended for inclusion in requirements for other packages.
-The package name is ``miutil``. Options include:
+The package name is ``miutil``. Extra install options include:
 
 - nii
+
+  - provides `miutil.imio.nii <https://github.com/AMYPAD/miutil/blob/master/miutil/imio/nii.py>`_
+
 - plot
 
-To install options and their dependencies,
+  - provides `miutil.plot <https://github.com/AMYPAD/miutil/blob/master/miutil/plot.py>`_
+
+    - includes a useful 3D multi-volume ``imscroll`` function which depends only on ``matplotlib``
+
+- cuda
+
+  - provides `miutil.cuinfo <https://github.com/AMYPAD/miutil/blob/master/miutil/cuinfo.py>`_
+
+
+To install extras and their dependencies,
 use the package name ``miutil[option1,option2]``.
 
 
 .. |Tests| image:: https://img.shields.io/github/workflow/status/AMYPAD/miutil/Test
    :target: https://github.com/AMYPAD/miutil/actions
+.. |Coverage| image:: https://codecov.io/gh/AMYPAD/miutil/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/AMYPAD/miutil
 .. |Versions| image:: https://img.shields.io/pypi/v/miutil.svg
    :target: https://github.com/AMYPAD/miutil/releases
 .. |Py-Versions| image:: https://img.shields.io/pypi/pyversions/miutil.svg?logo=python&logoColor=white

miutil/cuinfo.py

@@ -0,0 +1,84 @@
+"""CUDA helpers
+Usage:
+  miutil.cuinfo [options]
+
+Options:
+  -n, --num-devices   : print number of devices (ignores `-d`)
+  -f, --nvcc-flags    : print out flags for use nvcc compilation
+  -d ID, --dev-id ID  : select device ID [default: None:int] for all
+"""
+from argopt import argopt
+import pynvml
+
+__all__ = ["num_devices", "compute_capability", "memory", "name", "nvcc_flags"]
+
+
+def nvmlDeviceGetCudaComputeCapability(handle):
+    major = pynvml.c_int()
+    minor = pynvml.c_int()
+    fn = pynvml.get_func_pointer("nvmlDeviceGetCudaComputeCapability")
+    ret = fn(handle, pynvml.byref(major), pynvml.byref(minor))
+    pynvml.check_return(ret)
+    return [major.value, minor.value]
+
+
+def num_devices():
+    """returns total number of devices"""
+    pynvml.nvmlInit()
+    return pynvml.nvmlDeviceGetCount()
+
+
+def get_handle(dev_id=-1):
+    """allows negative indexing"""
+    pynvml.nvmlInit()
+    dev_id = num_devices() + dev_id if dev_id < 0 else dev_id
+    try:
+        return pynvml.nvmlDeviceGetHandleByIndex(dev_id)
+    except pynvml.NVMLError:
+        raise IndexError("invalid dev_id")
+
+
+def compute_capability(dev_id=-1):
+    """returns compute capability (major, minor)"""
+    return tuple(nvmlDeviceGetCudaComputeCapability(get_handle(dev_id)))
+
+
+def memory(dev_id=-1):
+    """returns memory (total, free, used)"""
+    mem = pynvml.nvmlDeviceGetMemoryInfo(get_handle(dev_id))
+    return (mem.total, mem.free, mem.used)
+
+
+def name(dev_id=-1):
+    """returns device name"""
+    return pynvml.nvmlDeviceGetName(get_handle(dev_id)).decode("U8")
+
+
+def nvcc_flags(dev_id=-1):
+    return "-gencode=arch=compute_{0:d}{1:d},code=compute_{0:d}{1:d}".format(
+        *compute_capability(dev_id)
+    )
+
+
+def main(*args, **kwargs):
+    args = argopt(__doc__).parse_args(*args, **kwargs)
+    noargs = True
+    devices = range(num_devices()) if args.dev_id is None else [args.dev_id]
+
+    if args.num_devices:
+        print(num_devices())
+        noargs = False
+    if args.nvcc_flags:
+        print(" ".join(sorted(set(map(nvcc_flags, devices)))[::-1]))
+        noargs = False
+    if noargs:
+        for dev_id in devices:
+            print(
+                "Device {:2d}:{}:compute capability:{:d}.{:d}".format(
+                    dev_id, name(dev_id), *compute_capability(dev_id)
+                )
+            )
+
+
+if __name__ == "__main__":  # pragma: no cover
+    main()

miutil/imio/nii.py

@@ -10,7 +10,7 @@
 import numpy as np
 
 from . import RE_NII_GZ
-from ..fdio import create_dir
+from ..fdio import create_dir, hasext
 
 RE_GZ = re.compile(r"^(.+)(\.gz)$", flags=re.I)
 log = logging.getLogger(__name__)
@@ -25,11 +25,11 @@ def file_parts(fname, regex=RE_NII_GZ):
 
 def nii_ugzip(imfile, outpath=""):
     """Uncompress *.gz file"""
-    assert imfile[-3:].lower() == ".gz"
+    assert hasext(imfile, "gz")
+    fout, ext = file_parts(imfile, RE_GZ)
     with gzip.open(imfile, "rb") as f:
         s = f.read()
     # write the uncompressed data
-    fout = imfile[:-3]
     if outpath:
         fout = os.path.join(outpath, os.path.basename(fout))
     with open(fout, "wb") as f:
@@ -141,11 +141,11 @@ def array2nii(im, A, fnii, descrip="", trnsp=None, flip=None, storage_as=None):
         'descrip':  the description given to the file
         'trsnp':    transpose/permute the dimensions.
                     In NIfTI it has to be in this order: [x,y,z,t,...])
-        'flip':     flip tupple for flipping the direction of x,y,z axes.
+        'flip':     flip tuple for flipping the direction of x,y,z axes.
                     (1: no flip, -1: flip)
         'storage_as': uses the flip and displacement as given by the following
                     NifTI dictionary, obtained using
-                    nimpa.getnii(filepath, output='all').
+                    `getnii(filepath, output='all')`.
     """
     trnsp = trnsp or ()
     flip = flip or ()

setup.cfg

@@ -17,6 +17,8 @@ provides = miutil
 classifiers =
     Development Status :: 4 - Beta
     Intended Audience :: Developers
+    Environment :: GPU
+    Environment :: GPU :: NVIDIA CUDA
     Intended Audience :: Education
     Intended Audience :: Healthcare Industry
     Intended Audience :: Science/Research
@@ -54,13 +56,17 @@ dev =
     pytest-cov
     pytest-timeout
     pytest-xdist
+    codecov
 nii =
     nibabel
     numpy
 plot =
     matplotlib
     numpy
     scipy
+cuda =
+    argopt
+    pynvml
 [options.package_data]
 * = *.md, *.rst, *.m
 

tests/test_cuinfo.py

@@ -0,0 +1,48 @@
+from pytest import importorskip, raises
+
+cuinfo = importorskip("miutil.cuinfo")
+
+
+def test_num_devices():
+    devices = cuinfo.num_devices()
+    assert isinstance(devices, int)
+
+
+def test_compute_capability():
+    cc = cuinfo.compute_capability()
+    if cc:
+        assert len(cc) == 2, cc
+        assert all(isinstance(i, int) for i in cc), cc
+
+
+def test_memory():
+    mem = cuinfo.memory()
+    if mem:
+        assert len(mem) == 3, mem
+        assert all(isinstance(i, int) for i in mem), mem
+
+
+def test_cuinfo_cli(capsys):
+    cuinfo.main(["--num-devices"])
+    out, _ = capsys.readouterr()
+    devices = int(out)
+    assert devices >= 0
+
+    # individual dev_id
+    for dev_id in range(devices):
+        cuinfo.main(["--dev-id", str(dev_id)])
+        out, _ = capsys.readouterr()
+        assert len(out.split("Device ")) == devices + 1
+
+    # all dev_ids
+    cuinfo.main()
+    out, _ = capsys.readouterr()
+    assert len(out.split("Device ")) == devices + 1
+
+    # dev_id one too much
+    with raises(IndexError):
+        cuinfo.main(["--dev-id", str(devices)])
+
+    cuinfo.main(["--nvcc-flags"])
+    out, _ = capsys.readouterr()
+    assert not devices or out.startswith("-gencode=")

tests/test_fdio.py

@@ -0,0 +1,34 @@
+from os import path
+
+from miutil import fdio
+
+
+def test_create_dir(tmp_path):
+    tmpdir = str(tmp_path / "create_dir")
+    assert not path.exists(tmpdir)
+    fdio.create_dir(tmpdir)
+    assert path.exists(tmpdir)
+
+
+def test_hasext():
+    for fname, ext in [
+        ("foo.bar", ".bar"),
+        ("foo.bar", "bar"),
+        ("foo.bar.baz", "baz"),
+        ("foo/bar.baz", "baz"),
+    ]:
+        assert fdio.hasext(fname, ext)
+
+    for fname, ext in [
+        ("foo.bar", "baz"),
+        ("foo.bar.baz", "bar.baz"),
+        ("foo", "foo"),
+    ]:
+        assert not fdio.hasext(fname, ext)
+
+
+def test_tmpdir():
+    with fdio.tmpdir() as tmpdir:
+        assert path.exists(tmpdir)
+        res = tmpdir
+    assert not path.exists(res)

tests/test_imio.py

@@ -2,10 +2,10 @@
 
 from miutil.imio import imread
 
+np = importorskip("numpy")
 
-def test_imread(tmp_path):
-    np = importorskip("numpy")
 
+def test_imread(tmp_path):
     x = np.random.randint(10, size=(9, 9))
     fname = tmp_path / "test_imread.npy"
     np.save(fname, x)
@@ -17,3 +17,13 @@ def test_imread(tmp_path):
 
     np.savez(fname, x, x)
     assert (imread(str(fname))["arr_0"] == x).all()
+
+
+def test_nii(tmp_path):
+    nii = importorskip("miutil.imio.nii")
+
+    x = np.arange(2 * 2 * 3).reshape(2, 2, 3)
+    fname = str(tmp_path / "test_nii.nii")
+    nii.array2nii(x, np.eye(4), fname, flip=(1, 1, 1))
+    nii.nii_gzip(fname)
+    assert (imread(fname + ".gz") == x).all()