bump version, merge pull request #17 from AMYPAD/centiloid

centiloid

.github/workflows/test.yml

@@ -4,15 +4,12 @@ jobs:
   check:
     if: github.event_name != 'push' || github.ref != 'refs/heads/devel'
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python: [2.7, 3.6, 3.9]
-    name: Check py${{ matrix.python }}
+    name: Check
     steps:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
       with:
-        python-version: ${{ matrix.python }}
+        python-version: '3.x'
     - name: set PYSHA
       run: echo "PYSHA=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
     - uses: actions/cache@v1
@@ -35,14 +32,13 @@ jobs:
       env:
         REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         EVENT: ${{ github.event_name }}
-    - if: startsWith(matrix.python, '3')
-      run: pre-commit run -a --show-diff-on-failure
+    - run: pre-commit run -a --show-diff-on-failure
   test:
     if: github.event_name != 'pull_request' || github.head_ref != 'devel'
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [2.7, 3.6, 3.9]
+        python: [3.6, '3.10']
     name: Test py${{ matrix.python }}
     steps:
     - uses: actions/checkout@v2

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.3.0
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -36,10 +36,10 @@ repos:
     - flake8-debugger
     - flake8-string-format
 - repo: https://github.com/psf/black
-  rev: 21.7b0
+  rev: 22.6.0
   hooks:
   - id: black
 - repo: https://github.com/PyCQA/isort
-  rev: 5.9.3
+  rev: 5.10.1
   hooks:
   - id: isort

pyproject.toml

@@ -7,4 +7,5 @@ write_to = "spm12/_dist_ver.py"
 write_to_template = "__version__ = '{version}'\n"
 
 [tool.black]
-target_version = ["py27", "py36", "py38"]
+target_version = ["py36", "py310"]
+line_length = 99

setup.cfg

@@ -25,13 +25,12 @@ classifiers=
     Operating System :: Microsoft :: Windows
     Operating System :: POSIX :: Linux
     Programming Language :: Other Scripting Engines
-    Programming Language :: Python :: 2
-    Programming Language :: Python :: 2.7
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
     Topic :: Scientific/Engineering :: Medical Science Apps.
     Topic :: Software Development :: Libraries
     Topic :: System :: Installation/Setup
@@ -46,7 +45,7 @@ install_requires=
     scipy
 include_package_data=True
 packages=find:
-python_requires=>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*
+python_requires=>=3.6
 [options.extras_require]
 dev=
     pre-commit
@@ -72,12 +71,13 @@ exclude=tests
 universal = 1
 
 [flake8]
-max_line_length=88
-extend-ignore=E203,P1
+max_line_length=99
+extend_ignore=E203,P1
 exclude=.git,__pycache__,build,dist,.eggs
 
 [isort]
 profile=black
+line_length=99
 known_first_party=spm12,tests
 
 [tool:pytest]

spm12/amypad_normw.m

@@ -1,9 +1,10 @@
-function out = amypad_normw(def_file, flist4norm)
+function out = amypad_normw(def_file, flist4norm, voxsz, intrp, bbox)
     job.subj.def = {def_file};
     job.subj.resample = flist4norm;
-    job.woptions.bb = [NaN, NaN, NaN; NaN, NaN, NaN];
-    job.woptions.vox = [2, 2, 2];
-    job.woptions.interp = 4;
+    %job.woptions.bb = [NaN, NaN, NaN; NaN, NaN, NaN];
+    job.woptions.bb = bbox;
+    job.woptions.vox = [voxsz, voxsz, voxsz];
+    job.woptions.interp = intrp;
     job.woptions.prefix = 'w';
     spm_run_norm(job);
     out=0;

spm12/cli.py

@@ -13,9 +13,7 @@
 
 
 def main(argv=None):
-    logging.basicConfig(
-        level=logging.DEBUG, format="%(levelname)s:%(funcName)s:%(message)s"
-    )
+    logging.basicConfig(level=logging.DEBUG, format="%(levelname)s:%(funcName)s:%(message)s")
     args = argopt(__doc__).parse_args(argv)
     ensure_spm(cache=args.cache, version=args.spm_version)
     print("SPM{v} is successfully installed".format(v=args.spm_version))

spm12/regseg.py

@@ -3,6 +3,7 @@
 import os
 import re
 import shutil
+from pathlib import PurePath
 from textwrap import dedent
 
 import numpy as np
@@ -46,9 +47,7 @@ def smoothim(fim, fwhm=4, fout=""):
     )
     if not fout:
         f = nii.file_parts(fim)
-        fout = os.path.join(
-            f[0], "{}_smo{}{}".format(f[1], str(fwhm).replace(".", "-"), f[2])
-        )
+        fout = os.path.join(f[0], "{}_smo{}{}".format(f[1], str(fwhm).replace(".", "-"), f[2]))
     nii.array2nii(
         imsmo,
         imd["affine"],
@@ -63,13 +62,52 @@ def smoothim(fim, fwhm=4, fout=""):
     return {"im": imsmo, "fim": fout, "fwhm": fwhm, "affine": imd["affine"]}
 
 
+def get_bbox(fnii):
+    """get the SPM equivalent of the bounding box for
+    NIfTI image `fnii` which can be a dictionary or file.
+    """
+
+    if isinstance(fnii, (str, PurePath)):
+        niidct = nii.getnii(fnii, output="all")
+    elif isinstance(fnii, dict) and "hdr" in fnii:
+        niidct = fnii
+    else:
+        raise ValueError("incorrect input NIfTI file/dictionary")
+
+    dim = niidct["hdr"]["dim"]
+    corners = np.array(
+        [
+            [1, 1, 1, 1],
+            [1, 1, dim[3], 1],
+            [1, dim[2], 1, 1],
+            [1, dim[2], dim[3], 1],
+            [dim[1], 1, 1, 1],
+            [dim[1], 1, dim[3], 1],
+            [dim[1], dim[2], 1, 1],
+            [dim[1], dim[2], dim[3], 1],
+        ]
+    )
+
+    XYZ = np.dot(niidct["affine"][:3, :], corners.T)
+
+    # FIXME: weird correction for SPM bounding box (??)
+    crr = np.dot(niidct["affine"][:3, :3], [1, 1, 1])
+
+    # bounding box as matrix
+    bbox = np.concatenate((np.min(XYZ, axis=1) - crr, np.max(XYZ, axis=1) - crr))
+    bbox.shape = (2, 3)
+
+    return bbox
+
+
 def coreg_spm(
     imref,
     imflo,
     matlab_eng_name="",
     fwhm_ref=0,
     fwhm_flo=0,
     outpath="",
+    output_eng=False,
     fname_aff="",
     fcomment="",
     pickname="ref",
@@ -137,9 +175,7 @@ def coreg_spm(
         imrefu = smodct["fim"]
 
         log.info(
-            "smoothed the reference image with FWHM={} and saved to\n{}".format(
-                fwhm_ref, imrefu
-            )
+            "smoothed the reference image with FWHM={} and saved to\n{}".format(fwhm_ref, imrefu)
         )
 
     # floating
@@ -162,9 +198,7 @@ def coreg_spm(
         imflou = smodct["fim"]
 
         log.info(
-            "smoothed the floating image with FWHM={} and saved to\n{}".format(
-                fwhm_ref, imrefu
-            )
+            "smoothed the floating image with FWHM={} and saved to\n{}".format(fwhm_flo, imflou)
         )
 
     # run the MATLAB SPM registration
@@ -233,7 +267,8 @@ def coreg_spm(
     out["faff"] = faff
     out["rotations"] = x[3:]
     out["translations"] = x[:3]
-    out["matlab_eng"] = eng
+    if output_eng:
+        out["matlab_eng"] = eng
     return out
 
 
@@ -243,7 +278,7 @@ def resample_spm(
     M,
     matlab_eng_name="",
     fwhm=0,
-    intrp=1.0,
+    intrp=1,
     which=1,
     mask=0,
     mean=0,
@@ -299,9 +334,7 @@ def resample_spm(
             M = np.load(M)
             log.info("matrix M given in the form of NumPy file")
         else:
-            raise IOError(
-                errno.ENOENT, M, "Unrecognised file extension for the affine."
-            )
+            raise IOError(errno.ENOENT, M, "Unrecognised file extension for the affine.")
     elif isinstance(M, (np.ndarray, np.generic)):
         log.info("matrix M given in the form of Numpy array")
     else:
@@ -311,7 +344,14 @@ def resample_spm(
     import matlab as ml
 
     eng.amypad_resample(
-        imrefu, imflou, ml.double(M.tolist()), mask, mean, intrp, which, prefix
+        imrefu,
+        imflou,
+        ml.double(M.tolist()),
+        mask,
+        mean,
+        float(intrp),
+        which,
+        prefix,
     )
 
     # -compress the output
@@ -415,17 +455,32 @@ def seg_spm(
     return out
 
 
-def normw_spm(f_def, files4norm, matlab_eng_name="", outpath=None):
+def normw_spm(f_def, files4norm, voxsz=2, intrp=4, bbox=None, matlab_eng_name="", outpath=None):
     """
     Write normalisation output to NIfTI files using SPM12.
     Args:
       f_def: NIfTI file of definitions for non-rigid normalisation
       files4norm: list of input NIfTI file paths in format ['file, 1']
+      voxsz: voxel size of the output (normalised) images
+      intrp: interpolation level used for the normalised images
+             (4: B-spline, default)
       matlab_eng_name: name of the Python engine for Matlab.
       outpath: output folder path for the normalisation files
     """
+
+    import matlab as ml
+
+    if bbox is None:
+        bb = ml.double([[np.NaN, np.NaN, np.NaN], [np.NaN, np.NaN, np.NaN]])
+    elif isinstance(bbox, np.ndarray) and bbox.shape == (2, 3):
+        bb = ml.double(bbox.tolist())
+    elif isinstance(bbox, list) and len(bbox) == 2:
+        bb = ml.double(bbox)
+    else:
+        raise ValueError("unrecognised format for bounding box")
+
     eng = ensure_spm(matlab_eng_name)  # get_matlab
-    eng.amypad_normw(f_def, files4norm)
+    eng.amypad_normw(f_def, files4norm, float(voxsz), float(intrp), bb)
     out = []  # output list
     if outpath is not None:
         create_dir(outpath)

spm12/utils.py

@@ -1,5 +1,5 @@
 import logging
-from functools import wraps
+from functools import lru_cache, wraps
 from os import path
 from textwrap import dedent
 
@@ -8,11 +8,6 @@
 from miutil.web import urlopen_cached
 from pkg_resources import resource_filename
 
-try:
-    from functools import lru_cache
-except ImportError:  # fix py2.7
-    from backports.functools_lru_cache import lru_cache
-
 __all__ = ["ensure_spm", "get_matlab", "spm_dir"]
 PATH_M = resource_filename(__name__, "")
 log = logging.getLogger(__name__)
@@ -46,8 +41,7 @@ def ensure_spm(name=None, cache="~/.spm12", version=12):
         try:
             log.info("Downloading to %s", cache)
             with urlopen_cached(
-                "https://www.fil.ion.ucl.ac.uk/"
-                "spm/download/restricted/eldorado/spm12.zip",
+                "https://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip",
                 cache,
             ) as fd:
                 extractall(fd, cache)

tests/__main__.py

@@ -6,9 +6,7 @@
 from .conftest import HOME
 
 log = logging.getLogger(__name__)
-DATA_URL = (
-    "https://zenodo.org/record/3877529/files/amyloidPET_FBP_TP0_extra.zip?download=1"
-)
+DATA_URL = "https://zenodo.org/record/3877529/files/amyloidPET_FBP_TP0_extra.zip?download=1"
 
 
 def main():

tests/test_main.py

@@ -1,11 +1,6 @@
 from miutil.mlab import matlabroot
 from pytest import mark, skip
 
-try:
-    FileNotFoundError
-except NameError:  # fix py2.7
-    FileNotFoundError = OSError
-
 pytestmark = mark.filterwarnings("ignore:numpy.ufunc size changed.*:RuntimeWarning")
 
 

tests/test_regseg.py

@@ -22,7 +22,7 @@ def assert_equal_arrays(x, y, nmse_tol=0, denan=True):
     if denan:
         x, y = map(np.nan_to_num, (x, y))
     if nmse_tol:
-        if ((x - y) ** 2).mean() / (y ** 2).mean() < nmse_tol:
+        if ((x - y) ** 2).mean() / (y**2).mean() < nmse_tol:
             return
     elif (x == y).all():
         return