bump version, merge pull request #16 from NiftyPET/devel

.github/workflows/test.yml

@@ -53,8 +53,6 @@ jobs:
     - run: pip install -U .[dev]
     - run: pytest --cov=$HOME/.niftypet
     - run: codecov
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
   deploy:
     needs: [check, test]
     name: PyPI Deploy
@@ -67,8 +65,7 @@ jobs:
     - id: dist
       uses: casperdcl/deploy-pypi@v2
       with:
-        requirements: twine setuptools wheel setuptools_scm[toml] tqdm miutil[web]
-        build: true
+        pip: true
         password: ${{ secrets.PYPI_TOKEN }}
         upload: ${{ github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') }}
     - name: Changelog

.gitignore

@@ -11,3 +11,4 @@ MANIFEST
 
 /.coverage*
 /coverage.xml
+/.pytest_cache/

niftypet/ninst/install_tools.py

@@ -305,7 +305,10 @@ def download_dcm2niix(Cnt, dest):
 
     Cnt["DCM2NIIX"] = fspath(next(binpath.glob("dcm2niix*")))
     # ensure the permissions are given to the executable
-    os.chmod(Cnt["DCM2NIIX"], 755)
+    try:
+        os.chmod(Cnt["DCM2NIIX"], 0o755)
+    except PermissionError:
+        pass
     # update the resources.py file in ~/.niftypet
     Cnt = update_resources(Cnt)
     return Cnt

niftypet/ninst/raw/resources.py

@@ -1,6 +1,7 @@
 """Resources file for NiftyPET NIPET and NIMPA etc."""
 __author__ = ("Pawel J. Markiewicz", "Casper O. da Costa-Luis")
 __copyright__ = "Copyright 2018-20"
+
 from math import ceil, pi
 
 try:
@@ -104,6 +105,15 @@ def array(x):
 RNG_STRT = 0
 RNG_END = 64
 
+
+# ------------------------------------------------------
+# > scatter axial ring definition
+sct_irng = [0, 10, 19, 28, 35, 44, 53, 63]
+# > resulting number of rings used for scatter modelling
+NSRNG = len(sct_irng)
+# ------------------------------------------------------
+
+
 # no of sinos in a segment out of 11 segments
 seg = array([127, 115, 115, 93, 93, 71, 71, 49, 49, 27, 27])
 
@@ -121,7 +131,7 @@ def array(x):
 NTT = 10
 
 # > all voxels intersected by a given LOR
-NTV = 907
+NTV = 1807
 # ------------------------------------------------------
 
 # number of direct sinograms (i.e., for segment 0)
@@ -404,6 +414,9 @@ def get_mmr_constants():
         "LLD": LLD,  # lower energy threashold
         "E511": E511,
         "ER": ER,  # energy resolution
+        # > scatter:
+        "SIRNG": sct_irng,  # scatter ring indices
+        "NSRNG": NSRNG,  # number of rings for scatter modelling
         "COSUPSMX": COSUPSMX,  # cosine of max allowed scatter angle
         "NCOS": NCOS,  # number of cos samples for LUT
         "COSSTP": COSSTP,  # cosine step

setup.cfg

@@ -41,13 +41,13 @@ python_requires=>=3.6
 [options.extras_require]
 dev=
     pre-commit
-    twine
-    wheel
     pytest
     pytest-cov
     pytest-timeout
     pytest-xdist
     codecov
+[options.packages.find]
+exclude=tests
 [options.package_data]
 *=*.md, *.rst