bump version, merge branch 'devel'

.github/workflows/test.yml

@@ -94,7 +94,7 @@ jobs:
       env:
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
       with:
-        name: amypad ${{ steps.meta.outputs.tag }} alpha
+        name: amypet ${{ steps.meta.outputs.tag }} alpha
         body_path: _CHANGES.md
         draft: true
         files: |

.gitignore

@@ -1,11 +1,12 @@
-*.py[co]
+*.py[cod]
 __pycache__/
 
 # build
-/amypad/_dist_ver.py
+/amypet/_dist_ver.py
 /build/
 /dist/
 /*.egg*/
 
 /.coverage*
 /coverage.xml
+/.pytest_cache/

.pre-commit-config.yaml

@@ -31,20 +31,22 @@ repos:
   - id: flake8
     args: [-j8]
     additional_dependencies:
+    - flake8-broken-line
     - flake8-bugbear
     - flake8-comprehensions
     - flake8-debugger
+    - flake8-isort
     - flake8-string-format
 - repo: https://github.com/google/yapf
   rev: v0.31.0
   hooks:
   - id: yapf
     args: [-i]
 - repo: https://github.com/PyCQA/isort
-  rev: 5.9.3
+  rev: 5.10.1
   hooks:
   - id: isort
 - hooks:
   - id: mbeautify
   repo: https://github.com/AMYPAD/miutil
-  rev: v0.9.0
+  rev: v0.9.1

README.rst

@@ -1,6 +1,6 @@
 |Logo|
 
-AMYPAD
+AMYPET
 ======
 
 Amyloid imaging to prevent Alzheimer's Disease.
@@ -13,17 +13,17 @@ Choose one of the following:
 
 .. code:: sh
 
-    pip install amypad  # command line interface (CLI) version
-    pip install amypad[gui]  # CLI and graphical user interface (GUI) version
+    pip install amypet  # command line interface (CLI) version
+    pip install amypet[gui]  # CLI and graphical user interface (GUI) version
 
 
 Usage
 -----
 
 .. code:: sh
 
-    amypad --help  # CLI version
-    amypad.gui     # GUI version
+    amypet --help  # CLI version
+    amypet.gui     # GUI version
 
 
 .. |Logo| image:: https://amypad.eu/wp-content/themes/AMYPAD/images/AMYPAD_Logo.jpg

amypad/__init__.py → amypet/__init__.py

@@ -14,7 +14,7 @@
         __version__ = "UNKNOWN"
 
 try:
-    __licence__ = get_distribution("amypad").get_metadata("LICENCE.md")
+    __licence__ = get_distribution("amypet").get_metadata("LICENCE.md")
 except (DistributionNotFound, FileNotFoundError):
     try:
         __licence__ = (Path(__file__).parent.parent / "LICENCE.md").read_text()

amypad/gui.py → amypet/gui.py

@@ -232,15 +232,15 @@ def print_not_none(value, **kwargs):
 # progress_expr="float(percent or 0)",
 # hide_progress_msg=True,
 # richtext_controls=True,
-@Gooey(default_size=(768, 768), program_name="amypad", sidebar_title="pipeline",
+@Gooey(default_size=(768, 768), program_name="amypet", sidebar_title="pipeline",
        image_dir=resource_filename(__name__, ""), show_restart_button=False,
        header_bg_color="#ffffff", sidebar_bg_color="#a3b5cd", body_bg_color="#a3b5cd",
        footer_bg_color="#2a569f", terminal_font_family="monospace", menu=[{
            "name": "Help", "items": [{
                "type": "Link", "menuTitle": "🌐 View source (online)",
-               "url": "https://github.com/AMYPAD/amypad"}, {
-                   "type": "AboutDialog", "menuTitle": "🔍 About", "name": "AMYPAD Pipeline",
-                   "description": "GUI to run AMYPAD tools", "version": __version__,
+               "url": "https://github.com/AMYPAD/amypet"}, {
+                   "type": "AboutDialog", "menuTitle": "🔍 About", "name": "AMYPET Pipeline",
+                   "description": "GUI to run AMYPET tools", "version": __version__,
                    "copyright": "2021", "website": "https://amypad.eu",
                    "developer": "https://github.com/AMYPAD", "license": __licence__}]}])
 def main(args=None, gui_mode=True):
@@ -249,9 +249,9 @@ def main(args=None, gui_mode=True):
     import niftypad.api
     import niftypad.models
 
-    from amypad import centiloid, imscroll, imtrimup
+    from amypet import centiloid, imscroll, imtrimup
 
-    parser = fix_subparser(MyParser(prog=None if gui_mode else "amypad"), gui_mode=gui_mode)
+    parser = fix_subparser(MyParser(prog=None if gui_mode else "amypet"), gui_mode=gui_mode)
     sub_kwargs = {}
     if sys.version_info[:2] >= (3, 7):
         sub_kwargs["required"] = True
@@ -290,11 +290,11 @@ def argparser(prog, description=None, epilog=None, formatter_class=None):
           <src>  : Input file/folder [default: FileChooser]
 
         Options:
-          -d PATH, --dst PATH      : Output file/folder (default: input folder)
-                                     [default: FileChooser]
-          -m MODEL, --model MODEL  : model [default: srtmb_basis]
-          -p FILE, --params FILE   : config file hint (relative to `--input`)
-                                     [default: FileChooser]
+          --dst PATH           : Output file/folder (default: input folder)
+            [default: FileChooser]
+          --model MODEL        : model [default: srtmb_basis]
+          --params FILE        : config file hint (relative to `src` input).
+            Default: search for {config,params}.{yaml,json}.
           --w W                : (default: None)
           --r1 R1              : [default: 0.905:float]
           --k2p K2P            : [default: 0.000250:float]
@@ -333,7 +333,7 @@ def argparser(prog, description=None, epilog=None, formatter_class=None):
     args = [i for i in args if i not in ("--dry-run",)] # strip args
 
     if gui_mode:
-        print(" ".join([Path(sys.executable).name, "-m amypad"] + args))
+        print(" ".join([Path(sys.executable).name, "-m amypet"] + args))
     if opts.dry_run:
         pass
     elif hasattr(opts, "main__"):                                                    # Cmd

pyproject.toml

@@ -2,5 +2,5 @@
 requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"]
 
 [tool.setuptools_scm]
-write_to = "amypad/_dist_ver.py"
+write_to = "amypet/_dist_ver.py"
 write_to_template = "__version__ = '{version}'\n"

setup.cfg

@@ -1,20 +1,20 @@
 [metadata]
-name=amypad
+name=amypet
 description=Amyloid imaging to prevent Alzheimer's Disease
 long_description=file: README.rst
 long_description_content_type=text/x-rst
 license=MPL 2.0
 license_file=LICENCE.md
 url=https://amypad.eu
 project_urls=
-    Repository=https://github.com/AMYPAD/amypad
-    Changelog=https://github.com/AMYPAD/amypad/releases
-    Documentation=https://github.com/AMYPAD/amypad/#amypad
+    Repository=https://github.com/AMYPAD/amypet
+    Changelog=https://github.com/AMYPAD/amypet/releases
+    Documentation=https://github.com/AMYPAD/amypet/#amypet
 maintainer=Casper da Costa-Luis
 [email protected]
 keywords=pet, alzheimers
 platforms=any
-provides=amypad
+provides=amypet
 classifiers=
     Development Status :: 3 - Alpha
     Intended Audience :: Developers
@@ -61,8 +61,8 @@ gui=Gooey>=1.0.8
 niftypet=niftypet>=0.0.1
 [options.entry_points]
 console_scripts=
-    amypad=amypad.cli:main
-    amypad.gui=amypad.gui:main
+    amypet=amypet.cli:main
+    amypet.gui=amypet.gui:main
 [options.packages.find]
 exclude=tests
 [options.package_data]
@@ -87,12 +87,12 @@ split_before_closing_bracket=False
 [isort]
 profile=black
 line_length=99
-known_first_party=amypad,tests
+known_first_party=amypet,tests
 
 [tool:pytest]
 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
+addopts=-v --tb=short -rxs -W=error -n=auto --durations=0 --durations-min=1 --cov=amypet --cov-report=term-missing --cov-report=xml
 filterwarnings=
     ignore:numpy.ufunc size changed.*:RuntimeWarning

tests/test_cli.py

@@ -1,4 +1,4 @@
-from amypad.cli import main
+from amypet.cli import main
 
 
 def test_run():

tests/test_imtrimup.py

@@ -5,22 +5,22 @@
 
 @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():
+    if res.is_dir() and len(list(res.glob('*.nii*'))) > 1:
         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
+    # frmdef = ["def", [4, 15], [8, 30], [9, 60], [2, 180], [8, 300]]
+    frmdef = ["def", [4, (hst['t1'] - hst['t0'] - toff) / 4]]
     frm_timings = nipet.lm.dynamic_timings(frmdef, offset=toff)
-    nipet.lm.draw_frames(hst, frm_timings["timings"])
+    # nipet.lm.draw_frames(hst, frm_timings["timings"]) # plot frames
     # hardware mu-map
     muhdct = nipet.hdw_mumap(datain, [1, 2, 4], mMRpars, outpath=opth, use_stored=True)
 
@@ -30,6 +30,7 @@ def dyndir(datain, mMRpars):
         mMRpars,
         outpath=opth,
         store=True,
+        use_stored=True,
         hst=hst,
         itr=2,
         petopt="ac",
@@ -44,7 +45,7 @@ def dyndir(datain, mMRpars):
         mMRpars,
         frames=frm_timings["timings"],
         mu_h=muhdct,
-        mu_o=mupdct,                   # muodct,
+        mu_o=mupdct,
         itr=5,
         fwhm=0.0,
         outpath=opth,
@@ -55,7 +56,7 @@ def dyndir(datain, mMRpars):
     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)
+@pytest.mark.timeout(30 * 60) # 30m
+def test_imtrimup(dyndir):
+    imtrimup = pytest.importorskip("amypet.imtrimup")
+    imtrimup.run(dyndir, glob='*_frm?_t*.nii*')