roifile 2024.3.20__tar.gz → 2024.9.15__tar.gz

{roifile-2024.3.20 → roifile-2024.9.15}/CHANGES.rst

@@ -1,6 +1,15 @@
 Revisions
 ---------
 
+2024.9.15
+
+- Improve typing.
+- Deprecate Python 3.9, support Python 3.13.
+
+2024.5.24
+
+- Fix docstring examples not correctly rendered on GitHub.
+
 2024.3.20
 
 - Fix writing generator of ROIs (#9).

{roifile-2024.3.20/roifile.egg-info → roifile-2024.9.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roifile
-Version: 2024.3.20
+Version: 2024.9.15
 Summary: Read and write ImageJ ROI format
 Home-page: https://www.cgohlke.com
 Author: Christoph Gohlke
@@ -15,10 +15,10 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: Developers
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
@@ -38,7 +38,7 @@ interest, geometric shapes, paths, text, and whatnot for image overlays.
 
 :Author: `Christoph Gohlke <https://www.cgohlke.com>`_
 :License: BSD 3-Clause
-:Version: 2024.3.20
+:Version: 2024.9.15
 :DOI: `10.5281/zenodo.6941603 <https://doi.org/10.5281/zenodo.6941603>`_
 
 Quickstart
@@ -64,14 +64,23 @@ Requirements
 This revision was tested with the following requirements and dependencies
 (other versions may work):
 
-- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.8, 3.12.2
-- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.4
-- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.2.12 (optional)
-- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.3 (optional)
+- `CPython <https://www.python.org>`_ 3.10.11, 3.11.9, 3.12.5, 3.13.0rc2
+- `Numpy <https://pypi.org/project/numpy/>`_ 2.2.1
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.8.30 (optional)
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.9.2 (optional)
 
 Revisions
 ---------
 
+2024.9.15
+
+- Improve typing.
+- Deprecate Python 3.9, support Python 3.13.
+
+2024.5.24
+
+- Fix docstring examples not correctly rendered on GitHub.
+
 2024.3.20
 
 - Fix writing generator of ROIs (#9).
@@ -156,11 +165,38 @@ array([[1.1, 2.2],
        [5.5, 6.6]], dtype=float32)
 >>> roi.left, roi.top, roi.right, roi.bottom
 (1, 2, 7, 8)
+>>> roi2.name = 'test'
 
 Plot the ROI using matplotlib:
 
 >>> roi.plot()
 
+Write the ROIs to a ZIP file:
+
+>>> roiwrite('_test.zip', [roi, roi2], mode='w')
+
+Read the ROIs from the ZIP file:
+
+>>> rois = roiread('_test.zip')
+>>> assert len(rois) == 2 and rois[0] == roi and rois[1].name == 'test'
+
+Write the ROIs to an ImageJ formatted TIFF file:
+
+>>> import tifffile
+>>> tifffile.imwrite(
+...     '_test.tif',
+...     numpy.zeros((9, 9), 'u1'),
+...     imagej=True,
+...     metadata={'Overlays': [roi.tobytes(), roi2.tobytes()]},
+... )
+
+Read the ROIs embedded in an ImageJ formatted TIFF file:
+
+>>> rois = roiread('_test.tif')
+>>> assert len(rois) == 2 and rois[0] == roi and rois[1].name == 'test'
+
 View the overlays stored in a ROI, ZIP, or TIFF file from a command line::
 
     python -m roifile _test.roi
+
+For an advanced example, see `roifile_demo.py` in the source distribution.

{roifile-2024.3.20 → roifile-2024.9.15}/README.rst

@@ -1,3 +1,6 @@
+..
+  This file is generated by setup.py
+
 Read and write ImageJ ROI format
 ================================
 
@@ -9,7 +12,7 @@ interest, geometric shapes, paths, text, and whatnot for image overlays.
 
 :Author: `Christoph Gohlke <https://www.cgohlke.com>`_
 :License: BSD 3-Clause
-:Version: 2024.3.20
+:Version: 2024.9.15
 :DOI: `10.5281/zenodo.6941603 <https://doi.org/10.5281/zenodo.6941603>`_
 
 Quickstart
@@ -35,14 +38,23 @@ Requirements
 This revision was tested with the following requirements and dependencies
 (other versions may work):
 
-- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.8, 3.12.2
-- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.4
-- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.2.12 (optional)
-- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.3 (optional)
+- `CPython <https://www.python.org>`_ 3.10.11, 3.11.9, 3.12.5, 3.13.0rc2
+- `Numpy <https://pypi.org/project/numpy/>`_ 2.2.1
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.8.30 (optional)
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.9.2 (optional)
 
 Revisions
 ---------
 
+2024.9.15
+
+- Improve typing.
+- Deprecate Python 3.9, support Python 3.13.
+
+2024.5.24
+
+- Fix docstring examples not correctly rendered on GitHub.
+
 2024.3.20
 
 - Fix writing generator of ROIs (#9).
@@ -101,37 +113,80 @@ Examples
 
 Create a new ImagejRoi instance from an array of x, y coordinates:
 
->>> roi = ImagejRoi.frompoints([[1.1, 2.2], [3.3, 4.4], [5.5, 6.6]])
->>> roi.roitype = ROI_TYPE.POINT
->>> roi.options |= ROI_OPTIONS.SHOW_LABELS
+.. code-block:: python
+
+    >>> roi = ImagejRoi.frompoints([[1.1, 2.2], [3.3, 4.4], [5.5, 6.6]])
+    >>> roi.roitype = ROI_TYPE.POINT
+    >>> roi.options |= ROI_OPTIONS.SHOW_LABELS
 
 Export the instance to an ImageJ ROI formatted byte string or file:
 
->>> out = roi.tobytes()
->>> out[:4]
-b'Iout'
->>> roi.tofile('_test.roi')
+.. code-block:: python
+
+    >>> out = roi.tobytes()
+    >>> out[:4]
+    b'Iout'
+    >>> roi.tofile('_test.roi')
 
 Read the ImageJ ROI from the file and verify the content:
 
->>> roi2 = ImagejRoi.fromfile('_test.roi')
->>> roi2 == roi
-True
->>> roi.roitype == ROI_TYPE.POINT
-True
->>> roi.subpixelresolution
-True
->>> roi.coordinates()
-array([[1.1, 2.2],
-       [3.3, 4.4],
-       [5.5, 6.6]], dtype=float32)
->>> roi.left, roi.top, roi.right, roi.bottom
-(1, 2, 7, 8)
+.. code-block:: python
+
+    >>> roi2 = ImagejRoi.fromfile('_test.roi')
+    >>> roi2 == roi
+    True
+    >>> roi.roitype == ROI_TYPE.POINT
+    True
+    >>> roi.subpixelresolution
+    True
+    >>> roi.coordinates()
+    array([[1.1, 2.2],
+           [3.3, 4.4],
+           [5.5, 6.6]], dtype=float32)
+    >>> roi.left, roi.top, roi.right, roi.bottom
+    (1, 2, 7, 8)
+    >>> roi2.name = 'test'
 
 Plot the ROI using matplotlib:
 
->>> roi.plot()
+.. code-block:: python
+
+    >>> roi.plot()
+
+Write the ROIs to a ZIP file:
+
+.. code-block:: python
+
+    >>> roiwrite('_test.zip', [roi, roi2], mode='w')
+
+Read the ROIs from the ZIP file:
+
+.. code-block:: python
+
+    >>> rois = roiread('_test.zip')
+    >>> assert len(rois) == 2 and rois[0] == roi and rois[1].name == 'test'
+
+Write the ROIs to an ImageJ formatted TIFF file:
+
+.. code-block:: python
+
+    >>> import tifffile
+    >>> tifffile.imwrite(
+    ...     '_test.tif',
+    ...     numpy.zeros((9, 9), 'u1'),
+    ...     imagej=True,
+    ...     metadata={'Overlays': [roi.tobytes(), roi2.tobytes()]},
+    ... )
+
+Read the ROIs embedded in an ImageJ formatted TIFF file:
+
+.. code-block:: python
+
+    >>> rois = roiread('_test.tif')
+    >>> assert len(rois) == 2 and rois[0] == roi and rois[1].name == 'test'
 
 View the overlays stored in a ROI, ZIP, or TIFF file from a command line::
 
     python -m roifile _test.roi
+
+For an advanced example, see `roifile_demo.py` in the source distribution.

{roifile-2024.3.20 → roifile-2024.9.15}/roifile/roifile.py

@@ -39,7 +39,7 @@ interest, geometric shapes, paths, text, and whatnot for image overlays.
 
 :Author: `Christoph Gohlke <https://www.cgohlke.com>`_
 :License: BSD 3-Clause
-:Version: 2024.3.20
+:Version: 2024.9.15
 :DOI: `10.5281/zenodo.6941603 <https://doi.org/10.5281/zenodo.6941603>`_
 
 Quickstart
@@ -65,14 +65,23 @@ Requirements
 This revision was tested with the following requirements and dependencies
 (other versions may work):
 
-- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.8, 3.12.2
-- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.4
-- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.2.12 (optional)
-- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.3 (optional)
+- `CPython <https://www.python.org>`_ 3.10.11, 3.11.9, 3.12.5, 3.13.0rc2
+- `Numpy <https://pypi.org/project/numpy/>`_ 2.2.1
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.8.30 (optional)
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.9.2 (optional)
 
 Revisions
 ---------
 
+2024.9.15
+
+- Improve typing.
+- Deprecate Python 3.9, support Python 3.13.
+
+2024.5.24
+
+- Fix docstring examples not correctly rendered on GitHub.
+
 2024.3.20
 
 - Fix writing generator of ROIs (#9).
@@ -157,20 +166,47 @@ array([[1.1, 2.2],
        [5.5, 6.6]], dtype=float32)
 >>> roi.left, roi.top, roi.right, roi.bottom
 (1, 2, 7, 8)
+>>> roi2.name = 'test'
 
 Plot the ROI using matplotlib:
 
 >>> roi.plot()
 
+Write the ROIs to a ZIP file:
+
+>>> roiwrite('_test.zip', [roi, roi2], mode='w')
+
+Read the ROIs from the ZIP file:
+
+>>> rois = roiread('_test.zip')
+>>> assert len(rois) == 2 and rois[0] == roi and rois[1].name == 'test'
+
+Write the ROIs to an ImageJ formatted TIFF file:
+
+>>> import tifffile
+>>> tifffile.imwrite(
+...     '_test.tif',
+...     numpy.zeros((9, 9), 'u1'),
+...     imagej=True,
+...     metadata={'Overlays': [roi.tobytes(), roi2.tobytes()]},
+... )
+
+Read the ROIs embedded in an ImageJ formatted TIFF file:
+
+>>> rois = roiread('_test.tif')
+>>> assert len(rois) == 2 and rois[0] == roi and rois[1].name == 'test'
+
 View the overlays stored in a ROI, ZIP, or TIFF file from a command line::
 
     python -m roifile _test.roi
 
+For an advanced example, see `roifile_demo.py` in the source distribution.
+
 """
 
 from __future__ import annotations
 
-__version__ = '2024.3.20'
+__version__ = '2024.9.15'
 
 __all__ = [
     'roiread',
@@ -197,8 +233,9 @@ import numpy
 
 if TYPE_CHECKING:
     from collections.abc import Iterable
-    from typing import Any, Literal
+    from typing import Any, Iterator, Literal
 
+    from matplotlib.axes import Axes
     from numpy.typing import ArrayLike, NDArray
 
 
@@ -888,15 +925,16 @@ class ImagejRoi:
 
     def plot(
         self,
-        ax: Any | None = None,
+        ax: Axes | None = None,
         *,
         rois: Iterable[ImagejRoi] | None = None,
         title: str | None = None,
         bounds: bool = False,
         invert_yaxis: bool | None = None,
-        **kwargs,
+        **kwargs: Any,
     ) -> None:
         """Plot a draft of coordinates using matplotlib."""
+        fig: Any
         roitype = self.roitype
         subtype = self.subtype
 
@@ -938,8 +976,6 @@ class ImagejRoi:
             pyplot.show()
             return
 
-        if kwargs is None:
-            kwargs = {}
         if 'color' not in kwargs and 'c' not in kwargs:
             kwargs['color'] = self.hexcolor(self.stroke_color)
         if 'linewidth' not in kwargs and 'lw' not in kwargs:
@@ -970,7 +1006,8 @@ class ImagejRoi:
             if 'fontsize' not in kwargs and self.text_size > 0:
                 kwargs['fontsize'] = self.text_size
             text = ax.text(
-                *coords[1],
+                coords[1][0],
+                coords[1][1],
                 self.text,
                 va='center_baseline',
                 rotation=self.text_angle,
@@ -1176,17 +1213,37 @@ class ImagejRoi:
         return indent(*info, end='\n)')
 
 
-def scale_text(text: Any, width: float) -> None:
+def scale_text(
+    text: Any,
+    width: float,
+    *,
+    offset: tuple[float, float] | None = None,
+) -> None:
     """Scale matplotlib text to width in data coordinates."""
     from matplotlib.patheffects import AbstractPathEffect
     from matplotlib.transforms import Bbox
 
     class TextScaler(AbstractPathEffect):
-        def __init__(self, text, width):
+        def __init__(
+            self,
+            text: Any,
+            width: float,
+            offset: tuple[float, float] | None = None,
+        ) -> None:
+            if offset is None:
+                offset = (0.0, 0.0)
+            super().__init__(offset)
             self._text = text
             self._width = width
 
-        def draw_path(self, renderer, gc, tpath, affine, rgbFace=None):
+        def draw_path(
+            self,
+            renderer: Any,
+            gc: Any,
+            tpath: Any,
+            affine: Any,
+            rgbFace: Any = None,
+        ) -> None:
             ax = self._text.axes
             renderer = ax.get_figure().canvas.get_renderer()
             bbox = text.get_window_extent(renderer=renderer)
@@ -1196,7 +1253,7 @@ def scale_text(text: Any, width: float) -> None:
                 affine = affine.from_values(scale, 0, 0, scale, 0, 0) + affine
             renderer.draw_path(gc, tpath, affine, rgbFace)
 
-    text.set_path_effects([TextScaler(text, width)])
+    text.set_path_effects([TextScaler(text, width, offset)])
 
 
 def oval(rect: ArrayLike, /, points: int = 33) -> NDArray[numpy.float32]:
@@ -1211,9 +1268,9 @@ def oval(rect: ArrayLike, /, points: int = 33) -> NDArray[numpy.float32]:
     return c
 
 
-def indent(*args: Any, sep='', end='') -> str:
+def indent(*args: Any, sep: str = '', end: str = '') -> str:
     """Return joined string representations of objects with indented lines."""
-    text = (sep + '\n').join(
+    text: str = (sep + '\n').join(
         arg if isinstance(arg, str) else repr(arg) for arg in args
     )
     return (
@@ -1252,7 +1309,7 @@ def logger() -> logging.Logger:
 def test(verbose: bool = False) -> None:
     """Test roifile.ImagejRoi class."""
     # test ROIs from a ZIP file
-    rois = ImagejRoi.fromfile('tests/ijzip.zip')
+    rois: Any = ImagejRoi.fromfile('tests/ijzip.zip')
     assert isinstance(rois, list)
     assert len(rois) == 7
     for roi in rois:
@@ -1268,7 +1325,7 @@ def test(verbose: bool = False) -> None:
     except OSError:
         pass
 
-    def roi_iter():
+    def roi_iter() -> Iterator[ImagejRoi]:
         # issue #9
         yield from rois
 

{roifile-2024.3.20 → roifile-2024.9.15/roifile.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: roifile
-Version: 2024.3.20
+Version: 2024.9.15
 Summary: Read and write ImageJ ROI format
 Home-page: https://www.cgohlke.com
 Author: Christoph Gohlke
@@ -15,10 +15,10 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: Developers
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
@@ -38,7 +38,7 @@ interest, geometric shapes, paths, text, and whatnot for image overlays.
 
 :Author: `Christoph Gohlke <https://www.cgohlke.com>`_
 :License: BSD 3-Clause
-:Version: 2024.3.20
+:Version: 2024.9.15
 :DOI: `10.5281/zenodo.6941603 <https://doi.org/10.5281/zenodo.6941603>`_
 
 Quickstart
@@ -64,14 +64,23 @@ Requirements
 This revision was tested with the following requirements and dependencies
 (other versions may work):
 
-- `CPython <https://www.python.org>`_ 3.9.13, 3.10.11, 3.11.8, 3.12.2
-- `Numpy <https://pypi.org/project/numpy/>`_ 1.26.4
-- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.2.12 (optional)
-- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.8.3 (optional)
+- `CPython <https://www.python.org>`_ 3.10.11, 3.11.9, 3.12.5, 3.13.0rc2
+- `Numpy <https://pypi.org/project/numpy/>`_ 2.2.1
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2024.8.30 (optional)
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.9.2 (optional)
 
 Revisions
 ---------
 
+2024.9.15
+
+- Improve typing.
+- Deprecate Python 3.9, support Python 3.13.
+
+2024.5.24
+
+- Fix docstring examples not correctly rendered on GitHub.
+
 2024.3.20
 
 - Fix writing generator of ROIs (#9).
@@ -156,11 +165,38 @@ array([[1.1, 2.2],
        [5.5, 6.6]], dtype=float32)
 >>> roi.left, roi.top, roi.right, roi.bottom
 (1, 2, 7, 8)
+>>> roi2.name = 'test'
 
 Plot the ROI using matplotlib:
 
 >>> roi.plot()
 
+Write the ROIs to a ZIP file:
+
+>>> roiwrite('_test.zip', [roi, roi2], mode='w')
+
+Read the ROIs from the ZIP file:
+
+>>> rois = roiread('_test.zip')
+>>> assert len(rois) == 2 and rois[0] == roi and rois[1].name == 'test'
+
+Write the ROIs to an ImageJ formatted TIFF file:
+
+>>> import tifffile
+>>> tifffile.imwrite(
+...     '_test.tif',
+...     numpy.zeros((9, 9), 'u1'),
+...     imagej=True,
+...     metadata={'Overlays': [roi.tobytes(), roi2.tobytes()]},
+... )
+
+Read the ROIs embedded in an ImageJ formatted TIFF file:
+
+>>> rois = roiread('_test.tif')
+>>> assert len(rois) == 2 and rois[0] == roi and rois[1].name == 'test'
+
 View the overlays stored in a ROI, ZIP, or TIFF file from a command line::
 
     python -m roifile _test.roi
+
+For an advanced example, see `roifile_demo.py` in the source distribution.

{roifile-2024.3.20 → roifile-2024.9.15}/roifile_demo.py

@@ -9,11 +9,10 @@ segmentation from/to ImageJ TIFF files.
 
 import numpy
 from matplotlib import pyplot
+from roifile import ImagejRoi
 from skimage.measure import find_contours, label, regionprops
 from tifffile import TiffFile, imwrite
 
-from roifile import ImagejRoi
-
 
 def plot_image_overlays(image, overlays, **kwargs):
     """Plot image and overlays (bytes) using matplotlib."""

{roifile-2024.3.20 → roifile-2024.9.15}/setup.py

@@ -8,14 +8,32 @@ import sys
 from setuptools import setup
 
 
-def search(pattern, code, flags=0):
-    # return first match for pattern in code
-    match = re.search(pattern, code, flags)
+def search(pattern, string, flags=0):
+    """Return first match of pattern in string."""
+    match = re.search(pattern, string, flags)
     if match is None:
         raise ValueError(f'{pattern!r} not found')
     return match.groups()[0]
 
 
+def fix_docstring_examples(docstring):
+    """Return docstring with examples fixed for GitHub."""
+    start = True
+    indent = False
+    lines = ['..', '  This file is generated by setup.py', '']
+    for line in docstring.splitlines():
+        if not line.strip():
+            start = True
+            indent = False
+        if line.startswith('>>> '):
+            indent = True
+            if start:
+                lines.extend(['.. code-block:: python', ''])
+                start = False
+        lines.append(('    ' if indent else '') + line)
+    return '\n'.join(lines)
+
+
 with open('roifile/roifile.py', encoding='utf-8') as fh:
     code = fh.read().replace('\r\n', '\n').replace('\r', '\n')
 
@@ -36,7 +54,7 @@ if 'sdist' in sys.argv:
     # update README, LICENSE, and CHANGES files
 
     with open('README.rst', 'w', encoding='utf-8') as fh:
-        fh.write(readme)
+        fh.write(fix_docstring_examples(readme))
 
     license = search(
         r'(# Copyright.*?(?:\r\n|\r|\n))(?:\r\n|\r|\n)+""',
@@ -92,9 +110,9 @@ setup(
         'Intended Audience :: Developers',
         'Operating System :: OS Independent',
         'Programming Language :: Python :: 3 :: Only',
-        'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
 )