feat(itkwasm-image-io): initial addition

packages/image-io/python/itkwasm-image-io-wasi/tests/test_read_write_image.py

@@ -1,5 +1,3 @@
-from pathlib import Path
-
 from itkwasm import PixelTypes, IntTypes
 
 from itkwasm_image_io_wasi import read_image, imread, write_image, imwrite

packages/image-io/python/itkwasm-image-io/README.md

@@ -0,0 +1,11 @@
+# itkwasm-image-io
+
+[![PyPI version](https://badge.fury.io/py/itkwasm-image-io.svg)](https://badge.fury.io/py/itkwasm-image-io)
+
+Input and output for scientific and medical image file formats.
+
+## Installation
+
+```sh
+pip install itkwasm-image-io
+```

packages/image-io/python/itkwasm-image-io/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

packages/image-io/python/itkwasm-image-io/docs/conf.py

@@ -0,0 +1,56 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+from datetime import date
+
+project = 'itkwasm-image-io'
+copyright = f'{date.today().year}, NumFOCUS'
+author = 'Insight Software Consortium'
+
+extensions = [
+    'sphinx.ext.autosummary',
+    'autodoc2',
+    'myst_parser',
+    'sphinx.ext.intersphinx',
+    'sphinx_copybutton',
+    'sphinxext.opengraph',
+    'sphinx_design',
+]
+
+myst_enable_extensions = ["colon_fence", "fieldlist"]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+autodoc2_packages = [
+    {
+        "path": "../itkwasm_image_io",
+        "exclude_files": ["_version.py"],
+    },
+]
+autodoc2_render_plugin = "myst"
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "itkwasm": ("https://itkwasm.readthedocs.io/en/latest/", None),
+}
+
+html_theme = 'furo'
+html_static_path = ['_static']
+html_logo = "_static/logo.svg"
+html_favicon = "_static/favicon.png"
+html_title = f"{project}"
+
+# Furo options
+html_theme_options = {
+    "top_of_page_button": "edit",
+    "source_repository": "https://github.com/InsightSoftwareConsortium/itk-wasm",
+    "source_branch": "main",
+    "source_directory": "docs",
+}

packages/image-io/python/itkwasm-image-io/docs/index.md

@@ -0,0 +1,35 @@
+itkwasm-image-io
+=======
+
+> Input and output for scientific and medical image file formats.
+
+[![itkwasm-image-io version](https://badge.fury.io/py/itkwasm_image_io.svg)](https://pypi.org/project/itkwasm_image_io/)
+
+## Installation
+
+::::{tab-set}
+
+:::{tab-item} System
+```shell
+pip install itkwasm-image-io
+```
+:::
+
+:::{tab-item} Browser
+In Pyodide, e.g. the [Pyodide REPL](https://pyodide.org/en/stable/console.html) or [JupyterLite](https://jupyterlite.readthedocs.io/en/latest/try/lab),
+
+```python
+import micropip
+await micropip.install('itkwasm-image-io')
+:::
+
+::::
+
+```{toctree}
+:hidden:
+:maxdepth: 3
+:caption: 📖 Reference
+
+apidocs/index.rst
+itkwasm docs <https://itkwasm.readthedocs.io/>
+```

packages/image-io/python/itkwasm-image-io/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

packages/image-io/python/itkwasm-image-io/docs/requirements.txt

@@ -0,0 +1,8 @@
+astroid<3
+sphinx
+furo
+sphinx-autodoc2
+myst-parser
+sphinx-copybutton
+sphinxext-opengraph
+sphinx-design

packages/image-io/python/itkwasm-image-io/itkwasm_image_io/__init__.py

@@ -0,0 +1,91 @@
+"""itkwasm-image-io: Input and output for scientific and medical image file formats."""
+
+from .read_image import read_image, imread
+from .write_image import write_image, imwrite
+
+from .bio_rad_read_image_async import bio_rad_read_image_async
+from .bio_rad_read_image import bio_rad_read_image
+from .bio_rad_write_image_async import bio_rad_write_image_async
+from .bio_rad_write_image import bio_rad_write_image
+from .bmp_read_image_async import bmp_read_image_async
+from .bmp_read_image import bmp_read_image
+from .bmp_write_image_async import bmp_write_image_async
+from .bmp_write_image import bmp_write_image
+from .fdf_read_image_async import fdf_read_image_async
+from .fdf_read_image import fdf_read_image
+from .fdf_write_image_async import fdf_write_image_async
+from .fdf_write_image import fdf_write_image
+from .gdcm_read_image_async import gdcm_read_image_async
+from .gdcm_read_image import gdcm_read_image
+from .gdcm_write_image_async import gdcm_write_image_async
+from .gdcm_write_image import gdcm_write_image
+from .ge_adw_read_image_async import ge_adw_read_image_async
+from .ge_adw_read_image import ge_adw_read_image
+from .ge_adw_write_image_async import ge_adw_write_image_async
+from .ge_adw_write_image import ge_adw_write_image
+from .ge4_read_image_async import ge4_read_image_async
+from .ge4_read_image import ge4_read_image
+from .ge4_write_image_async import ge4_write_image_async
+from .ge4_write_image import ge4_write_image
+from .ge5_read_image_async import ge5_read_image_async
+from .ge5_read_image import ge5_read_image
+from .ge5_write_image_async import ge5_write_image_async
+from .ge5_write_image import ge5_write_image
+from .gipl_read_image_async import gipl_read_image_async
+from .gipl_read_image import gipl_read_image
+from .gipl_write_image_async import gipl_write_image_async
+from .gipl_write_image import gipl_write_image
+from .jpeg_read_image_async import jpeg_read_image_async
+from .jpeg_read_image import jpeg_read_image
+from .jpeg_write_image_async import jpeg_write_image_async
+from .jpeg_write_image import jpeg_write_image
+from .lsm_read_image_async import lsm_read_image_async
+from .lsm_read_image import lsm_read_image
+from .lsm_write_image_async import lsm_write_image_async
+from .lsm_write_image import lsm_write_image
+from .meta_read_image_async import meta_read_image_async
+from .meta_read_image import meta_read_image
+from .meta_write_image_async import meta_write_image_async
+from .meta_write_image import meta_write_image
+from .mgh_read_image_async import mgh_read_image_async
+from .mgh_read_image import mgh_read_image
+from .mgh_write_image_async import mgh_write_image_async
+from .mgh_write_image import mgh_write_image
+from .mrc_read_image_async import mrc_read_image_async
+from .mrc_read_image import mrc_read_image
+from .mrc_write_image_async import mrc_write_image_async
+from .mrc_write_image import mrc_write_image
+from .nifti_read_image_async import nifti_read_image_async
+from .nifti_read_image import nifti_read_image
+from .nifti_write_image_async import nifti_write_image_async
+from .nifti_write_image import nifti_write_image
+from .nrrd_read_image_async import nrrd_read_image_async
+from .nrrd_read_image import nrrd_read_image
+from .nrrd_write_image_async import nrrd_write_image_async
+from .nrrd_write_image import nrrd_write_image
+from .png_read_image_async import png_read_image_async
+from .png_read_image import png_read_image
+from .png_write_image_async import png_write_image_async
+from .png_write_image import png_write_image
+from .scanco_read_image_async import scanco_read_image_async
+from .scanco_read_image import scanco_read_image
+from .scanco_write_image_async import scanco_write_image_async
+from .scanco_write_image import scanco_write_image
+from .tiff_read_image_async import tiff_read_image_async
+from .tiff_read_image import tiff_read_image
+from .tiff_write_image_async import tiff_write_image_async
+from .tiff_write_image import tiff_write_image
+from .vtk_read_image_async import vtk_read_image_async
+from .vtk_read_image import vtk_read_image
+from .vtk_write_image_async import vtk_write_image_async
+from .vtk_write_image import vtk_write_image
+from .wasm_read_image_async import wasm_read_image_async
+from .wasm_read_image import wasm_read_image
+from .wasm_write_image_async import wasm_write_image_async
+from .wasm_write_image import wasm_write_image
+from .wasm_zstd_read_image_async import wasm_zstd_read_image_async
+from .wasm_zstd_read_image import wasm_zstd_read_image
+from .wasm_zstd_write_image_async import wasm_zstd_write_image_async
+from .wasm_zstd_write_image import wasm_zstd_write_image
+
+from ._version import __version__

packages/image-io/python/itkwasm-image-io/itkwasm_image_io/_version.py

@@ -0,0 +1 @@
+__version__ = "0.3.0"

packages/image-io/python/itkwasm-image-io/itkwasm_image_io/bio_rad_read_image.py

@@ -0,0 +1,32 @@
+# Generated file. Do not edit.
+
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from itkwasm import (
+    environment_dispatch,
+    BinaryFile,
+    Image,
+)
+
+def bio_rad_read_image(
+    serialized_image: os.PathLike,
+    information_only: bool = False,
+) -> Tuple[Any, Image]:
+    """Read an image file format and convert it to the itk-wasm file format
+
+    :param serialized_image: Input image serialized in the file format
+    :type  serialized_image: os.PathLike
+
+    :param information_only: Only read image metadata -- do not read pixel data.
+    :type  information_only: bool
+
+    :return: Whether the input could be read. If false, the output image is not valid.
+    :rtype:  Any
+
+    :return: Output image
+    :rtype:  Image
+    """
+    func = environment_dispatch("itkwasm_image_io", "bio_rad_read_image")
+    output = func(serialized_image, information_only=information_only)
+    return output

packages/image-io/python/itkwasm-image-io/itkwasm_image_io/bio_rad_read_image_async.py

@@ -0,0 +1,32 @@
+# Generated file. Do not edit.
+
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from itkwasm import (
+    environment_dispatch,
+    BinaryFile,
+    Image,
+)
+
+async def bio_rad_read_image_async(
+    serialized_image: os.PathLike,
+    information_only: bool = False,
+) -> Tuple[Any, Image]:
+    """Read an image file format and convert it to the itk-wasm file format
+
+    :param serialized_image: Input image serialized in the file format
+    :type  serialized_image: os.PathLike
+
+    :param information_only: Only read image metadata -- do not read pixel data.
+    :type  information_only: bool
+
+    :return: Whether the input could be read. If false, the output image is not valid.
+    :rtype:  Any
+
+    :return: Output image
+    :rtype:  Image
+    """
+    func = environment_dispatch("itkwasm_image_io", "bio_rad_read_image_async")
+    output = await func(serialized_image, information_only=information_only)
+    return output

packages/image-io/python/itkwasm-image-io/itkwasm_image_io/bio_rad_write_image.py

@@ -0,0 +1,37 @@
+# Generated file. Do not edit.
+
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from itkwasm import (
+    environment_dispatch,
+    Image,
+    BinaryFile,
+)
+
+def bio_rad_write_image(
+    image: Image,
+    serialized_image: str,
+    information_only: bool = False,
+    use_compression: bool = False,
+) -> Tuple[Any]:
+    """Write an itk-wasm file format converted to an image file format
+
+    :param image: Input image
+    :type  image: Image
+
+    :param serialized_image: Output image serialized in the file format.
+    :type  serialized_image: str
+
+    :param information_only: Only write image metadata -- do not write pixel data.
+    :type  information_only: bool
+
+    :param use_compression: Use compression in the written file
+    :type  use_compression: bool
+
+    :return: Whether the input could be written. If false, the output image is not valid.
+    :rtype:  Any
+    """
+    func = environment_dispatch("itkwasm_image_io", "bio_rad_write_image")
+    output = func(image, serialized_image, information_only=information_only, use_compression=use_compression)
+    return output