obffile 2026.2.20__tar.gz

obffile-2026.2.20/LICENSE

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+BSD-3-Clause license
+
+Copyright (c) 2025-2026, Christoph Gohlke
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

obffile-2026.2.20/MANIFEST.in

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+include LICENSE
+include README.rst
+include CHANGES.rst
+include pyproject.toml
+
+include obffile/py.typed
+
+include docs/conf.py
+include docs/index.rst
+include docs/_static/custom.css
+
+# include .github/workflows/wheel.yml
+
+exclude .env
+exclude *.cmd
+exclude *.yaml
+exclude mypy.ini
+exclude ruff.toml
+recursive-exclude doc *
+recursive-exclude docs *
+recursive-exclude test *
+recursive-exclude tests *
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude * *Copy*
+
+# recursive-include tests readme.txt
+
+include tests/conftest.py
+include tests/test_obffile.py

obffile-2026.2.20/PKG-INFO

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+Metadata-Version: 2.4
+Name: obffile
+Version: 2026.2.20
+Summary: Read Imspector object binary format files (OBF and MSR)
+Home-page: https://www.cgohlke.com
+Author: Christoph Gohlke
+Author-email: cgohlke@cgohlke.com
+License: BSD-3-Clause
+Project-URL: Bug Tracker, https://github.com/cgohlke/obffile/issues
+Project-URL: Source Code, https://github.com/cgohlke/obffile
+Platform: any
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.11
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: numpy
+Provides-Extra: all
+Requires-Dist: xarray; extra == "all"
+Requires-Dist: tifffile; extra == "all"
+Requires-Dist: matplotlib; extra == "all"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+Read Imspector object binary format files (OBF and MSR)
+=======================================================
+
+Obffile is a Python library to read image and metadata from
+Object Binary Format (OBF) and Measurement Summary Record (MSR) image files.
+These files are written by Imspector software to store image and metadata
+from microscopy experiments.
+
+:Author: `Christoph Gohlke <https://www.cgohlke.com>`_
+:License: BSD-3-Clause
+:Version: 2026.2.20
+
+Quickstart
+----------
+
+Install the obffile package and all dependencies from the
+`Python Package Index <https://pypi.org/project/obffile/>`_::
+
+    python -m pip install -U obffile[all]
+
+See `Examples`_ for using the programming interface.
+
+Source code and support are available on
+`GitHub <https://github.com/cgohlke/obffile>`_.
+
+Requirements
+------------
+
+This revision was tested with the following requirements and dependencies
+(other versions may work):
+
+- `CPython <https://www.python.org>`_ 3.11.9, 3.12.10, 3.13.12, 3.14.3 64-bit
+- `NumPy <https://pypi.org/project/numpy>`_ 2.4.2
+- `Xarray <https://pypi.org/project/xarray>`_ 2026.2.0 (recommended)
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.10.8 (optional)
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2026.2.16 (optional)
+
+Revisions
+---------
+
+2026.2.20
+
+- Initial alpha release.
+- …
+
+Notes
+-----
+
+`Imspector <https://imspectordocs.readthedocs.io>`_ is a software platform for
+super-resolution and confocal microscopy developed by Abberior Instruments.
+
+This library is in its early stages of development. It is not feature-complete.
+Large, backwards-incompatible changes may occur between revisions.
+
+Specifically, the following features are not supported:
+writing or modifying OBF/MSR files, non-OBF based MSR files, reading
+MSR-specific non-image data (window positions, hardware configuration),
+and compression types other than zlib.
+
+The library has been tested with a limited number of files only.
+
+The Imspector image file formats are documented at
+https://imspectordocs.readthedocs.io/en/latest/fileformat.html.
+
+Other implementations for reading Imspector image files are
+`msr-reader <https://github.com/hoerlteam/msr-reader>`_,
+`obf_support.py <https://github.com/biosciflo/VISION>`_, and
+`bio-formats <https://github.com/ome/bioformats>`_.
+
+Examples
+--------
+
+Read an image stack and metadata from a OBF file:
+
+>>> with ObfFile('tests/data/Test.obf') as obf:
+...     assert obf.header.metadata['ome_xml'].startswith('<?xml')
+...     for stack in obf.stacks:
+...         _ = stack.name, stack.dims, stack.shape, stack.dtype
+...     obf.stacks[0].asxarray()
+...
+<xarray.DataArray 'Abberior STAR RED.Confocal' (T: 18, Z: 2, Y: 339, X: 381)...
+array([[[[0, 0, 0, ..., 3, 3, 3],
+         [0, 0, 0, ..., 4, 3, 3],
+         ...,
+         [0, 0, 0, ..., 0, 0, 0],
+         [0, 0, 0, ..., 0, 0, 0]]]], shape=(18, 2, 339, 381), dtype=int16)
+Coordinates:
+    * T        (T) float64 144B 0.0 0.0 0.0 0.0 0.0 0.0 ...
+    * Z        (Z) float64 16B 1.25e-07 3.75e-07
+    * Y        (Y) float64 3kB 0.0 2e-07 4e-07 ...
+    * X        (X) float64 3kB 0.0 2.002e-07 4.003e-07 ...
+...
+
+View the image stack and metadata in a OBF file from the console::
+
+    $ python -m obffile tests/data/Test.obf

obffile-2026.2.20/README.rst

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+..
+  This file is generated by setup.py
+
+Read Imspector object binary format files (OBF and MSR)
+=======================================================
+
+Obffile is a Python library to read image and metadata from
+Object Binary Format (OBF) and Measurement Summary Record (MSR) image files.
+These files are written by Imspector software to store image and metadata
+from microscopy experiments.
+
+:Author: `Christoph Gohlke <https://www.cgohlke.com>`_
+:License: BSD-3-Clause
+:Version: 2026.2.20
+
+Quickstart
+----------
+
+Install the obffile package and all dependencies from the
+`Python Package Index <https://pypi.org/project/obffile/>`_::
+
+    python -m pip install -U obffile[all]
+
+See `Examples`_ for using the programming interface.
+
+Source code and support are available on
+`GitHub <https://github.com/cgohlke/obffile>`_.
+
+Requirements
+------------
+
+This revision was tested with the following requirements and dependencies
+(other versions may work):
+
+- `CPython <https://www.python.org>`_ 3.11.9, 3.12.10, 3.13.12, 3.14.3 64-bit
+- `NumPy <https://pypi.org/project/numpy>`_ 2.4.2
+- `Xarray <https://pypi.org/project/xarray>`_ 2026.2.0 (recommended)
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.10.8 (optional)
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2026.2.16 (optional)
+
+Revisions
+---------
+
+2026.2.20
+
+- Initial alpha release.
+- …
+
+Notes
+-----
+
+`Imspector <https://imspectordocs.readthedocs.io>`_ is a software platform for
+super-resolution and confocal microscopy developed by Abberior Instruments.
+
+This library is in its early stages of development. It is not feature-complete.
+Large, backwards-incompatible changes may occur between revisions.
+
+Specifically, the following features are not supported:
+writing or modifying OBF/MSR files, non-OBF based MSR files, reading
+MSR-specific non-image data (window positions, hardware configuration),
+and compression types other than zlib.
+
+The library has been tested with a limited number of files only.
+
+The Imspector image file formats are documented at
+https://imspectordocs.readthedocs.io/en/latest/fileformat.html.
+
+Other implementations for reading Imspector image files are
+`msr-reader <https://github.com/hoerlteam/msr-reader>`_,
+`obf_support.py <https://github.com/biosciflo/VISION>`_, and
+`bio-formats <https://github.com/ome/bioformats>`_.
+
+Examples
+--------
+
+Read an image stack and metadata from a OBF file:
+
+.. code-block:: python
+
+    >>> with ObfFile('tests/data/Test.obf') as obf:
+    ...     assert obf.header.metadata['ome_xml'].startswith('<?xml')
+    ...     for stack in obf.stacks:
+    ...         _ = stack.name, stack.dims, stack.shape, stack.dtype
+    ...     obf.stacks[0].asxarray()
+    ...
+    <xarray.DataArray 'Abberior STAR RED.Confocal' (T: 18, Z: 2, Y: 339, X: 381)...
+    array([[[[0, 0, 0, ..., 3, 3, 3],
+             [0, 0, 0, ..., 4, 3, 3],
+             ...,
+             [0, 0, 0, ..., 0, 0, 0],
+             [0, 0, 0, ..., 0, 0, 0]]]], shape=(18, 2, 339, 381), dtype=int16)
+    Coordinates:
+        * T        (T) float64 144B 0.0 0.0 0.0 0.0 0.0 0.0 ...
+        * Z        (Z) float64 16B 1.25e-07 3.75e-07
+        * Y        (Y) float64 3kB 0.0 2e-07 4e-07 ...
+        * X        (X) float64 3kB 0.0 2.002e-07 4.003e-07 ...
+    ...
+
+View the image stack and metadata in a OBF file from the console::
+
+    $ python -m obffile tests/data/Test.obf

obffile-2026.2.20/obffile/__init__.py

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+# obffile/__init__.py
+
+from .obffile import *
+from .obffile import __all__, __doc__, __version__
+
+# constants are repeated for documentation
+
+__version__ = __version__
+"""Obffile version string."""

obffile-2026.2.20/obffile/__main__.py

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+# obffile/__main__.py
+
+"""Obffile package command line script."""
+
+import sys
+
+from .obffile import main
+
+sys.exit(main())