pylibCZIrw


NamepylibCZIrw JSON
Version 4.1.3 PyPI version JSON
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home_pageNone
SummaryA python wrapper around the libCZI C++ library with reading and writing functionality.
upload_time2024-08-27 05:00:27
maintainerNone
docs_urlNone
authorSebastian Soyer
requires_python<3.12,>=3.7
licenseNone
keywords czi imaging
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls.
            # pylibCZIrw - Python wrapper for libCZI

This project provides a simple and easy-to-use Python wrapper for [libCZI](https://github.com/ZEISS/libczi) - a cross-platform C++ library intended for providing read and write access to CZI image documents.

## Important Remarks

* At the moment, **pylibCZIrw** completely abstracts away the subblock concept, both in the reading and in the writing APIs.
* The core concept of pylibCZIrw is focussing on reading and writing 2D image planes by specifying the dimension indices and its location in order to only read or write **what is really needed**.
* It allows reading data via http/https-protocol enabling cloud storage scenarios.

## Example Usage

```python
from pylibCZIrw import czi as pyczi

filepath = "myimagefile.czi"

# open the CZI document to read the
with pyczi.open_czi(filepath) as czidoc:
    # get the image dimensions as a dictionary, where the key identifies the dimension
    total_bounding_box = czidoc.total_bounding_box

    # get the total bounding box for all scenes
    total_bounding_rectangle = czidoc.total_bounding_rectangle

    # get the bounding boxes for each individual scene
    scenes_bounding_rectangle = czidoc.scenes_bounding_rectangle

    # read a 2D image plane and optionally specify planes, zoom levels and ROIs
    image2d = czidoc.read(plane={"T": 1, "Z": 2, "C": 0}, zoom=1.0, roi=(0, 0, 50, 100))
```

The detailed usage can be inferred from the [sample notebooks](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).  

For more detailed information (on the latest version) refer to <https://zeiss.github.io/pylibczirw/>.  

## Installation
In case there is no wheel available for your system configuration, you can:  
- try to install from the provided source distribution  
  **For Windows**:
  - try to [keep paths short on systems with maximum path lengths](https://github.com/pypa/pip/issues/3055)
  - make [Win10 accept file paths over 260 characters](https://www.howtogeek.com/266621/how-to-make-windows-10-accept-file-paths-over-260-characters/)
- reach out to the maintainers of this project to add more wheels

## Disclaimer

The library and the notebook are free to use for everybody. Carl Zeiss Microscopy GmbH undertakes no warranty concerning the use of those tools. Use them at your own risk.

**By using any of those examples you agree to this disclaimer.**

Version: 2023.11.20

Copyright (c) 2023 Carl Zeiss AG, Germany. All Rights Reserved.


# CHANGELOG



## v4.1.3 (2024-08-26)

### Fix

* fix: Channel ID and Name in display settings metadata (#37)

This PR inlcudes the latest version ov libczirw to fix #13 
Fixes #13 ([`04316fe`](https://github.com/ZEISS/pylibczirw/commit/04316fe5861f4e3a5f7a5cb6797903cf75c770e6))


## v4.1.2 (2024-08-06)

### Chore

* chore: remove temporary debugging logic to push to PyPI (#30)

[x] I followed the [How to structure your
PR](https://github.com/ZEISS/pylibczirw/blob/main/CONTRIBUTING.md#creating-a-pr).
[ ] Based on [Commit
Parsing](https://python-semantic-release.readthedocs.io/en/latest/commit-parsing.html):
In case a new **major** release will be created (because the body or
footer begins with &#39;BREAKING CHANGE:&#39;), I created a new [Jupyter
notebook with a matching
version](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).
[ ] Based on [Commit
Parsing](https://python-semantic-release.readthedocs.io/en/latest/commit-parsing.html):
In case a new **minor/patch** release will be created (because PR title
begins with &#39;feat&#39;/(&#39;fix&#39; or &#39;perf&#39;)), I optionally created a new
[Jupyter notebook with a matching
version](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).
[ ] In case of API changes, I updated
[API.md](https://github.com/ZEISS/pylibczirw/blob/main/API.md).

Remove debugging code for temporaily pushing to testpypi until
infrastructure properly set up. ([`3b2ea06`](https://github.com/ZEISS/pylibczirw/commit/3b2ea0610baaa0608156426e5c7d781ca7bcdfcb))

### Fix

* fix: consider only dimensions with size &gt;1 for plane-coordinate (#28)

[x] I followed the [How to structure your
PR](https://github.com/ZEISS/pylibczirw/blob/main/CONTRIBUTING.md#creating-a-pr).
[ ] Based on [Commit
Parsing](https://python-semantic-release.readthedocs.io/en/latest/commit-parsing.html):
In case a new **major** release will be created (because the body or
footer begins with &#39;BREAKING CHANGE:&#39;), I created a new [Jupyter
notebook with a matching
version](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).
[ ] Based on [Commit
Parsing](https://python-semantic-release.readthedocs.io/en/latest/commit-parsing.html):
In case a new **minor/patch** release will be created (because PR title
begins with &#39;feat&#39;/(&#39;fix&#39; or &#39;perf&#39;)), I optionally created a new
[Jupyter notebook with a matching
version](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).
[ ] In case of API changes, I updated
[API.md](https://github.com/ZEISS/pylibczirw/blob/main/API.md).

Re-write of #16 due to changes in infrastructure.

Fixes #10

---------

Co-authored-by: Soyer, Sebastian &lt;sebastian.soyer@zeiss.com&gt;
Co-authored-by: soyers &lt;soyer.sebastian@gmail.com&gt; ([`264fcb4`](https://github.com/ZEISS/pylibczirw/commit/264fcb4ab95274e54433a0054d69f07c402582f4))


## v4.1.1 (2024-07-26)

### Chore

* chore: Add codeowners (#27)

Add CODEOWNERS file ([`dc1717b`](https://github.com/ZEISS/pylibczirw/commit/dc1717b88e4141546f4e9c29d4c3fa91a2c9ea95))

### Deps

* deps: bump codecov/codecov-action from 3 to 4 (#2)

Bumps
[codecov/codecov-action](https://github.com/codecov/codecov-action) from
3 to 4.
---------

Signed-off-by: dependabot[bot] &lt;support@github.com&gt;
Co-authored-by: dependabot[bot] &lt;49699333+dependabot[bot]@users.noreply.github.com&gt;
Co-authored-by: Felix Scheffler &lt;felix.scheffler@zeiss.com&gt; ([`dab7b18`](https://github.com/ZEISS/pylibczirw/commit/dab7b1807486f8eee57c9a565912d1337621cddd))

### Refactor

* refactor: Megalinter and infrastructure (#19)

[x] I followed the [How to structure your
PR](https://github.com/ZEISS/pylibczirw/blob/main/CONTRIBUTING.md#creating-a-pr).
[ ] Based on [Commit
Parsing](https://python-semantic-release.readthedocs.io/en/latest/commit-parsing.html):
In case a new **major** release will be created (because the body or
footer begins with &#39;BREAKING CHANGE:&#39;), I created a new [Jupyter
notebook with a matching
version](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).
[ ] Based on [Commit
Parsing](https://python-semantic-release.readthedocs.io/en/latest/commit-parsing.html):
In case a new **minor/patch** release will be created (because PR title
begins with &#39;feat&#39;/(&#39;fix&#39; or &#39;perf&#39;)), I optionally created a new
[Jupyter notebook with a matching
version](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).
[ ] In case of API changes, I updated
[API.md](https://github.com/ZEISS/pylibczirw/blob/main/API.md).

Infrastructure related changes, linting ([`2e60a2b`](https://github.com/ZEISS/pylibczirw/commit/2e60a2bc15933e92e75d96dce34171de07d109b7))

### Unknown

            

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    "description": "# pylibCZIrw - Python wrapper for libCZI\n\nThis project provides a simple and easy-to-use Python wrapper for [libCZI](https://github.com/ZEISS/libczi) - a cross-platform C++ library intended for providing read and write access to CZI image documents.\n\n## Important Remarks\n\n* At the moment, **pylibCZIrw** completely abstracts away the subblock concept, both in the reading and in the writing APIs.\n* The core concept of pylibCZIrw is focussing on reading and writing 2D image planes by specifying the dimension indices and its location in order to only read or write **what is really needed**.\n* It allows reading data via http/https-protocol enabling cloud storage scenarios.\n\n## Example Usage\n\n```python\nfrom pylibCZIrw import czi as pyczi\n\nfilepath = \"myimagefile.czi\"\n\n# open the CZI document to read the\nwith pyczi.open_czi(filepath) as czidoc:\n    # get the image dimensions as a dictionary, where the key identifies the dimension\n    total_bounding_box = czidoc.total_bounding_box\n\n    # get the total bounding box for all scenes\n    total_bounding_rectangle = czidoc.total_bounding_rectangle\n\n    # get the bounding boxes for each individual scene\n    scenes_bounding_rectangle = czidoc.scenes_bounding_rectangle\n\n    # read a 2D image plane and optionally specify planes, zoom levels and ROIs\n    image2d = czidoc.read(plane={\"T\": 1, \"Z\": 2, \"C\": 0}, zoom=1.0, roi=(0, 0, 50, 100))\n```\n\nThe detailed usage can be inferred from the [sample notebooks](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).  \n\nFor more detailed information (on the latest version) refer to <https://zeiss.github.io/pylibczirw/>.  \n\n## Installation\nIn case there is no wheel available for your system configuration, you can:  \n- try to install from the provided source distribution  \n  **For Windows**:\n  - try to [keep paths short on systems with maximum path lengths](https://github.com/pypa/pip/issues/3055)\n  - make [Win10 accept file paths over 260 characters](https://www.howtogeek.com/266621/how-to-make-windows-10-accept-file-paths-over-260-characters/)\n- reach out to the maintainers of this project to add more wheels\n\n## Disclaimer\n\nThe library and the notebook are free to use for everybody. Carl Zeiss Microscopy GmbH undertakes no warranty concerning the use of those tools. Use them at your own risk.\n\n**By using any of those examples you agree to this disclaimer.**\n\nVersion: 2023.11.20\n\nCopyright (c) 2023 Carl Zeiss AG, Germany. 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([`3b2ea06`](https://github.com/ZEISS/pylibczirw/commit/3b2ea0610baaa0608156426e5c7d781ca7bcdfcb))\n\n### Fix\n\n* fix: consider only dimensions with size &gt;1 for plane-coordinate (#28)\n\n[x] I followed the [How to structure your\nPR](https://github.com/ZEISS/pylibczirw/blob/main/CONTRIBUTING.md#creating-a-pr).\n[ ] Based on [Commit\nParsing](https://python-semantic-release.readthedocs.io/en/latest/commit-parsing.html):\nIn case a new **major** release will be created (because the body or\nfooter begins with &#39;BREAKING CHANGE:&#39;), I created a new [Jupyter\nnotebook with a matching\nversion](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).\n[ ] Based on [Commit\nParsing](https://python-semantic-release.readthedocs.io/en/latest/commit-parsing.html):\nIn case a new **minor/patch** release will be created (because PR title\nbegins with &#39;feat&#39;/(&#39;fix&#39; or &#39;perf&#39;)), I optionally created a new\n[Jupyter notebook with a matching\nversion](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).\n[ ] In case of API changes, I updated\n[API.md](https://github.com/ZEISS/pylibczirw/blob/main/API.md).\n\nRe-write of #16 due to changes in infrastructure.\n\nFixes #10\n\n---------\n\nCo-authored-by: Soyer, Sebastian &lt;sebastian.soyer@zeiss.com&gt;\nCo-authored-by: soyers &lt;soyer.sebastian@gmail.com&gt; ([`264fcb4`](https://github.com/ZEISS/pylibczirw/commit/264fcb4ab95274e54433a0054d69f07c402582f4))\n\n\n## v4.1.1 (2024-07-26)\n\n### Chore\n\n* chore: Add codeowners (#27)\n\nAdd CODEOWNERS file ([`dc1717b`](https://github.com/ZEISS/pylibczirw/commit/dc1717b88e4141546f4e9c29d4c3fa91a2c9ea95))\n\n### Deps\n\n* deps: bump codecov/codecov-action from 3 to 4 (#2)\n\nBumps\n[codecov/codecov-action](https://github.com/codecov/codecov-action) from\n3 to 4.\n---------\n\nSigned-off-by: dependabot[bot] &lt;support@github.com&gt;\nCo-authored-by: dependabot[bot] &lt;49699333+dependabot[bot]@users.noreply.github.com&gt;\nCo-authored-by: Felix Scheffler &lt;felix.scheffler@zeiss.com&gt; ([`dab7b18`](https://github.com/ZEISS/pylibczirw/commit/dab7b1807486f8eee57c9a565912d1337621cddd))\n\n### Refactor\n\n* refactor: Megalinter and infrastructure (#19)\n\n[x] I followed the [How to structure your\nPR](https://github.com/ZEISS/pylibczirw/blob/main/CONTRIBUTING.md#creating-a-pr).\n[ ] Based on [Commit\nParsing](https://python-semantic-release.readthedocs.io/en/latest/commit-parsing.html):\nIn case a new **major** release will be created (because the body or\nfooter begins with &#39;BREAKING CHANGE:&#39;), I created a new [Jupyter\nnotebook with a matching\nversion](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).\n[ ] Based on [Commit\nParsing](https://python-semantic-release.readthedocs.io/en/latest/commit-parsing.html):\nIn case a new **minor/patch** release will be created (because PR title\nbegins with &#39;feat&#39;/(&#39;fix&#39; or &#39;perf&#39;)), I optionally created a new\n[Jupyter notebook with a matching\nversion](https://github.com/ZEISS/pylibczirw/tree/main/doc/jupyter_notebooks).\n[ ] In case of API changes, I updated\n[API.md](https://github.com/ZEISS/pylibczirw/blob/main/API.md).\n\nInfrastructure related changes, linting ([`2e60a2b`](https://github.com/ZEISS/pylibczirw/commit/2e60a2bc15933e92e75d96dce34171de07d109b7))\n\n### Unknown\n",
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