https://github.com/tlambert03/bioformats_jar

(deprecated) meta-package to import bioformats_jar from scyjava
https://github.com/tlambert03/bioformats_jar

bioformats ome python

Last synced: 9 days ago
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(deprecated) meta-package to import bioformats_jar from scyjava

• Host: GitHub
• URL: https://github.com/tlambert03/bioformats_jar
• Owner: tlambert03
• License: gpl-2.0
• Created: 2021-09-14T19:08:57.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2022-05-27T21:02:28.000Z (over 2 years ago)
• Last Synced: 2024-10-11T21:54:41.702Z (about 1 month ago)
• Topics: bioformats, ome, python
• Language: Python
• Homepage:
• Size: 39.1 MB
• Stars: 0
• Watchers: 5
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# bioformats_jar

[![License](https://img.shields.io/pypi/l/bioformats_jar.svg?color=green)](https://github.com/tlambert03/bioformats_jar/raw/master/LICENSE)

[![PyPI](https://img.shields.io/pypi/v/bioformats_jar.svg?color=green)](https://pypi.org/project/bioformats_jar)

[![Python Version](https://img.shields.io/pypi/pyversions/bioformats_jar.svg?color=green)](https://python.org)

[![CI](https://github.com/tlambert03/bioformats_jar/actions/workflows/ci.yml/badge.svg)](https://github.com/tlambert03/bioformats_jar/actions/workflows/ci.yml)

## deprecated

This package is deprecated.  You should use [scyjava](https://github.com/scijava/scyjava) to download and import jars.  The functionality in this

package can be accomplished using scyjava as follows:

```python

import jpype

import scyjava

scyjava.config.endpoints.append('ome:formats-gpl:6.7.0')

scyjava.start_jvm()

loci = jpype.JPackage("loci")

loci.common.DebugTools.setRootLevel("ERROR")

```

This package remains only for packages that already depend on it.

## usage

```python

from bioformats_jar import get_loci, set_loci_log_level

# start the JVM and get the loci module

loci = get_loci()

# optionally:

set_loci_log_level("DEBUG")  # by default "ERROR"

```

The following environment variables can also be used:

- `BIOFORMATS_VERSION` - version of bioformats to use.  by default "LATEST"

- `BIOFORMATS_LOG_LEVEL` - logging level for loci tools. by default "ERROR"

- `BIOFORMATS_LICENSE` - license version of bioformats to use.  must be either

  `"gpl"` or `"bsd"`.  By default `"gpl"`

*see also:*

- [Bioformats Docs](https://docs.openmicroscopy.org/bio-formats/latest)

- [Javadocs](https://downloads.openmicroscopy.org/bio-formats/latest/api/) with the loci API

## install

```sh

pip install bioformats-jar

```

```sh

conda install -c conda-forge bioformats-jar

```