Metadata-Version: 2.1
Name: pyoformats
Version: 1.1.0
Summary: PyoFormats: Simple wrapper for python-bioformats
Home-page: https://git.ist.ac.at/csommer/pyoformats
Author: Christoph Sommer, Wiebke Jahr
Author-email: christoph.sommer23@gmail.com, wiebke.jahr@ist.ac.at
License: BSD
Description: # PyoFormats
        Simple wrapper for python-formats
        ---
        ## Example
        ```python
        from pyoformats import read
        
        # start JVM
        read.JVM().start()
        
        # displays names and shapes of all available series in file
        read.file_info("test.msr")
        
        # get series count of file
        n_series = read.series_count("test.msr")
        
        # returns 5d numpy array of image in series
        my_image = read.image_5d("test.msr", series=1)
        
        # read only certain z-slices. (Note, also channels and frames can be selected)
        my_image = read.image_5d("test.msr", series=1, zslices=[2, 3, 5, 8, 13])
        
        # get physical pixel sizes
        xyz_sizes = read.pixel_sizes_xyz("test.msr", series=0)
        
        # get physical pixel units
        xyz_sizes = read.pixel_sizes_xyz_units("test.msr", series=0)
        
        # iterate over all series and extract name and pixel data
        for s, data in read.image_5d_iterator("test.msr"):
            print(s, data.shape)
        
        
        # at end of script
        read.JVM().shutdown()
        ```
        
        ## Installation
        
        #### Detailed How-To for installing dependencies (Windows/ MacOS)
        
        Before you install the pyformats Python package, check out detailed instructions for [installing dependencies](Installation.md).
        
        #### pyoformats directly from gitlab
        `pip install git+https://git.ist.ac.at/csommer/pyoformats.git`
        
        #### or local
        
        1. `git clone https://git.ist.ac.at/csommer/pyoformats.git`
        2. `cd pyoformats`
        3.  `pip install -e .`
        
        ## Dependencies
        * numpy
        * javabridge
        * python-bioformats
        
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Description-Content-Type: text/markdown
