Metadata-Version: 2.1
Name: smalldataviewer
Version: 0.4.3
Summary: Command-line tool and python library for visualising small 3D datasets
Home-page: https://github.com/clbarnes/smalldataviewer
Author: Chris L Barnes
Author-email: barnesc@janelia.hhmi.org
License: MIT
Description: .. image:: https://travis-ci.org/clbarnes/smalldataviewer.svg?branch=master
            :target: https://travis-ci.org/clbarnes/smalldataviewer
        
        smalldataviewer
        ===============
        
        Simple matplotlib-based tool for viewing small amounts of 3D image data;
        helpful for debugging. Supports python 2.7 and 3.4+.
        
        Adapted from `this matplotlib recipe <https://matplotlib.org/gallery/animation/image_slices_viewer.html>`_.
        
        Installation
        ------------
        
        .. code:: bash
        
            pip install smalldataviewer
        
        Some file types require additional dependencies:
        
        -  HDF5: h5py_
        
           -  ``pip install h5py``
        
        -  zarr, N5: z5py_
        
           -  ``conda install -c cpape -c conda-forge z5py``
        
        .. _h5py: http://docs.h5py.org/en/latest/build.html
        .. _z5py: https://github.com/constantinpape/z5
        
        Usage
        -----
        
        As executable
        ~~~~~~~~~~~~~
        
        .. code::
        
            usage: smalldataviewer [-h] [-i INTERNAL_PATH] [-t TYPE] [-o ORDER]
                                   [-f OFFSET] [-s SHAPE] [-v]
                                   path
        
            positional arguments:
              path                  Path to HDF5, N5, zarr, npy, npz or JSON file
                                    containing a 3D dataset
        
            optional arguments:
              -h, --help            show this help message and exit
              -i INTERNAL_PATH, --internal_path INTERNAL_PATH
                                    Internal path of dataset inside HDF5, N5, zarr or npz
                                    file. If JSON, assumes the outerobject is a dict, and
                                    internal_path is the key of the array
              -t TYPE, --type TYPE  Dataset file type. Inferred from extension if not
                                    given.
              -o ORDER, --order ORDER
                                    Order of spatial axes for axis labelling purposes.
                                    Data is not transposed: dimension 0 will be scrolled
                                    through, dimension 1 will be on the up-down axis,
                                    dimension 2 will be on the left-right axis,
                                    anddimension 3, if it exists, will be used as the
                                    colour channels. Default "zyx".
              -f OFFSET, --offset OFFSET
                                    3D offset of ROI from (0, 0, 0) in pixels, in the form
                                    "<scroll>,<vertical>,<horizontal>"
              -s SHAPE, --shape SHAPE
                                    3D shape of ROI in pixels, in the form
                                    "<scroll>,<vertical>,<horizontal>"
              -v, --verbose         Increase logging verbosity
        
        .. code:: bash
        
            smalldataviewer my_data.hdf5 -i /my_group/my_volume
        
        Note: because of the circumstances under which python holds file descriptors open,
        and under which matplotlib blocks, the executable form reads the data into memory
        in its entirety. If your data are too big for this, look at small chunks with the
        oFfset and Shape options.
        
        As library
        ~~~~~~~~~~
        
        .. code:: python
        
            from smalldataviewer import DataViewer, dataviewer_from_file
        
            import numpy as np
            data = np.random.random((30, 100, 100))
        
            viewer = DataViewer(data)
            viewer.show()  # or matplotlib.pyplot.show()
        
            viewer2 = dataviewer_from_file(dataviewer, "my_data.npz", "volume")
            viewer2.show()
        
        Note: ``dataviewer_from_file`` reads the requested data into memory. ``DataViewer``
        does not, by default. However, you may need to, depending on the rest of your script.
        
Keywords: image volume 3d
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 2.7
Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*
Provides-Extra: hdf5
Provides-Extra: full
