Metadata-Version: 1.1
Name: pims-nd2
Version: 1.0
Summary: An image reader for nd2 (NIS Elements) multidimensional images
Home-page: https://github.com/soft-matter/pims_nd2
Author: Casper van der Wel
Author-email: caspervdw@gmail.com
License: UNKNOWN
Download-URL: https://github.com/soft-matter/pims_nd2/tarball/1.0
Description: pims_nd2 : A reader for Nikon .ND2
        ==================================
        [![build status](https://travis-ci.org/soft-matter/pims_nd2.png?branch=master)](https://travis-ci.org/soft-matter/pims_nd2)
        
        `pims_nd2` contains a reader for nd2 files produced by NIS Elements. The reader is based on the included [SDK](http://www.nd2sdk.com) from Nikon, which makes it compatible with older versions of nd2 files. The reader is written in the [pims](https://github.com/soft-matter/pims) framework, enabling easy access to multidimensional files, lazy slicing, and nice display in IPython.
        
        Installation
        ------------
        
        `pims_nd2` is implemented on Windows, Linux and OSX systems. To obtain the latest stable version, install via PyPi:
        
            pip install pims_nd2
        
        The ND2 SDK binaries are included in the package and will be copied into the `pims_nd2` package folder.
        
        Dependencies
        ------------
        
        This reader requires [pims](https://github.com/soft-matter/pims) version 0.3.0.
        
        Examples
        --------
        
        The following code opens a movie file and displays a frame. Note that frames are only actually read when necessary:
        
            from pims import ND2_Reader
            frames = ND2_Reader('some_movie.nd2')
            frames[82]  # display frame 82
            frames.close()
        
        The following code opens the multidimensional demo file included in the package and iterates through the first 3 frames. Note that we use a context manager here. We tell the reader which axis to iterate over and which axes to include in one frame. Also we select which channel to read.
        
            from pims import ND2_Reader
            with ND2_Reader('cluster.nd2') as frames:
        		frames.iter_axes = 't'  # 't' is the default already
        		frames.bundle_axes = 'zyx'  # when 'z' is available, this will be default
        		frames.default_coords['c'] = 1  # 0 is the default setting
        		for frame in frames[:3]:
        			# do something with 3D frames in channel 1
        
        The best way to use the reader is using a context manager. If you do not use a context manager, make sure to call `frames.close()` at the end of your script.
        
        Metadata access can be done on two levels: reader level and frame level.
        
        	frames.metadata['mpp']  # calibration in microns per pixel
        	frames[0].metadata['t_ms']  # time of frame in milliseconds
        
        Supporting Grant
        ----------------
        This reader was developed by Casper van der Wel, as part of his PhD thesis work in Daniela Kraft's group at the Huygens-Kamerlingh-Onnes laboratory, Institute of Physics, Leiden University, The Netherlands. This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW).
        
Platform: MacOS X
Platform: Windows
Platform: Linux CentOs 6.5/7
Platform: Linux Debian 7/8
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: C
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
