Metadata-Version: 1.2
Name: oiffile
Version: 2018.8.29
Summary: Read Olympus(r) image files (OIF and OIB)
Home-page: https://www.lfd.uci.edu/~gohlke/
Author: Christoph Gohlke
Author-email: cgohlke@uci.edu
License: BSD
Description: Read Olympus(r) image files (OIF and OIB)
        =========================================
        
        The Olympus Image Format is the native file format of the Olympus FluoView(tm)
        software for confocal microscopy.
        OIF (Olympus Image File) is a multi-file format that includes a main setting
        file (.oif) and an associated directory with data and setting files (.tif,
        .bmp, .txt, .pyt, .roi, and .lut).
        OIB (Olympus Image Binary) is a compound document file, storing OIF and
        associated files within a single file.
        
        :Author:
          `Christoph Gohlke <https://www.lfd.uci.edu/~gohlke/>`_
        
        :Organization:
          Laboratory for Fluorescence Dynamics. University of California, Irvine
        
        :Version: 2018.8.29
        
        Requirements
        ------------
        * `CPython 2.7 or 3.5+ <https://www.python.org>`_
        * `Numpy 1.14 <https://www.numpy.org>`_
        * `Tiffile 2018.8.28 <https://www.lfd.uci.edu/~gohlke/>`_
        
        Notes
        -----
        The API is not stable yet and might change between revisions.
        
        Python 2.7 and 3.4 are deprecated.
        
        No specification document is available.
        
        Tested only with files produced on Olympus FV1000 hardware.
        
        Examples
        --------
        
        Read the image from an OIB file as numpy array:
        
        >>> image = imread('test.oib')
        >>> image.shape
        (3, 256, 256)
        >>> image[:, 95, 216]
        array([820,  50, 436], dtype=uint16)
        
        Read the image from a single TIFF file in an OIB file:
        
        >>> with OifFile('test.oib') as oib:
        ...     filename = natural_sorted(oib.glob('*.tif'))[0]
        ...     image = oib.asarray(filename)
        >>> filename
        'Storage00001/s_C001.tif'
        >>> image[95, 216]
        820
        
        Access information in an OIB main file:
        
        >>> with OifFile('test.oib') as oib:
        ...     dataname = oib.mainfile['File Info']['DataName']
        >>> dataname
        'Cell 1 mitoEGFP.oib'
        
        Extract the OIB file content to an OIF file and associated data directory:
        
        >>> tempdir = tempfile.mkdtemp()
        >>> oib2oif('test.oib', location=tempdir)
        Saving ... done.
        
        Read the image from the extracted OIF file:
        
        >>> oif_filename = '%s/%s.oif' % (tempdir, dataname[:-4])
        >>> image = imread(oif_filename)
        >>> image[:, 95, 216]
        array([820,  50, 436], dtype=uint16)
        
        Read OLE compound file and access the 'OibInfo.txt' settings file:
        
        >>> with CompoundFile('test.oib') as oib:
        ...     info = oib.open_file('OibInfo.txt')
        >>> info = SettingsFile(info, 'OibInfo.txt')
        >>> info['OibSaveInfo']['Version']
        '2.0.0.0'
        
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=2.7
