python-microscopy 25.11.20__cp313-cp313-win_amd64.whl

PYME/contrib/gohlke/tifffile.py

@@ -0,0 +1,3095 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# tifffile.py
+
+# Copyright (c) 2008-2012, Christoph Gohlke
+# Copyright (c) 2008-2012, The Regents of the University of California
+# Produced at the Laboratory for Fluorescence Dynamics
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright
+#   notice, this list of conditions and the following disclaimer.
+# * Redistributions in binary form must reproduce the above copyright
+#   notice, this list of conditions and the following disclaimer in the
+#   documentation and/or other materials provided with the distribution.
+# * Neither the name of the copyright holders nor the names of any
+#   contributors may be used to endorse or promote products derived
+#   from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+
+"""Read and write image data from and to TIFF files.
+
+Image and meta-data can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH,
+and FluoView files. Only a subset of the TIFF specification is supported,
+mainly uncompressed and losslessly compressed 2**(0 to 6) bit integer,
+16, 32 and 64-bit float, grayscale and RGB(A) images, which are commonly
+used in bio-scientific imaging. Specifically, reading JPEG or CCITT
+compressed image data is not implemented. Only primary info records are
+read for STK, FluoView, and NIH image formats.
+
+TIFF, the Tagged Image File Format, is under the control of Adobe Systems.
+BigTIFF allows for files greater than 4 GB. STK, LSM, FluoView, and OME-TIFF
+are custom extensions defined by MetaMorph, Carl Zeiss MicroImaging,
+Olympus, and the Open Microscopy Environment consortium respectively.
+
+The API is not stable yet and might change between revisions.
+Tested on little-endian platforms only.
+
+For command line usage run ``python tifffile.py --help``
+
+:Authors:
+  `Christoph Gohlke <http://www.lfd.uci.edu/~gohlke/>`__,
+  Laboratory for Fluorescence Dynamics, University of California, Irvine
+
+:Version: 2012.04.21
+
+Requirements
+------------
+
+* `Python 2.7 or 3.2 <http://www.python.org>`__
+* `Numpy 1.6 <http://numpy.scipy.org>`__
+* `Matplotlib 1.1 <http://matplotlib.sourceforge.net>`__
+  (optional for plotting)
+* `tifffile.c 2012.01.01 <http://www.lfd.uci.edu/~gohlke/>`__
+  (optional for faster decoding of PackBits and LZW encoded strings)
+
+Acknowledgements
+----------------
+*  Egor Zindy, University of Manchester, for cz_lsm_scan_info specifics.
+*  Wim Lewis, for a bug fix and some read_cz_lsm functions.
+
+References
+----------
+
+(1) TIFF 6.0 Specification and Supplements. Adobe Systems Incorporated.
+    http://partners.adobe.com/public/developer/tiff/
+(2) TIFF File Format FAQ. http://www.awaresystems.be/imaging/tiff/faq.html
+(3) MetaMorph Stack (STK) Image File Format.
+    http://support.meta.moleculardevices.com/docs/t10243.pdf
+(4) File Format Description - LSM 5xx Release 2.0.
+    http://ibb.gsf.de/homepage/karsten.rodenacker/IDL/Lsmfile.doc
+(5) BioFormats. http://www.loci.wisc.edu/ome/formats.html
+(6) The OME-TIFF format.
+    http://www.openmicroscopy.org/site/support/file-formats/ome-tiff
+
+Examples
+--------
+
+>>> data = numpy.random.rand(301, 219)
+>>> imsave('temp.tif', data)
+>>> image = imread('temp.tif')
+>>> assert numpy.all(image == data)
+
+>>> tif = TIFFfile('test.tif')
+>>> images = tif.asarray()
+>>> image0 = tif[0].asarray()
+>>> for page in tif:
+...     for tag in page.tags.values():
+...         t = tag.name, tag.value
+...     image = page.asarray()
+...     if page.is_rgb: pass
+...     if page.is_palette:
+...         t = page.color_map
+...     if page.is_stk:
+...         t = page.mm_uic_tags.number_planes
+...     if page.is_lsm:
+...         t = page.cz_lsm_info
+>>> tif.close()
+
+"""
+
+from __future__ import division, print_function
+
+import sys
+import os
+import math
+import zlib
+import time
+import struct
+import warnings
+import datetime
+import collections
+from xml.etree import cElementTree as ElementTree
+
+import numpy
+
+__all__ = ['imsave', 'imread', 'imshow', 'TIFFfile']
+
+
+def imsave(filename, data, photometric=None, planarconfig=None,
+           resolution=None, description=None, software='tifffile.py',
+           byteorder=None, bigtiff=False):
+    """Write image data to TIFF file.
+
+    Image data are written uncompressed in one stripe per plane.
+    Dimensions larger than 2 or 3 (depending on photometric mode and
+    planar configuration) are flattened and saved as separate pages.
+
+    Arguments
+    ---------
+
+    filename : str
+        Name of file to write.
+
+    data : array_like
+        Input image. The last dimensions are assumed to be image height,
+        width, and samples.
+
+    photometric : {'minisblack', 'miniswhite', 'rgb'}
+        The color space of the image data.
+        By default this setting is inferred from the data shape.
+
+    planarconfig : {'contig', 'planar'}
+        Specifies if samples are stored contiguous or in separate planes.
+        By default this setting is inferred from the data shape.
+        'contig': last dimension contains samples.
+        'planar': third last dimension contains samples.
+
+    resolution : ((int, int), (int, int))
+        X and Y resolution in dots per inch as rational numbers.
+
+    description : str
+        The subject of the image. Saved with the first page only.
+
+    software : str
+        Name of the software used to create the image.
+        Saved with the first page only.
+
+    byteorder : {'<', '>'}
+        The endianness of the data in the file.
+        By default this is the system's native byte order.
+
+    bigtiff : bool
+        If True the BigTIFF format is used.
+        By default the standard TIFF format is used for data less than 2040 MB.
+
+    Example
+    -------
+
+    >>> data = numpy.random.rand(10, 3, 301, 219)
+    >>> imsave('temp.tif', data)
+
+    """
+    assert(photometric in (None, 'minisblack', 'miniswhite', 'rgb'))
+    assert(planarconfig in (None, 'contig', 'planar'))
+    assert(byteorder in (None, '<', '>'))
+
+    if byteorder is None:
+        byteorder = '<' if sys.byteorder == 'little' else '>'
+
+    data = numpy.asarray(data, dtype=byteorder+data.dtype.char, order='C')
+    data_shape = shape = data.shape
+    data = numpy.atleast_2d(data)
+
+    if not bigtiff and data.size * data.dtype.itemsize < 2040*2**20:
+        bigtiff = False
+        offset_size = 4
+        tag_size = 12
+        numtag_format = 'H'
+        offset_format = 'I'
+        val_format = '4s'
+    else:
+        bigtiff = True
+        offset_size = 8
+        tag_size = 20
+        numtag_format = 'Q'
+        offset_format = 'Q'
+        val_format = '8s'
+
+    # unify shape of data
+    samplesperpixel = 1
+    extrasamples = 0
+    if photometric is None:
+        if data.ndim > 2 and (shape[-3] in (3, 4) or shape[-1] in (3, 4)):
+            photometric = 'rgb'
+        else:
+            photometric = 'minisblack'
+    if photometric == 'rgb':
+        if len(shape) < 3:
+            raise ValueError("not a RGB(A) image")
+        if planarconfig is None:
+            planarconfig = 'planar' if shape[-3] in (3, 4) else 'contig'
+        if planarconfig == 'contig':
+            if shape[-1] not in (3, 4):
+                raise ValueError("not a contiguous RGB(A) image")
+            data = data.reshape((-1, 1) + shape[-3:])
+            samplesperpixel = shape[-1]
+        else:
+            if shape[-3] not in (3, 4):
+                raise ValueError("not a planar RGB(A) image")
+            data = data.reshape((-1, ) + shape[-3:] + (1, ))
+            samplesperpixel = shape[-3]
+        if samplesperpixel == 4:
+            extrasamples = 1
+    elif planarconfig and len(shape) > 2:
+        if planarconfig == 'contig':
+            data = data.reshape((-1, 1) + shape[-3:])
+            samplesperpixel = shape[-1]
+        else:
+            data = data.reshape((-1, ) + shape[-3:] + (1, ))
+            samplesperpixel = shape[-3]
+        extrasamples = samplesperpixel - 1
+    else:
+        planarconfig = None
+        data = data.reshape((-1, 1) + shape[-2:] + (1, ))
+
+    shape = data.shape  # (pages, planes, height, width, contig samples)
+
+    bytestr = bytes if sys.version[0] == '2' else lambda x: bytes(x, 'ascii')
+    tifftypes = {'B': 1, 's': 2, 'H': 3, 'I': 4, '2I': 5, 'b': 6,
+                 'h': 8, 'i': 9, 'f': 11, 'd': 12, 'Q': 16, 'q': 17}
+    tifftags = {'new_subfile_type': 254, 'subfile_type': 255,
+        'image_width': 256, 'image_length': 257, 'bits_per_sample': 258,
+        'compression': 259, 'photometric': 262, 'fill_order': 266,
+        'document_name': 269, 'image_description': 270, 'strip_offsets': 273,
+        'orientation': 274, 'samples_per_pixel': 277, 'rows_per_strip': 278,
+        'strip_byte_counts': 279, 'x_resolution': 282, 'y_resolution': 283,
+        'planar_configuration': 284, 'page_name': 285, 'resolution_unit': 296,
+        'software': 305, 'datetime': 306, 'predictor': 317, 'color_map': 320,
+        'extra_samples': 338, 'sample_format': 339}
+
+    tags = []
+    tag_data = []
+
+    def pack(fmt, *val):
+        return struct.pack(byteorder+fmt, *val)
+
+    def tag(name, dtype, number, value, offset=[0]):
+        # append tag binary string to tags list
+        # append (offset, value as binary string) to tag_data list
+        # increment offset by tag_size
+        if dtype == 's':
+            value = bytestr(value) + b'\0'
+            number = len(value)
+            value = (value, )
+        t = [pack('HH', tifftags[name], tifftypes[dtype]),
+             pack(offset_format, number)]
+        if len(dtype) > 1:
+            number *= int(dtype[:-1])
+            dtype = dtype[-1]
+        if number == 1:
+            if isinstance(value, (tuple, list)):
+                value = value[0]
+            t.append(pack(val_format, pack(dtype, value)))
+        elif struct.calcsize(dtype) * number <= offset_size:
+            t.append(pack(val_format, pack(str(number)+dtype, *value)))
+        else:
+            t.append(pack(offset_format, 0))
+            tag_data.append((offset[0] + offset_size + 4,
+                             pack(str(number)+dtype, *value)))
+        tags.append(b''.join(t))
+        offset[0] += tag_size
+
+    if software:
+        tag('software', 's', 0, software)
+    if description:
+        tag('image_description', 's', 0, description)
+    elif shape != data_shape:
+        tag('image_description', 's', 0,
+            "shape=(%s)" % (",".join('%i' % i for i in data_shape)))
+    tag('datetime', 's', 0,
+        datetime.datetime.now().strftime("%Y:%m:%d %H:%M:%S"))
+    # write previous tags only once
+    writeonce = (len(tags), len(tag_data)) if shape[0] > 1 else None
+    tag('compression', 'H', 1, 1)
+    tag('orientation', 'H', 1, 1)
+    tag('image_width', 'I', 1, shape[-2])
+    tag('image_length', 'I', 1, shape[-3])
+    tag('new_subfile_type', 'I', 1, 0 if shape[0] == 1 else 2)
+    tag('sample_format', 'H', 1,
+        {'u': 1, 'i': 2, 'f': 3, 'c': 6}[data.dtype.kind])
+    tag('photometric', 'H', 1,
+        {'miniswhite': 0, 'minisblack': 1, 'rgb': 2}[photometric])
+    tag('samples_per_pixel', 'H', 1, samplesperpixel)
+    if planarconfig:
+        tag('planar_configuration', 'H', 1, 1 if planarconfig=='contig' else 2)
+        tag('bits_per_sample', 'H', samplesperpixel,
+            (data.dtype.itemsize * 8, ) * samplesperpixel)
+    else:
+        tag('bits_per_sample', 'H', 1, data.dtype.itemsize * 8)
+    if extrasamples:
+        if photometric == 'rgb':
+            tag('extra_samples', 'H', 1, 1)  # alpha channel
+        else:
+            tag('extra_samples', 'H', extrasamples, (0, ) * extrasamples)
+    if resolution:
+        tag('x_resolution', '2I', 1, resolution[0])
+        tag('y_resolution', '2I', 1, resolution[1])
+        tag('resolution_unit', 'H', 1, 2)
+    tag('rows_per_strip', 'I', 1, shape[-3])
+    # use one strip per plane
+    strip_byte_counts = (data[0, 0].size * data.dtype.itemsize, ) * shape[1]
+    tag('strip_byte_counts', offset_format, shape[1], strip_byte_counts)
+    # strip_offsets must be the last tag; will be updated later
+    tag('strip_offsets', offset_format, shape[1], (0, ) * shape[1])
+
+    fd = open(filename, 'wb')
+    seek = fd.seek
+    tell = fd.tell
+
+    def write(arg, *args):
+        fd.write(pack(arg, *args) if args else arg)
+
+    write({'<': b'II', '>': b'MM'}[byteorder])
+    if bigtiff:
+        write('HHH', 43, 8, 0)
+    else:
+        write('H', 42)
+    ifd_offset = tell()
+    write(offset_format, 0)  # first IFD
+    for i in range(shape[0]):
+        # update pointer at ifd_offset
+        pos = tell()
+        seek(ifd_offset)
+        write(offset_format, pos)
+        seek(pos)
+        # write tags
+        write(numtag_format, len(tags))
+        tag_offset = tell()
+        write(b''.join(tags))
+        ifd_offset = tell()
+        write(offset_format, 0)  # offset to next ifd
+        # write extra tag data and update pointers
+        for off, dat in tag_data:
+            pos = tell()
+            seek(tag_offset + off)
+            write(offset_format, pos)
+            seek(pos)
+            write(dat)
+        # update strip_offsets
+        pos = tell()
+        if len(strip_byte_counts) == 1:
+            seek(ifd_offset - offset_size)
+            write(offset_format, pos)
+        else:
+            seek(pos - offset_size*shape[1])
+            strip_offset = pos
+            for size in strip_byte_counts:
+                write(offset_format, strip_offset)
+                strip_offset += size
+        seek(pos)
+        # write data
+        data[i].tofile(fd)  # if this fails, try update Python and numpy
+        fd.flush()
+        # remove tags that should be written only once
+        if writeonce:
+            tags = tags[writeonce[0]:]
+            d = writeonce[0] * tag_size
+            tag_data = [(o-d, v) for (o, v) in tag_data[writeonce[1]:]]
+            writeonce = None
+    fd.close()
+
+
+#modified by D. Baddeley for different image dimensionality and to avoid the
+#requirement for the whole image to be in memory
+#also saves each colour channel as an individual plane for better compatibility with 
+#ImageJ / OME
+def imsave_f(filename, data,
+           resolution=None, description=None, software='tifffile.py',
+           byteorder=None, bigtiff=False):
+    """Write image data to TIFF file.
+
+    Image data are written uncompressed in one stripe per plane.
+    Dimensions larger than 2 are flattened and saved as separate pages.
+
+    Arguments
+    ---------
+
+    filename : str
+        Name of file to write.
+
+    data : array_like
+        Input image. The first two dimensions are assumed to be imagewidth and height (x & y)
+        The following ones, time/z and colour.
+
+    resolution : ((int, int), (int, int))
+        X and Y resolution in dots per inch as rational numbers.
+
+    description : str
+        The subject of the image. Saved with the first page only.
+
+    software : str
+        Name of the software used to create the image.
+        Saved with the first page only.
+
+    byteorder : {'<', '>'}
+        The endianness of the data in the file.
+        By default this is the system's native byte order.
+
+    bigtiff : bool
+        If True the BigTIFF format is used.
+        By default the standard TIFF format is used for data less than 2040 MB.
+
+    Example
+    -------
+
+    >>> data = numpy.random.rand(10, 3, 301, 219)
+    >>> imsave('temp.tif', data)
+
+    """
+    #assert(photometric in (None, 'minisblack', 'miniswhite', 'rgb'))
+    #assert(planarconfig in (None, 'contig', 'planar'))
+    photometric = 'minisblack'
+    assert(byteorder in (None, '<', '>'))
+
+    if byteorder is None:
+        byteorder = '<' if sys.byteorder == 'little' else '>'
+
+    #don't modify data here (forces copy or bringing it into memory)    
+    #data = numpy.asarray(data, dtype=byteorder+data.dtype.char, order='C')
+    data_shape = shape = data.shape
+    #data = numpy.atleast_2d(data)
+    num_planes = numpy.prod(shape[2:])
+    
+    frame0 = data[:,:,0,0,0]
+    data_type = frame0.dtype
+    
+    if data_type == 'float64':
+        #force downcast as no-one understands 64bit float tiffs
+        #NB actual downcast occurs on a per-frame basis just before write so we 
+        #don't need to load everything into memory here
+        data_type = numpy.dtype('float32')
+    
+    data_size = frame0.size*data_type.itemsize*num_planes
+
+    if not bigtiff and data_size < 2040*2**20:
+        bigtiff = False
+        offset_size = 4
+        tag_size = 12
+        numtag_format = 'H'
+        offset_format = 'I'
+        val_format = '4s'
+    else:
+        bigtiff = True
+        offset_size = 8
+        tag_size = 20
+        numtag_format = 'Q'
+        offset_format = 'Q'
+        val_format = '8s'
+
+    # unify shape of data
+    samplesperpixel = 1
+    #extrasamples = 0
+#    if photometric is None:
+#        if data.ndim > 2 and (shape[-3] in (3, 4) or shape[-1] in (3, 4)):
+#            photometric = 'rgb'
+#        else:
+#            photometric = 'minisblack'
+#    if photometric == 'rgb':
+#        if len(shape) < 3:
+#            raise ValueError("not a RGB(A) image")
+#        if planarconfig is None:
+#            planarconfig = 'planar' if shape[-3] in (3, 4) else 'contig'
+#        if planarconfig == 'contig':
+#            if shape[-1] not in (3, 4):
+#                raise ValueError("not a contiguous RGB(A) image")
+#            data = data.reshape((-1, 1) + shape[-3:])
+#            samplesperpixel = shape[-1]
+#        else:
+#            if shape[-3] not in (3, 4):
+#                raise ValueError("not a planar RGB(A) image")
+#            data = data.reshape((-1, ) + shape[-3:] + (1, ))
+#            samplesperpixel = shape[-3]
+#        if samplesperpixel == 4:
+#            extrasamples = 1
+#    elif planarconfig and len(shape) > 2:
+#        if planarconfig == 'contig':
+#            data = data.reshape((-1, 1) + shape[-3:])
+#            samplesperpixel = shape[-1]
+#        else:
+#            data = data.reshape((-1, ) + shape[-3:] + (1, ))
+#            samplesperpixel = shape[-3]
+#        extrasamples = samplesperpixel - 1
+#    else:
+#        planarconfig = None
+#        data = data.reshape((-1, 1) + shape[-2:] + (1, ))
+
+    shape = data.shape  # (pages, planes, height, width, contig samples)
+    
+
+    bytestr = bytes if sys.version[0] == '2' else lambda x: bytes(x, 'ascii')
+    tifftypes = {'B': 1, 's': 2, 'H': 3, 'I': 4, '2I': 5, 'b': 6,
+                 'h': 8, 'i': 9, 'f': 11, 'd': 12, 'Q': 16, 'q': 17}
+    tifftags = {'new_subfile_type': 254, 'subfile_type': 255,
+        'image_width': 256, 'image_length': 257, 'bits_per_sample': 258,
+        'compression': 259, 'photometric': 262, 'fill_order': 266,
+        'document_name': 269, 'image_description': 270, 'strip_offsets': 273,
+        'orientation': 274, 'samples_per_pixel': 277, 'rows_per_strip': 278,
+        'strip_byte_counts': 279, 'x_resolution': 282, 'y_resolution': 283,
+        'planar_configuration': 284, 'page_name': 285, 'resolution_unit': 296,
+        'software': 305, 'datetime': 306, 'predictor': 317, 'color_map': 320,
+        'extra_samples': 338, 'sample_format': 339}
+
+    tags = []
+    tag_data = []
+
+    def pack(fmt, *val):
+        return struct.pack(byteorder+fmt, *val)
+
+    def tag(name, dtype, number, value, offset=[0]):
+        # append tag binary string to tags list
+        # append (offset, value as binary string) to tag_data list
+        # increment offset by tag_size
+        if dtype == 's':
+            value = bytestr(value) + b'\0'
+            number = len(value)
+            value = (value, )
+        t = [pack('HH', tifftags[name], tifftypes[dtype]),
+             pack(offset_format, number)]
+        if len(dtype) > 1:
+            number *= int(dtype[:-1])
+            dtype = dtype[-1]
+        if number == 1:
+            if isinstance(value, (tuple, list)):
+                value = value[0]
+            t.append(pack(val_format, pack(dtype, value)))
+        elif struct.calcsize(dtype) * number <= offset_size:
+            t.append(pack(val_format, pack(str(number)+dtype, *value)))
+        else:
+            t.append(pack(offset_format, 0))
+            tag_data.append((offset[0] + offset_size + 4,
+                             pack(str(number)+dtype, *value)))
+        tags.append(b''.join(t))
+        offset[0] += tag_size
+
+    if software:
+        tag('software', 's', 0, software)
+    if description:
+        tag('image_description', 's', 0, description)
+    elif shape != data_shape:
+        tag('image_description', 's', 0,
+            "shape=(%s)" % (",".join('%i' % i for i in data_shape)))
+    tag('datetime', 's', 0,
+        datetime.datetime.now().strftime("%Y:%m:%d %H:%M:%S"))
+    # write previous tags only once
+    writeonce = (len(tags), len(tag_data)) if num_planes > 1 else None
+    tag('compression', 'H', 1, 1)
+    tag('orientation', 'H', 1, 1)
+    tag('image_width', 'I', 1, shape[1])
+    tag('image_length', 'I', 1, shape[0])
+    tag('new_subfile_type', 'I', 1, 0 if num_planes == 1 else 2)
+    tag('sample_format', 'H', 1,
+        {'u': 1, 'i': 2, 'f': 3, 'c': 6}[data_type.kind])
+    tag('photometric', 'H', 1,
+        {'miniswhite': 0, 'minisblack': 1, 'rgb': 2}[photometric])
+    tag('samples_per_pixel', 'H', 1, samplesperpixel)
+    
+#    if False:#planarconfig:
+#        tag('planar_configuration', 'H', 1, 1 if planarconfig=='contig' else 2)
+#        tag('bits_per_sample', 'H', samplesperpixel,
+#           (data.dtype.itemsize * 8, ) * samplesperpixel)
+#    else:
+    tag('bits_per_sample', 'H', 1, data_type.itemsize * 8)
+    
+#    if extrasamples:
+#        if photometric == 'rgb':
+#            tag('extra_samples', 'H', 1, 1)  # alpha channel
+#        else:
+#            tag('extra_samples', 'H', extrasamples, (0, ) * extrasamples)
+    
+    if resolution:
+        tag('x_resolution', '2I', 1, resolution[0])
+        tag('y_resolution', '2I', 1, resolution[1])
+        tag('resolution_unit', 'H', 1, 2)
+    tag('rows_per_strip', 'I', 1, shape[0])
+    # use one strip per plane
+    strip_byte_counts = (frame0.size * data_type.itemsize, )
+    tag('strip_byte_counts', offset_format, len(strip_byte_counts), strip_byte_counts)
+    # strip_offsets must be the last tag; will be updated later
+    tag('strip_offsets', offset_format, len(strip_byte_counts), (0, ) * len(strip_byte_counts))
+
+    fd = open(filename, 'wb')
+    seek = fd.seek
+    tell = fd.tell
+
+    def write(arg, *args):
+        fd.write(pack(arg, *args) if args else arg)
+
+    write({'<': b'II', '>': b'MM'}[byteorder])
+    if bigtiff:
+        write('HHH', 43, 8, 0)
+    else:
+        write('H', 42)
+    ifd_offset = tell()
+    write(offset_format, 0)  # first IFD    
+    
+    for k in range(shape[4]):
+        for j in range(shape[3]):
+            for i in range(shape[2]):
+                # update pointer at ifd_offset
+                pos = tell()
+                seek(ifd_offset)
+                write(offset_format, pos)
+                seek(pos)
+                # write tags
+                write(numtag_format, len(tags))
+                tag_offset = tell()
+                write(b''.join(tags))
+                ifd_offset = tell()
+                write(offset_format, 0)  # offset to next ifd
+                # write extra tag data and update pointers
+                for off, dat in tag_data:
+                    pos = tell()
+                    seek(tag_offset + off)
+                    write(offset_format, pos)
+                    seek(pos)
+                    write(dat)
+                # update strip_offsets
+                pos = tell()
+                if len(strip_byte_counts) == 1:
+                    seek(ifd_offset - offset_size)
+                    write(offset_format, pos)
+                else:
+                    seek(pos - offset_size*shape[1])
+                    strip_offset = pos
+                    for size in strip_byte_counts:
+                        write(offset_format, strip_offset)
+                        strip_offset += size
+                seek(pos)
+                # write data
+                data[:,:,i,j,k].astype(data_type).tofile(fd)  # if this fails, try update Python and numpy
+                fd.flush()
+                # remove tags that should be written only once
+                if writeonce:
+                    tags = tags[writeonce[0]:]
+                    d = writeonce[0] * tag_size
+                    tag_data = [(o-d, v) for (o, v) in tag_data[writeonce[1]:]]
+                    writeonce = None
+    fd.close()
+
+def imread(filename, *args, **kwargs):
+    """Return image data from TIFF file as numpy array.
+
+    The first image series is returned if no arguments are provided.
+
+    Arguments
+    ---------
+
+    key : int, slice, or sequence of page indices
+        Defines which pages to return as array.
+
+    series : int
+        Defines which series of pages to return as array.
+
+    Example
+    -------
+
+    >>> image = imread('test.tif', 0)
+
+    """
+    with TIFFfile(filename) as tif:
+        return tif.asarray(*args, **kwargs)
+
+
+class lazyattr(object):
+    """Lazy object attribute whose value is computed on first access."""
+    def __init__(self, func):
+        self.func = func
+
+    def __get__(self, instance, owner):
+        if instance is None:
+            return self
+        result = self.func(instance)
+        if result is NotImplemented:
+            return getattr(super(owner, instance), self.func.__name__)
+        setattr(instance, self.func.__name__, result)
+        return result
+
+
+class TIFFfile(object):
+    """Read image and meta-data from TIFF, STK, LSM, and FluoView files.
+
+    TIFFfile instances must be closed using the close method.
+
+    Attributes
+    ----------
+
+    pages : list
+        All TIFFpages in file.
+
+    series : list of Records(shape, dtype, axes, TIFFpages)
+        TIFF pages with compatible shapes and types.
+
+    All attributes are read-only.
+
+    Example
+    -------
+
+    >>> tif = TIFFfile('test.tif')
+    ... try:
+    ...     images = tif.asarray()
+    ... except Exception as e:
+    ...     print(e)
+    ... finally:
+    ...     tif.close()
+
+    """
+    def __init__(self, filename):
+        """Initialize instance from file."""
+        from PYME.IO import unifiedIO
+        #filename = unifiedIO.local_or_temp_filename(filename)
+        #filename = os.path.abspath(filename)
+        #self._fd = open(filename, 'rb')
+        self._fd = unifiedIO.openFile(filename)
+        self.fname = os.path.basename(filename)
+        self.fpath = os.path.dirname(filename)
+        self._tiffs = {self.fname: self}  # cache of TIFFfiles
+        self.offset_size = None
+        self.pages = []
+        try:
+            self._fromfile()
+        except Exception:
+            self._fd.close()
+            raise
+
+    def close(self):
+        """Close open file handle(s)."""
+        if not hasattr(self, 'tiffs'):
+            return
+        for tif in self._tiffs.values():
+            if tif._fd:
+                tif._fd.close()
+                tif._fd = None
+
+    def _fromfile(self):
+        """Read TIFF header and all page records from file."""
+        self._fd.seek(0)
+        try:
+            self.byte_order = {b'II': '<', b'MM': '>'}[self._fd.read(2)]
+        except KeyError:
+            raise ValueError("not a valid TIFF file")
+        version = struct.unpack(self.byte_order+'H', self._fd.read(2))[0]
+        if version == 43:  # BigTiff
+            self.offset_size, zero = struct.unpack(self.byte_order+'HH',
+                                                   self._fd.read(4))
+            if zero or self.offset_size != 8:
+                raise ValueError("not a valid BigTIFF file")
+        elif version == 42:
+            self.offset_size = 4
+        else:
+            raise ValueError("not a TIFF file")
+        self.pages = []
+        while True:
+            try:
+                page = TIFFpage(self)
+                self.pages.append(page)
+            except StopIteration:
+                break
+        if not self.pages:
+            raise ValueError("empty TIFF file")
+
+    @lazyattr
+    def series(self):
+        """Return series of TIFFpage with compatible shape and properties."""
+        if self.is_ome:
+            series = self._omeseries()
+        elif self.is_fluoview:
+            dims = {b'X': 'X', b'Y': 'Y', b'Z': 'Z', b'T': 'T',
+                    b'WAVELENGTH': 'C', b'TIME': 'T', b'XY': 'R',
+                    b'EVENT': 'V', b'EXPOSURE': 'L'}
+            mmhd = list(reversed(self.pages[0].mm_header.dimensions))
+            series = [Record(
+                axes=''.join(dims.get(i[0].strip().upper(), 'O')
+                             for i in mmhd if i[1] > 1),
+                shape=tuple(int(i[1]) for i in mmhd if i[1] > 1),
+                pages=self.pages, dtype=numpy.dtype(self.pages[0].dtype))]
+        elif self.is_lsm:
+            lsmi = self.pages[0].cz_lsm_info
+            axes = CZ_SCAN_TYPES[lsmi.scan_type]
+            if self.pages[0].is_rgb:
+                axes = axes.replace('C', '').replace('XY', 'XYC')
+            axes = axes[::-1]
+            shape = [getattr(lsmi, CZ_DIMENSIONS[i]) for i in axes]
+            pages = [p for p in self.pages if not p.is_reduced]
+            series = [Record(axes=axes, shape=shape, pages=pages,
+                             dtype=numpy.dtype(pages[0].dtype))]
+            if len(pages) != len(self.pages):  # reduced RGB pages
+                pages = [p for p in self.pages if p.is_reduced]
+                cp = 1
+                i = 0
+                while cp < len(pages) and i < len(shape)-2:
+                    cp *= shape[i]
+                    i += 1
+                shape = shape[:i] + list(pages[0].shape)
+                axes = axes[:i] + 'CYX'
+                series.append(Record(axes=axes, shape=shape, pages=pages,
+                                     dtype=numpy.dtype(pages[0].dtype)))
+        elif self.is_nih:
+            series = [Record(pages=self.pages,
+                             shape=(len(self.pages),) + self.pages[0].shape,
+                             axes='I' + self.pages[0].axes,
+                             dtype=numpy.dtype(self.pages[0].dtype))]
+        elif self.pages[0].is_shaped:
+            shape = self.pages[0].tags['image_description'].value[7:-1]
+            shape = tuple(int(i) for i in shape.split(b','))
+            series = [Record(pages=self.pages, shape=shape,
+                             axes='O' * len(shape),
+                             dtype=numpy.dtype(self.pages[0].dtype))]
+        else:
+            shapes = []
+            pages = {}
+            for page in self.pages:
+                shape = page.shape + (page.axes,
+                                      page.compression in TIFF_DECOMPESSORS)
+                if not shape in pages:
+                    shapes.append(shape)
+                    pages[shape] = [page]
+                else:
+                    pages[shape].append(page)
+            series = [Record(pages=pages[s],
+                             axes=(('I' + s[-2])
+                                   if len(pages[s]) > 1 else s[-2]),
+                             dtype=numpy.dtype(pages[s][0].dtype),
+                             shape=((len(pages[s]), ) + s[:-2]
+                                    if len(pages[s]) > 1 else s[:-2]))
+                      for s in shapes]
+        return series
+
+    def asarray(self, key=None, series=None):
+        """Return image data of multiple TIFF pages as numpy array.
+
+        By default the first image series is returned.
+
+        Arguments
+        ---------
+
+        key : int, slice, or sequence of page indices
+            Defines which pages to return as array.
+
+        series : int
+            Defines which series of pages to return as array.
+
+        """
+        if key is None and series is None:
+            series = 0
+        if series is not None:
+            pages = self.series[series].pages
+        else:
+            pages = self.pages
+
+        if key is None:
+            pass
+        elif isinstance(key, int):
+            pages = [pages[key]]
+        elif isinstance(key, slice):
+            pages = pages[key]
+        elif isinstance(key, collections.Iterable):
+            pages = [pages[k] for k in key]
+        else:
+            raise TypeError('key must be an int, slice, or sequence')
+
+        if len(pages) == 1:
+            return pages[0].asarray()
+        elif self.is_nih:
+            result = numpy.vstack(p.asarray(colormapped=False,
+                                            squeeze=False) for p in pages)
+            if pages[0].is_palette:
+                result = numpy.take(pages[0].color_map, result, axis=1)
+                result = numpy.swapaxes(result, 0, 1)
+        else:
+            if self.is_ome and any(p is None for p in pages):
+                firstpage = next(p for p in pages if p)
+                nopage = numpy.zeros_like(
+                    firstpage.asarray())
+            result = numpy.vstack((p.asarray() if p else nopage)
+                                  for p in pages)
+        if key is None:
+            try:
+                result.shape = self.series[series].shape
+            except ValueError:
+                warnings.warn("failed to reshape %s to %s" % (
+                              result.shape, self.series[series].shape))
+                result.shape = (-1,) + pages[0].shape
+        else:
+            result.shape = (-1,) + pages[0].shape
+        return result
+
+    def _omeseries(self):
+        """Return image series in OME-TIFF files."""
+        root = ElementTree.XML(self.pages[0].tags['image_description'].value)
+        uuid = root.attrib.get('UUID', None)
+        self._tiffs = {uuid: self}
+        modulo = {}
+        result = []
+        for element in root:
+            if element.tag.endswith('BinaryOnly'):
+                warnings.warn("not an OME-TIFF master file")
+                break
+            if element.tag.endswith('StructuredAnnotations'):
+                for annot in element:
+                    if not annot.attrib.get('Namespace',
+                                            '').endswith('modulo'):
+                        continue
+                    for value in annot:
+                        for modul in value:
+                            for along in modul:
+                                if not along.tag[:-1].endswith('Along'):
+                                    continue
+                                axis = along.tag[-1]
+                                newaxis = along.attrib.get('Type', 'other')
+                                newaxis = AXES_LABELS[newaxis]
+                                if 'Start' in along.attrib:
+                                    labels = range(
+                                        int(along.attrib['Start']),
+                                        int(along.attrib['End']) + 1,
+                                        int(along.attrib.get('Step', 1)))
+                                else:
+                                    labels = [label.text for label in along
+                                              if label.tag.endswith('Label')]
+                                modulo[axis] = (newaxis, labels)
+            if not element.tag.endswith('Image'):
+                continue
+            for pixels in element:
+                if not pixels.tag.endswith('Pixels'):
+                    continue
+                atr = pixels.attrib
+                axes = "".join(reversed(atr['DimensionOrder']))
+                shape = list(int(atr['Size'+ax]) for ax in axes)
+                size = numpy.prod(shape[:-2])
+                ifds = [None] * size
+                for data in pixels:
+                    if not data.tag.endswith('TiffData'):
+                        continue
+                    atr = data.attrib
+                    ifd = int(atr.get('IFD', 0))
+                    num = int(atr.get('NumPlanes', 1 if 'IFD' in atr else 0))
+                    num = int(atr.get('PlaneCount', num))
+                    idx = [int(atr.get('First'+ax, 0)) for ax in axes[:-2]]
+                    idx = numpy.ravel_multi_index(idx, shape[:-2])
+                    for uuid in data:
+                        if uuid.tag.endswith('UUID'):
+                            if uuid.text not in self._tiffs:
+                                fn = uuid.attrib['FileName']
+                                try:
+                                    tf = TIFFfile(os.path.join(self.fpath, fn))
+                                except (IOError, ValueError):
+                                    warnings.warn("failed to read %s" % fn)
+                                    break
+                                self._tiffs[uuid.text] = tf
+                            pages = self._tiffs[uuid.text].pages
+                            try:
+                                for i in range(num if num else len(pages)):
+                                    ifds[idx + i] = pages[ifd + i]
+                            except IndexError:
+                                warnings.warn("ome-xml: index out of range")
+                            break
+                    else:
+                        pages = self.pages
+                        try:
+                            for i in range(num if num else len(pages)):
+                                ifds[idx + i] = pages[ifd + i]
+                        except IndexError:
+                            warnings.warn("ome-xml: index out of range")
+                result.append(Record(axes=axes, shape=shape, pages=ifds,
+                                     dtype=numpy.dtype(ifds[0].dtype)))
+
+        for record in result:
+            for axis, (newaxis, labels) in modulo.items():
+                i = record.axes.index(axis)
+                size = len(labels)
+                if record.shape[i] == size:
+                    record.axes = record.axes.replace(axis, newaxis, 1)
+                else:
+                    record.shape[i] //= size
+                    record.shape.insert(i+1, size)
+                    record.axes = record.axes.replace(axis, axis+newaxis, 1)
+
+        return result
+
+    def __len__(self):
+        """Return number of image pages in file."""
+        return len(self.pages)
+
+    def __getitem__(self, key):
+        """Return specified page."""
+        return self.pages[key]
+
+    def __iter__(self):
+        """Return iterator over pages."""
+        return iter(self.pages)
+
+    def __str__(self):
+        """Return string containing information about file."""
+        result = [self.fname.capitalize(),
+            "%.2f MB" % (self.fstat[6] / 1048576),
+            {'<': 'little endian', '>': 'big endian'}[self.byte_order]]
+        if self.is_bigtiff:
+            result.append("bigtiff")
+        if len(self.pages) > 1:
+            result.append("%i pages" % len(self.pages))
+        if len(self.series) > 1:
+            result.append("%i series" % len(self.series))
+        if len(self._tiffs) > 1:
+            result.append("%i files" % (len(self._tiffs)))
+        return ", ".join(result)
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, *args):
+        self.close()
+
+    @lazyattr
+    def fstat(self):
+        return os.fstat(self._fd.fileno())
+
+    @lazyattr
+    def is_bigtiff(self):
+        return self.offset_size != 4
+
+    @lazyattr
+    def is_rgb(self):
+        return all(p.is_rgb for p in self.pages)
+
+    @lazyattr
+    def is_palette(self):
+        return all(p.is_palette for p in self.pages)
+
+    @lazyattr
+    def is_stk(self):
+        return all(p.is_stk for p in self.pages)
+
+    @lazyattr
+    def is_lsm(self):
+        return self.pages[0].is_lsm
+
+    @lazyattr
+    def is_nih(self):
+        return self.pages[0].is_nih
+
+    @lazyattr
+    def is_fluoview(self):
+        return self.pages[0].is_fluoview
+
+    @lazyattr
+    def is_ome(self):
+        return self.pages[0].is_ome
+
+
+class TIFFpage(object):
+    """A TIFF image file directory (IFD).
+
+    Attributes
+    ----------
+
+    index : int
+        Index of page in file.
+
+    dtype : str {TIFF_SAMPLE_DTYPES}
+        Data type of image, colormapped if applicable.
+
+    shape : tuple
+        Dimensions of the image array in TIFF page,
+        colormapped and with one alpha channel if applicable.
+
+    axes : str
+        Axes label codes:
+        'X' width, 'Y' height, 'S' sample, 'P' plane, 'I' image series,
+        'Z' depth, 'C' color|em-wavelength|channel, 'E' ex-wavelength|lambda,
+        'T' time, 'R' region|tile, 'A' angle, 'F' phase, 'H' lifetime,
+        'L' exposure, 'V' event, 'O' unknown, '_' missing
+
+    tags : TiffTags
+        Dictionary of tags in page.
+        Tag values are also directly accessible as attributes.
+
+    color_map : numpy array
+        Color look up table if exists.
+
+    mm_uic_tags: Record(dict)
+        Consolidated MetaMorph mm_uic# tags, if exists.
+
+    cz_lsm_scan_info: Record(dict)
+        LSM scan info attributes, if exists.
+
+    All attributes are read-only.
+
+    """
+    def __init__(self, parent):
+        """Initialize instance from file."""
+        self.parent = parent
+        self.index = len(parent.pages)
+        self.shape = self._shape = ()
+        self.dtype = self._dtype = None
+        self.axes = ""
+        self.tags = TiffTags()
+
+        self._fromfile()
+        self._process_tags()
+
+    def _fromfile(self):
+        """Read TIFF IFD structure and its tags from file.
+
+        File cursor must be at storage position of IFD offset and is left at
+        offset to next IFD.
+
+        Raises StopIteration if offset (first bytes read) is 0.
+
+        """
+        fd = self.parent._fd
+        byte_order = self.parent.byte_order
+        offset_size = self.parent.offset_size
+
+        fmt = {4: 'I', 8: 'Q'}[offset_size]
+        offset = struct.unpack(byte_order + fmt, fd.read(offset_size))[0]
+        if not offset:
+            raise StopIteration()
+
+        # read standard tags
+        tags = self.tags
+        fd.seek(offset, 0)
+        fmt, size = {4: ('H', 2), 8: ('Q', 8)}[offset_size]
+        try:
+            numtags = struct.unpack(byte_order + fmt, fd.read(size))[0]
+        except Exception:
+            warnings.warn("corrupted page list")
+            raise StopIteration()
+
+        for _ in range(numtags):
+            tag = TIFFtag(self.parent)
+            tags[tag.name] = tag
+
+        # read custom tags
+        for name, readtag in CUSTOM_TAGS.values():
+            if name in tags and readtag:
+                pos = fd.tell()
+                value = readtag(fd, byte_order, tags[name])
+                if isinstance(value, dict):  # numpy.core.records.record
+                    value = Record(value)
+                tags[name].value = value
+                fd.seek(pos)
+
+        # read LSM info subrecords
+        if self.is_lsm:
+            pos = fd.tell()
+            for name, reader in CZ_LSM_INFO_READERS.items():
+                try:
+                    offset = self.cz_lsm_info["offset_"+name]
+                except KeyError:
+                    continue
+                if not offset:
+                    continue
+                fd.seek(offset)
+                try:
+                    setattr(self, "cz_lsm_"+name, reader(fd, byte_order))
+                except ValueError:
+                    pass
+            fd.seek(pos)
+
+    def _process_tags(self):
+        """Validate standard tags and initialize attributes.
+
+        Raise ValueError if tag values are not supported.
+
+        """
+        tags = self.tags
+        for code, (name, default, dtype, count, validate) in TIFF_TAGS.items():
+            if not (name in tags or default is None):
+                tags[name] = TIFFtag(code, dtype=dtype, count=count,
+                                     value=default, name=name)
+            if name in tags and validate:
+                try:
+                    if tags[name].count == 1:
+                        setattr(self, name, validate[tags[name].value])
+                    else:
+                        setattr(self, name, tuple(validate[value]
+                                            for value in tags[name].value))
+                except KeyError:
+                    raise ValueError("%s.value (%s) not supported" %
+                                     (name, tags[name].value))
+
+        tag = tags['bits_per_sample']
+        if tag.count == 1:
+            self.bits_per_sample = tag.value
+        else:
+            value = tag.value[:self.samples_per_pixel]
+            if any((v-value[0] for v in value)):
+                self.bits_per_sample = value
+            else:
+                self.bits_per_sample = value[0]
+
+        tag = tags['sample_format']
+        if tag.count == 1:
+            self.sample_format = TIFF_SAMPLE_FORMATS[tag.value]
+        else:
+            value = tag.value[:self.samples_per_pixel]
+            if any((v-value[0] for v in value)):
+                self.sample_format = [TIFF_SAMPLE_FORMATS[v] for v in value]
+            else:
+                self.sample_format = TIFF_SAMPLE_FORMATS[value[0]]
+
+        self.strips_per_image = int(math.floor(float(self.image_length +
+                            self.rows_per_strip - 1) / self.rows_per_strip))
+
+        key = (self.sample_format, self.bits_per_sample)
+        self.dtype = self._dtype = TIFF_SAMPLE_DTYPES.get(key, None)
+
+        if self.is_stk:
+            planes = tags['mm_uic2'].count
+            # consolidate mm_uci tags
+            self.mm_uic_tags = Record(tags['mm_uic2'].value)
+            for key in ('mm_uic3', 'mm_uic4', 'mm_uic1'):
+                if key in tags:
+                    self.mm_uic_tags.update(tags[key].value)
+            if self.planar_configuration == 'contig':
+                self._shape = (planes, 1, self.image_length,
+                               self.image_width, self.samples_per_pixel)
+                self.shape = tuple(self._shape[i] for i in (0, 2, 3, 4))
+                self.axes = "PYXS"
+            else:
+                self._shape = (planes, self.samples_per_pixel,
+                               self.image_length, self.image_width, 1)
+                self.shape = self._shape[:4]
+                self.axes = "PSYX"
+        elif self.is_palette:
+            self.dtype = self.tags['color_map'].dtype[1]
+            self.color_map = numpy.array(self.color_map, self.dtype)
+            dmax = self.color_map.max()
+            if dmax < 256:
+                self.dtype = numpy.uint8
+                self.color_map = self.color_map.astype(self.dtype)
+            #else:
+            #    self.dtype = numpy.uint8
+            #    self.color_map >>= 8
+            #    self.color_map = self.color_map.astype(self.dtype)
+            self.color_map.shape = (3, -1)
+            self._shape = (1, 1, self.image_length, self.image_width, 1)
+            if self.color_map.shape[1] >= 2**self.bits_per_sample:
+                self.shape = (3, self.image_length, self.image_width)
+                self.axes = "SYX"
+            else:
+                # LSM and FluoView
+                self.shape = (self.image_length, self.image_width)
+                self.axes = "YX"
+        elif self.is_rgb or self.samples_per_pixel > 1:
+            if self.planar_configuration == 'contig':
+                self._shape = (1, 1, self.image_length, self.image_width,
+                               self.samples_per_pixel)
+                self.shape = (self.image_length, self.image_width,
+                              self.samples_per_pixel)
+                self.axes = "YXS"
+            else:
+                self._shape = (1, self.samples_per_pixel, self.image_length,
+                               self.image_width, 1)
+                self.shape = self._shape[1:-1]
+                self.axes = "SYX"
+            if self.is_rgb and 'extra_samples' in self.tags:
+                extra_samples = self.extra_samples
+                if self.tags['extra_samples'].count == 1:
+                    extra_samples = (extra_samples, )
+                for exs in extra_samples:
+                    if exs in ('unassalpha', 'assocalpha'):
+                        if self.planar_configuration == 'contig':
+                            self.shape = self.shape[:2] + (4,)
+                        else:
+                            self.shape = (4,) + self.shape[1:]
+                        break
+        else:
+            self._shape = (1, 1, self.image_length, self.image_width, 1)
+            self.shape = self._shape[2:4]
+            self.axes = "YX"
+
+        if not self.compression and not 'strip_byte_counts' in tags:
+            self.strip_byte_counts = numpy.prod(self.shape) * (
+                self.bits_per_sample // 8)
+
+    def asarray(self, squeeze=True, colormapped=True, rgbonly=True):
+        """Read image data from file and return as numpy array.
+
+        Raise ValueError if format is unsupported.
+        If any argument is False, the shape of the returned array might be
+        different from the page shape.
+
+        Arguments
+        ---------
+
+        squeeze : bool
+            If True all length-1 dimensions (except X and Y) are
+            squeezed out from result.
+
+        colormapped : bool
+            If True color mapping is applied for palette-indexed images.
+
+        rgbonly : bool
+            If True return RGB(A) image without additional extra samples.
+
+        """
+        fd = self.parent._fd
+        if not fd:
+            raise IOError("TIFF file is not open")
+        if self.dtype is None:
+            raise ValueError("data type not supported: %s%i" % (
+                self.sample_format, self.bits_per_sample))
+        if self.compression not in TIFF_DECOMPESSORS:
+            raise ValueError("cannot decompress %s" % self.compression)
+        if ('ycbcr_subsampling' in self.tags and
+            self.tags['ycbcr_subsampling'].value not in (1, (1, 1))):
+            raise ValueError("YCbCr subsampling not supported")
+        tag = self.tags['sample_format']
+        if tag.count != 1 and any((i-tag.value[0] for i in tag.value)):
+            raise ValueError("sample formats don't match %s" % str(tag.value))
+
+        dtype = self._dtype
+        shape = self._shape
+        image_width = self.image_width
+        image_length = self.image_length
+        typecode = self.parent.byte_order + dtype
+        bits_per_sample = self.bits_per_sample
+
+        if self.is_tiled:
+            if 'tile_offsets' in self.tags:
+                byte_counts = self.tile_byte_counts
+                offsets = self.tile_offsets
+            else:
+                byte_counts = self.strip_byte_counts
+                offsets = self.strip_offsets
+            tile_width = self.tile_width
+            tile_length = self.tile_length
+            tw = (image_width + tile_width - 1) // tile_width
+            tl = (image_length + tile_length - 1) // tile_length
+            shape = shape[:-3] + (tl*tile_length, tw*tile_width, shape[-1])
+            tile_shape = (tile_length, tile_width, shape[-1])
+            runlen = tile_width
+        else:
+            byte_counts = self.strip_byte_counts
+            offsets = self.strip_offsets
+            runlen = image_width
+
+        try:
+            offsets[0]
+        except TypeError:
+            offsets = (offsets, )
+            byte_counts = (byte_counts, )
+        if any(o < 2 for o in offsets):
+            raise ValueError("corrupted file")
+
+        if (not self.is_tiled and (self.is_stk or (not self.compression
+            and bits_per_sample in (8, 16, 32, 64)
+            and all(offsets[i] == offsets[i+1] - byte_counts[i]
+                    for i in range(len(offsets)-1))))):
+            # contiguous data
+            fd.seek(offsets[0], 0)
+            if not hasattr(fd, 'name'):
+                # handle reading from BytesIO and similar 'file like' objects
+                # np.fromfile memmaps and hence doesn't work for things which aren't a physical file
+                # we look for the name attribute as a python version independent way of telling the difference
+                result = numpy.frombuffer(fd.read(int(numpy.prod(shape)*numpy.dtype(typecode).itemsize)), typecode)
+            else:
+                result = numpy.fromfile(fd, typecode, numpy.prod(shape))
+            
+            result = result.astype('=' + dtype)
+        else:
+            if self.planar_configuration == 'contig':
+                runlen *= self.samples_per_pixel
+            if bits_per_sample in (8, 16, 32, 64, 128):
+                if (bits_per_sample * runlen) % 8:
+                    raise ValueError("data and sample size mismatch")
+                unpack = lambda x: numpy.fromstring(x, typecode)
+            elif isinstance(bits_per_sample, tuple):
+                unpack = lambda x: unpackrgb(x, typecode, bits_per_sample)
+            else:
+                unpack = lambda x: unpackints(x, typecode, bits_per_sample,
+                                              runlen)
+            decompress = TIFF_DECOMPESSORS[self.compression]
+            if self.is_tiled:
+                result = numpy.empty(shape, dtype)
+                tw, tl, pl = 0, 0, 0
+                for offset, bytecount in zip(offsets, byte_counts):
+                    fd.seek(offset, 0)
+                    tile = unpack(decompress(fd.read(bytecount)))
+                    tile.shape = tile_shape
+                    result[0, pl, tl:tl+tile_length,
+                           tw:tw+tile_width, :] = tile
+                    del tile
+                    tw += tile_width
+                    if tw >= shape[-2]:
+                        tw, tl = 0, tl + tile_length
+                        if tl >= shape[-3]:
+                            tl, pl = 0, pl + 1
+                result = result[..., :image_length, :image_width, :]
+            else:
+                result = numpy.empty(shape, dtype).reshape(-1)
+                index = 0
+                for offset, bytecount in zip(offsets, byte_counts):
+                    fd.seek(offset, 0)
+                    stripe = unpack(decompress(fd.read(bytecount)))
+                    size = min(result.size, stripe.size)
+                    result[index:index+size] = stripe[:size]
+                    del stripe
+                    index += size
+
+        result.shape = self._shape
+
+        if self.predictor == 'horizontal':
+            # workaround bug in LSM510 software
+            if not (self.parent.is_lsm and not self.compression):
+                numpy.cumsum(result, axis=3, dtype=dtype, out=result)
+
+        if colormapped and self.is_palette:
+            if self.color_map.shape[1] >= 2**bits_per_sample:
+                # FluoView and LSM might fail here
+                result = numpy.take(self.color_map, result, axis=1)
+        elif rgbonly and self.is_rgb and 'extra_samples' in self.tags:
+            # return only RGB and first alpha channel if exists
+            extra_samples = self.extra_samples
+            if self.tags['extra_samples'].count == 1:
+                extra_samples = (extra_samples, )
+            for i, exs in enumerate(extra_samples):
+                if exs in ('unassalpha', 'assocalpha'):
+                    if self.planar_configuration == 'contig':
+                        result = result[..., [0, 1, 2, 3+i]]
+                    else:
+                        result = result[:, [0, 1, 2, 3+i]]
+                    break
+            else:
+                if self.planar_configuration == 'contig':
+                    result = result[..., :3]
+                else:
+                    result = result[:, :3]
+
+        if squeeze:
+            try:
+                result.shape = self.shape
+            except ValueError:
+                pass
+
+        return result
+
+    def __str__(self):
+        """Return string containing information about page."""
+        s = ', '.join(s for s in (
+            ' x '.join(str(i) for i in self.shape),
+            str(numpy.dtype(self.dtype)),
+            '%s bit' % str(self.bits_per_sample),
+            self.photometric,
+            self.compression if self.compression else 'raw',
+            ','.join(t[3:] for t in ('is_stk', 'is_lsm', 'is_nih', 'is_ome',
+                                     'is_fluoview', 'is_reduced', 'is_tiled')
+                     if getattr(self, t))) if s)
+        return "Page %i: %s" % (self.index, s)
+
+    def __getattr__(self, name):
+        """Return tag value."""
+        if name in self.tags:
+            value = self.tags[name].value
+            setattr(self, name, value)
+            return value
+        raise AttributeError(name)
+
+    @lazyattr
+    def is_rgb(self):
+        """True if page contains a RGB image."""
+        return self.tags['photometric'].value == 2
+
+    @lazyattr
+    def is_palette(self):
+        """True if page contains a palette-colored image."""
+        return self.tags['photometric'].value == 3
+
+    @lazyattr
+    def is_tiled(self):
+        """True if page contains tiled image."""
+        return 'tile_width' in self.tags
+
+    @lazyattr
+    def is_reduced(self):
+        """True if page is a reduced image of another image."""
+        return bool(self.tags['new_subfile_type'].value & 1)
+
+    @lazyattr
+    def is_stk(self):
+        """True if page contains MM_UIC2 tag."""
+        return 'mm_uic2' in self.tags
+
+    @lazyattr
+    def is_lsm(self):
+        """True if page contains LSM CZ_LSM_INFO tag."""
+        return 'cz_lsm_info' in self.tags
+
+    @lazyattr
+    def is_fluoview(self):
+        """True if page contains FluoView MM_STAMP tag."""
+        return 'mm_stamp' in self.tags
+
+    @lazyattr
+    def is_nih(self):
+        """True if page contains NIH image header."""
+        return 'nih_image_header' in self.tags
+
+    @lazyattr
+    def is_ome(self):
+        """True if page contains OME-XML in image_description tag."""
+        return ('image_description' in self.tags and self.tags[
+            'image_description'].value.startswith(b'<?xml version='))
+
+    @lazyattr
+    def is_shaped(self):
+        """True if page contains shape in image_description tag."""
+        return ('image_description' in self.tags and self.tags[
+            'image_description'].value.startswith(b'shape=('))
+
+
+class TIFFtag(object):
+    """A TIFF tag structure.
+
+    Attributes
+    ----------
+
+    name : string
+        Attribute name of tag.
+
+    code : int
+        Decimal code of tag.
+
+    dtype : str
+        Datatype of tag data. One of TIFF_DATA_TYPES.
+
+    count : int
+        Number of values.
+
+    value : various types
+        Tag data. For codes in CUSTOM_TAGS the 4 bytes file content.
+
+    value_offset : int
+        Location of value in file
+
+    All attributes are read-only.
+
+    """
+    __slots__ = ('code', 'name', 'count', 'dtype', 'value', 'value_offset',
+                 '_offset')
+
+    def __init__(self, arg, **kwargs):
+        """Initialize instance from file or arguments."""
+        self._offset = None
+        if hasattr(arg, '_fd'):
+            self._fromfile(arg, **kwargs)
+        else:
+            self._fromdata(arg, **kwargs)
+
+    def _fromdata(self, code, dtype, count, value, name=None):
+        """Initialize instance from arguments."""
+        self.code = int(code)
+        self.name = name if name else str(code)
+        self.dtype = TIFF_DATA_TYPES[dtype]
+        self.count = int(count)
+        self.value = value
+
+    def _fromfile(self, parent):
+        """Read tag structure from open file. Advances file cursor."""
+        fd = parent._fd
+        byte_order = parent.byte_order
+
+        self._offset = fd.tell()
+        self.value_offset = self._offset + parent.offset_size + 4
+
+        fmt, size = {4: ('HHI4s', 12), 8: ('HHQ8s', 20)}[parent.offset_size]
+        data = fd.read(size)
+        code, dtype = struct.unpack(byte_order + fmt[:2], data[:4])
+        count, value = struct.unpack(byte_order + fmt[2:], data[4:])
+
+        if code in TIFF_TAGS:
+            name = TIFF_TAGS[code][0]
+        elif code in CUSTOM_TAGS:
+            name = CUSTOM_TAGS[code][0]
+        else:
+            name = str(code)
+
+        try:
+            dtype = TIFF_DATA_TYPES[dtype]
+        except KeyError:
+            raise ValueError("unknown TIFF tag data type %i" % dtype)
+
+        if not code in CUSTOM_TAGS:
+            fmt = '%s%i%s' % (byte_order, count*int(dtype[0]), dtype[1])
+            size = struct.calcsize(fmt)
+            if size <= parent.offset_size:
+                value = struct.unpack(fmt, value[:size])
+            else:
+                pos = fd.tell()
+                tof = {4: 'I', 8: 'Q'}[parent.offset_size]
+                self.value_offset = struct.unpack(byte_order+tof, value)[0]
+                fd.seek(self.value_offset)
+                value = struct.unpack(fmt, fd.read(size))
+                fd.seek(pos)
+            if len(value) == 1:
+                value = value[0]
+            if dtype == '1s':
+                value = stripnull(value)
+
+        self.code = code
+        self.name = name
+        self.dtype = dtype
+        self.count = count
+        self.value = value
+
+    def __str__(self):
+        """Return string containing information about tag."""
+        return ' '.join(str(getattr(self, s)) for s in self.__slots__)
+
+
+class Record(dict):
+    """Dictionary with attribute access.
+
+    Can also be initialized with numpy.core.records.record.
+
+    """
+    __slots__ = ()
+
+    def __init__(self, arg=None, **kwargs):
+        if kwargs:
+            arg = kwargs
+        elif arg is None:
+            arg = {}
+        try:
+            dict.__init__(self, arg)
+        except TypeError:
+            for i, name in enumerate(arg.dtype.names):
+                v = arg[i]
+                self[name] = v if v.dtype.char != 'S' else stripnull(v)
+
+    def __getattr__(self, name):
+        return self[name]
+
+    def __setattr__(self, name, value):
+        self.__setitem__(name, value)
+
+    def __str__(self):
+        """Pretty print Record."""
+        s = []
+        lists = []
+        for k in sorted(self):
+            if k.startswith('_'):
+                continue
+            v = self[k]
+            if isinstance(v, (list, tuple)) and len(v):
+                if isinstance(v[0], Record):
+                    lists.append((k, v))
+                    continue
+                elif isinstance(v[0], TIFFpage):
+                    v = [i.index for i in v if i]
+            s.append(("* %s: %s" % (k, str(v))).split("\n",
+                                                      1)[0][:PRINT_LINE_LEN])
+        for k, v in lists:
+            l = []
+            for i, w in enumerate(v):
+                l.append("* %s[%i]\n  %s" % (k, i,
+                                             str(w).replace("\n", "\n  ")))
+            s.append('\n'.join(l))
+        return '\n'.join(s)
+
+
+class TiffTags(Record):
+    """Dictionary of TIFFtags with attribute access."""
+    def __str__(self):
+        """Return string with information about all tags."""
+        s = []
+        #sortbycode = lambda a, b: cmp(a.code, b.code)
+        #for tag in sorted(self.values(), sortbycode):
+        for tag in sorted(self.values(), key=lambda x: x.code):
+            typecode = "%i%s" % (tag.count * int(tag.dtype[0]), tag.dtype[1])
+            line = "* %i %s (%s) %s" % (tag.code, tag.name, typecode,
+                                        str(tag.value).split('\n', 1)[0])
+            s.append(line[:PRINT_LINE_LEN])
+        return '\n'.join(s)
+
+
+def read_nih_image_header(fd, byte_order, tag):
+    """Read NIH_IMAGE_HEADER tag from file and return as dictionary."""
+    fd.seek(12 + struct.unpack(byte_order+'I', tag.value)[0])
+    return {'version': struct.unpack(byte_order+'H', fd.read(2))[0]}
+
+
+def read_mm_header(fd, byte_order, tag):
+    """Read MM_HEADER tag from file and return as numpy.rec.array."""
+    fd.seek(struct.unpack(byte_order+'I', tag.value)[0])
+    return numpy.rec.fromfile(fd, MM_HEADER, 1, byteorder=byte_order)[0]
+
+
+def read_mm_stamp(fd, byte_order, tag):
+    """Read MM_STAMP tag from file and return as numpy.array."""
+    fd.seek(struct.unpack(byte_order+'I', tag.value)[0])
+    return numpy.fromfile(fd, byte_order+'8f8', 1)[0]
+
+
+def read_mm_uic1(fd, byte_order, tag):
+    """Read MM_UIC1 tag from file and return as dictionary."""
+    fd.seek(struct.unpack(byte_order+'I', tag.value)[0])
+    t = fd.read(8*tag.count)
+    t = struct.unpack('%s%iI' % (byte_order, 2*tag.count), t)
+    return dict((MM_TAG_IDS[k], v) for k, v in zip(t[::2], t[1::2])
+                if k in MM_TAG_IDS)
+
+
+def read_mm_uic2(fd, byte_order, tag):
+    """Read MM_UIC2 tag from file and return as dictionary."""
+    result = {'number_planes': tag.count}
+    fd.seek(struct.unpack(byte_order+'I', tag.value)[0])
+    values = numpy.fromfile(fd, byte_order+'I', 6*tag.count)
+    result['z_distance'] = values[0::6] // values[1::6]
+    #result['date_created'] = tuple(values[2::6])
+    #result['time_created'] = tuple(values[3::6])
+    #result['date_modified'] = tuple(values[4::6])
+    #result['time_modified'] = tuple(values[5::6])
+    return result
+
+
+def read_mm_uic3(fd, byte_order, tag):
+    """Read MM_UIC3 tag from file and return as dictionary."""
+    fd.seek(struct.unpack(byte_order+'I', tag.value)[0])
+    t = numpy.fromfile(fd, '%sI' % byte_order, 2*tag.count)
+    return {'wavelengths': t[0::2] // t[1::2]}
+
+
+def read_mm_uic4(fd, byte_order, tag):
+    """Read MM_UIC4 tag from file and return as dictionary."""
+    fd.seek(struct.unpack(byte_order+'I', tag.value)[0])
+    t = struct.unpack(byte_order + 'hI'*tag.count, fd.read(6*tag.count))
+    return dict((MM_TAG_IDS[k], v) for k, v in zip(t[::2], t[1::2])
+                if k in MM_TAG_IDS)
+
+
+def read_cz_lsm_info(fd, byte_order, tag):
+    """Read CS_LSM_INFO tag from file and return as numpy.rec.array."""
+    fd.seek(struct.unpack(byte_order+'I', tag.value)[0])
+    result = numpy.rec.fromfile(fd, CZ_LSM_INFO, 1,
+                                byteorder=byte_order)[0]
+    {50350412: '1.3', 67127628: '2.0'}[result.magic_number]  # validation
+    return result
+
+
+def read_cz_lsm_time_stamps(fd, byte_order):
+    """Read LSM time stamps from file and return as list."""
+    size, count = struct.unpack(byte_order+'II', fd.read(8))
+    if size != (8 + 8 * count):
+        raise ValueError("lsm_time_stamps block is too short")
+    return struct.unpack(('%s%dd' % (byte_order, count)),
+                         fd.read(8*count))
+
+
+def read_cz_lsm_event_list(fd, byte_order):
+    """Read LSM events from file and return as list of (time, type, text)."""
+    count = struct.unpack(byte_order+'II', fd.read(8))[1]
+    events = []
+    while count > 0:
+        esize, etime, etype = struct.unpack(byte_order+'IdI', fd.read(16))
+        etext = stripnull(fd.read(esize - 16))
+        events.append((etime, etype, etext))
+        count -= 1
+    return events
+
+
+def read_cz_lsm_scan_info(fd, byte_order):
+    """Read LSM scan information from file and return as Record."""
+    block = Record()
+    blocks = [block]
+    unpack = struct.unpack
+
+    if 0x10000000 != struct.unpack(byte_order+"I", fd.read(4))[0]:
+        raise ValueError("not a lsm_scan_info structure")
+    fd.read(8)
+
+    while True:
+        entry, dtype, size = unpack(byte_order+"III", fd.read(12))
+        if dtype == 2:
+            value = stripnull(fd.read(size))
+        elif dtype == 4:
+            value = unpack(byte_order+"i", fd.read(4))[0]
+        elif dtype == 5:
+            value = unpack(byte_order+"d", fd.read(8))[0]
+        else:
+            value = 0
+
+        if entry in CZ_LSM_SCAN_INFO_ARRAYS:
+            blocks.append(block)
+            name = CZ_LSM_SCAN_INFO_ARRAYS[entry]
+            newobj = []
+            setattr(block, name, newobj)
+            block = newobj
+        elif entry in CZ_LSM_SCAN_INFO_STRUCTS:
+            blocks.append(block)
+            newobj = Record()
+            block.append(newobj)
+            block = newobj
+        elif entry in CZ_LSM_SCAN_INFO_ATTRIBUTES:
+            name = CZ_LSM_SCAN_INFO_ATTRIBUTES[entry]
+            setattr(block, name, value)
+        elif entry == 0xffffffff:
+            block = blocks.pop()
+        else:
+            setattr(block, "unknown_%x" % entry, value)
+
+        if not blocks:
+            break
+    return block
+
+
+def _replace_by(module_function, warn=True):
+    """Try replace decorated function by module.function."""
+
+    def decorate(func, module_function=module_function, warn=warn):
+        sys.path.append(os.path.dirname(__file__))
+        try:
+            module, function = module_function.split('.')
+            func, oldfunc = getattr(__import__(module), function), func
+            globals()['__old_' + func.__name__] = oldfunc
+        except Exception:
+            if warn:
+                warnings.warn("failed to import %s" % module_function)
+        sys.path.pop()
+        return func
+
+    return decorate
+
+
+@_replace_by('_tifffile.decodepackbits')
+def decodepackbits(encoded):
+    """Decompress PackBits encoded byte string.
+
+    PackBits is a simple byte-oriented run-length compression scheme.
+
+    """
+    func = ord if sys.version[0] == '2' else lambda x: x
+    result = []
+    i = 0
+    try:
+        while True:
+            n = func(encoded[i]) + 1
+            i += 1
+            if n < 129:
+                result.extend(encoded[i:i+n])
+                i += n
+            elif n > 129:
+                result.extend(encoded[i:i+1] * (258-n))
+                i += 1
+    except IndexError:
+        pass
+    return b''.join(result) if sys.version[0] == '2' else bytes(result)
+
+
+@_replace_by('_tifffile.decodelzw')
+def decodelzw(encoded):
+    """Decompress LZW (Lempel-Ziv-Welch) encoded TIFF strip (byte string).
+
+    The strip must begin with a CLEAR code and end with an EOI code.
+
+    This is an implementation of the LZW decoding algorithm described in (1).
+    It is not compatible with old style LZW compressed files like quad-lzw.tif.
+
+    """
+    unpack = struct.unpack
+
+    if sys.version[0] == '2':
+        newtable = [chr(i) for i in range(256)]
+    else:
+        newtable = [bytes([i]) for i in range(256)]
+    newtable.extend((0, 0))
+
+    def next_code():
+        """Return integer of `bitw` bits at `bitcount` position in encoded."""
+        start = bitcount // 8
+        s = encoded[start:start+4]
+        try:
+            code = unpack('>I', s)[0]
+        except Exception:
+            code = unpack('>I', s + b'\x00'*(4-len(s)))[0]
+        code = code << (bitcount % 8)
+        code = code & mask
+        return code >> shr
+
+    switchbitch = {  # code: bit-width, shr-bits, bit-mask
+        255: (9, 23, int(9*'1'+'0'*23, 2)),
+        511: (10, 22, int(10*'1'+'0'*22, 2)),
+        1023: (11, 21, int(11*'1'+'0'*21, 2)),
+        2047: (12, 20, int(12*'1'+'0'*20, 2)), }
+    bitw, shr, mask = switchbitch[255]
+    bitcount = 0
+
+    if len(encoded) < 4:
+        raise ValueError("strip must be at least 4 characters long")
+
+    if next_code() != 256:
+        raise ValueError("strip must begin with CLEAR code")
+
+    code = oldcode = 0
+    result = []
+    while True:
+        code = next_code()  # ~5% faster when inlining this function
+        bitcount += bitw
+        if code == 257:  # EOI
+            break
+        if code == 256:  # CLEAR
+            table = newtable[:]
+            lentable = 258
+            bitw, shr, mask = switchbitch[255]
+            code = next_code()
+            bitcount += bitw
+            if code == 257:  # EOI
+                break
+            result.append(table[code])
+        else:
+            if code < lentable:
+                decoded = table[code]
+                newcode = table[oldcode] + decoded[:1]
+            else:
+                newcode = table[oldcode]
+                newcode += newcode[:1]
+                decoded = newcode
+            result.append(decoded)
+            table.append(newcode)
+            lentable += 1
+        oldcode = code
+        if lentable in switchbitch:
+            bitw, shr, mask = switchbitch[lentable]
+
+    if code != 257:
+        raise ValueError("unexpected end of stream (code %i)" % code)
+
+    return b''.join(result)
+
+
+@_replace_by('_tifffile.unpackints')
+def unpackints(data, dtype, itemsize, runlen=0):
+    """Decompress byte string to array of integers of any bit size <= 32.
+
+    data : byte str
+
+    dtype : numpy.dtype or str
+        A numpy boolean or integer type.
+
+    itemsize : int
+        Number of bits per integer.
+
+    runlen : int
+        Number of consecutive integers, after which to start at next byte.
+
+    """
+    if itemsize == 1:  # bitarray
+        data = numpy.fromstring(data, '|B')
+        data = numpy.unpackbits(data)
+        if runlen % 8:
+            data = data.reshape(-1, runlen+(8-runlen%8))
+            data = data[:, :runlen].reshape(-1)
+        return data.astype(dtype)
+
+    dtype = numpy.dtype(dtype)
+    if itemsize in (8, 16, 32, 64):
+        return numpy.fromstring(data, dtype)
+    if itemsize < 1 or itemsize > 32:
+        raise ValueError("itemsize out of range: %i" % itemsize)
+    if dtype.kind not in "biu":
+        raise ValueError("invalid dtype")
+
+    itembytes = next(i for i in (1, 2, 4, 8) if 8 * i >= itemsize)
+    if itembytes != dtype.itemsize:
+        raise ValueError("dtype.itemsize too small")
+    if runlen == 0:
+        runlen = len(data) // itembytes
+    skipbits = runlen*itemsize % 8
+    if skipbits:
+        skipbits = 8 - skipbits
+    shrbits = itembytes*8 - itemsize
+    bitmask = int(itemsize*'1'+'0'*shrbits, 2)
+    dtypestr = '>' + dtype.char  # dtype always big endian?
+
+    unpack = struct.unpack
+    l = runlen * (len(data)*8 // (runlen*itemsize + skipbits))
+    result = numpy.empty((l, ), dtype)
+    bitcount = 0
+    for i in range(len(result)):
+        start = bitcount // 8
+        s = data[start:start+itembytes]
+        try:
+            code = unpack(dtypestr, s)[0]
+        except Exception:
+            code = unpack(dtypestr, s + b'\x00'*(itembytes-len(s)))[0]
+        code = code << (bitcount % 8)
+        code = code & bitmask
+        result[i] = code >> shrbits
+        bitcount += itemsize
+        if (i+1) % runlen == 0:
+            bitcount += skipbits
+    return result
+
+
+def unpackrgb(data, dtype, bitspersample):
+    """Unpack RGB565 from byte string."""
+    if not (len(bitspersample) == 3
+            and all(i <= 8 for i in bitspersample)
+            and numpy.sum(bitspersample) == 16):
+        raise ValueError("sample size not supported %s" % str(bitspersample))
+    data = numpy.fromstring(data, dtype[0]+'H')
+    r, g, b = bitspersample
+    result = numpy.zeros((data.size, 3), 'uint8')
+    result[:, 0] = ((data >> (r+g)) & (int('0b'+'1'*r, 2))) << (8 - r)
+    result[:, 1] = ((data >> r) & (int('0b'+'1'*g, 2))) << (8 - g)
+    result[:, 2] = (data & (int('0b'+'1'*b, 2))) << (8 - b)
+    return result.reshape(-1)
+
+
+def reorient(image, orientation):
+    """Return reoriented view of image array.
+
+    image : numpy array
+        Non-squeezed output of asarray() functions.
+        Axes -3 and -2 must be image length and width respectively.
+
+    orientation : int or str
+        One of TIFF_ORIENTATIONS keys or values
+
+    """
+    o = TIFF_ORIENTATIONS.get(orientation, orientation)
+    if o == 'top_left':
+        return image
+    elif o == 'top_right':
+        return image[..., ::-1, :]
+    elif o == 'bottom_left':
+        return image[..., ::-1, :, :]
+    elif o == 'bottom_right':
+        return image[..., ::-1, ::-1, :]
+    elif o == 'left_top':
+        return numpy.swapaxes(image, -3, -2)
+    elif o == 'right_top':
+        return numpy.swapaxes(image, -3, -2)[..., ::-1, :]
+    elif o == 'left_bottom':
+        return numpy.swapaxes(image, -3, -2)[..., ::-1, :, :]
+    elif o == 'right_bottom':
+        return numpy.swapaxes(image, -3, -2)[..., ::-1, ::-1, :]
+
+
+def stripnull(string):
+    """Return string truncated at first null character."""
+    i = string.find(b'\x00')
+    return string if (i < 0) else string[:i]
+
+
+def datetime_from_timestamp(n, epoch=datetime.datetime.fromordinal(693594)):
+    """Return datetime object from timestamp in Excel serial format.
+
+    >>> datetime_from_timestamp(40237.029999999795)
+    datetime.datetime(2010, 2, 28, 0, 43, 11, 999982)
+
+    """
+    return epoch + datetime.timedelta(n)
+
+
+def test_tifffile(directory='testimages', verbose=True):
+    """Read all images in directory. Print error message on failure.
+
+    >>> test_tifffile(verbose=False)
+
+    """
+    import glob
+
+    successful = 0
+    failed = 0
+    start = time.time()
+    for f in glob.glob(os.path.join(directory, '*.*')):
+        if verbose:
+            print("\n%s>\n" % f.lower(), end='')
+        t0 = time.time()
+        try:
+            tif = TIFFfile(f)
+        except Exception as e:
+            if not verbose:
+                print(f, end=' ')
+            print("ERROR:", e)
+            failed += 1
+            continue
+        try:
+            img = tif.asarray()
+        except ValueError:
+            try:
+                img = tif[0].asarray()
+            except Exception as e:
+                if not verbose:
+                    print(f, end=' ')
+                print("ERROR:", e)
+                failed += 1
+                continue
+        finally:
+            tif.close()
+        successful += 1
+        if verbose:
+            print("%s, %s %s, %s, %.0f ms" % (str(tif), str(img.shape),
+                img.dtype, tif[0].compression, (time.time()-t0) * 1e3))
+    if verbose:
+        print("\nSuccessfully read %i of %i files in %.3f s\n" % (
+            successful, successful+failed, time.time()-start))
+
+
+class TIFF_SUBFILE_TYPES(object):
+    def __getitem__(self, key):
+        result = []
+        if key & 1:
+            result.append('reduced_image')
+        if key & 2:
+            result.append('page')
+        if key & 4:
+            result.append('mask')
+        return tuple(result)
+
+
+TIFF_PHOTOMETRICS = {
+    0: 'miniswhite',
+    1: 'minisblack',
+    2: 'rgb',
+    3: 'palette',
+    4: 'mask',
+    5: 'separated',
+    6: 'cielab',
+    7: 'icclab',
+    8: 'itulab',
+    32844: 'logl',
+    32845: 'logluv'}
+
+TIFF_COMPESSIONS = {
+    1: None,
+    2: 'ccittrle',
+    3: 'ccittfax3',
+    4: 'ccittfax4',
+    5: 'lzw',
+    6: 'ojpeg',
+    7: 'jpeg',
+    8: 'adobe_deflate',
+    9: 't85',
+    10: 't43',
+    32766: 'next',
+    32771: 'ccittrlew',
+    32773: 'packbits',
+    32809: 'thunderscan',
+    32895: 'it8ctpad',
+    32896: 'it8lw',
+    32897: 'it8mp',
+    32898: 'it8bl',
+    32908: 'pixarfilm',
+    32909: 'pixarlog',
+    32946: 'deflate',
+    32947: 'dcs',
+    34661: 'jbig',
+    34676: 'sgilog',
+    34677: 'sgilog24',
+    34712: 'jp2000'}
+
+TIFF_DECOMPESSORS = {
+    None: lambda x: x,
+    'adobe_deflate': zlib.decompress,
+    'deflate': zlib.decompress,
+    'packbits': decodepackbits,
+    'lzw': decodelzw}
+
+TIFF_DATA_TYPES = {
+    1: '1B',   # BYTE 8-bit unsigned integer.
+    2: '1s',   # ASCII 8-bit byte that contains a 7-bit ASCII code;
+               #   the last byte must be NULL (binary zero).
+    3: '1H',   # SHORT 16-bit (2-byte) unsigned integer
+    4: '1I',   # LONG 32-bit (4-byte) unsigned integer.
+    5: '2I',   # RATIONAL Two LONGs: the first represents the numerator of
+               #   a fraction; the second, the denominator.
+    6: '1b',   # SBYTE An 8-bit signed (twos-complement) integer.
+    7: '1B',   # UNDEFINED An 8-bit byte that may contain anything,
+               #   depending on the definition of the field.
+    8: '1h',   # SSHORT A 16-bit (2-byte) signed (twos-complement) integer.
+    9: '1i',   # SLONG A 32-bit (4-byte) signed (twos-complement) integer.
+    10: '2i',  # SRATIONAL Two SLONGs: the first represents the numerator
+               #   of a fraction, the second the denominator.
+    11: '1f',  # FLOAT Single precision (4-byte) IEEE format.
+    12: '1d',  # DOUBLE Double precision (8-byte) IEEE format.
+    13: '1I',  # IFD unsigned 4 byte IFD offset.
+    #14: '',   # UNICODE
+    #15: '',   # COMPLEX
+    16: '1Q',  # LONG8 unsigned 8 byte integer (BigTiff)
+    17: '1q',  # SLONG8 signed 8 byte integer (BigTiff)
+    18: '1Q'}  # IFD8 unsigned 8 byte IFD offset (BigTiff)
+
+TIFF_SAMPLE_FORMATS = {
+    1: 'uint',
+    2: 'int',
+    3: 'float',
+    #4: 'void',
+    #5: 'complex_int',
+    6: 'complex'}
+
+TIFF_SAMPLE_DTYPES = {
+    ('uint', 1): '?',  # bitmap
+    ('uint', 2): 'B',
+    ('uint', 3): 'B',
+    ('uint', 4): 'B',
+    ('uint', 5): 'B',
+    ('uint', 6): 'B',
+    ('uint', 7): 'B',
+    ('uint', 8): 'B',
+    ('uint', 9): 'H',
+    ('uint', 10): 'H',
+    ('uint', 11): 'H',
+    ('uint', 12): 'H',
+    ('uint', 13): 'H',
+    ('uint', 14): 'H',
+    ('uint', 15): 'H',
+    ('uint', 16): 'H',
+    ('uint', 17): 'I',
+    ('uint', 18): 'I',
+    ('uint', 19): 'I',
+    ('uint', 20): 'I',
+    ('uint', 21): 'I',
+    ('uint', 22): 'I',
+    ('uint', 23): 'I',
+    ('uint', 24): 'I',
+    ('uint', 25): 'I',
+    ('uint', 26): 'I',
+    ('uint', 27): 'I',
+    ('uint', 28): 'I',
+    ('uint', 29): 'I',
+    ('uint', 30): 'I',
+    ('uint', 31): 'I',
+    ('uint', 32): 'I',
+    ('uint', 64): 'Q',
+    ('int', 8): 'b',
+    ('int', 16): 'h',
+    ('int', 32): 'i',
+    ('int', 64): 'q',
+    ('float', 16): 'e',
+    ('float', 32): 'f',
+    ('float', 64): 'd',
+    ('complex', 64): 'F',
+    ('complex', 128): 'D',
+    ('uint', (5, 6, 5)): 'B'}
+
+TIFF_ORIENTATIONS = {
+    1: 'top_left',
+    2: 'top_right',
+    3: 'bottom_right',
+    4: 'bottom_left',
+    5: 'left_top',
+    6: 'right_top',
+    7: 'right_bottom',
+    8: 'left_bottom'}
+
+AXES_LABELS = {
+    'X': 'width',
+    'Y': 'height',
+    'Z': 'depth',
+    'S': 'sample',
+    'P': 'plane',
+    'T': 'time',
+    'C': 'channel',  # color, emission wavelength
+    'A': 'angle',
+    'F': 'phase',
+    'R': 'tile',  # region
+    'H': 'lifetime',  # histogram
+    'E': 'lambda',  # excitation wavelength
+    'L': 'exposure',  # lux
+    'V': 'event',
+    'O': 'other'}
+
+AXES_LABELS.update(dict((v, k) for k, v in AXES_LABELS.items()))
+
+# MetaMorph STK tags
+MM_TAG_IDS = {
+    0: 'auto_scale',
+    1: 'min_scale',
+    2: 'max_scale',
+    3: 'spatial_calibration',
+    #4: 'x_calibration',
+    #5: 'y_calibration',
+    #6: 'calibration_units',
+    #7: 'name',
+    8: 'thresh_state',
+    9: 'thresh_state_red',
+    11: 'thresh_state_green',
+    12: 'thresh_state_blue',
+    13: 'thresh_state_lo',
+    14: 'thresh_state_hi',
+    15: 'zoom',
+    #16: 'create_time',
+    #17: 'last_saved_time',
+    18: 'current_buffer',
+    19: 'gray_fit',
+    20: 'gray_point_count',
+    #21: 'gray_x',
+    #22: 'gray_y',
+    #23: 'gray_min',
+    #24: 'gray_max',
+    #25: 'gray_unit_name',
+    26: 'standard_lut',
+    27: 'wavelength',
+    #28: 'stage_position',
+    #29: 'camera_chip_offset',
+    #30: 'overlay_mask',
+    #31: 'overlay_compress',
+    #32: 'overlay',
+    #33: 'special_overlay_mask',
+    #34: 'special_overlay_compress',
+    #35: 'special_overlay',
+    36: 'image_property',
+    #37: 'stage_label',
+    #38: 'autoscale_lo_info',
+    #39: 'autoscale_hi_info',
+    #40: 'absolute_z',
+    #41: 'absolute_z_valid',
+    #42: 'gamma',
+    #43: 'gamma_red',
+    #44: 'gamma_green',
+    #45: 'gamma_blue',
+    #46: 'camera_bin',
+    47: 'new_lut',
+    #48: 'image_property_ex',
+    49: 'plane_property',
+    #50: 'user_lut_table',
+    51: 'red_autoscale_info',
+    #52: 'red_autoscale_lo_info',
+    #53: 'red_autoscale_hi_info',
+    54: 'red_minscale_info',
+    55: 'red_maxscale_info',
+    56: 'green_autoscale_info',
+    #57: 'green_autoscale_lo_info',
+    #58: 'green_autoscale_hi_info',
+    59: 'green_minscale_info',
+    60: 'green_maxscale_info',
+    61: 'blue_autoscale_info',
+    #62: 'blue_autoscale_lo_info',
+    #63: 'blue_autoscale_hi_info',
+    64: 'blue_min_scale_info',
+    65: 'blue_max_scale_info'}
+    #66: 'overlay_plane_color',
+
+# Olymus Fluoview
+MM_DIMENSION = [
+    ('name', 'a16'),
+    ('size', 'i4'),
+    ('origin', 'f8'),
+    ('resolution', 'f8'),
+    ('unit', 'a64')]
+
+MM_HEADER = [
+    ('header_flag', 'i2'),
+    ('image_type', 'u1'),
+    ('image_name', 'a257'),
+    ('offset_data', 'u4'),
+    ('palette_size', 'i4'),
+    ('offset_palette0', 'u4'),
+    ('offset_palette1', 'u4'),
+    ('comment_size', 'i4'),
+    ('offset_comment', 'u4'),
+    ('dimensions', MM_DIMENSION, 10),
+    ('offset_position', 'u4'),
+    ('map_type', 'i2'),
+    ('map_min', 'f8'),
+    ('map_max', 'f8'),
+    ('min_value', 'f8'),
+    ('max_value', 'f8'),
+    ('offset_map', 'u4'),
+    ('gamma', 'f8'),
+    ('offset', 'f8'),
+    ('gray_channel', MM_DIMENSION),
+    ('offset_thumbnail', 'u4'),
+    ('voice_field', 'i4'),
+    ('offset_voice_field', 'u4')]
+
+# Carl Zeiss LSM
+CZ_LSM_INFO = [
+    ('magic_number', 'i4'),
+    ('structure_size', 'i4'),
+    ('dimension_x', 'i4'),
+    ('dimension_y', 'i4'),
+    ('dimension_z', 'i4'),
+    ('dimension_channels', 'i4'),
+    ('dimension_time', 'i4'),
+    ('dimension_data_type', 'i4'),
+    ('thumbnail_x', 'i4'),
+    ('thumbnail_y', 'i4'),
+    ('voxel_size_x', 'f8'),
+    ('voxel_size_y', 'f8'),
+    ('voxel_size_z', 'f8'),
+    ('origin_x', 'f8'),
+    ('origin_y', 'f8'),
+    ('origin_z', 'f8'),
+    ('scan_type', 'u2'),
+    ('spectral_scan', 'u2'),
+    ('data_type', 'u4'),
+    ('offset_vector_overlay', 'u4'),
+    ('offset_input_lut', 'u4'),
+    ('offset_output_lut', 'u4'),
+    ('offset_channel_colors', 'u4'),
+    ('time_interval', 'f8'),
+    ('offset_channel_data_types', 'u4'),
+    ('offset_scan_information', 'u4'),
+    ('offset_ks_data', 'u4'),
+    ('offset_time_stamps', 'u4'),
+    ('offset_event_list', 'u4'),
+    ('offset_roi', 'u4'),
+    ('offset_bleach_roi', 'u4'),
+    ('offset_next_recording', 'u4'),
+    ('display_aspect_x', 'f8'),
+    ('display_aspect_y', 'f8'),
+    ('display_aspect_z', 'f8'),
+    ('display_aspect_time', 'f8'),
+    ('offset_mean_of_roi_overlay', 'u4'),
+    ('offset_topo_isoline_overlay', 'u4'),
+    ('offset_topo_profile_overlay', 'u4'),
+    ('offset_linescan_overlay', 'u4'),
+    ('offset_toolbar_flags', 'u4')]
+
+# Import functions for LSM_INFO subrecords
+CZ_LSM_INFO_READERS = {
+    'scan_information': read_cz_lsm_scan_info,
+    'time_stamps': read_cz_lsm_time_stamps,
+    'event_list': read_cz_lsm_event_list}
+
+# Map cz_lsm_info.scan_type to dimension order
+CZ_SCAN_TYPES = {
+    0: 'XYZCT',  # x-y-z scan
+    1: 'XYZCT',  # z scan (x-z plane)
+    2: 'XYZCT',  # line scan
+    3: 'XYTCZ',  # time series x-y
+    4: 'XYZTC',  # time series x-z
+    5: 'XYTCZ',  # time series 'Mean of ROIs'
+    6: 'XYZTC',  # time series x-y-z
+    7: 'XYCTZ',  # spline scan
+    8: 'XYCZT',  # spline scan x-z
+    9: 'XYTCZ',  # time series spline plane x-z
+    10: 'XYZCT'}  # point mode
+
+# Map dimension codes to cz_lsm_info attribute
+CZ_DIMENSIONS = {
+    'X': 'dimension_x',
+    'Y': 'dimension_y',
+    'Z': 'dimension_z',
+    'C': 'dimension_channels',
+    'T': 'dimension_time'}
+
+# Descriptions of cz_lsm_info.data_type
+CZ_DATA_TYPES = {
+    0: 'varying data types',
+    2: '12 bit unsigned integer',
+    5: '32 bit float'}
+
+CZ_LSM_SCAN_INFO_ARRAYS = {
+    0x20000000: "tracks",
+    0x30000000: "lasers",
+    0x60000000: "detectionchannels",
+    0x80000000: "illuminationchannels",
+    0xa0000000: "beamsplitters",
+    0xc0000000: "datachannels",
+    0x13000000: "markers",
+    0x11000000: "timers"}
+
+CZ_LSM_SCAN_INFO_STRUCTS = {
+    0x40000000: "tracks",
+    0x50000000: "lasers",
+    0x70000000: "detectionchannels",
+    0x90000000: "illuminationchannels",
+    0xb0000000: "beamsplitters",
+    0xd0000000: "datachannels",
+    0x14000000: "markers",
+    0x12000000: "timers"}
+
+CZ_LSM_SCAN_INFO_ATTRIBUTES = {
+    0x10000001: "name",
+    0x10000002: "description",
+    0x10000003: "notes",
+    0x10000004: "objective",
+    0x10000005: "processing_summary",
+    0x10000006: "special_scan_mode",
+    0x10000007: "oledb_recording_scan_type",
+    0x10000008: "oledb_recording_scan_mode",
+    0x10000009: "number_of_stacks",
+    0x1000000a: "lines_per_plane",
+    0x1000000b: "samples_per_line",
+    0x1000000c: "planes_per_volume",
+    0x1000000d: "images_width",
+    0x1000000e: "images_height",
+    0x1000000f: "images_number_planes",
+    0x10000010: "images_number_stacks",
+    0x10000011: "images_number_channels",
+    0x10000012: "linscan_xy_size",
+    0x10000013: "scan_direction",
+    0x10000014: "time_series",
+    0x10000015: "original_scan_data",
+    0x10000016: "zoom_x",
+    0x10000017: "zoom_y",
+    0x10000018: "zoom_z",
+    0x10000019: "sample_0x",
+    0x1000001a: "sample_0y",
+    0x1000001b: "sample_0z",
+    0x1000001c: "sample_spacing",
+    0x1000001d: "line_spacing",
+    0x1000001e: "plane_spacing",
+    0x1000001f: "plane_width",
+    0x10000020: "plane_height",
+    0x10000021: "volume_depth",
+    0x10000023: "nutation",
+    0x10000034: "rotation",
+    0x10000035: "precession",
+    0x10000036: "sample_0time",
+    0x10000037: "start_scan_trigger_in",
+    0x10000038: "start_scan_trigger_out",
+    0x10000039: "start_scan_event",
+    0x10000040: "start_scan_time",
+    0x10000041: "stop_scan_trigger_in",
+    0x10000042: "stop_scan_trigger_out",
+    0x10000043: "stop_scan_event",
+    0x10000044: "stop_scan_time",
+    0x10000045: "use_rois",
+    0x10000046: "use_reduced_memory_rois",
+    0x10000047: "user",
+    0x10000048: "use_bccorrection",
+    0x10000049: "position_bccorrection1",
+    0x10000050: "position_bccorrection2",
+    0x10000051: "interpolation_y",
+    0x10000052: "camera_binning",
+    0x10000053: "camera_supersampling",
+    0x10000054: "camera_frame_width",
+    0x10000055: "camera_frame_height",
+    0x10000056: "camera_offset_x",
+    0x10000057: "camera_offset_y",
+    # lasers
+    0x50000001: "name",
+    0x50000002: "acquire",
+    0x50000003: "power",
+    # tracks
+    0x40000001: "multiplex_type",
+    0x40000002: "multiplex_order",
+    0x40000003: "sampling_mode",
+    0x40000004: "sampling_method",
+    0x40000005: "sampling_number",
+    0x40000006: "acquire",
+    0x40000007: "sample_observation_time",
+    0x4000000b: "time_between_stacks",
+    0x4000000c: "name",
+    0x4000000d: "collimator1_name",
+    0x4000000e: "collimator1_position",
+    0x4000000f: "collimator2_name",
+    0x40000010: "collimator2_position",
+    0x40000011: "is_bleach_track",
+    0x40000012: "is_bleach_after_scan_number",
+    0x40000013: "bleach_scan_number",
+    0x40000014: "trigger_in",
+    0x40000015: "trigger_out",
+    0x40000016: "is_ratio_track",
+    0x40000017: "bleach_count",
+    0x40000018: "spi_center_wavelength",
+    0x40000019: "pixel_time",
+    0x40000021: "condensor_frontlens",
+    0x40000023: "field_stop_value",
+    0x40000024: "id_condensor_aperture",
+    0x40000025: "condensor_aperture",
+    0x40000026: "id_condensor_revolver",
+    0x40000027: "condensor_filter",
+    0x40000028: "id_transmission_filter1",
+    0x40000029: "id_transmission1",
+    0x40000030: "id_transmission_filter2",
+    0x40000031: "id_transmission2",
+    0x40000032: "repeat_bleach",
+    0x40000033: "enable_spot_bleach_pos",
+    0x40000034: "spot_bleach_posx",
+    0x40000035: "spot_bleach_posy",
+    0x40000036: "spot_bleach_posz",
+    0x40000037: "id_tubelens",
+    0x40000038: "id_tubelens_position",
+    0x40000039: "transmitted_light",
+    0x4000003a: "reflected_light",
+    0x4000003b: "simultan_grab_and_bleach",
+    0x4000003c: "bleach_pixel_time",
+    # detection_channels
+    0x70000001: "integration_mode",
+    0x70000002: "special_mode",
+    0x70000003: "detector_gain_first",
+    0x70000004: "detector_gain_last",
+    0x70000005: "amplifier_gain_first",
+    0x70000006: "amplifier_gain_last",
+    0x70000007: "amplifier_offs_first",
+    0x70000008: "amplifier_offs_last",
+    0x70000009: "pinhole_diameter",
+    0x7000000a: "counting_trigger",
+    0x7000000b: "acquire",
+    0x7000000c: "point_detector_name",
+    0x7000000d: "amplifier_name",
+    0x7000000e: "pinhole_name",
+    0x7000000f: "filter_set_name",
+    0x70000010: "filter_name",
+    0x70000013: "integrator_name",
+    0x70000014: "detection_channel_name",
+    0x70000015: "detection_detector_gain_bc1",
+    0x70000016: "detection_detector_gain_bc2",
+    0x70000017: "detection_amplifier_gain_bc1",
+    0x70000018: "detection_amplifier_gain_bc2",
+    0x70000019: "detection_amplifier_offset_bc1",
+    0x70000020: "detection_amplifier_offset_bc2",
+    0x70000021: "detection_spectral_scan_channels",
+    0x70000022: "detection_spi_wavelength_start",
+    0x70000023: "detection_spi_wavelength_stop",
+    0x70000026: "detection_dye_name",
+    0x70000027: "detection_dye_folder",
+    # illumination_channels
+    0x90000001: "name",
+    0x90000002: "power",
+    0x90000003: "wavelength",
+    0x90000004: "aquire",
+    0x90000005: "detchannel_name",
+    0x90000006: "power_bc1",
+    0x90000007: "power_bc2",
+    # beam_splitters
+    0xb0000001: "filter_set",
+    0xb0000002: "filter",
+    0xb0000003: "name",
+    # data_channels
+    0xd0000001: "name",
+    0xd0000003: "acquire",
+    0xd0000004: "color",
+    0xd0000005: "sample_type",
+    0xd0000006: "bits_per_sample",
+    0xd0000007: "ratio_type",
+    0xd0000008: "ratio_track1",
+    0xd0000009: "ratio_track2",
+    0xd000000a: "ratio_channel1",
+    0xd000000b: "ratio_channel2",
+    0xd000000c: "ratio_const1",
+    0xd000000d: "ratio_const2",
+    0xd000000e: "ratio_const3",
+    0xd000000f: "ratio_const4",
+    0xd0000010: "ratio_const5",
+    0xd0000011: "ratio_const6",
+    0xd0000012: "ratio_first_images1",
+    0xd0000013: "ratio_first_images2",
+    0xd0000014: "dye_name",
+    0xd0000015: "dye_folder",
+    0xd0000016: "spectrum",
+    0xd0000017: "acquire",
+    # markers
+    0x14000001: "name",
+    0x14000002: "description",
+    0x14000003: "trigger_in",
+    0x14000004: "trigger_out",
+    # timers
+    0x12000001: "name",
+    0x12000002: "description",
+    0x12000003: "interval",
+    0x12000004: "trigger_in",
+    0x12000005: "trigger_out",
+    0x12000006: "activation_time",
+    0x12000007: "activation_number"}
+
+# Map TIFF tag code to attribute name, default value, type, count, validator
+TIFF_TAGS = {
+    254: ('new_subfile_type', 0, 4, 1, TIFF_SUBFILE_TYPES()),
+    255: ('subfile_type', None, 3, 1,
+          {0: 'undefined', 1: 'image', 2: 'reduced_image', 3: 'page'}),
+    256: ('image_width', None, 4, 1, None),
+    257: ('image_length', None, 4, 1, None),
+    258: ('bits_per_sample', 1, 3, 1, None),
+    259: ('compression', 1, 3, 1, TIFF_COMPESSIONS),
+    262: ('photometric', None, 3, 1, TIFF_PHOTOMETRICS),
+    266: ('fill_order', 1, 3, 1, {1: 'msb2lsb', 2: 'lsb2msb'}),
+    269: ('document_name', None, 2, None, None),
+    270: ('image_description', None, 2, None, None),
+    271: ('make', None, 2, None, None),
+    272: ('model', None, 2, None, None),
+    273: ('strip_offsets', None, 4, None, None),
+    274: ('orientation', 1, 3, 1, TIFF_ORIENTATIONS),
+    277: ('samples_per_pixel', 1, 3, 1, None),
+    278: ('rows_per_strip', 2**32-1, 4, 1, None),
+    279: ('strip_byte_counts', None, 4, None, None),
+    #280: ('min_sample_value', 0, 3, None, None),
+    #281: ('max_sample_value', None, 3, None, None),  # 2**bits_per_sample
+    282: ('x_resolution', None, 5, 1, None),
+    283: ('y_resolution', None, 5, 1, None),
+    284: ('planar_configuration', 1, 3, 1, {1: 'contig', 2: 'separate'}),
+    285: ('page_name', None, 2, None, None),
+    296: ('resolution_unit', 2, 4, 1, {1: 'none', 2: 'inch', 3: 'centimeter'}),
+    305: ('software', None, 2, None, None),
+    306: ('datetime', None, 2, None, None),
+    315: ('artist', None, 2, None, None),
+    316: ('host_computer', None, 2, None, None),
+    317: ('predictor', 1, 3, 1, {1: None, 2: 'horizontal'}),
+    320: ('color_map', None, 3, None, None),
+    322: ('tile_width', None, 4, 1, None),
+    323: ('tile_length', None, 4, 1, None),
+    324: ('tile_offsets', None, 4, None, None),
+    325: ('tile_byte_counts', None, 4, None, None),
+    338: ('extra_samples', None, 3, None,
+          {0: 'unspecified', 1: 'assocalpha', 2: 'unassalpha'}),
+    339: ('sample_format', 1, 3, 1, TIFF_SAMPLE_FORMATS),
+    530: ('ycbcr_subsampling', 1, 3, 2, None),
+    531: ('ycbcr_positioning', 1, 3, 1, None),
+    #700: ('xmp', None, 1, None, None),
+    33432: ('copyright', None, 1, None, None),
+    32997: ('image_depth', None, 4, 1, None),
+    32998: ('tile_depth', None, 4, 1, None),
+    34665: ('exif_ifd', None, 4, 1, None)}
+
+# Map custom TIFF tag codes to attribute names and import functions
+CUSTOM_TAGS = {
+    33628: ('mm_uic1', read_mm_uic1),
+    33629: ('mm_uic2', read_mm_uic2),
+    33630: ('mm_uic3', read_mm_uic3),
+    33631: ('mm_uic4', read_mm_uic4),
+    34361: ('mm_header', read_mm_header),
+    34362: ('mm_stamp', read_mm_stamp),
+    34386: ('mm_user_block', None),
+    34412: ('cz_lsm_info', read_cz_lsm_info),
+    43314: ('nih_image_header', read_nih_image_header)}
+
+# Max line length of printed output
+PRINT_LINE_LEN = 79
+
+
+def imshow(data, title=None, vmin=0, vmax=None, cmap=None,
+           bitspersample=None, photometric='rgb', interpolation='nearest',
+           dpi=96, figure=None, subplot=111, maxdim=4096, **kwargs):
+    """Plot n-dimensional images using matplotlib.pyplot.
+
+    Return figure, subplot and plot axis.
+    Requires pyplot already imported ``from matplotlib import pyplot``.
+
+    Arguments
+    ---------
+
+    bitspersample : int or None
+        Number of bits per channel in integer RGB images.
+
+    photometric : {'miniswhite', 'minisblack', 'rgb', or 'palette'}
+        The color space of the image data.
+
+    title : str
+        Window and subplot title.
+
+    figure : matplotlib.figure.Figure instance (optional).
+
+    subplot : int
+        A matplotlib.pyplot.subplot axis.
+
+    maxdim : int
+        maximum image size in any dimension.
+
+    kwargs : optional arguments for matplotlib.pyplot.imshow.
+
+    """
+    #if photometric not in ('miniswhite', 'minisblack', 'rgb', 'palette'):
+    #    raise ValueError("Can't handle %s photometrics" % photometric)
+    isrgb = photometric in ('rgb', 'palette')
+    data = numpy.atleast_2d(data.squeeze())
+    data = data[(slice(0, maxdim), ) * len(data.shape)]
+
+    dims = data.ndim
+    if dims < 2:
+        raise ValueError("not an image")
+    elif dims == 2:
+        dims = 0
+        isrgb = False
+    else:
+        if (isrgb and data.shape[-3] in (3, 4)):
+            data = numpy.swapaxes(data, -3, -2)
+            data = numpy.swapaxes(data, -2, -1)
+        elif (not isrgb and data.shape[-1] in (3, 4)):
+            data = numpy.swapaxes(data, -3, -1)
+            data = numpy.swapaxes(data, -2, -1)
+        isrgb = isrgb and data.shape[-1] in (3, 4)
+        dims -= 3 if isrgb else 2
+
+    if photometric == 'palette':
+        datamax = data.max()
+        if datamax > 255:
+            data >>= 8  # possible precision loss
+        data = data.astype('B')
+    elif data.dtype.kind in 'ui':
+        if not isrgb or bitspersample is None:
+            bitspersample = int(math.ceil(math.log(data.max(), 2)))
+        elif not isinstance(bitspersample, int):
+            # bitspersample can be tuple, e.g. (5, 6, 5)
+            bitspersample = data.dtype.itemsize * 8
+        datamax = 2**bitspersample
+        if isrgb:
+            if bitspersample < 8:
+                data <<= 8 - bitspersample
+            elif bitspersample > 8:
+                data >>= bitspersample - 8  # precision loss
+            data = data.astype('B')
+    elif data.dtype.kind == 'f':
+        datamax = data.max()
+        if isrgb and datamax > 1.0:
+            if data.dtype.char == 'd':
+                data = data.astype('f')
+            data /= datamax
+    elif data.dtype.kind == 'b':
+        datamax = 1
+
+    if vmax is None:
+        vmax = datamax
+    if vmin is None:
+        if data.dtype.kind != 'f':
+            vmin = 0
+
+    pyplot = sys.modules['matplotlib.pyplot']
+
+    if figure is None:
+        pyplot.rc('font', family='sans-serif', weight='normal', size=8)
+        figure = pyplot.figure(dpi=dpi, figsize=(10.3, 6.3), frameon=True,
+                               facecolor='1.0', edgecolor='w')
+        try:
+            figure.canvas.manager.window.title(title)
+        except Exception:
+            pass
+        pyplot.subplots_adjust(bottom=0.03*(dims+2), top=0.9,
+                               left=0.1, right=0.95, hspace=0.05, wspace=0.0)
+    subplot = pyplot.subplot(subplot)
+
+    if title:
+        pyplot.title(title, size=11)
+
+    if cmap is None:
+        if photometric == 'miniswhite':
+            cmap = pyplot.cm.gray_r
+        else:
+            cmap = pyplot.cm.gray
+
+    image = pyplot.imshow(data[(0, ) * dims].squeeze(), vmin=vmin, vmax=vmax,
+                          cmap=cmap, interpolation=interpolation, **kwargs)
+
+    if not isrgb:
+        pyplot.colorbar()  # panchor=(0.55, 0.5), fraction=0.05
+
+    def format_coord(x, y):
+        # callback function to format coordinate display in toolbar
+        x = int(x + 0.5)
+        y = int(y + 0.5)
+        try:
+            if dims:
+                return "%s @ %s [%4i, %4i]" % (cur_ax_dat[1][y, x],
+                                               current, x, y)
+            else:
+                return "%s @ [%4i, %4i]" % (data[y, x], x, y)
+        except IndexError:
+            return ""
+
+    pyplot.gca().format_coord = format_coord
+
+    if dims:
+        current = list((0, ) * dims)
+        cur_ax_dat = [0, data[tuple(current)].squeeze()]
+        sliders = [pyplot.Slider(
+            pyplot.axes([0.125, 0.03*(axis+1), 0.725, 0.025]),
+            'Dimension %i' % axis, 0, data.shape[axis]-1, 0, facecolor='0.5',
+            valfmt='%%.0f [%i]' % data.shape[axis]) for axis in range(dims)]
+        for slider in sliders:
+            slider.drawon = False
+
+        def set_image(current, sliders=sliders, data=data):
+            # change image and redraw canvas
+            cur_ax_dat[1] = data[tuple(current)].squeeze()
+            image.set_data(cur_ax_dat[1])
+            for ctrl, index in zip(sliders, current):
+                ctrl.eventson = False
+                ctrl.set_val(index)
+                ctrl.eventson = True
+            figure.canvas.draw()
+
+        def on_changed(index, axis, data=data, current=current):
+            # callback function for slider change event
+            index = int(round(index))
+            cur_ax_dat[0] = axis
+            if index == current[axis]:
+                return
+            if index >= data.shape[axis]:
+                index = 0
+            elif index < 0:
+                index = data.shape[axis] - 1
+            current[axis] = index
+            set_image(current)
+
+        def on_keypressed(event, data=data, current=current):
+            # callback function for key press event
+            key = event.key
+            axis = cur_ax_dat[0]
+            if str(key) in '0123456789':
+                on_changed(key, axis)
+            elif key == 'right':
+                on_changed(current[axis] + 1, axis)
+            elif key == 'left':
+                on_changed(current[axis] - 1, axis)
+            elif key == 'up':
+                cur_ax_dat[0] = 0 if axis == len(data.shape)-1 else axis + 1
+            elif key == 'down':
+                cur_ax_dat[0] = len(data.shape)-1 if axis == 0 else axis - 1
+            elif key == 'end':
+                on_changed(data.shape[axis] - 1, axis)
+            elif key == 'home':
+                on_changed(0, axis)
+
+        figure.canvas.mpl_connect('key_press_event', on_keypressed)
+        for axis, ctrl in enumerate(sliders):
+            ctrl.on_changed(lambda k, a=axis: on_changed(k, a))
+
+    return figure, subplot, image
+
+
+def _app_show():
+    """Block the GUI. For use as skimage plugin."""
+    pyplot = sys.modules['matplotlib.pyplot']
+    pyplot.show()
+
+
+def main(argv=None):
+    """Command line usage main function."""
+    if float(sys.version[0:3]) < 2.6:
+        print("This script requires Python version 2.6 or better.")
+        print("This is Python version %s" % sys.version)
+        return 0
+    if argv is None:
+        argv = sys.argv
+
+    import re
+    import optparse
+
+    search_doc = lambda r, d: re.search(r, __doc__).group(1) if __doc__ else d
+    parser = optparse.OptionParser(
+        usage="usage: %prog [options] path",
+        description=search_doc("\n\n([^|]*?)\n\n", ''),
+        version="%%prog %s" % search_doc(":Version: (.*)", "Unknown"))
+    opt = parser.add_option
+    opt('-p', '--page', dest='page', type='int', default=-1,
+        help="display single page")
+    opt('-s', '--series', dest='series', type='int', default=-1,
+        help="display series of pages of same shape")
+    opt('--noplot', dest='noplot', action='store_true', default=False,
+        help="don't display images")
+    opt('--interpol', dest='interpol', metavar='INTERPOL', default='bilinear',
+        help="image interpolation method")
+    opt('--dpi', dest='dpi', type='int', default=96,
+        help="set plot resolution")
+    opt('--debug', dest='debug', action='store_true', default=False,
+        help="raise exception on failures")
+    opt('--test', dest='test', action='store_true', default=False,
+        help="try read all images in path")
+    opt('--doctest', dest='doctest', action='store_true', default=False,
+        help="runs the internal tests")
+    opt('-v', '--verbose', dest='verbose', action='store_true', default=True)
+    opt('-q', '--quiet', dest='verbose', action='store_false')
+
+    settings, path = parser.parse_args()
+    path = ' '.join(path)
+
+    if settings.doctest:
+        import doctest
+        doctest.testmod()
+        return 0
+    if not path:
+        parser.error("No file specified")
+    if settings.test:
+        test_tifffile(path, settings.verbose)
+        return 0
+
+    print("Reading file structure...", end=' ')
+    start = time.time()
+    try:
+        tif = TIFFfile(path)
+    except Exception as e:
+        if settings.debug:
+            raise
+        else:
+            print("\n", e)
+            sys.exit(0)
+    print("%.3f ms" % ((time.time()-start) * 1e3))
+
+    if tif.is_ome:
+        settings.norgb = True
+
+    images = [(None, tif[0 if settings.page < 0 else settings.page])]
+    if not settings.noplot:
+        print("Reading image data... ", end=' ')
+        notnone = lambda x: next(i for i in x if i is not None)
+        start = time.time()
+        try:
+            if settings.page >= 0:
+                images = [(tif.asarray(key=settings.page),
+                           tif[settings.page])]
+            elif settings.series >= 0:
+                images = [(tif.asarray(series=settings.series),
+                           notnone(tif.series[settings.series].pages))]
+            else:
+                images = []
+                for i, s in enumerate(tif.series):
+                    try:
+                        images.append(
+                            (tif.asarray(series=i), notnone(s.pages)))
+                    except ValueError as e:
+                        images.append((None, notnone(s.pages)))
+                        if settings.debug:
+                            raise
+                        else:
+                            print("\n* series %i failed: %s... " % (i, e),
+                                  end='')
+            print("%.3f ms" % ((time.time()-start) * 1e3))
+        except Exception as e:
+            if settings.debug:
+                raise
+            else:
+                print(e)
+    tif.close()
+
+    print("\nTIFF file:", tif)
+    print()
+    for i, s in enumerate(tif.series):
+        print("Series %i" % i)
+        print(s)
+        print()
+    for i, page in images:
+        print(page)
+        print(page.tags)
+        if page.is_palette:
+            print("\nColor Map:", page.color_map.shape, page.color_map.dtype)
+        for attr in ('cz_lsm_info', 'cz_lsm_scan_information',
+                     'mm_uic_tags', 'mm_header', 'nih_image_header'):
+            if hasattr(page, attr):
+                print("", attr.upper(), Record(getattr(page, attr)), sep="\n")
+        print()
+
+    if images and not settings.noplot:
+        try:
+            import matplotlib
+            matplotlib.use('TkAgg')
+            from matplotlib import pyplot
+        except ImportError as e:
+            warnings.warn("failed to import matplotlib.\n%s" % e)
+        else:
+            for img, page in images:
+                if img is None:
+                    continue
+                vmin, vmax = None, None
+                if page.is_stk:
+                    try:
+                        vmin = page.mm_uic_tags['min_scale']
+                        vmax = page.mm_uic_tags['max_scale']
+                    except KeyError:
+                        pass
+                    else:
+                        if vmax <= vmin:
+                            vmin, vmax = None, None
+                title = "%s\n %s" % (str(tif), str(page))
+                imshow(img, title=title, vmin=vmin, vmax=vmax,
+                       bitspersample=page.bits_per_sample,
+                       photometric=page.photometric,
+                       interpolation=settings.interpol,
+                       dpi=settings.dpi)
+            pyplot.show()
+
+
+__version__ = '2012.04.21'
+__docformat__ = 'restructuredtext en'
+
+if __name__ == "__main__":
+    sys.exit(main())