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Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH,
SGI, ImageJ, MicroManager, FluoView, ScanImage, SEQ, GEL, and GeoTIFF files.
Tifffile is not a general-purpose TIFF library.
Only a subset of the TIFF specification is supported, mainly uncompressed and
losslessly compressed 1, 8, 16, 32 and 64 bit integer, 16, 32 and 64-bit float,
grayscale and RGB(A) images, which are commonly used in scientific imaging.
Specifically, reading slices of image data, image trees defined via SubIFDs,
CCITT and OJPEG compression, chroma subsampling without JPEG compression,
or IPTC and XMP metadata are not implemented.
TIFF(R), the tagged Image File Format, is a trademark and under control of
Adobe Systems Incorporated. BigTIFF allows for files greater than 4 GB.
STK, LSM, FluoView, SGI, SEQ, GEL, and OME-TIFF, are custom extensions
defined by Molecular Devices (Universal Imaging Corporation), Carl Zeiss
MicroImaging, Olympus, Silicon Graphics International, Media Cybernetics,
Molecular Dynamics, and the Open Microscopy Environment consortium
respectively.
For command line usage run C{python -m tifffile --help}
:Author:
`Christoph Gohlke `_
:Organization:
Laboratory for Fluorescence Dynamics, University of California, Irvine
:Version: 2018.06.15
Requirements
------------
* `CPython 3.6 64-bit `_
* `Numpy 1.14 `_
* `Matplotlib 2.2 `_ (optional for plotting)
* `Tifffile.c 2018.02.10 `_
(recommended for faster decoding of PackBits and LZW encoded strings)
* `Tifffile_geodb.py 2018.02.10 `_
(optional enums for GeoTIFF metadata)
* Python 2 requires 'futures', 'enum34', 'pathlib'.
Revisions
---------
2018.06.15
Pass 2680 tests.
Towards reading JPEG and other compressions via imagecodecs package (WIP).
Add function to validate TIFF using 'jhove -m TIFF-hul'.
Save bool arrays as bilevel TIFF.
Accept pathlib.Path as filenames.
Move 'software' argument from TiffWriter __init__ to save.
Raise DOS limit to 16 TB.
Lazy load lzma and zstd compressors and decompressors.
Add option to save IJMetadata tags.
Return correct number of pages for truncated series (bug fix).
Move EXIF tags to TIFF.TAG as per TIFF/EP standard.
2018.02.18
Pass 2293 tests.
Always save RowsPerStrip and Resolution tags as required by TIFF standard.
Do not use badly typed ImageDescription.
Coherce bad ASCII string tags to bytes.
Tuning of __str__ functions.
Fix reading 'undefined' tag values (bug fix).
Read and write ZSTD compressed data.
Use hexdump to print byte strings.
Determine TIFF byte order from data dtype in imsave.
Add option to specify RowsPerStrip for compressed strips.
Allow memory map of arrays with non-native byte order.
Attempt to handle ScanImage <= 5.1 files.
Restore TiffPageSeries.pages sequence interface.
Use numpy.frombuffer instead of fromstring to read from binary data.
Parse GeoTIFF metadata.
Add option to apply horizontal differencing before compression.
Towards reading PerkinElmer QPTIFF (no test files).
Do not index out of bounds data in tifffile.c unpackbits and decodelzw.
2017.09.29 (tentative)
Many backwards incompatible changes improving speed and resource usage:
Pass 2268 tests.
Add detail argument to __str__ function. Remove info functions.
Fix potential issue correcting offsets of large LSM files with positions.
Remove TiffFile sequence interface; use TiffFile.pages instead.
Do not make tag values available as TiffPage attributes.
Use str (not bytes) type for tag and metadata strings (WIP).
Use documented standard tag and value names (WIP).
Use enums for some documented TIFF tag values.
Remove 'memmap' and 'tmpfile' options; use out='memmap' instead.
Add option to specify output in asarray functions.
Add option to concurrently decode image strips or tiles using threads.
Add TiffPage.asrgb function (WIP).
Do not apply colormap in asarray.
Remove 'colormapped', 'rgbonly', and 'scale_mdgel' options from asarray.
Consolidate metadata in TiffFile _metadata functions.
Remove non-tag metadata properties from TiffPage.
Add function to convert LSM to tiled BIN files.
Align image data in file.
Make TiffPage.dtype a numpy.dtype.
Add 'ndim' and 'size' properties to TiffPage and TiffPageSeries.
Allow imsave to write non-BigTIFF files up to ~4 GB.
Only read one page for shaped series if possible.
Add memmap function to create memory-mapped array stored in TIFF file.
Add option to save empty arrays to TIFF files.
Add option to save truncated TIFF files.
Allow single tile images to be saved contiguously.
Add optional movie mode for files with uniform pages.
Lazy load pages.
Use lightweight TiffFrame for IFDs sharing properties with key TiffPage.
Move module constants to 'TIFF' namespace (speed up module import).
Remove 'fastij' option from TiffFile.
Remove 'pages' parameter from TiffFile.
Remove TIFFfile alias.
Deprecate Python 2.
Require enum34 and futures packages on Python 2.7.
Remove Record class and return all metadata as dict instead.
Add functions to parse STK, MetaSeries, ScanImage, SVS, Pilatus metadata.
Read tags from EXIF and GPS IFDs.
Use pformat for tag and metadata values.
Fix reading some UIC tags (bug fix).
Do not modify input array in imshow (bug fix).
Fix Python implementation of unpack_ints.
2017.05.23
Pass 1961 tests.
Write correct number of SampleFormat values (bug fix).
Use Adobe deflate code to write ZIP compressed files.
Add option to pass tag values as packed binary data for writing.
Defer tag validation to attribute access.
Use property instead of lazyattr decorator for simple expressions.
2017.03.17
Write IFDs and tag values on word boundaries.
Read ScanImage metadata.
Remove is_rgb and is_indexed attributes from TiffFile.
Create files used by doctests.
2017.01.12
Read Zeiss SEM metadata.
Read OME-TIFF with invalid references to external files.
Rewrite C LZW decoder (5x faster).
Read corrupted LSM files missing EOI code in LZW stream.
2017.01.01
Add option to append images to existing TIFF files.
Read files without pages.
Read S-FEG and Helios NanoLab tags created by FEI software.
Allow saving Color Filter Array (CFA) images.
Add info functions returning more information about TiffFile and TiffPage.
Add option to read specific pages only.
Remove maxpages argument (backwards incompatible).
Remove test_tifffile function.
2016.10.28
Pass 1944 tests.
Improve detection of ImageJ hyperstacks.
Read TVIPS metadata created by EM-MENU (by Marco Oster).
Add option to disable using OME-XML metadata.
Allow non-integer range attributes in modulo tags (by Stuart Berg).
2016.06.21
Do not always memmap contiguous data in page series.
2016.05.13
Add option to specify resolution unit.
Write grayscale images with extra samples when planarconfig is specified.
Do not write RGB color images with 2 samples.
Reorder TiffWriter.save keyword arguments (backwards incompatible).
2016.04.18
Pass 1932 tests.
TiffWriter, imread, and imsave accept open binary file streams.
2016.04.13
Correctly handle reversed fill order in 2 and 4 bps images (bug fix).
Implement reverse_bitorder in C.
2016.03.18
Fix saving additional ImageJ metadata.
2016.02.22
Pass 1920 tests.
Write 8 bytes double tag values using offset if necessary (bug fix).
Add option to disable writing second image description tag.
Detect tags with incorrect counts.
Disable color mapping for LSM.
2015.11.13
Read LSM 6 mosaics.
Add option to specify directory of memory-mapped files.
Add command line options to specify vmin and vmax values for colormapping.
2015.10.06
New helper function to apply colormaps.
Renamed is_palette attributes to is_indexed (backwards incompatible).
Color-mapped samples are now contiguous (backwards incompatible).
Do not color-map ImageJ hyperstacks (backwards incompatible).
Towards reading Leica SCN.
2015.09.25
Read images with reversed bit order (FillOrder is LSB2MSB).
2015.09.21
Read RGB OME-TIFF.
Warn about malformed OME-XML.
2015.09.16
Detect some corrupted ImageJ metadata.
Better axes labels for 'shaped' files.
Do not create TiffTag for default values.
Chroma subsampling is not supported.
Memory-map data in TiffPageSeries if possible (optional).
2015.08.17
Pass 1906 tests.
Write ImageJ hyperstacks (optional).
Read and write LZMA compressed data.
Specify datetime when saving (optional).
Save tiled and color-mapped images (optional).
Ignore void bytecounts and offsets if possible.
Ignore bogus image_depth tag created by ISS Vista software.
Decode floating point horizontal differencing (not tiled).
Save image data contiguously if possible.
Only read first IFD from ImageJ files if possible.
Read ImageJ 'raw' format (files larger than 4 GB).
TiffPageSeries class for pages with compatible shape and data type.
Try to read incomplete tiles.
Open file dialog if no filename is passed on command line.
Ignore errors when decoding OME-XML.
Rename decoder functions (backwards incompatible).
2014.08.24
TiffWriter class for incremental writing images.
Simplify examples.
2014.08.19
Add memmap function to FileHandle.
Add function to determine if image data in TiffPage is memory-mappable.
Do not close files if multifile_close parameter is False.
2014.08.10
Pass 1730 tests.
Return all extrasamples by default (backwards incompatible).
Read data from series of pages into memory-mapped array (optional).
Squeeze OME dimensions (backwards incompatible).
Workaround missing EOI code in strips.
Support image and tile depth tags (SGI extension).
Better handling of STK/UIC tags (backwards incompatible).
Disable color mapping for STK.
Julian to datetime converter.
TIFF ASCII type may be NULL separated.
Unwrap strip offsets for LSM files greater than 4 GB.
Correct strip byte counts in compressed LSM files.
Skip missing files in OME series.
Read embedded TIFF files.
2014.02.05
Save rational numbers as type 5 (bug fix).
2013.12.20
Keep other files in OME multi-file series closed.
FileHandle class to abstract binary file handle.
Disable color mapping for bad OME-TIFF produced by bio-formats.
Read bad OME-XML produced by ImageJ when cropping.
2013.11.03
Allow zlib compress data in imsave function (optional).
Memory-map contiguous image data (optional).
2013.10.28
Read MicroManager metadata and little-endian ImageJ tag.
Save extra tags in imsave function.
Save tags in ascending order by code (bug fix).
2012.10.18
Accept file like objects (read from OIB files).
2012.08.21
Rename TIFFfile to TiffFile and TIFFpage to TiffPage.
TiffSequence class for reading sequence of TIFF files.
Read UltraQuant tags.
Allow float numbers as resolution in imsave function.
2012.08.03
Read MD GEL tags and NIH Image header.
2012.07.25
Read ImageJ tags.
...
Notes
-----
The API is not stable yet and might change between revisions.
Tested on little-endian platforms only.
Other Python packages and modules for reading (bio) scientific TIFF files:
* `python-bioformats `_
* `Imread `_
* `PyLibTiff `_
* `ITK `_
* `PyLSM `_
* `PyMca.TiffIO.py `_ (same as fabio.TiffIO)
* `BioImageXD.Readers `_
* `Cellcognition.io `_
* `pymimage `_
* `pytiff `_
Acknowledgements
----------------
* Egor Zindy, University of Manchester, for lsm_scan_info specifics.
* Wim Lewis for a bug fix and some LSM functions.
* Hadrien Mary for help on reading MicroManager files.
* Christian Kliche for help writing tiled and color-mapped files.
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) Image File Format Description LSM 5/7 Release 6.0 (ZEN 2010).
Carl Zeiss MicroImaging GmbH. BioSciences. May 10, 2011
5) The OME-TIFF format.
http://www.openmicroscopy.org/site/support/file-formats/ome-tiff
6) UltraQuant(r) Version 6.0 for Windows Start-Up Guide.
http://www.ultralum.com/images%20ultralum/pdf/UQStart%20Up%20Guide.pdf
7) Micro-Manager File Formats.
http://www.micro-manager.org/wiki/Micro-Manager_File_Formats
8) Tags for TIFF and Related Specifications. Digital Preservation.
http://www.digitalpreservation.gov/formats/content/tiff_tags.shtml
9) ScanImage BigTiff Specification - ScanImage 2016.
http://scanimage.vidriotechnologies.com/display/SI2016/
ScanImage+BigTiff+Specification
10) CIPA DC-008-2016: Exchangeable image file format for digital still cameras:
Exif Version 2.31.
http://www.cipa.jp/std/documents/e/DC-008-Translation-2016-E.pdf
Examples
--------
>>> # write numpy array to TIFF file
>>> data = numpy.random.rand(4, 301, 219)
>>> imsave('temp.tif', data, photometric='minisblack')
>>> # read numpy array from TIFF file
>>> image = imread('temp.tif')
>>> numpy.testing.assert_array_equal(image, data)
>>> # iterate over pages and tags in TIFF file
>>> with TiffFile('temp.tif') as tif:
... images = tif.asarray()
... for page in tif.pages:
... for tag in page.tags.values():
... _ = tag.name, tag.value
... image = page.asarray()
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S( s Return image data from TIFF file(s) as numpy array.
Refer to the TiffFile class and member functions for documentation.
Parameters
----------
files : str, binary stream, or sequence
File name, seekable binary stream, glob pattern, or sequence of
file names.
kwargs : dict
Parameters 'multifile' and 'is_ome' are passed to the TiffFile class.
The 'pattern' parameter is passed to the TiffSequence class.
Other parameters are passed to the asarray functions.
The first image series is returned if no arguments are provided.
Examples
--------
>>> # get image from first page
>>> imsave('temp.tif', numpy.random.rand(3, 4, 301, 219))
>>> im = imread('temp.tif', key=0)
>>> im.shape
(4, 301, 219)
>>> # get images from sequence of files
>>> ims = imread(['temp.tif', 'temp.tif'])
>>> ims.shape
(2, 3, 4, 301, 219)
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>>> data = numpy.random.randint(0, 255, (256, 256, 3), 'uint8')
>>> imsave('temp.tif', data, photometric='rgb')
>>> # save a random array and metadata, using compression
>>> data = numpy.random.rand(2, 5, 3, 301, 219)
>>> imsave('temp.tif', data, compress=6, metadata={'axes': 'TZCYX'})
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Memory-mapping requires data stored in native byte order, without tiling,
compression, predictors, etc.
If 'shape' and 'dtype' are provided, existing files will be overwritten or
appended to depending on the 'append' parameter.
Otherwise the image data of a specified page or series in an existing
file will be memory-mapped. By default, the image data of the first page
series is memory-mapped.
Call flush() to write any changes in the array to the file.
Raise ValueError if the image data in the file is not memory-mappable.
Parameters
----------
filename : str
Name of the TIFF file which stores the array.
shape : tuple
Shape of the empty array.
dtype : numpy.dtype
Data-type of the empty array.
page : int
Index of the page which image data to memory-map.
series : int
Index of the page series which image data to memory-map.
mode : {'r+', 'r', 'c'}, optional
The file open mode. Default is to open existing file for reading and
writing ('r+').
kwargs : dict
Additional parameters passed to imsave() or TiffFile().
Examples
--------
>>> # create an empty TIFF file and write to memory-mapped image
>>> im = memmap('temp.tif', shape=(256, 256), dtype='float32')
>>> im[255, 255] = 1.0
>>> im.flush()
>>> im.shape, im.dtype
((256, 256), dtype('float32'))
>>> del im
>>> # memory-map image data in a TIFF file
>>> im = memmap('temp.tif', page=0)
>>> im[255, 255]
1.0
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TiffWriter's main purpose is saving nD numpy array's as TIFF,
not to create any possible TIFF format. Specifically, JPEG compression,
SubIFDs, ExifIFD, or GPSIFD tags are not supported.
Examples
--------
>>> # successively append images to BigTIFF file
>>> data = numpy.random.rand(2, 5, 3, 301, 219)
>>> with TiffWriter('temp.tif', bigtiff=True) as tif:
... for i in range(data.shape[0]):
... tif.save(data[i], compress=6, photometric='minisblack')
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An empty TIFF file is created if the file does not exist, else the
file is overwritten with an empty TIFF file unless 'append'
is true. Use bigtiff=True when creating files larger than 4 GB.
Parameters
----------
file : str, binary stream, or FileHandle
File name or writable binary stream, such as an open file
or BytesIO.
bigtiff : bool
If True, the BigTIFF format is used.
byteorder : {'<', '>', '=', '|'}
The endianness of the data in the file.
By default, this is the system's native byte order.
append : bool
If True and 'file' is an existing standard TIFF file, image data
and tags are appended to the file.
Appending data may corrupt specifically formatted TIFF files
such as LSM, STK, ImageJ, NIH, or FluoView.
imagej : bool
If True, write an ImageJ hyperstack compatible file.
This format can handle data types uint8, uint16, or float32 and
data shapes up to 6 dimensions in TZCYXS order.
RGB images (S=3 or S=4) must be uint8.
ImageJ's default byte order is big-endian but this implementation
uses the system's native byte order by default.
ImageJ does not support BigTIFF format or LZMA compression.
The ImageJ file format is undocumented.
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d" d k st< | d) | d | }> d }H x | |? D]r }I xi tU |> D][ }P |I d |P | |P d | f }Q | |Q }Q | jV |Q t8 |Q |; |H <|H d 7}H qWqWn | j }@ xFtZ D]8\ }B }C |C d |3 k r |C d" r| jW |D |F }R xd |; D]& }S | jV |R |R |S 7}R qWq | jW |A |B | d | jV |F qp|C d |2 k rp| r |C d" rj | jW |E x^ |; D] }S | jV |S qG Wq | jW |A |B | d | jV |; d n PqpqpW| jW |@ | j] |? d k rAg D] }C |C d s |C ^ q qAqAW| | _^ d | | _ | | _ |F | __ |; | _` | rR | _ | rR |F ta |; f Sn d S( s Write numpy array and tags to TIFF file.
The data shape's last dimensions are assumed to be image depth,
height (length), width, and samples.
If a colormap is provided, the data's dtype must be uint8 or uint16
and the data values are indices into the last dimension of the
colormap.
If 'shape' and 'dtype' are specified, an empty array is saved.
This option cannot be used with compression or multiple tiles.
Image data are written uncompressed in one strip per plane by default.
Dimensions larger than 2 to 4 (depending on photometric mode, planar
configuration, and SGI mode) are flattened and saved as separate pages.
The SampleFormat and BitsPerSample tags are derived from the data type.
Parameters
----------
data : numpy.ndarray or None
Input image array.
shape : tuple or None
Shape of the empty array to save. Used only if 'data' is None.
dtype : numpy.dtype or None
Data-type of the empty array to save. Used only if 'data' is None.
returnoffset : bool
If True and the image data in the file is memory-mappable, return
the offset and number of bytes of the image data in the file.
photometric : {'MINISBLACK', 'MINISWHITE', 'RGB', 'PALETTE', 'CFA'}
The color space of the image data.
By default, this setting is inferred from the data shape and the
value of colormap.
For CFA images, DNG tags must be specified in 'extratags'.
planarconfig : {'CONTIG', 'SEPARATE'}
Specifies if samples are stored contiguous or in separate planes.
By default, this setting is inferred from the data shape.
If this parameter is set, extra samples are used to store grayscale
images.
'CONTIG': last dimension contains samples.
'SEPARATE': third last dimension contains samples.
tile : tuple of int
The shape (depth, length, width) of image tiles to write.
If None (default), image data are written in strips.
The tile length and width must be a multiple of 16.
If the tile depth is provided, the SGI ImageDepth and TileDepth
tags are used to save volume data.
Unless a single tile is used, tiles cannot be used to write
contiguous files.
Few software can read the SGI format, e.g. MeVisLab.
contiguous : bool
If True (default) and the data and parameters are compatible with
previous ones, if any, the image data are stored contiguously after
the previous one. Parameters 'photometric' and 'planarconfig'
are ignored. Parameters 'description', datetime', and 'extratags'
are written to the first page of a contiguous series only.
align : int
Byte boundary on which to align the image data in the file.
Default 16. Use mmap.ALLOCATIONGRANULARITY for memory-mapped data.
Following contiguous writes are not aligned.
truncate : bool
If True, only write the first page including shape metadata if
possible (uncompressed, contiguous, not tiled).
Other TIFF readers will only be able to read part of the data.
compress : int or 'LZMA', 'ZSTD'
Values from 0 to 9 controlling the level of zlib compression.
If 0 (default), data are written uncompressed.
Compression cannot be used to write contiguous files.
If 'LZMA' or 'ZSTD', LZMA or ZSTD compression is used, which is
not available on all platforms.
rowsperstrip : int
The number of rows per strip used for compression.
Uncompressed data are written in one strip per plane.
predictor : bool
If True, apply horizontal differencing to integer type images
before compression.
colormap : numpy.ndarray
RGB color values for the corresponding data value.
Must be of shape (3, 2**(data.itemsize*8)) and dtype uint16.
description : str
The subject of the image. Must be 7-bit ASCII. Cannot be used with
the ImageJ format. Saved with the first page only.
datetime : datetime
Date and time of image creation in '%Y:%m:%d %H:%M:%S' format.
If None (default), the current date and time is used.
Saved with the first page only.
resolution : (float, float[, str]) or ((int, int), (int, int)[, str])
X and Y resolutions in pixels per resolution unit as float or
rational numbers. A third, optional parameter specifies the
resolution unit, which must be None (default for ImageJ),
'INCH' (default), or 'CENTIMETER'.
software : str
Name of the software used to create the file. Must be 7-bit ASCII.
Saved with the first page only.
metadata : dict
Additional meta data to be saved along with shape information
in JSON or ImageJ formats in an ImageDescription tag.
If None, do not write a second ImageDescription tag.
Strings must be 7-bit ASCII. Saved with the first page only.
ijmetadata : dict
Additional meta data to be saved in application specific
IJMetadata and IJMetadataByteCounts tags. Refer to the
imagej_metadata_tags function for valid keys and values.
Saved with the first page only.
extratags : sequence of tuples
Additional tags as [(code, dtype, count, value, writeonce)].
code : int
The TIFF tag Id.
dtype : str
Data type of items in 'value' in Python struct format.
One of B, s, H, I, 2I, b, h, i, 2i, f, d, Q, or q.
count : int
Number of data values. Not used for string or byte string
values.
value : sequence
'Count' values compatible with 'dtype'.
Byte strings must contain count values of dtype packed as
binary data.
writeonce : bool
If True, the tag is written to the first page only.
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TiffFile instances must be closed using the 'close' method, which is
automatically called when using the 'with' context manager.
Attributes
----------
pages : TiffPages
Sequence of TIFF pages in file.
series : list of TiffPageSeries
Sequences of closely related TIFF pages. These are computed
from OME, LSM, ImageJ, etc. metadata or based on similarity
of page properties such as shape, dtype, and compression.
byteorder : '>', '<'
The endianness of data in the file.
'>': big-endian (Motorola).
'>': little-endian (Intel).
is_flag : bool
If True, file is of a certain format.
Flags are: bigtiff, movie, shaped, ome, imagej, stk, lsm, fluoview,
nih, vista, 'micromanager, metaseries, mdgel, mediacy, tvips, fei,
sem, scn, svs, scanimage, andor, epics, pilatus, qptiff.
All attributes are read-only.
Examples
--------
>>> # read image array from TIFF file
>>> imsave('temp.tif', numpy.random.rand(5, 301, 219))
>>> with TiffFile('temp.tif') as tif:
... data = tif.asarray()
>>> data.shape
(5, 301, 219)
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j+ n Xd$ S(& s Initialize instance from file.
Parameters
----------
arg : str or open file
Name of file or open file object.
The file objects are closed in TiffFile.close().
name : str
Optional name of file in case 'arg' is a file handle.
offset : int
Optional start position of embedded file. By default, this is
the current file position.
size : int
Optional size of embedded file. By default, this is the number
of bytes from the 'offset' to the end of the file.
multifile : bool
If True (default), series may include pages from multiple files.
Currently applies to OME-TIFF only.
movie : bool
If True, assume that later pages differ from first page only by
data offsets and byte counts. Significantly increases speed and
reduces memory usage when reading movies with thousands of pages.
Enabling this for non-movie files will result in data corruption
or crashes. Python 3 only.
kwargs : bool
'is_ome': If False, disable processing of OME-XML metadata.
t fastijs! the fastij option will be removedi Rb s unexpected keyword argument: %sRK R` t nameRG R< i Rl Rt Rm Ru i s not a TIFF filet bigRk Rp i+ R i i s invalid BigTIFF fileRn i t Q8si* Rq i t I4ss invalid TIFF filei i NI (, t DeprecationWarningt itemsRA t
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sys_byteorderR R t zero( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRP sr # $
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c C s | j S( s Return file handle.( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR
s c C s
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r. d SXd S( s3 Return status of file handle as stat_result object.N( t ost fstatR t filenoR2 R- ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s
c C s4 x$ | j j D] } | j j q Wi | _ d S( s Close open file handle(s).N( R t valuesR Ru ( RO R& ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRu s i c
C s; | j s t j g S| d k r7 | d k r7 d } n | d k rz y | j | } Wn t t f k
rm n X| j } n | j } | d k r ny t | t r | | g } nZ t | t
r | | } n> t | t j r g | D] } | | ^ q } n t d | s t
d n | j rJt | d | d | d t } n| d k r| r| j r| j | j j } | d k r| d j r| j j | | j | j } qb| d k rt | | j | j } n | j j | j | j j | t | j d | d t } nI t | d k rJ| d j d | d
| } n t | d | d | } | d k rrd S| d k ry | j | _ Wq7t
k
ry1 t j! d | j | j f d | j | _ Wqt
k
rd | d j | _ qXq7Xn9 t | d k r#| d j | _ n d | d j | _ | S( sB Return image data from multiple TIFF pages as numpy array.
By default, the data from the first series is returned.
Parameters
----------
key : int, slice, or sequence of page indices
Defines which pages to return as array.
series : int or TiffPageSeries
Defines which series of pages to return as array.
out : numpy.ndarray, str, or file-like object; optional
Buffer where image data will be saved.
If None (default), a new array will be created.
If numpy.ndarray, a writable array of compatible dtype and shape.
If 'memmap', directly memory-map the image data in the TIFF file
if possible; else create a memory-mapped array in a temporary file.
If str or open file, the file name or file object used to
create a memory-map to an array stored in a binary file on disk.
validate : bool
If True (default), validate various tags.
Passed to TiffPage.asarray().
maxworkers : int
Maximum number of threads to concurrently get data from pages.
Default is 1. If None, up to half the CPU cores are used.
Reading data from file is limited to a single thread.
Using multiple threads can significantly speed up this function
if the bottleneck is decoding compressed data, e.g. in case of
large LZW compressed LSM files.
If the bottleneck is I/O or pure Python code, using multiple
threads might be detrimental.
i s& key must be an int, slice, or sequences no pages selectedt outt
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q W| S( s Return related pages as TiffPageSeries.
Side effect: after calling this function, TiffFile.pages might contain
TiffPage and TiffFrame instances.
s( ome imagej lsm fluoview nih mdgel shapedRb s
_%s_seriesi ( RC R t keyframet splitRT R4 t _generic_seriesR% R9 R! R8 ( RO R R RF R| R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRF s" .
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MM_DIMENSIONSR3 R ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s s c s s/ | ]% } | d d k r t | d Vq d S( i N( R ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys u s R| t ImageNameR t FluoView( R5 RC R R R t fluoview_metadataR t reversedR R R R/ ( RO t mmt mmhdR R9 ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt _fluoview_seriesl s
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k r t j d } | d d d | d d k r f d } q f d } n d } | j d } t | g | j
| | j d
| d d g S( s# Return image series in MD Gel file.i t FileTagi i t float32t
ScalePixeli c s | j d d S( NR i ( t astype( Rc ( t scale( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt transform s c s | j d S( NR ( R ( Rc ( R ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s R R t MDGel( i i N( R4 RC R R R t mdgel_metadataR. R/ R- R R9 R ( RO t mdR/ R RJ ( ( R s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt
_mdgel_seriesy s
c C s t | j _ d | j _ | j j | j d } t | j d k r\ | j } | j } n& t | j f | j } d | j } t | j | | j | d d g S( s Return image series in NIH file.i i Rq R t NIH(
R5 RC R R R R! R9 R R R/ ( RO t page0R9 R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt _nih_series s
c ( s d d l m } | j d j } y | j | } Wnj | j k
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PlaneCountt Firsts ome-xml: invalid TiffData indext FileNames ome-xml: failed to read '%s's ome-xml: index out of rangec s s | ] } | d k Vq d S( N( R- ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys % s t parentR| R t OME(< t xml.etreeR RC R- t
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ParseErrorR R t decodeRq R2 R5 R R R t attribR3 R- R R t dirnameRT R" RA t AXES_LABELSt floatR. t aranget textR R R R R R t ravel_multi_indexR R R t pathR| R} Ru R R! t
IndexErrort allR! R8 R R/ R( R R9 R R t replaceR R t squeeze_axes(( RO t etreet omexmlt rootR[ t uuidR R RF t elementt annotRZ t modult alongR t newaxist stept startt stopt labelst labelR| t pixelsR/ R R9 R< t ifdst sppR8 Rj t numR t idxt fnameR& RC R R t serie( ( R s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt _ome_series s(
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s | j t j d } | j d j d k rQ | j d d j d d } n j d d d k rv | d
7} n j d d d k r | d 7} n | d
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| | | | d | d d g } | j d j rd | j _ | j d d
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} | | d } | j t
| | | | d | d d n | S( s6 Return main image series in LSM file. Skip thumbnails.t ScanTypei i R? R t XYt XYCt
DimensionPi t Pt
DimensionMt MNic 3 s& | ] } t t j | Vq d S( N( R RA t CZ_LSMINFO_DIMENSIONS( R R ( t lsmi( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys \ s R R| R t LSMt CYXt
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is_reducedR! R9 R( ( RO R R9 R| RC R/ RF t cpR ( ( R8 s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt _lsm_seriesQ s: !
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c C s t | j _ t | j _ d | j _ | j d } x' | j d d d D] } | | _ qH Wd | j _ | j d } x' | j d d d D] } | | _ q Wd S( s Load all pages from LSM file.i Ni i ( R5 RC t cacheR R ( RO R RJ ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s s
c C s# | j j d
k r d S| j } t | } | j d } | j } d } x5 d D]- } | j | d k rN | | j | 9} qN qN W| d k rCd } x/ d D]' } | | d k r | j | } Pq q W| r^t | d | | \ } } | d k s t | | | d f }
t j
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xt | j D]i } | | } g } xA | j D]6 } | |
k r| d
7} n | j | | | }
qWt | | _ qWd S( s Unwrap strip offsets for LSM files greater than 4 GB.
Each series and position require separate unwrapping (undocumented).
i i Ni i t PMR i.I ( i i ( i i I ( R R< RC R! RF R R9 R R R. R R R t moveaxist dataoffsetst flatR( R ( RO RC R RF R t positionsR t ntimest divR R9 t indicest wrapt previousoffsetRJ RD t
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c s | j } | d j d k r d St | d d } t | d } x t | D] \ } } | j d rq qR n | j | j } | | k r | | d j d } n% t d d | d | j j
} | f t f d t t | D | _ qR Wd S( s Set databytecounts to size of compressed data.
The StripByteCounts tag in LSM files contains the number of bytes
for the uncompressed data.
i i NR c S s | j d S( Ni ( RD ( t p( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR R i ic 3 s% | ] } | d | Vq d S( i N( ( R R ( t offsets( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s (
RC R R R! R! R8 RD t databytecountsR# R R< R R ( RO RC R R RJ t
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c C sp | d t j k rP | j s t St t | j d | } t | | | | St d | j j | f d S( s, Return 'is_flag' attributes from first page.i i s! '%s' object has no attribute '%s'N(
RA R RC R4 R RT RW RQ t __class__RV ( RO R| RZ ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt __getattr__ s c C s | S( N( ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRv s c C s | j d S( N( Ru ( RO Rw Rx Ry ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRz s i iO c s d t | j j i d d 6d d 6| j g } | j rI | j d n | j d j d | j D t | j d k r | j d
t | j n t | j
d k r | j d t | j
n t | j d k r| j d t | j n d
j | } | j d d
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} | t
| j j t d d t | } d k ro| S| g } | j d j d | j
D d k r| j f d | j D n# | j f d | j
D d k r~x t | j D]k } t | | d r t | | d } | rw| j d | j t | d d d f qwq q Wn d j | j d d S( s Return string containing information about file.
The detail parameter specifies the level of detail returned:
0: file only.
1: all series, first page of series and its tags.
2: large tag values and file metadata.
3: all pages.
s
TiffFile '%s't LittleEndianRl t BigEndianRm t BigTiffRj c s s | ] } | j Vq d S( N( R ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s i s %i Pagess %i Seriess %i Filess s s i i i s
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s i c 3 s6 | ], } | d k r t j | d d Vq d S( t detailt widthN( R- t TiffPaget __str__( R RM ( RW RX ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys
s c 3 sD | ]: } | j d d k r t j | j d d d Vq d S( i RW RX N( RC R- RY RZ ( R R ( RW RX ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys
s R s %s_METADATA
%sRX t heights
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( R R R< R* Rx R( R t flagsR! RC RF R R t snipstrR| t maxR R R RT R t pformat( RO RW RX t infoR| t m( ( RW RX s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRZ sD # 0 # c s# t f d t t j D S( s Return set of file flags.c 3 s. | ]$ } t d | r | j Vq d S( Rb N( RT t lower( R R| ( RO ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys
s ( t setR RA R ( RO ( ( RO s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR\
s c C s; y" | j d j p | j d j SWn t k
r6 t SXd S( s File has MD Gel format.i i N( RC t is_mdgelR R4 ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRd
s "
c C s
| j j S( s Return if file is a movie.( RC R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt is_movie$
s c C s$ | j s
d St d | j D S( s9 Return Tifffile metadata from JSON descriptions as dicts.Nc s s: | ]0 } | j j d k r t | j d j Vq d S( t shapedi N( R Rb R RC R ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys .
s ( R R RF ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt shaped_metadata)
s c C s% | j s
d St | j d j d S( s Return OME XML as dict.Ni R ( R R RC R- ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt ome_metadata1
s c C sE | j s
d Sd } | j d j j d | d | } t | | S( s< Return PerkinElmer-QPI-ImageDescription XML element as dict.Ns PerkinElmer-QPI-ImageDescriptioni t ( t is_qptiffRC R- R R ( RO R t xml( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt qptiff_metadata9
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$c C s" | j s
d S| j d j d j S( s0 Return LSM metadata from CZ_LSMINFO tag as dict.Ni t
CZ_LSMINFO( R RC R RZ ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR< B
s c C s | j s
d S| j d } | j } i } | d j | d <| j r\ | j j d | d | j s
d St | j } | j | j d j d j | S( s2 Return consolidated MicroManager metadata as dict.Ni t MicroManagerMetadata( t is_micromanagert read_micromanager_metadataR R@ RC R RZ ( RO RL ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt micromanager_metadata
s
c C s | j s
d Si } y0 t | j \ } } | | d <| j | Wn t k
rV n Xy t | j d j | d y | | V| d 7} Wq t k
r: Pq Xq Wd S( s Return iterator over all pages.i i N( R5 R ( RO R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt __iter__ s
i @ ( RV R] R^ RP R RA t setterR R Ry R R5 R R R R R R ( ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR
s "
> RY c B s) e Z d Z d Z d Z d Z d Z d Z d Z d Z d Z
d Z d5 Z d Z
d Z d Z d Z d Z d Z d6 Z d Z d Z d Z d6 d Z d6 e d6 e d7 e d Z e d6 d6 d6 d6 d Z d
Z e d Z e j d Z e! d
Z" e! d Z# e! d Z$ e! d Z% d d d Z& e! d Z' e d Z( e d Z) e! d Z* e! d Z+ e! d Z, e d Z- e d Z. e d Z/ e! d Z0 e! d Z1 e d Z2 e d Z3 e d Z4 e d! Z5 e d" Z6 e d# Z7 e d$ Z8 e d% Z9 e d& Z: e d' Z; e d( Z< e d) Z= e d* Z> e d+ Z? e d, Z@ e d- ZA e d. ZB e d/ ZC e d0 ZD e d1 ZE e d2 ZF e d3 ZG RS(8 s TIFF image file directory (IFD).
Attributes
----------
index : int
Index of page in file.
dtype : numpy.dtype or None
Data type (native byte order) of the image in IFD.
shape : tuple
Dimensions of the image in IFD.
axes : str
Axes label codes:
'X' width, 'Y' height, 'S' sample, 'I' image series|page|plane,
'Z' depth, 'C' color|em-wavelength|channel, 'E' ex-wavelength|lambda,
'T' time, 'R' region|tile, 'A' angle, 'P' phase, 'H' lifetime,
'L' exposure, 'V' event, 'Q' unknown, '_' missing
tags : dict
Dictionary of tags in IFD. {tag.name: TiffTag}
colormap : numpy.ndarray
Color look up table, if exists.
All attributes are read-only.
Notes
-----
The internal, normalized '_shape' attribute is 6 dimensional:
0 : number planes/images (stk, ij).
1 : planar samplesperpixel.
2 : imagedepth Z (sgi).
3 : imagelength Y.
4 : imagewidth X.
5 : contig samplesperpixel.
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S(, sl Initialize instance from file.
The file handle position must be at offset to a valid IFD.
R i i s suspicious number of tagss corrupted tag list at offset %ii s %s%ii s sof desNR Rq Rn R t IJMetadataByteCountsc 3 s | ] } | d Vq d S( i N( ( R t v( RZ ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s R c 3 s | ] } | d Vq d S( i N( ( R R ( RZ ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s R R t YXt YXSt SYXRt R Ru R Rq i t ZYXSt SZYXt ZYXt TileOffsetst StripOffsetst TileByteCountst StripByteCountsi s" required ByteCounts tag is missing( ( ( ( ( i (D R R8 R9 R R- R/ R R R RD RO R Rw RG R R R; R R R R2 R< R t TiffTagt ErrorR R R{ R| R5 RA t TAG_ATTRIBUTESR3 R RZ RW t is_andorR t is_epicsR R t _fix_lsm_bitspersamplet is_vistat
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rj | jF n | S(, s4 Read image data from file and return as numpy array.
Raise ValueError if format is unsupported.
Parameters
----------
out : numpy.ndarray, str, or file-like object; optional
Buffer where image data will be saved.
If None (default), a new array will be created.
If numpy.ndarray, a writable array of compatible dtype and shape.
If 'memmap', directly memory-map the image data in the TIFF file
if possible; else create a memory-mapped array in a temporary file.
If str or open file, the file name or file object used to
create a memory-map to an array stored in a binary file on disk.
squeeze : bool
If True, all length-1 dimensions (except X and Y) are
squeezed out from the array.
If False, the shape of the returned array might be different from
the page.shape.
lock : {RLock, NullContext}
A reentrant lock used to syncronize reads from file.
If None (default), the lock of the parent's filehandle is used.
reopen : bool
If True (default) and the parent file handle is closed, the file
is temporarily re-opened and closed if no exception occurs.
maxsize: int or None
Maximum size of data before a ValueError is raised.
Can be used to catch DOS. Default: 16 TB.
validate : bool
If True (default), validate various parameters.
If None, only validate parameters and return None.
i Ns data are too large %ss data type not supported: %s%is cannot decompress %sR i c 3 s | ] } | j d Vq d S( i N( RZ ( R R ( RT ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys 5
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s s invalid tile datat WRITEABLER iR/ i i .s failed to reshape from %s to %s( i i ( i i i i@ i ( i i i i (G R R R R R- R R{ R/ RI R R RA R R| R R RZ t is_chroma_subsampledR' t NotImplementedErrorR R t lockR t openR| R R R R R* RH t fillordert offsets_bytecountst is_tiledt tilewidtht
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j k rt n t | S( sA Return image data as RGB(A).
Work in progress.
i i R s cannot apply colormapi i t uint8t S.i R i N( .i ( R" R R& RA R R R, R9 R R/ RH R R^ R R R' t apply_colormapR R R- t EXTRASAMPLERD R R! R R R t SEPARATED( RO R t alphaR, t dmint dmaxt argsR# R8 R& R RD R t exs( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt asrgb
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& #& c C s | S( N( ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt aspage( s c C s | S( N( ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR + s c C s d S( N( ( RO R8 ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR / s c C s; | j r( | j \ } } | g | g f St | j | j S( s) Return simplified offsets and bytecounts.( RE t clean_offsets_countsRD RO ( RO RG t
byte_count( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR 3 s c s> | j d k s | j d k r" d Sd | j k r | j | j k sm | j | j sm | j d sm | j d rq d Sd | j k r d | j k r | j | j k s | j | j r d Sn | j | j
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sl Return offset and size of contiguous data, else None.
Excludes prediction and fill_order.
i i i i i@ NR R R i c 3 sC | ]9 } | | | d k p: | d d k Vq d S( i i N( ( R R ( RP RN ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys S s ( i i i i@ ( R R R R R R R R R RD RO R! R{ R R R% ( RO ( ( RP RN s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRE ; s& c C s/ | j o. | j d k o. | j d k o. | j S( s` Return if page's image data are stored in final form.
Excludes byte-swapping.
i ( RE R R+ R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR X s c C s3 | j j j o2 | j o2 | j d | j j d k S( s9 Return if page's image data in file can be memory-mapped.i ( R R t is_fileR RE R/ R0 ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRD b s iO c
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rRqVXn d j | S(" s0 Return string containing information about page.R t memmappablet finalR) Rb s c s s | ] } | r | Vq d S( N( ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s s R c s s | ] } t | Vq d S( N( R{ ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys t s s %s%sRj c s s | ] } | r | Vq d S( N( ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys w s t TILEDi c s s | ] } | j Vq d S( N( R ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s s TiffPage %i @%i %si R c S s | j S( N( R ( R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR R RX i t COUNTSt OFFSETSR[ i i s %s
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%si ( R R R) ( R R RZ RT R R R9 RA t SAMPLEFORMATRI R| R R R& R R R' R+ R R\ R8 RG R R R R( Ra R! R_ RZ R" R2 ( RO RW RX R R| R` R t tlinest vlinesRT RZ ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRZ i s^
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c s# t f d t t j D S( s Return set of flags.c 3 s. | ]$ } t d | r | j Vq d S( Rb N( RT Rb ( R R| ( RO ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s ( Rc R RA R ( RO ( ( RO s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR\ s c C s
t | j S( s" Return number of array dimensions.( R! R9 ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRB s c C s
t | j S( s# Return number of elements in array.( R R9 ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR< s c C s | j s
d S| j } i | d j d 6} x t | j j D]y } | j } d | k of d k n sq q@ n | j } t | j d k r | j d n | j } | | | <| | j =q@ W| S( sj Return consolidated metadata from Andor tags as dict.
Remove Andor tags from self.tags.
Nt AndorIdt Idi i i ( R R RZ R R R R! R| ( RO R RL RT R RZ R| ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s +
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d Si } | j } x t | j j D] } | j } d | k oX d k n sc q2 n | j } | d k r t j j t | | d | d k r>| d d k r>| d } n | d k rP| n | d } | | k ry | | | } Wqt k
rqXn | | | F s c C s# d | j k o" | j d j d k S( s& Page contains chroma subsampled image.t YCbCrSubSamplingi ( i i ( R RZ ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR L s c C s? x8 | j | j f D]$ } | s# d S| d d k r | Sq Wd S( s/ Return ImageJ description if exists, else None.Ni s ImageJ=( R- t description1( RO R- ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR R s
c C s_ xX | j | j f D]D } | s# d S| d d k rC d | k rC | S| d d k r | Sq Wd S( s? Return description containing array shape if exists, else None.Ni t {s "shape":i s shape=( R- RR ( RO R- ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR [ s c C s
d | j k S( s Page contains MDFileTag tag.R ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRd f s c C s' d | j k o& | j d j d d k S( s' Page contains Media Cybernetics Id tag.t MC_Idi s MC TIFF( R RZ ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt
is_mediacyk s c C s
d | j k S( s Page contains UIC2Tag tag.Rn ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR{ q s c C s
d | j k S( s Page contains CZ_LSMINFO tag.Rm ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR v s c C s
d | j k S( s$ Page contains FluoView MM_STAMP tag.R ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR { s c C s
d | j k S( s Page contains NIH image header.R ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s d | j k o d | j k S( s, Page contains SGI image and tile depth tags.R R ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt is_sgi s c C s
| j d k S( s Software tag is 'ISS Vista'.s ISS Vista( R0 ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C sG | j d k s | j d k r" t S| j } | j d oF | j d S( s> Page contains MDS MetaSeries metadata in ImageDescription tag.i t
MetaSeriess
s ( R8 R0 R4 R- t
startswithR" ( RO t d( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C sD | j d k s | j r t S| j } | d d k oC | d d k S( s. Page contains OME-XML in ImageDescription tag.i i s ( R8 R- R4 ( RO RY ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C sD | j d k s | j r t S| j } | d d k oC | d d k S( s4 Page contains Leica SCN XML in ImageDescription tag.i i s ( R8 R- R4 ( RO RY ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt is_scn s c C s
d | j k S( s% Page contains Micro-Manager metadata.R ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s
d | j k S( s$ Page contains Andor Technology tags.R ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s$ | j d d k o# | j d d k S( s Page contains Pilatus tags.i s TVX TIFFi s # ( R0 R- ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s | j d k p | j d k S( s& Page contains EPICS areaDetector tags.s EPICS areaDetector( R- R0 ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s
d | j k S( s Page contains TVIPS metadata.R ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s d | j k p d | j k S( s& Page contains SFEG or HELIOS metadata.R R ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s
d | j k S( s! Page contains Zeiss SEM metadata.R ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s | j d d k S( s Page contains Aperio metadata.i s Aperio Image Library( R- ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt is_svs s c C s7 | j d d k p6 | j d d k p6 d | j d k S( s! Page contains ScanImage metadata.i s state.configi s SI.LINE_FORMAT_VERSIONs
scanimage.SI.i ( R- R0 ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s | j d d k S( s1 Page contains PerkinElmer tissue images metadata.i s PerkinElmer-QPI( R0 ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRj s c C s
d | j k S( s Page contains GeoTIFF metadata.R# ( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s I I NI (H RV R] R^ R R R R R R R RC RI R* R R' R R& R+ RD R- R, R0 R- RR RP R5 R" R4 R R R R R R
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5 _ R c B s e Z d Z d Z e Z i Z d Z d Z d Z d
Z
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Z d Z d d Z RS( s Lightweight TIFF image file directory (IFD).
Only a limited number of tag values are read from file, e.g. StripOffsets,
and StripByteCounts. Other tag values are assumed to be identical with a
specified TiffPage instance, the keyframe.
TiffFrame is intended to reduce resource usage and speed up reading data
from file, not for introspection of metadata.
Not compatible with Python 2.
R R R8 RG RD RO c C s | | _ | | _ | | _ d | _ d | _ t j } | j } | j | _
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sp Read specified tags from file.
The file handle position must be at the offset to a valid IFD.
i i s suspicious number of tagss corrupted page list at offset %ii i iD iE i RD RO N( R R R8 R- RD RO R R R Rw RG R; R R R R2 R< R R R R R R R{ RW RZ ( RO R R8 R R R R t tagcodesR< t
codeformatR8 RM R RT R[ ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRP sB "
c C s2 | j j j | j t | j d | j d d S( s Return TiffPage from file.R8 R N( R R R RG RY R8 R- ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR , s c O s t | d Read image data from file and return RGB image as numpy array.R ( R4 RY R ( RO R R# ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR 9 s
c C s: | j j r' | j d | j j d f St | j | j S( s) Return simplified offsets and bytecounts.i ( R RE RD R RO ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR > s c C s+ | j j r' | j d | j j d f Sd S( s5 Return offset and size of contiguous data, else None.i i N( R RE RD ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRE E s c C s
| j j S( s9 Return if page's image data in file can be memory-mapped.( R RD ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRD K s c C s? | t j k r t | j | St d | j j | f d S( s Return attribute from keyframe.s! '%s' object has no attribute '%s'N( RA t FRAME_ATTRSRT R RQ RR RV ( RO R| ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRS P s i c C sU d j d d j d | j D t | j f D } d | j | j | f S( s1 Return string containing information about frame.s c s s | ] } | Vq d S( N( ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys [ s R c s s | ] } t | Vq d S( N( R{ ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys \ s s TiffFrame %i @%i %s( R R9 R{ R/ R8 RG ( RO RW R` ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRZ Y s ( R R R8 RG RD RO ( RV R] R^ R_ R4 Rd R RP R R" R R R RE RD RS RZ ( ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s 4 R c B sZ e Z d Z d Z d e f d YZ d Z e d Z d
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RS( s TIFF tag structure.
Attributes
----------
name : string
Name of tag.
code : int
Decimal code of tag.
dtype : str
Datatype of tag data. One of TIFF DATA_FORMATS.
count : int
Number of values.
value : various types
Tag data as Python object.
ImageSourceData : int
Location of value in file.
All attributes are read-only.
R R R/ RZ R R c B s e Z RS( ( RV R] ( ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR x s c s | j } | j } t j } | j } | j | d | _ | | j | d \ } } | | j | d \ }
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read_bytesR R t
read_numpyt TAG_TUPLER R t bytes2strt
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c C s t j j | j t | j S( N( RA R R3 R R{ ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR| s c C s | j d k r | j d k r t j d | j | j } t j | | j d | _ | j
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n d S( s Correct LSM bitspersample tag.
Old LSM writers may use a separate region for two 16-bit values,
although they fit into the tag value element of the tag.
i i s correcting LSM bitspersample tagi s s RX R[ s
( R R R/ R R| R RA Rh RZ R_ R ( RO RW RX R[ t tcodet lineRZ ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRZ s + "
( R R R/ RZ R ( RV R] R^ R_ R2 R RP R R| R RZ ( ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR a s B R c B s e Z d Z d d d d e d Z d d Z e d Z e d Z
e d Z e d Z d Z
d Z d Z d
Z RS( s Series of TIFF pages with compatible shape and data type.
Attributes
----------
pages : list of TiffPage
Sequence of TiffPages in series.
dtype : numpy.dtype
Data type (native byte order) of the image array in series.
shape : tuple
Dimensions of the image array in series.
axes : str
Labels of axes in shape. See TiffPage.axes.
offset : int or None
Position of image data in file if memory-mappable, else None.
c
C s d | _ | | _ t | | _ d j | | _ t j | | _ | rQ | n d | _ | rf | n d | _ | | _
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| d k r | r t t | j t | d j | _ n t
| | _ d S( s Initialize instance.i R i N( R8 R R R9 R R R. R/ R R| R R R- R! R R t _len(
RO RC R9 R/ R R R| R R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRP s ,c C sM | j rI | j j d | d | } | j d k rE | j | } n | Sd S( s; Return image data from series of TIFF pages as numpy array.RF R N( R R" R R- ( RO R RL ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR" s
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k r | Sd S( s- Return offset to series data in file, if any.Ni i ( R R- R RE R R R! R R9 R/ R0 ( RO R RJ RG ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRG s(
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t | j S( s" Return number of array dimensions.( R! R9 ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRB 1 s c C s t t | j S( s# Return number of elements in array.( R R R9 ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR< 6 s c C s | S( s' Return sequence of all pages in series.( ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRC ; s c C s | j S( s% Return number of TiffPages in series.( Rq ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR A s c C sa t | j d k rV d | k o/ | j k n rV | j d j } | j j | | S| j | S( s Return specified TiffPage.i i ( R! R Rq R8 R RC ( RO R R8 ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR E s 4c c s{ t | j | j k r4 x\ | j D] } | Vq" WnC | j j } | j d j } x$ t | j D] } | | | Vq` Wd S( s) Return iterator over TiffPages in series.i N( R! R Rq R RC R8 R ( RO RJ RC R8 R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR L s c
C s d j d | j r+ t d | j d n d d j d | j D t | j | j | j d t | j | j
r d | j
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| j | f S( s, Return string with information about series.s c s s | ] } | r | Vq d S( N( ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys Y s s '%s'i R R c s s | ] } t | Vq d S( N( R{ ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys [ s s %i Pagess Offset=%is TiffPageSeries %i %s( R R| R] R9 R{ R/ R R R! RC RG R8 ( RO R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRZ W s " &N( RV R] R^ R- R4 RP R" R
RG R RB R< RC R R R RZ ( ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c B s e Z d Z i d d 6Z d e f d YZ e d d Z d Z d Z d Z
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d Z d Z RS( s Sequence of TIFF files.
The image data in all files must match shape, dtype, etc.
Attributes
----------
files : list
List of file names.
shape : tuple
Shape of image sequence. Excludes shape of image array.
axes : str
Labels of axes in shape.
Examples
--------
>>> # read image stack from sequence of TIFF files
>>> imsave('temp_C001T001.tif', numpy.random.rand(64, 64))
>>> imsave('temp_C001T002.tif', numpy.random.rand(64, 64))
>>> tifs = TiffSequence('temp_C001*.tif')
>>> tifs.shape
(1, 2)
>>> tifs.axes
'CT'
>>> data = tifs.asarray()
>>> data.shape
(1, 2, 64, 64)
s
# matches Olympus OIF and Leica TIFF series
_?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))
_?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))?
_?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))?
_?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))?
_?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))?
_?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))?
_?(?:(q|l|p|a|c|t|x|y|z|ch|tp)(\d{1,4}))?
R R c B s e Z RS( ( RV R] ( ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c s t | t j r! t | } n t | t rH t t j | } n t | } | si t d n t | d t j r g | D] } t t j | ^ q } n" t | d t s t d n | | _ t
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s\ Initialize instance from multiple files.
Parameters
----------
files : str, pathlib.Path, or sequence thereof
Glob pattern or sequence of file names.
Binary streams are not supported.
imread : function or class
Image read function or class with asarray function returning numpy
array from single file.
pattern : str
Regular expression pattern that matches axes names and sequence
indices in file names.
By default, the pattern matches Olympus OIF and Leica TIFF series.
s no files foundi s not a file nameR" c s) | } | j | | SWd QXd S( N( R" ( R- R R# t im( t _imread( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s Rq c s s | ] } | f Vq d S( N( ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s N( i ( R t pathlibt PathR{ R R R R R R R R t _patternsR3 R t _parseR R R! R9 t _startindexR R t _indices( RO R R R R R# R ( ( Rs s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRP s4 +
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shape: %s( R R R! R R{ R9 ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRZ s
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IGNORECASEt VERBOSEt findallR R! R R R( R R R. R^ R# R| R R R R R R9 Ry Rx ( RO R t matchesR RI R- Ra R9 t
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d Z d Z d Z d d Z d Z d! Z d" Z d# Z e d$ Z e d% Z e d& Z e d' Z e d( Z e d) Z e j d* Z RS(. s Binary file handle.
A limited, special purpose file handler that can:
* handle embedded files (for CZI within CZI files)
* re-open closed files (for multi-file formats, such as OME-TIFF)
* read and write numpy arrays and records from file like objects
Only 'rb' and 'wb' modes are supported. Concurrently reading and writing
of the same stream is untested.
When initialized from another file handle, do not use it unless this
FileHandle is closed.
Attributes
----------
name : str
Name of the file.
path : str
Absolute path to file.
size : int
Size of file in bytes.
is_file : bool
If True, file has a filno and can be memory-mapped.
All attributes are read-only.
R t _filet _modet _namet _dirt _lockt _offsett _sizet _closeR R` c C sk | | _ d | _ | | _ | | _ d | _ | | _ | | _ t | _ t
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| j d S( s Initialize file handle from file name or another file handle.
Parameters
----------
file : str, pathlib.Path, binary stream, or FileHandle
File name or seekable binary stream, such as an open file
or BytesIO.
mode : str
File open mode in case 'file' is a file name. Must be 'rb' or 'wb'.
name : str
Optional name of file in case 'file' is a binary stream.
offset : int
Optional start position of embedded file. By default, this is
the current file position.
size : int
Optional size of embedded file. By default, this is the number
of bytes from the 'offset' to the end of the file.
R N( R R- R R R R R R R5 R R4 R t NullContextR R ( RO R7 RK R| RG R< ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRP - s c C s} | j r
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| j | j | _ t | _ | j d k rd | _ qn t | j t r| j j | _ | j d k r d | _ n | j | j j 7_ t | _ | j sy| j rgt j j | j j \ } } d | | j | f | _ qy| j j | _ n | j r| j | j j k rt d n | j j | _ | j j | _ nt | j d ry | j j Wn t k
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| j j S( s" Flush write buffers if applicable.( R R$ ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR$ s i t rR? c C sM | j s t d n t j | j d | d | d | j | d | d | S( s+ Return numpy.memmap of data stored in file.s% Cannot memory-map file without filenoR/ RK RG R9 t order( R R R. R R R ( RO R/ R9 RG RK R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s
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j 7} qWt | d r| j n | j | S( s Return numpy array from file.
Work around numpy issue #2230, "numpy.fromfile does not accept
StringIO object" https://github.com/numpy/numpy/issues/2230.
i iR$ N( R R. R/ R R0 R- t fromfileR| R R R R R R5 R R9 R# R1 R R! R< R R$ ( RO R/ R t sept chunksizeR R R R< RL R8 R9 R8 R9 ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s: "
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r t j | } | d k ri | j | j } n t t
| | j } | j j | } | j | | | d | } n X| d k r | d S| S( s Return numpy record from file.R* i i N(
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c C s; | d k r d S| j j | d d | j j d d S( s; Append size bytes to file. Position must be at end of file.i Ns ( R R R ( RO R< ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C sB y | j | j Wn' t k
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c C s | j j | j S( s Return file's current position.( R Rw R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRw s c C s | j rv | d k r3 | j j | j | | d S| d k rv | j d k rv | j j | j | j | d d Sn | j j | | d S( s Set file's current position.i Ni ( R R R R ( RO RG t whence( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s !c C s/ | j r+ | j r+ | j j d | _ n d S( s Close file.N( R R Ru R- ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRu s
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s c C s- | j r t j d | n t | j | S( s- Return attribute from underlying file object.s3 FileHandle: '%s' not implemented for embedded files( R R R RT R ( RO R| ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRS
s c C s | j S( N( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR| s c C s | j S( N( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s t j j | j | j S( N( R R R R R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s | j S( N( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR< s c C s
| j d k S( N( R R- ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR $ s c C s | j S( N( R ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR ( s c C s" | r t j n t | _ d S( N( t threadingt RLockR R ( RO RZ ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR , s (
R R R R R R R R R R Ni ( RV R] R^ R_ R- RP R R R R$ R R4 R R R R Rw R Ru Rv Rz RS R R| R R R< R R R ( ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR
s6 F + R c B s e Z d Z d Z d Z RS( sI Null context manager.
>>> with NullContext():
... pass
c C s | S( N( ( RO ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRv 8 s c C s d S( N( ( RO Rw Rx Ry ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRz ; s ( RV R] R^ Rv Rz ( ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR 1 s t
OpenFileCachec B s; e Z d Z d Z d
d Z d Z d Z d Z RS( s Keep files open.R t pastR R< c C sC g | _ i | _ | d k r' t n | | _ t | | _ d S( s Initialize open file cache.N( R R R- R R R R< ( RO R< R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRP D s c C sl | j ] | | j k r/ | j | c d 7 d= Z? d> Z@ RS(? s Namespace for module constants.c C s iGd d 6d d 6d d 6d d 6d d
6d d 6d
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d6dd6dd6dd6dd6dd6dd6dd 6d d 6d d 6d!d"6d#d$6d%d&6d'd(6d)d*6d+d,6d-d.6d/d06d1d26d3d46d5d66d7d86d9d:6d;d<6d=d>6d?d@6dAdB6dCdD6dEdF6dGdH6dIdJ6dKdL6dMdN6dOdP6dQdR6dSdT6dUdV6dWdX6dYdZ6d[d\6d]d^6d_d`6dadb6dcdd6dedf6dgdh6didj6dkdl6dmdn6dodp6dqdr6dsdt6dudv6dwdx6dydz6d{d|6d}d~6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd6dd 6dd6dd6dd6dd6d d
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d6dd6dd6dd6dd6dd6dd6dd 6d d 6d d 6d!d"6d#d$6d%d&6d'd(6d)d*6d+d,6d-d.6d/d06d1d26d3d46d5d66d7d86d9d:6d;d<6d=d>6d?d@6dAdB6dCdD6dEdF6dGdH6dIdJ6dKdL6dMdN6dOdP6dQdR6dSdT6dUdV6dWdX6dYdZ6d[d\6d]d^6d_d`6dadb6dcdd6dedf6dgdh6didj6dkdl6dmdn6dodp6dqdr6dsdt6dudv6dwdx6dydz6d{d|6d}d~6dd6dd6dd6dd6dd6dd6dd6dd6S( Nt ProcessingSoftwarei R i t SubfileTypei R i R i R i R i R i t Thresholdingi t CellWidthi t
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currentBuffert grayFitt grayPointCountt grayXt grayYt grayMint grayMaxt grayUnitNamet StandardLUTt
wavelengtht
StagePositions
(%i,2,2)u4t CameraChipOffsett OverlayMaskt OverlayCompresst Overlayt SpecialOverlayMaskt SpecialOverlayCompresst SpecialOverlayt
ImagePropertyt
StageLabels %ipt AutoScaleLoInfot AutoScaleHiInfot AbsoluteZs (%i,2)u4t AbsoluteZValids (%i,)u4R# Rq t GammaRedt
GammaGreent GammaBluet CameraBinR t NewLUTt ImagePropertyExt
PlanePropertyt UserLutTables (256,3)u1t RedAutoScaleInfot RedAutoScaleLoInfot RedAutoScaleHiInfot RedMinScaleInfot RedMaxScaleInfot GreenAutoScaleInfot GreenAutoScaleLoInfot GreenAutoScaleHiInfot GreenMinScaleInfot GreenMaxScaleInfot BlueAutoScaleInfot BlueAutoScaleLoInfot BlueAutoScaleHiInfot BlueMinScaleInfot BlueMaxScaleInfo( R N( R N( R N( R s
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rxt j d | q|Xn | | | Read LSM sequence of float pairs from file and return as list.s Read LSM ChannelColors structure from file and return as dict.t MonoR t
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| j s s no ImageJ metadatai R R s invalid ImageJ metadatai i i$ s# invalid ImageJ metadata header sizei t 4sINi i ( R R (
R@ Ru R R R R R| R3 Re Rb R R( Ra ( R8 RP R* R R R R R t header_sizet ntypesRt R t counterRL R R R R| RN RM t pos1( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR k sH
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r qz Xqz W| | | >> description = 'ImageJ=1.11a\nimages=510\nhyperstack=true\n'
>>> imagej_description_metadata(description) # doctest: +SKIP
{'ImageJ': '1.11a', 'images': 510, 'hyperstack': True}
c S s i t d 6t d 6| j S( Nt truet false( R5 R4 Rb ( R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt _bool s Ri R s not a ImageJ image description( Rw R R2 Ra R R R ( R- R RL Rp R R R/ ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s&
s 1.11ac K s | r t d n t | d | } | d d k } d | g } g } | j d t | d | d k r t } | j d n | j d
t | | d d k r | j d
| d n | d k r | r d } n | r| r| j d | n | d d k r*| j d | d n | d d k rn| j d | d | d k rn| j d qnn | d k r| j d t | n x7 | j D]) \ }
} | j d |
j | f qWd j | | d g S( s5 Return ImageJ image description from data shape.
ImageJ can handle up to 6 dimensions in order TZCYXS.
>>> imagej_description((51, 5, 2, 196, 171)) # doctest: +SKIP
ImageJ=1.11a
images=510
channels=2
slices=5
frames=51
hyperstack=true
mode=grayscale
loop=false
s! ImageJ colormapping not supportedt rgbii i s ImageJ=%ss images=%iis hyperstack=trues
hyperstack=%si i s channels=%it grayscales mode=%ss slices=%ii s frames=%is
loop=falses loop=%ss %s=%ss
R ( i i N(
R R R( R R- R5 R R Rb R ( R9 R t
colormapedR R RK t loopR# RL R( R RZ ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s8
!c C s t d | D } t | } d | k o9 d k n rM t d n | d k rx | d d
k or | d k } n | r | d d k r t d n | r | d k r | d d k r t d
n | s | d d k r d d | | Sd d | | d S( s Return shape normalized to 6D ImageJ hyperstack TZCYXS.
Raise ValueError if not a valid ImageJ hyperstack shape.
>>> imagej_shape((2, 3, 4, 5, 3), False)
(2, 3, 4, 5, 3, 1)
c s s | ] } t | Vq d S( N( R ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s i i s1 invalid ImageJ hyperstack: not 2 to 6 dimensionalii i i s* invalid ImageJ hyperstack: not a RGB images. invalid ImageJ hyperstack: not a non-RGB imagei N( i i ( i i ( i ( i ( i ( R R! R R- ( R9 R RB ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s #c K s | j d | t j | S( s Return JSON image description from data shape and other meta data.
Return UTF-8 encoded JSON.
>>> json_description((256, 256, 3), axes='YXS') # doctest: +SKIP
b'{"shape": [256, 256, 3], "axes": "YXS"}'
R9 ( R@ RJ t dumps( R9 R1 ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s c C s | d d k rC t d | d d !j d D } t d | S| d d k rp | d d
k rp t j | St d | d S(
s Return metatata from JSON formated image description as dict.
Raise ValuError if description is of unknown format.
>>> description = '{"shape": [256, 256, 3], "axes": "YXS"}'
>>> json_description_metadata(description) # doctest: +SKIP
{'shape': [256, 256, 3], 'axes': 'YXS'}
>>> json_description_metadata('shape=(256, 256, 3)')
{'shape': (256, 256, 3)}
i s shape=c s s | ] } t | Vq d S( N( R ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys , s i it ,R9 i RS t }s invalid JSON image descriptionN( R R Ru RJ RK R ( R- R9 ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s &
c C sF | j d s t d n | d k r9 d d h } n i } | g } t } x| j D]} | sv | j } n | s q[ n | d d k r| d d k r%| d =| d } | d d !} | r d
j | | | | >> descr = ('[Intensity Mapping]\nMap Ch0: Range=00000 to 02047\n'
... '[Intensity Mapping End]')
>>> fluoview_description_metadata(descr)
{'Intensity Mapping': {'Map Ch0: Range': '00000 to 02047'}}
Rv s" invalid FluoView image descriptions Region Info (Fields)s Protocol Descriptioni is End]ii s
i s LUT R/ R i Ri s RGB c s s | ] } t | Vq d S( N( R ( R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys p s N( ii ( RX R R- R4 Rw Ra R R. R R9 R5 R( R R! R R ( R- t ignoresectionsRL t sectionst commentRp Rx R| Rc R RZ ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt fluoview_description_metadata4 s^
c s i } | j d s | Sx d D] } | j | d } q Wx| j d D]} | d d k rh qL n | j } | d } | d t j k r y& t j j d j | d | d >> pilatus_description_metadata('# Pixel_size 172e-6 m x 172e-6 m')
{'Pixel_size': (0.000172, 0.000172)}
s # s #:=,()Ri s
i s i s %Y-%m-%dT%H %M %S.%fR i t nott NaNc 3 s | ] } | Vq d S( N( ( R R ( R/ ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s ( RX R R RA R= R. t strptimeR R2 R R R R R{ R! ( R- RL R Rp R| RI R R ( ( R/ s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR v s<
c C s | j d s t d n i } | j d } | d j j d d \ } } | j | | j >> svs_description_metadata('Aperio Image Library v1.0')
{'Aperio Image Library': 'v1.0'}
s Aperio Image Library s invalid Aperio image descriptions
i i Rj R s = N( RX R R Ra t rsplitR- R! R ( R- RL t linesR RZ R R\ ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt svs_description_metadata s " c C s. | j } | s g Sy t | } Wn t k
rG t j d g SXg } x | j d D] } i } x | j d D] } | j d d } t | d k r | \ } } t | j | | j s$ invalid MetaSeries image descriptioni( R R R c S s t | d d S( Nt onRT ( t asbool( R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR R R c s x | D] } | j } | s8 | i | | j | } | j }
d } | d \ } | } | 7 | d k r-Pn | | | ng | | k ri| | } | | | d } n | | } | | d 7} | } | | |
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j d | n d j |
S(# s+ 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 implementation of the LZW decoding algorithm is described in (1) and
is not compatible with old style LZW compressed files like quad-lzw.tif.
i i R i c s d } | | d !} y d | d } Wn6 t k
rj d | d d t | d } n X| d K} | M} | ?S( s@ Return integer of 'bitw' bits at 'bitcount' position in encoded.i i s >Ii s ( R2 R! ( R$ R R ( t bitcountR t maskt shrR ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt next_code s
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i i t 1t 0i i i
i i i i i i i i i s( strip must be at least 4 characters longs strip must begin with CLEAR codei i i s& unexpected end of LZW stream (code %i)R ( i i t 111111111t
1111111111t 11111111111t 111111111111t 00000000000000000000( R! R R R~ R R t chrR R R R R( R5 R R R ( R t len_encodedt bitcount_maxR t newtableR t switchbitcht bitwR t oldcodeRL t
result_appendR t table_appendt lentablet decodedt newcode( ( R R R R R s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR s sj
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s _tifffile.unpack_intsc s d k r t j | d } t j | } | d r} | j d | d | d } | d d d | f j d } n | j | St j | } d k r t j | | S d k r t d n | j d k r t d
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<| 7} |
d | d k r| | 7} qqW| S( s Decompress byte string to array of integers of any bit size <= 32.
This Python implementation is slow and only handles itemsizes 1, 2, 4, 8,
16, 32, and 64.
Parameters
----------
data : byte str
Data to decompress.
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.
Examples
--------
>>> unpack_ints(b'a', 'B', 1)
array([0, 1, 1, 0, 0, 0, 0, 1], dtype=uint8)
>>> unpack_ints(b'ab', 'B', 2)
array([1, 2, 0, 1, 1, 2, 0, 2], dtype=uint8)
i s |Bi iNi i i@ i i s itemsize not supported: %it bius
invalid dtypec 3 s% | ] } d | k r | Vq d S( i N( ( R R ( R0 ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys s s dtype.itemsize too smalli R R Rm s ( i i i i@ ( i i i i i i ( i i i i ( R. R t
unpackbitsR R R/ R R t nextR0 R! R RH R R R R R2 ( R8 R/ R0 R t itembytest skipbitst shrbitst bitmaskt dtypestrR R< RL R R R$ R R ( ( R0 s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR sV
(
)
s >> data = struct.pack('BBBB', 0x21, 0x08, 0xff, 0xff)
>>> print(unpack_rgb(data, '>> print(unpack_rgb(data, '>> print(unpack_rgb(data, '6! s s sample size not supported: %sc 3 s1 | ]' } t j | j d k r | Vq d S( i N( R. R/ R0 ( R R ( t bits( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys 8! s t BHIi t 0bR i i Rq Ni( R. R/ R R% R R R{ R
R R* R R< R! RH R! R0 R R (
R8 R/ R t rescaleR RL R RZ R t o( ( R
R/ s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR ! s$ !( $! s _tifffile.reverse_bitorderc C sm y, | j d } t j t j | d | Wn: t k
rL | j t j St k
rh t d n Xd S( sj Reverse bits in each byte of byte string or numpy array.
Decode data where pixels with lower column values are stored in the
lower-order bits of the bytes (FillOrder is LSB2MSB).
Parameters
----------
data : byte string or ndarray
The data to be bit reversed. If byte string, a new bit-reversed byte
string is returned. Numpy arrays are bit-reversed in-place.
Examples
--------
>>> reverse_bitorder(b'\x01\x64')
b'\x80&'
>>> data = numpy.array([1, 666], dtype='uint16')
>>> reverse_bitorder(data)
>>> data
array([ 128, 16473], dtype=uint16)
R R s slices of arrays not supportedN(
R R. t takeRA R? RQ t translateR> R R ( R8 R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR H! s
c C sL t j | | d d } t j | d | j } | rH t j | } n | S( s Return palette-colored image.
The image values are used to index the colormap on axis 1. The returned
image is of shape image.shape+colormap.shape[0] and dtype colormap.dtype.
Parameters
----------
image : numpy.ndarray
Indexes into the colormap.
colormap : numpy.ndarray
RGB lookup table aka palette of shape (3, 2**bits_per_sample).
contig : bool
If True, return a contiguous array.
Examples
--------
>>> image = numpy.arange(256, dtype='uint8')
>>> colormap = numpy.vstack([image, image, image]).astype('uint16') * 256
>>> apply_colormap(image, colormap)[-1]
array([65280, 65280, 65280], dtype=uint16)
R i i ( R. R
t rollaxisRB R ( t imageR, t contig( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR h! s
c C s t j } t | | } | | j k r+ | S| | j k rZ | d d d d d d f S| | j k r | d d d d d d d d f S| | j k r | d d d d d d d d d f S| | j k r t j | d d S| | j
k r-t j | d d d d d d d d f S| | j k rtt j | d d d d d d d d d d f S| | j k rt j | d d d d d d d d d d d f Sd S( s+ Return reoriented view of image array.
Parameters
----------
image : numpy.ndarray
Non-squeezed output of asarray() functions.
Axes -3 and -2 must be image length and width respectively.
orientation : int or str
One of TIFF.ORIENTATION names or values.
.Niii(
RA R R R R R R
R R. R R R R ( R
t orientationR ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt reorient! s$ ),/8c C s t j | } g } g } g } x` t | j | j | D]F \ } } } | j | | f | j | d f | j | | q: Wt j j j | | | d t
j | S( s Return read-only view into input array with elements repeated.
Zoom nD image by integer factors using nearest neighbor interpolation
(box filter).
Parameters
----------
a : array_like
Input array.
repeats : sequence of int
The number of repetitions to apply along each dimension of input array.
Example
-------
>>> repeat_nd([[1, 2], [3, 4]], (2, 2))
array([[1, 1, 2, 2],
[1, 1, 2, 2],
[3, 3, 4, 4],
[3, 3, 4, 4]])
i t writeable( R. R" R| t stridesR9 R R( t libt
stride_trickst
as_stridedR4 R ( Rc t repeatsR R9 R
R R R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR ! s ( c C si t | t } | r | n | j } t | | k r: | Sd | t | | } | r\ | S| j | S( s Return image array or shape with at least ndim dimensions.
Prepend 1s to image shape as necessary.
>>> reshape_nd(numpy.empty(0), 1).shape
(0,)
>>> reshape_nd(numpy.empty(1), 2).shape
(1, 1)
>>> reshape_nd(numpy.empty((2, 3)), 3).shape
(1, 2, 3)
>>> reshape_nd(numpy.empty((3, 4, 5)), 3).shape
(3, 4, 5)
>>> reshape_nd((2, 3), 3)
(1, 2, 3)
i ( i ( R R R9 R! R ( t
data_or_shapeRB t is_shapeR9 ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR ! s R1 c sk t | t | k r' t d n t f d t | | D \ } } t | d j | f S( s Return shape and axes with single-dimensional entries removed.
Remove unused dimensions unless their axes are listed in 'skip'.
>>> squeeze_axes((5, 1, 2, 1, 1), 'TZYXC')
((5, 2, 1), 'TYX')
s) dimensions of axes and shape do not matchc 3 s5 | ]+ } | d d k s) | d k r | Vq d S( i i N( ( R R ( RX ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys ! s R ( R! R R| R R ( R9 R RX ( ( RX s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR ! s +t CTZYXc C s x- | D]% } | | k r t d | q q W| j } x7 t | D]) } | | k rF | | } d | } qF qF W| j | } | j g | D] } | j | ^ q } | S( s Return image with its axes permuted to match specified axes.
A view is returned if possible.
>>> transpose_axes(numpy.zeros((2, 3, 4, 5)), 'TYXC', asaxes='CTZYX').shape
(5, 2, 1, 3, 4)
s unknown axis %si ( i ( R R9 R R t transposeR8 ( R
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+Rn c C s t | } t | } t | t | k r? t d n t | } t | } | | k r| t d | | f n | s | r d St d t | t | } | r | d | } n t | d } d } d } g }
x | d d d D] } | | 9} x6 | d k rB| | d k rB| d k rB| d 8} q
W| | | k r| | | | k r| | | 9} |
j | | | d 8} q |
j | q Wd j t |
| S( s Return axes matching new shape.
Unknown dimensions are labelled 'Q'.
>>> reshape_axes('YXS', (219, 301, 1), (219, 301))
'YX'
>>> reshape_axes('IYX', (12, 219, 301), (3, 4, 219, 1, 301, 1))
'QQYQXQ'
s axes do not match shapes cannot reshape %s to %sR i i Ni( i ( R R! R R R^ R( R R ( R R9 t newshapet unknownR< t newsizet lendiffR t prodnst prodsRL t ns( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR
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i c O s t | } | d k r' t d n | d k rM | d j d | | | St d | D } | j d d | f | j j } | j j } t | | | } | d k r t j
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j |
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s Read data from sequence of TiffPage and stack them vertically.
Additional parameters are passsed to the TiffPage.asarray function.
i s no pagesi R c s s! | ] } | d k r | Vq d S( N( R- ( R RM ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pys D" s R i R< i R c S sd | d k r` | j | j j | j d | j d t d t | | | | <| j | j j n d S( s! Read, decode, and copy page data.R R R N( R- R R R R" R R4 Ru ( RJ R8 R t filecacheR R# ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyRN Q" s
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c C s t | } t | } t | t | k s6 t d } x t t | | D] \ } \ } } | d k r | d k r | | k r | | | <| | | >> matlabstr2py('1')
1
>>> matlabstr2py("['x y z' true false; 1 2.0 -3e4; NaN Inf @class]")
[['x y z', True, False], [1, 2.0, -30000.0], [nan, inf, '@class']]
>>> d = matlabstr2py("SI.hChannels.channelType = {'stripe' 'stripe'}\n"
... "SI.hChannels.channelsActive = 2")
>>> d['SI.hChannels.channelType']
['stripe', 'stripe']
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Clean NULL terminated C strings. For unicode strings use null='\0'.
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b'string'
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'string'
i ( R ( RU Rr R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyR
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Clean NULL separated and terminated TIFF strings.
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b'string\x00string\n'
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b''
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False
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r[ q( Xq( W| S( s Return argument as one of types if possible.
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42
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3.14
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True
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'Neee-Wom'
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'1234 B'
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'11.50 GiB'
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'arg'
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>>> nullfunc('arg', kwarg='kwarg')
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r) | f SXd S( s{ Return tuple containing value if value is not a sequence.
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(1,)
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[1]
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Multiplying numpy integers might overflow.
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274877906944
>>> product([])
1
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['f1', 'f2', 'f10']
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Convert LSM time stamps.
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datetime.datetime(2010, 2, 28, 0, 43, 11, 999982)
( R. t timedelta( t timestampt epoch( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt excel_datetime# s c C sd | d k r d S| d } | d k rV t j | d d } | d | | d 7} n | | d k rk d n d } t j | d d
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Convert Julian dates according to MetaMorph.
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datetime.datetime(2000, 2, 2, 15, 6, 2, 783)
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c C sP | d k s | t j k r t Si d d 6d d 6} | j | | | t j k S( sc Return if byteorder matches the system's byteorder.
>>> byteorder_isnative('=')
True
Ri Rm R} Rl Rk ( R~ R* R5 R3 ( R* R ( ( s8 lib/python2.7/site-packages/imageio/plugins/_tifffile.pyt byteorder_isnative"$ s c C s i } x t | j j | D]i \ } } | d \ } } | d d k r] t t | } n | j d k r{ | j } n | | | >> xml2dict('1')
{'root': {'key': 1, 'attr': 'name'}}
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'49 49 2a 00 08 00 00 00 0e 00 fe 00 04 00 01 00 II*.............'
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False
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'abc...op'
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True
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True
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f S(Z s Plot n-dimensional images using matplotlib.pyplot.
Return figure, subplot and plot axis.
Requires pyplot already imported C{from matplotlib import pyplot}.
Parameters
----------
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 (optional).
Matplotlib to use for plotting.
subplot : int
A matplotlib.pyplot.subplot axis.
maxdim : int
maximum image width and length.
kwargs : optional
Arguments for matplotlib.pyplot.imshow.
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