Skip to content

descarteslabs/tifffile

BranchesTags
 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

280 Commits
tests
tests
 
 
tifffile
tifffile
 
 
.gitattributes
.gitattributes
 
 
.gitignore
.gitignore
 
 
ACKNOWLEDGEMENTS.rst
ACKNOWLEDGEMENTS.rst
 
 
CHANGES.rst
CHANGES.rst
 
 
LICENSE
LICENSE
 
 
MANIFEST.in
MANIFEST.in
 
 
README.rst
README.rst
 
 
setup.py
setup.py
 
 

Repository files navigation

Read and write TIFF files

Tifffile is a Python library to

  1. store numpy arrays in TIFF (Tagged Image File Format) files, and
  2. read image and metadata from TIFF-like files used in bioimaging.

Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, SGI, NIHImage, ImageJ, MicroManager, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, ZIF (Zoomable Image File Format), QPTIFF (QPI), NDPI, and GeoTIFF files.

Image data can be read as numpy arrays or zarr arrays/groups from strips, tiles, pages (IFDs), SubIFDs, higher order series, and pyramidal levels.

Numpy arrays can be written to TIFF, BigTIFF, OME-TIFF, and ImageJ hyperstack compatible files in multi-page, volumetric, pyramidal, memory-mappable, tiled, predicted, or compressed form.

A subset of the TIFF specification is supported, mainly 8, 16, 32 and 64-bit integer, 16, 32 and 64-bit float, grayscale and multi-sample images. Specifically, CCITT and OJPEG compression, chroma subsampling without JPEG compression, color space transformations, samples with differing types, or IPTC and XMP metadata are not implemented.

TIFF, the Tagged Image File Format, was created by the Aldus Corporation and Adobe Systems Incorporated. BigTIFF allows for files larger than 4 GB. STK, LSM, FluoView, SGI, SEQ, GEL, QPTIFF, NDPI, SCN, ZIF, and OME-TIFF, are custom extensions defined by Molecular Devices (Universal Imaging Corporation), Carl Zeiss MicroImaging, Olympus, Silicon Graphics International, Media Cybernetics, Molecular Dynamics, PerkinElmer, Hamamatsu, Leica, ObjectivePathology, and the Open Microscopy Environment consortium, respectively.

For command line usage run python -m tifffile --help

Author:Christoph Gohlke
Organization:Laboratory for Fluorescence Dynamics, University of California, Irvine
License:BSD 3-Clause
Version:2021.6.6

Requirements

This release has been tested with the following requirements and dependencies (other versions may work):

Revisions

2021.6.6
Pass 4405 tests. Fix TIFF.COMPESSOR typo (#85). Round resolution numbers that do not fit in 64-bit rationals (#81). Add support for JPEG XL compression. Add numcodecs compatible TIFF codec. Rename ZarrFileStore to ZarrFileSequenceStore (breaking). Add method to export fsspec ReferenceFileSystem from ZarrFileStore. Fix fsspec ReferenceFileSystem v1 for multifile series. Fix creating OME-TIFF with micron character in OME-XML.
2021.4.8
Fix reading OJPEG with wrong photometric or samplesperpixel tags (#75). Fix fsspec ReferenceFileSystem v1 and JPEG compression. Use TiffTagRegistry for NDPI_TAGS, EXIF_TAGS, GPS_TAGS, IOP_TAGS constants. Make TIFF.GEO_KEYS an Enum (breaking).
2021.3.31
Use JPEG restart markers as tile offsets in NDPI. Support version 1 and more codecs in fsspec ReferenceFileSystem (untested).
2021.3.17
Fix regression reading multi-file OME-TIFF with missing files (#72). Fix fsspec ReferenceFileSystem with non-native byte order (#56).
2021.3.16
TIFF is no longer a defended trademark. Add method to export fsspec ReferenceFileSystem from ZarrTiffStore (#56).
2021.3.5
Preliminary support for EER format (#68). Do not warn about unknown compression (#68).
2021.3.4
Fix reading multi-file, multi-series OME-TIFF (#67). Detect ScanImage 2021 files (#46). Shape new version ScanImage series according to metadata (breaking). Remove Description key from TiffFile.scanimage_metadata dict (breaking). Also return ScanImage version from read_scanimage_metadata (breaking). Fix docstrings.
2021.2.26
Squeeze axes of LSM series by default (breaking). Add option to preserve single dimensions when reading from series (WIP). Do not allow appending to OME-TIFF files. Fix reading STK files without name attribute in metadata. Make TIFF constants multi-thread safe and pickleable (#64). Add detection of NDTiffStorage MajorVersion to read_micromanager_metadata. Support ScanImage v4 files in read_scanimage_metadata.
2021.2.1
Fix multi-threaded access of ZarrTiffStores using same TiffFile instance. Use fallback zlib and lzma codecs with imagecodecs lite builds. Open Olympus and Panasonic RAW files for parsing, albeit not supported. Support X2 and X4 differencing found in DNG. Support reading JPEG_LOSSY compression found in DNG.
2021.1.14
Try ImageJ series if OME series fails (#54) Add option to use pages as chunks in ZarrFileStore (experimental). Fix reading from file objects with no readinto function.
2021.1.11
Fix test errors on PyPy. Fix decoding bitorder with imagecodecs >= 2021.1.11.
2021.1.8
Decode float24 using imagecodecs >= 2021.1.8. Consolidate reading of segments if possible.
2020.12.8
Fix corrupted ImageDescription in multi shaped series if buffer too small. Fix libtiff warning that ImageDescription contains null byte in value. Fix reading invalid files using JPEG compression with palette colorspace.
2020.12.4
Fix reading some JPEG compressed CFA images. Make index of SubIFDs a tuple. Pass through FileSequence.imread arguments in imread. Do not apply regex flags to FileSequence axes patterns (breaking).
2020.11.26
Add option to pass axes metadata to ImageJ writer. Pad incomplete tiles passed to TiffWriter.write (#38). Split TiffTag constructor (breaking). Change TiffTag.dtype to TIFF.DATATYPES (breaking). Add TiffTag.overwrite method. Add script to change ImageDescription in files. Add TiffWriter.overwrite_description method (WIP).
2020.11.18
Support writing SEPARATED color space (#37). Use imagecodecs.deflate codec if available. Fix SCN and NDPI series with Z dimensions. Add TiffReader alias for TiffFile. TiffPage.is_volumetric returns True if ImageDepth > 1. Zarr store getitem returns numpy arrays instead of bytes.
2020.10.1
Formally deprecate unused TiffFile parameters (scikit-image #4996).
2020.9.30
Allow to pass additional arguments to compression codecs. Deprecate TiffWriter.save method (use TiffWriter.write). Deprecate TiffWriter.save compress parameter (use compression). Remove multifile parameter from TiffFile (breaking). Pass all is_flag arguments from imread to TiffFile. Do not byte-swap JPEG2000, WEBP, PNG, JPEGXR segments in TiffPage.decode.
2020.9.29
Fix reading files produced by ScanImage > 2015 (#29).
2020.9.28
Derive ZarrStore from MutableMapping. Support zero shape ZarrTiffStore. Fix ZarrFileStore with non-TIFF files. Fix ZarrFileStore with missing files. Cache one chunk in ZarrFileStore. Keep track of already opened files in FileCache. Change parse_filenames function to return zero-based indices. Remove reopen parameter from asarray (breaking). Rename FileSequence.fromfile to imread (breaking).
2020.9.22
Add experimental zarr storage interface (WIP). Remove unused first dimension from TiffPage.shaped (breaking). Move reading of STK planes to series interface (breaking). Always use virtual frames for ScanImage files. Use DimensionOrder to determine axes order in OmeXml. Enable writing striped volumetric images. Keep complete dataoffsets and databytecounts for TiffFrames. Return full size tiles from Tiffpage.segments. Rename TiffPage.is_sgi property to is_volumetric (breaking). Rename TiffPageSeries.is_pyramid to is_pyramidal (breaking). Fix TypeError when passing jpegtables to non-JPEG decode method (#25).
2020.9.3
Do not write contiguous series by default (breaking). Allow to write to SubIFDs (WIP). Fix writing F-contiguous numpy arrays (#24).
2020.8.25
Do not convert EPICS timeStamp to datetime object. Read incompletely written Micro-Manager image file stack header (#23). Remove tag 51123 values from TiffFile.micromanager_metadata (breaking).
2020.8.13
Use tifffile metadata over OME and ImageJ for TiffFile.series (breaking). Fix writing iterable of pages with compression (#20). Expand error checking of TiffWriter data, dtype, shape, and tile arguments.
2020.7.24
Parse nested OmeXml metadata argument (WIP). Do not lazy load TiffFrame JPEGTables. Fix conditionally skipping some tests.
2020.7.22
Do not auto-enable OME-TIFF if description is passed to TiffWriter.save. Raise error writing empty bilevel or tiled images. Allow to write tiled bilevel images. Allow to write multi-page TIFF from iterable of single page images (WIP). Add function to validate OME-XML. Correct Philips slide width and length.
2020.7.17
Initial support for writing OME-TIFF (WIP). Return samples as separate dimension in OME series (breaking). Fix modulo dimensions for multiple OME series. Fix some test errors on big endian systems (#18). Fix BytesWarning. Allow to pass TIFF.PREDICTOR values to TiffWriter.save.
2020.7.4
Deprecate support for Python 3.6 (NEP 29). Move pyramidal subresolution series to TiffPageSeries.levels (breaking). Add parser for SVS, SCN, NDPI, and QPI pyramidal series. Read single-file OME-TIFF pyramids. Read NDPI files > 4 GB (#15). Include SubIFDs in generic series. Preliminary support for writing packed integer arrays (#11, WIP). Read more LSM info subrecords. Fix missing ReferenceBlackWhite tag for YCbCr photometrics. Fix reading lossless JPEG compressed DNG files.
2020.6.3
...

Refer to the CHANGES file for older revisions.

Notes

The API is not stable yet and might change between revisions.

Tested on little-endian platforms only.

Python 32-bit versions are deprecated. Python <= 3.7 are no longer supported.

Tifffile relies on the imagecodecs package for encoding and decoding LZW, JPEG, and other compressed image segments.

Several TIFF-like formats do not strictly adhere to the TIFF6 specification, some of which allow file or data sizes to exceed the 4 GB limit:

  • BigTIFF is identified by version number 43 and uses different file header, IFD, and tag structures with 64-bit offsets. It adds more data types. Tifffile can read and write BigTIFF files.
  • ImageJ hyperstacks store all image data, which may exceed 4 GB, contiguously after the first IFD. Files > 4 GB contain one IFD only. The size (shape and dtype) of the up to 6-dimensional image data can be determined from the ImageDescription tag of the first IFD, which is Latin-1 encoded. Tifffile can read and write ImageJ hyperstacks.
  • OME-TIFF stores up to 8-dimensional data in one or multiple TIFF of BigTIFF files. The 8-bit UTF-8 encoded OME-XML metadata found in the ImageDescription tag of the first IFD defines the position of TIFF IFDs in the high dimensional data. Tifffile can read OME-TIFF files, except when the OME-XML metadata are stored in a separate file. Tifffile can write numpy arrays to single-file OME-TIFF.
  • LSM stores all IFDs below 4 GB but wraps around 32-bit StripOffsets. The StripOffsets of each series and position require separate unwrapping. The StripByteCounts tag contains the number of bytes for the uncompressed data. Tifffile can read large LSM files.
  • STK (MetaMorph Stack) contains additional image planes stored contiguously after the image data of the first page. The total number of planes is equal to the counts of the UIC2tag. Tifffile can read STK files.
  • NDPI uses some 64-bit offsets in the file header, IFD, and tag structures. Tag values/offsets can be corrected using high bits stored after IFD structures. Tifffile can read NDPI files > 4 GB. JPEG compressed segments with dimensions >65530 or missing restart markers are not readable with libjpeg. Tifffile works around this limitation by separately decoding the MCUs between restart markers.
  • Philips TIFF slides store wrong ImageWidth and ImageLength tag values for tiled pages. The values can be corrected using the DICOM_PIXEL_SPACING attributes of the XML formatted description of the first page. Tifffile can read Philips slides.
  • ScanImage optionally allows corrupt non-BigTIFF files > 2 GB. The values of StripOffsets and StripByteCounts can be recovered using the constant differences of the offsets of IFD and tag values throughout the file. Tifffile can read such files if the image data are stored contiguously in each page.
  • GeoTIFF sparse files allow strip or tile offsets and byte counts to be 0. Such segments are implicitly set to 0 or the NODATA value on reading. Tifffile can read GeoTIFF sparse files.

Other libraries for reading scientific TIFF files from Python:

Some libraries are using tifffile to write OME-TIFF files:

Other tools for inspecting and manipulating TIFF files:

References

Examples

Write a numpy array to a single-page RGB TIFF file:

>>> data = numpy.random.randint(0, 255, (256, 256, 3), 'uint8')
>>> imwrite('temp.tif', data, photometric='rgb')

Read the image from the TIFF file as numpy array:

>>> image = imread('temp.tif')
>>> image.shape
(256, 256, 3)

Write a 3D numpy array to a multi-page, 16-bit grayscale TIFF file:

>>> data = numpy.random.randint(0, 2**12, (64, 301, 219), 'uint16')
>>> imwrite('temp.tif', data, photometric='minisblack')

Read the whole image stack from the TIFF file as numpy array:

>>> image_stack = imread('temp.tif')
>>> image_stack.shape
(64, 301, 219)
>>> image_stack.dtype
dtype('uint16')

Read the image from the first page in the TIFF file as numpy array:

>>> image = imread('temp.tif', key=0)
>>> image.shape
(301, 219)

Read images from a selected range of pages:

>>> image = imread('temp.tif', key=range(4, 40, 2))
>>> image.shape
(18, 301, 219)

Iterate over all pages in the TIFF file and successively read images:

>>> with TiffFile('temp.tif') as tif:
...     for page in tif.pages:
...         image = page.asarray()

Get information about the image stack in the TIFF file without reading the image data:

>>> tif = TiffFile('temp.tif')
>>> len(tif.pages)  # number of pages in the file
64
>>> page = tif.pages[0]  # get shape and dtype of the image in the first page
>>> page.shape
(301, 219)
>>> page.dtype
dtype('uint16')
>>> page.axes
'YX'
>>> series = tif.series[0]  # get shape and dtype of the first image series
>>> series.shape
(64, 301, 219)
>>> series.dtype
dtype('uint16')
>>> series.axes
'QYX'
>>> tif.close()

Inspect the "XResolution" tag from the first page in the TIFF file:

>>> with TiffFile('temp.tif') as tif:
...     tag = tif.pages[0].tags['XResolution']
>>> tag.value
(1, 1)
>>> tag.name
'XResolution'
>>> tag.code
282
>>> tag.count
1
>>> tag.dtype
<DATATYPES.RATIONAL: 5>

Iterate over all tags in the TIFF file:

>>> with TiffFile('temp.tif') as tif:
...     for page in tif.pages:
...         for tag in page.tags:
...             tag_name, tag_value = tag.name, tag.value

Overwrite the value of an existing tag, e.g. XResolution:

>>> with TiffFile('temp.tif', mode='r+b') as tif:
...     _ = tif.pages[0].tags['XResolution'].overwrite(tif, (96000, 1000))

Write a floating-point ndarray and metadata using BigTIFF format, tiling, compression, and planar storage:

>>> data = numpy.random.rand(2, 5, 3, 301, 219).astype('float32')
>>> imwrite('temp.tif', data, bigtiff=True, photometric='minisblack',
...         compression='deflate', planarconfig='separate', tile=(32, 32),
...         metadata={'axes': 'TZCYX'})

Write a 10 fps time series of volumes with xyz voxel size 2.6755x2.6755x3.9474 micron^3 to an ImageJ hyperstack formatted TIFF file:

>>> volume = numpy.random.randn(6, 57, 256, 256).astype('float32')
>>> imwrite('temp.tif', volume, imagej=True, resolution=(1./2.6755, 1./2.6755),
...         metadata={'spacing': 3.947368, 'unit': 'um', 'finterval': 1/10,
...                   'axes': 'TZYX'})

Read the volume and metadata from the ImageJ file:

>>> with TiffFile('temp.tif') as tif:
...     volume = tif.asarray()
...     axes = tif.series[0].axes
...     imagej_metadata = tif.imagej_metadata
>>> volume.shape
(6, 57, 256, 256)
>>> axes
'TZYX'
>>> imagej_metadata['slices']
57
>>> imagej_metadata['frames']
6

Create an empty TIFF file and write to the memory-mapped numpy array:

>>> memmap_image = memmap('temp.tif', shape=(3, 256, 256), dtype='float32')
>>> memmap_image[1, 255, 255] = 1.0
>>> memmap_image.flush()
>>> del memmap_image

Memory-map image data of the first page in the TIFF file:

>>> memmap_image = memmap('temp.tif', page=0)
>>> memmap_image[1, 255, 255]
1.0
>>> del memmap_image

Write two numpy arrays to a multi-series TIFF file:

>>> series0 = numpy.random.randint(0, 255, (32, 32, 3), 'uint8')
>>> series1 = numpy.random.randint(0, 1023, (4, 256, 256), 'uint16')
>>> with TiffWriter('temp.tif') as tif:
...     tif.write(series0, photometric='rgb')
...     tif.write(series1, photometric='minisblack')

Read the second image series from the TIFF file:

>>> series1 = imread('temp.tif', series=1)
>>> series1.shape
(4, 256, 256)

Successively write the frames of one contiguous series to a TIFF file:

>>> data = numpy.random.randint(0, 255, (30, 301, 219), 'uint8')
>>> with TiffWriter('temp.tif') as tif:
...     for frame in data:
...         tif.write(frame, contiguous=True)

Append an image series to the existing TIFF file:

>>> data = numpy.random.randint(0, 255, (301, 219, 3), 'uint8')
>>> imwrite('temp.tif', data, append=True)

Create a TIFF file from a generator of tiles:

>>> data = numpy.random.randint(0, 2**12, (31, 33, 3), 'uint16')
>>> def tiles(data, tileshape):
...     for y in range(0, data.shape[0], tileshape[0]):
...         for x in range(0, data.shape[1], tileshape[1]):
...             yield data[y : y + tileshape[0], x : x + tileshape[1]]
>>> imwrite('temp.tif', tiles(data, (16, 16)), tile=(16, 16),
...         shape=data.shape, dtype=data.dtype)

Write two numpy arrays to a multi-series OME-TIFF file:

>>> series0 = numpy.random.randint(0, 255, (32, 32, 3), 'uint8')
>>> series1 = numpy.random.randint(0, 1023, (4, 256, 256), 'uint16')
>>> with TiffWriter('temp.ome.tif') as tif:
...     tif.write(series0, photometric='rgb')
...     tif.write(series1, photometric='minisblack',
...              metadata={'axes': 'ZYX', 'SignificantBits': 10,
...                        'Plane': {'PositionZ': [0.0, 1.0, 2.0, 3.0]}})

Write a tiled, multi-resolution, pyramidal, OME-TIFF file using JPEG compression. Sub-resolution images are written to SubIFDs:

>>> data = numpy.arange(1024*1024*3, dtype='uint8').reshape((1024, 1024, 3))
>>> with TiffWriter('temp.ome.tif', bigtiff=True) as tif:
...     options = dict(tile=(256, 256), compression='jpeg')
...     tif.write(data, subifds=2, **options)
...     # save pyramid levels to the two subifds
...     # in production use resampling to generate sub-resolutions
...     tif.write(data[::2, ::2], subfiletype=1, **options)
...     tif.write(data[::4, ::4], subfiletype=1, **options)

Access the image levels in the pyramidal OME-TIFF file:

>>> baseimage = imread('temp.ome.tif')
>>> second_level = imread('temp.ome.tif', series=0, level=1)
>>> with TiffFile('temp.ome.tif') as tif:
...     baseimage = tif.series[0].asarray()
...     second_level = tif.series[0].levels[1].asarray()

Iterate over and decode single JPEG compressed tiles in the TIFF file:

>>> with TiffFile('temp.ome.tif') as tif:
...     fh = tif.filehandle
...     for page in tif.pages:
...         for index, (offset, bytecount) in enumerate(
...             zip(page.dataoffsets, page.databytecounts)
...         ):
...             fh.seek(offset)
...             data = fh.read(bytecount)
...             tile, indices, shape = page.decode(
...                 data, index, jpegtables=page.jpegtables
...             )

Use zarr to read parts of the tiled, pyramidal images in the TIFF file:

>>> import zarr
>>> store = imread('temp.ome.tif', aszarr=True)
>>> z = zarr.open(store, mode='r')
>>> z
<zarr.hierarchy.Group '/' read-only>
>>> z[0]  # base layer
<zarr.core.Array '/0' (1024, 1024, 3) uint8 read-only>
>>> z[0][256:512, 512:768].shape  # read a tile from the base layer
(256, 256, 3)
>>> store.close()

Read images from a sequence of TIFF files as numpy array:

>>> imwrite('temp_C001T001.tif', numpy.random.rand(64, 64))
>>> imwrite('temp_C001T002.tif', numpy.random.rand(64, 64))
>>> image_sequence = imread(['temp_C001T001.tif', 'temp_C001T002.tif'])
>>> image_sequence.shape
(2, 64, 64)

Read an image stack from a series of TIFF files with a file name pattern as numpy or zarr arrays:

>>> image_sequence = TiffSequence('temp_C001*.tif', pattern='axes')
>>> image_sequence.shape
(1, 2)
>>> image_sequence.axes
'CT'
>>> data = image_sequence.asarray()
>>> data.shape
(1, 2, 64, 64)
>>> with image_sequence.aszarr() as store:
...     zarr.open(store, mode='r')
<zarr.core.Array (1, 2, 64, 64) float64 read-only>
>>> image_sequence.close()

About

Read and write TIFF files. Forked from https://pypi.org/project/tifffile

Resources

Readme

License

BSD-3-Clause license
Activity
Custom properties

Stars

1 star

Watchers

0 watching

Forks

0 forks
Report repository

Releases

52 tags

Packages

No packages published

Languages

  • Python 100.0%