external.tifffile
Module: external.tifffile
skimage.external.tifffile.imread (files, **kwargs) | Return image data from TIFF file(s) as numpy array. |
skimage.external.tifffile.imsave (filename, ...) | Write image data to TIFF file. |
skimage.external.tifffile.imshow (data[, ...]) | Plot n-dimensional images using matplotlib.pyplot. |
skimage.external.tifffile.TiffFile (arg[, ...]) | Read image and metadata from TIFF, STK, LSM, and FluoView files. |
skimage.external.tifffile.TiffSequence (files) | Sequence of image files. |
skimage.external.tifffile.TiffWriter (filename) | Write image data to TIFF file. |
imread
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skimage.external.tifffile.imread(files, **kwargs)
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Return image data from TIFF file(s) as numpy array.
The first image series is returned if no arguments are provided.
Parameters: files : str or list
File name, glob pattern, or list of file names.
key : int, slice, or sequence of page indices
Defines which pages to return as array.
series : int
Defines which series of pages in file to return as array.
multifile : bool
If True (default), OME-TIFF data may include pages from multiple files.
pattern : str
Regular expression pattern that matches axes names and indices in file names.
kwargs : dict
Additional parameters passed to the TiffFile or TiffSequence asarray function.
Examples
>>> im = imread('test.tif', key=0) >>> im.shape (256, 256, 4) >>> ims = imread(['test.tif', 'test.tif']) >>> ims.shape (2, 256, 256, 4)
imsave
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skimage.external.tifffile.imsave(filename, data, **kwargs)
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Write image data to TIFF file.
Refer to the TiffWriter class and member functions for documentation.
Parameters: filename : str
Name of file to write.
data : array_like
Input image. The last dimensions are assumed to be image depth, height, width, and samples.
kwargs : dict
Parameters ‘byteorder’, ‘bigtiff’, and ‘software’ are passed to the TiffWriter class. Parameters ‘photometric’, ‘planarconfig’, ‘resolution’, ‘description’, ‘compress’, ‘volume’, and ‘extratags’ are passed to the TiffWriter.save function.
Examples
>>> data = numpy.random.rand(2, 5, 3, 301, 219) >>> description = u'{"shape": %s}' % str(list(data.shape)) >>> imsave('temp.tif', data, compress=6, ... extratags=[(270, 's', 0, description, True)])
imshow
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skimage.external.tifffile.imshow(data, title=None, vmin=0, vmax=None, cmap=None, bitspersample=None, photometric='rgb', interpolation='nearest', dpi=96, figure=None, subplot=111, maxdim=8192, **kwargs)
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Plot n-dimensional images using matplotlib.pyplot.
Return figure, subplot and plot axis. Requires pyplot already imported
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 size in any dimension.
kwargs : optional
Arguments for matplotlib.pyplot.imshow.
TiffFile
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class skimage.external.tifffile.TiffFile(arg, name=None, offset=None, size=None, multifile=True, multifile_close=True)
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Bases:
object
Read image and metadata from TIFF, STK, LSM, and FluoView files.
TiffFile instances must be closed using the close method, which is automatically called when using the ‘with’ statement.
Examples
>>> with TiffFile('test.tif') as tif: ... data = tif.asarray() ... data.shape (256, 256, 4)
Attributes
pages (list) All TIFF pages in file. series (list of Records(shape, dtype, axes, TiffPages)) TIFF pages with compatible shapes and types. micromanager_metadata: dict Extra MicroManager non-TIFF metadata in the file, if exists. All attributes are read-only. -
__init__(arg, name=None, offset=None, size=None, multifile=True, multifile_close=True)
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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.
multifile_close : bool
If True (default), keep the handles of other files in multifile series closed. This is inefficient when few files refer to many pages. If False, the C runtime may run out of resources.
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asarray(key=None, series=None, memmap=False)
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Return image data from multiple TIFF pages as numpy array.
By default the first image series is returned.
Parameters: key : int, slice, or sequence of page indices
Defines which pages to return as array.
series : int
Defines which series of pages to return as array.
memmap : bool
If True, return an array stored in a binary file on disk if possible.
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close()
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Close open file handle(s).
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filehandle
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Return file handle.
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filename
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Return name of file handle.
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fstat
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Lazy object attribute whose value is computed on first access.
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is_bigtiff
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Lazy object attribute whose value is computed on first access.
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is_fluoview
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Lazy object attribute whose value is computed on first access.
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is_imagej
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Lazy object attribute whose value is computed on first access.
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is_lsm
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Lazy object attribute whose value is computed on first access.
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is_mdgel
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Lazy object attribute whose value is computed on first access.
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is_mediacy
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Lazy object attribute whose value is computed on first access.
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is_micromanager
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Lazy object attribute whose value is computed on first access.
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is_nih
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Lazy object attribute whose value is computed on first access.
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is_ome
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Lazy object attribute whose value is computed on first access.
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is_palette
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Lazy object attribute whose value is computed on first access.
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is_rgb
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Lazy object attribute whose value is computed on first access.
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is_stk
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Lazy object attribute whose value is computed on first access.
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series
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Lazy object attribute whose value is computed on first access.
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TiffSequence
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class skimage.external.tifffile.TiffSequence(files, imread=<class 'skimage.external.tifffile.tifffile.TiffFile'>, pattern='axes', *args, **kwargs)
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Bases:
object
Sequence of image files.
The data shape and dtype of all files must match.
Examples
>>> tifs = TiffSequence("test.oif.files/*.tif") >>> tifs.shape, tifs.axes ((2, 100), 'CT') >>> data = tifs.asarray() >>> data.shape (2, 100, 256, 256)
Attributes
files (list) List of file names. shape (tuple) Shape of image sequence. axes (str) Labels of axes in shape. -
__init__(files, imread=<class 'skimage.external.tifffile.tifffile.TiffFile'>, pattern='axes', *args, **kwargs)
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Initialize instance from multiple files.
Parameters: files : str, or sequence of str
Glob pattern or sequence of file names.
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 this matches Olympus OIF and Leica TIFF series.
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exception ParseError
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Bases:
exceptions.Exception
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TiffSequence.asarray(memmap=False, *args, **kwargs)
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Read image data from all files and return as single numpy array.
If memmap is True, return an array stored in a binary file on disk. The args and kwargs parameters are passed to the imread function.
Raise IndexError or ValueError if image shapes don’t match.
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TiffSequence.close()
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TiffWriter
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class skimage.external.tifffile.TiffWriter(filename, bigtiff=False, byteorder=None, software='tifffile.py')
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Bases:
object
Write image data to TIFF file.
TiffWriter instances must be closed using the close method, which is automatically called when using the ‘with’ statement.
Examples
>>> 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)
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__init__(filename, bigtiff=False, byteorder=None, software='tifffile.py')
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Create a new TIFF file for writing.
Use bigtiff=True when creating files greater than 2 GB.
Parameters: filename : str
Name of file to write.
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.
software : str
Name of the software used to create the image. Saved with the first page only.
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TAGS = {'strip_byte_counts': 279, 'strip_offsets': 273, 'resolution_unit': 296, 'x_resolution': 282, 'photometric': 262, 'y_resolution': 283, 'subfile_type': 255, 'tile_byte_counts': 325, 'tile_offsets': 324, 'tile_width': 322, 'image_depth': 32997, 'bits_per_sample': 258, 'tile_depth': 32998, 'image_length': 257, 'datetime': 306, 'document_name': 269, 'orientation': 274, 'planar_configuration': 284, 'sample_format': 339, 'compression': 259, 'image_description': 270, 'fill_order': 266, 'image_width': 256, 'rows_per_strip': 278, 'color_map': 320, 'page_name': 285, 'samples_per_pixel': 277, 'new_subfile_type': 254, 'tile_length': 323, 'extra_samples': 338, 'predictor': 317, 'software': 305}
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TYPES = {'B': 1, 'I': 4, 'H': 3, 'Q': 16, '2I': 5, 'b': 6, 'd': 12, 'f': 11, 'i': 9, 'h': 8, 'q': 17, 's': 2}
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close()
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save(data, photometric=None, planarconfig=None, resolution=None, description=None, volume=False, writeshape=False, compress=0, extratags=())
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Write image data to TIFF file.
Image data are written in one stripe per plane. Dimensions larger than 2 to 4 (depending on photometric mode, planar configuration, and SGI mode) are flattened and saved as separate pages. The ‘sample_format’ and ‘bits_per_sample’ TIFF tags are derived from the data type.
Parameters: data : array_like
Input image. The last dimensions are assumed to be image depth, height, width, and samples.
photometric : {‘minisblack’, ‘miniswhite’, ‘rgb’}
The color space of the image data. By default this setting is inferred from the data shape.
planarconfig : {‘contig’, ‘planar’}
Specifies if samples are stored contiguous or in separate planes. By default this setting is inferred from the data shape. ‘contig’: last dimension contains samples. ‘planar’: third last dimension contains samples.
resolution : (float, float) or ((int, int), (int, int))
X and Y resolution in dots per inch as float or rational numbers.
description : str
The subject of the image. Saved with the first page only.
compress : int
Values from 0 to 9 controlling the level of zlib compression. If 0, data are written uncompressed (default).
volume : bool
If True, volume data are stored in one tile (if applicable) using the SGI image_depth and tile_depth tags. Image width and depth must be multiple of 16. Few software can read this format, e.g. MeVisLab.
writeshape : bool
If True, write the data shape to the image_description tag if necessary and no other description is given.
extratags: sequence of tuples
Additional tags as [(code, dtype, count, value, writeonce)].
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code : int
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The TIFF tag Id.
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dtype : str
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Data type of items in ‘value’ in Python struct format. One of B, s, H, I, 2I, b, h, i, f, d, Q, or q.
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count : int
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Number of data values. Not used for string values.
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value : sequence
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‘Count’ values compatible with ‘dtype’.
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writeonce : bool
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If True, the tag is written to the first page only.
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© 2011 the scikit-image team
Licensed under the BSD 3-clause License.
http://scikit-image.org/docs/0.12.x/api/skimage.external.tifffile.html