TIF#

TIF module provides interface to read and write tif image files.

Note

This modules relies on the tifffile library.

class Source(location, series=0, multi_file=False)[source]#

Bases: Source

Class to handle a tif file source

Note

Its assumed that the image data is stored in a series of the tif file.

as_buffer()[source]#

as_memmap()[source]#

as_real()[source]#

as_virtual()[source]#

Return virtual source without array data to pass in parallel processing.

Returns

sourceSource class: The source class without array data.

metadata(info=None)[source]#

Returns metadata from this tif file.

Arguments

sourcestr or Source: The filename or data source.
infolist or all: Optional list of keywords, if all return full tif metadata, if None return default set info.

Returns

metadatadict: Dictionary with the meta data.

property array#

property dtype#

The data type of the source.

Returns

dtypedtype: The data type of the source.

property element_strides#

The strides of the array elements.

Returns

stridestuple: Strides of the array elements.

Note

The strides of the elements module itemsize instead of bytes.

property location#

The location where the data of the source is stored.

Returns

locationstr or None: Returns the location of the data source or None if this source lives in memory only.

property name#

The name of this source.

Returns

namestr: Name of this source.

series#: Attribute whose value is computed on first access.

property shape#

The shape of the source.

Returns

shapetuple: The shape of the source.

property tif_shape#

class VirtualSource(source=None, shape=None, dtype=None, order=None, location=None, name=None)[source]#

Bases: VirtualSource

as_buffer()[source]#

as_real()[source]#

as_virtual()[source]#

Return virtual source without array data to pass in parallel processing.

Returns

sourceSource class: The source class without array data.

property name#

The name of this source.

Returns

namestr: Name of this source.

array_from_tif(array)[source]#

array_to_tif(array)[source]#

create(location=None, shape=None, dtype=None, mode=None, as_source=True, **kwargs)[source]#

Create a memory map.

Arguments

locationstr: The filename of the memory mapped array.
shapetuple or None: The shape of the memory map to create.
dtypedtype: The data type of the memory map.
mode‘r’, ‘w’, ‘w+’, None: The mode to open the memory map.
as_sourcebool: If True, return as Source class.

Returns

memmapnp.memmap: The memory map.

Note

By default memmaps are initialized as fortran contiguous if order is None.

is_tif(source)[source]#: Checks if this source a TIF source

read(source, slicing=None, sink=None, **args)[source]#

Read data from a tif file.

Arguments

sourcestr or TIF class: The name of the tif file or a TIF class.
slicingslice, Slice or None: An optional sub-slice to consider.

Returns

dataarray: The image data in the tif file.

shape_from_tif(shape)[source]#

shape_to_tif(shape)[source]#

write(sink, data, **args)[source]#

Write data to a tif file

Arguments

sinkstr: The name of the tif file.

Returns

sinkstr: The name of the tif file.