Table of contents¶

jicbioimage.core.image¶

Module for managing and accessing images.

class jicbioimage.core.image.History(creation=None)[source]¶

Class for storing the provenance of an image.

class Event(function, args, kwargs)[source]¶

An event in the history of an image.

History.add_event(function, args, kwargs)[source]¶

Return event added to the history.

class jicbioimage.core.image.Image(shape, dtype=<type 'numpy.uint8'>, buffer=None, offset=0, strides=None, order=None, name=None, log_in_history=True)[source]¶

Image class.

classmethod from_file(fpath, name=None, log_in_history=True)[source]¶

Return jicbioimage.core.image.Image instance from a file.

Parameters:	fpath – path to the image file name – name of the image log_in_history – whether or not to log the creation event in the image’s history
Returns:	jicbioimage.core.image.Image

class jicbioimage.core.image.Image3D(shape, dtype=<type 'numpy.uint8'>, buffer=None, offset=0, strides=None, order=None, name=None, log_in_history=True)[source]¶

Image3D class; in other words a 3D stack.

classmethod from_directory(directory)[source]¶

Return jicbioimage.core.image.Image3D from directory.

Parameters:	directory – name of input directory
Returns:	jicbioimage.core.image.Image3D

to_directory(directory)[source]¶

Write slices from 3D image to directory.

write(name)[source]¶

Write slices from 3D image to disk.

Parameters:	name – name of output directory

class jicbioimage.core.image.ImageCollection(fpath=None)[source]¶

Class for storing related images.

image(index=0)[source]¶

Return image as a jicbioimage.core.image.Image.

Parameters:	index – list index
Returns:	jicbioimage.core.image.Image

parse_manifest(fpath)[source]¶

Parse manifest file to build up the collection of images.

Parameters:	fpath – path to the manifest file
Raises:	RuntimeError

proxy_image(index=0)[source]¶

Return a jicbioimage.core.image.ProxyImage instance.

Parameters:	index – list index
Returns:	jicbioimage.core.image.ProxyImage

class jicbioimage.core.image.MicroscopyCollection(fpath=None)[source]¶

Collection of jicbioimage.core.image.MicroscopyImage instances.

channels(s=0)[source]¶

Return list of channels in the collection.

Parameters:	s – series
Returns:	list of channel identifiers

image(s=0, c=0, z=0, t=0)[source]¶

Return image as a jicbioimage.core.image.Image.

Parameters:	s – series c – channel z – zslice t – timepoint
Returns:	jicbioimage.core.image.Image

proxy_image(s=0, c=0, z=0, t=0)[source]¶

Return a jicbioimage.core.image.MicroscopyImage instance.

Parameters:	s – series c – channel z – zslice t – timepoint
Returns:	jicbioimage.core.image.MicroscopyImage

series¶

Return list of series in the collection.

timepoints(s=0)[source]¶

Return list of time points in the collection.

Parameters:	s – series
Returns:	list of time point identifiers

zslices(s=0)[source]¶

Return list of z-slices in the collection.

Parameters:	s – series
Returns:	list of zslice identifiers

zstack(s=0, c=0, t=0)[source]¶

Return zstack as a jicbioimage.core.image.Image3D.

Parameters:	s – series c – channel t – timepoint
Returns:	zstack as a jicbioimage.core.image.Image3D

zstack_array(s=0, c=0, t=0)[source]¶

Return zstack as a numpy.ndarray.

Parameters:	s – series c – channel t – timepoint
Returns:	zstack as a numpy.ndarray

zstack_proxy_iterator(s=0, c=0, t=0)[source]¶

Return zstack jicbioimage.core.image.ProxyImage iterator.

Parameters:	s – series c – channel t – timepoint
Returns:	zstack as a jicbioimage.core.image.ProxyImage iterator

class jicbioimage.core.image.MicroscopyImage(fpath, metadata={})[source]¶

Lightweight image class with microscopy meta data.

in_zstack(s, c, t)[source]¶

Return True if I am in the zstack.

Parameters:	s – series c – channel t – timepoint
Returns:	bool

is_me(s, c, z, t)[source]¶

Return True if arguments match my meta data.

Parameters:	s – series c – channel z – zslice t – timepoint
Returns:	bool

class jicbioimage.core.image.ProxyImage(fpath, metadata={})[source]¶

Lightweight image class.

image¶

Underlying jicbioimage.core.image.Image instance.

jicbioimage.core.io¶

Module for reading and writing images.

class jicbioimage.core.io.AutoName[source]¶

Class for generating output file names automatically.

directory = None¶

Output directory to save images to.

classmethod name(func)[source]¶

Return auto generated file name.

namespace = ''¶

Image file namespace.

classmethod prefix()[source]¶

Return auto generated file prefix.

prefix_format = '{:d}_'¶

Image file prefix format.

class jicbioimage.core.io.AutoWrite[source]¶

Class for writing images automatically.

on = True¶

Whether or not auto writing of images is enabled.

class jicbioimage.core.io.BFConvertWrapper(backend)[source]¶

Class for unpacking microscopy files using bfconvert.

already_converted(fpath)[source]¶

Return true if the file already has a manifest file in the backend.

Parameters:	fpath – potential path to the manifest file
Returns:	bool

manifest(entry)[source]¶

Returns manifest as a list.

Parameters:	entry – jicbioimage.core.io.FileBackend.Entry
Returns:	jicbioimage.core.io.Manifest

metadata_from_fname(fname, md5_hexdigest)[source]¶

Return meta data extracted from file name.

Parameters:	fname – metadata file name
Returns:	dictionary with meta data required by

run_command(input_file, output_dir=None)[source]¶

Return the command for running bfconvert as a list.

Parameters:	input_file – path to microscopy image to be converted ouput_dir – directory to write output tiff files to
Returns:	list

split_pattern(win32=False)[source]¶

Pattern used to split the input file.

class jicbioimage.core.io.DataManager(backend=None)[source]¶

Manage jicbioimage.core.image.ImageCollection instances.

load(fpath)[source]¶

Load a microscopy file.

Parameters:	fpath – path to microscopy file

class jicbioimage.core.io.FileBackend(directory)[source]¶

Class for storing image files.

class Entry(base_dir, fpath)[source]¶

Class representing a backend entry.

directory¶

Where the images are stored.

FileBackend.directory¶

Where the entries are stored.

FileBackend.new_entry(fpath)[source]¶

Return a new entry; to be populated with images.

Parameters:	fpath – path to microscopy image
Returns:	jiciimagelib.image.FileBackend.Entry instance

class jicbioimage.core.io.Manifest[source]¶

Class for generating backend entry manifest files.

add(filename, **kwargs)[source]¶

Add an entry to the manifest.

Parameters:	filename – relative path to image kwargs – custom parameters, e.g. series, channel, zslice
Returns:	the added entry

json¶

Return json representation.

jicbioimage.core.transform¶

Module containing image transformation functions.

This module contains the function decorator jicbioimage.core.transform.transformation() that can be used to turn functions into image transformations.

Below is an example of how to create a transformation that inverts an image.

>>> import numpy as np
>>> @transformation
... def invert(image):
...     "Return the inverted image."
...     maximum = np.iinfo(image.dtype).max
...     maximum_array = np.ones(image.shape, dtype=image.dtype) * maximum
...     return maximum_array - image
...

jicbioimage.core.transform.transformation(func)[source]¶

Function decorator to turn another function into a transformation.

jicbioimage.core.util.array¶

Module containing utility functions for manipulating numpy arrays.

jicbioimage.core.util.array.check_dtype(array, allowed)[source]¶

Raises TypeError if the array is not of an allowed dtype.

Parameters:	array – array whose dtype is to be checked allowed – instance or list of allowed dtypes
Raises:	TypeError

jicbioimage.core.util.array.color_array(array, color_dict)[source]¶

Return RGB color array.

Assigning a unique RGB color value to each unique element of the input array and return an array of shape (array.shape, 3).

Parameters:	array – input numpy.array color_dict – dictionary with keys/values corresponding to identifiers and RGB tuples respectively

jicbioimage.core.util.array.dtype_contract(input_dtype=None, output_dtype=None)[source]¶

Function decorator for specifying input and/or output array dtypes.

Parameters:	input_dtype – dtype of input array output_dtype – dtype of output array
Returns:	function decorator

jicbioimage.core.util.array.map_stack(array3D, z_function)[source]¶

Return 3D array where each z-slice has had the function applied to it.

Parameters:	array3D – 3D numpy.array z_function – function to be mapped to each z-slice

jicbioimage.core.util.array.normalise(array)[source]¶

Return array normalised such that all values are between 0 and 1.

If all the values in the array are the same the function will return: - np.zeros(array.shape, dtype=np.float) if the value is 0 or less - np.ones(array.shape, dtype=np.float) if the value is greater than 0

Parameters:	array – numpy.array
Returns:	numpy.array.astype(numpy.float)

jicbioimage.core.util.array.pretty_color_array(array, keep_zero_black=True)[source]¶

Return a RGB pretty color array.

Assigning a pretty RGB color value to each unique element of the input array and return an array of shape (array.shape, 3).

Parameters:	array – input numpy.array keep_zero_black – whether or not the background should be black
Returns:	numpy.array

jicbioimage.core.util.array.reduce_stack(array3D, z_function)[source]¶

Return 2D array projection of the input 3D array.

The input function is applied to each line of an input x, y value.

Parameters:	array3D – 3D numpy.array z_function – function to use for the projection (e.g. max())

jicbioimage.core.util.array.unique_color_array(array)[source]¶

Return a RGB unique color array.

Assigning a unique RGB color value to each unique element of the input array and return an array of shape (array.shape, 3).

Parameters:	array – input numpy.array
Returns:	numpy.array

jicbioimage.core.util.color¶

Module for generating RGB tuples for use as colors in images.

jicbioimage.core.util.color.identifier_from_unique_color(unique_color)[source]¶

Return identifier from unique RGB tuple.

Parameters:	unique_color – RGB tuple
Returns:	positive integer in range from 0 to 16777215 inclusive

jicbioimage.core.util.color.pretty_color_from_identifier(identifier)[source]¶

Return deterministic aesthetically pleasing RGB tuple.

Returns:	RGB tuple

jicbioimage.core.util.color.pretty_color_palette(identifiers, keep_zero_black=True)[source]¶

Return dictionary with pretty colors.

Parameters:	identifiers – set of unique identifiers keep_zero_black – whether or not the background should be black
Returns:	dictionary

jicbioimage.core.util.color.random_pretty_color()[source]¶

Return random aesthetically pleasing RGB tuple.

Returns:	RGB tuple

jicbioimage.core.util.color.unique_color_from_identifier(identifier)[source]¶

Return unique color as RGB tuple.

Useful for creating PNG images where each color is used as an identifier.

Raises TypeError if the identifier is not an integer.

Raises ValueError if the identifier is not in the range 0 to 16777215 inclusive.

Parameters:	identifier – positive integer in range from 0 to 16777215 inclusive
Raises:	TypeError, ValueError
Returns:	RGB tuple

jicbioimage.core.util.color.unique_color_palette(identifiers)[source]¶

Return dictionary with unique colors.

Parameters:	identifiers – set of unique identifiers
Returns:	dictionary