ClearMap.IO

This module handels data reading and writing in ClearMap via sources and sinks.

The base class for IO is a Source that automatically detects file type and gathers some basic infomration about the file.

The IO module is the main module organizing all the IO functionailty.

>>> import numpy as np
>>> import ClearMap.IO.IO as io
>>> x = np.random.rand(30,40,50);
>>> s = io.as_source(x);
>>> print(s);
Numpy-Source(30, 40, 50)[float64]|C|

The first tuple is the shape of the array, the next list contains the datype or data structure, the |.| bracket denotes the order of this array, which can be |C| for c-contigous, |F| for Fortran contigous or ‘’ if the array is non-contigous.

File sources contain further information about the location of the files etc.

The FileList source allows to turn a list of files into a sinlge source, e.g. for microscope data in which each imageing plane comes in a separate file.

Supported source types include:

Format	Module	Description
tif	TIF	tif images and stacks
raw / mhd	MHD	raw image files with optional mhd header file
nrrd	NRRD	nearly raw raster data files
csv	CSV	text files as comma separated values
npy	NPY	numpy binary file
gt	GT	graph tool file
file list	FileList	folder, file list or file expression for a list source files
	MMP	memory mapped file
	SMA	shared memory array

Note

Sources can be sliced as numpy arrays using the Slice module.

Note

All sources can be made virtual, containing only pointers to data in order to use them in parallel processing via the as_virtual function.

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Sub-packages and modules

ClearMap.IO.CSV	Interface to read and write csv files.
ClearMap.IO.FileList	Module to handle sources distributed over a list of files.
ClearMap.IO.FileUtils	This module provides utilities for file management used by various IO modules.
ClearMap.IO.GT	Interface to read and write graph tool files.
ClearMap.IO.IO	IO interface to read files as sources.
ClearMap.IO.MHD	IO interface to mhd / raw files.
ClearMap.IO.MMP	Interface to numpy memmaps
ClearMap.IO.NPY	IO interface to numpy arrays.
ClearMap.IO.NRRD	IO interface to NRRD volumetric image data files.
ClearMap.IO.SMA	Shared memory arrays for parallel processing.
ClearMap.IO.Slice	This module provides basic handling of slicing of sources.
ClearMap.IO.Source	This module provides the base class for data sources and sinks.
ClearMap.IO.TIF	TIF module provides interface to read and write tif image files.
ClearMap.IO.Temporary	Utility functions to create temporary files.
ClearMap.IO.Workspace	The Workspace module keeps track of the data files of a project.
ClearMap.IO.assets_constants
ClearMap.IO.elastix_config
ClearMap.IO.metadata