FileList

Module to handle sources distributed over a list of files.

File lists ar specified using a TagExpression.

class Source(expression=None, file_list=None, axes_order=None, shape=None, dtype=None, order=None, name=None)[source]

Bases: ClearMap.IO.Source.VirtualSource

File list source.

Note

The full shape of the file list source is the shape of the expression and the shape of the data in each file, i.e. shape = file_list_shape + array_shape.

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.

axes_to_tag_order()[source]

Map from axes of this source to the tag list from the file expression.

tag_to_axes_order()[source]

Map from the tag list from the file expression and the axes of this source.

property array
property axes_file

Source axes that constitute individual file dimensions in the full array.

property axes_list

Source axes that constitute the dimensions of the file list in the full array.

property axes_order

Optional ordering of the tag names.

Returns

axes_orderlist of str

The ordered axis names.

property dtype

The data type of the source.

Returns

dtypedtype

The data type of the source.

property element_strides
property expression

The underlying expression of this file list.

Returns

expressionstr

The underlying expression of this source.

property file_list

The underlying file list.

Returns

filelistlist

The underlying sources of this source.

property name

The name of this source.

Returns

namestr

Name of this source.

property ndim_file

Source dimension of the individual files.

property ndim_list

Source dimensions of the file list.

property shape

The shape of the source.

Returns

shapetuple

The shape of the source.

property shape_file

Source shape of the individual files.

property shape_list

Source shape of the file list.

class VirtualSource(expression=None, file_list=None, shape=None, dtype=None, order=None, axes_order=None, source=None, name=None)[source]

Bases: ClearMap.IO.Source.VirtualSource

Virtual file list source.

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 array
property axes_order
property dtype

The data type of the source.

Returns

dtypedtype

The data type of the source.

property element_strides
property expression

The underlying expression of this file list.

Returns

expressionstr

The underlying expression of this source.

property file_list
property name

The name of this source.

Returns

namestr

Name of this source.

property shape

The shape of the source.

Returns

shapetuple

The shape of the source.

convert(source, sink, processes=None, verbose=False)[source]

Converts list of files to a sink in parallel

Arguments

sourceSource

File list source.

sinkSource

A sink to write the source to.

Returns

sinkSource

The sink the data was converted to.

create(location=None, shape=None, dtype=None, array=None, as_source=True)[source]
dtype(expression=None, file_list=None)[source]

Returns data type of the array stored in a file list.

Arguments

expressionstr

The regular epression for the file list.

Returns

dtypedtype

The data type of the file list.

is_file_list(expression, exists=False, tag_names=None, n_tags=-1, verbose=False)[source]

Checks if the expression is a valid file list.

Arguments

expressionstr

The regular expression to check.

existsbool

If True, check if at least one file exists.

tag_nameslist of str or None

List of tag names expected to be present in the expression.

n_Tagsint or None

Number of tags to expect.

verbosebool

If True, print reason why the epxression does not represent the desired file list.

Returns

is_expressionbool

Returns True if the expression fullfills the desired criteria and at least one file matching the expression exists.

ndim(expression=None, file_list=None)[source]

Calculates the dimension of the file list given by an expression.

Arguments

expressionstr

The expression for the file_list.

file_listlist

Optional file_list to speed up calculation.

Returns

ndimint

The dimension of the file list given by the expression.

order(expression=None, file_list=None)[source]

Returns order of the array stored in a file list.

Arguments

expressionstr

The regular epression for the file list.

Returns

dtypedtype

The data type of the file list.

read(source, slicing=None, axes_order=None, **kwargs)[source]
shape(expression=None, file_list=None, axes_order=None, axis=None)[source]

Calculates the shape of the data in a file list.

Arguments

expressionstr or None

The regular epression for the file list.

file_listlist or None

List of files.

axisint or None

The shape along a specific axis. Can speed up the shape calculation.

axes_orderlist or None

The names of how to order the different tag names in the expression. If None, use ordering of the tags in the expression.

Returns

shapeint or tuple of ints

The shape of the array st ored in a file list.

shape_file(expression=None, file_list=None)[source]

Calculates the shape of the data in a file list.

Arguments

expressionstr or None

The regular epression for the file list.

file_listlist or None

List of files.

Returns

shapeint or tuple of ints

The shape of the array st ored in a file list.

shape_list(expression=None, file_list=None, axes_order=None)[source]

Calculates the shape of the data in a file list.

Arguments

expressionstr or None

The regular epression for the file list.

file_listlist or None

List of files.

axes_orderlist or None

The names of how to order the different tag names in the expression. If None, use ordering of the tags in the expression.

Returns

shapeint or tuple of ints

The shape of the array along the dimensions created by the file list.

write(sink, data, slicing=None, axes_order=None, processes=None, **kwargs)[source]