GT#

Interface to read and write graph tool files.

Note

The module utilizes the gt writer/reader from graph_tool.

See also

:mod`ClearMap.Analysis.Graphs`

class Source(location=None, graph=None, name=None)[source]#

Bases: Source

GT graph 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.

copy()[source]#

info()[source]#

read(location=None)[source]#

write(location=None)[source]#

property graph#

The underlying graph.

Returns

graphGraph: The underlying graph of this source.

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.

property shape#

The shape of the source.

Returns

shapetuple: The shape of the source.

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

Bases: VirtualSource

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 graph#

The underlying graph.

Returns

graphGraph: The underlying graph of this source.

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.

create(location=None, **kwargs)[source]#

is_graph(source)[source]#: Checks if this source is a graph source

read(source, as_source=None, **kwargs)[source]#

Read graph from a file.

Arguments

sourcestr: The name of the graph file.
slicingslice, Slice or None: An optional sub-slice to consider.
as_sourcebool: If True, return results as a source.

Returns

graphGraph or Source: The graph as a Graph class or source.

test()[source]#: Test GT module

write(sink, graph, **kwargs)[source]#

Write graph to a file.

Arguments

sinkstr: The name of the CSV file.
graphGraph: The data to write into the CSV file.

Returns

sinkgrpah or source: The sink graph file.