Source code for ClearMap.IO.GT
# -*- coding: utf-8 -*-
"""
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`
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ = 'GPLv3 - GNU General Public License v3 (see LICENSE.txt)'
__copyright__ = 'Copyright © 2020 by Christoph Kirst'
__webpage__ = 'https://idisco.info'
__download__ = 'https://www.github.com/ChristophKirst/ClearMap2'
from ClearMap.Analysis.graphs import graph_gt
import ClearMap.IO.Source as src
###############################################################################
### Source class
###############################################################################
[docs]
class Source(src.Source):
"""GT graph source."""
def __init__(self, location=None, graph=None, name=None, mode=None):
"""GT source class constructor.
Arguments
---------
location : str or None
The filename of the graph source.
graph : Graph or None
The graph object
"""
super().__init__(name=name, mode=mode)
if isinstance(location, graph_gt.Graph):
graph = location
location = None
self._location = location
self._graph = graph
@property
def location(self):
return self._location
@location.setter
def location(self, value):
if value != self.location:
self._location = value
@property
def graph(self):
"""The underlying graph.
Returns
-------
graph : Graph
The underlying graph of this source.
"""
if self._graph is None:
self._graph = _graph(self.location)
return self._graph
@graph.setter
def graph(self, value):
self._graph = value
@property
def shape(self):
"""The shape of the source.
Returns
-------
shape : tuple
The shape of the source.
"""
return self.graph.shape
@shape.setter
def shape(self, value):
self.graph.shape = value
[docs]
def as_virtual(self):
return VirtualSource(source=self)
[docs]
def as_real(self):
return self
### Generic
[docs]
def info(self):
self.graph.info()
[docs]
def write(self, location = None):
if location is None:
location = self.location
return _write(location, self.graph)
[docs]
def read(self, location = None):
if location is None:
location = self.location
self._graph = _graph(location)
[docs]
def copy(self):
return Source(graph=self.graph.copy())
### Formatting
def __str__(self):
try:
name = self.name
name = '%s' % name if name is not None else ''
except:
name =''
try:
graph = self._graph.__str__()[5:]
except:
graph = ''
try:
location = self.location
location = '%s' % location if location is not None else ''
if len(location) > 100:
location = location[:50] + '...' + location[-50:]
if len(location) > 0:
location = '{%s}' % location
except:
location = ''
return name + graph + location
[docs]
class VirtualSource(src.VirtualSource):
_real_class = Source
def __init__(self, source=None, location=None, name=None, mode=None):
if source is not None and location is None:
location = source.location
super().__init__(location=location, name=name, mode=mode)
[docs]
def as_buffer(self):
raise NotImplementedError('Cannot convert virtual graph to buffer')
@property
def graph(self):
"""The underlying graph.
Returns
-------
graph : Graph
The underlying graph of this source.
"""
if self._graph is None:
self._graph = _graph(self.location)
return self._graph
@graph.setter
def graph(self, value):
raise NotImplementedError("Cannot set virtual graph")
@property
def shape(self):
"""The shape of the source.
Returns
-------
shape : tuple
The shape of the source.
"""
return self.graph.shape
@shape.setter
def shape(self, value):
raise NotImplementedError("Cannot set shape of virtual graph")
###############################################################################
### IO Interface
###############################################################################
[docs]
def is_graph(source):
"""Checks if this source is a graph source"""
if isinstance(source, Source):
return True
if isinstance(source, str) and len(source) >= 2 and source[-2:] == 'gt':
return True
return False
[docs]
def read(source, as_source = None, **kwargs):
"""Read graph from a file.
Arguments
---------
source : str
The name of the graph file.
slicing : slice, Slice or None
An optional sub-slice to consider.
as_source : bool
If True, return results as a source.
Returns
-------
graph : Graph or Source
The graph as a Graph class or source.
"""
if not isinstance(source, Source):
source = Source(source)
if as_source:
return source
else:
return source.graph
[docs]
def write(sink, graph, **kwargs):
"""Write graph to a file.
Arguments
---------
sink : str
The name of the CSV file.
graph : Graph
The data to write into the CSV file.
Returns
-------
sink : grpah or source
The sink graph file.
"""
if not isinstance(sink, Source):
sink = Source(sink)
return _write(sink, graph)
[docs]
def create(location = None, **kwargs):
raise NotImplementedError('Creating graph files not implemented yet!')
###############################################################################
### Helpers
###############################################################################
def _graph(location, **kwargs):
"""Read graph from file.
Arguments
---------
location : str
Location of the csv array data.
Returns
-------
graph : Graph
The graph as a Graph object.
"""
graph = graph_gt.load(location)
return graph
def _write(filename, graph, **args):
"""Write graph to file."""
graph_gt.save(filename, graph)
return filename
###############################################################################
### Tests
###############################################################################
[docs]
def test():
"""Test GT module"""
import os
from ClearMap.Analysis.graphs import graph_gt
import ClearMap.IO.GT as gt
location = 'test.gt'
g = graph_gt.Graph(n_vertices=10)
s = gt.Source(graph=g, location=location)
s.shape = (1,2,3)
print(s)
s.write()
r = gt.Source(location=location)
print(r.shape)
os.remove(location)
