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# -*- coding: utf-8 -*-
import os
from os import path as op
title = 'mne-python flow diagram'
font_face = 'Arial'
node_size = 12
node_small_size = 9
edge_size = 9
sensor_color = '#7bbeca'
source_color = '#ff6347'
legend = """
<<FONT POINT-SIZE="%s">
<TABLE BORDER="0" CELLBORDER="0" CELLSPACING="4" CELLPADDING="4">
<TR><TD BGCOLOR="%s"> </TD><TD ALIGN="left">
Sensor (M/EEG) space</TD></TR>
<TR><TD BGCOLOR="%s"> </TD><TD ALIGN="left">
Source (brain) space</TD></TR>
</TABLE></FONT>>""" % (edge_size, sensor_color, source_color)
legend = ''.join(legend.split('\n'))
nodes = dict(
T1='T1',
flashes='Flash5/30',
trans='Head-MRI trans',
recon='Freesurfer surfaces',
bem='BEM',
src='Source space\nmne.SourceSpaces',
cov='Noise covariance\nmne.Covariance',
fwd='Forward solution\nmne.forward.Forward',
inv='Inverse operator\nmne.minimum_norm.InverseOperator',
stc='Source estimate\nmne.SourceEstimate',
raw='Raw data\nmne.io.Raw',
epo='Epoched data\nmne.Epochs',
evo='Averaged data\nmne.Evoked',
pre='Preprocessed data\nmne.io.Raw',
legend=legend,
)
sensor_space = ('raw', 'pre', 'epo', 'evo', 'cov')
source_space = ('src', 'stc', 'bem', 'flashes', 'recon', 'T1')
edges = (
('T1', 'recon'),
('flashes', 'bem'),
('recon', 'bem'),
('recon', 'src', 'mne.setup_source_space'),
('src', 'fwd'),
('bem', 'fwd'),
('trans', 'fwd', 'mne.make_forward_solution'),
('fwd', 'inv'),
('cov', 'inv', 'mne.make_inverse_operator'),
('inv', 'stc'),
('evo', 'stc', 'mne.minimum_norm.apply_inverse'),
('raw', 'pre', 'raw.filter\n'
'mne.preprocessing.ICA\n'
'mne.preprocessing.compute_proj_eog\n'
'mne.preprocessing.compute_proj_ecg\n'
'...'),
('pre', 'epo', 'mne.Epochs'),
('epo', 'evo', 'epochs.average'),
('epo', 'cov', 'mne.compute_covariance'),
)
subgraphs = (
[('T1', 'flashes', 'recon', 'bem', 'src'),
('<Structural information<BR/><FONT POINT-SIZE="%s"><I>'
'Freesurfer / MNE-C</I></FONT>>' % node_small_size)],
)
def setup(app):
app.connect('builder-inited', generate_flow_diagram)
app.add_config_value('make_flow_diagram', True, 'html')
def setup_module():
# HACK: Stop nosetests running setup() above
pass
def generate_flow_diagram(app):
out_dir = op.join(app.builder.outdir, '_static')
if not op.isdir(out_dir):
os.makedirs(out_dir)
out_fname = op.join(out_dir, 'mne-python_flow.svg')
make_flow_diagram = app is None or \
bool(app.builder.config.make_flow_diagram)
if not make_flow_diagram:
print('Skipping flow diagram, webpage will have a missing image')
return
import pygraphviz as pgv
g = pgv.AGraph(name=title, directed=True)
for key, label in nodes.items():
label = label.split('\n')
if len(label) > 1:
label[0] = ('<<FONT POINT-SIZE="%s">' % node_size
+ label[0] + '</FONT>')
for li in range(1, len(label)):
label[li] = ('<FONT POINT-SIZE="%s"><I>' % node_small_size
+ label[li] + '</I></FONT>')
label[-1] = label[-1] + '>'
label = '<BR/>'.join(label)
else:
label = label[0]
g.add_node(key, shape='plaintext', label=label)
# Create and customize nodes and edges
for edge in edges:
g.add_edge(*edge[:2])
e = g.get_edge(*edge[:2])
if len(edge) > 2:
e.attr['label'] = ('<<I>' +
'<BR ALIGN="LEFT"/>'.join(edge[2].split('\n')) +
'<BR ALIGN="LEFT"/></I>>')
e.attr['fontsize'] = edge_size
# Change colors
for these_nodes, color in zip((sensor_space, source_space),
(sensor_color, source_color)):
for node in these_nodes:
g.get_node(node).attr['fillcolor'] = color
g.get_node(node).attr['style'] = 'filled'
# Create subgraphs
for si, subgraph in enumerate(subgraphs):
g.add_subgraph(subgraph[0], 'cluster%s' % si,
label=subgraph[1], color='black')
# Format (sub)graphs
for gr in g.subgraphs() + [g]:
for x in [gr.node_attr, gr.edge_attr]:
x['fontname'] = font_face
g.node_attr['shape'] = 'box'
# A couple of special ones
for ni, node in enumerate(('fwd', 'inv', 'trans')):
node = g.get_node(node)
node.attr['gradientangle'] = 270
colors = (source_color, sensor_color)
colors = colors if ni == 0 else colors[::-1]
node.attr['fillcolor'] = ':'.join(colors)
node.attr['style'] = 'filled'
del node
g.get_node('legend').attr.update(shape='plaintext', margin=0, rank='sink')
# put legend in same rank/level as inverse
leg = g.add_subgraph(['legend', 'inv'], name='legendy')
leg.graph_attr['rank'] = 'same'
g.layout('dot')
g.draw(out_fname, format='svg')
return g
# This is useful for testing/iterating to see what the result looks like
if __name__ == '__main__':
from mne.io.constants import Bunch
out_dir = op.abspath(op.join(op.dirname(__file__), '..', '_build', 'html'))
app = Bunch(builder=Bunch(outdir=out_dir,
config=Bunch(make_flow_diagram=True)))
g = generate_flow_diagram(app)
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