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000000000..1559e9446 --- /dev/null +++ b/doc/source/images/generate_io_overview.py @@ -0,0 +1,114 @@ +# -*- coding: utf-8 -*- + +""" +This generate diagram of the (raw)ios and formats + + +Author: Julia Sprenger +""" + +import pygraphviz +import neo + +# from datetime import datetime +# +# import numpy as np +# import quantities as pq +# from matplotlib import pyplot +# from matplotlib.patches import Rectangle, ArrowStyle, FancyArrowPatch +# from matplotlib.font_manager import FontProperties +# +# from neo.test.generate_datasets import fake_neo +# +# line_heigth = .22 +# fontsize = 10.5 +# left_text_shift = .1 +# dpi = 100 + + +default_style = {'shape': 'rectangle', + 'color': 'black', + 'fontcolor': 'black'} +IO_style = default_style.copy() +IO_style['fontsize'] = '30' +IO_style['penwidth'] = 6 + +styles = {'IO': {'ro': IO_style.copy(), + 'rw': IO_style.copy(), + 'raw': IO_style.copy() + }, + 'main': default_style.copy(), + 'ext': default_style.copy()} + +styles['IO']['ro']['color'] = '#20B2AA ' +styles['IO']['rw']['color'] = '#4169E1 ' +styles['IO']['raw']['color'] = '#008080 ' +styles['ext']['shape'] = 'circle' +styles['ext']['fillcolor'] = 'red' +styles['ext']['style'] = 'filled' + + +# styles['ext']['fixedsize'] = 'True' + + +def generate_diagram(filename, plot_extensions=False): + dia = pygraphviz.AGraph(strict=False, splines='true') + G = dia + G.node_attr['fontname'] = 'Arial' + # G.node_attr['shape'] = 'circle' + # G.node_attr['fixedsize'] = 'true' + # G.node_attr['sep'] = '-100' + G.node_attr['fixedsize'] = 'False' + # G.graph_attr['overlap'] = 'False' + G.graph_attr['packMode'] = 'clust' + # G.graph_attr['levelsgap'] = -500 + G.node_attr['fontsize'] = '20' + G.edge_attr['minlen'] = '0' + # G.node_attr['style'] = 'filled' + # G.graph_attr['outputorder'] = 'edgesfirst' + # G.graph_attr['splines'] = "compound" + G.graph_attr['label'] = "NEO {}".format(neo.__version__) + G.graph_attr['ratio'] = '1.0' + # G.edge_attr['color'] = '#1100FF' + + G.edge_attr['style'] = 'setlinewidth(4)' + + dia.add_node('NEO', shape='circle', fontsize=50) + + for io in neo.io.iolist: + io_name = io.name + rawio = False + if issubclass(io, neo.io.basefromrawio.BaseFromRaw): + rawio = True + if io_name == 'BaseIO': + io_name = io.__name__.rstrip('RawIO') + if io_name is None: + io_name = io.__name__.rstrip('IO') + if 'example' in io_name: + continue + + if io.is_writable and io.is_readable: + mode = 'rw' + elif io.is_readable: + mode = 'ro' + if rawio: + mode = 'raw' + + dia.add_node(io_name, **styles['IO'][mode]) + dia.add_edge('NEO', io_name) + + if plot_extensions: + for ext in io.extensions: + dia.add_node(ext, **styles['ext']) + dia.add_edge(io_name, ext, minlen=0) + + dia.layout(prog='fdp') # neato, dot, twopi, circo, fdp, nop, wc, acyclic, gvpr, gvcolor, + # ccomps, sccmap, tred, sfdp. + for ext in ['png', 'svg', 'eps']: + dia.draw('{}.{}'.format(filename, ext)) + + +if __name__ == '__main__': + generate_diagram('IODiagram', plot_extensions=False) + generate_diagram('IODiagram_ext', plot_extensions=True) + # pyplot.show() diff --git a/doc/source/images/neo_UML_French_workshop.dia b/doc/source/images/neo_UML_French_workshop.dia deleted file mode 100644 index e26f3860e..000000000 Binary files a/doc/source/images/neo_UML_French_workshop.dia and /dev/null differ diff --git a/doc/source/images/neo_UML_French_workshop.png b/doc/source/images/neo_UML_French_workshop.png deleted file mode 100644 index f2bdd516e..000000000 Binary files a/doc/source/images/neo_UML_French_workshop.png and /dev/null differ diff --git a/doc/source/images/neo_ecosystem.drawio b/doc/source/images/neo_ecosystem.drawio new file mode 100644 index 000000000..290e34c37 --- /dev/null +++ b/doc/source/images/neo_ecosystem.drawio @@ -0,0 +1,193 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/doc/source/images/neo_ecosystem.svg b/doc/source/images/neo_ecosystem.svg index 0c7c8b0c2..2d65930a5 100644 --- a/doc/source/images/neo_ecosystem.svg +++ b/doc/source/images/neo_ecosystem.svg @@ -1,905 +1,4 @@ - - - - - - - - - - - - - - - - - - - - - - image/svg+xml - - - - - -   - - - Neo - - - Plexon - - - - NeuroExplorer   - - - - Axon - - - - TuckerDavis - - - - NIX - - - - - NWB - - - - - Klustakwik - - - - Blackrock - - - - - - - - - - - - - - - - - - - - - - - - PyNN - - - OpenElectrophy - - - G-Node - - - - SpykeViewer - - - - Elephant - - - - - Helmholtz - - - - spykeutils - - - - Dataanalysis - Visualization - Databases - Simulation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Matlab - - - - - HDF5 - - - - - - - - + + + +BlackRockNeuralynxPlexonOpenEphysPhyNWBNIX...SpikeGLXMaxwell
Simulation
Simulation
Data sharing
Data sharing
Visualization
Visualization
Data processing
Data processing
Data analysis
Data analysisPyNNTridesclousSpikeInterfaceNixViewerBIDSDANDIElephantephyviewerViewer does not support full SVG 1.1 \ No newline at end of file