def tryout_web_graphs(self, infr):
"""
https://plot.ly/python/
http://bokeh.pydata.org/en/latest/
pip install bokeh
Notes:
http://www.coppelia.io/2014/07/an-a-to-z-of-extra-features-for-the-d3-force-layout/
http://andrewmellor.co.uk/blog/articles/2014/12/14/d3-networks/
pip install plotly # eww need to sign up and get a key
http://igraph.org/
import mpld3
mpld3.save_html(fig, open('fig.html', 'w'))
mpld3.save_json(fig, open('fig.json', 'w'))
fig = pt.gcf()
"""
#import plottool as pt
# http://andrewmellor.co.uk/blog/articles/2014/12/14/d3-networks/
from networkx.readwrite import json_graph
G = infr.graph
data = json_graph.node_link_data(G)
json_text = ut.to_json(data, pretty=True)
ut.writeto('graph.json', json_text)
ut.editfile('graph.json')
ut.startfile('d3_example.html')
def autogen_ipynb(ibs, launch=None, run=None):
r"""
Autogenerates standard IBEIS Image Analysis IPython notebooks.
CommandLine:
python -m ibeis --tf autogen_ipynb --run --db lynx
python -m ibeis --tf autogen_ipynb --ipynb --db PZ_MTEST --asreport
python -m ibeis --tf autogen_ipynb --ipynb --db PZ_MTEST --noexample --withtags
python -m ibeis --tf autogen_ipynb --db PZ_MTEST
# TODO: Add support for dbdir to be specified
python -m ibeis --tf autogen_ipynb --db ~/work/PZ_MTEST
python -m ibeis --tf autogen_ipynb --ipynb --db Oxford -a default:qhas_any=\(query,\),dpername=1,exclude_reference=True,dminqual=good
python -m ibeis --tf autogen_ipynb --ipynb --db PZ_MTEST -a default -t best:lnbnn_normalizer=[None,normlnbnn-test]
python -m ibeis.templates.generate_notebook --exec-autogen_ipynb --db wd_peter_blinston --ipynb
python -m ibeis --tf autogen_ipynb --db PZ_Master1 --ipynb
python -m ibeis --tf autogen_ipynb --db PZ_Master1 -a timectrl:qindex=0:100 -t best best:normsum=True --ipynb --noexample
python -m ibeis --tf autogen_ipynb --db PZ_Master1 -a timectrl --run
jupyter-notebook Experiments-lynx.ipynb
killall python
python -m ibeis --tf autogen_ipynb --db humpbacks --ipynb -t default:proot=BC_DTW -a default:has_any=hasnotch
python -m ibeis --tf autogen_ipynb --db humpbacks --ipynb -t default:proot=BC_DTW default:proot=vsmany -a default:has_any=hasnotch,mingt=2,qindex=0:50 --noexample
Example:
>>> # SCRIPT
>>> from ibeis.templates.generate_notebook import * # NOQA
>>> import ibeis
>>> ibs = ibeis.opendb(defaultdb='testdb1')
>>> result = autogen_ipynb(ibs)
>>> print(result)
"""
dbname = ibs.get_dbname()
fname = 'Experiments-' + dbname
nb_fpath = fname + '.ipynb'
if ut.get_argflag('--cells'):
notebook_cells = make_ibeis_cell_list(ibs)
print('\n# ---- \n'.join(notebook_cells))
return
# TODO: Add support for dbdir to be specified
notebook_str = make_ibeis_notebook(ibs)
ut.writeto(nb_fpath, notebook_str)
run = ut.get_argflag('--run') if run is None else run
launch = launch if launch is not None else ut.get_argflag('--ipynb')
if run:
run_nb = ut.run_ipython_notebook(notebook_str)
output_fpath = ut.export_notebook(run_nb, fname)
ut.startfile(output_fpath)
elif launch:
ut.cmd('jupyter-notebook', nb_fpath, detatch=True)
#ut.cmd('ipython-notebook', nb_fpath)
#ut.startfile(nb_fpath)
else:
print('notebook_str =\n%s' % (notebook_str,))
def autogen_ipynb(ibs, launch=None, run=None):
r"""
Autogenerates standard IBEIS Image Analysis IPython notebooks.
CommandLine:
python -m ibeis --tf autogen_ipynb --run --db lynx
python -m ibeis --tf autogen_ipynb --ipynb --db PZ_MTEST --asreport
python -m ibeis --tf autogen_ipynb --ipynb --db PZ_MTEST --noexample --withtags
python -m ibeis --tf autogen_ipynb --db PZ_MTEST
# TODO: Add support for dbdir to be specified
python -m ibeis --tf autogen_ipynb --db ~/work/PZ_MTEST
python -m ibeis --tf autogen_ipynb --ipynb --db Oxford -a default:qhas_any=\(query,\),dpername=1,exclude_reference=True,dminqual=good
python -m ibeis --tf autogen_ipynb --ipynb --db PZ_MTEST -a default -t best:lnbnn_normalizer=[None,normlnbnn-test]
python -m ibeis.templates.generate_notebook --exec-autogen_ipynb --db wd_peter_blinston --ipynb
python -m ibeis --tf autogen_ipynb --db PZ_Master1 --ipynb
python -m ibeis --tf autogen_ipynb --db PZ_Master1 -a timectrl:qindex=0:100 -t best best:normsum=True --ipynb --noexample
python -m ibeis --tf autogen_ipynb --db PZ_Master1 -a timectrl --run
jupyter-notebook Experiments-lynx.ipynb
killall python
python -m ibeis --tf autogen_ipynb --db humpbacks --ipynb -t default:proot=BC_DTW -a default:has_any=hasnotch
python -m ibeis --tf autogen_ipynb --db humpbacks --ipynb -t default:proot=BC_DTW default:proot=vsmany -a default:has_any=hasnotch,mingt=2,qindex=0:50 --noexample
Example:
>>> # SCRIPT
>>> from ibeis.templates.generate_notebook import * # NOQA
>>> import ibeis
>>> ibs = ibeis.opendb(defaultdb='testdb1')
>>> result = autogen_ipynb(ibs)
>>> print(result)
"""
dbname = ibs.get_dbname()
fname = 'Experiments-' + dbname
nb_fpath = fname + '.ipynb'
if ut.get_argflag('--cells'):
notebook_cells = make_ibeis_cell_list(ibs)
print('\n# ---- \n'.join(notebook_cells))
return
# TODO: Add support for dbdir to be specified
notebook_str = make_ibeis_notebook(ibs)
ut.writeto(nb_fpath, notebook_str)
run = ut.get_argflag('--run') if run is None else run
launch = launch if launch is not None else ut.get_argflag('--ipynb')
if run:
run_nb = ut.run_ipython_notebook(notebook_str)
output_fpath = ut.export_notebook(run_nb, fname)
ut.startfile(output_fpath)
elif launch:
ut.cmd('jupyter-notebook', nb_fpath, detatch=True)
#ut.cmd('ipython-notebook', nb_fpath)
#ut.startfile(nb_fpath)
else:
print('notebook_str =\n%s' % (notebook_str, ))
def imwrite_theano_symbolic_graph(thean_expr):
import theano
graph_dpath = '.'
graph_fname = 'symbolic_graph.png'
graph_fpath = ut.unixjoin(graph_dpath, graph_fname)
ut.ensuredir(graph_dpath)
theano.printing.pydotprint(
thean_expr, outfile=graph_fpath, var_with_name_simple=True)
ut.startfile(graph_fpath)
return graph_fpath
def render_latex_text(input_text, nest_in_doc=False, appname='utool', verbose=None):
""" testing function """
import utool as ut
if verbose is None:
verbose = ut.VERBOSE
dpath = ut.get_app_resource_dir(appname)
# put a latex framgent in a full document
print(input_text)
pdf_fpath = ut.compile_latex_text(input_text, dpath=dpath, verbose=verbose)
ut.startfile(pdf_fpath)
return pdf_fpath
def make_bayes_notebook():
r"""
CommandLine:
python -m wbia.unstable.demobayes --exec-make_bayes_notebook
Example:
>>> # DISABLE_DOCTEST
>>> from wbia.unstable.demobayes import * # NOQA
>>> result = make_bayes_notebook()
>>> print(result)
"""
from wbia.templates import generate_notebook
initialize = ut.codeblock(r"""
# STARTBLOCK
import os
os.environ['UTOOL_NO_CNN'] = 'True'
from wbia.unstable.demobayes import * # NOQA
# Matplotlib stuff
import matplotlib as mpl
%matplotlib inline
%load_ext autoreload
%autoreload
from IPython.core.display import HTML
HTML("<style>body .container { width:99% !important; }</style>")
# ENDBLOCK
""")
cell_list_def = [
initialize,
show_model_templates,
demo_modes,
demo_name_annot_complexity,
# demo_model_idependencies,
demo_single_add,
demo_ambiguity,
demo_conflicting_evidence,
demo_annot_idependence_overlap,
]
def format_cell(cell):
if ut.is_funclike(cell):
header = '# ' + ut.to_title_caps(ut.get_funcname(cell))
code = (header,
ut.get_func_sourcecode(cell, stripdef=True, stripret=True))
else:
code = (None, cell)
return generate_notebook.format_cells(code)
cell_list = ut.flatten([format_cell(cell) for cell in cell_list_def])
nbstr = generate_notebook.make_notebook(cell_list)
logger.info('nbstr = %s' % (nbstr, ))
fpath = 'demobayes.ipynb'
ut.writeto(fpath, nbstr)
ut.startfile(fpath)
def make_bayes_notebook():
r"""
CommandLine:
python -m ibeis.algo.hots.demobayes --exec-make_bayes_notebook
Example:
>>> # DISABLE_DOCTEST
>>> from ibeis.algo.hots.demobayes import * # NOQA
>>> result = make_bayes_notebook()
>>> print(result)
"""
from ibeis.templates import generate_notebook
initialize = ut.codeblock(
r'''
# STARTBLOCK
import os
os.environ['UTOOL_NO_CNN'] = 'True'
from ibeis.algo.hots.demobayes import * # NOQA
# Matplotlib stuff
import matplotlib as mpl
%matplotlib inline
%load_ext autoreload
%autoreload
from IPython.core.display import HTML
HTML("<style>body .container { width:99% !important; }</style>")
# ENDBLOCK
'''
)
cell_list_def = [
initialize,
show_model_templates,
demo_modes,
demo_name_annot_complexity,
###demo_model_idependencies,
demo_single_add,
demo_ambiguity,
demo_conflicting_evidence,
demo_annot_idependence_overlap,
]
def format_cell(cell):
if ut.is_funclike(cell):
header = '# ' + ut.to_title_caps(ut.get_funcname(cell))
code = (header, ut.get_func_sourcecode(cell, stripdef=True, stripret=True))
else:
code = (None, cell)
return generate_notebook.format_cells(code)
cell_list = ut.flatten([format_cell(cell) for cell in cell_list_def])
nbstr = generate_notebook.make_notebook(cell_list)
print('nbstr = %s' % (nbstr,))
fpath = 'demobayes.ipynb'
ut.writeto(fpath, nbstr)
ut.startfile(fpath)
def plot_gps_html(gps_list):
""" Plots gps coordinates on a map projection
InstallBasemap:
sudo apt-get install libgeos-dev
pip install git+https://github.com/matplotlib/basemap
http://matplotlib.org/basemap/users/examples.html
pip install gmplot
sudo apt-get install netcdf-bin
sudo apt-get install libnetcdf-dev
pip install netCDF4
Ignore:
pip install git+git://github.com/myuser/foo.git@v123
Example:
>>> # DISABLE_DOCTEST
>>> from wbia.algo.preproc.preproc_occurrence import * # NOQA
>>> import wbia
>>> ibs = wbia.opendb(defaultdb='testdb1')
>>> images = ibs.images()
>>> # Setup GPS points to draw
>>> print('Setup GPS points')
>>> gps_list_ = np.array(images.gps2)
>>> unixtime_list_ = np.array(images.unixtime2)
>>> has_gps = np.all(np.logical_not(np.isnan(gps_list_)), axis=1)
>>> has_unixtime = np.logical_not(np.isnan(unixtime_list_))
>>> isvalid = np.logical_and(has_gps, has_unixtime)
>>> gps_list = gps_list_.compress(isvalid, axis=0)
>>> unixtime_list = unixtime_list_.compress(isvalid) # NOQA
>>> plot_image_gps(gps_list)
"""
import wbia.plottool as pt
import gmplot
import matplotlib as mpl
import vtool as vt
pt.qt4ensure()
lat = gps_list.T[0]
lon = gps_list.T[1]
# Get extent of
bbox = vt.bbox_from_verts(gps_list)
centerx, centery = vt.bbox_center(bbox)
gmap = gmplot.GoogleMapPlotter(centerx, centery, 13)
color = mpl.colors.rgb2hex(pt.ORANGE)
gmap.scatter(lat, lon, color=color, size=100, marker=False)
gmap.draw('mymap.html')
ut.startfile('mymap.html')
def _on_doubleclick(wgt, qtindex):
print('[wgt] _on_doubleclick: ')
col = qtindex.column()
if wgt.api.col_edit_list[col]:
print('do nothing special for editable columns')
return
model = qtindex.model()
colname = model.get_header_name(col)
if colname.endswith('fpath'):
print('showing fpath')
fpath = model.get_header_data(colname, qtindex)
ut.startfile(fpath)
def _on_doubleclick(wgt, qtindex):
print('[wgt] _on_doubleclick: ')
col = qtindex.column()
if wgt.api.col_edit_list[col]:
print('do nothing special for editable columns')
return
model = qtindex.model()
colname = model.get_header_name(col)
if colname.endswith('fpath'):
print('showing fpath')
fpath = model.get_header_data(colname, qtindex)
ut.startfile(fpath)
def render_latex_text(input_text,
nest_in_doc=False,
appname='utool',
verbose=None):
""" testing function """
import utool as ut
if verbose is None:
verbose = ut.VERBOSE
dpath = ut.get_app_resource_dir(appname)
# put a latex framgent in a full document
print(input_text)
pdf_fpath = ut.compile_latex_text(input_text, dpath=dpath, verbose=verbose)
ut.startfile(pdf_fpath)
return pdf_fpath
def render_latex_text(input_text, nest_in_doc=False, preamb_extra=None,
appname='utool', verbose=None):
""" compiles latex and shows the result """
import utool as ut
if verbose is None:
verbose = ut.VERBOSE
dpath = ut.ensure_app_resource_dir(appname, 'latex_tmp')
# put a latex framgent in a full document
# print(input_text)
fname = 'temp_render_latex'
pdf_fpath = ut.compile_latex_text(
input_text, dpath=dpath, fname=fname, preamb_extra=preamb_extra,
verbose=verbose)
ut.startfile(pdf_fpath)
return pdf_fpath
def customize_figure(fig, docla):
#if 'user_stat_list' not in fig.__dict__.keys() or docla:
# fig.user_stat_list = []
# fig.user_notes = []
fig.df2_closed = False
fig.pt_save = functools.partial(save_figure, fig=fig)
fig.pt_save_and_view = lambda *args, **kwargs: ut.startfile(fig.pt_save(*args, **kwargs))
def delayed_screenshot_func():
if done[0] == 500:
#back.mainwin.menubar.triggered.emit(back.mainwin.menuFile)
print('Mouseclick')
QTest.mouseClick(back.mainwin.menuFile, Qt.LeftButton)
# This works
#QTest.mouseClick(back.front.import_button, Qt.LeftButton)
if done[0] == 1:
timer2.stop()
print('screengrab to %r' % (fpath,))
screenimg = QPixmap.grabWindow(back.mainwin.winId())
screenimg.save(fpath, 'jpg')
ut.startfile(fpath)
print('lub dub2')
done[0] -= 1
return None
def delayed_screenshot_func():
if done[0] == 500:
#back.mainwin.menubar.triggered.emit(back.mainwin.menuFile)
print('Mouseclick')
QTest.mouseClick(back.mainwin.menuFile, Qt.LeftButton)
# This works
#QTest.mouseClick(back.front.import_button, Qt.LeftButton)
if done[0] == 1:
timer2.stop()
print('screengrab to %r' % (fpath,))
screenimg = QPixmap.grabWindow(back.mainwin.winId())
screenimg.save(fpath, 'jpg')
ut.startfile(fpath)
print('lub dub2')
done[0] -= 1
return None
def customize_figure(fig, docla):
#if 'user_stat_list' not in fig.__dict__.keys() or docla:
# fig.user_stat_list = []
# fig.user_notes = []
fig.df2_closed = False
fig.pt_save = functools.partial(save_figure, fig=fig)
fig.pt_save_and_view = lambda *args, **kwargs: ut.startfile(
fig.pt_save(*args, **kwargs))
def draw_serial(ChapX, expt_name, dbnames, *args):
dbnames = ut.smart_cast(dbnames, list)
mpl.rcParams.update(TMP_RC)
for dbname in dbnames:
self = ChapX(dbname)
if expt_name == 'all':
self.draw_all()
else:
draw_func = getattr(self, 'draw_' + expt_name, None)
if draw_func is None:
draw_func = getattr(self, 'write_' + expt_name, None)
if draw_func is None:
raise ValueError('Cannot find a way to draw ' + expt_name)
fpath = draw_func(*args)
if ut.get_argflag('--diskshow'):
if isinstance(fpath, six.text_type):
ut.startfile(fpath)
elif fpath is not None:
fpath_list = fpath
for fpath in fpath_list:
ut.startfile(fpath)
def visualize():
import networkx as nx
import torch
from torch.autograd import Variable
def make_nx(var, params):
param_map = {id(v): k for k, v in params.items()}
print(param_map)
node_attr = dict(style='filled',
shape='box',
align='left',
fontsize='12',
ranksep='0.1',
height='0.2')
seen = set()
G = nx.DiGraph()
def size_to_str(size):
return '(' + (', ').join(['%d' % v for v in size]) + ')'
def build_graph(var):
if var not in seen:
if torch.is_tensor(var):
G.add_node(id(var),
label=size_to_str(var.size()),
fillcolor='orange',
**node_attr)
elif hasattr(var, 'variable'):
u = var.variable
node_name = '%s\n %s' % (param_map.get(
id(u)), size_to_str(u.size()))
G.add_node(id(var),
label=node_name,
fillcolor='lightblue',
**node_attr)
else:
G.add_node(id(var),
label=str(type(var).__name__),
**node_attr)
seen.add(var)
if hasattr(var, 'next_functions'):
for u in var.next_functions:
if u[0] is not None:
G.add_edge(id(u[0]), id(var))
build_graph(u[0])
if hasattr(var, 'saved_tensors'):
for t in var.saved_tensors:
G.add_edge(id(t), id(var))
build_graph(t)
build_graph(var.grad_fn)
return G
# inputs = torch.randn(1, 3, 224, 224)
# resnet18 = models.resnet18()
# y = resnet18(Variable(inputs))
inputs = torch.randn(1, 3, 224, 224)
# model = torchvision.models.resnet18()
model = torchvision.models.resnet50()
model = Siamese()
# y = model(Variable(inputs))
y = model(Variable(inputs), Variable(inputs))
params = model.state_dict()
G = make_nx(y, params)
import plottool as pt
pt.dump_nx_ondisk(G, './pytorch_network.png')
ut.startfile('./pytorch_network.png')
def draw_twoday_count(ibs, visit_info_list_):
import copy
visit_info_list = copy.deepcopy(visit_info_list_)
aids_day1, aids_day2 = ut.take_column(visit_info_list_, 'aids')
nids_day1, nids_day2 = ut.take_column(visit_info_list_, 'unique_nids')
resight_nids = ut.isect(nids_day1, nids_day2)
if False:
# HACK REMOVE DATA TO MAKE THIS FASTER
num = 20
for info in visit_info_list:
non_resight_nids = list(set(info['unique_nids']) - set(resight_nids))
sample_nids2 = non_resight_nids[0:num] + resight_nids[:num]
info['grouped_aids'] = ut.dict_subset(info['grouped_aids'], sample_nids2)
info['unique_nids'] = sample_nids2
# Build a graph of matches
if False:
debug = False
for info in visit_info_list:
edges = []
grouped_aids = info['grouped_aids']
aids_list = list(grouped_aids.values())
ams_list = ibs.get_annotmatch_rowids_in_cliques(aids_list)
aids1_list = ibs.unflat_map(ibs.get_annotmatch_aid1, ams_list)
aids2_list = ibs.unflat_map(ibs.get_annotmatch_aid2, ams_list)
for ams, aids, aids1, aids2 in zip(ams_list, aids_list, aids1_list, aids2_list):
edge_nodes = set(aids1 + aids2)
##if len(edge_nodes) != len(set(aids)):
# #print('--')
# #print('aids = %r' % (aids,))
# #print('edge_nodes = %r' % (edge_nodes,))
bad_aids = edge_nodes - set(aids)
if len(bad_aids) > 0:
print('bad_aids = %r' % (bad_aids,))
unlinked_aids = set(aids) - edge_nodes
mst_links = list(ut.itertwo(list(unlinked_aids) + list(edge_nodes)[:1]))
bad_aids.add(None)
user_links = [(u, v) for (u, v) in zip(aids1, aids2) if u not in bad_aids and v not in bad_aids]
new_edges = mst_links + user_links
new_edges = [(int(u), int(v)) for u, v in new_edges if u not in bad_aids and v not in bad_aids]
edges += new_edges
info['edges'] = edges
# Add edges between days
grouped_aids1, grouped_aids2 = ut.take_column(visit_info_list, 'grouped_aids')
nids_day1, nids_day2 = ut.take_column(visit_info_list, 'unique_nids')
resight_nids = ut.isect(nids_day1, nids_day2)
resight_aids1 = ut.take(grouped_aids1, resight_nids)
resight_aids2 = ut.take(grouped_aids2, resight_nids)
#resight_aids3 = [list(aids1) + list(aids2) for aids1, aids2 in zip(resight_aids1, resight_aids2)]
ams_list = ibs.get_annotmatch_rowids_between_groups(resight_aids1, resight_aids2)
aids1_list = ibs.unflat_map(ibs.get_annotmatch_aid1, ams_list)
aids2_list = ibs.unflat_map(ibs.get_annotmatch_aid2, ams_list)
between_edges = []
for ams, aids1, aids2, rawaids1, rawaids2 in zip(ams_list, aids1_list, aids2_list, resight_aids1, resight_aids2):
link_aids = aids1 + aids2
rawaids3 = rawaids1 + rawaids2
badaids = ut.setdiff(link_aids, rawaids3)
assert not badaids
user_links = [(int(u), int(v)) for (u, v) in zip(aids1, aids2)
if u is not None and v is not None]
# HACK THIS OFF
user_links = []
if len(user_links) == 0:
# Hack in an edge
between_edges += [(rawaids1[0], rawaids2[0])]
else:
between_edges += user_links
assert np.all(0 == np.diff(np.array(ibs.unflat_map(ibs.get_annot_nids, between_edges)), axis=1))
import plottool_ibeis as pt
import networkx as nx
#pt.qt4ensure()
#len(list(nx.connected_components(graph1)))
#print(ut.graph_info(graph1))
# Layout graph
layoutkw = dict(
prog='neato',
draw_implicit=False, splines='line',
#splines='curved',
#splines='spline',
#sep=10 / 72,
#prog='dot', rankdir='TB',
)
def translate_graph_to_origin(graph):
x, y, w, h = ut.get_graph_bounding_box(graph)
ut.translate_graph(graph, (-x, -y))
def stack_graphs(graph_list, vert=False, pad=None):
graph_list_ = [g.copy() for g in graph_list]
for g in graph_list_:
translate_graph_to_origin(g)
bbox_list = [ut.get_graph_bounding_box(g) for g in graph_list_]
if vert:
dim1 = 3
dim2 = 2
else:
dim1 = 2
dim2 = 3
dim1_list = np.array([bbox[dim1] for bbox in bbox_list])
dim2_list = np.array([bbox[dim2] for bbox in bbox_list])
if pad is None:
pad = np.mean(dim1_list) / 2
offset1_list = ut.cumsum([0] + [d + pad for d in dim1_list[:-1]])
max_dim2 = max(dim2_list)
offset2_list = [(max_dim2 - d2) / 2 for d2 in dim2_list]
if vert:
t_xy_list = [(d2, d1) for d1, d2 in zip(offset1_list, offset2_list)]
else:
t_xy_list = [(d1, d2) for d1, d2 in zip(offset1_list, offset2_list)]
for g, t_xy in zip(graph_list_, t_xy_list):
ut.translate_graph(g, t_xy)
nx.set_node_attributes(g, name='pin', values='true')
new_graph = nx.compose_all(graph_list_)
#pt.show_nx(new_graph, layout='custom', node_labels=False, as_directed=False) # NOQA
return new_graph
# Construct graph
for count, info in enumerate(visit_info_list):
graph = nx.Graph()
edges = [(int(u), int(v)) for u, v in info['edges']
if u is not None and v is not None]
graph.add_edges_from(edges, attr_dict={'zorder': 10})
nx.set_node_attributes(graph, name='zorder', values=20)
# Layout in neato
_ = pt.nx_agraph_layout(graph, inplace=True, **layoutkw) # NOQA
# Extract components and then flatten in nid ordering
ccs = list(nx.connected_components(graph))
root_aids = []
cc_graphs = []
for cc_nodes in ccs:
cc = graph.subgraph(cc_nodes)
try:
root_aids.append(list(ut.nx_source_nodes(cc.to_directed()))[0])
except nx.NetworkXUnfeasible:
root_aids.append(list(cc.nodes())[0])
cc_graphs.append(cc)
root_nids = ibs.get_annot_nids(root_aids)
nid2_graph = dict(zip(root_nids, cc_graphs))
resight_nids_ = set(resight_nids).intersection(set(root_nids))
noresight_nids_ = set(root_nids) - resight_nids_
n_graph_list = ut.take(nid2_graph, sorted(noresight_nids_))
r_graph_list = ut.take(nid2_graph, sorted(resight_nids_))
if len(n_graph_list) > 0:
n_graph = nx.compose_all(n_graph_list)
_ = pt.nx_agraph_layout(n_graph, inplace=True, **layoutkw) # NOQA
n_graphs = [n_graph]
else:
n_graphs = []
r_graphs = [stack_graphs(chunk) for chunk in ut.ichunks(r_graph_list, 100)]
if count == 0:
new_graph = stack_graphs(n_graphs + r_graphs, vert=True)
else:
new_graph = stack_graphs(r_graphs[::-1] + n_graphs, vert=True)
#pt.show_nx(new_graph, layout='custom', node_labels=False, as_directed=False) # NOQA
info['graph'] = new_graph
graph1_, graph2_ = ut.take_column(visit_info_list, 'graph')
if False:
_ = pt.show_nx(graph1_, layout='custom', node_labels=False, as_directed=False) # NOQA
_ = pt.show_nx(graph2_, layout='custom', node_labels=False, as_directed=False) # NOQA
graph_list = [graph1_, graph2_]
twoday_graph = stack_graphs(graph_list, vert=True, pad=None)
nx.set_node_attributes(twoday_graph, name='pin', values='true')
if debug:
ut.nx_delete_None_edge_attr(twoday_graph)
ut.nx_delete_None_node_attr(twoday_graph)
print('twoday_graph(pre) info' + ut.repr3(ut.graph_info(twoday_graph), nl=2))
# Hack, no idea why there are nodes that dont exist here
between_edges_ = [edge for edge in between_edges
if twoday_graph.has_node(edge[0]) and twoday_graph.has_node(edge[1])]
twoday_graph.add_edges_from(between_edges_, attr_dict={'alpha': .2, 'zorder': 0})
ut.nx_ensure_agraph_color(twoday_graph)
layoutkw['splines'] = 'line'
layoutkw['prog'] = 'neato'
agraph = pt.nx_agraph_layout(twoday_graph, inplace=True, return_agraph=True, **layoutkw)[-1] # NOQA
if False:
fpath = ut.truepath('~/ggr_graph.png')
agraph.draw(fpath)
ut.startfile(fpath)
if debug:
print('twoday_graph(post) info' + ut.repr3(ut.graph_info(twoday_graph)))
_ = pt.show_nx(twoday_graph, layout='custom', node_labels=False, as_directed=False) # NOQA
def autogen_ipynb(ibs, launch=None, run=None):
r"""
Autogenerates standard IBEIS Image Analysis IPython notebooks.
CommandLine:
python -m wbia autogen_ipynb --run --db lynx
python -m wbia autogen_ipynb --run --db lynx
python -m wbia autogen_ipynb --ipynb --db PZ_MTEST -p :proot=smk,num_words=64000 default
python -m wbia autogen_ipynb --ipynb --db PZ_MTEST --asreport
python -m wbia autogen_ipynb --ipynb --db PZ_MTEST --noexample --withtags
python -m wbia autogen_ipynb --ipynb --db PZ_MTEST
python -m wbia autogen_ipynb --ipynb --db STS_SandTigers
python -m wbia autogen_ipynb --db PZ_MTEST
# TODO: Add support for dbdir to be specified
python -m wbia autogen_ipynb --db ~/work/PZ_MTEST
python -m wbia autogen_ipynb --ipynb --db Oxford -a default:qhas_any=\(query,\),dpername=1,exclude_reference=True,dminqual=good
python -m wbia autogen_ipynb --ipynb --db PZ_MTEST -a default -t best:lnbnn_normalizer=[None,normlnbnn-test]
python -m wbia.templates.generate_notebook --exec-autogen_ipynb --db wd_peter_blinston --ipynb
python -m wbia autogen_ipynb --db PZ_Master1 --ipynb
python -m wbia autogen_ipynb --db PZ_Master1 -a timectrl:qindex=0:100 -t best best:normsum=True --ipynb --noexample
python -m wbia autogen_ipynb --db PZ_Master1 -a timectrl --run
jupyter-notebook Experiments-lynx.ipynb
killall python
python -m wbia autogen_ipynb --db humpbacks --ipynb -t default:proot=BC_DTW -a default:has_any=hasnotch
python -m wbia autogen_ipynb --db humpbacks --ipynb -t default:proot=BC_DTW default:proot=vsmany -a default:has_any=hasnotch,mingt=2,qindex=0:50 --noexample
python -m wbia autogen_ipynb --db testdb_curvrank --ipynb -t default:proot=CurvRankDorsal
python -m wbia autogen_ipynb --db testdb_curvrank --ipynb -t default:proot=CurvRankFluke
python -m wbia autogen_ipynb --db PW_Master --ipynb -t default:proot=CurvRankDorsal
python -m wbia autogen_ipynb --db testdb_identification --ipynb -t default:proot=Deepsense
Ignore:
python -m wbia autogen_ipynb --db WS_ALL
Example:
>>> # SCRIPT
>>> from wbia.templates.generate_notebook import * # NOQA
>>> import wbia
>>> ibs = wbia.opendb(defaultdb='testdb1')
>>> result = autogen_ipynb(ibs)
>>> print(result)
"""
dbname = ibs.get_dbname()
fname = 'Experiments-' + dbname
nb_fpath = fname + '.ipynb'
if ut.get_argflag('--cells'):
notebook_cells = make_wbia_cell_list(ibs)
print('\n# ---- \n'.join(notebook_cells))
return
# TODO: Add support for dbdir to be specified
notebook_str = make_wbia_notebook(ibs)
ut.writeto(nb_fpath, notebook_str)
run = ut.get_argflag('--run') if run is None else run
launch = launch if launch is not None else ut.get_argflag('--ipynb')
if run:
run_nb = ut.run_ipython_notebook(notebook_str)
output_fpath = ut.export_notebook(run_nb, fname)
ut.startfile(output_fpath)
elif launch:
command = ' '.join(
[
'jupyter-notebook',
'--NotebookApp.iopub_data_rate_limit=10000000',
'--NotebookApp.token=',
nb_fpath,
]
)
ut.cmd2(command, detatch=True, verbose=True)
else:
print('notebook_str =\n%s' % (notebook_str,))
