def print_feat_stats(kpts, vecs):
assert len(vecs) == len(kpts), 'disagreement'
print('keypoints and vecs agree')
flat_kpts = np.vstack(kpts)
num_kpts = list(map(len, kpts))
kpt_scale = vt.get_scales(flat_kpts)
num_kpts_stats = ut.get_stats(num_kpts)
scale_kpts_stats = ut.get_stats(kpt_scale)
print('Number of ' + prefix + ' keypoints: ' + ut.repr3(num_kpts_stats, nl=0, precision=2))
print('Scale of ' + prefix + ' keypoints: ' + ut.repr3(scale_kpts_stats, nl=0, precision=2))
def __init__(self, qdup_pos_map={}, ddup_pos_map={}):
message = ('Some UUIDs are specified more than once at positions:\n'
'duplicate_data_uuids=%s\n'
'duplicate_query_uuids=%s\n') % (
ut.repr3(qdup_pos_map, nl=1),
ut.repr3(ddup_pos_map, nl=1))
qdup_pos_map_ = { str(k): v for k, v in qdup_pos_map.iteritems() }
ddup_pos_map_ = { str(k): v for k, v in ddup_pos_map.iteritems() }
rawreturn = {
'qdup_pos_map' : qdup_pos_map_,
'ddup_pos_map' : ddup_pos_map_,
}
code = 601
super(DuplicateUUIDException, self).__init__(message, rawreturn, code)
def _test_indent_print():
# Indent test code doesnt work in doctest blocks.
import utool as ut
flag = ut.ensure_logging()
print('Checking indent. Should have none')
with ut.Indenter('[INDENT] '):
print('Checking indent. Should be indented')
print('Should no longer be indented')
text = ut.get_current_log_text()
# The last line might sometimes be empty or not.
# Not sure.
# New hack: had to put in stride. Seems like logs get written
# with two line breaks now
last_lines = text.split('\n')[-8::2]
if last_lines[-1] != '':
assert False, 'DEV ERROR. REMOVE FIRST LINE INSTEAD OF LAST'
last_lines = last_lines[:-1]
#print('last_lines = %r' % (ut.repr3(last_lines)))
try:
assert last_lines[0].find('[INDENT] ') == -1, last_lines[0]
assert last_lines[1].find('[INDENT] ') >= 0, 'did not indent %r' % (last_lines[1],)
assert last_lines[2].find('[INDENT] ') == -1, last_lines[2]
except AssertionError:
print('Error. Last 3 lines')
print(ut.repr3(last_lines))
raise
if not flag:
ut.stop_logging()
def make_ibeis_cell_list(ibs):
cell_template_list = get_default_cell_template_list(ibs)
autogen_str = make_autogen_str()
dbname = ibs.get_dbname()
#if ut.get_argflag('--hacktestscore'):
# annotconfig_list_body = ut.codeblock(
# '''
# 'timectrl',
# '''
# )
#else:
default_acfgstr = ut.get_argval('-a', type_=str, default='default:is_known=True')
annotconfig_list_body = ut.codeblock(
ut.repr2(default_acfgstr) + '\n' +
ut.codeblock('''
# See ibeis/expt/annotation_configs.py for names of annot configuration options
#'default:has_any=(query,),dpername=1,exclude_reference=True',
#'default:is_known=True',
#'default:qsame_encounter=True,been_adjusted=True,excluderef=True'
#'default:qsame_encounter=True,been_adjusted=True,excluderef=True,qsize=10,dsize=20',
#'default:require_timestamp=True,min_timedelta=3600',
#'default:species=primary',
#'timectrl:',
#'timectrl:been_adjusted=True,dpername=3',
#'timectrl:qsize=10,dsize=20',
#'unctrl:been_adjusted=True',
''')
)
#if ut.get_argflag('--hacktestscore'):
# pipeline_list_body = ut.codeblock(
# '''
# # See ibeis/algo/Config.py for names of pipeline config options
# 'default:lnbnn_on=True,bar_l2_on=False,normonly_on=False,fg_on=True',
# 'default:lnbnn_on=False,bar_l2_on=True,normonly_on=False,fg_on=True',
# 'default:lnbnn_on=False,bar_l2_on=False,normonly_on=True,fg_on=True',
# 'default:lnbnn_on=True,bar_l2_on=False,normonly_on=False,fg_on=False',
# 'default:lnbnn_on=False,bar_l2_on=True,normonly_on=False,fg_on=False',
# 'default:lnbnn_on=False,bar_l2_on=False,normonly_on=True,fg_on=False',
# '''
# )
#elif True:
default_pcfgstr_list = ut.get_argval(('-t', '-p'), type_=list, default='default')
default_pcfgstr = ut.repr3(default_pcfgstr_list, nobr=True)
pipeline_list_body = ut.codeblock(
default_pcfgstr + '\n' +
ut.codeblock('''
#'default',
#'default:K=1',
#'default:K=1,AI=False',
#'default:K=1,AI=False,QRH=True',
#'default:K=1,RI=True,AI=False',
#'default:K=1,adapteq=True',
#'default:fg_on=[True,False]',
''')
)
locals_ = locals()
_format = partial(format_cells, locals_=locals_)
cell_list = ut.flatten(map(_format, cell_template_list))
return cell_list
def print_tree_struct(*args, **kwargs):
tree_str = (ut.indent(ut.repr3(get_tree_info(*args, **kwargs), nl=1)))
print(tree_str)
#bytes_str = ut.byte_str2(drive.get_total_nbytes(dpath_to_unique_fidx[path]))
#print('path = %r, %s' % (path, bytes_str))
#print(ut.repr3(key_list))
return tree_str
def print_tree(root, path, dpath_to_unique_fidx=dpath_to_unique_fidx, drive=drive, depth=None):
print('path = %r' % (path,))
print(ut.byte_str2(drive.get_total_nbytes(dpath_to_unique_fidx[path])))
path_components = ut.dirsplit(path)
# Navigate to correct spot in tree
current = root
for c in path_components:
current = current[c]
print(ut.repr3(current, truncate=1))
def hello_world(*args, **kwargs):
"""
CommandLine:
python -m ibeis.web.apis --exec-hello_world:0
python -m ibeis.web.apis --exec-hello_world:1
Example:
>>> # WEB_DOCTEST
>>> from ibeis.web.app import * # NOQA
>>> import ibeis
>>> web_ibs = ibeis.opendb_bg_web(browser=True, url_suffix='/api/test/helloworld/?test0=0') # start_job_queue=False)
>>> print('Server will run until control c')
>>> #web_ibs.terminate2()
Example1:
>>> # WEB_DOCTEST
>>> from ibeis.web.app import * # NOQA
>>> import ibeis
>>> import requests
>>> import ibeis
>>> web_ibs = ibeis.opendb_bg_web('testdb1', start_job_queue=False)
>>> domain = 'http://127.0.0.1:5000'
>>> url = domain + '/api/test/helloworld/?test0=0'
>>> payload = {
>>> 'test1' : 'test1',
>>> 'test2' : None, # NOTICE test2 DOES NOT SHOW UP
>>> }
>>> resp = requests.post(url, data=payload)
>>> print(resp)
>>> web_ibs.terminate2()
"""
print('+------------ HELLO WORLD ------------')
print('Args: %r' % (args,))
print('Kwargs: %r' % (kwargs,))
print('request.args: %r' % (request.args,))
print('request.form: %r' % (request.form,))
print('request.url; %r' % (request.url,))
print('request.environ: %s' % (ut.repr3(request.environ),))
print('request: %s' % (ut.repr3(request.__dict__),))
print('L____________ HELLO WORLD ____________')
def make_ibeis_cell_list(ibs):
cell_template_list = get_default_cell_template_list(ibs)
autogen_str = ut.make_autogen_str()
dbname = ibs.get_dbname()
default_acfgstr = ut.get_argval('-a', type_=str, default='default:is_known=True')
asreport = ut.get_argflag('--asreport')
default_pcfgstr_list = ut.get_argval(('-t', '-p'), type_=list, default='default')
default_pcfgstr = ut.repr3(default_pcfgstr_list, nobr=True)
if asreport:
annotconfig_list_body = ut.codeblock(
ut.repr2(default_acfgstr) )
pipeline_list_body = ut.codeblock(
default_pcfgstr
)
else:
annotconfig_list_body = ut.codeblock(
ut.repr2(default_acfgstr) + '\n' +
ut.codeblock('''
# See ibeis/expt/annotation_configs.py for names of annot configuration options
#'default:has_any=(query,),dpername=1,exclude_reference=True',
#'default:is_known=True',
#'default:qsame_imageset=True,been_adjusted=True,excluderef=True,qsize=10,dsize=20',
#'default:require_timestamp=True,min_timedelta=3600',
#'default:species=primary',
#'timectrl:',
#'unctrl:been_adjusted=True',
''')
)
pipeline_list_body = ut.codeblock(
default_pcfgstr + '\n' +
ut.codeblock('''
#'default',
#'default:K=1,AI=False,QRH=True',
#'default:K=1,RI=True,AI=False',
#'default:K=1,adapteq=True',
#'default:fg_on=[True,False]',
''')
)
locals_ = locals()
_format = partial(ut.format_cells, locals_=locals_)
cell_list = ut.flatten(map(_format, cell_template_list))
return cell_list
def collector_loop(dbdir):
"""
Service that stores completed algorithm results
"""
import ibeis
update_proctitle('collector_loop')
print = partial(ut.colorprint, color='yellow')
with ut.Indenter('[collect] '):
collect_rout_sock = ctx.socket(zmq.ROUTER)
collect_rout_sock.setsockopt_string(zmq.IDENTITY, 'collect.ROUTER')
collect_rout_sock.connect(collect_url2)
if VERBOSE_JOBS:
print('connect collect_url2 = %r' % (collect_url2,))
ibs = ibeis.opendb(dbdir=dbdir, use_cache=False, web=False)
# shelve_path = join(ut.get_shelves_dir(appname='ibeis'), 'engine')
shelve_path = ibs.get_shelves_path()
ut.delete(shelve_path)
ut.ensuredir(shelve_path)
collecter_data = {}
awaiting_data = {}
try:
while True:
# several callers here
# CALLER: collector_notify
# CALLER: collector_store
# CALLER: collector_request_status
# CALLER: collector_request_result
idents, collect_request = rcv_multipart_json(collect_rout_sock, print=print)
try:
reply = on_collect_request(collect_request, collecter_data,
awaiting_data, shelve_path)
except Exception as ex:
print(ut.repr3(collect_request))
ut.printex(ex, 'ERROR in collection')
send_multipart_json(collect_rout_sock, idents, reply)
except KeyboardInterrupt:
print('Caught ctrl+c in collector loop. Gracefully exiting')
if VERBOSE_JOBS:
print('Exiting collector')
def _wrapper(*args, **kwargs):
try:
return func(*args, **kwargs)
except Exception as ex:
import utool as ut
ut.printex(ex)
import inspect # NOQA
trace = inspect.trace()
locals_ = trace[-1][0].f_locals
print('-- <TRACE LOCALS> --')
for level, t in enumerate(trace[1:]):
frame = t[0]
locals_ = frame.f_locals
local_repr_dict = {key: ut.trunc_repr(val)
for key, val in locals_.items()}
print('LOCALS LEVEL %d' % (level,))
print(ut.repr3(local_repr_dict, strvals=True, nl=1))
print('-- </TRACE LOCALS> --')
#import utool
#utool.embed()
raise
def graph_info(graph, verbose=False):
import utool as ut
node_attrs = list(graph.node.values())
edge_attrs = list(ut.take_column(graph.edges(data=True), 2))
node_attr_hist = ut.dict_hist(ut.flatten([attr.keys() for attr in node_attrs]))
edge_attr_hist = ut.dict_hist(ut.flatten([attr.keys() for attr in edge_attrs]))
node_type_hist = ut.dict_hist(list(map(type, graph.nodes())))
info_dict = ut.odict([
('directed', graph.is_directed()),
('multi', graph.is_multigraph()),
('num_nodes', len(graph)),
('num_edges', len(list(graph.edges()))),
('edge_attr_hist', ut.sort_dict(edge_attr_hist)),
('node_attr_hist', ut.sort_dict(node_attr_hist)),
('node_type_hist', ut.sort_dict(node_type_hist)),
('graph_attrs', graph.graph),
('graph_name', graph.name),
])
#unique_attrs = ut.map_dict_vals(ut.unique, ut.dict_accum(*node_attrs))
#ut.dict_isect_combine(*node_attrs))
#[list(attrs.keys())]
if verbose:
print(ut.repr3(info_dict))
return info_dict
def get_toy_data_1vM(num_annots, num_names=None, **kwargs):
r"""
Args:
num_annots (int):
num_names (int): (default = None)
Kwargs:
initial_aids, initial_nids, nid_sequence, seed
Returns:
tuple: (pair_list, feat_list)
CommandLine:
python -m ibeis.algo.hots.demobayes --exec-get_toy_data_1vM --show
Example:
>>> # DISABLE_DOCTEST
>>> from ibeis.algo.hots.demobayes import * # NOQA
>>> num_annots = 1000
>>> num_names = 40
>>> get_toy_data_1vM(num_annots, num_names)
>>> ut.quit_if_noshow()
>>> import plottool as pt
>>> ut.show_if_requested()
"""
import vtool as vt
tup_ = get_toy_annots(num_annots, num_names, **kwargs)
aids, nids, aids1, nids1, all_aids, all_nids = tup_
rng = vt.ensure_rng(None)
# Test a simple SVM classifier
nid2_nexemp = ut.dict_hist(nids1)
aid2_nid = dict(zip(aids, nids))
ut.fix_embed_globals()
#def add_to_globals(globals_, subdict):
# globals_.update(subdict)
unique_nids = list(nid2_nexemp.keys())
def annot_to_class_feats2(aid, aid2_nid, top=None):
pair_list = []
score_list = []
nexemplar_list = []
for nid in unique_nids:
label = (aid2_nid[aid] == nid)
num_exemplars = nid2_nexemp.get(nid, 0)
if num_exemplars == 0:
continue
params = toy_params[label]
mu, sigma = ut.dict_take(params, ['mu', 'sigma'])
score_ = rng.normal(mu, sigma, size=num_exemplars).max()
score = np.clip(score_, 0, np.inf)
pair_list.append((aid, nid))
score_list.append(score)
nexemplar_list.append(num_exemplars)
rank_list = ut.argsort(score_list, reverse=True)
feat_list = np.array([score_list, rank_list, nexemplar_list]).T
sortx = np.argsort(rank_list)
feat_list = feat_list.take(sortx, axis=0)
pair_list = np.array(pair_list).take(sortx, axis=0)
if top is not None:
feat_list = feat_list[:top]
pair_list = pair_list[0:top]
return pair_list, feat_list
toclass_features = [annot_to_class_feats2(aid, aid2_nid, top=5) for aid in aids]
aidnid_pairs = np.vstack(ut.get_list_column(toclass_features, 0))
feat_list = np.vstack(ut.get_list_column(toclass_features, 1))
score_list = feat_list.T[0:1].T
lbl_list = [aid2_nid[aid] == nid for aid, nid in aidnid_pairs]
from sklearn import svm
#clf1 = svm.LinearSVC()
print('Learning classifiers')
clf3 = svm.SVC()
clf3.fit(feat_list, lbl_list)
clf1 = svm.LinearSVC()
clf1.fit(score_list, lbl_list)
# Score new annots against the training database
tup_ = get_toy_annots(num_annots * 2, num_names, initial_aids=all_aids, initial_nids=all_nids)
aids, nids, aids1, nids1, all_aids, all_nids = tup_
aid2_nid = dict(zip(aids, nids))
toclass_features = [annot_to_class_feats2(aid, aid2_nid) for aid in aids]
aidnid_pairs = np.vstack(ut.get_list_column(toclass_features, 0))
feat_list = np.vstack(ut.get_list_column(toclass_features, 1))
lbl_list = np.array([aid2_nid[aid] == nid for aid, nid in aidnid_pairs])
print('Running tests')
score_list = feat_list.T[0:1].T
tp_feat_list = feat_list[lbl_list]
tn_feat_list = feat_list[~lbl_list]
tp_lbls = lbl_list[lbl_list]
tn_lbls = lbl_list[~lbl_list]
print('num tp: %d' % len(tp_lbls))
print('num fp: %d' % len(tn_lbls))
tp_score_list = score_list[lbl_list]
tn_score_list = score_list[~lbl_list]
print('tp_feat' + ut.repr3(ut.get_stats(tp_feat_list, axis=0), precision=2))
print('tp_feat' + ut.repr3(ut.get_stats(tn_feat_list, axis=0), precision=2))
print('tp_score' + ut.repr2(ut.get_stats(tp_score_list), precision=2))
print('tp_score' + ut.repr2(ut.get_stats(tn_score_list), precision=2))
tp_pred3 = clf3.predict(tp_feat_list)
tn_pred3 = clf3.predict(tn_feat_list)
print((tp_pred3.sum(), tp_pred3.shape))
print((tn_pred3.sum(), tn_pred3.shape))
tp_score3 = clf3.score(tp_feat_list, tp_lbls)
tn_score3 = clf3.score(tn_feat_list, tn_lbls)
tp_pred1 = clf1.predict(tp_score_list)
tn_pred1 = clf1.predict(tn_score_list)
print((tp_pred1.sum(), tp_pred1.shape))
print((tn_pred1.sum(), tn_pred1.shape))
tp_score1 = clf1.score(tp_score_list, tp_lbls)
tn_score1 = clf1.score(tn_score_list, tn_lbls)
print('tp score with rank = %r' % (tp_score3,))
print('tn score with rank = %r' % (tn_score3,))
print('tp score without rank = %r' % (tp_score1,))
print('tn score without rank = %r' % (tn_score1,))
toy_data = {}
return toy_data
def classify_k(cfg={}):
"""
CommandLine:
python -m ibeis.algo.hots.demobayes --exec-classify_k --show --ev :nA=3
python -m ibeis.algo.hots.demobayes --exec-classify_k --show --ev :nA=3,k=1
python -m ibeis.algo.hots.demobayes --exec-classify_k --show --ev :nA=3,k=0 --method=approx
python -m ibeis.algo.hots.demobayes --exec-classify_k --show --ev :nA=10,k=1 --method=approx
Example:
>>> from ibeis.algo.hots.demobayes import * # NOQA
>>> cfg_list = testdata_demo_cfgs()
>>> classify_k(cfg_list[0])
>>> ut.show_if_requested()
"""
cfg = cfg.copy()
num_annots = cfg.pop('num_annots', 3)
num_scores = cfg.pop('num_scores', 2)
num_iter = cfg.pop('k', 0)
nid_sequence = np.array([0, 0, 1, 2, 2, 1, 1])
toy_data = get_toy_data_1v1(num_annots, nid_sequence=nid_sequence)
force_evidence = None
force_evidence = 0
diag_scores, = ut.dict_take(
toy_data, 'diag_scores'.split(', '))
#print('diag_scores = %r' % (diag_scores,))
#diag_labels = pairwise_matches.compress(is_diag)
#diag_pairs = ut.compress(pairwise_aidxs, is_diag)
discr_domain, discr_p_same = learn_prob_score(num_scores)[0:2]
def discretize_scores(scores):
# Assign continuous scores to closest discrete index
score_idxs = np.abs(1 - (discr_domain / scores[:, None])).argmin(axis=1)
return score_idxs
# Careful ordering is important here
score_evidence = discretize_scores(diag_scores)
if force_evidence is not None:
for x in range(len(score_evidence)):
score_evidence[x] = 0
model, evidence, query_results = test_model(
num_annots=num_annots, num_names=num_annots,
num_scores=num_scores,
mode=1,
score_evidence=score_evidence,
p_score_given_same=discr_p_same,
score_basis=discr_domain,
#verbose=True
)
print(query_results['top_assignments'][0])
toy_data1 = toy_data
print('toy_data1 = ' + ut.repr3(toy_data1, nl=1))
num_annots2 = num_annots + 1
score_evidence1 = [None] * len(score_evidence)
full_evidence = score_evidence.tolist()
factor_list = query_results['factor_list']
using_soft = False
if using_soft:
soft_evidence1 = [dict(zip(x.statenames[0], x.values)) for x in factor_list]
for _ in range(num_iter):
print('\n\n ---------- \n\n')
#toy_data1['all_nids'].max() + 1
num_names_gen = len(toy_data1['all_aids']) + 1
num_names_gen = toy_data1['all_nids'].max() + 2
toy_data2 = get_toy_data_1v1(
1, num_names_gen,
initial_aids=toy_data1['all_aids'],
initial_nids=toy_data1['all_nids'],
nid_sequence=nid_sequence)
diag_scores2, = ut.dict_take(
toy_data2, 'diag_scores'.split(', '))
print('toy_data2 = ' + ut.repr3(toy_data2, nl=1))
score_evidence2 = discretize_scores(diag_scores2).tolist()
if force_evidence is not None:
for x in range(len(score_evidence2)):
score_evidence2[x] = force_evidence
print('score_evidence2 = %r' % (score_evidence2,))
if using_soft:
# Demo with soft evidence
model, evidence, query_results2 = test_model(
num_annots=num_annots2, num_names=num_annots2,
num_scores=num_scores,
mode=1,
name_evidence=soft_evidence1,
#score_evidence=score_evidence1 + score_evidence2,
score_evidence=score_evidence2,
p_score_given_same=discr_p_same,
score_basis=discr_domain,
#verbose=True,
hack_score_only=len(score_evidence2),
)
if 1:
# Demo with full evidence
model, evidence, query_results2 = test_model(
num_annots=num_annots2, num_names=num_annots2,
num_scores=num_scores,
mode=1,
score_evidence=full_evidence + score_evidence2,
p_score_given_same=discr_p_same,
score_basis=discr_domain,
verbose=True
)
factor_list2 = query_results2['factor_list']
if using_soft:
soft_evidence1 = [dict(zip(x.statenames[0], x.values)) for x in factor_list2]
score_evidence1 += ([None] * len(score_evidence2))
full_evidence = full_evidence + score_evidence2
num_annots2 += 1
toy_data1 = toy_data2
def on_scroll(self, event):
if self.debug:
print('[pt.a] on_scroll')
print(ut.repr3(event.__dict__))
pass
def demo_bayesnet(cfg={}):
r"""
Make a model that knows who the previous annots are and tries to classify a new annot
CommandLine:
python -m ibeis --tf demo_bayesnet --diskshow --verbose --save demo4.png --dpath . --figsize=20,10 --dpi=128 --clipwhite
python -m ibeis --tf demo_bayesnet --ev :nA=3,Sab=0,Sac=0,Sbc=1
python -m ibeis --tf demo_bayesnet --ev :nA=4,Sab=0,Sac=0,Sbc=1,Sbd=1 --show
python -m ibeis --tf demo_bayesnet --ev :nA=4,Sab=0,Sac=0,Sbc=1,Scd=1 --show
python -m ibeis --tf demo_bayesnet --ev :nA=4,Sab=0,Sac=0,Sbc=1,Sbd=1,Scd=1 --show
python -m ibeis --tf demo_bayesnet --ev :nA=3,Sab=0,Sac=0,Sbc=1
python -m ibeis --tf demo_bayesnet --ev :nA=5,rand_scores=True --show
python -m ibeis --tf demo_bayesnet --ev :nA=4,nS=3,rand_scores=True --show --verbose
python -m ibeis --tf demo_bayesnet --ev :nA=5,nS=2,Na=fred,rand_scores=True --show --verbose
python -m ibeis --tf demo_bayesnet --ev :nA=5,nS=5,Na=fred,rand_scores=True --show --verbose
python -m ibeis --tf demo_bayesnet --ev :nA=4,nS=2,Na=fred,rand_scores=True --show --verbose
python -m ibeis.algo.hots.demobayes --exec-demo_bayesnet \
--ev =:nA=4,Sab=0,Sac=0,Sbc=1 \
:Sbd=1 :Scd=1 :Sbd=1,Scd=1 :Sbd=1,Scd=1,Sad=0 \
--show --present
Example:
>>> # DISABLE_DOCTEST
>>> from ibeis.algo.hots.demobayes import * # NOQA
>>> cfg_list = testdata_demo_cfgs()
>>> print('cfg_list = %r' % (cfg_list,))
>>> for cfg in cfg_list:
>>> demo_bayesnet(cfg)
>>> ut.show_if_requested()
"""
cfg = cfg.copy()
num_annots = cfg.pop('num_annots', 3)
num_names = cfg.pop('num_names', None)
num_scores = cfg.pop('num_scores', 2)
rand_scores = cfg.pop('rand_scores', False)
method = cfg.pop('method', 'bp')
other_evidence = {k: v for k, v in cfg.items() if not k.startswith('_')}
if rand_scores:
#import randomdotorg
#import sys
#r = randomdotorg.RandomDotOrg('ExampleCode')
#seed = int((1 - 2 * r.random()) * sys.maxint)
toy_data = get_toy_data_1v1(num_annots, nid_sequence=[0, 0, 1, 0, 1, 2])
print('toy_data = ' + ut.repr3(toy_data, nl=1))
diag_scores, = ut.dict_take(
toy_data, 'diag_scores'.split(', '))
discr_domain, discr_p_same = learn_prob_score(num_scores)[0:2]
def discretize_scores(scores):
# Assign continuous scores to discrete index
score_idxs = np.abs(1 - (discr_domain / scores[:, None])).argmin(axis=1)
return score_idxs
score_evidence = discretize_scores(diag_scores)
else:
score_evidence = []
discr_p_same = None
discr_domain = None
model, evidence, query_results = test_model(
num_annots=num_annots, num_names=num_names,
num_scores=num_scores,
score_evidence=score_evidence,
mode=1,
other_evidence=other_evidence,
p_score_given_same=discr_p_same,
score_basis=discr_domain,
method=method,
)
def fix_duplicates(drive):
r"""
for every duplicate file passing a (eg avi) filter, remove the file
that is in the smallest directory. On a tie use the smallest dpath.
This will filter all duplicate files in a folder into a single folder.
but... need to look at non-duplicates in that folder and decide if they
should be moved as well. So, should trigger on folders that have at
least 50% duplicate. Might not want to move curated folders.
Example:
cd ~/local/scripts
>>> from register_files import * # NOQA
>>> dpaths = ut.get_argval('--drives', type_=list, default=['E:/'])#'D:/', 'E:/', 'F:/'])
>>> drives = [Drive(root_dpath) for root_dpath in dpaths]
>>> E = drive = drives[0]
>>> #D, E, F = drives
"""
print('Fixing Duplicates in %r' % (drive,))
list_ = drive.fpath_hashX_list
multiindex_dict_ = build_multindex(list_)
duplicate_hashes = [
key for key, val in six.iteritems(multiindex_dict_)
if len(val) > 1
]
duplicate_idxs = ut.dict_take(multiindex_dict_, duplicate_hashes)
unflat_fpaths = ut.list_unflat_take(drive.fpath_list, duplicate_idxs)
# Check if any dups have been removed
still_exists = ut.unflat_map(exists, unflat_fpaths)
unflat_idxs2 = ut.zipcompress(duplicate_idxs, still_exists)
duplicate_idxs = [idxs for idxs in unflat_idxs2 if len(idxs) > 1]
# Look at duplicate files
unflat_fpaths = ut.list_unflat_take(drive.fpath_list, duplicate_idxs)
unflat_sizes = ut.list_unflat_take(drive.fpath_bytes_list, duplicate_idxs)
# Find highly coupled directories
if True:
coupled_dirs = []
for fpaths in unflat_fpaths:
#basedir = ut.longest_existing_path(commonprefix(fpaths))
dirs = sorted(list(map(dirname, fpaths)))
_list = list(range(len(dirs)))
idxs = ut.upper_diag_self_prodx(_list)
coupled_dirs.extend(list(map(tuple, ut.list_unflat_take(dirs, idxs))))
hist_ = ut.dict_hist(coupled_dirs)
coupled_idxs = ut.list_argsort(hist_.values())[::-1]
most_coupled = ut.take(list(hist_.keys()), coupled_idxs[0:100])
print('Coupled fpaths: ' + ut.list_str(most_coupled, nl=True))
print('%d unique files are duplicated' % (len(unflat_sizes),))
#print('Duplicate sizes: ' + ut.list_str(unflat_sizes[0:10], nl=True))
#print('Duplicate fpaths: ' + ut.list_str(unflat_fpaths[0:10], nl=True))
#print('Duplicate fpaths: ' + ut.list_str(unflat_fpaths[0::5], nl=True))
print('Duplicate fpaths: ' + ut.list_str(unflat_fpaths, nl=True))
# Find duplicate directories
dpath_list = list(drive.dpath_to_fidx.keys())
fidxs_list = ut.dict_take(drive.dpath_to_fidx, drive.dpath_list)
#exists_list = list(map(exists, drive.fpath_list))
#unflat_exists = ut.list_unflat_take(exists_list, fidxs_list)
fname_registry = [basename(fpath) for fpath in drive.fpath_list]
unflat_fnames = ut.list_unflat_take(fname_registry, fidxs_list)
def unsorted_list_hash(list_):
return ut.hashstr27(str(sorted(list_)))
unflat_fname_sets = list(map(unsorted_list_hash, ut.ProgIter(unflat_fnames, freq=10000)))
fname_based_duplicate_dpaths = []
multiindex_dict2_ = build_multindex(unflat_fname_sets)
fname_based_duplicate_hashes = [key for key, val in multiindex_dict2_.items() if len(val) > 1]
print('#fname_based_duplicate_dpaths = %r' % (len(fname_based_duplicate_hashes),))
fname_based_duplicate_didxs = ut.dict_take(multiindex_dict2_, fname_based_duplicate_hashes)
fname_based_duplicate_dpaths = ut.list_unflat_take(dpath_list, fname_based_duplicate_didxs)
print(ut.repr3(fname_based_duplicate_dpaths[0:10]))
def show_all_colormaps():
"""
Displays at a 90 degree angle. Weird
FIXME: Remove call to pylab
References:
http://wiki.scipy.org/Cookbook/Matplotlib/Show_colormaps
http://matplotlib.org/examples/color/colormaps_reference.html
Notes:
cmaps = [('Perceptually Uniform Sequential',
['viridis', 'inferno', 'plasma', 'magma']),
('Sequential', ['Blues', 'BuGn', 'BuPu',
'GnBu', 'Greens', 'Greys', 'Oranges', 'OrRd',
'PuBu', 'PuBuGn', 'PuRd', 'Purples', 'RdPu',
'Reds', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd']),
('Sequential (2)', ['afmhot', 'autumn', 'bone', 'cool',
'copper', 'gist_heat', 'gray', 'hot',
'pink', 'spring', 'summer', 'winter']),
('Diverging', ['BrBG', 'bwr', 'coolwarm', 'PiYG', 'PRGn', 'PuOr',
'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn', 'Spectral',
'seismic']),
('Qualitative', ['Accent', 'Dark2', 'Paired', 'Pastel1',
'Pastel2', 'Set1', 'Set2', 'Set3']),
('Miscellaneous', ['gist_earth', 'terrain', 'ocean', 'gist_stern',
'brg', 'CMRmap', 'cubehelix',
'gnuplot', 'gnuplot2', 'gist_ncar',
'nipy_spectral', 'jet', 'rainbow',
'gist_rainbow', 'hsv', 'flag', 'prism'])
]
CommandLine:
python -m plottool.color_funcs --test-show_all_colormaps --show
python -m plottool.color_funcs --test-show_all_colormaps --show --type=Miscellaneous
Example:
>>> # DISABLE_DOCTEST
>>> from plottool.color_funcs import * # NOQA
>>> import plottool as pt
>>> show_all_colormaps()
>>> pt.show_if_requested()
"""
from matplotlib import pyplot as plt
import pylab
import numpy as np
pylab.rc('text', usetex=False)
TRANSPOSE = True
a = np.outer(np.arange(0, 1, 0.01), np.ones(10))
if TRANSPOSE:
a = a.T
pylab.figure(figsize=(10, 5))
if TRANSPOSE:
pylab.subplots_adjust(right=0.8, left=0.05, bottom=0.01, top=0.99)
else:
pylab.subplots_adjust(top=0.8, bottom=0.05, left=0.01, right=0.99)
type_ = ut.get_argval('--type', str, default=None)
if type_ is None:
maps = [m for m in pylab.cm.datad if not m.endswith("_r")]
#maps += cmaps2.__all__
maps.sort()
else:
maps = CMAP_DICT[type_]
print('CMAP_DICT = %s' % (ut.repr3(CMAP_DICT),))
l = len(maps) + 1
for i, m in enumerate(maps):
if TRANSPOSE:
pylab.subplot(l, 1, i + 1)
else:
pylab.subplot(1, l, i + 1)
#pylab.axis("off")
ax = plt.gca()
ax.set_xticks([])
ax.set_yticks([])
#try:
cmap = pylab.get_cmap(m)
#except Exception:
# cmap = getattr(cmaps2, m)
pylab.imshow(a, aspect='auto', cmap=cmap) # , origin="lower")
if TRANSPOSE:
ax.set_ylabel(m, rotation=0, fontsize=10,
horizontalalignment='right', verticalalignment='center')
else:
pylab.title(m, rotation=90, fontsize=10)
def dummy_example_depcacahe():
r"""
CommandLine:
python -m dtool.example_depcache --exec-dummy_example_depcacahe
Example:
>>> # ENABLE_DOCTEST
>>> from dtool.example_depcache import * # NOQA
>>> depc = dummy_example_depcacahe()
>>> ut.show_if_requested()
"""
fname = None
# fname = 'dummy_default_depcache'
fname = ':memory:'
depc = testdata_depc(fname)
tablename = 'fgweight'
# print('[test] fgweight_path =\n%s' % (ut.repr3(depc.get_dependencies(tablename), nl=1),))
# print('[test] keypoint =\n%s' % (ut.repr3(depc.get_dependencies('keypoint'), nl=1),))
# print('[test] descriptor =\n%s' % (ut.repr3(depc.get_dependencies('descriptor'), nl=1),))
# print('[test] spam =\n%s' % (ut.repr3(depc.get_dependencies('spam'), nl=1),))
root_rowids = [5, 3]
desc_rowids = depc.get_rowids('descriptor', root_rowids) # NOQA
table = depc[tablename] # NOQA
#example_getter_methods(depc, 'vsmany', root_rowids)
# example_getter_methods(depc, 'chipmask', root_rowids)
# example_getter_methods(depc, 'keypoint', root_rowids)
# example_getter_methods(depc, 'chip', root_rowids)
test_getters(depc)
#import plottool as pt
# pt.ensure_pylab_qt4()
graph = depc.make_graph() # NOQA
#pt.show_nx(graph)
print('---------- 111 -----------')
# Try testing the algorithm
req = depc.new_request('vsmany', root_rowids, root_rowids, {})
print('req = %r' % (req,))
req.execute()
print('---------- 222 -----------')
cfgdict = {'sver_on': False}
req = depc.new_request('vsmany', root_rowids, root_rowids, cfgdict)
req.execute()
print('---------- 333 -----------')
cfgdict = {'sver_on': False, 'adapt_shape': False}
req = depc.new_request('vsmany', root_rowids, root_rowids, cfgdict)
req.execute()
print('---------- 444 -----------')
req = depc.new_request('vsmany', root_rowids, root_rowids, {})
req.execute()
#ut.InstanceList(
db = list(depc.fname_to_db.values())[0]
#db_list = ut.InstanceList(depc.fname_to_db.values())
#db_list.print_table_csv('config', exclude_columns='config_strid')
print('config table')
column_list, column_names = db.get_table_column_data(tablename,
['config_strid'])
print('\n'.join([ut.hz_str(*list(ut.interleave((r, [', '] * (len(r) - 1)))))
for r in list(zip(*[[ut.repr3(r, nl=2) for r in col] for col in column_list]))]))
return depc
def postload_commands(ibs, back):
"""
Postload commands deal with a specific ibeis database
ibeis --db PZ_MTEST --occur "*All Images" --query 1
ibeis --db PZ_MTEST --occur "*All Images" --query-intra
"""
if ut.NOT_QUIET:
print('\n[main_cmd] postload_commands')
if params.args.view_database_directory:
print('got arg --vdd')
vdd(ibs)
if params.args.set_default_dbdir:
sysres.set_default_dbdir(ibs.get_dbdir())
if params.args.update_query_cfg is not None:
# Set query parameters from command line using the --cfg flag
cfgdict = ut.parse_cfgstr_list(params.args.update_query_cfg)
print('Custom cfgdict specified')
print(ut.dict_str(cfgdict))
ibs.update_query_cfg(**cfgdict)
#print(ibs.cfg.query_cfg.get_cfgstr())
if params.args.edit_notes:
ut.editfile(ibs.get_dbnotes_fpath(ensure=True))
if params.args.delete_cache:
ibs.delete_cache()
if params.args.delete_cache_complete:
ibs.delete_cache(delete_chips=True, delete_imagesets=True)
if params.args.delete_query_cache:
ibs.delete_qres_cache()
if params.args.set_all_species is not None:
ibs._overwrite_all_annot_species_to(params.args.set_all_species)
if params.args.dump_schema:
ibs.db.print_schema()
# DEPRICATE
if params.args.set_notes is not None:
ibs.set_dbnotes(params.args.set_notes)
if params.args.set_aids_as_hard is not None:
aid_list = params.args.set_aids_as_hard
ibs.set_annot_is_hard(aid_list, [True] * len(aid_list))
#/DEPRICATE
if ut.get_argflag('--ipynb'):
back.launch_ipy_notebook()
select_imgsetid = ut.get_argval(('--select-imgsetid', '--imgsetid', '--occur'), None)
if select_imgsetid is not None:
print('\n+ --- CMD SELECT EID=%r ---' % (select_imgsetid,))
# Whoa: this doesnt work. weird.
#back.select_imgsetid(select_imgsetid)
# This might be the root of gui problems
#back.front._change_imageset(select_imgsetid)
back.front.select_imageset_tab(select_imgsetid)
print('L ___ CMD SELECT EID=%r ___\n' % (select_imgsetid,))
# Send commands to GUIBack
if params.args.select_aid is not None:
if back is not None:
try:
ibsfuncs.assert_valid_aids(ibs, (params.args.select_aid,))
except AssertionError:
print('Valid RIDs are: %r' % (ibs.get_valid_aids(),))
raise
back.select_aid(params.args.select_aid)
if params.args.select_gid is not None:
back.select_gid(params.args.select_gid)
if params.args.select_nid is not None:
back.select_nid(params.args.select_nid)
select_name = ut.get_argval('--select-name')
if select_name is not None:
import ibeis.gui.guiheaders as gh
back.ibswgt.select_table_indicies_from_text(gh.NAMES_TREE, select_name,
allow_table_change=True)
if ut.get_argflag(('--intra-occur-query', '--query-intra-occur', '--query-intra')):
back.special_query_funcs['intra_occurrence'](cfgdict={'use_k_padding': False})
qaid_list = ut.get_argval(('--query-aid', '--query'), type_=list, default=None)
if qaid_list is not None:
#qaid_list = params.args.query_aid
# fix stride case
if len(qaid_list) == 1 and isinstance(qaid_list[0], tuple):
qaid_list = list(qaid_list[0])
daids_mode = ut.get_argval('--daids-mode', type_=str, default=const.VS_EXEMPLARS_KEY)
back.compute_queries(qaid_list=qaid_list, daids_mode=daids_mode, ranks_lt=10)
if ut.get_argflag('--inc-query'):
back.incremental_query()
if ut.get_argflag(('--dbinfo', '--display_dbinfo')):
back.display_dbinfo()
pass
aidcmd = ut.get_argval('--aidcmd', default=None)
aid = ut.get_argval('--aid', type_=int, default=1)
if aidcmd:
#aidcmd = 'Interact image'
metadata = ibs.get_annot_lazy_dict(aid)
annot_context_options = metadata['annot_context_options']
aidcmd_dict = dict(annot_context_options)
print('aidcmd_dict = %s' % (ut.repr3(aidcmd_dict),))
command = aidcmd_dict[aidcmd]
command()
#import utool
#utool.embed()
#back.start_web_server_parallel()
if ut.get_argflag('--start-web'):
back.start_web_server_parallel()
screengrab_fpath = ut.get_argval('--screengrab')
if screengrab_fpath:
from guitool.__PYQT__.QtGui import QPixmap
from PyQt4.QtTest import QTest
from PyQt4.QtCore import Qt
fpath = ut.truepath(screengrab_fpath)
import guitool
#ut.embed()
timer2 = guitool.__PYQT__.QtCore.QTimer()
done = [1000]
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
CLICK_FILE_MENU = True
if CLICK_FILE_MENU:
#ut.embed()
#QTest::keyClick(menu, Qt::Key_Down)
pass
timer2.delayed_screenshot_func = delayed_screenshot_func
timer2.timeout.connect(timer2.delayed_screenshot_func)
timer2.start(1)
back.mainwin.timer2 = timer2
guitool.activate_qwindow(back.mainwin)
#QPixmap.grabWindow(back.mainwin.winId()).save(fpath, 'jpg')
#ut.startfile(fpath)
#ut.embed()
pass
if params.args.postload_exit:
print('[main_cmd] postload exit')
sys.exit(0)
def show_all_colormaps():
"""
Displays at a 90 degree angle. Weird
FIXME: Remove call to pylab
References:
http://wiki.scipy.org/Cookbook/Matplotlib/Show_colormaps
http://matplotlib.org/examples/color/colormaps_reference.html
Notes:
cmaps = [('Perceptually Uniform Sequential',
['viridis', 'inferno', 'plasma', 'magma']),
('Sequential', ['Blues', 'BuGn', 'BuPu',
'GnBu', 'Greens', 'Greys', 'Oranges', 'OrRd',
'PuBu', 'PuBuGn', 'PuRd', 'Purples', 'RdPu',
'Reds', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd']),
('Sequential (2)', ['afmhot', 'autumn', 'bone', 'cool',
'copper', 'gist_heat', 'gray', 'hot',
'pink', 'spring', 'summer', 'winter']),
('Diverging', ['BrBG', 'bwr', 'coolwarm', 'PiYG', 'PRGn', 'PuOr',
'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn', 'Spectral',
'seismic']),
('Qualitative', ['Accent', 'Dark2', 'Paired', 'Pastel1',
'Pastel2', 'Set1', 'Set2', 'Set3']),
('Miscellaneous', ['gist_earth', 'terrain', 'ocean', 'gist_stern',
'brg', 'CMRmap', 'cubehelix',
'gnuplot', 'gnuplot2', 'gist_ncar',
'nipy_spectral', 'jet', 'rainbow',
'gist_rainbow', 'hsv', 'flag', 'prism'])
]
CommandLine:
python -m wbia.plottool.color_funcs --test-show_all_colormaps --show
python -m wbia.plottool.color_funcs --test-show_all_colormaps --show --type=Miscellaneous
python -m wbia.plottool.color_funcs --test-show_all_colormaps --show --cmap=RdYlBu
Example:
>>> # DISABLE_DOCTEST
>>> from wbia.plottool.color_funcs import * # NOQA
>>> import wbia.plottool as pt
>>> show_all_colormaps()
>>> pt.show_if_requested()
"""
from matplotlib import pyplot as plt
import pylab
import numpy as np
pylab.rc('text', usetex=False)
TRANSPOSE = True
a = np.outer(np.arange(0, 1, 0.01), np.ones(10))
if TRANSPOSE:
a = a.T
pylab.figure(figsize=(10, 5))
if TRANSPOSE:
pylab.subplots_adjust(right=0.8, left=0.05, bottom=0.01, top=0.99)
else:
pylab.subplots_adjust(top=0.8, bottom=0.05, left=0.01, right=0.99)
type_ = ut.get_argval('--type', str, default=None)
if type_ is None:
maps = [m for m in pylab.cm.datad if not m.endswith('_r')]
# maps += cmaps2.__all__
maps.sort()
else:
maps = CMAP_DICT[type_]
print('CMAP_DICT = %s' % (ut.repr3(CMAP_DICT), ))
cmap_ = ut.get_argval('--cmap', default=None)
if cmap_ is not None:
maps = [getattr(plt.cm, cmap_)]
length = len(maps) + 1
for i, m in enumerate(maps):
if TRANSPOSE:
pylab.subplot(length, 1, i + 1)
else:
pylab.subplot(1, length, i + 1)
# pylab.axis("off")
ax = plt.gca()
ax.set_xticks([])
ax.set_yticks([])
# try:
cmap = pylab.get_cmap(m)
# except Exception:
# cmap = getattr(cmaps2, m)
pylab.imshow(a, aspect='auto', cmap=cmap) # , origin="lower")
if TRANSPOSE:
ax.set_ylabel(
m,
rotation=0,
fontsize=10,
horizontalalignment='right',
verticalalignment='center',
)
else:
pylab.title(m, rotation=90, fontsize=10)
def __repr__(group):
repr_ = ut.repr3(group.infohist, nl=1)
print(repr_)
return repr_
def compare_featscores():
"""
CommandLine:
ibeis --tf compare_featscores --db PZ_MTEST \
--nfscfg :disttype=[L2_sift,lnbnn],top_percent=[None,.5,.1] -a timectrl \
-p default:K=[1,2],normalizer_rule=name \
--save featscore{db}.png --figsize=13,20 --diskshow
ibeis --tf compare_featscores --db PZ_MTEST \
--nfscfg :disttype=[L2_sift,normdist,lnbnn],top_percent=[None,.5] -a timectrl \
-p default:K=[1],normalizer_rule=name,sv_on=[True,False] \
--save featscore{db}.png --figsize=13,10 --diskshow
ibeis --tf compare_featscores --nfscfg :disttype=[L2_sift,normdist,lnbnn] \
-a timectrl -p default:K=1,normalizer_rule=name --db PZ_Master1 \
--save featscore{db}.png --figsize=13,13 --diskshow
ibeis --tf compare_featscores --nfscfg :disttype=[L2_sift,normdist,lnbnn] \
-a timectrl -p default:K=1,normalizer_rule=name --db GZ_ALL \
--save featscore{db}.png --figsize=13,13 --diskshow
ibeis --tf compare_featscores --db GIRM_Master1 \
--nfscfg ':disttype=fg,L2_sift,normdist,lnbnn' \
-a timectrl -p default:K=1,normalizer_rule=name \
--save featscore{db}.png --figsize=13,13
ibeis --tf compare_featscores --nfscfg :disttype=[L2_sift,normdist,lnbnn] \
-a timectrl -p default:K=[1,2,3],normalizer_rule=name,sv_on=False \
--db PZ_Master1 --save featscore{db}.png \
--dpi=128 --figsize=15,20 --diskshow
ibeis --tf compare_featscores --show --nfscfg :disttype=[L2_sift,normdist] -a timectrl -p :K=1 --db PZ_MTEST
ibeis --tf compare_featscores --show --nfscfg :disttype=[L2_sift,normdist] -a timectrl -p :K=1 --db GZ_ALL
ibeis --tf compare_featscores --show --nfscfg :disttype=[L2_sift,normdist] -a timectrl -p :K=1 --db PZ_Master1
ibeis --tf compare_featscores --show --nfscfg :disttype=[L2_sift,normdist] -a timectrl -p :K=1 --db GIRM_Master1
ibeis --tf compare_featscores --db PZ_MTEST \
--nfscfg :disttype=[L2_sift,normdist,lnbnn],top_percent=[None,.5,.2] -a timectrl \
-p default:K=[1],normalizer_rule=name \
--save featscore{db}.png --figsize=13,20 --diskshow
ibeis --tf compare_featscores --db PZ_MTEST \
--nfscfg :disttype=[L2_sift,normdist,lnbnn],top_percent=[None,.5,.2] -a timectrl \
-p default:K=[1],normalizer_rule=name \
--save featscore{db}.png --figsize=13,20 --diskshow
Example:
>>> # DISABLE_DOCTEST
>>> from ibeis.algo.hots.scorenorm import * # NOQA
>>> result = compare_featscores()
>>> print(result)
>>> ut.quit_if_noshow()
>>> import plottool as pt
>>> ut.show_if_requested()
"""
import plottool as pt
import ibeis
nfs_cfg_list = NormFeatScoreConfig.from_argv_cfgs()
learnkw = {}
ibs, testres = ibeis.testdata_expts(
defaultdb='PZ_MTEST', a=['default'], p=['default:K=1'])
print('nfs_cfg_list = ' + ut.repr3(nfs_cfg_list))
encoder_list = []
lbl_list = []
varied_nfs_lbls = ut.get_varied_cfg_lbls(nfs_cfg_list)
varied_qreq_lbls = ut.get_varied_cfg_lbls(testres.cfgdict_list)
#varies_qreq_lbls
#func = ut.cached_func(cache_dir='.')(learn_featscore_normalizer)
for datakw, nlbl in zip(nfs_cfg_list, varied_nfs_lbls):
for qreq_, qlbl in zip(testres.cfgx2_qreq_, varied_qreq_lbls):
lbl = qlbl + ' ' + nlbl
cfgstr = '_'.join([datakw.get_cfgstr(), qreq_.get_full_cfgstr()])
try:
encoder = vt.ScoreNormalizer()
encoder.load(cfgstr=cfgstr)
except IOError:
print('datakw = %r' % (datakw,))
encoder = learn_featscore_normalizer(qreq_, datakw, learnkw)
encoder.save(cfgstr=cfgstr)
encoder_list.append(encoder)
lbl_list.append(lbl)
fnum = 1
# next_pnum = pt.make_pnum_nextgen(nRows=len(encoder_list), nCols=3)
next_pnum = pt.make_pnum_nextgen(nRows=len(encoder_list) + 1, nCols=3, start=3)
iconsize = 94
if len(encoder_list) > 3:
iconsize = 64
icon = qreq_.ibs.get_database_icon(max_dsize=(None, iconsize), aid=qreq_.qaids[0])
score_range = (0, .6)
for encoder, lbl in zip(encoder_list, lbl_list):
#encoder.visualize(figtitle=encoder.get_cfgstr(), with_prebayes=False, with_postbayes=False)
encoder._plot_score_support_hist(fnum, pnum=next_pnum(), titlesuf='\n' + lbl, score_range=score_range)
encoder._plot_prebayes(fnum, pnum=next_pnum())
encoder._plot_roc(fnum, pnum=next_pnum())
if icon is not None:
pt.overlay_icon(icon, coords=(1, 0), bbox_alignment=(1, 0))
nonvaried_lbl = ut.get_nonvaried_cfg_lbls(nfs_cfg_list)[0]
figtitle = qreq_.__str__() + '\n' + nonvaried_lbl
pt.set_figtitle(figtitle)
pt.adjust_subplots(hspace=.5, top=.92, bottom=.08, left=.1, right=.9)
pt.update_figsize()
pt.plt.tight_layout()
for repo_dpath in IBEIS_REPO_DIRS:
# ut.getp_
mod_dpaths = ut.get_submodules_from_dpath(repo_dpath, recursive=False,
only_packages=True)
modname_list = ut.lmap(ut.get_modname_from_modpath, mod_dpaths)
print('Checking modules = %r' % (modname_list,))
for modname in modname_list:
try:
ut.import_modname(modname)
print(modname + ' success')
except ImportError as ex:
failures += [modname]
print(modname + ' failure')
print('failures = %s' % (ut.repr3(failures),))
# print('repo_dpath = %r' % (repo_dpath,))
# print('modules = %r' % (modules,))
# import ibeis
# print('found ibeis=%r' % (ibeis,))
if GET_ARGFLAG('--push'):
ut.gg_command('git push')
commit_msg = GET_ARGVAL('--commit', type_=str, default=None)
if commit_msg is not None:
ut.gg_command('git commit -am "{commit_msg}"'.format(**locals()))
if GET_ARGFLAG('--clean'):
def basic_infostr(card):
basic_infostr_ = ut.repr3(card.basic_infodict, nl=1)
return basic_infostr_
def infostr(card):
infostr_ = ut.repr3(card.infodict, nl=1)
return infostr_
def detect_opencv_keypoints():
import cv2
import vtool as vt
import numpy as np # NOQA
#img_fpath = ut.grab_test_imgpath(ut.get_argval('--fname', default='lena.png'))
img_fpath = ut.grab_test_imgpath(ut.get_argval('--fname', default='zebra.png'))
imgBGR = vt.imread(img_fpath)
imgGray = cv2.cvtColor(imgBGR, cv2.COLOR_BGR2GRAY)
def from_cv2_kpts(cv2_kp):
kp = (cv2_kp.pt[0], cv2_kp.pt[1], cv2_kp.size, 0, cv2_kp.size, cv2_kp.angle)
return kp
print('\n'.join(ut.search_module(cv2, 'create', recursive=True)))
detect_factory = {
#'BLOB': cv2.SimpleBlobDetector_create,
#'HARRIS' : HarrisWrapper.create,
#'SIFT': cv2.xfeatures2d.SIFT_create, # really DoG
'SURF': cv2.xfeatures2d.SURF_create, # really harris corners
'MSER': cv2.MSER_create,
#'StarDetector_create',
}
extract_factory = {
'SIFT': cv2.xfeatures2d.SIFT_create,
'SURF': cv2.xfeatures2d.SURF_create,
#'DAISY': cv2.xfeatures2d.DAISY_create,
'FREAK': cv2.xfeatures2d.FREAK_create,
#'LATCH': cv2.xfeatures2d.LATCH_create,
#'LUCID': cv2.xfeatures2d.LUCID_create,
#'ORB': cv2.ORB_create,
}
mask = None
type_to_kpts = {}
type_to_desc = {}
key = 'BLOB'
key = 'MSER'
for key in detect_factory.keys():
factory = detect_factory[key]
extractor = factory()
# For MSERS need to adapt shape and then convert into a keypoint repr
if hasattr(extractor, 'detectRegions'):
# bboxes are x,y,w,h
regions, bboxes = extractor.detectRegions(imgGray)
# ellipse definition from [Fitzgibbon95]
# http://www.bmva.org/bmvc/1995/bmvc-95-050.pdf p518
# ell = [c_x, c_y, R_x, R_y, theta]
# (cx, cy) = conic center
# Rx and Ry = conic radii
# theta is the counterclockwise angle
fitz_ellipses = [cv2.fitEllipse(mser) for mser in regions]
# http://answers.opencv.org/question/19015/how-to-use-mser-in-python/
#hulls = [cv2.convexHull(p.reshape(-1, 1, 2)) for p in regions]
#hull_ells = [cv2.fitEllipse(hull[:, 0]) for hull in hulls]
kpts_ = []
for ell in fitz_ellipses:
((cx, cy), (rx, ry), degrees) = ell
theta = np.radians(degrees) # opencv lives in radians
S = vt.scale_mat3x3(rx, ry)
T = vt.translation_mat3x3(cx, cy)
R = vt.rotation_mat3x3(theta)
#R = np.eye(3)
invVR = T.dot(R.dot(S))
kpt = vt.flatten_invV_mats_to_kpts(np.array([invVR]))[0]
kpts_.append(kpt)
kpts_ = np.array(kpts_)
tt = ut.tic('Computing %r keypoints' % (key,))
try:
cv2_kpts = extractor.detect(imgGray, mask)
except Exception as ex:
ut.printex(ex, 'Failed to computed %r keypoints' % (key,), iswarning=True)
pass
else:
ut.toc(tt)
type_to_kpts[key] = cv2_kpts
print(list(type_to_kpts.keys()))
print(ut.depth_profile(list(type_to_kpts.values())))
print('type_to_kpts = ' + ut.repr3(type_to_kpts, truncate=True))
cv2_kpts = type_to_kpts['MSER']
kp = cv2_kpts[0] # NOQA
#cv2.fitEllipse(cv2_kpts[0])
cv2_kpts = type_to_kpts['SURF']
for key in extract_factory.keys():
factory = extract_factory[key]
extractor = factory()
tt = ut.tic('Computing %r descriptors' % (key,))
try:
filtered_cv2_kpts, desc = extractor.compute(imgGray, cv2_kpts)
except Exception as ex:
ut.printex(ex, 'Failed to computed %r descriptors' % (key,), iswarning=True)
pass
else:
ut.toc(tt)
type_to_desc[key] = desc
print(list(type_to_desc.keys()))
print(ut.depth_profile(list(type_to_desc.values())))
print('type_to_desc = ' + ut.repr3(type_to_desc, truncate=True))
def translated_call(**kwargs):
def html_newlines(text):
r = '<br />\n'
text = text.replace(' ', ' ')
text = text.replace('\r\n', r).replace('\n\r', r).replace('\r', r).replace('\n', r)
return text
__format__ = False # Default __format__ value
ignore_cookie_set = False
try:
#print('Processing: %r with args: %r and kwargs: %r' % (func, args, kwargs, ))
# Pipe web input into Python web call
kwargs2 = _process_input(flask.request.args)
kwargs3 = _process_input(flask.request.form)
kwargs.update(kwargs2)
kwargs.update(kwargs3)
jQuery_callback = None
if 'callback' in kwargs and 'jQuery' in kwargs['callback']:
jQuery_callback = str(kwargs.pop('callback', None))
kwargs.pop('_', None)
#print('KWARGS: %s' % (kwargs, ))
#print('COOKIES: %s' % (request.cookies, ))
__format__ = request.cookies.get('__format__', None)
__format__ = kwargs.pop('__format__', __format__)
if __format__ is not None:
__format__ = str(__format__).lower()
ignore_cookie_set = __format__ in ['onetime', 'true']
__format__ = __format__ in ['true', 'enabled', 'enable']
resp_tup = translate_ibeis_webcall(func, **kwargs)
rawreturn, success, code, message = resp_tup
except WebException as webex:
ut.printex(webex)
rawreturn = webex.get_rawreturn(
DEBUG_PYTHON_STACK_TRACE_JSON_RESPONSE)
success = False
code = webex.code
message = webex.message
jQuery_callback = None
except Exception as ex:
ut.printex(ex)
rawreturn = ''
if DEBUG_PYTHON_STACK_TRACE_JSON_RESPONSE:
rawreturn = str(traceback.format_exc())
success = False
code = 500
errmsg = str(ex)
message = 'API error, Python Exception thrown: %s' % (errmsg)
if "'int' object is not iterable" in message:
rawreturn = (
'HINT: the input for this call is most likely '
'expected to be a list. Try adding a comma at '
'the end of the input (to cast the conversion '
'into a list) or encapsualte the input with '
'[].')
jQuery_callback = None
#print('RECEIVED FORMAT: %r' % (__format__, ))
if __format__:
# Hack for readable error messages
webreturn = translate_ibeis_webreturn(
rawreturn, success, code, message, jQuery_callback)
webreturn = ut.repr3(ut.from_json(webreturn), strvals=True)
try:
from ansi2html import Ansi2HTMLConverter
conv = Ansi2HTMLConverter()
webreturn = conv.convert(webreturn)
except ImportError as ex:
ut.printex(ex, 'pip install ansi2html', iswarning=True)
webreturn = ut.strip_ansi(webreturn)
webreturn = '<p><samp>\n' + html_newlines(webreturn) + '\n</samp></p>'
webreturn = '<meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-8">\n' + webreturn
def get_func_href(funcname):
url = 'http://' + request.environ['HTTP_HOST'] + flask.url_for(funcname) + '?__format__=True'
return '<a href="{url}">{url}</a>'.format(url=url)
if not success:
webreturn += '<pre>See logs for details: %s</pre>' % get_func_href('get_current_log_text')
webreturn += '<pre>Might also look into db_info: %s</pre>' % get_func_href('get_dbinfo')
else:
webreturn = translate_ibeis_webreturn(
rawreturn, success, code, message, jQuery_callback)
webreturn = ut.strip_ansi(webreturn)
resp = flask.make_response(webreturn, code)
if not ignore_cookie_set:
if __format__:
resp.set_cookie('__format__', 'enabled')
else:
resp.set_cookie('__format__', '', expires=0)
return resp
def detect(rf, forest, input_gpath_list, **kwargs):
"""
Run detection with a given loaded forest on a list of images
Args:
forest (object): the forest obejct that you want to use during
detection
input_gpath_list (list of str): the list of image paths that you want
to test
Kwargs:
output_gpath_list (list of str, optional): the paralell list of output
image paths for detection debugging or results; defaults to None
When this list is None no images are outputted for any test
images, whereas the list can be a parallel list where some values
are strings and others are None
output_scale_gpath_list (list of str, optional): the paralell list of output
scale image paths for detection debugging or results; defaults
to None
When this list is None no images are outputted for any test
images, whereas the list can be a parallel list where some values
are strings and others are None
mode (int, optional): the mode that the detector outputs; detaults to 0
0 - Hough Voting - the output is a Hough image that predicts the
locations of the obejct centeroids
0 - Classification Map - the output is a classification probability
map across the entire image where no regression information
is utilized
sensitivity (float, optional): the sensitivity of the detector;
mode = 0 - defaults to 128.0
mode = 1 - defaults to 255.0
scale_list (list of float, optional): the list of floats that specifies the scales
to try during testing;
defaults to [1.0, 0.80, 0.65, 0.50, 0.40, 0.30, 0.20, 0.10]
scale > 1.0 - Upscale the image
scale = 1.0 - Original image size
scale < 1.0 - Downscale the image
The list of scales highly impacts the performance of the detector and
should be carefully chosen
The scales are applied to BOTH the width and the height of the image
in order to scale the image and an interpolation of OpenCV's
CV_INTER_LANCZOS4 is used
batch_size (int, optional): the number of images to test at a single
time in paralell (if None, the number of CPUs is used); defaults to None
nms_min_area_contour (int, optional): the minimum size of a centroid
candidate region; defaults to 300
nms_min_area_overlap (float, optional, DEPRICATED): the allowable overlap in
bounding box predictions; defaults to 0.75
serial (bool, optional): flag to signify if to run detection in serial;
len(input_gpath_list) >= batch_size - defaults to False
len(input_gpath_list) < batch_size - defaults to False
verbose (bool, optional): verbose flag; defaults to object's verbose or
selectively enabled for this function
Yields:
(str, (list of dict)): tuple of the input image path and a list
of dictionaries specifying the detected bounding boxes
The dictionaries returned by this function are of the form:
centerx (int): the x position of the object's centroid
Note that the center of the bounding box and the location of
the object's centroid can be different
centery (int): the y position of the obejct's centroid
Note that the center of the bounding box and the location of
the object's centroid can be different
xtl (int): the top left x position of the bounding box
ytl (int): the top left y position of the bounding box
width (int): the width of the bounding box
height (int): the hiehgt of the bounding box
confidence (float): the confidence that this bounding box is of
the class specified by the trees used during testing
suppressed (bool, DEPRICATED): the flag of if this bounding
box has been marked to be suppressed by the detection
algorithm
"""
# Default values
params = odict([
('output_gpath_list', None),
('output_scale_gpath_list', None),
('mode', 0),
('sensitivity', None),
('scale_list', [1.0, 0.80, 0.65, 0.50, 0.40, 0.30, 0.20, 0.10]),
('_scale_num', None), # This value always gets overwritten
('batch_size', None),
('nms_min_area_contour', 100),
('nms_min_area_overlap', 0.75),
('results_val_array', None), # This value always gets overwritten
('results_len_array', None), # This value always gets overwritten
('RESULT_LENGTH', None), # This value always gets overwritten
('serial', False),
('verbose', rf.verbose),
('quiet', rf.quiet),
])
ut.update_existing(params, kwargs)
#print('Unused kwargs %r' % (set(kwargs.keys()) - set(params.keys()),))
params['RESULT_LENGTH'] = RESULT_LENGTH
output_gpath_list = params['output_gpath_list']
output_scale_gpath_list = params['output_scale_gpath_list']
# We no longer want these parameters in params
del params['output_gpath_list']
del params['output_scale_gpath_list']
if params['sensitivity'] is None:
assert params['mode'] in [0, 1], 'Invalid mode provided'
if params['mode'] == 0:
params['sensitivity'] = 128.0
elif params['mode'] == 1:
params['sensitivity'] = 255.0
# Try to determine the parallel processing batch size
if params['batch_size'] is None:
try:
cpu_count = multiprocessing.cpu_count()
if not params['quiet']:
print('[pyrf py] Detecting with %d CPUs' % (cpu_count, ))
params['batch_size'] = cpu_count
except:
params['batch_size'] = 8
# To eleminate downtime, add 1 to batch_size
# params['batch_size'] +=
# Data integrity
assert params['mode'] >= 0, \
'Detection mode must be non-negative'
assert 0.0 <= params['sensitivity'], \
'Sensitivity must be non-negative'
assert len(params['scale_list']) > 0 , \
'The scale list cannot be empty'
assert all( [ scale > 0.0 for scale in params['scale_list'] ]), \
'All scales must be positive'
assert params['batch_size'] > 0, \
'Batch size must be positive'
assert params['nms_min_area_contour'] > 0, \
'Non-maximum suppression minimum contour area cannot be negative'
assert 0.0 <= params['nms_min_area_overlap'] and params['nms_min_area_overlap'] <= 1.0, \
'Non-maximum supression minimum area overlap percentage must be between 0 and 1 (inclusive)'
# Convert optional parameters to C-valid default options
if output_gpath_list is None:
output_gpath_list = [''] * len(input_gpath_list)
elif output_gpath_list is not None:
assert len(output_gpath_list) == len(input_gpath_list), \
'Output image path list is invalid or is not the same length as the input list'
for index in range(len(output_gpath_list)):
if output_gpath_list[index] is None:
output_gpath_list[index] = ''
output_gpath_list = _cast_list_to_c(ensure_bytes_strings(output_gpath_list), C_CHAR)
if output_scale_gpath_list is None:
output_scale_gpath_list = [''] * len(input_gpath_list)
elif output_scale_gpath_list is not None:
assert len(output_scale_gpath_list) == len(input_gpath_list), \
'Output scale image path list is invalid or is not the same length as the input list'
for index in range(len(output_scale_gpath_list)):
if output_scale_gpath_list[index] is None:
output_scale_gpath_list[index] = ''
output_scale_gpath_list = _cast_list_to_c(ensure_bytes_strings(output_scale_gpath_list), C_CHAR)
# Prepare for C
params['_scale_num'] = len(params['scale_list'])
params['scale_list'] = _cast_list_to_c(params['scale_list'], C_FLOAT)
if not params['quiet']:
print('[pyrf py] Detecting over %d scales' % (params['_scale_num'], ))
# Run training algorithm
batch_size = params['batch_size']
del params['batch_size'] # Remove this value from params
batch_num = int(len(input_gpath_list) / batch_size) + 1
# Detect for each batch
for batch in ut.ProgressIter(range(batch_num), lbl="[pyrf py]", freq=1, invert_rate=True):
begin = time.time()
start = batch * batch_size
end = start + batch_size
if end > len(input_gpath_list):
end = len(input_gpath_list)
input_gpath_list_ = input_gpath_list[start:end]
output_gpath_list_ = output_gpath_list[start:end]
output_scale_gpath_list_ = output_scale_gpath_list[start:end]
num_images = len(input_gpath_list_)
# Set image detection to be run in serial if less than half a batch to run
if num_images < min(batch_size / 2, 8):
params['serial'] = True
# Final sanity check
assert len(input_gpath_list_) == len(output_gpath_list_) and len(input_gpath_list_) == len(output_scale_gpath_list_)
params['results_val_array'] = np.empty(num_images, dtype=NP_ARRAY_FLOAT)
params['results_len_array'] = np.empty(num_images, dtype=C_INT)
# Make the params_list
params_list = [
forest,
_cast_list_to_c(ensure_bytes_strings(input_gpath_list_), C_CHAR),
num_images,
_cast_list_to_c(ensure_bytes_strings(output_gpath_list_), C_CHAR),
_cast_list_to_c(ensure_bytes_strings(output_scale_gpath_list_), C_CHAR)
] + list(params.values())
try:
RF_CLIB.detect(rf.detector_c_obj, *params_list)
except C.ArgumentError as ex:
print('ERROR passing arguments to pyrf')
print(' * params_list = %s' % (ut.repr3(params_list, nl=3),))
ut.printex(ex)
results_list = _extract_np_array(params['results_len_array'], params['results_val_array'], NP_ARRAY_FLOAT, NP_FLOAT32, RESULT_LENGTH)
conclude = time.time()
if not params['quiet']:
print('[pyrf py] Took %r seconds to compute %d images' % (conclude - begin, num_images, ))
for input_gpath, result_list in zip(input_gpath_list_, results_list):
if params['mode'] == 0:
result_list_ = []
for result in result_list:
# Unpack result into a nice Python dictionary and return
temp = {}
temp['centerx'] = int(result[0])
temp['centery'] = int(result[1])
temp['xtl'] = int(result[2])
temp['ytl'] = int(result[3])
temp['width'] = int(result[4])
temp['height'] = int(result[5])
temp['confidence'] = float(np.round(result[6], decimals=4))
temp['suppressed'] = int(result[7]) == 1
result_list_.append(temp)
yield (input_gpath, result_list_)
else:
yield (input_gpath, None)
results_list = None
params['results_val_array'] = None
params['results_len_array'] = None
def learn_featscore_normalizer(qreq_, datakw={}, learnkw={}):
r"""
Takes the result of queries and trains a score encoder
Args:
qreq_ (ibeis.QueryRequest): query request object with hyper-parameters
Returns:
vtool.ScoreNormalizer: encoder
CommandLine:
python -m ibeis --tf learn_featscore_normalizer --show -t default:
python -m ibeis --tf learn_featscore_normalizer --show --fsvx=0 --threshx=1 --show
python -m ibeis --tf learn_featscore_normalizer --show -a default:size=40 -t default:fg_on=False,lnbnn_on=False,ratio_thresh=1.0,K=1,Knorm=6,sv_on=False,normalizer_rule=name --fsvx=0 --threshx=1 --show
python -m ibeis --tf learn_featscore_normalizer --show --disttype=ratio
python -m ibeis --tf learn_featscore_normalizer --show --disttype=lnbnn
python -m ibeis --tf learn_featscore_normalizer --show --disttype=L2_sift -t default:K=1
python -m ibeis --tf learn_featscore_normalizer --show --disttype=L2_sift -a timectrl -t default:K=1 --db PZ_Master1
python -m ibeis --tf learn_featscore_normalizer --show --disttype=ratio -a timectrl -t default:K=1 --db PZ_Master1
python -m ibeis --tf learn_featscore_normalizer --show --disttype=lnbnn -a timectrl -t default:K=1 --db PZ_Master1
# LOOK AT THIS
python -m ibeis --tf learn_featscore_normalizer --show --disttype=normdist -a timectrl -t default:K=1 --db PZ_Master1
#python -m ibeis --tf learn_featscore_normalizer --show --disttype=parzen -a timectrl -t default:K=1 --db PZ_Master1
#python -m ibeis --tf learn_featscore_normalizer --show --disttype=norm_parzen -a timectrl -t default:K=1 --db PZ_Master1
python -m ibeis --tf learn_featscore_normalizer --show --disttype=lnbnn --db PZ_Master1 -a timectrl -t best
Example:
>>> # ENABLE_DOCTEST
>>> from ibeis.algo.hots.scorenorm import * # NOQA
>>> import ibeis
>>> learnkw = {}
>>> datakw = NormFeatScoreConfig.from_argv_dict()
>>> qreq_ = ibeis.testdata_qreq_(
>>> defaultdb='PZ_MTEST', a=['default'], p=['default'])
>>> encoder = learn_featscore_normalizer(qreq_, datakw, learnkw)
>>> ut.quit_if_noshow()
>>> encoder.visualize(figtitle=encoder.get_cfgstr())
>>> ut.show_if_requested()
"""
cm_list = qreq_.execute()
print('learning scorenorm')
print('datakw = %s' % ut.repr3(datakw))
tp_scores, tn_scores, scorecfg = get_training_featscores(
qreq_, cm_list, **datakw)
_learnkw = dict(monotonize=True, adjust=2)
_learnkw.update(learnkw)
encoder = vt.ScoreNormalizer(**_learnkw)
encoder.fit_partitioned(tp_scores, tn_scores, verbose=False)
# ut.hashstr27(qreq_.get_cfgstr())
# Maintain regen command info: TODO: generalize and integrate
encoder._regen_info = {
'cmd': 'python -m ibeis --tf learn_featscore_normalizer',
'scorecfg': scorecfg,
'learnkw': learnkw,
'datakw': datakw,
'qaids': qreq_.qaids,
'daids': qreq_.daids,
'qreq_cfg': qreq_.get_full_cfgstr(),
'qreq_regen_info': getattr(qreq_, '_regen_info', {}),
}
# 'timestamp': ut.get_printable_timestamp(),
scorecfg_safe = scorecfg
scorecfg_safe = re.sub('[' + re.escape('()= ') + ']', '', scorecfg_safe)
scorecfg_safe = re.sub('[' + re.escape('+*<>[]') + ']', '_', scorecfg_safe)
hashid = ut.hashstr27(ut.to_json(encoder._regen_info))
naidinfo = ('q%s_d%s' % (len(qreq_.qaids), len(qreq_.daids)))
cfgstr = 'featscore_{}_{}_{}_{}'.format(scorecfg_safe, qreq_.ibs.get_dbname(), naidinfo, hashid)
encoder.cfgstr = cfgstr
return encoder
def merge_level_order(level_orders, topsort):
"""
Merge orders of individual subtrees into a total ordering for
computation.
>>> level_orders = {
>>> 'multi_chip_multitest': [['dummy_annot'], ['chip'], ['multitest'],
>>> ['multitest_score'], ],
>>> 'multi_fgweight_multitest': [ ['dummy_annot'], ['chip', 'probchip'],
>>> ['keypoint'], ['fgweight'], ['multitest'], ['multitest_score'], ],
>>> 'multi_keypoint_nnindexer': [ ['dummy_annot'], ['chip'], ['keypoint'],
>>> ['nnindexer'], ['multitest'], ['multitest_score'], ],
>>> 'normal': [ ['dummy_annot'], ['chip', 'probchip'], ['keypoint'],
>>> ['fgweight'], ['spam'], ['multitest'], ['multitest_score'], ],
>>> 'nwise_notch_multitest_1': [ ['dummy_annot'], ['notch'], ['multitest'],
>>> ['multitest_score'], ],
>>> 'nwise_notch_multitest_2': [ ['dummy_annot'], ['notch'], ['multitest'],
>>> ['multitest_score'], ],
>>> 'nwise_notch_notchpair_1': [ ['dummy_annot'], ['notch'], ['notchpair'],
>>> ['multitest'], ['multitest_score'], ],
>>> 'nwise_notch_notchpair_2': [ ['dummy_annot'], ['notch'], ['notchpair'],
>>> ['multitest'], ['multitest_score'], ],
>>> }
>>> topsort = [u'dummy_annot', u'notch', u'probchip', u'chip', u'keypoint',
>>> u'fgweight', u'nnindexer', u'spam', u'notchpair', u'multitest',
>>> u'multitest_score']
>>> print(ut.repr3(ut.merge_level_order(level_orders, topsort)))
EG2:
level_orders = {u'normal': [[u'dummy_annot'], [u'chip', u'probchip'], [u'keypoint'], [u'fgweight'], [u'spam']]}
topsort = [u'dummy_annot', u'probchip', u'chip', u'keypoint', u'fgweight', u'spam']
"""
import utool as ut
if False:
compute_order = []
level_orders = ut.map_dict_vals(ut.total_flatten, level_orders)
level_sets = ut.map_dict_vals(set, level_orders)
for tablekey in topsort:
compute_order.append((tablekey, [groupkey for groupkey, set_ in level_sets.items() if tablekey in set_]))
return compute_order
else:
# Do on common subgraph
import itertools
# Pointer to current level.: Start at the end and
# then work your way up.
main_ptr = len(topsort) - 1
stack = []
#from six.moves import zip_longest
keys = list(level_orders.keys())
type_to_ptr = {key: -1 for key in keys}
print('level_orders = %s' % (ut.repr3(level_orders),))
for count in itertools.count(0):
print('----')
print('count = %r' % (count,))
ptred_levels = []
for key in keys:
levels = level_orders[key]
ptr = type_to_ptr[key]
try:
level = tuple(levels[ptr])
except IndexError:
level = None
ptred_levels.append(level)
print('ptred_levels = %r' % (ptred_levels,))
print('main_ptr = %r' % (main_ptr,))
# groupkeys, groupxs = ut.group_indices(ptred_levels)
# Group keys are tablenames
# They point to the (type) of the input
# num_levelkeys = len(ut.total_flatten(ptred_levels))
groupkeys, groupxs = ut.group_indices(ptred_levels)
main_idx = None
while main_idx is None and main_ptr >= 0:
target = topsort[main_ptr]
print('main_ptr = %r' % (main_ptr,))
print('target = %r' % (target,))
# main_idx = ut.listfind(groupkeys, (target,))
# if main_idx is None:
possible_idxs = [idx for idx, keytup in enumerate(groupkeys) if keytup is not None and target in keytup]
if len(possible_idxs) == 1:
main_idx = possible_idxs[0]
else:
main_idx = None
if main_idx is None:
main_ptr -= 1
if main_idx is None:
print('break I')
break
found_groups = ut.apply_grouping(keys, groupxs)[main_idx]
print('found_groups = %r' % (found_groups,))
stack.append((target, found_groups))
for k in found_groups:
type_to_ptr[k] -= 1
if len(found_groups) == len(keys):
main_ptr -= 1
if main_ptr < 0:
print('break E')
break
print('stack = %s' % (ut.repr3(stack),))
print('have = %r' % (sorted(ut.take_column(stack, 0)),))
print('need = %s' % (sorted(ut.total_flatten(level_orders.values())),))
compute_order = stack[::-1]
return compute_order
def cluster_query(model, query_vars=None, evidence=None, soft_evidence=None,
method=None, operation='maximize'):
"""
CommandLine:
python -m ibeis.algo.hots.bayes --exec-cluster_query --show
ParamGrid:
>>> param_grid = dict(
>>> #method=['approx', 'bf', 'bp'],
>>> method=['approx', 'bp'],
>>> )
>>> combos = ut.all_dict_combinations(param_grid)
>>> index = 0
>>> keys = 'method'.split(', ')
>>> method, = ut.dict_take(combos[index], keys)
Setup:
>>> from ibeis.algo.hots.bayes import * # NOQA
>>> verbose = True
>>> other_evidence = {}
>>> name_evidence = [1, None, None, 0]
>>> score_evidence = [2, 0, 2]
>>> special_names = ['fred', 'sue', 'tom', 'paul']
>>> model = make_name_model(
>>> num_annots=4, num_names=4, num_scores=3, verbose=True, mode=1,
>>> special_names=special_names)
>>> method = None
>>> model, evidence, soft_evidence = update_model_evidence(
>>> model, name_evidence, score_evidence, other_evidence)
>>> evidence = model._ensure_internal_evidence(evidence)
>>> query_vars = ut.list_getattr(model.ttype2_cpds['name'], 'variable')
Example:
>>> # DISABLE_DOCTEST
>>> query_results = cluster_query(model, query_vars, evidence,
>>> method=method)
>>> print(ut.repr2(query_results['top_assignments'], nl=1))
>>> ut.quit_if_noshow()
>>> pgm_ext.show_model(model, evidence=evidence, **query_results)
>>> ut.show_if_requested()
"""
evidence = model._ensure_internal_evidence(evidence)
if query_vars is None:
query_vars = model.nodes()
orig_query_vars = query_vars # NOQA
query_vars = ut.setdiff(query_vars, list(evidence.keys()))
if method is None:
method = ut.get_argval('--method', type_=str, default='bp')
reduced_joint = compute_reduced_joint(model, query_vars, evidence,
method, operation)
new_reduced_joint = collapse_factor_labels(model, reduced_joint, evidence)
if False:
report_partitioning_statistics(new_reduced_joint)
# FIXME: are these max marginals?
max_marginals = {}
for i, var in enumerate(query_vars):
one_out = query_vars[:i] + query_vars[i + 1:]
max_marginals[var] = new_reduced_joint.marginalize(one_out,
inplace=False)
# max_marginals[var] = joint2.maximize(one_out, inplace=False)
factor_list = max_marginals.values()
# Now find the most likely state
reduced_variables = new_reduced_joint.variables
new_state_idxs = np.array(new_reduced_joint._row_labels(asindex=True))
new_values = new_reduced_joint.values.ravel()
sortx = new_values.argsort()[::-1]
sort_new_state_idxs = new_state_idxs.take(sortx, axis=0)
sort_new_values = new_values.take(sortx)
sort_new_states = list(zip(*[
ut.dict_take(model.statename_dict[var], idx)
for var, idx in
zip(reduced_variables, sort_new_state_idxs.T)]))
# Better map assignment based on knowledge of labels
map_assign = dict(zip(reduced_variables, sort_new_states[0]))
sort_reduced_rowstr_lbls = [
ut.repr2(dict(zip(reduced_variables, lbls)), explicit=True,
nobraces=True,
strvals=True)
for lbls in sort_new_states
]
top_assignments = list(zip(sort_reduced_rowstr_lbls[:4], sort_new_values))
if len(sort_new_values) > 3:
top_assignments += [('other', 1 - sum(sort_new_values[:4]))]
query_results = {
'factor_list': factor_list,
'top_assignments': top_assignments,
'map_assign': map_assign,
'method': method,
}
print('query_results = %s' % (ut.repr3(query_results, nl=2),))
return query_results
def cluster_query(model, query_vars=None, evidence=None, soft_evidence=None,
method=None, operation='maximize'):
"""
CommandLine:
python -m ibeis.algo.hots.bayes --exec-cluster_query --show
GridParams:
>>> param_grid = dict(
>>> #method=['approx', 'bf', 'bp'],
>>> method=['approx', 'bp'],
>>> )
>>> combos = ut.all_dict_combinations(param_grid)
>>> index = 0
>>> keys = 'method'.split(', ')
>>> method, = ut.dict_take(combos[index], keys)
GridSetup:
>>> from ibeis.algo.hots.bayes import * # NOQA
>>> verbose = True
>>> other_evidence = {}
>>> name_evidence = [1, None, None, 0]
>>> score_evidence = [2, 0, 2]
>>> special_names = ['fred', 'sue', 'tom', 'paul']
>>> model = make_name_model(
>>> num_annots=4, num_names=4, num_scores=3, verbose=True, mode=1,
>>> special_names=special_names)
>>> method = None
>>> model, evidence, soft_evidence = update_model_evidence(
>>> model, name_evidence, score_evidence, other_evidence)
>>> evidence = model._ensure_internal_evidence(evidence)
>>> query_vars = ut.list_getattr(model.ttype2_cpds[NAME_TTYPE], 'variable')
GridExample:
>>> # DISABLE_DOCTEST
>>> query_results = cluster_query(model, query_vars, evidence,
>>> method=method)
>>> print(ut.repr2(query_results['top_assignments'], nl=1))
>>> ut.quit_if_noshow()
>>> from ibeis.algo.hots import pgm_viz
>>> pgm_viz.show_model(model, evidence=evidence, **query_results)
>>> ut.show_if_requested()
"""
evidence = model._ensure_internal_evidence(evidence)
if query_vars is None:
query_vars = model.nodes()
orig_query_vars = query_vars # NOQA
query_vars = ut.setdiff(query_vars, list(evidence.keys()))
if method is None:
method = ut.get_argval('--method', type_=str, default='bp')
reduced_joint = compute_reduced_joint(model, query_vars, evidence,
method, operation)
new_reduced_joint = collapse_factor_labels(model, reduced_joint, evidence)
if False:
report_partitioning_statistics(new_reduced_joint)
# FIXME: are these max marginals?
max_marginals = {}
for i, var in enumerate(query_vars):
one_out = query_vars[:i] + query_vars[i + 1:]
max_marginals[var] = new_reduced_joint.marginalize(one_out,
inplace=False)
# max_marginals[var] = joint2.maximize(one_out, inplace=False)
factor_list = max_marginals.values()
# Now find the most likely state
reduced_variables = new_reduced_joint.variables
new_state_idxs = np.array(new_reduced_joint._row_labels(asindex=True))
new_values = new_reduced_joint.values.ravel()
sortx = new_values.argsort()[::-1]
sort_new_state_idxs = new_state_idxs.take(sortx, axis=0)
sort_new_values = new_values.take(sortx)
sort_new_states = list(zip(*[
ut.dict_take(model.statename_dict[var], idx)
for var, idx in
zip(reduced_variables, sort_new_state_idxs.T)]))
# Better map assignment based on knowledge of labels
map_assign = dict(zip(reduced_variables, sort_new_states[0]))
sort_reduced_rowstr_lbls = [
ut.repr2(dict(zip(reduced_variables, lbls)), explicit=True,
nobraces=True,
strvals=True)
for lbls in sort_new_states
]
top_assignments = list(zip(sort_reduced_rowstr_lbls[:4], sort_new_values))
if len(sort_new_values) > 3:
top_assignments += [('other', 1 - sum(sort_new_values[:4]))]
query_results = {
'factor_list': factor_list,
'top_assignments': top_assignments,
'map_assign': map_assign,
'method': method,
}
print('query_results = %s' % (ut.repr3(query_results, nl=2),))
return query_results
