def get_obj_ids_for_timestamp( self, timestamp_string=None ):
(single_episode, kh5_file, stim_fname
) = self._get_episode_for_timestamp(timestamp_string=timestamp_string)
for include in single_episode.findall('include'):
raise ValueError('<single_episode> has <include> tag')
for exclude in single_episode.findall('exclude'):
raise ValueError('<single_episode> has <exclude> tag')
include_ids = None
exclude_ids = None
for include in kh5_file.findall('include'):
if include_ids is None:
include_ids = []
if include.text is not None:
obj_ids = parse_seq( include.text )
include_ids.extend( obj_ids )
else:
obj_ids = None
for exclude in kh5_file.findall('exclude'):
if exclude_ids is None:
exclude_ids = []
if exclude.text is not None:
obj_ids = parse_seq( exclude.text )
exclude_ids.extend( obj_ids )
else:
obj_ids = None
return include_ids, exclude_ids
def main():
usage = '%prog [options]'
parser = OptionParser(usage)
analysis_options.add_common_options(parser)
parser.add_option("--interactive", action='store_true', default=False)
parser.add_option(
"--fuse",
action='store_true',
help=
"fuse object ids corresponding to a single fly (requires stim-xml fanout)",
default=False)
(options, args) = parser.parse_args()
if options.obj_only is not None:
options.obj_only = core_analysis.parse_seq(options.obj_only)
if not options.interactive:
matplotlib.use('Agg')
if len(args):
parser.print_help()
return
if options.up_dir is not None:
options.up_dir = core_analysis.parse_seq(options.up_dir)
else:
options.up_dir = None
doit(options=options, )
def doit(options = None,
):
kalman_filename=options.kalman_filename
import pylab # do after matplotlib.use() call
fig = pylab.figure(figsize=(5,8))
figtitle = kalman_filename.split('.')[0]
pylab.figtext(0,0,figtitle)
ax = None
subplot ={}
subplots = ['xy','xz']
for i, name in enumerate(subplots):
ax = fig.add_subplot(len(subplots),1,i+1)#,sharex=ax)
subplot[name] = ax
if options.up_dir is not None:
options.up_dir = core_analysis.parse_seq(options.up_dir)
else:
options.up_dir = None
plot_top_and_side_views(subplot=subplot,
options=options,
)
pylab.show()
def main():
usage = '%prog [options]'
parser = OptionParser(usage)
analysis_options.add_common_options( parser )
parser.add_option("--ellipsoids", action='store_true', default=False)
parser.add_option("--show-obj-id", action='store_true', default=False)
parser.add_option("--show-observations", action='store_true', default=False)
parser.add_option("--markersize", type='float',default=0.5)
(options, args) = parser.parse_args()
if options.obj_only is not None:
options.obj_only = core_analysis.parse_seq(options.obj_only)
if len(args):
parser.print_help()
return
doit( options=options,
)
def main():
usage = '%prog [options] FILE1 [FILE2] ...'
parser = OptionParser(usage)
parser.add_option('-k',
"--kalman-file",
dest="kalman_filename",
type='string',
help=".h5 file with kalman data and 3D reconstructor")
parser.add_option("--spreadh5",
type='string',
help=(".spreadh5 file with frame synchronization info "
"(make with flydra_analysis_check_sync)"))
parser.add_option("--start",
dest="start",
type='int',
help="start frame (.h5 frame number reference)")
parser.add_option("--stop",
dest="stop",
type='int',
help="stop frame (.h5 frame number reference)")
parser.add_option("--disable-kalman-smoothing",
action='store_false',
dest='use_kalman_smoothing',
default=True,
help=("show original, causal Kalman filtered data "
"(rather than Kalman smoothed observations)"))
parser.add_option("--timestamps", action='store_true', default=False)
parser.add_option("--reproj-error",
action='store_true',
default=False,
help=("calculate and print to console the mean "
"reprojection error for each camera"))
parser.add_option("--hide-source-name",
action='store_false',
dest='show_source_name',
default=True,
help="show the source filename?")
parser.add_option("--fps",
dest='fps',
type='float',
help=("frames per second (used for Kalman "
"filtering/smoothing)"))
parser.add_option("--area-threshold",
type='float',
default=0.0,
help=("area of 2D point required for plotting (NOTE: "
"this is not related to the threshold used for "
"Kalmanization)"))
parser.add_option("--likely-only",
action='store_true',
default=False,
help=('plot only points that are deemed likely to '
'be true positives'))
parser.add_option("--save-fig",
type='string',
default=None,
help='path name of figure to save (exits script '
'immediately after save)')
parser.add_option(
"--dynamic-model",
type="string",
dest="dynamic_model",
default=None,
)
parser.add_option("--obj-only", type="string")
parser.add_option("--up-dir", type="string")
(options, args) = parser.parse_args()
if options.obj_only is not None:
options.obj_only = core_analysis.parse_seq(options.obj_only)
if options.up_dir is not None:
up_dir = core_analysis.parse_seq(options.up_dir)
else:
up_dir = None
doit(
filenames=args,
kalman_filename=options.kalman_filename,
start=options.start,
stop=options.stop,
fps=options.fps,
dynamic_model=options.dynamic_model,
use_kalman_smoothing=options.use_kalman_smoothing,
up_dir=up_dir,
options=options,
)
def main():
usage = '%prog [options]'
parser = OptionParser(usage)
analysis_options.add_common_options(parser)
parser.add_option(
"--frames",
action='store_true',
help="plot horizontal axis in frame number (not seconds)",
default=False)
parser.add_option(
"--fuse",
action='store_true',
help=
"fuse object ids corresponding to a single fly (requires stim-xml fanout)",
default=False)
parser.add_option("--P55",
action='store_true',
help="plot P[5,5] component of covariance matrix",
default=False)
parser.add_option(
"--timestamp-file",
type='string',
help="file with data2d_distorted table to get timestamps")
parser.add_option("--save-fig",
type='string',
default=None,
help='path name of figure to save (exits script '
'immediately after save)')
parser.add_option("--ori-qual",
type='float',
default=None,
help=('minimum orientation quality to use'))
parser.add_option("--smooth-orientations",
action='store_true',
help="if displaying orientations, use smoothed data",
default=False)
parser.add_option("--show-3d-orientations",
action='store_true',
help="show orientation data?",
default=False)
(options, args) = parser.parse_args()
if options.obj_only is not None:
options.obj_only = core_analysis.parse_seq(options.obj_only)
if len(args):
parser.print_help()
return
doit(options=options, )
def doit(options=None, ):
import pylab # do after matplotlib.use() call
if options.up_dir is not None:
options.up_dir = core_analysis.parse_seq(options.up_dir)
else:
options.up_dir = None
fig = pylab.figure() #figsize=(6,4))
figtitle = options.kalman_filename
pylab.figtext(0, 0, figtitle)
ax = None
subplot = {}
if options.show_3d_orientations:
subplots = ['x', 'y', 'z', 'dx', 'dy', 'dz']
else:
subplots = ['x', 'y', 'z', 'xy_vel', 'vel', 'accel', 'frame']
if options.P55:
subplots.append('P55')
#subplots = ['x','y','z','vel','accel']
for i, name in enumerate(subplots):
ax = fig.add_subplot(len(subplots), 1, i + 1, sharex=ax)
ax.grid(True)
subplot[name] = ax
fig.subplots_adjust(bottom=0.15)
if 0:
fig = pylab.figure()
figtitle = options.kalman_filename
pylab.figtext(0, 0, figtitle)
ax = fig.add_subplot(1, 1, 1)
subplot['vel_hist'] = ax
ax.grid(True)
line2obj_id = plot_timeseries(
subplot=subplot,
options=options,
)
class MyPickObj(object):
def __init__(self, line2obj_id):
self.line2obj_id = line2obj_id
self.obj_ids = []
def onpick(self, event):
if isinstance(event.artist, matplotlib.lines.Line2D):
thisline = event.artist
obj_id = self.line2obj_id[thisline]
if obj_id not in self.obj_ids:
self.obj_ids.append(obj_id)
self.obj_ids.sort()
print 'picked', obj_id
print 'all:'
print self.obj_ids
## else:
## print '(already had obj_id %d)'%obj_id
def on_key_press(self, event):
#print 'received key',repr(event.key)
if event.key == 'c':
del self.obj_ids[:]
print self.obj_ids
if event.key == 'l':
del self.obj_ids[-1]
print self.obj_ids
#print 'all:'
#print self.obj_ids
if options.save_fig is not None:
pylab.savefig(options.save_fig)
else:
pick_receiver = MyPickObj(line2obj_id)
fig.canvas.mpl_connect('pick_event', pick_receiver.onpick)
fig.canvas.mpl_connect('key_press_event', pick_receiver.on_key_press)
pylab.show()