def update_skill(self):
## plogp = np.zeros([2])
## plogp[0] = 0.5*(self.PD+self.PL)*np.log2(self.PD+self.PL)
## plogp[1] = 0.5*(1.0-self.PD+1.0-self.PL)*np.log2(1.0-self.PD+1.0-self.PL)
## self.contribution = np.sum(plogp)
self.skill = swap.expectedInformationGain(0.5, self.PL, self.PD)
return self.skill
def update_skill(self):
## plogp = np.zeros([2])
## plogp[0] = 0.5*(self.PD+self.PL)*np.log2(self.PD+self.PL)
## plogp[1] = 0.5*(1.0-self.PD+1.0-self.PL)*np.log2(1.0-self.PD+1.0-self.PL)
## self.contribution = np.sum(plogp)
self.skill = swap.expectedInformationGain(0.5, self.PL, self.PD)
return self.skill
plotplpd(final_PL1,final_PD1,information1,1,"Stage 1 Information")
plotplpd(final_PL2,final_PD2,information2,2,"Stage 2 Information")
savefig("information_plpd.png")
clf();
###########################
##Skill PL PD plot
###########################
bins=101
skill=np.zeros(bins*bins);
skill=np.reshape(skill,(bins,bins));
for ii in range(bins):
M_ll=0.01*ii;
for jj in range(bins):
M_nn=0.01*jj;
skill[ii][jj]=swap.expectedInformationGain(0.5, M_ll, M_nn);
ax=subplot(1,1,1);
im=ax.imshow(skill,origin='lower',extent=(0,1,0,1));
cbar=colorbar(im);
cbar.solids.set_edgecolor("face");
ax.set_xlim(0,1);
ax.set_ylim(0,1);
ax.set_xlabel("P$_L$");
ax.set_ylabel("P$_D$");
ax.set_title("Skill");
xx=np.arange(-0.1,2,0.1);
ax.axhline(0.5,color="k",linestyle='dashed');
ax.axvline(0.5,color="k",linestyle='dashed');
ax.plot(xx,1-xx,color="k");
def make_lens_catalog(args):
"""
NAME
make_lens_catalog
PURPOSE
Given location of collection pickle, this script produces a set of
annotated images of lenses (heatmaps for lens locations, markers for
where clicks were, etc).
COMMENTS
You have to download the file so it chooses whever your output
directory is to also download the raw images.
This should be pretty customizable.
FLAGS
-h Print this message
--skill Weight by skill
INPUTS
collection.pickle
OUTPUTS
lens.dat
Assumed format:
ID kind x y Prob N0 Skill Dist
Here:
ID = Space Warps subject ID
kind = Space Warps subject type (sim, dud, test)
x,y = object (cluster) centroid, in pixels
P = Space Warps subject probability
N0 = number of markers in the cluster
S = total skill per cluster, summed over markers
D = biggest distance within cluster
EXAMPLE
BUGS
AUTHORS
This file is part of the Space Warps project, and is distributed
under the GPL v2 by the Space Warps Science Team.
http://spacewarps.org/
HISTORY
2013-07-16 started Davis (KIPAC)
"""
# ------------------------------------------------------------------
# Some defaults:
flags = {'skill': False,
'output_directory': './',
'output_name': 'catalog.dat',
'image_y_size': 440,
'catalog_path': '',
'update_collection': '',}
# ------------------------------------------------------------------
# Read in options:
# this has to be easier to do...
for arg in args:
if arg in flags:
flags[arg] = args[arg]
elif arg == 'collection_path':
collection_path = args[arg]
else:
print "make_lens_atlas: unrecognized flag ",arg
print "make_lens_catalog: illustrating behaviour captured in collection file: "
print "make_lens_catalog: ",collection_path
memory = joblib.Memory(cachedir=flags['output_directory'])
memory.clear()
catalog_path = flags['output_directory'] + flags['output_name']
if len(flags['output_name']) > 0:
F = open(catalog_path, 'w')
F.write('id,kind,x,y,prob,n0,skill,dist\n')
# ------------------------------------------------------------------
# Read in files:
collection = swap.read_pickle(collection_path, 'collection')
ID_list = collection.list()
print "make_lens_catalog: collection numbers ", len(ID_list)
if flags['catalog_path'] != '':
print "make_lens_catalog: filtering from catalog ",flags['catalog_path']
catalog_in = csv2rec(flags['catalog_path'])
ID_list = np.unique(catalog_in['id'])
# ------------------------------------------------------------------
# Run through data:
catalog = {}
for ID in ID_list:
subject = collection.member[ID]
kind = subject.kind
P = subject.mean_probability
itwas = subject.annotationhistory['ItWas']
x_all = subject.annotationhistory['At_X']
y_all = subject.annotationhistory['At_Y']
x_markers = np.array([xi for xj in x_all for xi in xj])
y_markers = np.array([yi for yj in y_all for yi in yj])
catalog.update({ID: {'agents_reject': [],
'x': x_markers,
'y': y_markers,}})
PL_all = subject.annotationhistory['PL']
PD_all = subject.annotationhistory['PD']
# filter out the empty clicks
PL_list = []
PL_nots = []
for i, xj in enumerate(x_all):
# len(xj) of empty = 0
PL_list.append([PL_all[i]] * len(xj))
if len(xj) == 0:
PL_nots.append(PL_all[i])
PL = np.array([PLi for PLj in PL_list for PLi in PLj])
PL_nots = np.array(PL_nots)
# filter out the empty clicks
PD_list = []
PD_nots = []
for i, xj in enumerate(x_all):
PD_list.append([PD_all[i]] * len(xj))
if len(xj) == 0:
PD_nots.append(PD_all[i])
catalog[ID]['agents_reject'].append(i)
PD = np.array([PDi for PDj in PD_list for PDi in PDj])
PD_nots = np.array(PD_nots)
skill = swap.expectedInformationGain(0.5, PL, PD) # skill
# it is only fair to write out the NOTs, too
# do the empty guys
skill_nots = swap.expectedInformationGain(0.5, PL_nots, PD_nots) # skill
x, y = -1, -1
N0 = len(skill_nots)
S = np.sum(skill_nots)
D = 0
## catalog.append((ID, kind, x, y, P, N0, S, D))
if len(catalog)%500 == 0:
print len(catalog)
if len(flags['output_name']) > 0:
F.write('{0},{1},{2},{3},{4},{5},{6},{7}\n'.format(
ID, kind, x, y, P, N0, S, D))
if len(x_markers) == 0:
# apparently everyone was a not...
catalog[ID]['agents_labels'] = np.array([])
continue
# ------------------------------------------------------------------
# cluster
print 'make_lens_catalog: subject ID = ', ID
if flags['skill']:
cluster_centers, cluster_center_labels, cluster_labels, \
n_clusters, dist_within = outlier_clusters(x_markers, y_markers, skill, memory=memory)
else:
cluster_centers, cluster_center_labels, cluster_labels, \
n_clusters, dist_within = outlier_clusters(x_markers, y_markers, None, memory=memory)
# need to get: x, y, N0, S
catalog[ID]['agents_labels'] = cluster_labels
for cluster_center_label in cluster_center_labels:
cluster_center = cluster_centers[cluster_center_label]
members = (cluster_labels == cluster_center_label)
x, y = cluster_center
# convert y to catalog convention
y = flags['image_y_size'] - y
N0 = np.sum(members)
S = np.sum(skill[members])
D = dist_within[cluster_center_label]
if cluster_center_label == -1:
# outlier cluster
# so really every point is its own cluster...
D = 0
## catalog.append((ID, kind, x, y, P, N0, S, D))
## if len(catalog)%500 == 0:
## print len(catalog)
# TODO: make some requirement to be included (exclude outliers)
if len(flags['output_name']) > 0:
F.write('{0},{1},{2},{3},{4},{5},{6},{7}\n'.format(
ID, kind, x, y, P, N0, S, D))
print 'make_lens_catalog: Clearing memory'
# clear memory
memory.clear()
if len(flags['output_name']) > 0:
print 'make_lens_catalog: closing file!'
F.close()
if len(flags['update_collection']) > 0:
print 'make_lens_catalog: writing updated collection to', flags['update_collection']
# TODO: get the other params correct!!!!
collection_fat = swap.collection.Collection()
for ID in catalog:
subject = collection.member[ID]
atx = subject.annotationhistory['At_X']
labels_in = list(catalog[ID]['agents_labels'])
labels_fat = []
for atx_i in atx:
labels_fat.append([])
for atx_ij in atx_i:
labels_fat[-1].append(labels_in.pop(0))
subject.annotationhistory.update({'labels': labels_fat})
collection_fat.member.update({ID: subject})
swap.write_pickle(collection_fat, flags['update_collection'])
print 'make_lens_catalog: All done!'
return catalog
plotplpd(final_PL1,final_PD1,information1,1,"Stage 1 Information")
plotplpd(final_PL2,final_PD2,information2,2,"Stage 2 Information")
savefig("information_plpd.png")
clf();
###########################
##Skill PL PD plot
###########################
bins=101
skill=np.zeros(bins*bins);
skill=np.reshape(skill,(bins,bins));
for ii in range(bins):
M_ll=0.01*ii;
for jj in range(bins):
M_nn=0.01*jj;
skill[ii][jj]=swap.expectedInformationGain(0.5, M_ll, M_nn);
ax=subplot(1,1,1);
im=ax.imshow(skill,origin='lower',extent=(0,1,0,1));
cbar=colorbar(im);
cbar.solids.set_edgecolor("face");
ax.set_xlim(0,1);
ax.set_ylim(0,1);
ax.set_xlabel("P$_L$");
ax.set_ylabel("P$_D$");
ax.set_title("Skill");
xx=np.arange(-0.1,2,0.1);
ax.axhline(0.5,color="k",linestyle='dashed');
ax.axvline(0.5,color="k",linestyle='dashed');
ax.plot(xx,1-xx,color="k");
def make_lens_atlas(args):
"""
NAME
make_lens_atlas
PURPOSE
Given location of bureau and collection pickles as well as a list of
subjects, this script produces a set of annotated images of lenses
(heatmaps for lens locations, markers for where clicks were, etc).
COMMENTS
You have to download the file so it chooses whever your output
directory is to also download the raw images.
This should be pretty customizable.
FLAGS
-h Print this message
--heatmap Do heatmaps
--contour Do contours
--field Do full image
--stamp Do cutouts
--alpha Do alpha
--points N Take N agents and plot them. Any number < 0 = do all
--skill Weight agent markers by skill
INPUTS
collection collection.pickle
catalog catalog.dat
Assumed format:
ID kind x y Prob N0 Skill Dist
Here:
ID = Space Warps subject ID
kind = Space Warps subject type (sim, dud, test)
x,y = object (cluster) centroid, in pixels
P = Space Warps subject probability
N0 = number of markers in the cluster
S = total skill per cluster, summed over markers
D = biggest distance within cluster
OUTPUTS
EXAMPLE
BUGS
TODO: incorporate some of these defaults into the flags dictionary
AUTHORS
This file is part of the Space Warps project, and is distributed
under the GPL v2 by the Space Warps Science Team.
http://spacewarps.org/
HISTORY
2013-07-16 started Davis (KIPAC)
"""
# ------------------------------------------------------------------
# Some defaults:
flags = {'points': 30,
'heatmap': False,
'contour': False,
'field': False,
'stamp': False,
'alpha': False,
'skill': False,
'output_directory': './',
'output_format': 'png',
'stamp_size': 50,
'dist_max': 30,
'stamp_min': 1,
'smooth_click': 3,
'figsize_stamp': 5,
'figsize_field': 10,
'image_y_size': 440,
'diagnostics': False,
}
# ------------------------------------------------------------------
# Read in options:
# this has to be easier to do...
for arg in args:
if arg in flags:
flags[arg] = args[arg]
elif arg == 'collection':
collection_path = args[arg]
elif arg == 'catalog':
catalog_path = args[arg]
else:
print "make_lens_atlas: unrecognized flag ",arg
xbins = np.arange(flags['stamp_size'] * 2)
ybins = np.arange(flags['stamp_size'] * 2)
figsize_stamp = (flags['figsize_stamp'], flags['figsize_stamp'])
figsize_field = (flags['figsize_field'], flags['figsize_field'])
image_y_size = flags['image_y_size']
print "make_lens_atlas: illustrating behaviour captured in collection, and lens files: "
print "make_lens_atlas: ", collection_path
print "make_lens_atlas: ", catalog_path
# ------------------------------------------------------------------
# Read in files:
#bureau = swap.read_pickle(bureau_path, 'bureau') # TODO: needed?
collection = swap.read_pickle(collection_path, 'collection')
catalog = csv2rec(catalog_path)
#print "make_lens_atlas: bureau numbers ", len(bureau.list())
print "make_lens_atlas: collection numbers ", len(collection.list())
print "make_lens_atlas: catalog numbers ", len(catalog)
# ------------------------------------------------------------------
# Run through data:
# ------------------------------------------------------------------
# Stamps:
if flags['stamp']:
print "make_lens_atlas: running stamps"
for lens_i in range(len(catalog)):
ID = catalog[lens_i]['id']
kind = catalog[lens_i]['kind']
x = catalog[lens_i]['x']
# flip y axis
y = image_y_size - catalog[lens_i]['y']
N0 = catalog[lens_i]['n0']
if 'dist' in catalog.dtype.names:
if catalog[lens_i]['dist'] == 0:
continue
if ((x < 0)):
# this is one of the 'non points'; skip
continue
if (N0 < flags['stamp_min']):
# not enough points!
continue
subject = collection.member[ID]
annotationhistory = subject.annotationhistory
# ------------------------------------------------------------------
# download png
url = subject.location
outname = flags['output_directory'] + '{0}_field.png'.format(ID)
im = get_online_png(url, outname)
min_x = np.int(np.max((x - flags['stamp_size'], 0)))
max_x = np.int(np.min((x + flags['stamp_size'], im.shape[0])))
min_y = np.int(np.max((y - flags['stamp_size'], 0)))
max_y = np.int(np.min((y + flags['stamp_size'], im.shape[1])))
min_member_x = np.int(np.max((x - flags['dist_max'], 0)))
max_member_x = np.int(np.min((x + flags['dist_max'], im.shape[0])))
min_member_y = np.int(np.max((y - flags['dist_max'], 0)))
max_member_y = np.int(np.min((y + flags['dist_max'], im.shape[1])))
if (min_x >= max_x) + (min_y >= max_y):
print "make_lens_atlas: misshapen lens for ID ", ID
continue
# if it is a training image, claim the alpha parameter
if im.shape[2] == 4:
alpha = im[:, :, 3][min_y: max_y, min_x: max_x]
im = im[:, :, :3][min_y: max_y, min_x: max_x]
else:
alpha = None
im = im[min_y: max_y, min_x: max_x]
fig = plt.figure(figsize=figsize_stamp)
ax = fig.add_subplot(111)
ax.imshow(im, origin=origin)
ax.scatter(x - min_x,
y - min_y,
marker='d',
c=(0, 1.0, 0), s=100,
alpha=0.75)
if ((flags['contour'])
+ (flags['heatmap'])
+ (flags['points'] != 0)):
itwas = annotationhistory['ItWas']
x_all = annotationhistory['At_X']
y_all = annotationhistory['At_Y']
x_markers_all = np.array([xi for xj in x_all for xi in xj])
y_markers_all = np.array([yi for yj in y_all for yi in yj])
agents_numbers = np.arange(
x_markers_all.size)
if 'labels' in annotationhistory:
# find which label is closest to your folks
labels_all = annotationhistory['labels']
labels = np.array([xi for xj in labels_all for xi in xj])
cluster_labels = list(set(labels))
data = np.vstack((x_markers_all, y_markers_all)).T
cluster_centers = np.array([np.mean(data[labels == i], axis=0)
for i in cluster_labels])
# find which label is closest to the (x,y)
label_center = cluster_labels[np.argmin(np.sum(np.square(cluster_centers - np.vstack((x, y)).T), axis=1))]
conds = (labels == label_center)
else:
# now filter markers by those that are within
# dist_max of the center (since I don't record cluster
# members...)
conds = ((x_markers_all >= min_member_x) *
(x_markers_all <= max_member_x) *
(y_markers_all >= min_member_y) *
(y_markers_all <= max_member_y))
agents = agents_numbers[conds]
x_markers = x_markers_all[agents]
y_markers = y_markers_all[agents]
# filter markers
n_catalog = len(agents)
if (flags['points'] > 0) * \
(flags['points'] < n_catalog):
agents_points = np.random.choice(
agents,
size=flags['points'], replace=False)
else:
agents_points = agents
x_markers_filtered = x_markers_all[agents_points]
y_markers_filtered = y_markers_all[agents_points]
if (flags['skill']) * (len(agents) > 0):
PL_all = annotationhistory['PL']
PD_all = annotationhistory['PD']
# filter out the empty clicks
PL_list = []
for i, xj in enumerate(x_all):
PL_list.append([PL_all[i]] * len(xj))
PL = np.array([PLi for PLj in PL_list for PLi in PLj])
# filter out the empty clicks
PD_list = []
for i, xj in enumerate(x_all):
PD_list.append([PD_all[i]] * len(xj))
PD = np.array([PDi for PDj in PD_list for PDi in PDj])
skill_all = swap.expectedInformationGain(0.5, PL, PD)
skill = skill_all[agents]
smax = 100
smin = 5
if np.max(skill) != np.min(skill):
sizes_all = (skill_all - np.min(skill)) * (smax - smin) / \
(np.max(skill) - np.min(skill))
sizes_filtered = sizes_all[agents_points]
else:
sizes_filtered = 50
else:
skill = None
sizes_filtered = 50
colors = (0, 1.0, 0)
# ----------------------------------------------------------
# heatmaps
if (flags['heatmap']) * (len(agents) > 0):
fig_heatmap = plt.figure(figsize=figsize_stamp)
ax_heatmap = fig_heatmap.add_subplot(111)
# now do the lens locations
# don't need to filter the x's since that is filtered by
# xbins and ybins anyways
pdf2d(x_markers - min_x, y_markers - min_y,
xbins=xbins, ybins=ybins,
weights=skill, smooth=flags['smooth_click'],
color=(0, 1.0, 0),
style='hist',
axis=ax_heatmap)
if flags['alpha'] * (alpha != None):
contour_hist(alpha.T,
extent=(xbins[0], xbins[-1], ybins[0], ybins[-1]),
color='w', style='contour', axis=ax_heatmap)
ax_heatmap.tick_params(\
axis='both', # changes apply to the x-axis
which='both', # both major and minor ticks are affected
bottom='off', # ticks along the bottom edge are off
top='off', # ticks along the top edge are off
left='off',
right='off',
labelleft='off',
labelbottom='off') # labels along the bottom edge are off
# CPD 04.08.14: Flip axis to old conventions
ax_heatmap.invert_yaxis()
try:
outfile = flags['output_directory'] + \
'{0}_cluster_{1}_heatmap.{2}'.format(
ID, lens_i, flags['output_format'])
# fig_heatmap.savefig(outfile)
#fig_heatmap.canvas.print_png(outfile)
fig_heatmap.savefig(outfile, bbox_inches='tight', pad_inches=0)
except:
print 'make_lens_catalog: heatmap problem with ', ID, lens_i
# import ipdb; ipdb.set_trace()
# ---------------------------------------------------------
# back to our other plots
# contours
if (flags['contour']) * (len(agents) > 0):
# now do the lens locations
# don't need to filter the x's since that is filtered by
# xbins and ybins anyways
pdf2d(x_markers - min_x, y_markers - min_y,
xbins=xbins, ybins=ybins,
weights=skill, smooth=flags['smooth_click'],
color=(0, 1.0, 0),
style='contour',
axis=ax)
# plot points
if (flags['points'] != 0) * (len(agents) > 0):
ax.scatter(x_markers_filtered - min_x,
y_markers_filtered - min_y,
c=colors, s=sizes_filtered,
alpha=0.25)
# plot alpha
if flags['alpha'] * (alpha != None):
contour_hist(alpha.T,
extent=(xbins[0], xbins[-1], ybins[0], ybins[-1]),
color='w', style='contour', axis=ax)
# ----------------------------------------------------------
ax.tick_params(\
axis='both', # changes apply to the x-axis
which='both', # both major and minor ticks are affected
bottom='off', # ticks along the bottom edge are off
top='off', # ticks along the top edge are off
left='off',
right='off',
labelleft='off',
labelbottom='off') # labels along the bottom edge are off
ax.invert_yaxis()
try:
outfile = flags['output_directory'] + \
'{0}_cluster_{1}_contour.{2}'.format(
ID, lens_i, flags['output_format']
)
# fig.savefig(outfile)
fig.savefig(outfile, bbox_inches='tight', pad_inches=0)
# fig.canvas.print_png(outfile)
except:
print 'make_lens_catalog: contour problem with ', ID, lens_i
# import ipdb; ipdb.set_trace()
plt.close('all')
# ------------------------------------------------------------------
# Fields
if flags['field']:
print "make_lens_atlas: running fields"
# find the unique IDs. mark centers and also centrals if clustering is
# done
#import ipdb; ipdb.set_trace()
unique_IDs = np.unique(catalog['id'])
for ID in unique_IDs:
mini_catalog = catalog[catalog['id'] == ID]
subject = collection.member[ID]
annotationhistory = subject.annotationhistory
# plot cluster centers
kind = mini_catalog['kind']
x_centers = mini_catalog['x']
# flip y from catalog
y_centers = image_y_size - mini_catalog['y']
skill_centers = mini_catalog['skill']
# filter out the -1 entry
center_cond = (x_centers > 0) * (y_centers > 0)
# filter outliers if possible
if 'dist' in mini_catalog.dtype.names:
center_cond *= mini_catalog['dist'] > 0
skill_centers = skill_centers[center_cond]
x_centers = x_centers[center_cond]
y_centers = y_centers[center_cond]
colors_centers = [(0, 1.0, 0) for i in x_centers]
if len(colors_centers) == 0:
#welp, nothing here
continue
# ------------------------------------------------------------------
# download png
url = subject.location
outname = flags['output_directory'] + '{0}_field.png'.format(ID)
im = get_online_png(url, outname)
# if it is a training image, claim the alpha parameter
if im.shape[2] == 4:
alpha = im[:, :, 3]
im = im[:, :, :3]
else:
alpha = None
fig = plt.figure(figsize=figsize_field)
ax = fig.add_subplot(111)
ax.imshow(im, origin=origin)
xbins = np.arange(im.shape[0])
ybins = np.arange(im.shape[1])
min_x = 0
min_y = 0
max_x = im.shape[0]
max_y = im.shape[1]
if (flags['skill']) * (np.max(skill_centers) != np.min(skill_centers)):
sizes_centers = (
(skill_centers - np.min(skill_centers)) *
(200 - 10) /
(np.max(skill_centers) - np.min(skill_centers)))
else:
sizes_centers = [100 for i in x_centers]
sizes_centers = [100 for i in x_centers]
ax.scatter(x_centers, y_centers,
marker='d', c=colors_centers,
s=sizes_centers, alpha=0.75)
if flags['diagnostics']:
r = flags['dist_max']
b = flags['stamp_size']
b_ones = np.ones(100) * b
b_arr = np.linspace(-b, b, 100)
def xy(x0, y0, r, phi):
return x0 + r * np.cos(phi), y0 + r * np.sin(phi)
phis = np.arange(0, 6.28, 0.01)
for i in xrange(len(x_centers)):
x_center = x_centers[i]
y_center = y_centers[i]
ax.plot( *xy(x_center, y_center, r, phis), c='w', ls='-', linewidth=4)
# plot box
ax.plot(x_center + b_ones, y_center + b_arr, c='r', ls='--', linewidth=4)
ax.plot(x_center - b_ones, y_center + b_arr, c='r', ls='--', linewidth=4)
ax.plot(x_center + b_arr, y_center + b_ones, c='r', ls='--', linewidth=4)
ax.plot(x_center + b_arr, y_center - b_ones, c='r', ls='--', linewidth=4)
itwas = annotationhistory['ItWas']
x_all = annotationhistory['At_X']
y_all = annotationhistory['At_Y']
x_markers_all = np.array([xi for xj in x_all for xi in xj])
y_markers_all = np.array([yi for yj in y_all for yi in yj])
# now filter markers by those that are within
# stamp_size of the stamp
# I'm pretty sure this step is redundant when going over the full
# image?
agents_numbers = np.arange(
x_markers_all.size)
conds = ((x_markers_all >= min_x) * (x_markers_all <= max_x) *
(y_markers_all >= min_y) * (y_markers_all <= max_y))
agents = agents_numbers[conds]
x_markers = x_markers_all[agents]
y_markers = y_markers_all[agents]
# filter markers
n_catalog = len(agents)
if (flags['points'] > 0) * \
(flags['points'] < n_catalog):
agents_points = np.random.choice(
agents,
size=flags['points'], replace=False)
else:
agents_points = agents
x_markers_filtered = x_markers_all[agents_points]
y_markers_filtered = y_markers_all[agents_points]
if flags['skill']:
PL_all = annotationhistory['PL']
PD_all = annotationhistory['PD']
# filter out the empty clicks
PL_list = []
for i, xj in enumerate(x_all):
PL_list.append([PL_all[i]] * len(xj))
PL = np.array([PLi for PLj in PL_list for PLi in PLj])
# filter out the empty clicks
PD_list = []
for i, xj in enumerate(x_all):
PD_list.append([PD_all[i]] * len(xj))
PD = np.array([PDi for PDj in PD_list for PDi in PDj])
skill_all = swap.expectedInformationGain(0.5, PL, PD)
skill = skill_all[agents]
smax = 100
smin = 5
if np.max(skill) != np.min(skill):
sizes_all = (skill_all - np.min(skill)) * (smax - smin) / \
(np.max(skill) - np.min(skill))
sizes_filtered = sizes_all[agents_points]
else:
sizes_filtered = 50
else:
skill = None
sizes_filtered = 50
if 'labels' in annotationhistory:
# find which label is closest to your folks
labels_all = annotationhistory['labels']
labels = np.array([xi for xj in labels_all for xi in xj])
labels_filtered = labels[agents_points]
colors = []
alpha = 0.75
for label in labels_filtered:
if label == -1:
colors.append((1.0, 0.0, 0))
else:
colors.append((0, 1.0, 0))
else:
colors = (0, 1.0, 0)
alpha = 0.25
# ----------------------------------------------------------
# contours
if flags['contour'] * (len(x_markers) >= flags['stamp_min']):
# now do the lens locations
# don't need to filter the x's since that is filtered by
# xbins and ybins anyways
pdf2d(x_markers - min_x, y_markers - min_y,
xbins=xbins, ybins=ybins,
weights=skill, smooth=flags['smooth_click'],
color=(0, 1.0, 0),
style='contour',
axis=ax)
# ----------------------------------------------------------
# plot points
if flags['points'] != 0:
ax.scatter(x_markers_filtered - min_x,
y_markers_filtered - min_y,
c=colors, s=sizes_filtered,
alpha=alpha)
# ----------------------------------------------------------
# do alpha
if flags['alpha'] * (alpha != None):
contour_hist(alpha.T,
extent=(xbins[0], xbins[-1], ybins[0], ybins[-1]),
color='w', style='contour', axis=ax)
ax.tick_params(\
axis='both', # changes apply to the x-axis
which='both', # both major and minor ticks are affected
bottom='off', # ticks along the bottom edge are off
top='off', # ticks along the top edge are off
left='off',
right='off',
labelleft='off',
labelbottom='off') # labels along the bottom edge are off
ax.invert_yaxis()
try:
outfile = flags['output_directory'] + '{0}_field_output.{1}'.format(ID, flags['output_format'])
# fig.savefig(outfile)
fig.savefig(outfile, bbox_inches='tight', pad_inches=0)
#fig.canvas.print_png(outfile)
except:
print 'make_lens_catalog: field problem with field ', ID
plt.close('all')
print 'make_lens_catalog: All done!'
def make_lens_catalog(args):
"""
NAME
make_lens_catalog
PURPOSE
Given location of collection pickle, this script produces a set of
annotated images of lenses (heatmaps for lens locations, markers for
where clicks were, etc).
COMMENTS
You have to download the file so it chooses whever your output
directory is to also download the raw images.
This should be pretty customizable.
FLAGS
-h Print this message
--skill Weight by skill
INPUTS
collection.pickle
OUTPUTS
lens.dat
Assumed format:
ID kind x y Prob N0 Skill Dist
Here:
ID = Space Warps subject ID
kind = Space Warps subject type (sim, dud, test)
x,y = object (cluster) centroid, in pixels
P = Space Warps subject probability
N0 = number of markers in the cluster
S = total skill per cluster, summed over markers
D = biggest distance within cluster
EXAMPLE
BUGS
AUTHORS
This file is part of the Space Warps project, and is distributed
under the GPL v2 by the Space Warps Science Team.
http://spacewarps.org/
HISTORY
2013-07-16 started Davis (KIPAC)
"""
# ------------------------------------------------------------------
# Some defaults:
flags = {
'skill': False,
'output_directory': './',
'output_name': 'catalog.dat',
'image_y_size': 440,
'catalog_path': '',
'update_collection': '',
}
# ------------------------------------------------------------------
# Read in options:
# this has to be easier to do...
for arg in args:
if arg in flags:
flags[arg] = args[arg]
elif arg == 'collection_path':
collection_path = args[arg]
else:
print "make_lens_atlas: unrecognized flag ", arg
print "make_lens_catalog: illustrating behaviour captured in collection file: "
print "make_lens_catalog: ", collection_path
memory = joblib.Memory(cachedir=flags['output_directory'])
memory.clear()
catalog_path = flags['output_directory'] + flags['output_name']
if len(flags['output_name']) > 0:
F = open(catalog_path, 'w')
F.write('id,kind,x,y,prob,n0,skill,dist\n')
# ------------------------------------------------------------------
# Read in files:
collection = swap.read_pickle(collection_path, 'collection')
ID_list = collection.list()
print "make_lens_catalog: collection numbers ", len(ID_list)
if flags['catalog_path'] != '':
print "make_lens_catalog: filtering from catalog ", flags[
'catalog_path']
catalog_in = csv2rec(flags['catalog_path'])
ID_list = np.unique(catalog_in['id'])
# ------------------------------------------------------------------
# Run through data:
catalog = {}
for ID in ID_list:
subject = collection.member[ID]
kind = subject.kind
P = subject.mean_probability
itwas = subject.annotationhistory['ItWas']
x_all = subject.annotationhistory['At_X']
y_all = subject.annotationhistory['At_Y']
x_markers = np.array([xi for xj in x_all for xi in xj])
y_markers = np.array([yi for yj in y_all for yi in yj])
catalog.update(
{ID: {
'agents_reject': [],
'x': x_markers,
'y': y_markers,
}})
PL_all = subject.annotationhistory['PL']
PD_all = subject.annotationhistory['PD']
# filter out the empty clicks
PL_list = []
PL_nots = []
for i, xj in enumerate(x_all):
# len(xj) of empty = 0
PL_list.append([PL_all[i]] * len(xj))
if len(xj) == 0:
PL_nots.append(PL_all[i])
PL = np.array([PLi for PLj in PL_list for PLi in PLj])
PL_nots = np.array(PL_nots)
# filter out the empty clicks
PD_list = []
PD_nots = []
for i, xj in enumerate(x_all):
PD_list.append([PD_all[i]] * len(xj))
if len(xj) == 0:
PD_nots.append(PD_all[i])
catalog[ID]['agents_reject'].append(i)
PD = np.array([PDi for PDj in PD_list for PDi in PDj])
PD_nots = np.array(PD_nots)
skill = swap.expectedInformationGain(0.5, PL, PD) # skill
# it is only fair to write out the NOTs, too
# do the empty guys
skill_nots = swap.expectedInformationGain(0.5, PL_nots,
PD_nots) # skill
x, y = -1, -1
N0 = len(skill_nots)
S = np.sum(skill_nots)
D = 0
## catalog.append((ID, kind, x, y, P, N0, S, D))
if len(catalog) % 500 == 0:
print len(catalog)
if len(flags['output_name']) > 0:
F.write('{0},{1},{2},{3},{4},{5},{6},{7}\n'.format(
ID, kind, x, y, P, N0, S, D))
if len(x_markers) == 0:
# apparently everyone was a not...
catalog[ID]['agents_labels'] = np.array([])
continue
# ------------------------------------------------------------------
# cluster
print 'make_lens_catalog: subject ID = ', ID
if flags['skill']:
cluster_centers, cluster_center_labels, cluster_labels, \
n_clusters, dist_within = outlier_clusters(x_markers, y_markers, skill, memory=memory)
else:
cluster_centers, cluster_center_labels, cluster_labels, \
n_clusters, dist_within = outlier_clusters(x_markers, y_markers, None, memory=memory)
# need to get: x, y, N0, S
catalog[ID]['agents_labels'] = cluster_labels
for cluster_center_label in cluster_center_labels:
cluster_center = cluster_centers[cluster_center_label]
members = (cluster_labels == cluster_center_label)
x, y = cluster_center
# convert y to catalog convention
y = flags['image_y_size'] - y
N0 = np.sum(members)
S = np.sum(skill[members])
D = dist_within[cluster_center_label]
if cluster_center_label == -1:
# outlier cluster
# so really every point is its own cluster...
D = 0
## catalog.append((ID, kind, x, y, P, N0, S, D))
## if len(catalog)%500 == 0:
## print len(catalog)
# TODO: make some requirement to be included (exclude outliers)
if len(flags['output_name']) > 0:
F.write('{0},{1},{2},{3},{4},{5},{6},{7}\n'.format(
ID, kind, x, y, P, N0, S, D))
print 'make_lens_catalog: Clearing memory'
# clear memory
memory.clear()
if len(flags['output_name']) > 0:
print 'make_lens_catalog: closing file!'
F.close()
if len(flags['update_collection']) > 0:
print 'make_lens_catalog: writing updated collection to', flags[
'update_collection']
# TODO: get the other params correct!!!!
collection_fat = swap.collection.Collection()
for ID in catalog:
subject = collection.member[ID]
atx = subject.annotationhistory['At_X']
labels_in = list(catalog[ID]['agents_labels'])
labels_fat = []
for atx_i in atx:
labels_fat.append([])
for atx_ij in atx_i:
labels_fat[-1].append(labels_in.pop(0))
subject.annotationhistory.update({'labels': labels_fat})
collection_fat.member.update({ID: subject})
swap.write_pickle(collection_fat, flags['update_collection'])
print 'make_lens_catalog: All done!'
return catalog
def make_lens_atlas(args):
"""
NAME
make_lens_atlas
PURPOSE
Given location of bureau and collection pickles as well as a list of
subjects, this script produces a set of annotated images of lenses
(heatmaps for lens locations, markers for where clicks were, etc).
COMMENTS
You have to download the file so it chooses whever your output
directory is to also download the raw images.
This should be pretty customizable.
FLAGS
-h Print this message
--heatmap Do heatmaps
--contour Do contours
--field Do full image
--stamp Do cutouts
--alpha Do alpha
--points N Take N agents and plot them. Any number < 0 = do all
--skill Weight agent markers by skill
INPUTS
collection collection.pickle
catalog catalog.dat
Assumed format:
ID kind x y Prob N0 Skill Dist
Here:
ID = Space Warps subject ID
kind = Space Warps subject type (sim, dud, test)
x,y = object (cluster) centroid, in pixels
P = Space Warps subject probability
N0 = number of markers in the cluster
S = total skill per cluster, summed over markers
D = biggest distance within cluster
OUTPUTS
EXAMPLE
BUGS
TODO: incorporate some of these defaults into the flags dictionary
AUTHORS
This file is part of the Space Warps project, and is distributed
under the GPL v2 by the Space Warps Science Team.
http://spacewarps.org/
HISTORY
2013-07-16 started Davis (KIPAC)
"""
# ------------------------------------------------------------------
# Some defaults:
flags = {
'points': 30,
'heatmap': False,
'contour': False,
'field': False,
'stamp': False,
'alpha': False,
'skill': False,
'output_directory': './',
'output_format': 'png',
'stamp_size': 50,
'dist_max': 30,
'stamp_min': 1,
'smooth_click': 3,
'figsize_stamp': 5,
'figsize_field': 10,
'image_y_size': 440,
'diagnostics': False,
}
# ------------------------------------------------------------------
# Read in options:
# this has to be easier to do...
for arg in args:
if arg in flags:
flags[arg] = args[arg]
elif arg == 'collection':
collection_path = args[arg]
elif arg == 'catalog':
catalog_path = args[arg]
else:
print "make_lens_atlas: unrecognized flag ", arg
print(flags)
xbins = np.arange(flags['stamp_size'] * 2)
ybins = np.arange(flags['stamp_size'] * 2)
figsize_stamp = (flags['figsize_stamp'], flags['figsize_stamp'])
figsize_field = (flags['figsize_field'], flags['figsize_field'])
image_y_size = flags['image_y_size']
print "make_lens_atlas: illustrating behaviour captured in collection, and lens files: "
print "make_lens_atlas: ", collection_path
print "make_lens_atlas: ", catalog_path
# ------------------------------------------------------------------
# Read in files:
#bureau = swap.read_pickle(bureau_path, 'bureau') # TODO: needed?
collection = swap.read_pickle(collection_path, 'collection')
catalog = csv2rec(catalog_path)
#print "make_lens_atlas: bureau numbers ", len(bureau.list())
print "make_lens_atlas: collection numbers ", len(collection.list())
print "make_lens_atlas: catalog numbers ", len(catalog)
# ------------------------------------------------------------------
# Run through data:
# ------------------------------------------------------------------
# Stamps:
if flags['stamp']:
print "make_lens_atlas: running stamps"
for lens_i in range(len(catalog)):
ID = catalog[lens_i]['id']
kind = catalog[lens_i]['kind']
x = catalog[lens_i]['x']
# flip y axis
y = image_y_size - catalog[lens_i]['y']
N0 = catalog[lens_i]['n0']
if 'dist' in catalog.dtype.names:
if catalog[lens_i]['dist'] == 0:
continue
if ((x < 0)):
# this is one of the 'non points'; skip
print(lens_i, 'x < 0!')
continue
if (N0 < flags['stamp_min']):
# not enough points!
print(lens_i, '{0} < {1}'.format(N0, flags['stamp_min']))
continue
subject = collection.member[ID]
annotationhistory = subject.annotationhistory
# ------------------------------------------------------------------
# download png
url = subject.location
outname = flags['output_directory'] + '{0}_field.png'.format(ID)
im = get_online_png(url, outname)
min_x = np.int(np.max((x - flags['stamp_size'], 0)))
max_x = np.int(np.min((x + flags['stamp_size'], im.shape[0])))
min_y = np.int(np.max((y - flags['stamp_size'], 0)))
max_y = np.int(np.min((y + flags['stamp_size'], im.shape[1])))
min_member_x = np.int(np.max((x - flags['dist_max'], 0)))
max_member_x = np.int(np.min((x + flags['dist_max'], im.shape[0])))
min_member_y = np.int(np.max((y - flags['dist_max'], 0)))
max_member_y = np.int(np.min((y + flags['dist_max'], im.shape[1])))
if (min_x >= max_x) + (min_y >= max_y):
print "make_lens_atlas: misshapen lens for ID ", ID
continue
# if it is a training image, claim the alpha parameter
if im.shape[2] == 4:
alpha = im[:, :, 3][min_y:max_y, min_x:max_x]
im = im[:, :, :3][min_y:max_y, min_x:max_x]
else:
alpha = None
im = im[min_y:max_y, min_x:max_x]
fig = plt.figure(figsize=figsize_stamp)
ax = fig.add_subplot(111)
ax.imshow(im, origin=origin)
ax.scatter(x - min_x,
y - min_y,
marker='d',
c=(0, 1.0, 0),
s=100,
alpha=0.75)
if ((flags['contour']) + (flags['heatmap']) +
(flags['points'] != 0)):
itwas = annotationhistory['ItWas']
x_all = annotationhistory['At_X']
y_all = annotationhistory['At_Y']
x_markers_all = np.array([xi for xj in x_all for xi in xj])
y_markers_all = np.array([yi for yj in y_all for yi in yj])
agents_numbers = np.arange(x_markers_all.size)
if 'labels' in annotationhistory:
# find which label is closest to your folks
labels_all = annotationhistory['labels']
labels = np.array([xi for xj in labels_all for xi in xj])
cluster_labels = list(set(labels))
data = np.vstack((x_markers_all, y_markers_all)).T
cluster_centers = np.array([
np.mean(data[labels == i], axis=0)
for i in cluster_labels
])
# find which label is closest to the (x,y)
label_center = cluster_labels[np.argmin(
np.sum(np.square(cluster_centers -
np.vstack((x, y)).T),
axis=1))]
conds = (labels == label_center)
else:
# now filter markers by those that are within
# dist_max of the center (since I don't record cluster
# members...)
conds = ((x_markers_all >= min_member_x) *
(x_markers_all <= max_member_x) *
(y_markers_all >= min_member_y) *
(y_markers_all <= max_member_y))
agents = agents_numbers[conds]
x_markers = x_markers_all[agents]
y_markers = y_markers_all[agents]
# filter markers
n_catalog = len(agents)
if n_catalog < 1:
print(lens_i, n_catalog)
if (flags['points'] > 0) * \
(flags['points'] < n_catalog):
agents_points = np.random.choice(agents,
size=flags['points'],
replace=False)
else:
agents_points = agents
x_markers_filtered = x_markers_all[agents_points]
y_markers_filtered = y_markers_all[agents_points]
if (flags['skill']) * (len(agents) > 0):
PL_all = annotationhistory['PL']
PD_all = annotationhistory['PD']
# filter out the empty clicks
PL_list = []
for i, xj in enumerate(x_all):
PL_list.append([PL_all[i]] * len(xj))
PL = np.array([PLi for PLj in PL_list for PLi in PLj])
# filter out the empty clicks
PD_list = []
for i, xj in enumerate(x_all):
PD_list.append([PD_all[i]] * len(xj))
PD = np.array([PDi for PDj in PD_list for PDi in PDj])
skill_all = swap.expectedInformationGain(0.5, PL, PD)
skill = skill_all[agents]
smax = 100
smin = 5
if np.max(skill) != np.min(skill):
sizes_all = (skill_all - np.min(skill)) * (smax - smin) / \
(np.max(skill) - np.min(skill))
sizes_filtered = sizes_all[agents_points]
else:
sizes_filtered = 50
else:
skill = None
sizes_filtered = 50
colors = (0, 1.0, 0)
# ----------------------------------------------------------
# heatmaps
if (flags['heatmap']) * (len(agents) > 0):
fig_heatmap = plt.figure(figsize=figsize_stamp)
ax_heatmap = fig_heatmap.add_subplot(111)
# now do the lens locations
# don't need to filter the x's since that is filtered by
# xbins and ybins anyways
pdf2d(x_markers - min_x,
y_markers - min_y,
xbins=xbins,
ybins=ybins,
weights=skill,
smooth=flags['smooth_click'],
color=(0, 1.0, 0),
style='hist',
axis=ax_heatmap)
if flags['alpha'] * (alpha != None):
contour_hist(alpha.T,
extent=(xbins[0], xbins[-1], ybins[0],
ybins[-1]),
color='w',
style='contour',
axis=ax_heatmap)
ax_heatmap.tick_params(\
axis='both', # changes apply to the x-axis
which='both', # both major and minor ticks are affected
bottom='off', # ticks along the bottom edge are off
top='off', # ticks along the top edge are off
left='off',
right='off',
labelleft='off',
labelbottom='off') # labels along the bottom edge are off
# CPD 04.08.14: Flip axis to old conventions
ax_heatmap.invert_yaxis()
try:
outfile = flags['output_directory'] + \
'{0}_cluster_{1}_heatmap.{2}'.format(
ID, lens_i, flags['output_format'])
# fig_heatmap.savefig(outfile)
#fig_heatmap.canvas.print_png(outfile)
fig_heatmap.savefig(outfile,
bbox_inches='tight',
pad_inches=0)
except:
print 'make_lens_catalog: heatmap problem with ', ID, lens_i
# import ipdb; ipdb.set_trace()
# ---------------------------------------------------------
# back to our other plots
# contours
if (flags['contour']) * (len(agents) > 0):
# now do the lens locations
# don't need to filter the x's since that is filtered by
# xbins and ybins anyways
pdf2d(x_markers - min_x,
y_markers - min_y,
xbins=xbins,
ybins=ybins,
weights=skill,
smooth=flags['smooth_click'],
color=(0, 1.0, 0),
style='contour',
axis=ax)
# plot points
if (flags['points'] != 0) * (len(agents) > 0):
ax.scatter(x_markers_filtered - min_x,
y_markers_filtered - min_y,
c=colors,
s=sizes_filtered,
alpha=0.25)
# plot alpha
if flags['alpha'] * (alpha != None):
contour_hist(alpha.T,
extent=(xbins[0], xbins[-1], ybins[0], ybins[-1]),
color='w',
style='contour',
axis=ax)
# ----------------------------------------------------------
ax.tick_params(\
axis='both', # changes apply to the x-axis
which='both', # both major and minor ticks are affected
bottom='off', # ticks along the bottom edge are off
top='off', # ticks along the top edge are off
left='off',
right='off',
labelleft='off',
labelbottom='off') # labels along the bottom edge are off
ax.invert_yaxis()
try:
outfile = flags['output_directory'] + \
'{0}_cluster_{1}_contour.{2}'.format(
ID, lens_i, flags['output_format']
)
# fig.savefig(outfile)
fig.savefig(outfile, bbox_inches='tight', pad_inches=0)
# fig.canvas.print_png(outfile)
except:
print 'make_lens_catalog: contour problem with ', ID, lens_i
# import ipdb; ipdb.set_trace()
plt.close('all')
# ------------------------------------------------------------------
# Fields
if flags['field']:
print "make_lens_atlas: running fields"
# find the unique IDs. mark centers and also centrals if clustering is
# done
#import ipdb; ipdb.set_trace()
unique_IDs = np.unique(catalog['id'])
for ID in unique_IDs:
mini_catalog = catalog[catalog['id'] == ID]
subject = collection.member[ID]
annotationhistory = subject.annotationhistory
# plot cluster centers
kind = mini_catalog['kind']
x_centers = mini_catalog['x']
# flip y from catalog
y_centers = image_y_size - mini_catalog['y']
skill_centers = mini_catalog['skill']
# filter out the -1 entry
center_cond = (x_centers > 0) * (y_centers > 0)
# filter outliers if possible
if 'dist' in mini_catalog.dtype.names:
center_cond *= mini_catalog['dist'] > 0
skill_centers = skill_centers[center_cond]
x_centers = x_centers[center_cond]
y_centers = y_centers[center_cond]
colors_centers = [(0, 1.0, 0) for i in x_centers]
if len(colors_centers) == 0:
#welp, nothing here
continue
# ------------------------------------------------------------------
# download png
url = subject.location
outname = flags['output_directory'] + '{0}_field.png'.format(ID)
im = get_online_png(url, outname)
# if it is a training image, claim the alpha parameter
if im.shape[2] == 4:
alpha = im[:, :, 3]
im = im[:, :, :3]
else:
alpha = None
fig = plt.figure(figsize=figsize_field)
ax = fig.add_subplot(111)
ax.imshow(im, origin=origin)
xbins = np.arange(im.shape[0])
ybins = np.arange(im.shape[1])
min_x = 0
min_y = 0
max_x = im.shape[0]
max_y = im.shape[1]
if (flags['skill']) * (np.max(skill_centers) !=
np.min(skill_centers)):
sizes_centers = (
(skill_centers - np.min(skill_centers)) * (200 - 10) /
(np.max(skill_centers) - np.min(skill_centers)))
else:
sizes_centers = [100 for i in x_centers]
sizes_centers = [100 for i in x_centers]
ax.scatter(x_centers,
y_centers,
marker='d',
c=colors_centers,
s=sizes_centers,
alpha=0.75)
if flags['diagnostics']:
r = flags['dist_max']
b = flags['stamp_size']
b_ones = np.ones(100) * b
b_arr = np.linspace(-b, b, 100)
def xy(x0, y0, r, phi):
return x0 + r * np.cos(phi), y0 + r * np.sin(phi)
phis = np.arange(0, 6.28, 0.01)
for i in xrange(len(x_centers)):
x_center = x_centers[i]
y_center = y_centers[i]
ax.plot(*xy(x_center, y_center, r, phis),
c='w',
ls='-',
linewidth=4)
# plot box
ax.plot(x_center + b_ones,
y_center + b_arr,
c='r',
ls='--',
linewidth=4)
ax.plot(x_center - b_ones,
y_center + b_arr,
c='r',
ls='--',
linewidth=4)
ax.plot(x_center + b_arr,
y_center + b_ones,
c='r',
ls='--',
linewidth=4)
ax.plot(x_center + b_arr,
y_center - b_ones,
c='r',
ls='--',
linewidth=4)
itwas = annotationhistory['ItWas']
x_all = annotationhistory['At_X']
y_all = annotationhistory['At_Y']
x_markers_all = np.array([xi for xj in x_all for xi in xj])
y_markers_all = np.array([yi for yj in y_all for yi in yj])
# now filter markers by those that are within
# stamp_size of the stamp
# I'm pretty sure this step is redundant when going over the full
# image?
agents_numbers = np.arange(x_markers_all.size)
conds = ((x_markers_all >= min_x) * (x_markers_all <= max_x) *
(y_markers_all >= min_y) * (y_markers_all <= max_y))
agents = agents_numbers[conds]
x_markers = x_markers_all[agents]
y_markers = y_markers_all[agents]
# filter markers
n_catalog = len(agents)
if (flags['points'] > 0) * \
(flags['points'] < n_catalog):
agents_points = np.random.choice(agents,
size=flags['points'],
replace=False)
else:
agents_points = agents
x_markers_filtered = x_markers_all[agents_points]
y_markers_filtered = y_markers_all[agents_points]
if flags['skill']:
PL_all = annotationhistory['PL']
PD_all = annotationhistory['PD']
# filter out the empty clicks
PL_list = []
for i, xj in enumerate(x_all):
PL_list.append([PL_all[i]] * len(xj))
PL = np.array([PLi for PLj in PL_list for PLi in PLj])
# filter out the empty clicks
PD_list = []
for i, xj in enumerate(x_all):
PD_list.append([PD_all[i]] * len(xj))
PD = np.array([PDi for PDj in PD_list for PDi in PDj])
skill_all = swap.expectedInformationGain(0.5, PL, PD)
skill = skill_all[agents]
smax = 100
smin = 5
if np.max(skill) != np.min(skill):
sizes_all = (skill_all - np.min(skill)) * (smax - smin) / \
(np.max(skill) - np.min(skill))
sizes_filtered = sizes_all[agents_points]
else:
sizes_filtered = 50
else:
skill = None
sizes_filtered = 50
if 'labels' in annotationhistory:
# find which label is closest to your folks
labels_all = annotationhistory['labels']
labels = np.array([xi for xj in labels_all for xi in xj])
labels_filtered = labels[agents_points]
colors = []
alpha = 0.75
for label in labels_filtered:
if label == -1:
colors.append((1.0, 0.0, 0))
else:
colors.append((0, 1.0, 0))
else:
colors = (0, 1.0, 0)
alpha = 0.25
# ----------------------------------------------------------
# contours
if flags['contour'] * (len(x_markers) >= flags['stamp_min']):
# now do the lens locations
# don't need to filter the x's since that is filtered by
# xbins and ybins anyways
pdf2d(x_markers - min_x,
y_markers - min_y,
xbins=xbins,
ybins=ybins,
weights=skill,
smooth=flags['smooth_click'],
color=(0, 1.0, 0),
style='contour',
axis=ax)
# ----------------------------------------------------------
# plot points
if flags['points'] != 0:
ax.scatter(x_markers_filtered - min_x,
y_markers_filtered - min_y,
c=colors,
s=sizes_filtered,
alpha=alpha)
# ----------------------------------------------------------
# do alpha
if flags['alpha'] * (alpha != None):
contour_hist(alpha.T,
extent=(xbins[0], xbins[-1], ybins[0], ybins[-1]),
color='w',
style='contour',
axis=ax)
ax.tick_params(\
axis='both', # changes apply to the x-axis
which='both', # both major and minor ticks are affected
bottom='off', # ticks along the bottom edge are off
top='off', # ticks along the top edge are off
left='off',
right='off',
labelleft='off',
labelbottom='off') # labels along the bottom edge are off
ax.invert_yaxis()
try:
outfile = flags[
'output_directory'] + '{0}_field_output.{1}'.format(
ID, flags['output_format'])
# fig.savefig(outfile)
fig.savefig(outfile, bbox_inches='tight', pad_inches=0)
#fig.canvas.print_png(outfile)
except:
print 'make_lens_catalog: field problem with field ', ID
plt.close('all')
print 'make_lens_catalog: All done!'