def findSuperClusters(self, basic_clusters, raw_data, raw_data_fullreso,
raw_data_fullreso_zs, iteration):
superClusters = []
superClusterContours = np.array([])
if len(basic_clusters):
# use the clustered points to get "seeds" for superclustering
# i.e. open a window to get back unclustered points with low light
seedsAndNeighbors = self.clusters_neighborood(
basic_clusters, raw_data)
# run the superclustering algorithm (GAC with 300 iterations)
superClusterContours = self.supercluster(seedsAndNeighbors)
# get the superclusters with the list of points of each one
superClusterWithPixels = self.supercluster_points(
superClusterContours)
# get a cluster object
rebin = int(2048 / self.shape)
for i, scpixels in enumerate(superClusterWithPixels):
sclu = Cluster(scpixels,
rebin,
raw_data_fullreso,
raw_data_fullreso_zs,
debug=False)
sclu.iteration = iteration
sclu.nclu = i
x = scpixels[:, 0]
y = scpixels[:, 1]
corr, p_value = pearsonr(x, y)
sclu.pearson = p_value
superClusters.append(sclu)
# return the supercluster collection
return superClusters, superClusterContours
def findSuperClusters(self,basic_clusters,raw_data,raw_data_fullreso,raw_data_fullreso_zs,iteration):
superClusters = []; superClusterContours = np.array([])
if len(basic_clusters):
# use the clustered points to get "seeds" for superclustering
# i.e. open a window to get back unclustered points with low light
seedsAndNeighbors = self.clusters_neighborood(basic_clusters,raw_data)
# run the superclustering algorithm (GAC with 300 iterations)
superClusterContours = self.supercluster(seedsAndNeighbors)
# get the superclusters with the list of points of each one
superClusterWithPixels = self.supercluster_points(superClusterContours)
# get a cluster object
rebin = int(2048/self.shape)
for i,scpixels in enumerate(superClusterWithPixels):
sclu = Cluster(scpixels,rebin,raw_data_fullreso,raw_data_fullreso_zs,debug=False)
sclu.iteration=iteration
sclu.nclu = i
x = scpixels[:, 0]; y = scpixels[:, 1]
corr, p_value = pearsonr(x, y)
sclu.pearson = p_value
if self.debug:
print ( "SUPERCLUSTER BARE INTEGRAL = {integral:.1f}".format(integral=sclu.integral()) )
sclu.calibratedEnergy = self.calibrator.calibratedEnergy(sclu.hits_fr)
sclu.pathlength = self.calibrator.clusterLength()
superClusters.append(sclu)
# if i==3:
# print(" === hits list ")
# print(scpixels)
# sclu.dumpToFile('supercluster3')
# return the supercluster collection
return superClusters,superClusterContours
def getClusters(self, plot=False):
from sklearn.cluster import DBSCAN
from iDBSCAN import iDBSCAN
from sklearn import metrics
from scipy.spatial import distance
from scipy.stats import pearsonr
from random import random
outname = self.options.plotDir
if outname and not os.path.exists(outname):
os.system("mkdir -p " + outname)
os.system("cp utils/index.php " + outname)
# Plot parameters #
vmin = 99
vmax = 125
# IDBSCAN parameters #
tip = self.options.tip
scale = 1
iterative = self.options.iterative # number of iterations for the IDBSC
vector_eps = self.options.vector_eps
vector_min_samples = self.options.vector_min_samples
vector_eps = list(np.array(vector_eps, dtype=float) * scale)
vector_min_samples = list(
np.array(vector_min_samples, dtype=float) * scale)
cuts = self.options.cuts
nb_it = 3
#-----Pre-Processing----------------#
rescale = int(2048 / self.rebin)
rebin_image = tl.rebin(self.img_ori, (rescale, rescale))
edges = median_filter(self.image, size=4)
edcopy = edges.copy()
edcopyTight = tl.noisereductor(edcopy, rescale,
self.options.min_neighbors_average)
# make the clustering with DBSCAN algo
# this kills all macrobins with N photons < 1
points = np.array(np.nonzero(np.round(edcopyTight))).astype(int).T
lp = points.shape[0]
if tip == '3D':
Xl = [(ix, iy) for ix, iy in points
] # Aux variable to simulate the Z-dimension
X1 = np.array(Xl).copy() # variable to keep the 2D coordinates
for ix, iy in points: # Looping over the non-empty coordinates
nreplicas = int(self.image[ix, iy]) - 1
for count in range(
nreplicas
): # Looping over the number of 'photons' in that coordinate
Xl.append((ix, iy)) # add a coordinate repeatedly
X = np.array(Xl) # Convert the list to an array
else:
X = points.copy()
X1 = X
if self.options.debug_mode == 0:
self.options.flag_plot_noise = 0
# returned collections
clusters = []
superclusters = []
# clustering will crash if the vector of pixels is empty (it may happen after the zero-suppression + noise filtering)
if len(X) == 0:
return clusters, superclusters
# - - - - - - - - - - - - - -
db = iDBSCAN(iterative=iterative,
vector_eps=vector_eps,
vector_min_samples=vector_min_samples,
cuts=cuts,
flag_plot_noise=self.options.flag_plot_noise).fit(X)
if self.options.debug_mode == 1 and self.options.flag_plot_noise == 1:
for ext in ['png', 'pdf']:
plt.savefig('{pdir}/{name}_{esp}.{ext}'.format(pdir=outname,
name=self.name,
esp='0th',
ext=ext),
bbox_inches='tight',
pad_inches=0)
plt.gcf().clear()
plt.close('all')
# Returning to '2' dimensions
if tip == '3D':
db.labels_ = db.labels_[range(
0, lp)] # Returning theses variables to the length
db.tag_ = db.tag_[range(
0,
lp)] # of the 'real' edges, to exclude the fake repetitions.
# - - - - - - - - - - - - - -
labels = db.labels_
# Number of clusters in labels, ignoring noise if present.
n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
##################### plot
# the following is to preserve the square aspect ratio with all the camera pixels
# plt.axes().set_aspect('equal','box')
# plt.ylim(0,2040)
# plt.xlim(0,2040)
# Black removed and is used for noise instead.
unique_labels = set(labels)
colors = [(random(), random(), random(), 1.0)
for each in range(len(unique_labels))]
# colors = [plt.cm.Spectral(each)
# for each in np.linspace(0, 1, len(unique_labels))]
#canv = ROOT.TCanvas('c1','',600,600)
if plot:
#fig_edges = plt.figure(figsize=(10, 10))
#plt.imshow(self.image.T, cmap='gray', vmin=0, vmax=1, origin='lower' )
#plt.savefig('{pdir}/{name}_edges.png'.format(pdir=outname,name=self.name))
fig = plt.figure(figsize=(10, 10))
plt.imshow(self.image,
cmap='viridis',
vmin=1,
vmax=25,
interpolation=None,
origin='lower')
#plt.savefig('{pdir}/{name}_edges.png'.format(pdir=outname,name=self.name))
for k, col in zip(unique_labels, colors):
if k == -1:
col = [0, 0, 0, 1]
break # noise: the unclustered
class_member_mask = (labels == k)
#xy = X[class_member_mask & core_samples_mask]
xy = X1[class_member_mask]
x = xy[:, 0]
y = xy[:, 1]
# only add the cores to the clusters saved in the event
if k > -1 and len(x) > 1:
cl = Cluster(xy,
self.rebin,
self.image_fr,
self.image_fr_zs,
debug=False)
cl.iteration = db.tag_[labels == k][0]
cl.nclu = k
#corr, p_value = pearsonr(x, y)
cl.pearson = 999 #p_value
clusters.append(cl)
if plot:
xri, yri = tl.getContours(y, x)
cline = {1: 'r', 2: 'b', 3: 'y'}
plt.plot(xri,
yri,
'-{lcol}'.format(lcol=cline[cl.iteration]),
linewidth=0.5)
# if plot: cl.plotAxes(plot=plt,num_steps=100)
# cl.calcProfiles(plot=None)
# for dir in ['long','lat']:
# prof = cl.getProfile(dir)
# if prof and cl.widths[dir]>10: # plot the profiles only of sufficiently long snakes
# prof.Draw()
# for ext in ['png','pdf']:
# canv.SaveAs('{pdir}/{name}_snake{iclu}_{dir}profile.{ext}'.format(pdir=outname,name=self.name,iclu=k,dir=dir,ext=ext))
## SUPERCLUSTERING
from supercluster import SuperClusterAlgorithm
superclusterContours = []
scAlgo = SuperClusterAlgorithm(shape=rescale,
debugmode=self.options.debug_mode)
u, indices = np.unique(db.labels_, return_index=True)
allclusters_it1 = [
X1[db.labels_ == i]
for i in u[list(np.where(db.tag_[indices] == 1)[0])].tolist()
]
allclusters_it2 = [
X1[db.labels_ == i]
for i in u[list(np.where(db.tag_[indices] == 2)[0])].tolist()
]
allclusters_it12 = allclusters_it1 + allclusters_it2
# note: passing the edges, not the filtered ones for deeper information
superclusters, superclusterContours = scAlgo.findSuperClusters(
allclusters_it12, edges, self.image_fr, self.image_fr_zs, 0)
if plot:
for ext in ['png', 'pdf']:
plt.savefig('{pdir}/{name}.{ext}'.format(pdir=outname,
name=self.name,
ext=ext),
bbox_inches='tight',
pad_inches=0)
plt.gcf().clear()
plt.close('all')
## DEBUG MODE
if self.options.debug_mode == 1:
print('[DEBUG-MODE ON]')
print('[%s Method]' % (self.options.tip))
if self.options.flag_full_image or self.options.flag_rebin_image or self.options.flag_edges_image or self.options.flag_first_it or self.options.flag_second_it or self.options.flag_third_it or self.options.flag_all_it or self.options.flag_supercluster:
import matplotlib.pyplot as plt
if self.options.flag_full_image == 1:
fig = plt.figure(figsize=(self.options.figsizeX,
self.options.figsizeY))
plt.imshow(self.image_fr.T,
cmap=self.options.cmapcolor,
vmin=1,
vmax=25,
origin='upper')
plt.title("Original Image")
for ext in ['png', 'pdf']:
plt.savefig('{pdir}/{name}_{esp}.{ext}'.format(
pdir=outname, name=self.name, esp='oriIma', ext=ext),
bbox_inches='tight',
pad_inches=0)
with open(
'{pdir}/{name}_{esp}.pkl'.format(pdir=outname,
name=self.name,
esp='oriIma',
ext=ext), "wb") as fp:
pickle.dump(fig, fp, protocol=4)
plt.gcf().clear()
plt.close('all')
if self.options.flag_rebin_image == 1:
fig = plt.figure(figsize=(self.options.figsizeX,
self.options.figsizeY))
plt.imshow(rebin_image,
cmap=self.options.cmapcolor,
vmin=vmin,
vmax=vmax,
origin='lower')
plt.title("Rebin Image")
for ext in ['png', 'pdf']:
plt.savefig('{pdir}/{name}_{esp}.{ext}'.format(
pdir=outname, name=self.name, esp='rebinIma', ext=ext),
bbox_inches='tight',
pad_inches=0)
plt.gcf().clear()
plt.close('all')
if self.options.flag_edges_image == 1:
fig = plt.figure(figsize=(self.options.figsizeX,
self.options.figsizeY))
plt.imshow(edcopyTight,
cmap=self.options.cmapcolor,
vmin=0,
vmax=1,
origin='lower')
plt.title('Edges after Filtering')
for ext in ['png', 'pdf']:
plt.savefig('{pdir}/{name}_{esp}.{ext}'.format(
pdir=outname, name=self.name, esp='edgesIma', ext=ext),
bbox_inches='tight',
pad_inches=0)
plt.gcf().clear()
plt.close('all')
if self.options.flag_stats == 1:
print('[Statistics]')
n_clusters_ = len(set(
db.labels_)) - (1 if -1 in db.labels_ else 0)
print("Total number of Clusters: %d" % (n_clusters_))
u, indices = np.unique(db.labels_, return_index=True)
print("Clusters found in iteration 1: %d" %
(sum(db.tag_[indices] == 1)))
print("Clusters found in iteration 2: %d" %
(sum(db.tag_[indices] == 2)))
print("Clusters found in iteration 3: %d" %
(sum(db.tag_[indices] == 3)))
print("SuperClusters found: %d" % len(superclusters))
if self.options.flag_first_it == 1:
print('[Plotting 1st iteration]')
u, indices = np.unique(db.labels_, return_index=True)
clu = [
X1[db.labels_ == i]
for i in u[list(np.where(
db.tag_[indices] == 1)[0])].tolist()
]
fig = plt.figure(figsize=(self.options.figsizeX,
self.options.figsizeY))
plt.imshow(rebin_image,
cmap=self.options.cmapcolor,
vmin=vmin,
vmax=vmax,
origin='lower')
plt.title("Clusters found in iteration 1")
for j in range(0, np.shape(clu)[0]):
ybox = clu[j][:, 0]
xbox = clu[j][:, 1]
if (len(ybox) > 0) and (len(xbox) > 0):
contours = tl.findedges(ybox, xbox, self.rebin)
for n, contour in enumerate(contours):
plt.plot(contour[:, 1],
contour[:, 0],
'-r',
linewidth=2.5)
for ext in ['png', 'pdf']:
plt.savefig('{pdir}/{name}_{esp}_{tip}.{ext}'.format(
pdir=outname,
name=self.name,
esp='1st',
ext=ext,
tip=self.options.tip),
bbox_inches='tight',
pad_inches=0)
with open(
'{pdir}/{name}_{esp}_{tip}.pkl'.format(
pdir=outname,
name=self.name,
esp='1st',
ext=ext,
tip=self.options.tip), "wb") as fp:
pickle.dump(fig, fp, protocol=4)
plt.gcf().clear()
plt.close('all')
if self.options.flag_second_it == 1:
print('[Plotting 2nd iteration]')
u, indices = np.unique(db.labels_, return_index=True)
clu = [
X1[db.labels_ == i]
for i in u[list(np.where(
db.tag_[indices] == 2)[0])].tolist()
]
fig = plt.figure(figsize=(self.options.figsizeX,
self.options.figsizeY))
plt.imshow(rebin_image,
cmap=self.options.cmapcolor,
vmin=vmin,
vmax=vmax,
origin='lower')
plt.title("Clusters found in iteration 2")
for j in range(0, np.shape(clu)[0]):
ybox = clu[j][:, 0]
xbox = clu[j][:, 1]
if (len(ybox) > 0) and (len(xbox) > 0):
contours = tl.findedges(ybox, xbox, self.rebin)
for n, contour in enumerate(contours):
plt.plot(contour[:, 1],
contour[:, 0],
'-b',
linewidth=2.5)
for ext in ['png', 'pdf']:
plt.savefig('{pdir}/{name}_{esp}_{tip}.{ext}'.format(
pdir=outname,
name=self.name,
esp='2nd',
ext=ext,
tip=self.options.tip),
bbox_inches='tight',
pad_inches=0)
with open(
'{pdir}/{name}_{esp}_{tip}.pkl'.format(
pdir=outname,
name=self.name,
esp='2nd',
ext=ext,
tip=self.options.tip), "wb") as fp:
pickle.dump(fig, fp, protocol=4)
plt.gcf().clear()
plt.close('all')
if self.options.flag_third_it == 1:
print('[Plotting 3rd iteration]')
u, indices = np.unique(db.labels_, return_index=True)
clu = [
X1[db.labels_ == i]
for i in u[list(np.where(
db.tag_[indices] == 3)[0])].tolist()
]
fig = plt.figure(figsize=(self.options.figsizeX,
self.options.figsizeY))
plt.imshow(rebin_image,
cmap=self.options.cmapcolor,
vmin=vmin,
vmax=vmax,
origin='lower')
plt.title("Clusters found in iteration 3")
for j in range(0, np.shape(clu)[0]):
ybox = clu[j][:, 0]
xbox = clu[j][:, 1]
if (len(ybox) > 0) and (len(xbox) > 0):
contours = tl.findedges(ybox, xbox, self.rebin)
for n, contour in enumerate(contours):
plt.plot(contour[:, 1],
contour[:, 0],
'-y',
linewidth=2.5)
for ext in ['png', 'pdf']:
plt.savefig('{pdir}/{name}_{esp}_{tip}.{ext}'.format(
pdir=outname,
name=self.name,
esp='3rd',
ext=ext,
tip=self.options.tip),
bbox_inches='tight',
pad_inches=0)
plt.gcf().clear()
plt.close('all')
if self.options.flag_all_it == 1:
print('[Plotting ALL iteration]')
u, indices = np.unique(db.labels_, return_index=True)
clu = [
X1[db.labels_ == i]
for i in u[list(np.where(
db.tag_[indices] == 1)[0])].tolist()
]
fig = plt.figure(figsize=(self.options.figsizeX,
self.options.figsizeY))
plt.imshow(rebin_image,
cmap=self.options.cmapcolor,
vmin=vmin,
vmax=vmax,
origin='lower')
plt.title("Final Image")
for j in range(0, np.shape(clu)[0]):
ybox = clu[j][:, 0]
xbox = clu[j][:, 1]
if (len(ybox) > 0) and (len(xbox) > 0):
contours = tl.findedges(ybox, xbox, self.rebin)
for n, contour in enumerate(contours):
line, = plt.plot(contour[:, 1],
contour[:, 0],
'-r',
linewidth=2.5)
if j == 0:
line.set_label('1st Iteration')
clu = [
X1[db.labels_ == i]
for i in u[list(np.where(
db.tag_[indices] == 2)[0])].tolist()
]
for j in range(0, np.shape(clu)[0]):
ybox = clu[j][:, 0]
xbox = clu[j][:, 1]
if (len(ybox) > 0) and (len(xbox) > 0):
contours = tl.findedges(ybox, xbox, self.rebin)
for n, contour in enumerate(contours):
line, = plt.plot(contour[:, 1],
contour[:, 0],
'-b',
linewidth=2.5)
if j == 0:
line.set_label('2nd Iteration')
clu = [
X1[db.labels_ == i]
for i in u[list(np.where(
db.tag_[indices] == 3)[0])].tolist()
]
for j in range(0, np.shape(clu)[0]):
ybox = clu[j][:, 0]
xbox = clu[j][:, 1]
if (len(ybox) > 0) and (len(xbox) > 0):
contours = tl.findedges(ybox, xbox, self.rebin)
for n, contour in enumerate(contours):
line, = plt.plot(contour[:, 1],
contour[:, 0],
'-y',
linewidth=2.5)
if j == 0:
line.set_label('3rd Iteration')
plt.legend(loc='upper left')
if len(superclusters):
supercluster_contour = plt.contour(superclusterContours,
[0.5],
colors='limegreen',
linewidths=2)
supercluster_contour.collections[0].set_label(
'supercluster')
for ext in ['png', 'pdf']:
plt.savefig('{pdir}/{name}_{esp}_{tip}.{ext}'.format(
pdir=outname,
name=self.name,
esp='all',
ext=ext,
tip=self.options.tip),
bbox_inches='tight',
pad_inches=0)
with open(
'{pdir}/{name}_{esp}_{tip}.pkl'.format(
pdir=outname,
name=self.name,
esp='all',
ext=ext,
tip=self.options.tip), "wb") as fp:
pickle.dump(fig, fp, protocol=4)
plt.gcf().clear()
plt.close('all')
#################### PLOT SUPERCLUSTER ONLY ###############################
if self.options.flag_supercluster == 1:
if len(superclusters):
fig = plt.figure(figsize=(self.options.figsizeX,
self.options.figsizeY))
supercluster_contour = plt.contour(superclusterContours,
[0.5],
colors='limegreen',
linewidths=2,
alhpa=0.5)
#supercluster_contour.collections[0].set_label('supercluster it 1+2')
plt.imshow(rebin_image,
cmap=self.options.cmapcolor,
vmin=vmin,
vmax=vmax,
origin='lower')
plt.title("Superclusters found")
for ext in ['png', 'pdf']:
plt.savefig('{pdir}/{name}_{esp}_{tip}.{ext}'.format(
pdir=outname,
name=self.name,
esp='sc',
ext=ext,
tip=self.options.tip),
bbox_inches='tight',
pad_inches=0)
with open(
'{pdir}/{name}_{esp}_{tip}.pkl'.format(
pdir=outname,
name=self.name,
esp='sc',
ext=ext,
tip=self.options.tip), "wb") as fp:
pickle.dump(fig, fp, protocol=4)
plt.gcf().clear()
plt.close('all')
#################### PLOT SUPERCLUSTER ONLY ###############################
if self.options.nclu >= 0:
print('[Plotting just the cluster %d]' % (self.options.nclu))
fig = plt.figure(figsize=(self.options.figsizeX,
self.options.figsizeY))
plt.imshow(rebin_image,
cmap=self.options.cmapcolor,
vmin=vmin,
vmax=vmax,
origin='lower')
plt.title('Plotting just the cluster %d' % (self.options.nclu))
cl_mask = (db.labels_ == self.options.nclu)
xy = X1[cl_mask]
xbox = xy[:, 1]
ybox = xy[:, 0]
if (len(ybox) > 0) and (len(xbox) > 0):
contours = tl.findedges(ybox, xbox, self.rebin)
for n, contour in enumerate(contours):
line, = plt.plot(contour[:, 1],
contour[:, 0],
'-r',
linewidth=2.5)
for ext in ['png', 'pdf']:
plt.savefig('{pdir}/{name}_{tip}_{nclu}.{ext}'.format(
pdir=outname,
name=self.name,
ext=ext,
tip=self.options.tip,
nclu=self.options.nclu),
bbox_inches='tight',
pad_inches=0)
plt.gcf().clear()
plt.close('all')
return clusters, superclusters
def getTracks(self, plot=True):
from skimage.transform import (hough_line, hough_line_peaks)
# Classic straight-line Hough transform
image = self.imagelog
h, theta, d = hough_line(image)
print("tracks found")
tracks = []
thr = 0.8 * np.amax(h)
####################### IMPLEMENT HERE THE SAVING OF THE TRACKS ############
# loop over prominent tracks
itrk = 0
for _, angle, dist in zip(
*hough_line_peaks(h, theta, d, threshold=thr)):
print("Track # ", itrk)
#points_along_trk = np.zeros((self.image.shape[1],self.image.shape[0]))
points_along_trk = []
for x in range(self.image.shape[1]):
y = min(
self.image.shape[0],
max(0, int((dist - x * np.cos(angle)) / np.sin(angle))))
#points_along_trk[x,y] = self.image[y,x]
#print "adding point: %d,%d,%f" % (x,y,self.image[y,x])
# add a halo fo +/- 20 pixels to calculate the lateral profile
for iy in range(int(y) - 5, int(y) + 5):
if iy < 0 or iy >= self.image.shape[0]: continue
points_along_trk.append((x, iy, self.image[iy, x]))
xy = np.array(points_along_trk)
trk = Cluster(xy, self.rebin)
tracks.append(trk)
itrk += 1
###################################
if plot:
# Generating figure
from matplotlib import cm
fig, ax = plt.subplots(2, 1, figsize=(18, 6))
#ax = axes.ravel()
ax[0].imshow(image, cmap=cm.gray)
ax[0].set_title('Camera image')
#ax[0].set_axis_off()
ax[1].imshow(image, cmap=cm.gray)
for _, angle, dist in zip(
*hough_line_peaks(h, theta, d, threshold=thr)):
y0 = (dist - 0 * np.cos(angle)) / np.sin(angle)
y1 = (dist - image.shape[1] * np.cos(angle)) / np.sin(angle)
ax[1].plot((0, image.shape[1]), (y0, y1), '-r')
ax[1].set_xlim((0, image.shape[1]))
ax[1].set_ylim((image.shape[0], 0))
#ax[1].set_axis_off()
ax[1].set_title('Fitted tracks')
plt.tight_layout()
#plt.show()
outname = self.options.plotDir
if outname and not os.path.exists(outname):
os.system("mkdir -p " + outname)
os.system("cp ~/cernbox/www/Cygnus/index.php " + outname)
for ext in ['pdf']:
plt.savefig('{pdir}/{name}.{ext}'.format(pdir=outname,
name=self.name,
ext=ext))
plt.gcf().clear()
return tracks
def findSuperClusters(self, basic_clusters, raw_data, raw_data_fullreso,
raw_data_fullreso_zs, iteration):
superClusters = []
superClusterContours = np.array([])
if len(basic_clusters):
# use the clustered points to get "seeds" for superclustering
# i.e. open a window to get back unclustered points with low light
seedsAndNeighbors = self.clusters_neighborood(
basic_clusters, raw_data)
# run the superclustering algorithm (GAC with 300 iterations)
superClusterContours = self.supercluster(seedsAndNeighbors)
# get the superclusters with the list of points of each one
superClusterWithPixels = self.supercluster_points(
superClusterContours)
print("A questo punto")
# get a cluster object
rebin = int(self.cg.npixx / self.shape)
for i, scpixels in enumerate(superClusterWithPixels):
#print ("===> SC ",i)
sclu = Cluster(scpixels,
rebin,
raw_data_fullreso,
raw_data_fullreso_zs,
self.options.geometry,
debug=False)
#T2 = time.perf_counter()
sclu.iteration = iteration
sclu.nclu = i
sclu.ID = []
sclu.IDall = []
if sclu.integral() > 0 and sclu.hits_fr_zs != []:
sclu.nintpixels = sclu.sizeActive()
sclu.nallintpixels = sclu.size()
for k in range(sclu.nintpixels):
sclu.ID.append(i)
for k in range(sclu.nallintpixels):
sclu.IDall.append(i)
sclu.xpixelcoord = sclu.hits_fr_zs[:, 0]
sclu.ypixelcoord = sclu.hits_fr_zs[:, 1]
sclu.zpixel = sclu.hits_fr_zs[:, 2]
sclu.xallpixelcoord = sclu.hits_fr[:, 0]
sclu.yallpixelcoord = sclu.hits_fr[:, 1]
sclu.zallpixel = sclu.hits_fr[:, 2]
else:
sclu.ID.append(-1)
sclu.nintpixels = 1
sclu.IDall.append(-1)
sclu.nallintpixels = 1
if sclu.hits_fr_zs != []:
sclu.xpixelcoord = sclu.hits_fr_zs[
int(sclu.sizeActive() /
2):int(sclu.sizeActive() / 2) + 1, 0]
sclu.ypixelcoord = sclu.hits_fr_zs[
int(sclu.sizeActive() /
2):int(sclu.sizeActive() / 2) + 1, 1]
sclu.zpixel = sclu.hits_fr_zs[
int(sclu.sizeActive() /
2):int(sclu.sizeActive() / 2) + 1, 2]
else:
sclu.xpixelcoord = sclu.hits_fr[
int(sclu.size() / 2):int(sclu.size() / 2) + 1, 0]
sclu.ypixelcoord = sclu.hits_fr[
int(sclu.size() / 2):int(sclu.size() / 2) + 1, 1]
sclu.zpixel = sclu.hits_fr[int(sclu.size() /
2):int(sclu.size() /
2) + 1, 2]
sclu.xallpixelcoord = sclu.hits_fr[int(sclu.size() /
2):int(sclu.size() /
2) + 1, 0]
sclu.yallpixelcoord = sclu.hits_fr[int(sclu.size() /
2):int(sclu.size() /
2) + 1, 1]
sclu.zallpixel = sclu.hits_fr[int(sclu.size() /
2):int(sclu.size() / 2) +
1, 2]
x = scpixels[:, 0]
y = scpixels[:, 1]
corr, p_value = pearsonr(x, y)
sclu.pearson = p_value
# slicesCalEnergy is useful for the profile along the path
# this is time-consuming, though
if self.calibrate:
calEnergy, slicesCalEnergy, centers = self.calibrator.calibratedEnergy(
sclu.hits_fr)
#T3 = time.perf_counter()
#print(f"\t calibrated in {T3 - T2:0.4f} seconds")
else:
calEnergy, slicesCalEnergy, centers = -1, [], []
if self.debug:
print("SUPERCLUSTER BARE INTEGRAL = {integral:.1f}".format(
integral=sclu.integral()))
sclu.calibratedEnergy = calEnergy
sclu.nslices = len(slicesCalEnergy)
sclu.energyprofile = slicesCalEnergy
sclu.centers = centers
sclu.pathlength = -1 if self.calibrate == False else self.calibrator.clusterLength(
)
superClusters.append(sclu)
# test of the supercluster matcher
# sclu.dumpToFile('sclu_{i}'.format(i=i),zero_suppressed=True)
# test of the skeletonization
# if i==3:
# print(" === hits list ")
# print(scpixels)
# sclu.dumpToFile('supercluster3')
# return the supercluster collection
return superClusters, superClusterContours
hits = np.load('debug_code/sclu_{cand}.npy'.format(cand=cosm_cand))
fileParModule = open('modules_config/clusterMatcher.txt', 'r')
params = eval(fileParModule.read())
fileParGeometry = open('modules_config/geometry_lime.txt', 'r')
geo_params = eval(fileParGeometry.read())
params.update(geo_params)
print("full parameter set: ", params)
fitter = ClusterMatcher(params)
fitter.fitCluster(hits)
# test the cluster matcher
killer = Cluster(hits, 1, None, None, 'lime')
killer.shapes[
'long_width'] = 300 # cluster shapes are not calculated when running standalone. Just set to a value to pass the threshold
# this is to set the collection used in the reco
killer.hits_fr_zs = hits
targets = []
for icl in range(7):
if icl == cosm_cand:
continue
cluhits = np.load('debug_code/sclu_{i}.npy'.format(i=icl))
cl = Cluster(cluhits, 1, None, None, 'lime')
cl.hits_fr_zs = cluhits
targets.append(cl)
fitter.matchClusters(killer, targets)
# check if a cluster has been killed