def bulk_discretize(hdfPath, x_disc, y_disc, z_disc, charge, noise):
"""Discretizes all events in an HDF5 file using a grid geometry.
Parameters
----------
hdfPath : the system path to the hdf5 file to be
x_disc : number of slices in x
y_disc : number of slices in y
z_disc : number of slices in z
charge : boolean variable denoting whether or not charge will be included
in the discretization
noise : boolean variable to add noise to (simulated) data-processing
Returns
-------
A numpy array of shape (n, x_disc*y_disc*z_disc) where n is the number of
events in the provided hdf5 file.
"""
disc_evts = []
with pytpc.HDFDataFile(hdfPath, 'r') as f:
n_evts = len(f)
evt_id = 0
while evt_id < n_evts:
curEvt = f[evt_id]
curxyz = curEvt.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
if noise:
curxyz = add_noise(curxyz)
if charge:
disc_evts.append(
discretize_grid_charge(curxyz, x_disc, y_disc, z_disc))
else:
disc_evts.append(
discretize_grid(curxyz, x_disc, y_disc, z_disc))
if evt_id % 1000 == 0:
print("Discretized event " + str(evt_id))
evt_id += 1
discretized_data = sp.sparse.vstack(disc_evts, format='csr')
print("Data discretization complete.")
return discretized_data
def simulated(projection, data_dir, save_path, prefix):
# however many pads we're trying to predict
print('Processing data...')
print(data_dir)
proton_events = pytpc.HDFDataFile(os.path.join(data_dir, prefix + 'proton.h5'), 'r')
carbon_events = pytpc.HDFDataFile(os.path.join(data_dir, prefix + 'carbon.h5'), 'r')
# Create empty arrays to hold data
data = []
# Add proton events to data array
for i, event in enumerate(proton_events):
xyzs = event.xyzs(peaks_only=True, drift_vel=5.2, clock=12.5, return_pads=False,
baseline_correction=False, cg_times=False)
data.append([xyzs, 0])
if i % 50 == 0:
print('Proton event ' + str(i) + ' added.')
# Add carbon events to data array
for i, event in enumerate(carbon_events):
xyzs = event.xyzs(peaks_only=True, drift_vel=5.2, clock=12.5, return_pads=False,
baseline_correction=False, cg_times=False)
data.append([xyzs, 1])
if i % 50 == 0:
print('Carbon event ' + str(i) + ' added.')
# Take the log of charge data
log = np.vectorize(_l)
for event in data:
event[0][:, 3] = log(event[0][:, 3])
data = shuffle(data)
partition = int(len(data) * 0.8)
train = data[:partition]
test = data[partition:]
# Normalize
max_charge = np.array(list(map(lambda x: x[0][:, 3].max(), data))).max()
for e in data:
for point in e[0]:
point[3] = point[3] / max_charge
print('Making images...')
# Make Training sets
# Make numpy sets
train_image_contexts = np.zeros((len(train), 128, 128, 3), dtype=np.uint8)
train_images = np.zeros((len(train), 128, 128, 3), dtype=np.uint8)
for i, event in enumerate(train):
e = event[0]
z = e[:, 1]
c = e[:, 3]
if projection == 'zy':
x = e[:, 2]
elif projection == 'xy':
x = e[:, 0]
else:
raise ValueError('Invalid projection value.')
# create lists for missing regions
x_c = []
z_c = []
c_c = []
for j in range(len(e)):
# insert deleting condition here
if not (-10 <= x[j] <= 127.5 and -117.5 <= z[j] <= 20):
x_c.append(x[j])
z_c.append(z[j])
c_c.append(c[j])
# c[j] = 0
# make image context
fig = plt.figure(figsize=(1, 1), dpi=128)
ax = fig.add_axes([0, 0, 1, 1])
if projection == 'zy':
ax.set_xlim(0.0, 1250.0)
elif projection == 'xy':
ax.set_xlim(-275.0, 275.0)
ax.set_ylim((-275.0, 275.0))
ax.set_axis_off()
ax.scatter(x_c, z_c, s=0.01, c=c_c, cmap='Greys')
fig.canvas.draw()
data = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data = np.delete(data, 3, axis=2)
train_image_contexts[i] = data
plt.close()
# make image
fig = plt.figure(figsize=(1, 1), dpi=128)
ax = fig.add_axes([0, 0, 1, 1])
if projection == 'zy':
ax.set_xlim(0.0, 1250.0)
elif projection == 'xy':
ax.set_xlim(-275.0, 275.0)
ax.set_ylim((-275.0, 275.0))
ax.set_axis_off()
ax.scatter(x, z, s=0.01, c=c, cmap='Greys')
fig.canvas.draw()
data = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data = np.delete(data, 3, axis=2)
train_images[i] = data
plt.close()
# Make Testing sets
# Make numpy sets
test_image_contexts = np.zeros((len(test), 128, 128, 3), dtype=np.uint8)
test_images = np.zeros((len(test), 128, 128, 3), dtype=np.uint8)
for i, event in enumerate(test):
e = event[0]
z = e[:, 1]
c = e[:, 3]
if projection == 'zy':
x = e[:, 2]
elif projection == 'xy':
x = e[:, 0]
else:
raise ValueError('Invalid projection value.')
# create lists for missing regions
x_c = []
z_c = []
c_c = []
for j in range(len(e)):
# insert deleting condition here
if not (-10 <= x[j] <= 127.5 and -117.5 <= z[j] <= 20):
x_c.append(x[j])
z_c.append(z[j])
c_c.append(c[j])
# make image context
fig = plt.figure(figsize=(1, 1), dpi=128)
ax = fig.add_axes([0, 0, 1, 1])
if projection == 'zy':
ax.set_xlim(0.0, 1250.0)
elif projection == 'xy':
ax.set_xlim(-275.0, 275.0)
ax.set_ylim((-275.0, 275.0))
ax.set_axis_off()
ax.scatter(x_c, z_c, s=0.01, c=c_c, cmap='Greys')
fig.canvas.draw()
data = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data = np.delete(data, 3, axis=2)
test_image_contexts[i] = data
plt.close()
# make image
fig = plt.figure(figsize=(1, 1), dpi=128)
ax = fig.add_axes([0, 0, 1, 1])
if projection == 'zy':
ax.set_xlim(0.0, 1250.0)
elif projection == 'xy':
ax.set_xlim(-275.0, 275.0)
ax.set_ylim((-275.0, 275.0))
ax.set_axis_off()
ax.scatter(x, z, s=0.01, c=c, cmap='Greys')
fig.canvas.draw()
data = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data = np.delete(data, 3, axis=2)
test_images[i] = data
plt.close()
if not os.path.exists(save_path):
os.makedirs(save_path)
print('Saving file...')
filename = os.path.join(save_path, prefix + 'images.h5')
# Save to HDF5
h5 = h5py.File(filename, 'w')
h5.create_dataset('train_image_contexts', data=train_image_contexts)
h5.create_dataset('train_images', data=train_images)
h5.create_dataset('test_image_contexts', data=test_image_contexts)
h5.create_dataset('test_images', data=test_images)
# h5.create_dataset('max_charge', data=np.array([max_charge]))
h5.close()
def simulated_unlabeled(projection, noise, data_dir, save_path, prefix,
include_junk):
print('Processing data...')
proton_events = pytpc.HDFDataFile(
os.path.join(data_dir, prefix + 'proton.h5'), 'r')
carbon_events = pytpc.HDFDataFile(
os.path.join(data_dir, prefix + 'carbon.h5'), 'r')
# Create empty arrays to hold data
data = []
# Add proton events to data array
for i, event in enumerate(proton_events):
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
if noise:
# Add artificial noise
xyzs = dd.add_noise(xyzs).astype('float32')
data.append([xyzs, 0])
if i % 50 == 0:
print('Proton event ' + str(i) + ' added.')
# Add carbon events to data array
for i, event in enumerate(carbon_events):
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
if noise:
# Add artificial noise
xyzs = dd.add_noise(xyzs).astype('float32')
data.append([xyzs, 1])
if i % 50 == 0:
print('Carbon event ' + str(i) + ' added.')
# Create junk events
if include_junk:
for i in range(len(proton_events)):
xyzs = np.empty([1, 4])
if noise:
xyzs = dd.add_noise(xyzs).astype('float32')
data.append([xyzs, 2])
if i % 50 == 0:
print('Junk event ' + str(i) + ' added.')
# Take the log of charge data
log = np.vectorize(_l)
for event in data:
event[0][:, 3] = log(event[0][:, 3])
data = shuffle(data)
# Normalize
max_charge = np.array(list(map(lambda x: x[0][:, 3].max(), data))).max()
for e in data:
for point in e[0]:
point[3] = point[3] / max_charge
print('Making images...')
# Make numpy sets
images = np.empty((len(data), 128, 128, 3), dtype=np.uint8)
for i, event in enumerate(data):
e = event[0]
if projection == 'zy':
x = e[:, 2].flatten()
z = e[:, 1].flatten()
c = e[:, 3].flatten()
elif projection == 'xy':
x = e[:, 0].flatten()
z = e[:, 1].flatten()
c = e[:, 3].flatten()
else:
raise ValueError('Invalid projection value.')
fig = plt.figure(figsize=(1, 1), dpi=128)
if projection == 'zy':
plt.xlim(0.0, 1250.0)
elif projection == 'xy':
plt.xlim(-275.0, 275.0)
plt.ylim((-275.0, 275.0))
plt.axis('off')
plt.scatter(x, z, s=0.6, c=c, cmap='Greys')
fig.canvas.draw()
data = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data = np.delete(data, 3, axis=2)
images[i] = data
plt.close()
if not os.path.exists(save_path):
os.makedirs(save_path)
print('Saving file...')
filename = os.path.join(save_path, prefix + 'images.h5')
# Save to HDF5
h5 = h5py.File(filename, 'w')
h5.create_dataset('images', data=images)
h5.create_dataset('max_charge', data=np.array([max_charge]))
h5.close()
def real_labeled(projection, data_dir, save_path, prefix):
print('Processing data...')
data = []
for run in RUNS:
events_file = os.path.join(data_dir, 'run_{}.h5'.format(run))
labels_file = os.path.join(data_dir, 'run_{}_labels.csv'.format(run))
events = pytpc.HDFDataFile(events_file, 'r')
labels = pd.read_csv(labels_file, sep=',')
proton_indices = labels.loc[(labels['label'] == 'p')]['evt_id'].values
carbon_indices = labels.loc[(labels['label'] == 'c')]['evt_id'].values
junk_indices = labels.loc[(labels['label'] == 'j')]['evt_id'].values
for evt_id in proton_indices:
event = events[str(evt_id)]
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
data.append([xyzs, 0])
for evt_id in carbon_indices:
event = events[str(evt_id)]
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
data.append([xyzs, 1])
for evt_id in junk_indices:
event = events[str(evt_id)]
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
data.append([xyzs, 2])
log = np.vectorize(_l)
for event in data:
event[0][:, 3] = log(event[0][:, 3])
# Shuffle data
data = shuffle(data)
# Split into train and test sets
partition = int(len(data) * 0.8)
train = data[:partition]
test = data[partition:]
# Normalize
max_charge = np.array(list(map(lambda x: x[0][:, 3].max(), train))).max()
for e in train:
for point in e[0]:
point[3] = point[3] / max_charge
for e in test:
for point in e[0]:
point[3] = point[3] / max_charge
print('Making images...')
# Make train numpy sets
train_features = np.empty((len(train), 128, 128, 3), dtype=np.uint8)
train_targets = np.empty((len(train), ), dtype=np.uint8)
for i, event in enumerate(train):
e = event[0]
if projection == 'zy':
x = e[:, 2].flatten()
z = e[:, 1].flatten()
c = e[:, 3].flatten()
elif projection == 'xy':
x = e[:, 0].flatten()
z = e[:, 1].flatten()
c = e[:, 3].flatten()
else:
raise ValueError('Invalid projection value.')
fig = plt.figure(figsize=(1, 1), dpi=128)
if projection == 'zy':
plt.xlim(0.0, 1250.0)
elif projection == 'xy':
plt.xlim(-275.0, 275.0)
plt.ylim((-275.0, 275.0))
plt.axis('off')
plt.scatter(x, z, s=0.6, c=c, cmap='Greys')
fig.canvas.draw()
data = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data = np.delete(data, 3, axis=2)
train_features[i] = data
train_targets[i] = event[1]
plt.close()
# Make test numpy sets
test_features = np.empty((len(test), 128, 128, 3), dtype=np.uint8)
test_targets = np.empty((len(test), ), dtype=np.uint8)
for i, event in enumerate(test):
e = event[0]
if projection == 'zy':
x = e[:, 2].flatten()
z = e[:, 1].flatten()
c = e[:, 3].flatten()
elif projection == 'xy':
x = e[:, 0].flatten()
z = e[:, 1].flatten()
c = e[:, 3].flatten()
else:
raise ValueError('Invalid projection value.')
fig = plt.figure(figsize=(1, 1), dpi=128)
if projection == 'zy':
plt.xlim(0.0, 1250.0)
elif projection == 'xy':
plt.xlim(-275.0, 275.0)
plt.ylim((-275.0, 275.0))
plt.axis('off')
plt.scatter(x, z, s=0.6, c=c, cmap='Greys')
fig.canvas.draw()
data = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data = np.delete(data, 3, axis=2)
test_features[i] = data
test_targets[i] = event[1]
plt.close()
print('Saving file...')
if not os.path.exists(save_path):
os.makedirs(save_path)
filename = os.path.join(save_path, prefix + 'images.h5')
# Save to HDF5
h5 = h5py.File(filename, 'w')
h5.create_dataset('train_features', data=train_features)
h5.create_dataset('train_targets', data=train_targets)
h5.create_dataset('test_features', data=test_features)
h5.create_dataset('test_targets', data=test_targets)
h5.create_dataset('max_charge', data=np.array([max_charge]))
h5.close()
def real_unlabeled(projection, data_dir, save_path, prefix):
print('Processing data...')
data = []
for run in RUNS:
events_file = os.path.join(data_dir, 'run_{}.h5'.format(run))
events = pytpc.HDFDataFile(events_file, 'r')
for event in events:
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
data.append([xyzs, -1])
# Take the log of charge data
log = np.vectorize(_l)
for event in data:
event[0][:, 3] = log(event[0][:, 3])
# Shuffle data
data = shuffle(data)
# Normalize
max_charge = np.array(list(map(lambda x: x[0][:, 3].max(), data))).max()
for e in data:
for point in e[0]:
point[3] = point[3] / max_charge
print('Making images...')
# Make numpy sets
images = np.empty((len(data), 128, 128, 3), dtype=np.uint8)
for i, event in enumerate(data):
e = event[0]
if projection == 'zy':
x = e[:, 2].flatten()
z = e[:, 1].flatten()
c = e[:, 3].flatten()
elif projection == 'xy':
x = e[:, 0].flatten()
z = e[:, 1].flatten()
c = e[:, 3].flatten()
else:
raise ValueError('Invalid projection value.')
fig = plt.figure(figsize=(1, 1), dpi=128)
if projection == 'zy':
plt.xlim(0.0, 1250.0)
elif projection == 'xy':
plt.xlim(-275.0, 275.0)
plt.ylim((-275.0, 275.0))
plt.axis('off')
plt.scatter(x, z, s=0.6, c=c, cmap='Greys')
fig.canvas.draw()
data = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data = np.delete(data, 3, axis=2)
images[i] = data
plt.close()
print('Saving file...')
if not os.path.exists(save_path):
os.makedirs(save_path)
filename = os.path.join(save_path, prefix + 'images.h5')
# Save to HDF5
h5 = h5py.File(filename, 'w')
h5.create_dataset('images', data=images)
h5.create_dataset('max_charge', data=np.array([max_charge]))
h5.close()
import dataDiscretization as dd
import scipy as sp
import pandas as pd
import pytpc
data_path = '../data/real/'
disc_path = data_path + '50x50x50/'
runs = ['0130', '0210']
x_disc = 50
y_disc = 50
z_disc = 50
for run in runs:
data = pytpc.HDFDataFile(data_path + "run_" + run + ".h5", 'r')
labels = pd.read_csv(data_path + "run_" + run + "_labels.csv", sep=',')
print("Successfully loaded data and labels for run " + str(run) + ".")
#discretize proton events
p_indices = labels.loc[(labels['label'] == 'p')]['evt_id'].values
p_discEvts = []
for evt_id in p_indices:
curEvt = data[evt_id]
curxyz = curEvt.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
def simulated(projection, noise, data_dir, save_path, prefix):
print("We are in the simulared() function!")
print('Processing data...')
proton_events = pytpc.HDFDataFile(
os.path.join(data_dir, prefix + 'proton.h5'), 'r')
carbon_events = pytpc.HDFDataFile(
os.path.join(data_dir, prefix + 'carbon.h5'), 'r')
# Create empty arrays to hold data-processing
data = []
# Add proton events to data-processing array
for i, event in enumerate(proton_events):
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=True,
baseline_correction=False,
cg_times=False)
#if noise:
# Add artificial noise
#xyzs = dd.add_noise(xyzs).astype('float32')
data.append([xyzs, 0])
if i % 50 == 0:
print('Proton event ' + str(i) + ' added.')
for i, event in enumerate(carbon_events):
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=True,
baseline_correction=False,
cg_times=False)
#if noise:
# Add artificial noise
# xyzs = dd.add_noise(xyzs).astype('float32')
data.append([xyzs, 1])
if i % 50 == 0:
print('Carbon event ' + str(i) + ' added.')
# Create junk events
#for i in range(len(proton_events)):
#xyzs = np.empty([1, 4])
#xyzs = dd.add_noise(xyzs).astype('float32')
#data.append([xyzs, 2])
#if i % 50 == 0:
#print('Junk event ' + str(i) + ' added.')
# Take the log of charge data-processing
log = np.vectorize(_l)
for event in data:
event[0][:, 3] = log(event[0][:, 3])
# Split into train and test sets
data = shuffle(data)
partition = int(len(data) * 0.8)
train = data[:partition]
test = data[partition:]
# Normalize
max_charge = np.array(list(map(lambda x: x[0][:, 3].max(), train))).max()
for e in train:
for point in e[0]:
point[3] = point[3] / max_charge
for e in test:
for point in e[0]:
point[3] = point[3] / max_charge
# Make train numpy sets
train_features = np.empty((len(train), 128, 128, 3), dtype=np.uint8)
train_targets = np.empty((len(train), ), dtype=np.uint8)
# Make train numpy sets for the broken spiral
train_features_broken = np.empty((len(train), 32, 32, 3), dtype=np.uint8)
train_targets_broken = np.empty((len(train), ), dtype=np.uint8)
for i, event in enumerate(train):
e = event[0]
c = e[:, 3].flatten()
p = e[:, 4].flatten()
if projection == 'zy':
x = e[:, 2].flatten()
z = e[:, 1].flatten()
elif projection == 'xy':
x = e[:, 0].flatten()
z = e[:, 1].flatten()
else:
raise ValueError('Invalid projection value.')
# deleting part of the Spiral
x_b = []
z_b = []
c_b = []
for j in range(len(x)):
if -10 < x[j] < 127.5 and -117.5 < z[j] < 20:
x_b.append(x[j])
z_b.append(z[j])
c_b.append(c[j])
c[j] = 0
# Make numpy array image of spiral context
fig = plt.figure(figsize=(1, 1), dpi=128)
if projection == 'zy':
plt.xlim(0.0, 1250.0)
elif projection == 'xy':
plt.xlim(-275.0, 275.0)
plt.ylim((-275.0, 275.0))
plt.axis('off')
plt.scatter(x, z, s=0.6, c=c, cmap='Greys')
fig.canvas.draw()
data = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data = np.delete(data, 3, axis=2)
train_features[i] = data
train_targets[i] = event[1]
plt.close()
# Make numpy array image of broken spiral
fig = plt.figure(figsize=(1, 1), dpi=32)
if projection == 'zy':
plt.xlim(0.0, 1250.0)
elif projection == 'xy':
plt.xlim(-10, 127.5)
plt.ylim((-117.5, 20))
plt.axis('off')
plt.scatter(x_b, z_b, s=0.6, c=c_b, cmap='Greys')
fig.canvas.draw()
data_broken = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data_broken = np.delete(data_broken, 3, axis=2)
train_features_broken[i] = data_broken
train_targets[i] = event[1]
plt.close()
# Make test numpy sets
test_features = np.empty((len(test), 128, 128, 3), dtype=np.uint8)
test_targets = np.empty((len(test), ), dtype=np.uint8)
test_features_broken = np.empty((len(test), 32, 32, 3), dtype=np.uint8)
test_targets_broken = np.empty((len(test), ), dtype=np.uint8)
for i, event in enumerate(test):
e = event[0]
p = e[:, 4].flatten()
if projection == 'zy':
x = e[:, 2].flatten()
z = e[:, 1].flatten()
c = e[:, 3].flatten()
elif projection == 'xy':
x = e[:, 0].flatten()
z = e[:, 1].flatten()
c = e[:, 3].flatten()
else:
raise ValueError('Invalid projection value.')
fig = plt.figure(figsize=(1, 1), dpi=128)
x_b = []
z_b = []
c_b = []
for j in range(len(x)):
if -10 < x[j] < 127.5 and -117.5 < z[j] < 20:
x_b.append(x[j])
z_b.append(z[j])
c_b.append(c[j])
c[j] = 0
fig = plt.figure(figsize=(1, 1), dpi=128)
if projection == 'zy':
plt.xlim(0.0, 1250.0)
elif projection == 'xy':
plt.xlim(-275.0, 275.0)
plt.ylim((-275.0, 275.0))
plt.axis('off')
plt.scatter(x, z, s=0.6, c=c, cmap='Greys')
fig.canvas.draw()
data = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data = np.delete(data, 3, axis=2)
test_features[i] = data
test_targets[i] = event[1]
plt.close()
fig = plt.figure(figsize=(1, 1), dpi=32)
if projection == 'zy':
plt.xlim(0.0, 1250.0)
elif projection == 'xy':
plt.xlim(-10, 127.5)
plt.ylim((-117.5, 20))
plt.axis('off')
plt.scatter(x_b, z_b, s=0.6, c=c_b, cmap='Greys')
fig.canvas.draw()
data_broken = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
data_broken = np.delete(data_broken, 3, axis=2)
test_features_broken[i] = data_broken
test_targets_broken[i] = event[1]
plt.close()
if not os.path.exists(save_path):
os.makedirs(save_path)
filename = os.path.join(save_path, prefix + 'images.h5')
# Save to HDF5
h5 = h5py.File(filename, 'w')
h5.create_dataset('train_features', data=train_features)
h5.create_dataset('train_targets', data=train_targets)
h5.create_dataset('test_features', data=test_features)
h5.create_dataset('test_targets', data=test_targets)
h5.create_dataset('max_charge', data=np.array([max_charge]))
h5.create_dataset('train_features_broken', data=train_features_broken)
h5.create_dataset('train_targets_broken', data=train_targets_broken)
h5.create_dataset('test_features_broken', data=test_features_broken)
h5.create_dataset('test_targets_broken', data=test_targets_broken)
h5.close()
def real_unlabeled_events(projection, save_path, prefix):
print('Processing data...')
data = []
events = pytpc.HDFDataFile('corrected_run_0210.h5', 'r')
for x, event in enumerate(events):
# Get pytpc xyzs
xyzs = event.xyzs(peaks_only=True,
return_pads=True,
baseline_correction=False,
cg_times=False)
event_trace = np.ndarray(NUMBEROFPADS, dtype=object)
# Get the events trace across each pad
with h5py.File('corrected_run_0210.h5', 'r') as f:
dset = f['get/' + str(x + 1)]
trace = dset[:,
10:510] #works better when you exclude start and end
TRACELENGTH = len(trace[0])
for i in range(NUMBEROFPADS):
y = np.zeros(TRACELENGTH)
pad_number = dset[i, 4]
current_pad = trace[i]
for j in range(TRACELENGTH):
y[j] = current_pad[j]
event_trace[pad_number] = y
hit_peaks = []
for i in range(NUMBEROFPADS):
trace = event_trace[i]
trace_max = np.amax(trace)
trace_average = _average(trace)
charge = trace_max - trace_average
peak_time = np.argmax(trace)
#move window across trace
for timebucket in range(25, 475):
firstvalue = trace[timebucket - 25]
middlevalue = trace[timebucket]
lastvalue = trace[timebucket + 25]
average_first_last = (firstvalue + lastvalue) * 0.5
peakheight = middlevalue - average_first_last
if peakheight > THRESHOLD: # time charge padnumber
hit_peaks.append([peak_time, charge, i])
break
np.asarray(hit_peaks)
HITPEAKSLENGTH = len(hit_peaks)
# Merge pytpc xyzs array with correct charge values
plot_points = np.zeros(shape=(HITPEAKSLENGTH, 4))
for i in range(HITPEAKSLENGTH):
hitpeaks_padnum = hit_peaks[i][2]
for j in range(NUMBEROFPADS):
xyzs_padnum = xyzs[j][4]
if (hitpeaks_padnum == xyzs_padnum):
plot_points[i][0] = xyzs[j][0] #x
plot_points[i][1] = xyzs[j][1] #y
plot_points[i][2] = hit_peaks[i][0] #time
plot_points[i][3] = hit_peaks[i][1] #charge
data.append(plot_points)
# Take the log of charge data
log = np.vectorize(_l)
for event in data:
event[:, 3] = log(event[:, 3])
# Normalize
max_charge = np.array(list(map(lambda x: x[:, 3].max(), data))).max()
for e in data:
for point in e:
point[3] = point[3] / max_charge
print('Making images...')
# Make numpy set
images = np.empty((len(data), 128, 128, 3), dtype=np.uint8)
for i, event in enumerate(data):
e = event
if projection == 'zy':
x = e[:, 2] #actually z (time)
y = e[:, 1]
charge = e[:, 3]
elif projection == 'xy':
x = e[:, 0]
y = e[:, 1]
charge = e[:, 3]
else:
raise ValueError('Invalid projection value.')
fig = plt.figure(figsize=(1, 1), dpi=128)
if projection == 'zy':
plt.xlim(0.0, 512)
if projection == 'xy':
plt.xlim(-275.0, 275.0)
plt.ylim((-275.0, 275.0))
plt.axis('off')
#cmap='gray_r' the _r inverts greyscale so high charge is black
#while low charge is white
plt.scatter(x, y, s=0.6, c=charge, cmap='gray_r')
fig.canvas.draw()
eventData = np.array(fig.canvas.renderer._renderer, dtype=np.uint8)
eventData = np.delete(eventData, 3, axis=2)
images[i] = eventData
plt.close()
print('Saving file...')
if not os.path.exists(save_path):
os.makedirs(save_path)
filename = os.path.join(save_path, prefix + 'images.h5')
#save to HDF5 file
h5 = h5py.File(filename, 'w')
h5.create_dataset('images', data=images)
#h5.create_dataset('max_charge', data=np.array([max_charge]))
h5.close()
def simulated(data_dir, save_dir, prefix, noise):
print('Starting...')
proton_events = pytpc.HDFDataFile(
os.path.join(data_dir, prefix + 'proton.h5'), 'r')
carbon_events = pytpc.HDFDataFile(
os.path.join(data_dir, prefix + 'carbon.h5'), 'r')
# Create empty array to hold data
data = []
# Add proton events to data array
for i, event in enumerate(proton_events):
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
if noise:
xyzs = dd.add_noise(xyzs).astype('float32')
data.append(
[dd.discretize_grid_charge(xyzs, X_DISC, Y_DISC, Z_DISC), 0])
if i % 50 == 0:
print('Proton event ' + str(i) + ' added.')
# Add carbon events to data array
for i, event in enumerate(carbon_events):
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
if noise:
xyzs = dd.add_noise(xyzs).astype('float32')
data.append(
[dd.discretize_grid_charge(xyzs, X_DISC, Y_DISC, Z_DISC), 1])
if i % 50 == 0:
print('Carbon event ' + str(i) + ' added.')
# Create junk events
for i in range(len(proton_events)):
xyzs = np.empty([1, 4])
xyzs = dd.add_noise(xyzs).astype('float32')
data.append(
[dd.discretize_grid_charge(xyzs, X_DISC, Y_DISC, Z_DISC), 2])
if i % 50 == 0:
print('Junk event ' + str(i) + ' added.')
# Split into train and test sets
data = shuffle(data)
partition = int(len(data) * 0.8)
train = data[:partition]
test = data[partition:]
train_features = [t[0] for t in train]
train_targets = [t[1] for t in train]
test_features = [t[0] for t in test]
test_targets = [t[1] for t in test]
train_features = sp.sparse.vstack(train_features, format='csr')
test_features = sp.sparse.vstack(test_features, format='csr')
# Save
sp.sparse.save_npz(
os.path.join(save_dir, '{}train-features.npz'.format(prefix)),
train_features)
sp.sparse.save_npz(
os.path.join(save_dir, '{}test-features.npz'.format(prefix)),
test_features)
h5 = h5py.File(os.path.join(save_dir, '{}targets.h5'.format(prefix)), 'w')
h5.create_dataset('train_targets', data=train_targets)
h5.create_dataset('test_targets', data=test_targets)
h5.close()
def real(data_dir, save_dir, prefix):
# Create empty array to hold data
data = []
for run in RUNS:
run_filename = os.path.join(data_dir, 'run_{}.h5'.format(run))
labels_filename = os.path.join(data_dir,
'run_{}_labels.csv'.format(run))
events = pytpc.HDFDataFile(run_filename, 'r')
labels = pd.read_csv(labels_filename, sep=',')
proton_indices = labels.loc[(labels['label'] == 'p')]['evt_id'].values
carbon_indices = labels.loc[(labels['label'] == 'c')]['evt_id'].values
junk_indices = labels.loc[(labels['label'] == 'j')]['evt_id'].values
for evt_id in proton_indices:
event = events[str(evt_id)]
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
data.append(
[dd.discretize_grid_charge(xyzs, X_DISC, Y_DISC, Z_DISC), 0])
for evt_id in carbon_indices:
event = events[str(evt_id)]
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
data.append(
[dd.discretize_grid_charge(xyzs, X_DISC, Y_DISC, Z_DISC), 1])
for evt_id in junk_indices:
event = events[str(evt_id)]
xyzs = event.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
data.append(
[dd.discretize_grid_charge(xyzs, X_DISC, Y_DISC, Z_DISC), 2])
# Split into train and test sets
data = shuffle(data)
partition = int(len(data) * 0.8)
train = data[:partition]
test = data[partition:]
train_features = [t[0] for t in train]
train_targets = [t[1] for t in train]
test_features = [t[0] for t in test]
test_targets = [t[1] for t in test]
train_features = sp.sparse.vstack(train_features, format='csr')
test_features = sp.sparse.vstack(test_features, format='csr')
# Save
sp.sparse.save_npz(
os.path.join(save_dir, '{}train-features.npz'.format(prefix)),
train_features)
sp.sparse.save_npz(
os.path.join(save_dir, '{}test-features.npz'.format(prefix)),
test_features)
h5 = h5py.File(os.path.join(save_dir, '{}targets.h5'.format(prefix)), 'w')
h5.create_dataset('train_targets', data=train_targets)
h5.create_dataset('test_targets', data=test_targets)
h5.close()
repo = "/home/solli-comphys/github/attpc-classification-reproduction/"
data_repo = repo+"data/datapoints/"
import sys
n_samples = 4001
filenames_c = [data_repo+str(1e5+i)+".npy" for i in range(int(10*n_samples))]
filenames_p = [data_repo+str(2e5+i)+".npy" for i in range(int(10*n_samples))]
sys.path.insert(0, repo + "modules")
for i in tqdm(range(0, 10)):
c_name = repo+"data/C_40000_tilt_largeEvts_{}.h5".format(i)
p_name = repo+"data/p_40000_tilt_largeEvts_{}.h5".format(i)
with pytpc.HDFDataFile(c_name, "r") as f:
from representation_converter import TpcRepresent
convert_obj = TpcRepresent(filenames_c[i*n_samples: (i+1)*n_samples])
events = [f[i] for i in range(len(f))]
convert_obj.convert(events)
with pytpc.HDFDataFile(p_name, "r") as f:
from representation_converter import TpcRepresent
convert_obj = TpcRepresent(filenames_p[i*n_samples: (i+1)*n_samples])
events = [f[i] for i in range(len(f))]
convert_obj.convert(events)
carbon, and junk.
"""
import matplotlib.pyplot as plt
import scipy as sp
import numpy as np
import pytpc
import sys
sys.path.insert(0, '../modules/')
import dataDiscretization as dd
data_path = '../data/tilt/'
plot_path = '../cnn-plots/'
#proton events
with pytpc.HDFDataFile(data_path + 'p_40000_tilt_largeEvts.h5', 'r') as p_sim:
n_evts = len(p_sim)
evt_id = 0
while (evt_id < n_evts):
curEvt = p_sim[evt_id]
curxyz = curEvt.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
noise_xyz = dd.addNoise(curxyz)
plt.figure(figsize=(1.28, 1.28), dpi=100)
plt.plot(noise_xyz[:, 2],
from pytpc.hdfdata import HDFDataFile
import pytpc
from mpl_toolkits.mplot3d import Axes3D # noqa: F401 unused import
import matplotlib.pyplot as plt
repo = "/home/solli-comphys/github/attpc-classification-reproduction/"
evt = 0
with pytpc.HDFDataFile(repo + "/data/C_40000_tilt_largeEvts.h5", "r") as f:
evt = f[3]
space_distr = evt.xyzs(peaks_only=True,
drift_vel=5.2,
clock=12.5,
return_pads=False,
baseline_correction=False,
cg_times=False)
xs = space_distr[:, 0]
ys = space_distr[:, 1]
zs = space_distr[:, 2]
ch = space_distr[:, 3]
import pandas as pd
charge_series = pd.DataFrame(ch)
fig = plt.figure()
ax = fig.add_subplot(111, projection="3d")
