def plot_graphs(classifier_name):
fit_result = None
checkpoint_dir = os.path.join('.', 'checkpoints')
checkpoint_file = os.path.join(checkpoint_dir, classifier_name)
if os.path.isfile(
checkpoint_file
): # Loading the checkpoints if the models already trained with the same hyperparameters
fit_result = torch.load(checkpoint_file,
map_location=torch.device('cpu'))
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
if device.type == 'cpu':
plot_fit(fit_result, 'RNN classifier graph', legend='total')
def test_gp(plot=False, method='full'):
"""
Compares model prediction with an exact GP (without optimisation)
"""
# note that this test fails without latent noise in the case of full Gaussian
np.random.seed(111)
num_input_samples = 10
num_samples = 10000
gaussian_sigma = .2
X, Y, kernel = DataSource.normal_generate_samples(num_input_samples, gaussian_sigma, 1)
kernel = [GPy.kern.RBF(1, variance=1., lengthscale=np.array((1.,)))]
if method == 'full':
m = SAVIGP_SingleComponent(X, Y, num_input_samples, UnivariateGaussian(np.array(gaussian_sigma)),
kernel, num_samples, None, 0.001, True, True)
if method == 'diag':
m = SAVIGP_Diag(X, Y, num_input_samples, 1, UnivariateGaussian(np.array(gaussian_sigma)),
kernel, num_samples, None, 0.001, True, True)
# update model using optimal parameters
# gp = SAVIGP_Test.gpy_prediction(X, Y, gaussian_sigma, kernel[0])
# gp_mean, gp_var = gp.predict(X, full_cov=True)
# m.MoG.m[0,0] = gp_mean[:,0]
# m.MoG.update_covariance(0, gp_var - gaussian_sigma * np.eye(10))
try:
folder_name = 'test' + '_' + ModelLearn.get_ID()
logger = ModelLearn.get_logger(folder_name, logging.DEBUG)
Optimizer.optimize_model(m, 10000, logger, ['mog'])
except KeyboardInterrupt:
pass
sa_mean, sa_var = m.predict(X)
gp = SAVIGP_Test.gpy_prediction(X, Y, gaussian_sigma, deepcopy(kernel[0]))
gp_mean, gp_var = gp.predict(X)
mean_error = (np.abs(sa_mean - gp_mean)).sum() / sa_mean.shape[0]
var_error = (np.abs(sa_var - gp_var)).sum() / gp_var.T.shape[0]
if mean_error < 0.1:
print bcolors.OKBLUE, "passed: mean gp prediction ", mean_error
else:
print bcolors.WARNING, "failed: mean gp prediction ", mean_error
print bcolors.ENDC
if var_error < 0.1:
print bcolors.OKBLUE, "passed: var gp prediction ", var_error
else:
print bcolors.WARNING, "failed: var gp prediction ", var_error
print bcolors.ENDC
if plot:
plot_fit(m)
gp.plot()
show(block=True)
def print_with_plot(fit_result: FitResult):
print(fit_result)
plot_fit(fit_result)
# bgdsignal=ydata[bgd]/np.array([reference[bgd]]*len(ydata.T)).T
# print bgdsignal
bgdsignal = np.average(ydata[bgd] / np.array([reference[bgd]] * len(ydata.T)).T / 53 * 1000, axis=0)
# plt.plot(xdata,bgdsignal,'-')
# plt.plot(xdata,data.T[1],'-')
# print len(ydata.T)
# plt.show()
# plt.close()
# print bgdsignal
# signal=np.arange(9,44)
signal = ds.signalstack()
sig = ydata[signal] / np.array([reference[signal]] * len(ydata.T)).T / 53 * 1000
# sig_bgd_pair.shape(2,24)
# print sig_bgd_pair
binsize = xdata[3] - xdata[2]
print "#Num kobs(1/ms) height_err m1 c1 popt.a popt.b popt.c perr.a perr.b perr.c residual"
for i in range(0, len(sig)):
# Sig=(data.T[sig_bgd_pair[i][0]+1]/reference[sig_bgd_pair[i][0]]-data.T[sig_bgd_pair[i][1]+1]/reference[sig_bgd_pair[i][1]])/53*1000
# Time=data.T[0]
fit_data = np.vstack((xdata, sig[i] - bgdsignal))
raw_data = np.copy(fit_data)
# print fit_data
param_opt = fitting(fit_data.T, binsize)
kobs = param_opt.popt[1]
height_err = param_opt.popt[0] + param_opt.popt[2] - param_opt.trigger_h
print (signal[i]), kobs, height_err, param_opt.m1, param_opt.c1, " ".join(map(str, param_opt.popt)), " ".join(
map(str, param_opt.perr)
), param_opt.residual
plot_fit(raw_data.T, param_opt, str(signal[i]) + "-fig", binsize)
def print_fit_res(model_name: str):
checkpoint_filename = f'{model_name}.pt'
saved_state = torch.load(checkpoint_filename, 'cpu')
fit_res = saved_state['fit_result']
plot_fit(fit_res)
def main():
'''Produces results for report.'''
# simulations flag
simulations = 0
# if analysing simulations
if simulations == 1:
detector = 'BGO'
mus, mu_errs, Rs, R_errs, e_fs, e_f_errs, e_ps, e_p_errs, Gs, m, dEs, d_errs, sigmas, s_errs = sims(
)
else:
# name detector
detector = 'CdTe'
# empty arrays for plotting
Rs = []
R_errs = []
ang_Rs = []
ang_R_errs = []
e_fs = []
e_f_errs = []
ang_e_fs = []
ang_e_f_errs = []
e_ps = []
e_p_errs = []
ang_e_ps = []
ang_e_p_errs = []
angles = []
Gs = []
ang_Gs = []
mu_errs = []
s_errs = []
dEs = []
d_errs = []
sigmas = []
Cs = []
C_errs = []
C_thetas = []
C_theta_errs = []
# get clock drift
drift = get_detector_drift(detector)
# list of sample files
if detector == 'NaI': # NaI has different file format
samples = ['241Am.txt', '133Ba.txt', '137Cs.txt', '60Co.txt']
m, c, mus, ns = find_calibration(detector, samples)
elif detector == 'CdTe': # different file format, calibrate CdTe with 241Am
samples = ['241Am.mca', '133Ba.mca']
m, c, mus, ns = find_calibration(detector, ['241Am.mca'])
else: # HPGe, BGO
samples = ['241Am.spe', '133Ba.spe', '137Cs.spe', '60Co.spe']
m, c, mus, ns = find_calibration(detector, samples)
# for each sample listed
for sample in samples:
source = str(sample.split('.', 1)[0]) # find sample name
# get list of angles at which off-axis measurements have been made
angles = get_angles(detector, source)
# get on-axis angle
on_axis = int(get_on_axis_angle(detector, source))
# for each angle
for angle in angles:
# create filename
filename = angle + '_' + sample
# get live time from file
t_l = get_live_time(filename)
# for each combination of source and detector
# get number of peaks of interest in sample spectrum
no_peaks = get_no_peaks(detector, source)
# calculate time since initial activity measurement
lifetime = get_lifetime(detector, filename, drift)
# calculate current source activity
activity, a_err = calculate_activity(source, lifetime)
# for each peak
for no_peak in no_peaks:
# fit it
params, popt, perrs = fit_peak(detector, source, filename,
no_peak, angle)
# get gaussian parameters
mu, sigma, amp = popt[0], popt[1], popt[2]
# get actual energy n and decay fraction f
n, n_err, f = get_decay_fraction(
source, no_peak) # gets actual energy
# calculate resolution for peak centered on given energy n
R, R_err, dE, d_error = calculate_resolution(
sigma, perrs[1], n, n_err, m)
channel_min, channel_max = get_roi(
detector, source, no_peak) # get region of interest
# get greatest amplitude of gaussian curve, i.e. remove background
amplitude = remove_background(channel_min, channel_max, mu,
sigma, amp)
amp_err = perrs[2] / popt[2] * amplitude
# calculate FEP efficiency
e_f, e_f_err, C, C_err = calculate_e_f(
sigma * m, perrs[1] * m, amplitude, amp_err, activity,
a_err, t_l, f)
# calculate intrinsic peak efficiency
e_p, e_p_err, G = calculate_e_p_G(e_f, e_f_err, detector,
angle)
# add to on-axis arrays if angle is on-axis
if angle == str(on_axis):
Rs.append(R * 100)
R_errs.append(R_err * 100)
e_fs.append(e_f * 100)
e_f_errs.append(e_f_err * 100)
e_ps.append(e_p * 100)
e_p_errs.append(e_p_err * 100)
Gs.append(G)
mu_errs.append(perrs[0])
sigmas.append(popt[1])
s_errs.append(perrs[1])
dEs.append(dE)
d_errs.append(d_error)
# for calculating ratio
C_on_axis = C
# plot fit on-axis
plot_fit(channel_min, channel_max, detector, source,
no_peak, mu, sigma, amp, m, c)
if len(angles) > 6: # if off-axis
# if value not already in array, add it and its errors
if float(e_f) not in ang_e_fs:
ang_e_fs.append(e_f * 100)
ang_e_f_errs.append(e_f_err * 100)
if float(R) not in ang_Rs:
ang_Rs.append(R * 100)
ang_R_errs.append(R_err * 100)
if e_p not in ang_e_ps:
ang_e_ps.append(e_p * 100)
ang_e_p_errs.append(e_p_err * 100)
ang_Gs.append(G)
if C not in Cs:
Cs.append(C)
C_errs.append(C_err)
C_thetas.append(C / C_on_axis)
C_theta_errs.append(C_err / C_on_axis)
# convert list of angles to ints
int_angles = list(map(int, angles))
# for off-axis case, create plots vs angle
if len(angles) > 6:
write_count_errors(detector, source, int_angles, Cs, C_errs,
C_thetas, C_theta_errs)
# for more than one peak, i.e. 2
if len(int_angles) != len(ang_Rs):
# separate values for two peaks for plotting
# create resolution vs angle plot
plot_angle_vs_resolution(detector, source, int_angles,
ang_Rs[::2], 0)
plot_angle_vs_resolution(detector, source, int_angles,
ang_Rs[1::2], 1)
# create FEP efficiency vs angle plot
plot_angle_vs_fep(detector, source, int_angles,
ang_e_fs[::2], 0)
plot_angle_vs_fep(detector, source, int_angles,
ang_e_fs[1::2], 1)
# create geometry vs angle plot
plot_angle_vs_geometry(detector, source, int_angles,
ang_Gs[::2], 0)
plot_angle_vs_geometry(detector, source, int_angles,
ang_Gs[1::2], 1)
# create intrinsic peak efficiency vs angle plot
plot_angle_vs_ipe(detector, source, int_angles,
ang_e_ps[::2], 0)
plot_angle_vs_ipe(detector, source, int_angles,
ang_e_ps[1::2], 1)
else:
# create resolution vs angle plot
plot_angle_vs_resolution(detector, source, int_angles,
ang_Rs, 0)
# create FEP efficiency vs angle plot
plot_angle_vs_fep(detector, source, int_angles, ang_e_fs,
0)
# create geometry vs angle plot
plot_angle_vs_geometry(detector, source, int_angles,
ang_Gs, 0)
# create intrinsic peak efficiency vs angle plot
plot_angle_vs_ipe(detector, source, int_angles, ang_e_ps,
0)
# clear array for use with next source
ang_Rs.clear()
ang_e_fs.clear()
ang_Gs.clear()
ang_e_ps.clear()
# for simulated detector
if simulations == 1:
detector = 'simulated ' + detector
# plot resolution curve for detector
plot_resolution_curve(detector, mus, Rs)
# plot FEP effieciency curve for detector
plot_fp_efficiency_curve(detector, mus, e_fs)
# plot geometry curve for detector
plot_geometry_curve(detector, mus, Gs)
# plot intrinsic effieciency curve for detector
plot_ip_efficiency_curve(detector, mus, e_ps)
# for writing to file, uncalibrate to get raw data
for mu in mus:
mu = mu / m
for mu_err in mu_errs:
mu_err = mu_err / m
# write to file for tables
write_resolution_errors(detector, mus, mu_errs, dEs, d_errs, sigmas,
s_errs, Rs, R_errs)
write_efficiency_errors(detector, mus, mu_errs, e_fs, e_f_errs, e_ps,
e_p_errs)
def main():
# downloading the data
print("Downloading data...\n")
download.download_data(out_path, TCELL_CSV_FILENAME, TCELL_DOWNLOAD_URL)
downloaded_filename = TCELL_CSV_FILENAME
# parsing the downloaded data
print("Organizing data, checking for duplicates (it might take a while...)\n")
parser.make_samples(out_path, downloaded_filename,
PARSED_SAMPLES_FOLDER_NAME, BATCH_FILE_SIZE, BATCH_REQUEST_SIZE)
print("Finished parsing data\n")
# pre-proecessing the data
print("Clustering data for train-test independence\n")
parsed_samples_paths = get_parsed_samples_paths(
out_path, PARSED_SAMPLES_FOLDER_NAME)
run_processing.main(['-i', *parsed_samples_paths])
print("Done clustering\n")
parser.Clean_id_lines_from_samples(
out_path, processed_folder_name, CLEAN_PROCESSED_SAMPLES)
print("Loading the data to memory and partitioning to train and test groups\n")
# Create dataset of sequences
char_to_idx, idx_to_char = lstm_model.char_maps()
vocab_len = len(char_to_idx)
train_samples, train_labels, test_samples, test_labels = make_labelled_samples(
out_path, CLEAN_PROCESSED_SAMPLES, char_to_idx, idx_to_char, config["train_test_ratio"])
# ====================== MODEL AND TRAINING ======================
# Create DataLoader returning batches of samples.
dl_train, dl_test, _, ds_test = get_dataloaders(
train_samples, train_labels, test_samples, test_labels)
# get random subset text from test dataset
subset_text = get_subset_text(ds_test, idx_to_char)
# initialize a model and try to train it
in_local_maximum = True
while in_local_maximum:
try:
in_local_maximum = False
model_text = ''
model = None
print(
"\nInitializing a random model with a random enough capitalization before training\n")
while not is_random(model_text):
# init model
model = lstm_model.LSTMTagger(hidden_dim=config["hidden_dim"], input_dim=vocab_len, tagset_size=TAGSET_SIZE,
n_layers=config["n_layers"], bidirectional=(config["bidirectional"] == 1), drop_prob=config["dropout"], device=device)
model.to(device)
model_text = get_capitalized_model_text(
model, subset_text.lower(), (char_to_idx, idx_to_char))
# see how model works before training at all
print("Model capitalization before training:\n")
print(model_text)
# train the model
fit_res = train_model(model, subset_text, (char_to_idx,
idx_to_char), dl_train, dl_test)
print("\nFinished training\n")
except LocalMaximumError:
print("Stuck in local maximum of all non-epitopes! Retrying...")
checkpoint_file = config['checkpoint_file']
checkpoint_filename = f'{checkpoint_file}.pt'
if os.path.isfile(checkpoint_filename):
pathlib.Path(checkpoint_filename).unlink()
in_local_maximum = True
# plot the training results
training_plot_name = config['training_plot_name']
print(f"Saving training plot to: {training_plot_name}\n")
fig, _ = plot_fit(fit_res)
fig.savefig(training_plot_name)