def acquireProjection(self, idx, ts=20):
print("Acquire projection along axis: ", idx, "\n")
socket.write(struct.pack('<I', 7 << 28 | idx))
while (True): # Wait until bytes written
if not socket.waitForBytesWritten():
break
while True: # Read data
socket.waitForReadyRead()
datasize = socket.bytesAvailable()
# print(datasize)
time.sleep(0.0001)
if datasize == 8 * self.size:
print("Readout finished : ", datasize)
self.buffer[0:8 * self.size] = socket.read(8 * self.size)
t1 = time.time() # calculate time for acquisition
break
else:
continue
print("Start processing readout.")
self.process_readout(ts)
self.readout_finished.emit()
def acquire(self, ts=20):
t0 = time.time() # calculate time for acquisition
socket.write(struct.pack('<I', 1 << 28))
while (True): # Wait until bytes written
if not socket.waitForBytesWritten(): break
while True: # Read data
socket.waitForReadyRead()
datasize = socket.bytesAvailable()
# print(datasize)
time.sleep(0.0001)
if datasize == 8 * self.size:
print("Readout finished : ", datasize)
self.buffer[0:8 * self.size] = socket.read(8 * self.size)
t1 = time.time() # calculate time for acquisition
break
else:
continue
print("Start processing readout.")
self.process_readout(ts)
print("Start analyzing data.")
self.analytics()
print('Finished acquisition in {:.3f} ms'.format((t1 - t0) * 1000.0))
# Emit signal, when data was read
self.readout_finished.emit()
def acquireImage(self, npe=16, TR=4000, ts=4):
# Implement new concept:
# com.start_image(npe)
socket.write(struct.pack('<I', 6 << 28 | npe << 16 | TR))
while (True): # Wait until bytes written
if not socket.waitForBytesWritten(): break
t0 = time.time()
for n in range(npe):
while True: # Read data
socket.waitForReadyRead()
datasize = socket.bytesAvailable()
time.sleep(0.0001)
if datasize == 8 * self.size:
print("Readout finished : ", datasize)
self.buffer[0:8 * self.size] = socket.read(8 * self.size)
break
else:
continue
self.process_readout(ts)
self.readout_finished.emit()
t1 = time.time()
print('Finished image acquisition in {:.4f} min'.format(
(t1 - t0) / 60))
def acquireImage(self, npe=16, ts=20):
socket.write(struct.pack('<I', 6 << 28 | npe))
while (True): # Wait until bytes written
if not socket.waitForBytesWritten():
break
for n in range(npe):
while True: # Read data
socket.waitForReadyRead()
datasize = socket.bytesAvailable()
time.sleep(0.0001)
if datasize == 8 * self.size:
print("Readout finished : ", datasize)
self.buffer[0:8 * self.size] = socket.read(8 * self.size)
break
else:
continue
self.process_readout(ts)
self.readout_finished.emit()
def T2_measurement(self, values, freq, recovery, **kwargs):
print('T1 Measurement')
avgPoint = kwargs.get('avgP', 1)
avgMeas = kwargs.get('avgM', 1)
self.idxM = 0
self.idxP = 0
self.T2 = []
self.R2 = []
self.measurement = []
self.set_freq(freq)
while self.idxM < avgMeas:
print("Measurement : ", self.idxM + 1, "/", avgMeas)
self.measurement = []
for self.te in values:
self.peaks = []
self.set_SE(self.te)
while self.idxP < avgPoint:
print("Datapoint : ", self.idxP + 1, "/", avgPoint)
time.sleep(recovery / 1000)
socket.write(struct.pack('<I', 1 << 28))
while True:
socket.waitForReadyRead()
datasize = socket.bytesAvailable()
print(datasize)
time.sleep(0.1)
if datasize == 8 * self.size:
print("IR readout finished : ", datasize)
self.buffer[0:8 * self.size] = socket.read(
8 * self.size)
break
else:
continue
print("Start processing SE readout.")
self.process_readout()
print("Start analyzing SE data.")
self.analytics()
self.peaks.append(np.max(self.mag_con))
self.readout_finished.emit()
self.idxP += 1
self.measurement.append(np.mean(self.peaks))
self.idxP = 0
# Calculate T2 value and error
try:
p, cov = curve_fit(self.T2_fit,
values,
self.measurement,
bounds=([0, self.measurement[0],
0], [10, 50000, 0.5]))
# Calculation of T2: M(T2) = 0.37*(func(0)) = 0.37(A+B), T2 = -1/C * ln((M(T2)-A)/B)
self.T2.append(
round(
-(1 / p[2]) * np.log(
((0.37 * (p[0] + p[1])) - p[0]) / p[1]), 5))
self.R2.append(
round(
1 - (np.sum(
(self.measurement - self.T2_fit(values, *p))**2) /
(np.sum(
(self.measurement - np.mean(self.measurement))
**2))), 5))
self.x_fit = np.linspace(0, int(1.2 * values[-1]), 1000)
self.y_fit = self.T2_fit(self.x_fit, *p)
self.fit_params = p
self.t2_finished.emit()
self.idxM += 1
except:
self.T2.append(float('nan'))
self.R2.append(float('nan'))
self.x_fit = float('nan')
self.y_fit = float('nan')
self.fit_params = float('nan')
self.t2_finished.emit()
self.idxM += 1
return np.nanmean(self.T2), np.nanmean(self.R2)
def T1_measurement(self, values, freq, recovery, **kwargs):
print('T1 Measurement')
avgPoint = kwargs.get('avgP', 1)
avgMeas = kwargs.get('avgM', 1)
seq_type = kwargs.get('seqType', 1)
self.idxM = 0
self.idxP = 0
self.T1 = []
self.R2 = []
self.set_freq(freq)
while self.idxM < avgMeas:
print("Measurement : ", self.idxM + 1, "/", avgMeas)
self.measurement = []
for self.ti in values:
self.peaks = []
if seq_type == 'sir':
self.set_SIR(self.ti)
else:
self.set_IR(self.ti)
while self.idxP < avgPoint:
print("Datapoint : ", self.idxP + 1, "/", avgPoint)
time.sleep(recovery / 1000)
socket.write(struct.pack('<I', 1 << 28))
while True: # Readout data
socket.waitForReadyRead()
datasize = socket.bytesAvailable()
print(datasize)
time.sleep(0.1)
if datasize == 8 * self.size:
print("IR readout finished : ", datasize)
self.buffer[0:8 * self.size] = socket.read(
8 * self.size)
break
else:
continue
print("Start processing IR readout.")
self.process_readout()
print("Start analyzing IR data.")
self.analytics()
self.peaks.append(
np.max(self.mag_con) *
np.sign(self.real_con[np.argmin(self.real_con[0:50])]))
#self.peaks.append(self.peak_value*np.sign(self.real_con[np.argmin(self.real_con[0:50])]))
self.readout_finished.emit()
self.idxP += 1
self.measurement.append(np.mean(self.peaks))
self.idxP = 0
def func(x):
return p[0] - p[1] * np.exp(-p[2] * x)
try:
p, cov = curve_fit(self.T1_fit, values, self.measurement)
# Calculate T1 value and error
self.T1.append(
round(1.44 * brentq(func, values[0], values[-1]), 2))
self.R2.append(
round(
1 - (np.sum(
(self.measurement - self.T1_fit(values, *p))**2) /
(np.sum(
(self.measurement - np.mean(self.measurement))
**2))), 5))
self.x_fit = np.linspace(0, int(1.2 * values[-1]), 1000)
self.y_fit = self.T1_fit(self.x_fit, *p)
self.fit_params = p
except: # in case no fit found
self.T1.append(float('nan'))
self.R2.append(float('nan'))
self.x_fit = float('nan')
self.y_fit = float('nan')
self.fit_params = float('nan')
self.t1_finished.emit()
self.idxM += 1
return np.nanmean(self.T1), np.nanmean(self.R2)
def T1_measurement(self, values, freq, recovery, **kwargs):
print('T1 Measurement')
avgPoint = kwargs.get('avgP', 1)
avgMeas = kwargs.get('avgM', 1)
seq_type = kwargs.get('seqType', 1)
ts = 2
self.idxM = 0
self.idxP = 0
self.T1 = []
self.R2 = []
self.set_freq(freq)
#while self.idxM < avgMeas:
#print("Measurement : ", self.idxM+1, "/", avgMeas)
self.measurement = []
for self.ti in values:
self.peaks = []
if seq_type == 'sir':
self.set_SIR(self.ti)
else:
self.set_IR(self.ti)
while self.idxP < avgPoint:
print("Datapoint : ", self.idxP + 1, "/", avgPoint)
time.sleep(recovery / 1000)
socket.write(struct.pack('<I', 1 << 28))
while True: # Readout data
socket.waitForReadyRead()
datasize = socket.bytesAvailable()
print(datasize)
time.sleep(0.1)
if datasize == 8 * self.size:
print("IR readout finished : ", datasize)
self.buffer[0:8 * self.size] = socket.read(8 *
self.size)
break
else:
continue
print("Start processing IR readout.")
self.process_readout(ts)
print("Start analyzing IR data.")
self.analytics()
self.peaks.append(
np.max(self.mag_con) *
np.sign(self.real_con[np.argmin(self.real_con[0:50])]))
#self.peaks.append(self.peak_value*np.sign(self.real_con[np.argmin(self.real_con[0:50])]))
self.readout_finished.emit()
self.idxP += 1
self.measurement.append(np.mean(self.peaks))
self.idxP = 0
#self.calculateT1fit(values)
#bounds=([0, self.measurement[0], 0], [100, 50000, 1])
self.calculateT1fit(values) #, bounds)
self.t1_finished.emit()
#self.idxM += 1
return np.nanmean(self.T1), np.nanmean(self.R2)
if not socket.waitForBytesWritten(): break
# Test 2D SE acquisition
#socket.write(struct.pack('<I', 6 << 28 | npe))
# Test FID
socket.write(struct.pack('<I', 1 << 28))
while (True): # Wait until bytes written
if not socket.waitForBytesWritten(): break
# Perform npe-times readout
for n in range(npe):
while True: # Read data
socket.waitForReadyRead()
datasize = socket.bytesAvailable()
time.sleep(0.0001)
if datasize == 8 * size:
print("Readout finished : ", datasize)
buffer[0:8 * size] = socket.read(8 * size)
break
else:
continue
ax.plot(data[0:2000])
plt.show()
print("Acquisition finished.\n")
time.sleep(1)