def open_mri_se(self):
self.stop_all()
self.stacked_widget.setCurrentIndex(1)
self.mriSeWidget.set_freq(parameters.get_freq())
self.mriSeWidget.freqValue.setValue(parameters.get_freq())
# self.mriSeWidget.atValue.setValue(parameters.get_at())
self.setWindowTitle('MRI tabletop - SE GUI')
def open_mri_fid(self):
self.stop_all()
self.stacked_widget.setCurrentIndex(0)
# update frequency to server
self.mriFidWidget.set_freq(parameters.get_freq())
self.mriFidWidget.freqValue.setValue(
parameters.get_freq()) # maybe put this in lower funcs
self.setWindowTitle('MRI tabletop - FID GUI')
def init_var(self):
self.centeringFlag = False
self.attenuationFlag = False
self.acqTimeout = self.timeoutValue.value() / 1000
self.acqCount = 0
self.centerFreq = 0
self.centerPeak = 0
self.at_results = []
self.freqEstimation.setValue(parameters.get_freq())
self.freqSpan.setValue(0.60)
self.freqSteps.setValue(6)
self.atStart.setValue(16)
self.atStop.setValue(24)
self.atSteps.setValue(8)
def analytics(self):
self.peak_value = round(np.max(self.fft_mag), 2)
self.peak.setText(str(self.peak_value))
# Calculate fwhm
max_value = np.max(self.fft_mag)
self.max_index = np.argmax(self.fft_mag)
bound_high = self.max_index
bound_low = self.max_index
while 1:
if self.fft_mag[bound_low] < 0.5 * max_value:
break
bound_low = bound_low - 1
while 1:
if self.fft_mag[bound_high] < 0.5 * max_value:
break
bound_high = bound_high + 1
self.fwhm_value = bound_high - bound_low
freq_span = abs(np.min(self.freqaxis)) + abs(np.max(self.freqaxis))
self.fwhm.setText(
str(round(self.fwhm_value * freq_span / self.data_idx)) + " Hz")
# Calculate the SNR value inside a peak window
peak_window = self.fwhm_value * 5
self.noise_bound_low = int(self.max_index - peak_window / 2)
self.noise_bound_high = int(self.max_index + peak_window / 2)
# Join noise outside peak window, calculate std. dev. and snr = peak/std.dev.
noise = np.concatenate((self.fft_mag[0:self.noise_bound_low],
self.fft_mag[self.noise_bound_high:]))
self.snr_value = round(self.peak_value / np.std(noise), 2)
# print("snr_value: ", snr_value)
self.snr.setText(str(self.snr_value))
# Calculate center frequency
self.center_freq = parameters.get_freq() + (
(self.max_index - 5000 / 2) * 250000 / 5000) / 1.0e6
# 250000 sampling rate, 5000 number of samples for FFT
self.centerFreq.setText(str(round(self.center_freq, 5)))
print("\tData analysed.")
def open_mri_sd(self):
self.stop_all()
self.stacked_widget.setCurrentIndex(7)
self.mriRtWidget.set_freq(parameters.get_freq())
self.mriRtWidget.freqValue.setValue(parameters.get_freq())
self.setWindowTitle('MRI tabletop - Sequence Design GUI')
def open_mri_rt(self):
self.stop_all()
self.stacked_widget.setCurrentIndex(6)
self.mriRtWidget.set_freq(parameters.get_freq())
self.mriRtWidget.freqValue.setValue(parameters.get_freq())
self.setWindowTitle('MRI tabletop - Real-time Update GUI')
def open_mri_3dimag(self):
self.stop_all()
self.stacked_widget.setCurrentIndex(5)
self.mri3DImagWidget.set_freq(parameters.get_freq())
self.mri3DImagWidget.freqValue.setValue(parameters.get_freq())
self.setWindowTitle('MRI tabletop - 3D Image GUI')
def open_mri_proj(self):
self.stop_all()
self.stacked_widget.setCurrentIndex(3)
self.mriProjWidget.set_freq(parameters.get_freq())
self.mriProjWidget.freqValue.setValue(parameters.get_freq())
self.setWindowTitle('MRI tabletop - 1D Projection GUI')
def open_mri_sig(self):
self.stop_all()
self.stacked_widget.setCurrentIndex(2)
self.mriSigWidget.set_freq(parameters.get_freq())
self.mriSigWidget.freqValue.setValue(parameters.get_freq())
self.setWindowTitle('MRI tabletop - Signals GUI')
def display_data(self):
# Clear the plots: bottom-time domain, top-frequency domain
self.axes_bottom.clear()
self.axes_bottom.grid()
self.axes_top.clear()
self.axes_top.grid()
# Get magnitude, real and imaginary part of data
data = self.data
mag = np.abs(data)
real = np.real(data)
imag = np.imag(data)
# Plot the bottom (time domain): display time signal from 0~21ms [0~5250]
time = 20
data_idx = int(time * 250)
mag_t = mag[0:data_idx]
real_t = real[0:data_idx]
imag_t = imag[0:data_idx]
time_axis = np.linspace(0, time, data_idx)
self.curve_bottom = self.axes_bottom.plot(time_axis, mag_t) # blue
self.curve_bottom = self.axes_bottom.plot(time_axis, real_t) # red
self.curve_bottom = self.axes_bottom.plot(time_axis, imag_t) # green
self.axes_bottom.set_xlabel('time, ms')
# Plot the top (frequency domain): use signal from 0.5~20.5ms: first 0.5ms junk
# update: the junk is already taken care of by the sequence timing
dclip = data[0:data_idx]
freqaxis = np.linspace(-125000, 125000, data_idx) # 5000 points ~ 20ms
fft_mag = abs(np.fft.fftshift(np.fft.fft(np.fft.fftshift(dclip))))
if not self.freqCheckBox.isChecked(): # non zoomed
self.curve_top = self.axes_top.plot(
freqaxis[int(data_idx / 2 - data_idx / 10):int(data_idx / 2 +
data_idx / 10)],
fft_mag[int(data_idx / 2 - data_idx / 10):int(data_idx / 2 +
data_idx / 10)])
else: # zoomed
self.curve_top = self.axes_top.plot(
freqaxis[int(data_idx / 2 -
data_idx / 100):int(data_idx / 2 +
data_idx / 100)],
fft_mag[int(data_idx / 2 -
data_idx / 100):int(data_idx / 2 +
data_idx / 100)])
self.axes_top.set_xlabel('frequency, Hz')
# Update the figure
self.canvas.draw()
# Data Analysis
# Calculate and display properties of the frequency
peak_value = round(np.max(fft_mag), 2)
self.peak.setText(str(peak_value))
max_value = np.max(fft_mag)
max_index = np.argmax(fft_mag)
bound_high = max_index
bound_low = max_index
# print(max_index)
while 1:
if fft_mag[bound_low] < 0.5 * max_value:
break
bound_low = bound_low - 1
while 1:
if fft_mag[bound_high] < 0.5 * max_value:
break
bound_high = bound_high + 1
fwhm_value = bound_high - bound_low
self.fwhm.setText(str(fwhm_value))
# Calculate center frequency
self.center_freq = parameters.get_freq() + (
(max_index - 5000 / 2) * 250000 / 5000) / 1.0e6
# 250000 sampling rate, 5000 number of samples for FFT
self.centerFreq.setText(str(self.center_freq))
def open_mri_rt(self):
self.stop_all()
self.stacked_widget.setCurrentIndex(7)
self.mriRtWidget.set_freq(parameters.get_freq())
self.mriRtWidget.freqValue.setValue(parameters.get_freq())
self.setWindowTitle('Tabletop MRI - Real-time Rotation GUI')
def open_mri_2dimag(self):
self.stop_all()
self.stacked_widget.setCurrentIndex(5)
self.mri2DImagWidget.set_freq(parameters.get_freq())
self.mri2DImagWidget.freqValue.setValue(parameters.get_freq())
self.setWindowTitle('Tabletop MRI - 2D Imaging GUI')