def haste(self, plotSeq):
init_gpa = False # Starts the gpa
nScans = self.nScans # NEX
larmorFreq = self.larmorFreq # MHz, Larmor frequency
rfExAmp = self.rfExAmp # a.u., rf excitation pulse amplitude
rfReAmp = self.rfReAmp # a.u., rf refocusing pulse amplitude
rfExTime = self.rfExTime # us, rf excitation pulse time
rfReTime = self.rfReTime # us, rf refocusing pulse time
rfEnvelope = self.rfEnvelope # 'Rec' -> square pulse, 'Sinc' -> sinc pulse
echoSpacing = self.echoSpacing # ms, time between echoes
inversionTime = self.inversionTime # ms, Inversion recovery time
repetitionTime = self.repetitionTime # ms, TR
fov = np.array(self.fov) # mm, FOV along readout, phase and slice
dfov = np.array(self.dfov) # mm, displacement of fov center
nPoints = np.array(
self.nPoints) # Number of points along readout, phase and slice
acqTime = self.acqTime # ms, acquisition time
axes = np.array(self.axes) # 0->x, 1->y and 2->z defined as [rd,ph,sl]
axesEnable = self.axesEnable # 1-> Enable, 0-> Disable
sweepMode = self.sweepMode # 0->k2k (T2), 1->02k (T1), 2->k20 (T2), 3->Niquist modulated (T2)
rdGradTime = self.rdGradTime # ms, readout gradient time
rdDephTime = self.rdDephTime # ms, readout dephasing time
phGradTime = self.phGradTime # ms, phase and slice dephasing time
rdPreemphasis = self.rdPreemphasis # readout dephasing gradient is multiplied by this factor
ssPreemphasis = self.ssPreemphasis # slice rephasing gradient is multiplied by this factor
crusherDelay = self.crusherDelay # delay of the crusher gradient
drfPhase = self.drfPhase # degrees, phase of the excitation pulse
dummyPulses = self.dummyPulses # number of dummy pulses for T1 stabilization
shimming = self.shimming # a.u.*1e4, shimming along the X,Y and Z axes
parFourierFraction = self.parFourierFraction # fraction of acquired k-space along phase direction
freqCal = True
demo = False
# rawData fields
rawData = {}
# Conversion of variables to non-multiplied units
larmorFreq = larmorFreq * 1e6
rfExTime = rfExTime * 1e-6
rfReTime = rfReTime * 1e-6
fov = np.array(fov) * 1e-3
dfov = np.array(dfov) * 1e-3
echoSpacing = echoSpacing * 1e-3
acqTime = acqTime * 1e-3
shimming = np.array(shimming) * 1e-4
repetitionTime = repetitionTime * 1e-3
inversionTime = inversionTime * 1e-3
rdGradTime = rdGradTime * 1e-3
rdDephTime = rdDephTime * 1e-3
phGradTime = phGradTime * 1e-3
crusherDelay = crusherDelay * 1e-6
# Inputs for rawData
rawData['seqName'] = 'HASTE'
rawData['nScans'] = nScans
rawData['larmorFreq'] = larmorFreq # Larmor frequency
rawData['rfExAmp'] = rfExAmp # rf excitation pulse amplitude
rawData['rfReAmp'] = rfReAmp # rf refocusing pulse amplitude
rawData['rfExTime'] = rfExTime # rf excitation pulse time
rawData['rfReTime'] = rfReTime # rf refocusing pulse time
rawData['rfEnvelope'] = rfEnvelope
rawData['echoSpacing'] = echoSpacing # time between echoes
rawData['inversionTime'] = inversionTime # Inversion recovery time
rawData['repetitionTime'] = repetitionTime # TR
rawData['fov'] = fov # FOV along readout, phase and slice
rawData['dfov'] = dfov # Displacement of fov center
rawData[
'nPoints'] = nPoints # Number of points along readout, phase and slice
rawData['acqTime'] = acqTime # Acquisition time
rawData[
'axesOrientation'] = axes # 0->x, 1->y and 2->z defined as [rd,ph,sl]
rawData['axesEnable'] = axesEnable # 1-> Enable, 0-> Disable
rawData[
'sweepMode'] = sweepMode # 0->k2k (T2), 1->02k (T1), 2->k20 (T2), 3->Niquist modulated (T2)
rawData['rdPreemphasis'] = rdPreemphasis
rawData['ssPreemphasis'] = ssPreemphasis
rawData['drfPhase'] = drfPhase
rawData['dummyPulses'] = dummyPulses # Dummy pulses for T1 stabilization
rawData['partialFourierFraction'] = parFourierFraction
rawData['rdDephTime'] = rdDephTime
rawData['crusherDelay'] = crusherDelay
rawData['shimming'] = shimming
# Miscellaneous
slThickness = fov[2]
rfSincLobes = 7 # Number of lobes for sinc rf excitation, BW = rfSincLobes/rfTime
larmorFreq = larmorFreq * 1e-6
gradRiseTime = 200e-6 # Estimated gradient rise time
gSteps = int(gradRiseTime * 1e6 / 5)
addRdPoints = 10 # Initial rd points to avoid artifact at the begining of rd
if rfReAmp == 0:
rfReAmp = 2 * rfExAmp
if rfReTime == 0:
rfReTime = rfExTime
resolution = fov / nPoints
rawData['resolution'] = resolution
rawData['gradRiseTime'] = gradRiseTime
rawData['addRdPoints'] = addRdPoints
# Matrix size
nRD = nPoints[0] + 2 * addRdPoints
nPH = nPoints[1] * axesEnable[1] + (1 - axesEnable[1])
# parAcqLines
nPHreal = int(nPoints[1] * parFourierFraction)
parAcqLines = int(nPHreal - nPoints[1] / 2)
rawData['parAcqLines'] = parAcqLines
print(parAcqLines)
del nPHreal
# BW
BW = nPoints[0] / acqTime * 1e-6
BWov = BW * hw.oversamplingFactor
samplingPeriod = 1 / BWov
rawData['samplingPeriod'] = samplingPeriod
# Readout gradient time
if rdGradTime < acqTime:
rdGradTime = acqTime
rawData['rdGradTime'] = rdGradTime
# Phase de- and re-phasing time
if phGradTime == 0 or phGradTime > echoSpacing / 2 - rfExTime / 2 - rfReTime / 2 - 2 * gradRiseTime:
phGradTime = echoSpacing / 2 - rfExTime / 2 - rfReTime / 2 - 2 * gradRiseTime
rawData['phGradTime'] = phGradTime
# Slice selection dephasing gradient time
ssDephGradTime = (rfExTime - gradRiseTime) / 2
rawData['ssDephGradTime'] = ssDephGradTime
# Max redaout and phase gradient amplitude
rdGradAmplitude = nPoints[0] / (hw.gammaB * fov[0] *
acqTime) * axesEnable[0]
phGradAmplitude = nPH / (2 * hw.gammaB * fov[1] *
(phGradTime + gradRiseTime)) * axesEnable[1]
rawData['rdGradAmplitude'] = rdGradAmplitude
rawData['phGradAmplitude'] = phGradAmplitude
# Slice selection gradient
if rfEnvelope == 'Sinc':
ssGradAmplitude = rfSincLobes / (hw.gammaB * slThickness *
rfExTime) * axesEnable[2]
elif rfEnvelope == 'Rec':
ssGradAmplitude = 1 / (hw.gammaB * slThickness *
rfExTime) * axesEnable[2]
rawData['ssGradAmplitude'] = ssGradAmplitude
# Readout dephasing amplitude
rdDephAmplitude = 0.5 * rdGradAmplitude * (gradRiseTime + rdGradTime) / (
gradRiseTime + rdDephTime)
rawData['rdDephAmplitude'] = rdDephAmplitude
# Phase gradient vector
phGradients = np.linspace(-phGradAmplitude,
phGradAmplitude,
num=nPH,
endpoint=False)
# Get phase indexes for the given sweep mode
ind = mri.getIndex(2 * parAcqLines, 2 * parAcqLines, sweepMode)
ind = ind - parAcqLines + int(nPH / 2)
ind = np.int32(
np.concatenate((ind,
np.linspace(int(nPH / 2) - parAcqLines - 1,
-1,
num=int(nPH / 2) - parAcqLines,
endpoint=False)),
axis=0))
rawData['sweepOrder'] = ind
# Now fix the number of phases to partailly acquired k-space
nPH = (int(nPoints[1] / 2) + parAcqLines) * axesEnable[1] + (1 -
axesEnable[1])
phGradients = phGradients[0:nPH]
phGradients = phGradients[ind]
rawData['phGradients'] = phGradients
def createSequenceDemo():
nRepetitions = int(1 + dummyPulses)
scanTime = 20e3 + nRepetitions * repetitionTime
rawData['scanTime'] = scanTime * 1e-6
acqPoints = 0
data = []
for repeIndex in range(nRepetitions):
for echoIndex in range(nPH):
if (repeIndex == 0 or repeIndex >= dummyPulses):
acqPoints += nRD * hw.oversamplingFactor
data = np.concatenate(
(data, np.random.randn(nRD * hw.oversamplingFactor) +
1j * np.random.randn(nRD * hw.oversamplingFactor)),
axis=0)
return data, acqPoints
def createSequence():
nRepetitions = int(1 + dummyPulses)
scanTime = 20e3 + nRepetitions * repetitionTime
rawData['scanTime'] = scanTime * 1e-6
print('Scan Time = ', (scanTime * 1e-6), 's')
if rdGradTime == 0: # Check if readout gradient is dc or pulsed
dc = True
else:
dc = False
# Set shimming
mri.iniSequence(expt, 20, shimming)
for repeIndex in range(nRepetitions):
# Initialize time
tEx = 20e3 + repetitionTime * repeIndex + inversionTime
# Inversion pulse
if repeIndex >= dummyPulses and inversionTime != 0:
t0 = tEx - inversionTime - rfReTime / 2 - hw.blkTime
mri.rfRecPulse(expt, t0, rfReTime, rfReAmp / 180 * 180, 0)
mri.gradTrap(expt, t0 + hw.blkTime + rfReTime, gradRiseTime,
inversionTime * 0.5, 0.005, gSteps, axes[0],
shimming)
mri.gradTrap(expt, t0 + hw.blkTime + rfReTime, gradRiseTime,
inversionTime * 0.5, 0.005, gSteps, axes[1],
shimming)
mri.gradTrap(expt, t0 + hw.blkTime + rfReTime, gradRiseTime,
inversionTime * 0.5, 0.005, gSteps, axes[2],
shimming)
# DC radout gradient if desired
if (repeIndex == 0 or repeIndex >= dummyPulses) and dc == True:
t0 = tEx - rfExTime / 2 - gradRiseTime - hw.gradDelay
mri.gradTrap(expt, t0, echoSpacing * (nPH + 1),
rdGradAmplitude, axes[0])
# Slice selection gradient dephasing
if (slThickness != 0 and repeIndex >= dummyPulses):
t0 = tEx - rfExTime / 2 - gradRiseTime - hw.gradDelay
mri.gradTrap(expt, t0, gradRiseTime, rfExTime, ssGradAmplitude,
gSteps, axes[2], shimming)
# Excitation pulse
t0 = tEx - hw.blkTime - rfExTime / 2
if rfEnvelope == 'Rec':
mri.rfRecPulse(expt, t0, rfExTime, rfExAmp,
drfPhase * np.pi / 180)
elif rfEnvelope == 'Sinc':
mri.rfSincPulse(expt, t0, rfExTime, rfSincLobes, rfExAmp,
drfPhase * np.pi / 180)
# Slice selection gradient rephasing
if (slThickness != 0 and repeIndex >= dummyPulses):
t0 = tEx + rfExTime / 2 + gradRiseTime - hw.gradDelay
if rfEnvelope == 'Rec':
mri.gradTrap(expt, t0, gradRiseTime, 0.,
-ssGradAmplitude * ssPreemphasis, gSteps,
axes[2], shimming)
elif rfEnvelope == 'Sinc':
mri.gradTrap(expt, t0, gradRiseTime, ssDephGradTime,
-ssGradAmplitude * ssPreemphasis, gSteps,
axes[2], shimming)
# Dephasing readout
t0 = tEx + rfExTime / 2 - hw.gradDelay
if (repeIndex == 0 or repeIndex >= dummyPulses) and dc == False:
mri.gradTrap(expt, t0, gradRiseTime, rdDephTime,
rdDephAmplitude * rdPreemphasis, gSteps, axes[0],
shimming)
# Echo train
for echoIndex in range(nPH):
tEcho = tEx + echoSpacing * (echoIndex + 1)
# Crusher gradient
if repeIndex >= dummyPulses:
t0 = tEcho - echoSpacing / 2 - rfReTime / 2 - gradRiseTime - hw.gradDelay - crusherDelay
mri.gradTrap(expt, t0, gradRiseTime,
rfReTime + 2 * crusherDelay, ssGradAmplitude,
gSteps, axes[2], shimming)
# Refocusing pulse
t0 = tEcho - echoSpacing / 2 - rfReTime / 2 - hw.blkTime
if rfEnvelope == 'Rec':
mri.rfRecPulse(expt, t0, rfReTime, rfReAmp,
np.pi / 2 + drfPhase * np.pi / 180)
if rfEnvelope == 'Sinc':
mri.rfSincPulse(expt, t0, rfReTime, rfSincLobes, rfReAmp,
np.pi / 2 + drfPhase * np.pi / 180)
# Dephasing phase gradient
t0 = tEcho - echoSpacing / 2 + rfReTime / 2 - hw.gradDelay
if repeIndex >= dummyPulses: # This is to account for dummy pulses
mri.gradTrap(expt, t0, gradRiseTime, phGradTime,
phGradients[echoIndex], gSteps, axes[1],
shimming)
# Readout gradient
t0 = tEcho - rdGradTime / 2 - gradRiseTime - hw.gradDelay
if (repeIndex == 0 or repeIndex >= dummyPulses
) and dc == False: # This is to account for dummy pulses
mri.gradTrap(expt, t0, gradRiseTime, rdGradTime,
rdGradAmplitude, gSteps, axes[0], shimming)
# Rx gate
if (repeIndex == 0 or repeIndex >= dummyPulses):
t0 = tEcho - acqTime / 2 - addRdPoints / BW
mri.rxGate(expt, t0, acqTime + 2 * addRdPoints / BW)
# Rephasing phase and slice gradients
t0 = tEcho + acqTime / 2 + addRdPoints / BW - hw.gradDelay
if (echoIndex < nPH - 1 and repeIndex >= dummyPulses):
mri.gradTrap(expt, t0, gradRiseTime, phGradTime,
-phGradients[echoIndex], gSteps, axes[1],
shimming)
elif (echoIndex == nPH - 1 and repeIndex >= dummyPulses):
mri.gradTrap(expt, t0, gradRiseTime, phGradTime,
+phGradients[echoIndex], gSteps, axes[1],
shimming)
if repeIndex == nRepetitions - 1:
mri.endSequence(expt, scanTime)
# Changing time parameters to us
rfExTime = rfExTime * 1e6
rfReTime = rfReTime * 1e6
echoSpacing = echoSpacing * 1e6
repetitionTime = repetitionTime * 1e6
gradRiseTime = gradRiseTime * 1e6
phGradTime = phGradTime * 1e6
rdGradTime = rdGradTime * 1e6
rdDephTime = rdDephTime * 1e6
inversionTime = inversionTime * 1e6
crusherDelay = crusherDelay * 1e6
ssDephGradTime = ssDephGradTime * 1e6
# Calibrate frequency
if not demo and freqCal and (not plotSeq):
mri.freqCalibration(rawData, bw=0.05)
mri.freqCalibration(rawData, bw=0.005)
larmorFreq = rawData['larmorFreq'] * 1e-6
# Create full sequence
if not demo:
expt = ex.Experiment(lo_freq=larmorFreq,
rx_t=samplingPeriod,
init_gpa=init_gpa,
gpa_fhdo_offset_time=(1 / 0.2 / 3.1))
samplingPeriod = expt.get_rx_ts()[0]
BW = 1 / samplingPeriod / hw.oversamplingFactor
acqTime = nPoints[0] / BW # us
createSequence()
# Run the experiment
dataFull = []
dummyData = []
overData = []
for ii in range(nScans):
if plotSeq:
expt.plot_sequence()
plt.show()
break
else:
print("Scan %s ..." % (ii + 1))
if not demo:
rxd, msgs = expt.run()
rxd['rx0'] = rxd[
'rx0'] * 13.788 # Here I normalize to get the result in mV
else:
data, acqPoints = createSequenceDemo()
# Get data
if not demo:
if dummyPulses > 0:
dummyData = np.concatenate(
(dummyData,
rxd['rx0'][0:nRD * nPH * hw.oversamplingFactor]),
axis=0)
overData = np.concatenate(
(overData,
rxd['rx0'][nRD * nPH * hw.oversamplingFactor::]),
axis=0)
else:
overData = np.concatenate((overData, rxd['rx0']), axis=0)
else:
if dummyPulses > 0:
dummyData = np.concatenate(
(dummyData, data[0:nRD * nPH * hw.oversamplingFactor]),
axis=0)
overData = np.concatenate(
(overData, data[nRD * nPH * hw.oversamplingFactor::]),
axis=0)
else:
overData = np.concatenate((overData, data), axis=0)
if not demo: expt.__del__()
print('Scans done!')
rawData['overData'] = overData
# Fix the echo position using oversampled data
if dummyPulses > 0:
dummyData = np.reshape(dummyData,
(nScans, nPH, nRD * hw.oversamplingFactor))
dummyData = np.average(dummyData, axis=0)
rawData['dummyData'] = dummyData
overData = np.reshape(overData,
(nScans, 1, nPH, nRD * hw.oversamplingFactor))
for ii in range(nScans):
overData[ii, :, :, :] = mri.fixEchoPosition(
dummyData, overData[ii, :, :, :])
# Generate dataFull
overData = np.squeeze(
np.reshape(overData, (1, nRD * hw.oversamplingFactor * nPH * nScans)))
dataFull = sig.decimate(overData,
hw.oversamplingFactor,
ftype='fir',
zero_phase=True)
# Get index for krd = 0
# Average data
dataProv = np.reshape(dataFull, (nScans, nRD * nPH))
dataProv = np.average(dataProv, axis=0)
# Reorganize the data acording to sweep mode
dataProv = np.reshape(dataProv, (nPH, nRD))
dataTemp = dataProv * 0
for ii in range(nPH):
dataTemp[ind[ii], :] = dataProv[ii, :]
dataProv = dataTemp
# Check where is krd = 0
dataProv = dataProv[int(nPoints[1] / 2), :]
indkrd0 = np.argmax(np.abs(dataProv))
if indkrd0 < nRD / 2 - addRdPoints or indkrd0 > nRD / 2 + addRdPoints:
indkrd0 = int(nRD / 2)
# Get individual images
dataFull = np.reshape(dataFull, (nScans, nPH, nRD))
dataFull = dataFull[:, :, indkrd0 - int(nPoints[0] / 2):indkrd0 +
int(nPoints[0] / 2)]
dataTemp = dataFull * 0
for ii in range(nPH):
dataTemp[:, ind[ii], :] = dataFull[:, ii, :]
dataFull = dataTemp
imgFull = dataFull * 0
for ii in range(nScans):
imgFull[ii, :, :] = np.fft.ifftshift(
np.fft.ifftn(np.fft.ifftshift(dataFull[ii, :, :])))
rawData['dataFull'] = dataFull
rawData['imgFull'] = imgFull
# Average data
data = np.average(dataFull, axis=0)
data = np.reshape(data, (nPH, nPoints[0]))
# Do zero padding
dataTemp = np.zeros((nPoints[1], nPoints[0]))
dataTemp = dataTemp + 1j * dataTemp
dataTemp[0:nPH, :] = data
data = np.reshape(dataTemp, (1, nPoints[0] * nPoints[1]))
# Fix the position of the sample according to dfov
kMax = np.array(nPoints) / (2 * np.array(fov)) * np.array(axesEnable)
kRD = np.linspace(-kMax[0], kMax[0], num=nPoints[0], endpoint=False)
kPH = np.linspace(-kMax[1], kMax[1], num=nPoints[1], endpoint=False)
kPH, kRD = np.meshgrid(kPH, kRD)
kRD = np.reshape(kRD, (1, nPoints[0] * nPoints[1]))
kPH = np.reshape(kPH, (1, nPoints[0] * nPoints[1]))
dPhase = np.exp(-2 * np.pi * 1j * (dfov[0] * kRD + dfov[1] * kPH))
data = np.reshape(data * dPhase, (nPoints[1], nPoints[0]))
rawData['kSpace3D'] = data
img = np.fft.ifftshift(np.fft.ifftn(np.fft.ifftshift(data)))
rawData['image3D'] = img
data = np.reshape(data, (1, nPoints[0] * nPoints[1]))
# Create sampled data
kRD = np.reshape(kRD, (nPoints[0] * nPoints[1], 1))
kPH = np.reshape(kPH, (nPoints[0] * nPoints[1], 1))
data = np.reshape(data, (nPoints[0] * nPoints[1], 1))
rawData['kMax'] = kMax
rawData['sampled'] = np.concatenate((kRD, kPH, data), axis=1)
data = np.reshape(data, -1)
# Save data
mri.saveRawData(rawData)
return rawData, msgs, data, BW
def rare_standalone(
init_gpa=False, # Starts the gpa
nScans=1, # NEX
larmorFreq=3.08, # MHz, Larmor frequency
rfExAmp=0.3, # a.u., rf excitation pulse amplitude
rfReAmp=0.3, # a.u., rf refocusing pulse amplitude
rfExTime=35, # us, rf excitation pulse time
rfReTime=70, # us, rf refocusing pulse time
echoSpacing=10, # ms, time between echoes
preExTime=0., # ms, Time from preexcitation pulse to inversion pulse
inversionTime=0., # ms, Inversion recovery time
repetitionTime=200., # ms, TR
fov=np.array([140., 150., 180.]), # mm, FOV along readout, phase and slice
dfov=np.array([0., 0., 0.]), # mm, displacement of fov center
nPoints=np.array([140, 80,
10]), # Number of points along readout, phase and slice
etl=10, # Echo train length
acqTime=4, # ms, acquisition time
axes=np.array([2, 1, 0]), # 0->x, 1->y and 2->z defined as [rd,ph,sl]
axesEnable=np.array([1, 1, 1]), # 1-> Enable, 0-> Disable
sweepMode=1, # 0->k2k (T2), 1->02k (T1), 2->k20 (T2), 3->Niquist modulated (T2)
rdGradTime=5, # ms, readout gradient time
rdDephTime=2, # ms, readout dephasing time
phGradTime=1, # ms, phase and slice dephasing time
rdPreemphasis=1.00, # readout dephasing gradient is multiplied by this factor
drfPhase=0, # degrees, phase of the excitation pulse
dummyPulses=1, # number of dummy pulses for T1 stabilization
shimming=np.array([-70, -90.,
10]), # a.u.*1e4, shimming along the X,Y and Z axes
parFourierFraction=1.0 # fraction of acquired k-space along phase direction
):
freqCal = 1
# rawData fields
rawData = {}
# Conversion of variables to non-multiplied units
larmorFreq = larmorFreq * 1e6
rfExTime = rfExTime * 1e-6
rfReTime = rfReTime * 1e-6
fov = np.array(fov) * 1e-3
dfov = np.array(dfov) * 1e-3
echoSpacing = echoSpacing * 1e-3
acqTime = acqTime * 1e-3
shimming = shimming * 1e-4
repetitionTime = repetitionTime * 1e-3
preExTime = preExTime * 1e-3
inversionTime = inversionTime * 1e-3
rdGradTime = rdGradTime * 1e-3
rdDephTime = rdDephTime * 1e-3
phGradTime = phGradTime * 1e-3
# Inputs for rawData
rawData['seqName'] = 'RareBatches_Standalone'
rawData['nScans'] = nScans
rawData['larmorFreq'] = larmorFreq # Larmor frequency
rawData['rfExAmp'] = rfExAmp # rf excitation pulse amplitude
rawData['rfReAmp'] = rfReAmp # rf refocusing pulse amplitude
rawData['rfExTime'] = rfExTime # rf excitation pulse time
rawData['rfReTime'] = rfReTime # rf refocusing pulse time
rawData['echoSpacing'] = echoSpacing # time between echoes
rawData['preExTime'] = preExTime
rawData['inversionTime'] = inversionTime # Inversion recovery time
rawData['repetitionTime'] = repetitionTime # TR
rawData['fov'] = fov # FOV along readout, phase and slice
rawData['dfov'] = dfov # Displacement of fov center
rawData[
'nPoints'] = nPoints # Number of points along readout, phase and slice
rawData['etl'] = etl # Echo train length
rawData['acqTime'] = acqTime # Acquisition time
rawData[
'axesOrientation'] = axes # 0->x, 1->y and 2->z defined as [rd,ph,sl]
rawData['axesEnable'] = axesEnable # 1-> Enable, 0-> Disable
rawData[
'sweepMode'] = sweepMode # 0->k2k (T2), 1->02k (T1), 2->k20 (T2), 3->Niquist modulated (T2)
rawData['rdPreemphasis'] = rdPreemphasis
rawData['drfPhase'] = drfPhase
rawData['dummyPulses'] = dummyPulses # Dummy pulses for T1 stabilization
rawData['parFourierFraction'] = parFourierFraction
rawData['rdDephTime'] = rdDephTime
rawData['shimming'] = shimming
# Miscellaneous
larmorFreq = larmorFreq * 1e-6
gradRiseTime = 400e-6 # Estimated gradient rise time
gSteps = int(gradRiseTime * 1e6 / 5) * 0 + 1
addRdPoints = 10 # Initial rd points to avoid artifact at the begining of rd
randFactor = 0e-3 # Random amplitude to add to the phase gradients
if rfReAmp == 0:
rfReAmp = rfExAmp
if rfReTime == 0:
rfReTime = 2 * rfExTime
resolution = fov / nPoints
rawData['resolution'] = resolution
rawData['gradRiseTime'] = gradRiseTime
rawData['randFactor'] = randFactor
rawData['addRdPoints'] = addRdPoints
# Matrix size
nRD = nPoints[0] + 2 * addRdPoints
nPH = nPoints[1] * axesEnable[1] + (1 - axesEnable[1])
nSL = nPoints[2] * axesEnable[2] + (1 - axesEnable[2])
# ETL if nPH = 1
if etl > nPH:
etl = nPH
# parAcqLines in case parAcqLines = 0
parAcqLines = int(int(nPoints[2] * parFourierFraction) - nPoints[2] / 2)
rawData['partialAcquisition'] = parAcqLines
# BW
BW = nPoints[0] / acqTime * 1e-6
BWov = BW * hw.oversamplingFactor
samplingPeriod = 1 / BWov
rawData['bw'] = BW
rawData['samplingPeriod'] = samplingPeriod
# Readout gradient time
if rdGradTime > 0 and rdGradTime < acqTime:
rdGradTime = acqTime
rawData['rdGradTime'] = rdGradTime
# Phase and slice de- and re-phasing time
if phGradTime == 0 or phGradTime > echoSpacing / 2 - rfExTime / 2 - rfReTime / 2 - 2 * gradRiseTime:
phGradTime = echoSpacing / 2 - rfExTime / 2 - rfReTime / 2 - 2 * gradRiseTime
rawData['phGradTime'] = phGradTime
# Max gradient amplitude
rdGradAmplitude = nPoints[0] / (hw.gammaB * fov[0] *
acqTime) * axesEnable[0]
phGradAmplitude = nPH / (2 * hw.gammaB * fov[1] *
(phGradTime + gradRiseTime)) * axesEnable[1]
slGradAmplitude = nSL / (2 * hw.gammaB * fov[2] *
(phGradTime + gradRiseTime)) * axesEnable[2]
rawData['rdGradAmplitude'] = rdGradAmplitude
rawData['phGradAmplitude'] = phGradAmplitude
rawData['slGradAmplitude'] = slGradAmplitude
# Readout dephasing amplitude
rdDephAmplitude = 0.5 * rdGradAmplitude * (gradRiseTime + rdGradTime) / (
gradRiseTime + rdDephTime)
rawData['rdDephAmplitude'] = rdDephAmplitude
# Phase and slice gradient vector
phGradients = np.linspace(-phGradAmplitude,
phGradAmplitude,
num=nPH,
endpoint=False)
slGradients = np.linspace(-slGradAmplitude,
slGradAmplitude,
num=nSL,
endpoint=False)
# Now fix the number of slices to partailly acquired k-space
nSL = (int(nPoints[2] / 2) + parAcqLines) * axesEnable[2] + (1 -
axesEnable[2])
# Add random displacemnt to phase encoding lines
for ii in range(nPH):
if ii < np.ceil(nPH / 2 - nPH / 20) or ii > np.ceil(nPH / 2 +
nPH / 20):
phGradients[ii] = phGradients[ii] + randFactor * np.random.randn()
kPH = hw.gammaB * phGradients * (gradRiseTime + phGradTime)
rawData['phGradients'] = phGradients
rawData['slGradients'] = slGradients
# Set phase vector to given sweep mode
ind = mri.getIndex(etl, nPH, sweepMode)
rawData['sweepOrder'] = ind
phGradients = phGradients[ind]
def createSequence():
phIndex = 0
nRepetitions = int(nPH / etl + dummyPulses)
scanTime = 20e3 + nRepetitions * repetitionTime
rawData['batchTime'] = scanTime * 1e-6
if rdGradTime == 0: # Check if readout gradient is dc or pulsed
dc = True
else:
dc = False
# Set shimming
mri.iniSequence(expt, 20, shimming)
for repeIndex in range(nRepetitions):
# Initialize time
tEx = 20e3 + repetitionTime * repeIndex + inversionTime + preExTime
# First I do a noise measurement.
if repeIndex == 0:
t0 = tEx - preExTime - inversionTime - 4 * acqTime
mri.rxGate(expt, t0, acqTime + 2 * addRdPoints / BW)
# Pre-excitation pulse
if repeIndex >= dummyPulses and preExTime != 0:
t0 = tEx - preExTime - inversionTime - rfExTime / 2 - hw.blkTime
mri.rfRecPulse(expt, t0, rfExTime, rfExAmp / 90 * 90, 0)
mri.gradTrap(expt, t0 + hw.blkTime + rfReTime, gradRiseTime,
preExTime * 0.5, -0.005, gSteps, axes[0],
shimming)
mri.gradTrap(expt, t0 + hw.blkTime + rfReTime, gradRiseTime,
preExTime * 0.5, -0.005, gSteps, axes[1],
shimming)
mri.gradTrap(expt, t0 + hw.blkTime + rfReTime, gradRiseTime,
preExTime * 0.5, -0.005, gSteps, axes[2],
shimming)
# Inversion pulse
if repeIndex >= dummyPulses and inversionTime != 0:
t0 = tEx - inversionTime - rfReTime / 2 - hw.blkTime
mri.rfRecPulse(expt, t0, rfReTime, rfReAmp / 180 * 180, 0)
mri.gradTrap(expt, t0 + hw.blkTime + rfReTime, gradRiseTime,
inversionTime * 0.5, 0.005, gSteps, axes[0],
shimming)
mri.gradTrap(expt, t0 + hw.blkTime + rfReTime, gradRiseTime,
inversionTime * 0.5, 0.005, gSteps, axes[1],
shimming)
mri.gradTrap(expt, t0 + hw.blkTime + rfReTime, gradRiseTime,
inversionTime * 0.5, 0.005, gSteps, axes[2],
shimming)
# DC gradient if desired
if (repeIndex == 0 or repeIndex >= dummyPulses) and dc == True:
t0 = tEx - 10e3
mri.gradTrap(expt, t0, gradRiseTime,
10e3 + echoSpacing * (etl + 1), rdGradAmplitude,
gSteps, axes[0], shimming)
# Excitation pulse
t0 = tEx - hw.blkTime - rfExTime / 2
mri.rfRecPulse(expt, t0, rfExTime, rfExAmp, drfPhase)
# Dephasing readout
t0 = tEx + rfExTime / 2 - hw.gradDelay
if (repeIndex == 0 or repeIndex >= dummyPulses) and dc == False:
mri.gradTrap(expt, t0, gradRiseTime, rdDephTime,
rdDephAmplitude * rdPreemphasis, gSteps, axes[0],
shimming)
# Echo train
for echoIndex in range(etl):
tEcho = tEx + echoSpacing * (echoIndex + 1)
# Refocusing pulse
t0 = tEcho - echoSpacing / 2 - rfReTime / 2 - hw.blkTime
mri.rfRecPulse(expt, t0, rfReTime, rfReAmp,
drfPhase + np.pi / 2)
# Dephasing phase and slice gradients
if repeIndex >= dummyPulses: # This is to account for dummy pulses
t0 = tEcho - echoSpacing / 2 + rfReTime / 2 - hw.gradDelay
mri.gradTrap(expt, t0, gradRiseTime, phGradTime,
phGradients[phIndex], gSteps, axes[1],
shimming)
mri.gradTrap(expt, t0, gradRiseTime, phGradTime,
slGradients[slIndex], gSteps, axes[2],
shimming)
# Readout gradient
if (repeIndex == 0 or repeIndex >= dummyPulses
) and dc == False: # This is to account for dummy pulses
t0 = tEcho - rdGradTime / 2 - gradRiseTime - hw.gradDelay
mri.gradTrap(expt, t0, gradRiseTime, rdGradTime,
rdGradAmplitude, gSteps, axes[0], shimming)
# Rx gate
if (repeIndex == 0 or repeIndex >= dummyPulses):
t0 = tEcho - acqTime / 2 - addRdPoints / BW
mri.rxGate(expt, t0, acqTime + 2 * addRdPoints / BW)
# Rephasing phase and slice gradients
t0 = tEcho + acqTime / 2 + addRdPoints / BW - hw.gradDelay
if (echoIndex < etl - 1 and repeIndex >= dummyPulses):
mri.gradTrap(expt, t0, gradRiseTime, phGradTime,
-phGradients[phIndex], gSteps, axes[1],
shimming)
mri.gradTrap(expt, t0, gradRiseTime, phGradTime,
-slGradients[slIndex], gSteps, axes[2],
shimming)
elif (echoIndex == etl - 1 and repeIndex >= dummyPulses):
mri.gradTrap(expt, t0, gradRiseTime, phGradTime,
+phGradients[phIndex], gSteps, axes[1],
shimming)
mri.gradTrap(expt, t0, gradRiseTime, phGradTime,
+slGradients[slIndex], gSteps, axes[2],
shimming)
# Update the phase and slice gradient
if repeIndex >= dummyPulses:
phIndex += 1
if repeIndex == nRepetitions - 1:
mri.endSequence(expt, scanTime)
# Changing time parameters to us
rfExTime = rfExTime * 1e6
rfReTime = rfReTime * 1e6
echoSpacing = echoSpacing * 1e6
repetitionTime = repetitionTime * 1e6
gradRiseTime = gradRiseTime * 1e6
phGradTime = phGradTime * 1e6
rdGradTime = rdGradTime * 1e6
rdDephTime = rdDephTime * 1e6
inversionTime = inversionTime * 1e6
preExTime = preExTime * 1e6
# Calibrate frequency
if freqCal == 1:
mri.freqCalibration(rawData, bw=0.05)
mri.freqCalibration(rawData, bw=0.005)
larmorFreq = rawData['larmorFreq'] * 1e-6
drfPhase = rawData['drfPhase']
# Run the experiment
dataFull = []
dummyData = []
overData = []
noise = []
for slIndex in range(nSL):
expt = ex.Experiment(lo_freq=larmorFreq,
rx_t=samplingPeriod,
init_gpa=init_gpa,
gpa_fhdo_offset_time=(1 / 0.2 / 3.1))
samplingPeriod = expt.get_rx_ts()[0]
BW = 1 / samplingPeriod / hw.oversamplingFactor
acqTime = nPoints[0] / BW # us
createSequence()
for ii in range(nScans):
print("Scan %s, slice %s ..." % (ii + 1, slIndex + 1))
rxd, msgs = expt.run()
rxd['rx0'] = rxd[
'rx0'] * 13.788 # Here I normalize to get the result in mV
# Get noise data
noise = np.concatenate(
(noise, rxd['rx0'][0:nRD * hw.oversamplingFactor]), axis=0)
rxd['rx0'] = rxd['rx0'][nRD * hw.oversamplingFactor::]
# Get data
if dummyPulses > 0:
dummyData = np.concatenate(
(dummyData,
rxd['rx0'][0:nRD * etl * hw.oversamplingFactor]),
axis=0)
overData = np.concatenate(
(overData,
rxd['rx0'][nRD * etl * hw.oversamplingFactor::]),
axis=0)
else:
overData = np.concatenate((overData, rxd['rx0']), axis=0)
expt.__del__()
print('Scans done!')
rawData['noiseData'] = noise
rawData['overData'] = overData
# Fix the echo position using oversampled data
if dummyPulses > 0:
dummyData = np.reshape(
dummyData, (nSL * nScans, etl, nRD * hw.oversamplingFactor))
dummyData = np.average(dummyData, axis=0)
rawData['dummyData'] = dummyData
overData = np.reshape(
overData,
(nScans * nSL, int(nPH / etl), etl, nRD * hw.oversamplingFactor))
for ii in range(nScans * nSL):
overData[ii, :, :, :] = mri.fixEchoPosition(
dummyData, overData[ii, :, :, :])
overData = np.squeeze(
np.reshape(overData,
(1, nRD * hw.oversamplingFactor * nPH * nSL * nScans)))
# Generate dataFull
dataFull = sig.decimate(overData,
hw.oversamplingFactor,
ftype='fir',
zero_phase=True)
# Get index for krd = 0
# Average data
dataProv = np.reshape(dataFull, (nSL, nScans, nRD * nPH))
dataProv = np.average(dataProv, axis=1)
# Reorganize the data acording to sweep mode
dataProv = np.reshape(dataProv, (nSL, nPH, nRD))
dataTemp = dataProv * 0
for ii in range(nPH):
dataTemp[:, ind[ii], :] = dataProv[:, ii, :]
dataProv = dataTemp
# Check where is krd = 0
dataProv = dataProv[int(nPoints[2] / 2), int(nPH / 2), :]
indkrd0 = np.argmax(np.abs(dataProv))
if indkrd0 < nRD / 2 - addRdPoints or indkrd0 > nRD / 2 + addRdPoints:
indkrd0 = int(nRD / 2)
# indkrd0 = int(nRD/2)
# Get individual images
dataFull = np.reshape(dataFull, (nSL, nScans, nPH, nRD))
dataFull = dataFull[:, :, :, indkrd0 - int(nPoints[0] / 2):indkrd0 +
int(nPoints[0] / 2)]
dataTemp = dataFull * 0
for ii in range(nPH):
dataTemp[:, :, ind[ii], :] = dataFull[:, :, ii, :]
dataFull = dataTemp
imgFull = dataFull * 0
for ii in range(nScans):
imgFull[:, ii, :, :] = np.fft.ifftshift(
np.fft.ifftn(np.fft.ifftshift(np.squeeze(dataFull[:, ii, :, :]))))
rawData['dataFull'] = dataFull
rawData['imgFull'] = imgFull
# Average data
data = np.average(dataFull, axis=1)
# Do zero padding
dataTemp = np.zeros((nPoints[2], nPoints[1], nPoints[0]))
dataTemp = dataTemp + 1j * dataTemp
dataTemp[0:nSL, :, :] = data
data = np.reshape(dataTemp, (1, nPoints[0] * nPoints[1] * nPoints[2]))
# Fix the position of the sample according to dfov
kMax = np.array(nPoints) / (2 * np.array(fov)) * np.array(axesEnable)
kRD = np.linspace(-kMax[0], kMax[0], num=nPoints[0], endpoint=False)
# kPH = np.linspace(-kMax[1],kMax[1],num=nPoints[1],endpoint=False)
kSL = np.linspace(-kMax[2], kMax[2], num=nPoints[2], endpoint=False)
kPH = kPH[::-1]
kPH, kSL, kRD = np.meshgrid(kPH, kSL, kRD)
kRD = np.reshape(kRD, (1, nPoints[0] * nPoints[1] * nPoints[2]))
kPH = np.reshape(kPH, (1, nPoints[0] * nPoints[1] * nPoints[2]))
kSL = np.reshape(kSL, (1, nPoints[0] * nPoints[1] * nPoints[2]))
dPhase = np.exp(-2 * np.pi * 1j *
(dfov[0] * kRD + dfov[1] * kPH + dfov[2] * kSL))
data = np.reshape(data * dPhase, (nPoints[2], nPoints[1], nPoints[0]))
rawData['kSpace3D'] = data
img = np.fft.ifftshift(np.fft.ifftn(np.fft.ifftshift(data)))
rawData['image3D'] = img
data = np.reshape(data, (1, nPoints[0] * nPoints[1] * nPoints[2]))
# Create sampled data
kRD = np.reshape(kRD, (nPoints[0] * nPoints[1] * nPoints[2], 1))
kPH = np.reshape(kPH, (nPoints[0] * nPoints[1] * nPoints[2], 1))
kSL = np.reshape(kSL, (nPoints[0] * nPoints[1] * nPoints[2], 1))
data = np.reshape(data, (nPoints[0] * nPoints[1] * nPoints[2], 1))
rawData['kMax'] = kMax
rawData['sampled'] = np.concatenate((kRD, kPH, kSL, data), axis=1)
data = np.reshape(data, (nPoints[2], nPoints[1], nPoints[0]))
# Save data
mri.saveRawData(rawData)
# Plot data for 1D case
if (nPH == 1 and nSL == 1):
# Plot k-space
plt.figure(3)
dataPlot = data[0, 0, :]
plt.subplot(1, 2, 1)
if axesEnable[0] == 0:
tVector = np.linspace(
-acqTime / 2, acqTime / 2, num=nPoints[0],
endpoint=False) * 1e-3
sMax = np.max(np.abs(dataPlot))
indMax = np.argmax(np.abs(dataPlot))
timeMax = tVector[indMax]
sMax3 = sMax / 3
dataPlot3 = np.abs(np.abs(dataPlot) - sMax3)
indMin = np.argmin(dataPlot3)
timeMin = tVector[indMin]
T2 = np.abs(timeMax - timeMin)
plt.plot(tVector, np.abs(dataPlot))
plt.plot(tVector, np.real(dataPlot))
plt.plot(tVector, np.imag(dataPlot))
plt.xlabel('t (ms)')
plt.ylabel('Signal (mV)')
print("T2 = %s us" % (T2))
plt.title(rawData['fileName'])
plt.legend(['Abs', 'Real', 'Imag'])
else:
plt.plot(kRD[:, 0], np.abs(dataPlot))
plt.yscale('log')
plt.xlabel('krd (mm^-1)')
plt.ylabel('Signal (mV)')
echoTime = np.argmax(np.abs(dataPlot))
echoTime = kRD[echoTime, 0]
print("Echo position = %s mm^{-1}" % round(echoTime, 1))
plt.title(rawData['fileName'])
# Plot image
plt.subplot(122)
img = img[0, 0, :]
if axesEnable[0] == 0:
xAxis = np.linspace(
-BW / 2, BW / 2, num=nPoints[0], endpoint=False) * 1e3
plt.plot(xAxis, np.abs(img), '.')
plt.xlabel('Frequency (kHz)')
plt.ylabel('Density (a.u.)')
print("Smax = %s mV" % (np.max(np.abs(img))))
plt.title(rawData['fileName'])
else:
xAxis = np.linspace(-fov[0] / 2 * 1e2,
fov[0] / 2 * 1e2,
num=nPoints[0],
endpoint=False)
plt.plot(xAxis, np.abs(img))
plt.xlabel('Position RD (cm)')
plt.ylabel('Density (a.u.)')
plt.title(rawData['fileName'])
else:
# Plot k-space
plt.figure(3)
dataPlot = data[round(nSL / 2), :, :]
plt.subplot(131)
plt.imshow(np.log(np.abs(dataPlot)), cmap='gray')
plt.axis('off')
# Plot image
if sweepMode == 3:
imgPlot = img[round(nSL / 2), round(nPH / 4):round(3 * nPH / 4), :]
else:
imgPlot = img[round(nSL / 2), :, :]
plt.subplot(132)
plt.imshow(np.abs(imgPlot), cmap='gray')
plt.axis('off')
plt.title(rawData['fileName'])
plt.subplot(133)
plt.imshow(np.angle(imgPlot), cmap='gray')
plt.axis('off')
# plot full image
if nSL > 1:
plt.figure(4)
img2d = np.zeros((nPoints[1], nPoints[0] * nPoints[2]))
img2d = img2d + 1j * img2d
for ii in range(nPoints[2]):
img2d[:, ii * nPoints[0]:(ii + 1) * nPoints[0]] = img[ii, :, :]
plt.imshow(np.abs(img2d), cmap='gray')
plt.axis('off')
plt.title(rawData['fileName'])
plt.show()
def gre3d(self, plotSeq):
init_gpa = False, # Starts the gpa
nScans = self.nScans # NEX
larmorFreq = self.larmorFreq # MHz, Larmor frequency
rfExAmp = self.rfExAmp # a.u. rf excitation pulse amplitude
rfExTime = self.rfExTime # us, rf excitation pulse time
echoTime = self.echoTime # ms, TE
repetitionTime = self.repetitionTime # ms, TR
fov = self.fov # mm, FOV along readout, phase and slice
dfov = self.dfov # mm, Displacement of fov center
nPoints = self.nPoints # Number of points along readout, phase and slice
acqTime = self.acqTime # ms, Acquisition time
axes = self.axes # 0->x, 1->y and 2->z defined as [rd,ph,sl]
rdGradTime = self.rdGradTime # ms, readout rephasing gradient time
dephGradTime = self.dephGradTime # ms, Phase and slice dephasing time
dummyPulses = self.dummyPulses # Dummy pulses for T1 stabilization
shimming = self.shimming # a.u.*1e4, Shimming along the X,Y and Z axes
parFourierFraction = self.parFourierFractionSl # fraction of acquired k-space along phase direction
spoiler = self.spoiler # set 1 or 0 if you want or do not want to apply spoiler gradients
freqCal = False
demo = False
# rawData fields
rawData = {}
# Conversion of variables to non-multiplied units
larmorFreq = larmorFreq * 1e6
rfExTime = rfExTime * 1e-6
fov = np.array(fov) * 1e-3
dfov = np.array(dfov) * 1e-3
echoTime = echoTime * 1e-3
acqTime = acqTime * 1e-3
shimming = np.array(shimming) * 1e-4
nPoints = np.array(nPoints)
repetitionTime = repetitionTime * 1e-3
rdGradTime = rdGradTime * 1e-3
dephGradTime = dephGradTime * 1e-3
# Inputs for rawData
rawData['seqName'] = self.seq
rawData['nScans'] = nScans
rawData['larmorFreq'] = larmorFreq # Larmor frequency
rawData['rfExAmp'] = rfExAmp # rf excitation pulse amplitude
rawData['rfExTime'] = rfExTime # rf excitation pulse time
rawData['echoTime'] = echoTime # time between echoes
rawData['repetitionTime'] = repetitionTime # TR
rawData['fov'] = fov # FOV along readout, phase and slice
rawData['dfov'] = dfov # Displacement of fov center
rawData[
'nPoints'] = nPoints # Number of points along readout, phase and slice
rawData['acqTime'] = acqTime # Acquisition time
rawData[
'axesOrientation'] = axes # 0->x, 1->y and 2->z defined as [rd,ph,sl]
rawData['rdGradTime'] = rdGradTime
rawData['dephGradTime'] = dephGradTime
rawData['dummyPulses'] = dummyPulses # Dummy pulses for T1 stabilization
rawData['shimming'] = shimming
rawData['partialFourierFraction'] = parFourierFraction
rawData['spoiler'] = spoiler
# Miscellaneous
larmorFreq = larmorFreq * 1e-6
gradRiseTime = 100e-6 # Estimated gradient rise time
gSteps = int(gradRiseTime * 1e6 / 5) * 0 + 1
addRdPoints = 5 # Initial rd points to avoid artifact at the begining of rd
resolution = fov / nPoints
randFactor = 0.
axesEnable = np.array([1, 1, 1])
for ii in range(3):
if nPoints[ii] == 1: axesEnable[ii] = 0
if fov[0] > 1 and nPoints[1] == 1: axesEnable[0] = 0
rawData['randFactor'] = randFactor
rawData['resolution'] = resolution
rawData['gradRiseTime'] = gradRiseTime
rawData['addRdPoints'] = addRdPoints
# Matrix size
nRD = nPoints[0] + 2 * addRdPoints
nPH = nPoints[1]
nSL = nPoints[2]
# parAcqLines
nSLreal = int(nPoints[2] * parFourierFraction)
parAcqLines = int(nSLreal - nPoints[2] / 2)
rawData['parAcqLines'] = parAcqLines
del nSLreal
# BW
BW = nPoints[0] / acqTime * 1e-6
BWov = BW * hw.oversamplingFactor
samplingPeriod = 1 / BWov
rawData['samplingPeriod'] = samplingPeriod
# Check if dephasing grad time is ok
maxDephGradTime = echoTime - (rfExTime + rdGradTime) - 3 * gradRiseTime
if dephGradTime == 0 or dephGradTime > maxDephGradTime:
dephGradTime = maxDephGradTime
# Max gradient amplitude
rdGradAmplitude = nPoints[0] / (hw.gammaB * fov[0] * acqTime)
rdDephAmplitude = -rdGradAmplitude * (rdGradTime + gradRiseTime) / (
2 * (dephGradTime + gradRiseTime))
phGradAmplitude = nPH / (2 * hw.gammaB * fov[1] *
(dephGradTime + gradRiseTime)) * axesEnable[1]
slGradAmplitude = nSL / (2 * hw.gammaB * fov[2] *
(dephGradTime + gradRiseTime)) * axesEnable[2]
rawData['rdGradAmplitude'] = rdGradAmplitude
rawData['rdDephAmplitude'] = rdDephAmplitude
rawData['phGradAmplitude'] = phGradAmplitude
rawData['slGradAmplitude'] = slGradAmplitude
# Phase and slice gradient vector
phGradients = np.linspace(-phGradAmplitude,
phGradAmplitude,
num=nPH,
endpoint=False)
slGradients = np.linspace(-slGradAmplitude,
slGradAmplitude,
num=nSL,
endpoint=False)
# Now fix the number of slices to partailly acquired k-space
if nPoints[2] == 1:
nSL = 1
else:
nSL = int(nPoints[2] / 2) + parAcqLines
nRepetitions = nPH * nSL
# Add random displacemnt to phase encoding lines
for ii in range(nPH):
if ii < np.ceil(nPH / 2 - nPH / 20) or ii > np.ceil(nPH / 2 +
nPH / 20):
phGradients[ii] = phGradients[ii] + randFactor * np.random.randn()
kPH = hw.gammaB * phGradients * (gradRiseTime + dephGradTime)
rawData['phGradients'] = phGradients
rawData['slGradients'] = slGradients
# Changing time parameters to us
rfExTime = rfExTime * 1e6
echoTime = echoTime * 1e6
repetitionTime = repetitionTime * 1e6
gradRiseTime = gradRiseTime * 1e6
dephGradTime = dephGradTime * 1e6
rdGradTime = rdGradTime * 1e6
scanTime = nRepetitions * repetitionTime
rawData['scanTime'] = scanTime * nSL * 1e-6
# Create demo
def createSequenceDemo(phIndex=0, slIndex=0, repeIndexGlobal=0):
repeIndex = 0
acqPoints = 0
orders = 0
data = []
if (dummyPulses > 0 and nRD * 3 > hw.maxRdPoints) or (
dummyPulses == 0 and nRD * 2 > hw.maxRdPoints):
print(
'ERROR: Too many acquired points or orders to the red pitaya.')
return ()
while acqPoints + nRD <= hw.maxRdPoints and orders <= hw.maxOrders and repeIndexGlobal < nRepetitions:
# First I do a noise measurement
if repeIndex == 0:
acqPoints += nRD
data = np.concatenate(
(data, np.random.randn(nRD * hw.oversamplingFactor)),
axis=0)
# Dephasing readout, phase and slice
if (repeIndex == 0 or repeIndex >= dummyPulses):
orders = orders + gSteps * 2
if repeIndex >= dummyPulses:
orders = orders + gSteps * 4
# Rephasing readout gradient
if (repeIndex == 0 or repeIndex >= dummyPulses):
orders = orders + gSteps * 2
# Rx gate
if (repeIndex == 0 or repeIndex >= dummyPulses):
acqPoints += nRD
data = np.concatenate(
(data, np.random.randn(nRD * hw.oversamplingFactor)),
axis=0)
# Spoiler
if (repeIndex == 0 or repeIndex >= dummyPulses):
orders = orders + gSteps * 2
if repeIndex >= dummyPulses:
orders = orders + gSteps * 4
# Update the phase and slice gradient
if repeIndex >= dummyPulses:
if phIndex == nPH - 1:
phIndex = 0
slIndex += 1
else:
phIndex += 1
if repeIndex >= dummyPulses:
repeIndexGlobal += 1 # Update the global repeIndex
repeIndex += 1 # Update the repeIndex after the ETL
# Return the output variables
return (phIndex, slIndex, repeIndexGlobal, acqPoints, data)
# Create sequence instructions
def createSequence(phIndex=0, slIndex=0, repeIndexGlobal=0, rewrite=True):
repeIndex = 0
acqPoints = 0
orders = 0
# check in case of dummy pulse filling the cache
if (dummyPulses > 0 and nRD * 3 > hw.maxRdPoints) or (
dummyPulses == 0 and nRD * 2 > hw.maxRdPoints):
print(
'ERROR: Too many acquired points or orders to the red pitaya.')
return ()
# Set shimming
mri.iniSequence(expt, 20, shimming, rewrite=rewrite)
# Run sequence batch
while acqPoints + nRD <= hw.maxRdPoints and orders <= hw.maxOrders and repeIndexGlobal < nRepetitions:
# Initialize time
tEx = 20e3 + repetitionTime * repeIndex
# First I do a noise measurement
if repeIndex == 0:
t0 = tEx - 4 * acqTime
mri.rxGate(expt, t0, acqTime + 2 * addRdPoints / BW)
acqPoints += nRD
# Excitation pulse
t0 = tEx - hw.blkTime - rfExTime / 2
mri.rfRecPulse(expt, t0, rfExTime, rfExAmp, 0.)
# Dephasing readout, phase and slice
if (repeIndex == 0 or repeIndex >= dummyPulses):
t0 = tEx + rfExTime / 2 - hw.gradDelay
mri.gradTrap(expt, t0, gradRiseTime, dephGradTime,
rdDephAmplitude, gSteps, axes[0], shimming)
orders = orders + gSteps * 2
if repeIndex >= dummyPulses:
t0 = tEx + rfExTime / 2 - hw.gradDelay
mri.gradTrap(expt, t0, gradRiseTime, dephGradTime,
phGradients[phIndex], gSteps, axes[1], shimming)
mri.gradTrap(expt, t0, gradRiseTime, dephGradTime,
slGradients[slIndex], gSteps, axes[2], shimming)
orders = orders + gSteps * 4
# Rephasing readout gradient
if (repeIndex == 0 or repeIndex >= dummyPulses):
t0 = tEx + echoTime - rdGradTime / 2 - gradRiseTime - hw.gradDelay
mri.gradTrap(expt, t0, gradRiseTime, rdGradTime,
rdGradAmplitude, gSteps, axes[0], shimming)
orders = orders + gSteps * 2
# Rx gate
if (repeIndex == 0 or repeIndex >= dummyPulses):
t0 = tEx + echoTime - acqTime / 2 - addRdPoints / BW
mri.rxGate(expt, t0, acqTime + 2 * addRdPoints / BW)
acqPoints += nRD
# Spoiler
if spoiler:
t0 = tEx + echoTime + rdGradTime / 2 + gradRiseTime - hw.gradDelay
mri.gradTrap(expt, t0, gradRiseTime, dephGradTime,
-rdDephAmplitude, gSteps, axes[0], shimming)
orders = orders + gSteps * 2
# Update the phase and slice gradient
if repeIndex >= dummyPulses:
if phIndex == nPH - 1:
phIndex = 0
slIndex += 1
else:
phIndex += 1
if repeIndex >= dummyPulses:
repeIndexGlobal += 1 # Update the global repeIndex
repeIndex += 1 # Update the repeIndex after the ETL
# Turn off the gradients after the end of the batch
mri.endSequence(expt, repeIndex * repetitionTime)
# Return the output variables
return (phIndex, slIndex, repeIndexGlobal, acqPoints)
# Calibrate frequency
if (not demo) and freqCal and (not plotSeq):
mri.freqCalibration(rawData, bw=0.05)
mri.freqCalibration(rawData, bw=0.005)
larmorFreq = rawData['larmorFreq'] * 1e-6
drfPhase = rawData['drfPhase']
# Initialize the experiment
dataFull = []
dummyData = []
overData = []
noise = []
nBatches = 0
repeIndexArray = np.array([0])
repeIndexGlobal = repeIndexArray[0]
phIndex = 0
slIndex = 0
acqPointsPerBatch = []
while repeIndexGlobal < nRepetitions:
nBatches += 1
if not demo:
expt = ex.Experiment(lo_freq=larmorFreq,
rx_t=samplingPeriod,
init_gpa=init_gpa,
gpa_fhdo_offset_time=(1 / 0.2 / 3.1))
samplingPeriod = expt.get_rx_ts()[0]
BW = 1 / samplingPeriod / hw.oversamplingFactor
acqTime = nPoints[0] / BW # us
phIndex, slIndex, repeIndexGlobal, aa = createSequence(
phIndex=phIndex,
slIndex=slIndex,
repeIndexGlobal=repeIndexGlobal,
rewrite=False)
repeIndexArray = np.concatenate(
(repeIndexArray, np.array([repeIndexGlobal - 1])), axis=0)
acqPointsPerBatch.append(aa)
expt.plot_sequence()
else:
phIndex, slIndex, repeIndexGlobal, aa, dataA = createSequenceDemo(
phIndex=phIndex,
slIndex=slIndex,
repeIndexGlobal=repeIndexGlobal)
repeIndexArray = np.concatenate(
(repeIndexArray, np.array([repeIndexGlobal - 1])), axis=0)
acqPointsPerBatch.append(aa)
for ii in range(nScans):
print('Batch ', nBatches, ', Scan ', ii, ' runing...')
if not demo:
if plotSeq == 1: # What is the meaning of plotSeq??
print('Ploting sequence...')
expt.plot_sequence()
plt.show()
expt.__del__()
break
else:
rxd, msgs = expt.run()
rxd['rx0'] = rxd[
'rx0'] * 13.788 # Here I normalize to get the result in mV
# Get noise data
noise = np.concatenate(
(noise, rxd['rx0'][0:nRD * hw.oversamplingFactor]),
axis=0)
rxd['rx0'] = rxd['rx0'][nRD * hw.oversamplingFactor::]
# Get data
if dummyPulses > 0:
dummyData = np.concatenate(
(dummyData,
rxd['rx0'][0:nRD * hw.oversamplingFactor]),
axis=0)
overData = np.concatenate(
(overData,
rxd['rx0'][nRD * hw.oversamplingFactor::]),
axis=0)
else:
overData = np.concatenate((overData, rxd['rx0']),
axis=0)
else:
data = dataA
noise = np.concatenate(
(noise, data[0:nRD * hw.oversamplingFactor]), axis=0)
data = data[nRD * hw.oversamplingFactor::]
# Get data
if dummyPulses > 0:
dummyData = np.concatenate(
(dummyData, data[0:nRD * hw.oversamplingFactor]),
axis=0)
overData = np.concatenate(
(overData, data[nRD * hw.oversamplingFactor::]),
axis=0)
else:
overData = np.concatenate((overData, data), axis=0)
if not demo: expt.__del__()
if plotSeq == 1:
break
del aa
if not plotSeq:
acqPointsPerBatch = (acqPointsPerBatch - nRD *
(dummyPulses > 0) - nRD) * nScans
print('Scans done!')
rawData['noiseData'] = noise
rawData['overData'] = overData
# Fix the echo position using oversampled data
if dummyPulses > 0:
dummyData = np.reshape(
dummyData, (nBatches * nScans, 1, nRD * hw.oversamplingFactor))
dummyData = np.average(dummyData, axis=0)
rawData['dummyData'] = dummyData
overData = np.reshape(overData,
(-1, 1, nRD * hw.oversamplingFactor))
overData = mri.fixEchoPosition(dummyData, overData)
overData = np.reshape(overData, -1)
# Generate dataFull
dataFull = sig.decimate(overData,
hw.oversamplingFactor,
ftype='fir',
zero_phase=True)
if nBatches > 1:
dataFullA = dataFull[0:sum(acqPointsPerBatch[0:-1])]
dataFullB = dataFull[sum(acqPointsPerBatch[0:-1])::]
# Reorganize dataFull
dataProv = np.zeros([nScans, nSL * nPH * nRD])
dataProv = dataProv + 1j * dataProv
dataFull = np.reshape(dataFull, (nBatches, nScans, -1, nRD))
if nBatches > 1:
dataFullA = np.reshape(dataFullA, (nBatches - 1, nScans, -1, nRD))
dataFullB = np.reshape(dataFullB, (1, nScans, -1, nRD))
for scan in range(nScans):
if nBatches > 1:
dataProv[ii, :] = np.concatenate(
(np.reshape(dataFullA[:, ii, :, :],
-1), np.reshape(dataFullB[:, ii, :, :], -1)),
axis=0)
else:
dataProv[ii, :] = np.reshape(dataFull[:, ii, :, :], -1)
dataFull = np.reshape(dataProv, -1)
# Get index for krd = 0
# Average data
dataProv = np.reshape(dataFull, (nScans, nRD * nPH * nSL))
dataProv = np.average(dataProv, axis=0)
dataProv = np.reshape(dataProv, (nSL, nPH, nRD))
# Check where is krd = 0
dataProv = dataProv[int(nPoints[2] / 2), int(nPH / 2), :]
indkrd0 = np.argmax(np.abs(dataProv))
if indkrd0 < nRD / 2 - addRdPoints or indkrd0 > nRD / 2 + addRdPoints:
indkrd0 = int(nRD / 2)
# Get individual images
dataFull = np.reshape(dataFull, (nScans, nSL, nPH, nRD))
dataFull = dataFull[:, :, :, indkrd0 - int(nPoints[0] / 2):indkrd0 +
int(nPoints[0] / 2)]
imgFull = dataFull * 0
for ii in range(nScans):
imgFull[ii, :, :, :] = np.fft.ifftshift(
np.fft.ifftn(np.fft.ifftshift(dataFull[ii, :, :, :])))
rawData['dataFull'] = dataFull
rawData['imgFull'] = imgFull
# Average data
data = np.average(dataFull, axis=0)
data = np.reshape(data, (nSL, nPH, nPoints[0]))
# Do zero padding
dataTemp = np.zeros((nPoints[2], nPoints[1], nPoints[0]))
dataTemp = dataTemp + 1j * dataTemp
dataTemp[0:nSL, :, :] = data
data = np.reshape(dataTemp, (1, nPoints[0] * nPoints[1] * nPoints[2]))
# Fix the position of the sample according to dfov
kMax = np.array(nPoints) / (2 * np.array(fov)) * np.array(axesEnable)
kRD = np.linspace(-kMax[0], kMax[0], num=nPoints[0], endpoint=False)
# kPH = np.linspace(-kMax[1],kMax[1],num=nPoints[1],endpoint=False)
kSL = np.linspace(-kMax[2], kMax[2], num=nPoints[2], endpoint=False)
kPH = kPH[::-1]
kPH, kSL, kRD = np.meshgrid(kPH, kSL, kRD)
kRD = np.reshape(kRD, (1, nPoints[0] * nPoints[1] * nPoints[2]))
kPH = np.reshape(kPH, (1, nPoints[0] * nPoints[1] * nPoints[2]))
kSL = np.reshape(kSL, (1, nPoints[0] * nPoints[1] * nPoints[2]))
dPhase = np.exp(-2 * np.pi * 1j *
(dfov[0] * kRD + dfov[1] * kPH + dfov[2] * kSL))
data = np.reshape(data * dPhase, (nPoints[2], nPoints[1], nPoints[0]))
rawData['kSpace3D'] = data
img = np.fft.ifftshift(np.fft.ifftn(np.fft.ifftshift(data)))
rawData['image3D'] = img
data = np.reshape(data, (1, nPoints[0] * nPoints[1] * nPoints[2]))
# Create sampled data
kRD = np.reshape(kRD, (nPoints[0] * nPoints[1] * nPoints[2], 1))
kPH = np.reshape(kPH, (nPoints[0] * nPoints[1] * nPoints[2], 1))
kSL = np.reshape(kSL, (nPoints[0] * nPoints[1] * nPoints[2], 1))
data = np.reshape(data, (nPoints[0] * nPoints[1] * nPoints[2], 1))
rawData['kMax'] = kMax
rawData['sampled'] = np.concatenate((kRD, kPH, kSL, data), axis=1)
data = np.reshape(data, (nPoints[2], nPoints[1], nPoints[0]))
# Save data
mri.saveRawData(rawData)
# Reshape to 0 dimensional
data = np.reshape(data, -1)
return rawData, msgs, data, BW