def compress_shape(decompressed_shape):
"""
Returns a run-length encoded compressed shape.
Parameters
----------
decompressed_shape : ndarray
Decompressed shape.
Returns
-------
compressed_shape : Holder
A Holder object containing the shape of the compressed shape ndarray and the compressed shape ndarray itself.
"""
if decompressed_shape.shape[0] != 1:
raise ValueError("input should be of shape (1,x)")
if not isinstance(decompressed_shape, np.ndarray):
raise TypeError("input should be of type numpy.ndarray")
data = np.array([decompressed_shape[0][0]])
data = np.concatenate((data, np.diff(decompressed_shape[0])))
mask_changes = np.array([1])
diff_as_ones = (abs(np.diff(data)) > 1e-8).astype(int)
mask_changes = np.concatenate((mask_changes, diff_as_ones))
vals = data[np.nonzero(mask_changes)].astype(float)
k = np.array(np.nonzero(np.append(mask_changes, 1)))
k = k.reshape((1, k.shape[1]))
n = np.diff(k)[0]
n_extra = (n - 2).astype(float)
vals2 = np.copy(vals)
vals2[np.where(n_extra < 0)] = np.NAN
n_extra[np.where(n_extra < 0)] = np.NAN
v = np.array([vals, vals2, n_extra])
v = np.concatenate(np.hsplit(v, v.shape[1]))
finite_vals = np.isfinite(v)
v = v[finite_vals]
v_abs = abs(v)
smallest_indices = np.where(v_abs < 1e-10)
v[smallest_indices] = 0
compressed_shape = Holder()
compressed_shape.num_samples = decompressed_shape.shape[1]
compressed_shape.data = v.reshape([1, v.shape[0]])
return compressed_shape
def makedelay(d):
"""
Makes a Holder object for an delay Event.
Parameters
----------
d : float
Delay time, in seconds.
Returns
-------
delay : Holder
Delay Event.
"""
delay = Holder()
if d < 0:
raise ValueError('Delay {:.2f} ms is invalid'.format(d * 1e3))
delay.type = 'delay'
delay.delay = d
return delay
def makearbitrarygrad(kwargs):
"""
Makes a Holder object for an arbitrary gradient Event.
Parameters
----------
kwargs : dict
Key value mappings of RF Event parameters_params and values.
Returns
-------
grad : Holder
Trapezoidal gradient Event configured based on supplied kwargs.
"""
channel = kwargs.get("channel", "z")
system = kwargs.get("system", Opts())
waveform = kwargs.get("waveform")
max_grad_result = kwargs.get("max_grad", 0)
max_slew_result = kwargs.get("max_slew", 0)
max_grad = max_grad_result if max_grad_result > 0 else system.max_grad
max_slew = max_slew_result if max_slew_result > 0 else system.max_slew
g = waveform
slew = (g[0][1:] - g[0][0:-1]) / system.grad_raster_time
if max(abs(slew)) > max_slew:
raise ValueError('Slew rate violation {:f}'.format(
max(abs(slew)) / max_slew * 100))
if max(abs(g[0])) > max_grad:
raise ValueError('Gradient amplitude violation {:f}'.format(
max(abs(g)) / max_grad * 100))
grad = Holder()
grad.type = 'grad'
grad.channel = channel
grad.waveform = g
grad.t = np.array([[x * system.grad_raster_time
for x in range(len(g[0]))]])
return grad
def get_block(self, block_index):
"""
Returns Block at position specified by block_index.
Parameters
----------
block_index : int
Index of Block to be retrieved.
Returns
-------
block : dict
Block at position specified by block_index.
"""
block = {}
event_ind = self.block_events[block_index]
if event_ind[0] > 0:
delay = Holder()
delay.type = 'delay'
delay.delay = self.delay_library.data[event_ind[0]]
block['delay'] = delay
elif event_ind[1] > 0:
rf = Holder()
rf.type = 'rf'
lib_data = self.rf_library.data[event_ind[1]]
amplitude, mag_shape, phase_shape = lib_data[0], lib_data[1], lib_data[
2]
shape_data = self.shape_library.data[mag_shape]
compressed = Holder()
compressed.num_samples = shape_data[0][0]
compressed.data = shape_data[0][1:]
compressed.data = compressed.data.reshape(
(1, compressed.data.shape[0]))
mag = decompress_shape(compressed)
shape_data = self.shape_library.data[phase_shape]
compressed.num_samples = shape_data[0][0]
compressed.data = shape_data[0][1:]
compressed.data = compressed.data.reshape(
(1, compressed.data.shape[0]))
phase = decompress_shape(compressed)
rf.signal = 1j * 2 * np.pi * phase
rf.signal = amplitude * mag * np.exp(rf.signal)
rf.t = [(x * self.rf_raster_time)
for x in range(1,
max(mag.shape) + 1)]
rf.t = np.reshape(rf.t, (1, len(rf.t)))
rf.freq_offset = lib_data[3]
rf.phase_offset = lib_data[4]
if max(lib_data.shape) < 6:
lib_data = np.append(lib_data, 0)
rf.dead_time = lib_data[5]
block['rf'] = rf
grad_channels = ['gx', 'gy', 'gz']
for i in range(1, len(grad_channels) + 1):
if event_ind[2 + (i - 1)] > 0:
grad, compressed = Holder(), Holder()
type = self.grad_library.type[event_ind[2 + (i - 1)]]
lib_data = self.grad_library.data[event_ind[2 + (i - 1)]]
grad.type = 'trap' if type == 't' else 'grad'
grad.channel = grad_channels[i - 1][1]
if grad.type == 'grad':
amplitude = lib_data[0]
shape_id = lib_data[1]
shape_data = self.shape_library.data[shape_id]
compressed.num_samples = shape_data[0][0]
compressed.data = np.array([shape_data[0][1:]])
g = decompress_shape(compressed)
grad.waveform = amplitude * g
grad.t = np.array([[
x * self.grad_raster_time for x in range(1, g.size + 1)
]])
else:
grad.amplitude, grad.rise_time, grad.flat_time, grad.fall_time = [
lib_data[x] for x in range(4)
]
grad.area = grad.amplitude * (
grad.flat_time + grad.rise_time / 2 + grad.fall_time / 2)
grad.flat_area = grad.amplitude * grad.flat_time
block[grad_channels[i - 1]] = grad
if event_ind[5] > 0:
lib_data = self.adc_library.data[event_ind[5]]
if max(lib_data.shape) < 6:
lib_data = np.append(lib_data, 0)
adc = Holder()
adc.num_samples, adc.dwell, adc.delay, adc.freq_offset, adc.phase_offset, adc.dead_time = [
lib_data[x] for x in range(6)
]
adc.type = 'adc'
block['adc'] = adc
return block
def makeblockpulse(kwargs, nargout=1):
"""
Makes a Holder object for an RF pulse Event.
Parameters
----------
kwargs : dict
Key value mappings of RF Event parameters_params and values.
nargout: int
Number of output arguments to be returned. Default is 1, only RF Event is returned. Passing any number greater
than 1 will return the Gz Event along with the RF Event.
Returns
-------
Tuple consisting of:
rf : Holder
RF Event configured based on supplied kwargs.
gz : Holder
Slice select trapezoidal gradient Event.
"""
flip_angle = kwargs.get("flip_angle")
system = kwargs.get("system", Opts())
duration = kwargs.get("duration", 0)
freq_offset = kwargs.get("freq_offset", 0)
phase_offset = kwargs.get("phase_offset", 0)
time_bw_product = kwargs.get("time_bw_product", 4)
bandwidth = kwargs.get("bandwidth", 0)
max_grad = kwargs.get("max_grad", 0)
max_slew = kwargs.get("max_slew", 0)
slice_thickness = kwargs.get("slice_thickness", 0)
if duration == 0:
if time_bw_product > 0:
duration = time_bw_product / bandwidth
elif bandwidth > 0:
duration = 1 / (4 * bandwidth)
else:
raise ValueError('Either bandwidth or duration must be defined')
BW = 1 / (4 * duration)
N = round(duration / 1e-6)
t = [x * system.rf_raster_time for x in range(N)]
signal = flip_angle / (2 * np.pi) / duration * np.ones(len(t))
rf = Holder()
rf.type = 'rf'
rf.signal = signal
rf.t = t
rf.freq_offset = freq_offset
rf.phase_offset = phase_offset
rf.dead_time = system.rf_dead_time
fill_time = 0
if nargout > 1:
if slice_thickness < 0:
raise ValueError('Slice thickness must be provided')
if max_grad > 0:
system.max_grad = max_grad
if max_slew > 0:
system.max_slew = max_slew
amplitude = BW / slice_thickness
area = amplitude * duration
kwargs_for_trap = {'channel': 'z', 'system': system, 'flat_time': duration, 'flat_area': area}
gz = maketrapezoid(kwargs_for_trap)
fill_time = gz.rise_time
t_fill = np.array([x * 1e-6 for x in range(int(round(fill_time / 1e-6)))])
rf.t = np.array([t_fill, rf.t + t_fill[-1], t_fill + rf.t[-1] + t_fill[-1]])
rf.signal = np.array([np.zeros(t_fill.size), rf.signal, np.zeros(t_fill.size)])
if fill_time < rf.dead_time:
fill_time = rf.dead_time - fill_time
t_fill = np.array([x * 1e-6 for x in range(int(round(fill_time / 1e-6)))])
rf.t = np.insert(rf.t, 0, t_fill) + t_fill[-1]
rf.t = np.reshape(rf.t, (1, len(rf.t)))
rf.signal = np.insert(rf.signal, 0, np.zeros(t_fill.size))
rf.signal = np.reshape(rf.signal, (1, len(rf.signal)))
if nargout > 1:
return rf, gz
else:
return rf
def makearbitraryrf(kwargs, nargout=1):
"""
Makes a Holder object for an arbitrary RF pulse Event.
Parameters
----------
kwargs : dict
Key value mappings of RF Event parameters_params and values.
nargout: int
Number of output arguments to be returned. Default is 1, only RF Event is returned. Passing any number greater
than 1 will return the Gz Event along with the RF Event.
Returns
-------
rf : Holder
RF Event configured based on supplied kwargs.
gz : Holder
Slice select trapezoidal gradient Event.
"""
flip_angle = kwargs.get("flip_angle")
system = kwargs.get("system", Opts())
signal = kwargs.get("signal", 0)
freq_offset = kwargs.get("freq_offset", 0)
phase_offset = kwargs.get("phase_offset", 0)
time_bw_product = kwargs.get("time_bw_product", 0)
bandwidth = kwargs.get("bandwidth", 0)
max_grad = kwargs.get("max_grad", 0)
max_slew = kwargs.get("max_slew", 0)
slice_thickness = kwargs.get("slice_thickness", 0)
signal = signal / sum(
signal * system.rf_raster_time) * flip_angle / (2 * pi)
N = len(signal)
duration = N * system.rf_raster_time
t = [x * system.rfRasterTime for x in range(0, N)]
rf = Holder()
rf.type = 'rf'
rf.signal = signal
rf.t = t
rf.freq_offset = freq_offset
rf.phase_offset = phase_offset
rf.rf_dead_time = system.rf_dead_time
if nargout > 1:
if slice_thickness <= 0:
raise ValueError('Slice thickness must be provided')
if bandwidth <= 0:
raise ValueError('Bandwdith of pulse must be provided')
system.maxgrad = max_grad if max_grad > 0 else system.maxgrad
system.max_slew = max_slew if max_slew > 0 else system.max_slew
BW = bandwidth
if time_bw_product > 0:
BW = time_bw_product / duration
amplitude = BW / slice_thickness
area = amplitude * duration
kwargs_for_trap = {
"channel": 'z',
"system": system,
"flat_time": duration,
"flat_area": area
}
gz = maketrapezoid(**kwargs_for_trap)
t_fill = [x * 1e-6 for x in range(1, round(gz.riseTime / 1e-6))]
rf.t = [t_fill, rf.t + t_fill[-1], t_fill + rf.t[-1] + t_fill[-1]]
rf.signal = [np.zeros(len(t_fill)), rf.signal, np.zeros(len(t_fill))]
return rf, gz
def makesincpulse(kwargs, nargout=1):
"""
Makes a Holder object for an RF pulse Event.
Parameters
----------
kwargs : dict
Key value mappings of RF Event parameters_params and values.
nargout: int
Number of output arguments to be returned. Default is 1, only RF Event is returned. Passing any number greater
than 1 will return the Gz Event along with the RF Event.
Returns
-------
Tuple consisting of:
rf : Holder
RF Event configured based on supplied kwargs.
gz : Holder
Slice select trapezoidal gradient Event.
"""
flip_angle = kwargs.get("flip_angle")
system = kwargs.get("system", Opts())
duration = kwargs.get("duration", 0)
freq_offset = kwargs.get("freq_offset", 0)
phase_offset = kwargs.get("phase_offset", 0)
time_bw_product = kwargs.get("time_bw_product", 4)
apodization = kwargs.get("apodization", 0)
max_grad = kwargs.get("max_grad", 0)
max_slew = kwargs.get("max_slew", 0)
slice_thickness = kwargs.get("slice_thickness", 0)
BW = time_bw_product / duration
alpha = apodization
N = int(round(duration / 1e-6))
t = np.zeros((1, N))
for x in range(1, N + 1):
t[0][x - 1] = x * system.rf_raster_time
tt = t - (duration / 2)
window = np.zeros((1, tt.shape[1]))
for x in range(0, tt.shape[1]):
window[0][x] = 1.0 - alpha + alpha * np.cos(
2 * np.pi * tt[0][x] / duration)
signal = np.multiply(window, np.sinc(BW * tt))
flip = np.sum(signal) * system.rf_raster_time * 2 * np.pi
signal = signal * flip_angle / flip
rf = Holder()
rf.type = 'rf'
rf.signal = signal
rf.t = t
rf.freq_offset = freq_offset
rf.phase_offset = phase_offset
rf.dead_time = system.rf_dead_time
fill_time = 0
if nargout > 1:
if slice_thickness == 0:
raise ValueError('Slice thickness must be provided')
system.max_grad = max_grad if max_grad > 0 else system.max_grad
system.max_slew = max_slew if max_slew > 0 else system.max_slew
amplitude = BW / slice_thickness
area = amplitude * duration
kwargs_for_trap = {
"channel": 'z',
"system": system,
"flat_time": duration,
"flat_area": area
}
gz = maketrapezoid(kwargs_for_trap)
fill_time = gz.rise_time
nfill_time = int(round(fill_time / 1e-6))
t_fill = np.zeros((1, nfill_time))
for x in range(1, nfill_time + 1):
t_fill[0][x - 1] = x * 1e-6
temp = np.concatenate((t_fill[0], rf.t[0] + t_fill[0][-1]))
temp = temp.reshape((1, len(temp)))
rf.t = np.resize(rf.t, temp.shape)
rf.t[0] = temp
z = np.zeros((1, t_fill.shape[1]))
temp2 = np.concatenate((z[0], rf.signal[0]))
temp2 = temp2.reshape((1, len(temp2)))
rf.signal = np.resize(rf.signal, temp2.shape)
rf.signal[0] = temp2
if fill_time < rf.dead_time:
fill_time = rf.dead_time - fill_time
t_fill = np.array(
[x * 1e-6 for x in range(int(round(fill_time / 1e-6)))])
rf.t = np.insert(rf.t, 0, t_fill) + t_fill[-1]
rf.t = np.reshape(rf.t, (1, len(rf.t)))
rf.signal = np.insert(rf.signal, 0, (np.zeros(t_fill.size)))
rf.signal = np.reshape(rf.signal, (1, len(rf.signal)))
# Following 2 lines of code are workarounds for numpy returning 3.14... for np.angle(-0.00...)
negative_zero_indices = np.where(rf.signal == -0.0)
rf.signal[negative_zero_indices] = 0
if nargout > 1:
return rf, gz
else:
return rf
def makeadc(kwargs):
"""
Makes a Holder object for an ADC Event.
Parameters
----------
kwargs : dict
Key value mappings of ADC Event parameters_params and values.
Returns
-------
adc : Holder
ADC Event.
"""
num_samples = kwargs.get("num_samples", 0)
system = kwargs.get("system", Opts())
dwell = kwargs.get("dwell", 0)
duration = kwargs.get("duration", 0)
delay = kwargs.get("delay", 0)
freq_offset = kwargs.get("freq_offset", 0)
phase_offset = kwargs.get("phase_offset", 0)
adc = Holder()
adc.type = 'adc'
adc.num_samples = num_samples
adc.dwell = dwell
adc.delay = delay
adc.freq_offset = freq_offset
adc.phase_offset = phase_offset
adc.dead_time = system.adc_dead_time
if (dwell == 0 and duration == 0) or (dwell > 0 and duration > 0):
raise ValueError("Either dwell or duration must be defined, not both")
if duration > 0:
# getcontext().prec = 4
adc.dwell = float(Decimal(duration) / Decimal(num_samples))
adc.duration = dwell * num_samples if dwell > 0 else 0
return adc
def maketrapezoid(kwargs):
"""
Makes a Holder object for an trapezoidal gradient Event.
Parameters
----------
kwargs : dict
Key value mappings of trapezoidal gradient Event parameters_params and values.
Returns
-------
grad : Holder
Trapezoidal gradient Event configured based on supplied kwargs.
"""
channel = kwargs.get("channel", "z")
system = kwargs.get("system", Opts())
duration = kwargs.get("duration", 0)
area_result = kwargs.get("area", -1)
flat_time_result = kwargs.get("flat_time", 0)
flat_area_result = kwargs.get("flat_area", -1)
amplitude_result = kwargs.get("amplitude", -1)
max_grad = kwargs.get("max_grad", 0)
max_slew = kwargs.get("max_slew", 0)
rise_time = kwargs.get("rise_time", 0)
max_grad = max_grad if max_grad > 0 else system.max_grad
max_slew = max_slew if max_slew > 0 else system.max_slew
rise_time = rise_time if rise_time > 0 else system.rise_time
if area_result == -1 and flat_area_result == -1 and amplitude_result == -1:
raise ValueError('Must supply either '
'area'
', '
'flat_area'
' or '
'amplitude'
'')
if flat_time_result > 0:
amplitude = amplitude_result if (amplitude_result != -1) else (
flat_area_result / flat_time_result)
if rise_time == 0:
rise_time = abs(amplitude) / max_slew
rise_time = ceil(
rise_time / system.grad_raster_time) * system.grad_raster_time
fall_time, flat_time = rise_time, flat_time_result
elif duration > 0:
if amplitude_result != -1:
amplitude = amplitude_result
else:
if rise_time == 0:
dC = 1 / abs(2 * max_slew) + 1 / abs(2 * max_slew)
amplitude = (duration - sqrt(
pow(duration, 2) - 4 * abs(area_result) * dC)) / (2 * dC)
else:
amplitude = area_result / (duration - rise_time)
if rise_time == 0:
rise_time = ceil(amplitude / max_slew /
system.grad_raster_time) * system.grad_raster_time
fall_time = rise_time
flat_time = (duration - rise_time - fall_time)
amplitude = area_result / (rise_time / 2 + fall_time / 2 + flat_time
) if amplitude_result == -1 else amplitude
else:
raise ValueError('Must supply a duration')
if abs(amplitude) > max_grad:
raise ValueError("Amplitude violation")
grad = Holder()
grad.type = "trap"
grad.channel = channel
grad.amplitude = amplitude
grad.rise_time = rise_time
grad.flat_time = flat_time
grad.fall_time = fall_time
grad.area = amplitude * (flat_time + rise_time / 2 + fall_time / 2)
grad.flat_area = amplitude * flat_time
return grad