rf180 = makeblockpulse(kwargs_for_sinc) kwargs_for_gz_spoil = { "channel": 'z', "system": system, "area": gz.area * 2, "duration": 3 * pre_time } gz_spoil = maketrapezoid(kwargs_for_gz_spoil) duration_to_center = (Nx / 2 + 0.5) * calcduration(gx) + Ny / 2 * calcduration(gy) delayTE1 = TE / 2 - calcduration(gz) / 2 - pre_time - calcduration( gz_spoil) - calcduration(rf180) / 2 delayTE2 = TE / 2 - calcduration(rf180) / 2 - calcduration( gz_spoil) - duration_to_center delay1 = makedelay(delayTE1) delay2 = makedelay(delayTE2) seq.add_block(rf, gz) seq.add_block(gx_pre, gy_pre, gz_reph) seq.add_block(delay1) seq.add_block(gz_spoil) seq.add_block(rf180) seq.add_block(gz_spoil) seq.add_block(delay2) for i in range(Ny): seq.add_block(gx, adc) seq.add_block(gy) gx.amplitude = -gx.amplitude seq.add_block(makedelay(1))
def make_se_epi(self): kwargs_for_opts = {"max_grad": self.max_grad, "grad_unit": "mT/m", "max_slew": self.max_slew, "slew_unit": "T/m/s", "rf_dead_time": 10e-6, "adc_dead_time": 10e-6} system = Opts(kwargs_for_opts) seq = Sequence(system) slice_thickness = 3e-3 flip = 90 * pi / 180 kwargs_for_sinc = {"flip_angle": flip, "system": system, "duration": 3e-3, "slice_thickness": slice_thickness, "apodization": 0.5, "time_bw_product": 4} rf, gz = makesincpulse(kwargs_for_sinc, 2) # plt.plot(rf.t[0], rf.signal[0]) # plt.show() delta_k = 1 / self.fov k_width = self.Nx * delta_k readout_time = 3.2e-4 kwargs_for_gx = {"channel": 'x', "system": system, "flat_area": k_width, "flat_time": readout_time} gx = maketrapezoid(kwargs_for_gx) kwargs_for_adc = {"num_samples": self.Nx, "system": system, "duration": gx.flat_time, "delay": gx.rise_time} adc = makeadc(kwargs_for_adc) pre_time = 8e-4 kwargs_for_gxpre = {"channel": 'x', "system": system, "area": -gx.area / 2, "duration": pre_time} gx_pre = maketrapezoid(kwargs_for_gxpre) kwargs_for_gz_reph = {"channel": 'z', "system": system, "area": -gz.area / 2, "duration": pre_time} gz_reph = maketrapezoid(kwargs_for_gz_reph) kwargs_for_gy_pre = {"channel": 'y', "system": system, "area": -self.Ny / 2 * delta_k, "duration": pre_time} gy_pre = maketrapezoid(kwargs_for_gy_pre) dur = ceil(2 * sqrt(delta_k / system.max_slew) / 10e-6) * 10e-6 kwargs_for_gy = {"channel": 'y', "system": system, "area": delta_k, "duration": dur} gy = maketrapezoid(kwargs_for_gy) flip = 180 * pi / 180 kwargs_for_sinc = {"flip_angle": flip, "system": system, "duration": 500e-6} rf180 = makeblockpulse(kwargs_for_sinc) kwargs_for_gz_spoil = {"channel": 'z', "system": system, "area": gz.area * 2, "duration": 3 * pre_time} gz_spoil = maketrapezoid(kwargs_for_gz_spoil) TE = self.te duration_to_center = (self.Nx / 2 + 0.5) * calcduration(gx) + self.Ny / 2 * calcduration(gy) delayTE1 = TE / 2 - calcduration(gz) / 2 - pre_time - calcduration(gz_spoil) - calcduration(rf180) / 2 delayTE2 = TE / 2 - calcduration(rf180) / 2 - calcduration(gz_spoil) - duration_to_center delay1 = makedelay(delayTE1) delay2 = makedelay(delayTE2) seq.add_block(rf, gz) seq.add_block(gx_pre, gy_pre, gz_reph) seq.add_block(delay1) seq.add_block(gz_spoil) seq.add_block(rf180) seq.add_block(gz_spoil) seq.add_block(delay2) for i in range(self.Ny): seq.add_block(gx, adc) seq.add_block(gy) gx.amplitude = -gx.amplitude seq.add_block(makedelay(1)) return seq
gx_pre = maketrapezoid(kwargs_for_gxpre) kwargs_for_gz_reph = { "channel": 'z', "system": system, "area": -gz.area / 2, "duration": 2.5e-3 } gz_reph = maketrapezoid(kwargs_for_gz_reph) phase_areas = np.array(([x for x in range(0, Ny)])) phase_areas = (phase_areas - Ny / 2) * delta_k delayTE = TE - calcduration( gx_pre) - calcduration(rf) / 2 - calcduration(gx) / 2 delayTR = TR - calcduration(gx_pre) - calcduration(rf) - calcduration( gx) - delayTE delay1 = makedelay(delayTE) delay2 = makedelay(delayTR) for i in range(Ny): seq.add_block(rf, gz) kwargsForGyPre = { "channel": 'y', "system": system, "area": phase_areas[i], "duration": 2.5e-3 } gyPre = maketrapezoid(kwargsForGyPre) seq.add_block(gx_pre, gyPre, gz_reph) seq.add_block(delay1) seq.add_block(gx, adc) seq.add_block(delay2)
kwargs_for_gxpre = {"channel": 'x', "system": system, "area": -gx.area / 2, "duration": 2.5e-3} gx_pre = maketrapezoid(kwargs_for_gxpre) kwargs_for_gz_reph = {"channel": 'z', "system": system, "area": -gz.area / 2, "duration": 2.5e-3} gz_reph = maketrapezoid(kwargs_for_gz_reph) flip = 180 * pi / 180 kwargs_for_sinc = {"flip_angle": flip, "system": system, "duration": 2.5e-3, "slice_thickness": slice_thickness, "apodization": 0.5, "time_bw_product": 4} rf180, gz180 = makesincpulse(kwargs_for_sinc, 2) delayTE1 = TE / 2 - calcduration(gz_reph) - calcduration(rf) - calcduration(rf180) / 2 delayTE2 = TE / 2 - calcduration(gx) / 2 - calcduration(rf180) / 2 delayTE3 = TR - TE - calcduration(gx) delay1 = makedelay(delayTE1) delay2 = makedelay(delayTE2) delay3 = makedelay(delayTE3) phase_areas = np.array(([x for x in range(0, Ny)])) phase_areas = (phase_areas - Ny / 2) * delta_k for i in range(Ny): seq.add_block(rf, gz) kwargsForGyPre = {"channel": 'y', "system": system, "area": phase_areas[i], "duration": 2.5e-3} gyPre = maketrapezoid(kwargsForGyPre) seq.add_block(gx_pre, gyPre, gz_reph) seq.add_block(delay1) seq.add_block(rf180, gz180) seq.add_block(delay2) seq.add_block(gx, adc)
def make_event_holders(self): """Make appropriate Holder objects depending on the Event type.""" self.system = self.in_dict['system'] # arbgrad_file_path is only for arbitrary gradients arbgrad_file_path = self.all_event_def[ 'file_path'] if 'file_path' in self.all_event_def else None self.all_event_holders = {} for event in self.all_event_def: event_unique_name = event['event_unique_name'] event_name = event['event_name'] event_values = list(event['event_values'].values()) include_in_loop = event['include_in_loop'] if event_name == 'Delay': params = self.parse_config_params(event_values) delay = makedelay(params[0]) self.all_event_holders[ event_unique_name] = delay, include_in_loop elif event_name == 'SincRF': include_gz = event['include_gz'] max_grad, max_slew, flip_angle, duration, freq_offset, phase_offset, time_bw_product, apodization, slice_thickness = self.parse_config_params( event_values) flip_angle = math.radians(flip_angle) max_grad = convert.convert_from_to(max_grad, 'mT/m') max_slew = convert.convert_from_to(max_slew, 'mT/m/ms') max_grad = self.system.max_grad if max_grad == 0 else max_grad max_slew = self.system.max_slew if max_slew == 0 else max_slew kwargs_for_sinc = { "flip_angle": flip_angle, "system": self.system, "duration": duration, "freq_offset": freq_offset, "phase_offset": phase_offset, "time_bw_product": time_bw_product, "apodization": apodization, "max_grad": max_grad, "max_slew": max_slew, "slice_thickness": slice_thickness } if include_gz: rf, gz = makesincpulse(kwargs_for_sinc, 2) self.all_event_holders[ event_unique_name] = rf, include_in_loop self.all_event_holders[ 'gz_' + event_unique_name] = gz, include_in_loop else: rf = makesincpulse(kwargs_for_sinc) self.all_event_holders[ event_unique_name] = rf, include_in_loop elif event_name == 'BlockRF': include_gz = event['include_gz'] max_grad, max_slew, flip_angle, duration, freq_offset, phase_offset, time_bw_product, bandwidth, slice_thickness = self.parse_config_params( event_values) flip_angle = math.radians(flip_angle) max_grad = convert.convert_from_to(max_grad, 'mT/m') max_slew = convert.convert_from_to(max_slew, 'mT/m/ms') max_grad = self.system.max_grad if max_grad == 0 else max_grad max_slew = self.system.max_slew if max_slew == 0 else max_slew kwargs_for_block = { "flip_angle": flip_angle, "system": self.system, "duration": duration, "freq_offset": freq_offset, "phase_offset": phase_offset, "time_bw_product": time_bw_product, "bandwidth": bandwidth, "max_grad": max_grad, "max_slew": max_slew, "slice_thickness": slice_thickness } if include_gz: rf, gz = makeblockpulse(kwargs_for_block, 2) self.all_event_holders[ event_unique_name] = rf, include_in_loop self.all_event_holders[ 'gz_' + event_unique_name] = gz, include_in_loop else: rf = makeblockpulse(kwargs_for_block) self.all_event_holders[ event_unique_name] = rf, include_in_loop elif event_name == 'G': channel = event_values.pop(0) max_grad, max_slew, duration, area, flat_time, flat_area, amplitude, rise_time = self.parse_config_params( event_values) # area, flat_area and amplitude should be reset to -1 if user does not input any values. This is # because the default values are -1 in maketrap method. area = area if area != 0 else -1 flat_area = flat_area if flat_area != 0 else -1 amplitude = amplitude if amplitude != 0 else -1 max_grad = convert.convert_from_to(max_grad, 'mT/m') max_slew = convert.convert_from_to(max_slew, 'mT/m/ms') max_grad = self.system.max_grad if max_grad == 0 else max_grad max_slew = self.system.max_slew if max_slew == 0 else max_slew kwargs_for_trap = { "channel": channel, "system": self.system, "duration": duration, "area": area, "flat_time": flat_time, "flat_area": flat_area, "amplitude": amplitude, "max_grad": max_grad, "max_slew": max_slew, "rise_time": rise_time } trap = maketrapezoid(kwargs_for_trap) self.all_event_holders[ event_unique_name] = trap, include_in_loop elif event_name == 'GyPre': duration, area = self.parse_config_params(event_values) Ny = self.system.Ny delta_k = 1 / self.system.fov gy_pre_list = [] for i in range(int(Ny)): kwargs_for_gy_pre = { "channel": 'y', "system": self.system, "area": (i - Ny / 2) * delta_k, "duration": duration } if area != 0: kwargs_for_gy_pre['area'] = area gy_pre = maketrapezoid(kwargs_for_gy_pre) gy_pre_list.append(gy_pre) self.all_event_holders[event_unique_name] = gy_pre_list, True elif event_name == 'ArbGrad': channel = event_values.pop(0) max_grad, max_slew = self.parse_config_params(event_values) file = h5py.File(gpi.TranslateFileURI(arbgrad_file_path), "r") self.dataset = str() def append_if_dataset(name, obj): if isinstance(obj, h5py.Dataset): self.dataset = name return True file.visititems(append_if_dataset) waveform = file[self.dataset].value kwargs_for_arb_grad = { "channel": channel, "waveform": waveform, "max_grad": max_grad, "max_slew": max_slew, "system": self.system } arb_grad = makearbitrarygrad(kwargs_for_arb_grad) self.all_event_holders[ event_unique_name] = arb_grad, include_in_loop elif event_name == 'ADC': num_samples, dwell, duration, delay, freq_offset, phase_offset = self.parse_config_params( event_values) kwargs_for_adc = { "num_samples": num_samples, "system": self.system, "dwell": dwell, "duration": duration, "delay": delay, "freq_offset": freq_offset, "phase_offset": phase_offset } adc = makeadc(kwargs_for_adc) self.all_event_holders[ event_unique_name] = adc, include_in_loop