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pypulseq/pulseq/core/Sequence/write_seq.py
822297d0cbf0feature-spiral

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write_seq.py
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import numpy as np
import math
def write(self, file_name):
"""
Writes a .seq file from the Sequence object calling the method.
>.0f is used when only decimals have to be displayed.
>g is used when insignificant zeros have to be truncated.
Parameters
----------
file_name : str
File name of .seq file to be written.
"""
file_name += '.seq' if file_name[-4:] != '.seq' not in file_name else ''
output_file = open(file_name, 'w')
output_file.write("# Pulseq sequence file\n")
output_file.write("# Created by Python/GPI Lab\n\n")
output_file.write("# Format of blocks:\n")
output_file.write("# # D RF GX GY GZ ADC\n")
output_file.write("[BLOCKS]\n")
id_format_width = len(str(len(self.block_events)))
id_format_str = '{:>' + str(id_format_width) + '}'
id_format_str += ' {:>2.0f} {:>2.0f} {:>3.0f} {:>3.0f} {:>3.0f} {:>2.0f}\n'
for i in range(0, len(self.block_events)):
s = id_format_str.format(*np.insert(self.block_events[i + 1].astype(int), 0, (i + 1)))
output_file.write(s)
output_file.write('\n')
if len(self.rf_library.keys) != 0:
output_file.write('# Format of RF events:\n')
output_file.write('# id amplitude mag_id phase_id freq phase\n')
output_file.write('# .. Hz .... .... Hz rad\n')
output_file.write('[RF]\n')
rf_lib_keys = self.rf_library.keys
id_format_str = '{:>1.0f} {:>12g} {:>1.0f} {:>1.0f} {:>g} {:>g}\n'
for k in rf_lib_keys.keys():
lib_data = self.rf_library.data[k][0:5]
s = id_format_str.format(*np.insert(lib_data, 0, k))
output_file.write(s)
output_file.write('\n')
grad_lib_values = np.array(list(self.grad_library.type.values()))
arb_grad_mask = np.where(grad_lib_values == 'g')[0]
trap_grad_mask = np.where(grad_lib_values == 't')[0]
if any(arb_grad_mask):
output_file.write('# Format of arbitrary gradients:\n')
output_file.write('# id amplitude shape_id\n')
output_file.write('# .. Hz/m ....\n')
output_file.write('[GRADIENTS]\n')
keys = np.array(list(self.grad_library.keys.keys()))
id_format_str = '{:>1.0f} {:>12g} {:>1.0f} \n'
for k in keys[arb_grad_mask]:
s = id_format_str.format(*np.insert(self.grad_library.data[k], 0, k))
output_file.write(s)
output_file.write('\n')
if any(trap_grad_mask):
output_file.write('# Format of trapezoid gradients:\n')
output_file.write('# id amplitude rise flat fall\n')
output_file.write('# .. Hz/m us us us\n')
output_file.write('[TRAP]\n')
keys = np.array(list(self.grad_library.keys.keys()))
for k in keys[trap_grad_mask]:
id_format_str = '{:>2.0f} {:>12g} {:>3.0f} {:>4.0f} {:>3.0f}\n'
data = self.grad_library.data[k]
data = np.reshape(data, (1, data.shape[0]))
data[0][1:] = np.round(1e6 * data[0][1:], decimals=2)
s = id_format_str.format(*np.insert(data, 0, k))
output_file.write(s)
output_file.write('\n')
if len(self.adc_library.keys) != 0:
output_file.write('# Format of ADC events:\n')
output_file.write('# id num dwell delay freq phase\n')
output_file.write('# .. .. ns us Hz rad\n')
output_file.write('[ADC]\n')
keys = self.adc_library.keys
id_format_str = '{:>2.0f} {:>3.0f} {:>6.0f} {:>3.0f} {:>g} {:>g}\n'
for k in keys.values():
data = np.multiply(self.adc_library.data[k][0:5], [1, 1e9, 1e6, 1, 1])
s = id_format_str.format(*np.insert(data, 0, k))
output_file.write(s)
output_file.write('\n')
if len(self.delay_library.keys) != 0:
output_file.write('# Format of delays:\n')
output_file.write('# id delay (us)\n')
output_file.write('[DELAYS]\n')
keys = self.delay_library.keys
id_format_str = '{:>.0f} {:>.0f}\n'
for k in keys.values():
data = np.round(1e6 * self.delay_library.data[k])
s = id_format_str.format(*np.insert(data, 0, k))
output_file.write(s)
output_file.write('\n')
if len(self.shape_library.keys) != 0:
output_file.write('# Sequence Shapes\n')
output_file.write('[SHAPES]\n\n')
keys = self.shape_library.keys
for k in keys.values():
shape_data = self.shape_library.data[k]
s = 'shape_id {:>.0f}\n'
s = s.format(k)
output_file.write(s)
s = 'num_samples {:>g}\n'
s = s.format(shape_data[0][0])
output_file.write(s)
s = '{:g}\n'
for x in shape_data[0][1:]:
s1 = s.format(x)
output_file.write(s1)
output_file.write('\n')
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