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chatcannonchatcannon
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Code to read in Tecmag TNMR .tnt files
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‎nmrglue/fileio/__init__.py‎

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import rnmrtk
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import simpson
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import sparky
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import tecmag
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import varian
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import varian as agilent # replicate varian namespace in agilent
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import table

‎nmrglue/fileio/tecmag.py‎

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"""
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Functions for reading and Tecmag .tnt data files
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"""
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__developer_info__ = """
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Tecmag .tnt file format information
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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The Tecmag .tnt file format is documented with C pseudo-code in the file
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"A1 - TNMR File Format.doc" distributed with the TNMR software.
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This file is based on the pytnt module available at
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https://www.github.com/chatcannon/pytnt
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Please inform upstream if you find a bug or want a new feature.
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"""
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import io
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import re
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from collections import OrderedDict
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import numpy as np
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from . import fileiobase
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tntMagic_re = re.compile(b"^TNT1\.\d\d\d$")
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tntMagic = np.dtype('a8')
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tntTLV = np.dtype([('tag', 'a4'), ('bool', '<u4'), ('length', '<u4')])
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tntTMAG = np.dtype([
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('npts', '<i4', 4),
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('actual_npts', '<i4', 4),
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('acq_points', '<i4'),
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('npts_start', '<i4', 4),
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('scans', '<i4'),
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('actual_scans', '<i4'),
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('dummy_scans', '<i4'),
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('repeat_times', '<i4'),
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('sadimension', '<i4'),
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('samode', '<i4'),
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# ('space1', 'a0'),
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('magnet_field', '<f8'),
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('ob_freq', '<f8', 4),
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('base_freq', '<f8', 4),
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('offset_freq', '<f8', 4),
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('ref_freq', '<f8'),
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('NMR_frequency', '<f8'),
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('obs_channel', '<i2'),
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('space2', 'a42'),
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('sw', '<f8', 4),
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('dwell', '<f8', 4),
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('filter', '<f8'),
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('experiment_time', '<f8'),
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('acq_time', '<f8'),
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('last_delay', '<f8'),
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('spectrum_direction', '<i2'),
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('hardware_sideband', '<i2'),
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('Taps', '<i2'),
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('Type', '<i2'),
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('bDigRec', '<u4'),
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('nDigitalCenter', '<i4'),
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('space3', 'a16'),
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('transmitter_gain', '<i2'),
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('receiver_gain', '<i2'),
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('NumberOfReceivers', '<i2'),
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('RG2', '<i2'),
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('receiver_phase', '<f8'),
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('space4', 'a4'),
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('set_spin_rate', '<u2'),
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('actual_spin_rate', '<u2'),
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('lock_field', '<i2'),
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('lock_power', '<i2'),
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('lock_gain', '<i2'),
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('lock_phase', '<i2'),
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('lock_freq_mhz', '<f8'),
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('lock_ppm', '<f8'),
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('H2O_freq_ref', '<f8'),
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('space5', 'a16'),
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('set_temperature', '<f8'),
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('actual_temperature', '<f8'),
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('shim_units', '<f8'),
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('shims', '<i2', 36),
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('shim_FWHM', '<f8'),
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('HH_dcpl_attn', '<i2'),
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('DF_DN', '<i2'),
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('F1_tran_mode', '<i2', 7),
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('dec_BW', '<i2'),
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('grd_orientation', 'a4'),
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('LatchLP', '<i4'),
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('grd_Theta', '<f8'),
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('grd_Phi', '<f8'),
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('space6', 'a264'),
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('start_time', '<u4'),
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('finish_time', '<u4'),
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('elapsed_time', '<i4'),
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('date', 'a32'),
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('nuclei', 'a16', 4),
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('sequence', 'a32'),
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('lock_solvent', 'a16'),
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('lock_nucleus', 'a16')
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])
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tntGridAndAxis = np.dtype([
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('majorTickInc', '<f8', 12),
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('minorIntNum', '<i2', 12),
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('labelPrecision', '<i2', 12),
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('gaussPerCentimeter', '<f8'),
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('gridLines', '<i2'),
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('axisUnits', '<i2'),
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('showGrid', '<u4'),
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('showGridLabels', '<u4'),
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('adjustOnZoom', '<u4'),
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('showDistanceUnits', '<u4'),
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('axisName', 'a32'),
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('space', 'a52'),
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])
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tntTMG2 = np.dtype([
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('real_flag', '<u4'),
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('imag_flag', '<u4'),
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('magn_flag', '<u4'),
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('axis_visible', '<u4'),
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('auto_scale', '<u4'),
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('line_display', '<u4'),
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('show_shim_units', '<u4'),
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('integral_display', '<u4'),
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('fit_display', '<u4'),
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('show_pivot', '<u4'),
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('label_peaks', '<u4'),
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('keep_manual_peaks', '<u4'),
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('label_peaks_in_units', '<u4'),
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('integral_dc_average', '<u4'),
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('integral_show_multiplier', '<u4'),
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('Boolean_space', '<u4', 9),
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('all_ffts_done', '<u4', 4),
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('all_phase_done', '<u4', 4),
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('amp', '<f8'),
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('ampbits', '<f8'),
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('ampCtl', '<f8'),
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('offset', '<i4'),
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('axis_set', tntGridAndAxis),
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('display_units', '<i2', 4),
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('ref_point', '<i4', 4),
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('ref_value', '<f8', 4),
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('z_start', '<i4'),
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('z_end', '<i4'),
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('z_select_start', '<i4'),
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('z_select_end', '<i4'),
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('last_zoom_start', '<i4'),
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('last_zoom_end', '<i4'),
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('index_2D', '<i4'),
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('index_3D', '<i4'),
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('index_4D', '<i4'),
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('apodization_done', '<i4', 4),
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('linebrd', '<f8', 4),
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('gaussbrd', '<f8', 4),
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('dmbrd', '<f8', 4),
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('sine_bell_shift', '<f8', 4),
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('sine_bell_width', '<f8', 4),
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('sine_bell_skew', '<f8', 4),
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('Trapz_point_1', '<i4', 4),
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('Trapz_point_2', '<i4', 4),
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('Trapz_point_3', '<i4', 4),
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('Trapz_point_4', '<i4', 4),
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('trafbrd', '<f8', 4),
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('echo_center', '<i4', 4),
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('data_shift_points', '<i4'),
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('fft_flag', '<i2', 4),
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('unused', '<f8', 8),
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('pivot_point', '<i4', 4),
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('cumm_0_phase', '<f8', 4),
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('cumm_1_phase', '<f8', 4),
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('manual_0_phase', '<f8'),
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('manual_1_phase', '<f8'),
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('phase_0_value', '<f8'),
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('phase_1_value', '<f8'),
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('session_phase_0', '<f8'),
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('session_phase_1', '<f8'),
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('max_index', '<i4'),
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('min_index', '<i4'),
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('peak_threshold', '<f4'),
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('peak_noise', '<f4'),
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('integral_dc_points', '<i2'),
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('integral_label_type', '<i2'),
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('integral_scale_factor', '<f4'),
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('auto_integrate_shoulder', '<i4'),
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('auto_integrate_noise', '<f8'),
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('auto_integrate_threshold', '<f8'),
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('s_n_peak', '<i4'),
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('s_n_noise_start', '<i4'),
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('s_n_noise_end', '<i4'),
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('s_n_calculated', '<f4'),
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('Spline_point', '<i4', 14),
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('Spline_point_avr', '<i2'),
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('Poly_point', '<i4', 8),
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('Poly_point_avr', '<i2'),
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('Poly_order', '<i2'),
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('space', 'a610'),
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('line_simulation_name', 'a32'),
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('integral_template_name', 'a32'),
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('baseline_template_name', 'a32'),
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('layout_name', 'a32'),
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('relax_information_name', 'a32'),
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('username', 'a32'),
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('user_string_1', 'a16'),
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('user_string_2', 'a16'),
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('user_string_3', 'a16'),
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('user_string_4', 'a16')
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])
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def read(filename):
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"""
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Read a .tnt data file
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Parameters
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----------
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filename : str
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Name of file to read from
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Returns
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-------
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dic : dict
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Dictionary of Tecmag parameters.
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data : ndarray
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Array of NMR data.
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"""
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tnt_sections = OrderedDict()
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with open(filename, 'rb') as tntfile:
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tntmagic = np.fromstring(tntfile.read(tntMagic.itemsize),
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tntMagic, count=1)[0]
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if not tntMagic_re.match(tntmagic):
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raise ValueError("Invalid magic number (is '%s' really a TNMR file?): %s" % (filename, tntmagic))
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##Read in the section headers
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tnthdrbytes = tntfile.read(tntTLV.itemsize)
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while(tntTLV.itemsize == len(tnthdrbytes)):
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TLV = np.fromstring(tnthdrbytes, tntTLV)[0]
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data_length = TLV['length']
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hdrdict = {'offset': tntfile.tell(),
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'length': data_length,
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'bool': bool(TLV['bool'])}
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if data_length <= 4096:
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hdrdict['data'] = tntfile.read(data_length)
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assert(len(hdrdict['data']) == data_length)
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else:
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tntfile.seek(data_length, io.SEEK_CUR)
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tnt_sections[TLV['tag']] = hdrdict
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tnthdrbytes = tntfile.read(tntTLV.itemsize)
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assert(tnt_sections['TMAG']['length'] == tntTMAG.itemsize)
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TMAG = np.fromstring(tnt_sections['TMAG']['data'], tntTMAG, count=1)[0]
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assert(tnt_sections['DATA']['length'] ==
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TMAG['actual_npts'].prod() * 8)
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## For some reason we can't set offset and shape together
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#DATA = np.memmap(tntfilename,np.dtype('<c8'), mode='r',
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# offset=self.tnt_sections['DATA']['offset'],
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# shape=self.TMAG['actual_npts'].tolist(),order='F')
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DATA = np.memmap(filename, np.dtype('<c8'), mode='c',
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offset=tnt_sections['DATA']['offset'],
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shape=TMAG['actual_npts'].prod())
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DATA = np.reshape(DATA, TMAG['actual_npts'], order='F')
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assert(tnt_sections['TMG2']['length'] == tntTMG2.itemsize)
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TMG2 = np.fromstring(tnt_sections['TMG2']['data'], tntTMG2, count=1)[0]
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dic = dict()
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for name in tntTMAG.names:
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if not name.startswith('space'):
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dic[name] = TMAG[name]
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for name in tntTMG2.names:
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if name not in ['Boolean_space', 'unused', 'space', 'axis_set']:
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dic[name] = TMG2[name]
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for name in tntGridAndAxis.names:
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dic[name] = TMG2['axis_set'][name]
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return dic, DATA
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def guess_udic(dic, data):
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"""
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Guess parameters of universal dictionary from dic, data pair.
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Parameters
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----------
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dic : dict
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Dictionary of Tecmag parameters.
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data : ndarray
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Array of NMR data.
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Returns
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-------
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udic : dict
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Universal dictionary of spectral parameters.
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"""
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# create an empty universal dictionary
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udic = fileiobase.create_blank_udic(4)
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# update default values
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for i in xrange(4):
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udic[i]["size"] = dic['actual_npts'][i]
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udic[i]["sw"] = dic['sw'][i]
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udic[i]["complex"] = True
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udic[i]["obs"] = dic['ob_freq'] * 1e6
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# Not sure what the difference is here
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# N.B. base_freq is some bogus value like 1.4e-13
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udic[i]["car"] = dic['ob_freq'] * 1e6
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udic[i]["time"] = not bool(dic['fft_flag'])
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udic[i]["freq"] = bool(dic['fft_flag'])
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return udic

‎tests/test_tecmag.py‎

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import os
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import numpy as np
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from numpy.testing import assert_allclose
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from numpy.testing import assert_array_almost_equal
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import nmrglue as ng
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from setup import DATA_DIR
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def test_tecmag_load_time_domain():
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ref1, data = ng.tecmag.read(os.path.join(DATA_DIR, 'tecmag', 'LiCl_ref1.tnt'))
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real, imag, usec = np.loadtxt(os.path.join(DATA_DIR, 'tecmag', 'LiCl_ref1.txt'),
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skiprows=3, unpack=True)
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assert_array_almost_equal(data.real.squeeze(), real, decimal=3)
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assert_array_almost_equal(data.imag.squeeze(), imag, decimal=3)
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assert_array_almost_equal(np.arange(ref1['npts'][0]) *
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ref1['dwell'][0] * 1e6,
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usec, decimal=3)

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