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test_rnmrtk.py
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328 lines (283 loc) · 10.9 KB
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""" Tests for the fileio.rnmrtk submodule """
import tempfile
import os
import numpy as np
from numpy.testing import assert_array_equal
import nmrglue as ng
import pytest
from setup import DATA_DIR
# subroutines
def write_readback(dic, data):
""" write out and readback a RNMRTK file. """
tf = tempfile.mktemp(suffix='.sec', dir='.')
ng.rnmrtk.write(tf, dic, data)
rdic, rdata = ng.rnmrtk.read(tf)
os.remove(tf)
os.remove(tf.replace('.sec', '.par'))
assert_array_equal(data, rdata)
assert dic == rdic
def lowmem_write_readback(dic, data):
""" lowmemory write out and readback a RNMTRK file. """
tf = tempfile.mktemp(suffix='.sec', dir='.')
ng.rnmrtk.write_lowmem(tf, dic, data)
rdic, rdata = ng.rnmrtk.read_lowmem(tf)
# check value [0,1,...]
s = tuple(range(data.ndim))
assert data[s] == rdata[s]
assert dic == rdic
print(tf)
os.remove(tf)
os.remove(tf.replace('.sec', '.par'))
# tests
@pytest.mark.fast
def test_1d_time():
""" reading/writing of 1D RNMRTK time domain file """
dic, data = ng.rnmrtk.read(
os.path.join(DATA_DIR, 'rnmrtk_1d', 'time_1d.sec'))
assert data.shape == (1500, )
assert np.abs(data[0].real - 91899.24) <= 0.01
assert np.abs(data[0].imag - -1964.70) <= 0.01
assert np.abs(data[1].real - 168844.25) <= 0.01
assert np.abs(data[1].imag - -49503.41) <= 0.01
assert dic['sw'][0] == 50000.0
assert dic['sf'][0] == 125.68
assert dic['ppm'][0] == 99.0
write_readback(dic, data)
@pytest.mark.fast
def test_1d_freq():
""" reading/writing of 1D RNMRTK frequency domain file """
dic, data = ng.rnmrtk.read(
os.path.join(DATA_DIR, 'rnmrtk_1d', 'freq_1d.sec'))
assert data.shape == (4096, )
assert np.abs(data[0] - -1726.76) <= 0.01
assert np.abs(data[1] - -1702.76) <= 0.01
assert dic['sw'][0] == 50000.0
assert dic['sf'][0] == 125.68
assert dic['ppm'][0] == 99.0
write_readback(dic, data)
@pytest.mark.fast
def test_2d_time():
""" reading/writing of 2D RNMRTK time domain file """
dic, data = ng.rnmrtk.read(
os.path.join(DATA_DIR, "rnmrtk_2d", "time_2d.sec"))
assert data.shape == (332, 1500)
assert np.abs(data[0, 1].real - 360.07) <= 0.01
assert np.abs(data[0, 1].imag - -223.20) <= 0.01
assert np.abs(data[10, 18].real - 17.93) <= 0.01
assert np.abs(data[10, 18].imag - -67.20) <= 0.01
assert dic['sw'][1] == 50000.0
assert dic['sf'][1] == 125.69
assert dic['ppm'][1] == 55.0
assert dic['sw'][0] == 5555.556
assert dic['sf'][0] == 50.65
assert dic['ppm'][0] == 120.0
write_readback(dic, data)
@pytest.mark.fast
def test_2d_freq():
""" reading/writing of 2D RNMRTK frequency domain file """
dic, data = ng.rnmrtk.read(
os.path.join(DATA_DIR, "rnmrtk_2d", "freq_2d.sec"))
assert data.shape == (2048, 4096)
assert np.abs(data[0, 1] - -.19) <= 0.01
assert np.abs(data[10, 18] - 0.88) <= 0.01
assert dic['sw'][1] == 50000.0
assert dic['sf'][1] == 125.69
assert dic['ppm'][1] == 55.0
assert dic['sw'][0] == 5555.556
assert dic['sf'][0] == 50.65
assert dic['ppm'][0] == 120.0
write_readback(dic, data)
@pytest.mark.fast
def test_2d_time_lowmem():
""" low memory reading/writing of 2D RNMRTK time domain file """
dic, data = ng.rnmrtk.read_lowmem(
os.path.join(DATA_DIR, "rnmrtk_2d", "time_2d.sec"))
assert data.shape == (332, 1500)
assert np.abs(data[0, 1].real - 360.07) <= 0.01
assert np.abs(data[0, 1].imag - -223.20) <= 0.01
assert np.abs(data[10, 18].real - 17.93) <= 0.01
assert np.abs(data[10, 18].imag - -67.20) <= 0.01
assert dic['sw'][1] == 50000.0
assert dic['sf'][1] == 125.69
assert dic['ppm'][1] == 55.0
assert dic['sw'][0] == 5555.556
assert dic['sf'][0] == 50.65
assert dic['ppm'][0] == 120.0
lowmem_write_readback(dic, data)
@pytest.mark.fast
def test_2d_freq_lowmem():
""" low memory reading/writing of 2D RNMRTK frequency domain file """
dic, data = ng.rnmrtk.read_lowmem(
os.path.join(DATA_DIR, "rnmrtk_2d", "freq_2d.sec"))
assert data.shape == (2048, 4096)
assert np.abs(data[0, 1] - -.19) <= 0.01
assert np.abs(data[10, 18] - 0.88) <= 0.01
assert dic['sw'][1] == 50000.0
assert dic['sf'][1] == 125.69
assert dic['ppm'][1] == 55.0
assert dic['sw'][0] == 5555.556
assert dic['sf'][0] == 50.65
assert dic['ppm'][0] == 120.0
lowmem_write_readback(dic, data)
@pytest.mark.slow
def test_3d_time():
""" reading/writing of 3D RNMRTK time domain file """
dic, data = ng.rnmrtk.read(
os.path.join(DATA_DIR, "rnmrtk_3d", "time_3d.sec"))
assert data.shape == (128, 88, 1250)
assert np.abs(data[0, 1, 2].real - 7.98) <= 0.01
assert np.abs(data[0, 1, 2].imag - 33.82) <= 0.01
assert np.abs(data[10, 11, 18].real - -9.36) <= 0.01
assert np.abs(data[10, 11, 18].imag - -7.75) <= 0.01
assert dic['sw'][2] == 50000.0
assert dic['sf'][2] == 125.68
assert dic['ppm'][2] == 56.0
assert dic['sw'][1] == 2777.778
assert dic['sf'][1] == 50.65
assert dic['ppm'][1] == 120.0
assert dic['sw'][0] == 5555.556
assert dic['sf'][0] == 125.68
assert dic['ppm'][0] == 56.0
write_readback(dic, data)
@pytest.mark.slow
def test_3d_freq():
""" reading/writing of 3D RNMRTK frequency domain file """
dic, data = ng.rnmrtk.read(
os.path.join(DATA_DIR, "rnmrtk_3d", "freq_3d.sec"))
assert data.shape == (128, 128, 4096)
assert np.abs(data[0, 1, 2] - 3.23) <= 0.01
assert np.abs(data[10, 11, 18] - 1.16) <= 0.01
assert dic['sw'][2] == 50000.0
assert dic['sf'][2] == 125.68
assert dic['ppm'][2] == 56.0
assert dic['sw'][1] == 2777.778
assert dic['sf'][1] == 50.65
assert dic['ppm'][1] == 120.0
assert dic['sw'][0] == 5555.556
assert dic['sf'][0] == 125.68
assert dic['ppm'][0] == 56.0
write_readback(dic, data)
@pytest.mark.slow
def test_3d_time_lowmem():
""" low memory reading/writing of 3D RNMRTK time domain file """
dic, data = ng.rnmrtk.read_lowmem(
os.path.join(DATA_DIR, "rnmrtk_3d", "time_3d.sec"))
assert data.shape == (128, 88, 1250)
assert np.abs(data[0, 1, 2].real - 7.98) <= 0.01
assert np.abs(data[0, 1, 2].imag - 33.82) <= 0.01
assert np.abs(data[10, 11, 18].real - -9.36) <= 0.01
assert np.abs(data[10, 11, 18].imag - -7.75) <= 0.01
assert dic['sw'][2] == 50000.0
assert dic['sf'][2] == 125.68
assert dic['ppm'][2] == 56.0
assert dic['sw'][1] == 2777.778
assert dic['sf'][1] == 50.65
assert dic['ppm'][1] == 120.0
assert dic['sw'][0] == 5555.556
assert dic['sf'][0] == 125.68
assert dic['ppm'][0] == 56.0
lowmem_write_readback(dic, data)
@pytest.mark.slow
def test_3d_freq_lowmem():
""" low memory reading/writing of 3D RNMRTK frequency domain file """
dic, data = ng.rnmrtk.read_lowmem(
os.path.join(DATA_DIR, "rnmrtk_3d", "freq_3d.sec"))
assert data.shape == (128, 128, 4096)
assert np.abs(data[0, 1, 2] - 3.23) <= 0.01
assert np.abs(data[10, 11, 18] - 1.16) <= 0.01
assert dic['sw'][2] == 50000.0
assert dic['sf'][2] == 125.68
assert dic['ppm'][2] == 56.0
assert dic['sw'][1] == 2777.778
assert dic['sf'][1] == 50.65
assert dic['ppm'][1] == 120.0
assert dic['sw'][0] == 5555.556
assert dic['sf'][0] == 125.68
assert dic['ppm'][0] == 56.0
lowmem_write_readback(dic, data)
@pytest.mark.fast
def test_3d_transpose():
""" reading/writing of transposed 3D RNMRTK time domain file """
dir_3d = os.path.join(DATA_DIR, 'rnmrtk_3d')
# T1 T2 T3 ordering
dic, data = ng.rnmrtk.read(os.path.join(dir_3d, "time_3d_t1_t2_t3.sec"))
assert data.shape == (128, 88, 36)
assert np.abs(data[2, 6, 4].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
write_readback(dic, data)
# T1 T3 T2 ordering
dic, data = ng.rnmrtk.read(os.path.join(dir_3d, "time_3d_t1_t3_t2.sec"))
assert data.shape == (128, 72, 44)
assert np.abs(data[2, 8, 3].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
write_readback(dic, data)
# T2 T1 T3 ordering
dic, data = ng.rnmrtk.read(os.path.join(dir_3d, "time_3d_t2_t1_t3.sec"))
assert data.shape == (88, 128, 36)
assert np.abs(data[6, 2, 4].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
write_readback(dic, data)
# T2 T3 T1 ordering
dic, data = ng.rnmrtk.read(os.path.join(dir_3d, "time_3d_t2_t3_t1.sec"))
assert data.shape == (88, 72, 64)
assert np.abs(data[6, 8, 1].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
write_readback(dic, data)
# T3 T1 T2 ordering
dic, data = ng.rnmrtk.read(os.path.join(dir_3d, "time_3d_t3_t1_t2.sec"))
assert data.shape == (72, 128, 44)
assert np.abs(data[8, 2, 3].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
write_readback(dic, data)
# T3 T2 T1 ordering
dic, data = ng.rnmrtk.read(os.path.join(dir_3d, "time_3d_t3_t2_t1.sec"))
assert data.shape == (72, 88, 64)
assert np.abs(data[8, 6, 1].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
write_readback(dic, data)
@pytest.mark.slow
def test_3d_transpose_lowmem():
""" low mem. reading/writing of transposed 3D RNMRTK time domain file """
dir_3d = os.path.join(DATA_DIR, 'rnmrtk_3d')
# T1 T2 T3 ordering
dic, data = ng.rnmrtk.read_lowmem(os.path.join(
dir_3d, "time_3d_t1_t2_t3.sec"))
assert data.shape == (128, 88, 36)
assert np.abs(data[2, 6, 4].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
lowmem_write_readback(dic, data)
# T1 T3 T2 ordering
dic, data = ng.rnmrtk.read_lowmem(os.path.join(
dir_3d, "time_3d_t1_t3_t2.sec"))
assert data.shape == (128, 72, 44)
assert np.abs(data[2, 8, 3].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
lowmem_write_readback(dic, data)
# T2 T1 T3 ordering
dic, data = ng.rnmrtk.read_lowmem(os.path.join(
dir_3d, "time_3d_t2_t1_t3.sec"))
assert data.shape == (88, 128, 36)
assert np.abs(data[6, 2, 4].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
lowmem_write_readback(dic, data)
# T2 T3 T1 ordering
dic, data = ng.rnmrtk.read_lowmem(os.path.join(
dir_3d, "time_3d_t2_t3_t1.sec"))
assert data.shape == (88, 72, 64)
assert np.abs(data[6, 8, 1].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
lowmem_write_readback(dic, data)
# T3 T1 T2 ordering
dic, data = ng.rnmrtk.read_lowmem(os.path.join(
dir_3d, "time_3d_t3_t1_t2.sec"))
assert data.shape == (72, 128, 44)
assert np.abs(data[8, 2, 3].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
lowmem_write_readback(dic, data)
# T3 T2 T1 ordering
dic, data = ng.rnmrtk.read_lowmem(os.path.join(
dir_3d, "time_3d_t3_t2_t1.sec"))
assert data.shape == (72, 88, 64)
assert np.abs(data[8, 6, 1].real - -1.82) <= 0.01
assert dic['npts'] == [64, 44, 36]
lowmem_write_readback(dic, data)