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TST: unit tests for fileio/pipe module
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‎nmrglue/fileio/tests/create_test_data_nmrpipe.sh‎

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#!/bin/csh
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# nmrpipe_1d_time.fid
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# 1D time containing 1 - 1j, 2 - 2j, 0, 0, ...
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simTimeND \
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-xN 32 \
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-xT 16 \
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-xMODE Complex \
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-xSW 50000.000 \
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-xOBS 500.000 \
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-xCAR 99.000 \
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-xLAB H1 \
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-ndim 1 \
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-out data/nmrpipe_1d_time.fid -ov
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nmrPipe -in data/nmrpipe_1d_time.fid \
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| nmrPipe -fn SET -r 1.0 -i -1.0 -x1 1 -xn 1 \
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| nmrPipe -fn SET -r 2.0 -i -2.0 -x1 2 -xn 2 \
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-ov -out data/nmrpipe_1d_time.fid
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# nmrpipe_1d_freq.ft2
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# 1D NMRPipe freq containing 1, 2
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nmrPipe -in data/nmrpipe_1d_time.fid \
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| nmrPipe -fn SET \
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| nmrPipe -fn FT -di \
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| nmrPipe -fn SET -r 1.0 -x1 1 -xn 1 \
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| nmrPipe -fn SET -r 2.0 -x1 2 -xn 2 \
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-ov -out data/nmrpipe_1d_freq.fid
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# nmrpipe_1d_ext.ft2
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# 1D NMRPipe freq extracted containing 1, 2
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nmrPipe -in data/nmrpipe_1d_freq.fid \
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| nmrPipe -fn SET \
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| nmrPipe -fn EXT -x1 4 -xn 11 -sw \
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| nmrPipe -fn SET -r 1.0 -x1 1 -xn 1 \
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| nmrPipe -fn SET -r 2.0 -x1 2 -xn 2 \
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-ov -out data/nmrpipe_1d_ext.fid
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# nmrpipe_2d_time.fid
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# 2D NMRPipe time containing 1 - 1j, 2 - 2j, 0 + 0j along each vector
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simTimeND \
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-xN 16 -yN 4 \
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-xT 8 -yT 2 \
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-xMODE Complex -yMODE States \
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-xSW 50000.000 -ySW 20000.000 \
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-xOBS 500.000 -yOBS 125.000 \
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-xCAR 4.700 -yCAR 99.000 \
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-xLAB H1 -yLAB C13 \
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-ndim 2 -aq2D States \
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-out data/nmrpipe_2d_time.fid -ov
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nmrPipe -in data/nmrpipe_2d_time.fid \
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| nmrPipe -fn SET -r 1.0 -i -1.0 -x1 1 -xn 1 \
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| nmrPipe -fn SET -r 2.0 -i -2.0 -x1 2 -xn 2 \
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-ov -out data/nmrpipe_2d_time.fid
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# nmrpipe_2d_freq.ft2
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# 2D NMRPipe freq containing 1, 2
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nmrPipe -in data/nmrpipe_2d_time.fid \
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| nmrPipe -fn SET \
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| nmrPipe -fn FT -di \
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| nmrPipe -fn TP \
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| nmrPipe -fn FT -di \
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| nmrPipe -fn TP \
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| nmrPipe -fn SET -r 1.0 -x1 1 -xn 1 \
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| nmrPipe -fn SET -r 2.0 -x1 2 -xn 2 \
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-ov -out data/nmrpipe_2d_freq.ft2
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# nmrpipe_2d_time_tp.fid
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# 2D NMRPipe time transposed
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nmrPipe -in data/nmrpipe_2d_time.fid \
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| nmrPipe -fn TP -hyper \
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-ov -out data/nmrpipe_2d_time_tp.fid
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# nmrpipe_2d_freq_tp.ft2
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# 2D NMRPipe freq transposed
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nmrPipe -in data/nmrpipe_2d_freq.ft2 \
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| nmrPipe -fn TP \
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-ov -out data/nmrpipe_2d_freq_tp.ft2
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# nmrpipe_3d_time.fid
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# 3D NMRPipe time containing 1 - 1j, 2 - 2j, 0 + 0j along each vector
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simTimeND \
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-xN 16 -yN 6 -zN 4 \
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-xT 8 -yT 3 -zT 2 \
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-xMODE Complex -yMODE States -zMODE States \
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-xSW 50000.000 -ySW 20000.000 -zSW 10000.000 \
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-xOBS 500.000 -yOBS 125.000 -zOBS 50.000 \
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-xCAR 4.700 -yCAR 99.000 -zCAR 120.000 \
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-xLAB H1 -yLAB C13 -zLAB N15 \
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-ndim 3 -aq2D States \
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-out data/nmrpipe_3d_time.dir/nmrpipe_3d_time_%03d.fid -ov
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xyz2pipe -in data/nmrpipe_3d_time.dir/nmrpipe_3d_time_%03d.fid \
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| nmrPipe -fn SET -r 1.0 -i -1.0 -x1 1 -xn 1 \
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| nmrPipe -fn SET -r 2.0 -i -2.0 -x1 2 -xn 2 \
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| pipe2xyz -out data/nmrpipe_3d_time.dir/nmrpipe_3d_time_%03d.fid
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# nmrpipe_3d_freq.fid
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# 3D NMRPipe time containing 1 - 1j, 2 - 2j, 0 + 0j along each vector
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xyz2pipe -in data/nmrpipe_3d_time.dir/nmrpipe_3d_time_%03d.fid -x \
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| nmrPipe -fn SET \
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| nmrPipe -fn FT -di \
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| nmrPipe -fn TP \
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| nmrPipe -fn FT -di \
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| pipe2xyz -out data/nmrpipe_3d_freq.dir/nmrpipe_3d_freq_%03d.ft2 -y
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xyz2pipe -in data/nmrpipe_3d_freq.dir/nmrpipe_3d_freq_%03d.ft2 -z \
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| nmrPipe -fn FT -di \
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| nmrPipe -fn SET -r 1.0 -x1 1 -xn 1 \
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| nmrPipe -fn SET -r 2.0 -x1 2 -xn 2 \
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| pipe2xyz -out data/nmrpipe_3d_freq.dir/nmrpipe_3d_freq_%03d.ft3 -z
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rm data/nmrpipe_3d_freq.dir/*.ft2
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# nmrpipe_3d_time.fid
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# 3D NMRPipe stream file (single file 3D file)
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xyz2pipe -in data/nmrpipe_3d_time.dir/nmrpipe_3d_time_%03d.fid -x > data/nmrpipe_3d_time.fid
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xyz2pipe -in data/nmrpipe_3d_freq.dir/nmrpipe_3d_freq_%03d.ft3 -x > data/nmrpipe_3d_freq.ft3
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# nmrpipe_4d_time_2.dir
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# 4D NMRPipe time containing 1 - 1j, 2 - 2j, 0 + 0j along each vector
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simTimeND \
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-xN 10 -yN 8 -zN 6 -aN 4 \
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-xT 5 -yT 4 -zT 3 -aT 2 \
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-xMODE Complex -yMODE States -zMODE States -aMODE States \
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-xSW 50000.000 -ySW 20000.000 -zSW 10000.000 -aSW 30000.000 \
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-xOBS 500.000 -yOBS 125.000 -zOBS 50.000 -aOBS 150.000 \
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-xCAR 4.700 -yCAR 99.000 -zCAR 120.000 -aCAR 80.000 \
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-xLAB H1 -yLAB C13 -zLAB N15 -aLAB P31 \
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-ndim 4 -aq2D States \
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| pipe2xyz -out data/nmrpipe_4d_time_2.dir/nmrpipe_4d_time_%03d_%03d.fid -x -ov -to 0
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xyz2pipe -in data/nmrpipe_4d_time_2.dir/nmrpipe_4d_time_%03d_%03d.fid -x \
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| nmrPipe -fn SET -r 1.0 -i -1.0 -x1 1 -xn 1 \
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| nmrPipe -fn SET -r 2.0 -i -2.0 -x1 2 -xn 2 \
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| pipe2xyz -out data/nmrpipe_4d_time_2.dir/nmrpipe_4d_time_%03d_%03d.fid -x -ov
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# nmrpipe_4d_time_1.dir
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# 4D NMRPipe time containing 1 - 1j, 2 - 2j, 0 + 0j along each vector
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simTimeND \
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-xN 10 -yN 8 -zN 6 -aN 4 \
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-xT 5 -yT 4 -zT 3 -aT 2 \
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-xMODE Complex -yMODE States -zMODE States -aMODE States \
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-xSW 50000.000 -ySW 20000.000 -zSW 10000.000 -aSW 30000.000 \
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-xOBS 500.000 -yOBS 125.000 -zOBS 50.000 -aOBS 150.000 \
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-xCAR 4.700 -yCAR 99.000 -zCAR 120.000 -aCAR 80.000 \
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-xLAB H1 -yLAB C13 -zLAB N15 -aLAB P31 \
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-ndim 4 -aq2D States \
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-out data/nmrpipe_4d_time_1.dir/nmrpipe_4d_time_%03d.fid -verb -ov
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xyz2pipe -in data/nmrpipe_4d_time_1.dir/nmrpipe_4d_time_%03d.fid -x \
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| nmrPipe -fn SET -r 1.0 -i -1.0 -x1 1 -xn 1 \
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| nmrPipe -fn SET -r 2.0 -i -2.0 -x1 2 -xn 2 \
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| pipe2xyz -out data/nmrpipe_4d_time_1.dir/nmrpipe_4d_time_%03d.fid -x -ov
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# nmrpipe_4d_time.fid
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# 4D Stream file
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xyz2pipe -in data/nmrpipe_4d_time_2.dir/nmrpipe_4d_time_%03d_%03d.fid -x > data/nmrpipe_4d_time.fid
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# nmrpipe_4d_freq_1.dir
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# 4D NMRPipe time containing 1 - 1j, 2 - 2j, 0 + 0j along each vector
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xyz2pipe -in data/nmrpipe_4d_time_1.dir/nmrpipe_4d_time_%03d.fid -x -verb \
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| nmrPipe -fn SET \
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| nmrPipe -fn FT -di \
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| pipe2xyz -out data/nmrpipe_4d_freq_1.dir/nmrpipe_4d_freq_%03d.ft1 -x -ov
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xyz2pipe -in data/nmrpipe_4d_freq_1.dir/nmrpipe_4d_freq_%03d.ft1 -y -verb \
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| nmrPipe -fn SET \
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| nmrPipe -fn FT -di \
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| pipe2xyz -out data/nmrpipe_4d_freq_1.dir/nmrpipe_4d_freq_%03d.ft2 -y -ov
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xyz2pipe -in data/nmrpipe_4d_freq_1.dir/nmrpipe_4d_freq_%03d.ft2 -z -verb \
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| nmrPipe -fn SET \
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| nmrPipe -fn FT -di \
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| pipe2xyz -out data/nmrpipe_4d_freq_1.dir/nmrpipe_4d_freq_%03d.ft3 -z -ov
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xyz2pipe -in data/nmrpipe_4d_freq_1.dir/nmrpipe_4d_freq_%03d.ft3 -a -verb \
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| nmrPipe -fn SET \
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| nmrPipe -fn FT -di \
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| nmrPipe -fn SET -r 1.0 -i -1.0 -x1 1 -xn 1 \
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| nmrPipe -fn SET -r 2.0 -i -2.0 -x1 2 -xn 2 \
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| pipe2xyz -out data/nmrpipe_4d_freq_1.dir/nmrpipe_4d_freq_%03d.ft4 -a -ov
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rm data/nmrpipe_4d_freq_1.dir/*.ft1
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rm data/nmrpipe_4d_freq_1.dir/*.ft2
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rm data/nmrpipe_4d_freq_1.dir/*.ft3
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# nmrpipe_4d_freq_2.dir
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# 4D NMRPipe time containing 1 - 1j, 2 - 2j, 0 + 0j along each vector
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xyz2pipe -in data/nmrpipe_4d_time_2.dir/nmrpipe_4d_time_%03d_%03d.fid -x -verb \
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| nmrPipe -fn SET \
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| nmrPipe -fn FT -di \
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| pipe2xyz -out data/nmrpipe_4d_freq_2.dir/nmrpipe_4d_freq_%03d_%03d.ft1 -x -ov
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xyz2pipe -in data/nmrpipe_4d_freq_2.dir/nmrpipe_4d_freq_%03d_%03d.ft1 -y -verb \
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| nmrPipe -fn SET \
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| nmrPipe -fn FT -di \
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| pipe2xyz -out data/nmrpipe_4d_freq_2.dir/nmrpipe_4d_freq_%03d_%03d.ft2 -y -ov
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xyz2pipe -in data/nmrpipe_4d_freq_2.dir/nmrpipe_4d_freq_%03d_%03d.ft2 -z -verb \
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| nmrPipe -fn SET \
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| nmrPipe -fn FT -di \
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| pipe2xyz -out data/nmrpipe_4d_freq_2.dir/nmrpipe_4d_freq_%03d_%03d.ft3 -z -ov
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xyz2pipe -in data/nmrpipe_4d_freq_2.dir/nmrpipe_4d_freq_%03d_%03d.ft3 -a -verb \
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| nmrPipe -fn SET \
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| nmrPipe -fn FT -di \
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| nmrPipe -fn SET -r 1.0 -i -1.0 -x1 1 -xn 1 \
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| nmrPipe -fn SET -r 2.0 -i -2.0 -x1 2 -xn 2 \
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| pipe2xyz -out data/nmrpipe_4d_freq_2.dir/nmrpipe_4d_freq_%03d_%03d.ft4 -a -ov
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rm data/nmrpipe_4d_freq_2.dir/*.ft1
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rm data/nmrpipe_4d_freq_2.dir/*.ft2
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rm data/nmrpipe_4d_freq_2.dir/*.ft3
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# nmrpipe_4d_freq.ft4
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# 4D Stream file
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xyz2pipe -in data/nmrpipe_4d_freq_2.dir/nmrpipe_4d_freq_%03d_%03d.ft4 -x > data/nmrpipe_4d_freq.ft4

‎nmrglue/fileio/tests/data/nmrpipe_1d_ext.fid‎

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‎nmrglue/fileio/tests/data/nmrpipe_1d_freq.fid‎

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‎nmrglue/fileio/tests/data/nmrpipe_1d_time.fid‎

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‎nmrglue/fileio/tests/data/nmrpipe_2d_freq.ft2‎

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‎nmrglue/fileio/tests/data/nmrpipe_2d_freq_tp.ft2‎

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‎nmrglue/fileio/tests/data/nmrpipe_2d_time.fid‎

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‎nmrglue/fileio/tests/data/nmrpipe_2d_time_tp.fid‎

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‎nmrglue/fileio/tests/data/nmrpipe_3d_freq.dir/nmrpipe_3d_freq_001.ft3‎

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‎nmrglue/fileio/tests/data/nmrpipe_3d_freq.dir/nmrpipe_3d_freq_002.ft3‎

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