LMTOY>> seq_pipeline: 2-feb-2022 LMTOY>> READING lmtoy_functions 11-mar-2022 via /lma1/teuben/lmtoy/examples/seq_pipeline.sh Working directory ./2022S1SEQUOIACommissioning/94052 LMTOY>> reading lmtoy_94052.rc LMTOY>> updating LMTOY>> process_otf_map2 in 2 seconds {'--b_order': '0', '--b_regions': '[[-326,-76],[124,374]]', '--bank': '0', '--eliminate_list': '0', '--help': False, '--l_regions': '[[-76,124]]', '--obsnum': '94052', '--output': 'R-Cas_94052.nc', '--path': '/n/lma1/lmt/data_lmt/', '--pix_list': '0,1,2,3,4,6,7,9,10,11,14,15', '--restfreq': None, '--sample': None, '--save_tsys': False, '--slice': '[-326,374]', '--stype': '2', '--tsys': '250.0', '--use_cal': True, '--use_otf_cal': False, '--x_axis': 'VLSR'} program process_otf_map options stype = 2 obsnum = 94052 pix_list = [0, 1, 2, 3, 4, 6, 7, 9, 10, 11, 14, 15] path = /n/lma1/lmt/data_lmt/ eliminate_list = [0] use_otf_cal = False x_axis = VLSR data_path = /n/lma1/lmt/data_lmt/ slice = [-326, 374] l_regions = [[-76, 124]] output_file_name = R-Cas_94052.nc bank = 0 b_regions = [[-326, -76], [124, 374]] b_order = 0 output = R-Cas_94052.nc use_cal = True tsys = 250.0 2022-02-22T16:01:05 begin /n/lma1/lmt/data_lmt/ifproc/ifproc_2022-02-22_094052_00_0001.nc 2022-02-22T16:34:37 end /n/lma1/lmt/data_lmt/ifproc/ifproc_2022-02-22_094052_00_0001.nc BufPos 3 4.5 sec 94052 BufPos 2 4.0 sec 94052 BufPos 1 16.6 sec 94052 BufPos 0 35.6 sec 94052 BufPos 1 33.5 sec 94052 BufPos 0 35.7 sec 94052 BufPos 1 33.2 sec 94052 BufPos 0 36.3 sec 94052 BufPos 1 33.1 sec 94052 BufPos 0 36.2 sec 94052 BufPos 1 32.8 sec 94052 BufPos 0 35.6 sec 94052 BufPos 1 32.3 sec 94052 BufPos 0 35.0 sec 94052 BufPos 1 33.4 sec 94052 BufPos 0 35.8 sec 94052 BufPos 1 32.5 sec 94052 BufPos 0 35.8 sec 94052 BufPos 1 17.4 sec 94052 BufPos 3 4.4 sec 94052 BufPos 2 4.6 sec 94052 BufPos 1 16.6 sec 94052 BufPos 0 36.0 sec 94052 BufPos 1 33.5 sec 94052 BufPos 0 35.4 sec 94052 BufPos 1 32.1 sec 94052 BufPos 0 35.2 sec 94052 BufPos 1 32.8 sec 94052 BufPos 0 35.8 sec 94052 BufPos 1 32.0 sec 94052 BufPos 0 35.4 sec 94052 BufPos 1 31.6 sec 94052 BufPos 0 36.0 sec 94052 BufPos 1 32.2 sec 94052 BufPos 0 35.6 sec 94052 BufPos 1 32.4 sec 94052 BufPos 0 36.4 sec 94052 BufPos 1 16.4 sec 94052 BufPos 3 4.5 sec 94052 BufPos 2 4.3 sec 94052 BufPos 1 16.7 sec 94052 BufPos 0 35.8 sec 94052 BufPos 1 31.5 sec 94052 BufPos 0 36.9 sec 94052 BufPos 1 32.4 sec 94052 BufPos 0 35.2 sec 94052 BufPos 1 31.8 sec 94052 BufPos 0 35.2 sec 94052 BufPos 1 32.4 sec 94052 BufPos 0 36.2 sec 94052 BufPos 1 31.5 sec 94052 BufPos 0 37.5 sec 94052 BufPos 1 32.0 sec 94052 BufPos 0 35.4 sec 94052 BufPos 1 32.0 sec 94052 BufPos 0 36.3 sec 94052 BufPos 1 16.7 sec 94052 BufPos 3 4.5 sec 94052 BufPos 2 4.1 sec 94052 BufPos 1 16.8 sec 94052 BufPos 0 35.6 sec 94052 BufPos 1 32.2 sec 94052 BufPos 0 35.9 sec 94052 BufPos 1 32.0 sec 94052 BufPos 0 35.4 sec 94052 BufPos 1 33.4 sec 94052 BufPos 0 36.4 sec 94052 BufPos 1 31.8 sec 94052 BufPos 0 36.2 sec 94052 BufPos 1 10.2 sec 94052 before read npix from pixels npix = 16 from xlen npix = 16 Map Parameters: Ra Continuous HPBW= 16.0 XLength= 360.0 YLength= 360.0 XStep= 1.00 YStep= 0.50 /n/lma1/lmt/data_lmt/ifproc/ifproc_2022-02-22_094052_00_0001.nc does not have bs parameters 94052 is a Map observation get chop 'Data.Msip1mm.BeamChopperActPos' no chop 2022-02-22T15:49:24 begin /n/lma1/lmt/data_lmt/ifproc/ifproc_2022-02-22_094051_00_0001.nc 2022-02-22T15:58:05 end /n/lma1/lmt/data_lmt/ifproc/ifproc_2022-02-22_094051_00_0001.nc BufPos 3 4.2 sec 94051 BufPos 2 4.1 sec 94051 BufPos 1 20.9 sec 94051 BufPos 0 50.7 sec 94051 BufPos 1 21.7 sec 94051 BufPos 0 51.9 sec 94051 BufPos 1 22.0 sec 94051 BufPos 0 51.1 sec 94051 BufPos 1 22.2 sec 94051 BufPos 0 51.1 sec 94051 BufPos 1 23.8 sec 94051 BufPos 0 51.9 sec 94051 BufPos 1 20.7 sec 94051 BufPos 0 52.3 sec 94051 BufPos 1 20.7 sec 94051 BufPos 0 36.8 sec 94051 BufPos 1 15.1 sec 94051 before read npix from pixels npix = 16 from xlen npix = 16 /n/lma1/lmt/data_lmt/ifproc/ifproc_2022-02-22_094051_00_0001.nc does not have map parameters /n/lma1/lmt/data_lmt/ifproc/ifproc_2022-02-22_094051_00_0001.nc does not have bs parameters WARNING: 94051 is NOT a Cal observation : Lissajous get chop cal 'Data.Msip1mm.BeamChopperActPos' no chop cal read_roach /n/lma1/lmt/data_lmt/spectrometer/roach0/roach0_94052_0_1_R-Cas_2022-02-22_210056.nc nspec,nchan=55716,4096 r:0 inp:0 pix:0 time_offset:-0.030000 r:0 inp:1 pix:1 time_offset:-0.030000 r:0 inp:2 pix:2 time_offset:-0.030000 r:0 inp:3 pix:3 time_offset:-0.030000 read_roach /n/lma1/lmt/data_lmt/spectrometer/roach1/roach1_94052_0_1_R-Cas_2022-02-22_210056.nc nspec,nchan=56220,4096 r:1 inp:0 pix:4 time_offset:-0.030000 r:1 inp:2 pix:6 time_offset:-0.030000 r:1 inp:3 pix:7 time_offset:-0.030000 read_roach /n/lma1/lmt/data_lmt/spectrometer/roach2/roach2_94052_0_1_R-Cas_2022-02-22_210056.nc nspec,nchan=56456,4096 r:2 inp:1 pix:9 time_offset:-0.030000 r:2 inp:2 pix:10 time_offset:-0.030000 r:2 inp:3 pix:11 time_offset:-0.030000 read_roach /n/lma1/lmt/data_lmt/spectrometer/roach3/roach3_94052_0_1_R-Cas_2022-02-22_210056.nc nspec,nchan=56496,4096 r:3 inp:2 pix:14 time_offset:-0.030000 r:3 inp:3 pix:15 time_offset:-0.030000 RESTFREQ 86.2434 GHz read_roach /n/lma1/lmt/data_lmt/spectrometer/roach0/roach0_94051_0_1_R-Cas_2022-02-22_204915.nc nspec,nchan=15516,4096 r:0 inp:0 pix:0 time_offset:-0.030000 r:0 inp:1 pix:1 time_offset:-0.030000 r:0 inp:2 pix:2 time_offset:-0.030000 r:0 inp:3 pix:3 time_offset:-0.030000 read_roach /n/lma1/lmt/data_lmt/spectrometer/roach1/roach1_94051_0_1_R-Cas_2022-02-22_204915.nc nspec,nchan=15672,4096 r:1 inp:0 pix:4 time_offset:-0.030000 r:1 inp:2 pix:6 time_offset:-0.030000 r:1 inp:3 pix:7 time_offset:-0.030000 read_roach /n/lma1/lmt/data_lmt/spectrometer/roach2/roach2_94051_0_1_R-Cas_2022-02-22_204915.nc nspec,nchan=15580,4096 r:2 inp:1 pix:9 time_offset:-0.030000 r:2 inp:2 pix:10 time_offset:-0.030000 r:2 inp:3 pix:11 time_offset:-0.030000 read_roach /n/lma1/lmt/data_lmt/spectrometer/roach3/roach3_94051_0_1_R-Cas_2022-02-22_204915.nc nspec,nchan=15632,4096 r:3 inp:2 pix:14 time_offset:-0.030000 r:3 inp:3 pix:15 time_offset:-0.030000 TSYS[0] = 86.2398 +/- 19.8393 (4096 channels) TSYS[1] = 90.3174 +/- 2.81221 (4096 channels) TSYS[2] = 91.0246 +/- 7.77813 (4096 channels) TSYS[3] = 93.3239 +/- 10.4592 (4096 channels) TSYS[4] = 101.17 +/- 1.61268 (4096 channels) TSYS[6] = 90.7456 +/- 5.13059 (4096 channels) TSYS[7] = 97.1095 +/- 1.69747 (4096 channels) TSYS[9] = 88.798 +/- 10.0701 (4096 channels) TSYS[10] = 98.5395 +/- 3.97606 (4096 channels) TSYS[11] = 95.7014 +/- 5.0805 (4096 channels) TSYS[14] = 94.5544 +/- 6.04628 (4096 channels) TSYS[15] = 95.7098 +/- 10.3567 (4096 channels) Spectral Band velocity range: 684.293 -705.815 km/s Total Number of OTF Spectra = 95059 NSPEC: 95059 NCHAN: 2062 FAST_NC: True Looping over 12 pixel list [0, 1, 2, 3, 4, 6, 7, 9, 10, 11, 14, 15]: Processing 1 CAL's for Tsys Pix Nspec Mean Std MAD_std Min Max RMS_max Warnings TSYS[0] slice: 92.1964 (2.4985) minmax: 84.795 98.4205 0 7891 0.001 1.103 1.087 -5.946 88.845 1.105 1.216 TSYS[1] slice: 91.5444 (2.05004) minmax: 86.1105 96.2393 1 7891 0.001 1.056 1.041 -6.233 90.433 1.049 1.146 TSYS[2] slice: 94.7437 (2.52071) minmax: 83.9696 98.8945 2 7891 0.001 1.097 1.084 -5.746 87.496 1.092 1.178 TSYS[3] slice: 97.6328 (1.82338) minmax: 91.6834 101.334 3 7891 0.001 1.130 1.116 -5.850 93.438 1.124 1.216 TSYS[4] slice: 101.972 (1.24345) minmax: 98.7671 105.105 4 7943 0.002 1.148 1.133 -6.163 101.352 1.147 1.253 TSYS[6] slice: 92.8477 (2.13392) minmax: 87.4339 96.481 6 7943 0.001 1.066 1.052 -5.893 88.048 1.064 1.164 TSYS[7] slice: 96.8483 (1.90427) minmax: 92.2853 100.586 7 7943 0.001 1.113 1.101 -5.967 75.816 1.112 1.189 Traceback (most recent call last): File "/lma1/teuben/lmtoy/SpectralLineReduction/lmtslr/ifproc/ifproc.py", line 537, in __init__ self.chop = self.nc.variables['Data.Msip1mm.BeamChopperActPos'][:] KeyError: 'Data.Msip1mm.BeamChopperActPos' Traceback (most recent call last): File "/lma1/teuben/lmtoy/SpectralLineReduction/lmtslr/ifproc/ifproc.py", line 668, in __init__ self.chop = self.nc.variables['Data.Msip1mm.BeamChopperActPos'][:] KeyError: 'Data.Msip1mm.BeamChopperActPos' /lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/numpy/core/fromnumeric.py:748: UserWarning: Warning: 'partition' will ignore the 'mask' of the MaskedArray. a.partition(kth, axis=axis, kind=kind, order=order) /lma1/teuben/lmtoy/SpectralLineReduction/lmtslr/spec/spec.py:547: RuntimeWarning: invalid value encountered in true_divide self.tsys_spectrum = 280 * sky_spectrum / (hot_spectrum - /lma1/teuben/lmtoy/SpectralLineReduction/lmtslr/spec/spec.py:547: RuntimeWarning: divide by zero encountered in true_divide self.tsys_spectrum = 280 * sky_spectrum / (hot_spectrum - /lma1/teuben/lmtoy/SpectralLineReduction/lmtslr/spec/spec.py:392: RuntimeWarning: invalid value encountered in true_divide spectra.append((self.raw_spec[i,:] - ref) / ref) /lma1/teuben/lmtoy/SpectralLineReduction/lmtslr/spec/spec.py:392: RuntimeWarning: divide by zero encountered in true_divide spectra.append((self.raw_spec[i,:] - ref) / ref) /lma1/teuben/lmtoy/SpectralLineReduction/lmtslr/spec/spec.py:434: RuntimeWarning: invalid value encountered in multiply self.reduced_spectra = np.array(spectra) * tsys_spectrum TSYS[9] slice: 92.7834 (2.83822) minmax: 86.7659 97.9636 9 7946 0.001 1.100 1.085 -5.806 95.373 1.098 1.192 TSYS[10] slice: 99.9235 (1.98211) minmax: 94.9097 103.451 10 7946 0.002 1.139 1.126 -6.165 87.689 1.135 1.232 TSYS[11] slice: 97.2514 (2.64857) minmax: 90.3253 102.661 11 7946 0.003 1.174 1.156 -6.387 80.250 1.178 1.273 TSYS[14] slice: 96.2343 (3.22661) minmax: 87.8342 101.539 14 7914 0.001 1.142 1.126 -6.218 103.113 1.137 1.234 TSYS[15] slice: 99.427 (4.81068) minmax: 83.1038 105.585 15 7914 0.001 1.198 1.179 -6.424 94.611 1.194 1.298 CPU TIME: 63.5263 sec Traceback (most recent call last): File "/lma1/teuben/lmtoy/anaconda3/bin/process_otf_map2.py", line 7, in exec(compile(f.read(), __file__, 'exec')) File "/lma1/teuben/lmtoy/SpectralLineReduction/bin/process_otf_map2.py", line 110, in main(sys.argv[1:]) File "/lma1/teuben/lmtoy/SpectralLineReduction/bin/process_otf_map2.py", line 105, in main specfile.write_ncdata() File "/lma1/teuben/lmtoy/SpectralLineReduction/lmtslr/spec/specfile.py", line 325, in write_ncdata self._create_nc_data() File "/lma1/teuben/lmtoy/SpectralLineReduction/lmtslr/spec/specfile.py", line 286, in _create_nc_data nc_tsys[:,:,:] = tmp_tsys[:,:,:] File "src/netCDF4/_netCDF4.pyx", line 4918, in netCDF4._netCDF4.Variable.__setitem__ File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/netCDF4/utils.py", line 365, in _StartCountStride datashape = broadcasted_shape(shape, datashape) File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/netCDF4/utils.py", line 973, in broadcasted_shape return np.broadcast(a, b).shape ValueError: shape mismatch: objects cannot be broadcast to a single shape LMTOY>> view_spec_file {'--help': False, '--input': 'R-Cas_94052.nc', '--pix_list': '0,1,2,3,4,6,7,9,10,11,14,15', '--plot_range': '-1,3', '--plots': 'R-Cas_94052_specviews', '--rms_cut': '-4', '--show_pixel': None, '--skip_tsys': False} SLR Plots initialized with 1 method=R-Cas_94052_specviews Max sequence=7946 Plots saving in R-Cas_94052_specviews.1.png (overwriting the old one) Plots saving in R-Cas_94052_specviews.2.png (overwriting the old one) Plots saving in R-Cas_94052_specviews.3.png (overwriting the old one) Plots saving in R-Cas_94052_specviews.4.png (overwriting the old one) Plots saving in R-Cas_94052_specviews.5.png (overwriting the old one) NEW TSYS PIC SHAPE (1, 12, 2062) PIXEL: 0 [ 0 1 2 ... 7888 7889 7890] PIXEL: 1 [ 7891 7892 7893 ... 15779 15780 15781] PIXEL: 2 [15782 15783 15784 ... 23670 23671 23672] PIXEL: 3 [23673 23674 23675 ... 31561 31562 31563] PIXEL: 4 [31564 31565 31566 ... 39504 39505 39506] PIXEL: 6 [39507 39508 39509 ... 47447 47448 47449] PIXEL: 7 [47450 47451 47452 ... 55390 55391 55392] PIXEL: 9 [55393 55394 55395 ... 63336 63337 63338] PIXEL: 10 [63339 63340 63341 ... 71282 71283 71284] PIXEL: 11 [71285 71286 71287 ... 79228 79229 79230] PIXEL: 14 [79231 79232 79233 ... 87142 87143 87144] PIXEL: 15 [87145 87146 87147 ... 95056 95057 95058] Plots saving in R-Cas_94052_specviews.6.png (overwriting the old one) /lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/numpy/core/fromnumeric.py:748: UserWarning: Warning: 'partition' will ignore the 'mask' of the MaskedArray. a.partition(kth, axis=axis, kind=kind, order=order) SLR Plots initialized with 3 method=R-Cas_94052_specpoint,png,1 MAD: 0 1.1052498 0.022671848223860456 1.1959371554305371 MAD: 1 1.0484374 0.021024808563137997 1.1325365912014045 MAD: 2 1.091866 0.02144368226159408 1.1776407454343158 MAD: 3 1.1237948 0.022208259316244296 1.2126278313476189 MAD: 4 1.14641 0.022382878393912908 1.235941501978972 MAD: 6 1.0631942 0.021245556769623926 1.1481763827715499 MAD: 7 1.1116941 0.02165029127150765 1.1982952626049514 MAD: 9 1.0976901 0.02183100787769809 1.1850141369490248 MAD: 10 1.135165 0.022334805125566893 1.2245041966222627 MAD: 11 1.1779673 0.02377850546558314 1.2730813318141148 MAD: 14 1.1364782 0.023206751704188445 1.2293051924704403 MAD: 15 1.1938049 0.023492982064800102 1.2877767883742517 Plots saving in R-Cas_94052_specpoint.1.png (overwriting the old one) /lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/numpy/core/fromnumeric.py:748: UserWarning: Warning: 'partition' will ignore the 'mask' of the MaskedArray. a.partition(kth, axis=axis, kind=kind, order=order) SLR Plots initialized with 3 method=R-Cas_94052_specpoint,png,2 MAD: 0 1.1052498 0.022671848223860456 1.1959371554305371 MAD: 1 1.0484374 0.021024808563137997 1.1325365912014045 MAD: 2 1.091866 0.02144368226159408 1.1776407454343158 MAD: 3 1.1237948 0.022208259316244296 1.2126278313476189 MAD: 4 1.14641 0.022382878393912908 1.235941501978972 MAD: 6 1.0631942 0.021245556769623926 1.1481763827715499 MAD: 7 1.1116941 0.02165029127150765 1.1982952626049514 MAD: 9 1.0976901 0.02183100787769809 1.1850141369490248 MAD: 10 1.135165 0.022334805125566893 1.2245041966222627 MAD: 11 1.1779673 0.02377850546558314 1.2730813318141148 MAD: 14 1.1364782 0.023206751704188445 1.2293051924704403 MAD: 15 1.1938049 0.023492982064800102 1.2877767883742517 Plots saving in R-Cas_94052_specpoint.2.png (overwriting the old one) LMTOY>> make_spec_fits (waterfall) pix [0, 1, 2, 3, 4, 6, 7, 9, 10, 11, 14, 15] Min nsamp 7891 Binning [1, 1] FITS file will be 7891 x 2062 x 12 Written waterfall cube to R-Cas_94052.wf.fits pix [0, 1, 2, 3, 4, 6, 7, 9, 10, 11, 14, 15] Min nsamp 7891 Binning [10, 1] FITS file will be 789 x 2062 x 12 New shape: (12, 2062, 789) Written waterfall cube to R-Cas_94052.wf10.fits LMTOY>> grid_data {'--cell': '7.5', '--edge': '0', '--help': False, '--input': 'R-Cas_94052.nc', '--n_samples': '256', '--noise_sigma': '1', '--otf_a': '1.1', '--otf_b': '4.75', '--otf_c': '2', '--otf_select': '1', '--output': 'R-Cas_94052.fits', '--pix_list': '0,1,2,3,4,6,7,9,10,11,14,15', '--program_path': 'spec_driver_fits', '--resolution': '15', '--rmax': '3', '--rms_cut': '-4', '--sample': '-1', '--weight': 'R-Cas_94052.wt.fits', '--x_extent': '360', '--y_extent': '360'} Removing R-Cas_94052.fits Removing R-Cas_94052.wt.fits STDOUT **************************** spec_driver_fits LMTSLR 15-mar-2022 CMD: spec_driver_fits -i R-Cas_94052.nc -o R-Cas_94052.fits -w R-Cas_94052.wt.fits -l 15 -c 7.5 -u [0,1,2,3,4,6,7,9,10,11,14,15] -z -4 -s 1 -x 360 -y 360 -f 1 -r 3 -n 256 -0 1.1 -1 4.75 -2 2 -b -1 -e 0 file list=R-Cas_94052.nc DEBUG:7.5 sample_list=-1 Warning: sample list is not a multiple of 3 nsamples=1 Processing 1 SpecFiles: Opening SpecFile file R-Cas_94052.nc Error: NetCDF: Variable not found STDERR **************************** Exit Code: 2 LMTOY>> Some NEMO post-processing LMTOY>> Problems finding R-Cas_94052.fits. Skipping NEMO work. LMTOY>> skipping ADMIT post-processing LMTOY>> Created R-Cas_94052.fits and R-Cas_94052.wt.fits LMTOY>> Parameter file used: lmtoy_94052.rc LMTOY>> Making summary index.html: Making index.html for obsnum=94052 R-Cas_94052 R-Cas_94052_specviews R-Cas_94052_specpoint Writing index.html Writing index_pipeline.html Writing index_admit.html Writing index_pars.html Writing index_log.html