LMTOY>> seq_combine: 17-dec-2021 LMTOY>> READING lmtoy_functions 24-dec-2021 via /lma1/teuben/lmtoy/examples/seq_combine.sh No PDIR directory used, all work in the current directory OBSNUM: 85776 OBSNUMS: 85776,85778,85824 OBSNUMS1: 85776 85778 85824 85776 : 1 2018-S1-MU-46/85776/lmtoy_85776.rc 85778 : 1 2018-S1-MU-46/85778/lmtoy_85778.rc 85824 : 1 2018-S1-MU-46/85824/lmtoy_85824.rc First RC will be used : 2018-S1-MU-46/85776/lmtoy_85776.rc Using pdir=2018-S1-MU-46/85776_85824 src=Region_J-K ONS: 2018-S1-MU-46/85776/Region_J-K_85776.nc 2018-S1-MU-46/85778/Region_J-K_85778.nc 2018-S1-MU-46/85824/Region_J-K_85824.nc OBSNUM range: 85776 85824 FILES: s_nc: ../../2018-S1-MU-46/85776/Region_J-K_85776.nc,../../2018-S1-MU-46/85778/Region_J-K_85778.nc,../../2018-S1-MU-46/85824/Region_J-K_85824.nc LMTOY>> grid_data {'--cell': '5.5', '--edge': '0', '--help': False, '--input': '../../2018-S1-MU-46/85776/Region_J-K_85776.nc,../../2018-S1-MU-46/85778/Region_J-K_85778.nc,../../2018-S1-MU-46/85824/Region_J-K_85824.nc', '--n_samples': '256', '--noise_sigma': '1', '--otf_a': '1.1', '--otf_b': '4.75', '--otf_c': '2', '--otf_select': '1', '--output': 'Region_J-K_85776_85824.fits', '--pix_list': '0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15', '--program_path': 'spec_driver_fits', '--resolution': '11', '--rmax': '3', '--rms_cut': '4', '--sample': '-1', '--weight': 'Region_J-K_85776_85824.wt.fits', '--x_extent': '300', '--y_extent': '300'} STDOUT **************************** spec_driver_fits LMTSLR 26-jan-2022 CMD: spec_driver_fits -i ../../2018-S1-MU-46/85776/Region_J-K_85776.nc,../../2018-S1-MU-46/85778/Region_J-K_85778.nc,../../2018-S1-MU-46/85824/Region_J-K_85824.nc -o Region_J-K_85776_85824.fits -w Region_J-K_85776_85824.wt.fits -l 11 -c 5.5 -u [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15] -z 4 -s 1 -x 300 -y 300 -f 1 -r 3 -n 256 -0 1.1 -1 4.75 -2 2 -b -1 -e 0 file list=../../2018-S1-MU-46/85776/Region_J-K_85776.nc,../../2018-S1-MU-46/85778/Region_J-K_85778.nc,../../2018-S1-MU-46/85824/Region_J-K_85824.nc DEBUG:5.5 sample_list=-1 Warning: sample list is not a multiple of 3 nsamples=1 Processing 3 SpecFiles: Opening SpecFile file ../../2018-S1-MU-46/85776/Region_J-K_85776.nc file: ../../2018-S1-MU-46/85776/Region_J-K_85776.nc nspec= 213432 nchan= 689 SpecFile version 6-mar-2021 X-range: -216.22 192.529 Y-range: -185.827 224.666 arcsec X-ramp: -132.82 109.129 Y-ramp: -102.427 141.266 arcsec MapSize: 408.748 x 410.493 arcsec 85776 Region_J-K DATE-OBS 2019-10-31T03:01:57 CF.n_cells= 7 delta=0.129412 cell=5.5 resol=11 oft_select=1 C-AXIS 2 starts at 53.9848 C-AXIS 1 starts at -302.5 C-AXIS 0 starts at -302.5 P-AXIS 1 starts at -302.5 P-AXIS 0 starts at -302.5 P-AXIS 1 starts at -302.5 P-AXIS 0 starts at -302.5 WARNING fuzzy_edge=0 pixel: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 used?: 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 rms_stats: n=213432 rms_cutoff=4 Warning: no pixels found for pixel 3 Opening SpecFile file ../../2018-S1-MU-46/85778/Region_J-K_85778.nc file: ../../2018-S1-MU-46/85778/Region_J-K_85778.nc nspec= 214998 nchan= 689 SpecFile version 6-mar-2021 X-range: -215.71 190.878 Y-range: -185.766 222.952 arcsec X-ramp: -132.31 107.478 Y-ramp: -102.366 139.552 arcsec MapSize: 406.589 x 408.717 arcsec rms_stats: n=214998 rms_cutoff=4 Warning: no pixels found for pixel 3 Opening SpecFile file ../../2018-S1-MU-46/85824/Region_J-K_85824.nc file: ../../2018-S1-MU-46/85824/Region_J-K_85824.nc nspec= 215587 nchan= 689 SpecFile version 6-mar-2021 X-range: -216.685 194.43 Y-range: -185.993 223.181 arcsec X-ramp: -133.285 111.03 Y-ramp: -102.593 139.781 arcsec MapSize: 411.114 x 409.173 arcsec rms_stats: n=215587 rms_cutoff=4 Warning: no pixels found for pixel 3 Cube Completed, 644017/644017 Spectra accepted = 1.000 Weighting Completed, fuzzy_edge=0 Weight at 0.000000 0.000000 is 179.039536 write to Region_J-K_85776_85824.fits write weights to Region_J-K_85776_85824.wt.fits STDERR **************************** Exit Code: 0 LMTOY>> Some NEMO post-processing ### nemo Debug Info: FITS file: Image size 111 111 689 ### Warning [fitsccd]: Setting map minimum from 0 to -9.61546 ### Warning [fitsccd]: Setting map maximum from 0 to 9.99436 ### nemo Debug Info: There were 4732052 blank values in the image (55.742229 %) ### nemo Debug Info: FITS file: Image size 111 111 ### Warning [fitsccd]: Setting map minimum from 0 to -4.4765 ### Warning [fitsccd]: Setting map maximum from 0 to 213.951 ### nemo Debug Info: There were no blank values set in the image LMTOY>> STATS Region_J-K_85776_85824.ccd centerbox robust ### Warning [ccdsub]: Sampling will be done ### Warning [ccdsub]: Attempting to fix the WCS ### nemo Debug Info: WCS Corner: 10.6075 41.5549 53984.8 Number of points : 2160704 Min and Max : -0.661692 1.539258 Mean and dispersion : 0.003376 0.086430 Skewness and kurtosis : 0.981720 9.147128 Sum and Sum*Dx*Dy*Dz* : 7293.953365 17.295910 Points per beam (map) : 1 N Robust : 2126873 Mean Robust : 0.001647 Sigma Robust : 0.076357 Median Robust : 0.001556 0/2160704 out-of-range points discarded LMTOY>> STATS Region_J-K_85776_85824.wt.ccd centerbox robust ### Warning [ccdsub]: Sampling will be done ### Warning [ccdsub]: Attempting to fix the WCS ### nemo Debug Info: WCS Corner: 10.6075 41.5549 0 Number of points : 3136 Min and Max : 24.703348 213.951019 Mean and dispersion : 153.340260 33.786649 Skewness and kurtosis : -1.122404 0.529042 Sum and Sum*Dx*Dy* : 480875.055098 -1.122413 Points per beam (map) : 1 N Robust : 3048 Mean Robust : 156.047925 Sigma Robust : 30.176982 Median Robust : 171.643593 0/3136 out-of-range points discarded ### nemo Debug Info: Keeping 111*111*689 cube ### Warning [ccdfits]: Replacing header from Region_J-K_85776_85824.wt.fits SLABS: [[-646,-396],[-196,54]] == -646,-396,-196,54 ### Warning [ccdslice]: axis=1 not fully supported yet ### nemo Debug Info: Axis: 689 0 53984.8 -1015.92 ### nemo Debug Info: Axis min/max: 53984.8 -644969 ### nemo Debug Info: slab -646 -396 -> 689 442 ### nemo Debug Info: slab -196 54 -> 246 0 ### nemo Debug Info: Total planes: 495 ### Warning [ccdslice]: Code not converted to fix reference pixel value ### Warning [ccdfits]: Replacing header from Region_J-K_85776_85824.wt.fits ### Warning [ccdfits]: Replacing header from Region_J-K_85776_85824.wt.fits ### Warning [ccdfits]: Replacing header from Region_J-K_85776_85824.fits QAC_STATS: Region_J-K_85776_85824-full 0.00332504 0.174278 -9.61546 9.99436 12492.6 0.033481 ### Warning [ccdsub]: Sampling will be done ### Warning [ccdsub]: Attempting to fix the WCS ### nemo Debug Info: WCS Corner: 10.6075 41.5549 53984.8 QAC_STATS: Region_J-K_85776_85824-cent 0.00337573 0.0864295 -0.661692 1.53926 7293.95 0.0519187 ### nemo Debug Info: FITS file: Image size 111 111 689 ### Warning [fitsccd]: Setting map minimum from 0 to -0.0535417 ### Warning [fitsccd]: Setting map maximum from 0 to 0.796385 ### nemo Debug Info: There were no blank values set in the image spectab : # 55 55 689 min/mean/sig/max -0.227619 0.00232415 0.073246 0.219847 0.000286626 0.0953485 0.920482 specstab: # 55 55 689 min/mean/sig/max -0.035546 0.00213711 0.0134542 0.0509412 1.59951e-05 0.00400475 0.210476 Traceback (most recent call last): File "/lma1/teuben/lmtoy/examples/fitsplot.py", line 21, in f = aplpy.FITSFigure(fitsfile) File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/decorators.py", line 28, in wrapper return f(*args, **kwargs) File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/core.py", line 232, in __init__ self._get_hdu(data, hdu, north, convention=convention, File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/core.py", line 309, in _get_hdu raise IOError("File not found: " + filename) OSError: File not found: Region_J-K_85776_85824.mom0.fits Traceback (most recent call last): File "/lma1/teuben/lmtoy/examples/fitsplot.py", line 21, in f = aplpy.FITSFigure(fitsfile) File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/decorators.py", line 28, in wrapper return f(*args, **kwargs) File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/core.py", line 232, in __init__ self._get_hdu(data, hdu, north, convention=convention, File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/core.py", line 309, in _get_hdu raise IOError("File not found: " + filename) OSError: File not found: Region_J-K_85776_85824.mom1.fits Traceback (most recent call last): File "/lma1/teuben/lmtoy/examples/fitsplot.py", line 21, in f = aplpy.FITSFigure(fitsfile) File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/decorators.py", line 28, in wrapper return f(*args, **kwargs) File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/core.py", line 232, in __init__ self._get_hdu(data, hdu, north, convention=convention, File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/core.py", line 309, in _get_hdu raise IOError("File not found: " + filename) OSError: File not found: Region_J-K_85776_85824.mom2.fits INFO: Auto-setting vmin to -2.298e+01 [aplpy.core] INFO: Auto-setting vmax to 2.268e+02 [aplpy.core] INFO: Auto-setting vmin to -2.342e+01 [aplpy.core] INFO: Auto-setting vmax to 2.300e+02 [aplpy.core] Writing Region_J-K_85776_85824.wt.png INFO: Auto-setting vmin to -2.420e+01 [aplpy.core] INFO: Auto-setting vmax to 2.686e+02 [aplpy.core] INFO: Auto-setting vmin to -2.468e+01 [aplpy.core] INFO: Auto-setting vmax to 2.740e+02 [aplpy.core] Writing Region_J-K_85776_85824.wt2.png INFO: Auto-setting vmin to -2.492e+03 [aplpy.core] INFO: Auto-setting vmax to 2.766e+04 [aplpy.core] INFO: Auto-setting vmin to -1.061e+03 [aplpy.core] INFO: Auto-setting vmax to 1.177e+04 [aplpy.core] Writing Region_J-K_85776_85824.wt3.png Traceback (most recent call last): File "/lma1/teuben/lmtoy/examples/fitsplot.py", line 21, in f = aplpy.FITSFigure(fitsfile) File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/decorators.py", line 28, in wrapper return f(*args, **kwargs) File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/core.py", line 232, in __init__ self._get_hdu(data, hdu, north, convention=convention, File "/lma1/teuben/lmtoy/anaconda3/lib/python3.8/site-packages/aplpy/core.py", line 309, in _get_hdu raise IOError("File not found: " + filename) OSError: File not found: Region_J-K_85776_85824.wtn.fits INFO: Auto-setting vmin to -1.107e-01 [aplpy.core] INFO: Auto-setting vmax to 1.229e+00 [aplpy.core] INFO: Auto-setting vmin to -1.111e-01 [aplpy.core] INFO: Auto-setting vmax to 1.234e+00 [aplpy.core] Writing Region_J-K_85776_85824.wtr.png WARNING: FITSFixedWarning: RADECSYS= 'FK5 ' / the RADECSYS keyword is deprecated, use RADESYSa. [astropy.wcs.wcs] INFO: Setting slices=[0] [aplpy.core] INFO: Auto-setting vmin to -4.624e+03 [aplpy.core] INFO: Auto-setting vmax to 1.577e+04 [aplpy.core] INFO: Auto-setting vmin to -4.867e+03 [aplpy.core] INFO: Auto-setting vmax to 1.721e+04 [aplpy.core] Writing Region_J-K_85776_85824.mom0.png LMTOY>> Created Region_J-K_85776_85824.nf.fits and Region_J-K_85776_85824.nfs.fits LMTOY>> ADMIT post-processing LMTOY>> lmtoy_admit: 31-oct-2021 /lma1/teuben/lmtoy/examples/lmtoy_admit.sh: line 33: export: `Region_J-K_85776_85824.nfs.fits': not a valid identifier No PDIR directory used, all work in the current directory ADMIT = /lma1/teuben/lmtoy/admit version = 1.0.8.5 CASA_PATH = /n/astromake/opt/casa/58 linux admit lma.astro.umd.edu CASA_ROOT = /n/astromake/opt/casa/58 prefix = /an/terra_astromake/opt/casa/casa-release-5.8.0-109.el7 version = 5.8.0-rel-109 revision = 1 Trying CASA6, no worries if this fails Traceback (most recent call last): File "", line 1, in ImportError: No module named casatools LMTOY>> ADMIT post-processing Found 33 Xvfb 1260405 Sl Xvfb 1258093 Sl Xvfb 1256822 Sl Xvfb 1256146 Sl Xvfb ### (1/1) : processing Region_J-K_85776_85824.nfs.fits Region_J-K_85776_85824.nfs.fits [111, 111, 689] Region_J-K 10.64875 41.5137 5.398476e-05 0.032 /lma1/teuben/lmtoy/admit/admit/test/admit1.py --basename x Region_J-K_85776_85824.nfs.fits 134.179u 4.103s 2:41.78 85.4% 0+0k 704+328552io 0pf+0w Logfile: Region_J-K_85776_85824.nfs.fits.log LMTOY>> lmtoy_admit: 31-oct-2021 /lma1/teuben/lmtoy/examples/lmtoy_admit.sh: line 33: export: `Region_J-K_85776_85824.nf.fits': not a valid identifier No PDIR directory used, all work in the current directory ADMIT = /lma1/teuben/lmtoy/admit version = 1.0.8.5 CASA_PATH = /n/astromake/opt/casa/58 linux admit lma.astro.umd.edu CASA_ROOT = /n/astromake/opt/casa/58 prefix = /an/terra_astromake/opt/casa/casa-release-5.8.0-109.el7 version = 5.8.0-rel-109 revision = 1 Trying CASA6, no worries if this fails Traceback (most recent call last): File "", line 1, in ImportError: No module named casatools LMTOY>> ADMIT post-processing ### (1/1) : processing Region_J-K_85776_85824.nf.fits Region_J-K_85776_85824.nf.fits [111, 111, 689] Region_J-K 10.64875 41.5137 5.398476e-05 0.032 /lma1/teuben/lmtoy/admit/admit/test/admit1.py --basename x Region_J-K_85776_85824.nf.fits 66.515u 2.453s 1:20.94 85.1% 0+0k 312+190872io 0pf+0w Logfile: Region_J-K_85776_85824.nf.fits.log LMTOY>> Created Region_J-K_85776_85824.fits and Region_J-K_85776_85824.wt.fits LMTOY>> Parameter file used: 2018-S1-MU-46/85776/lmtoy_85776.rc LMTOY>> Making summary index.html: Making index.html for obsnum=85776_85824 Region_J-K_85776_85824_? Region_J-K_85776_85824_?_specviews Region_J-K_85776_85824_?_specpoint Writing index.html Writing index_pipeline.html cp: cannot stat 'Region_J-K_85776_85824_?_specviews.1.png': No such file or directory LMTOY>> Created Region_J-K_85776_85824.fits and Region_J-K_85776_85824.wt.fits LMTOY>> Parameter file used: 2018-S1-MU-46/85776/lmtoy_85776.rc