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: 90911 OBSNUMS: 90911,91112 OBSNUMS1: 90911 91112 90911 : 1 2018-S1-MU-8/90911/lmtoy_90911.rc 91112 : 1 2018-S1-MU-8/91112/lmtoy_91112.rc First RC will be used : 2018-S1-MU-8/90911/lmtoy_90911.rc Using pdir=2018-S1-MU-8/90911_91112 src=NGC5194 ONS: 2018-S1-MU-8/90911/NGC5194_90911.nc 2018-S1-MU-8/91112/NGC5194_91112.nc OBSNUM range: 90911 91112 FILES: s_nc: ../../2018-S1-MU-8/90911/NGC5194_90911.nc,../../2018-S1-MU-8/91112/NGC5194_91112.nc LMTOY>> grid_data {'--cell': '5.5', '--edge': '0', '--help': False, '--input': '../../2018-S1-MU-8/90911/NGC5194_90911.nc,../../2018-S1-MU-8/91112/NGC5194_91112.nc', '--n_samples': '256', '--noise_sigma': '1', '--otf_a': '1.1', '--otf_b': '4.75', '--otf_c': '2', '--otf_select': '1', '--output': 'NGC5194_90911_91112.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': 'NGC5194_90911_91112.wt.fits', '--x_extent': '420', '--y_extent': '600'} STDOUT **************************** spec_driver_fits LMTSLR 26-jan-2022 CMD: spec_driver_fits -i ../../2018-S1-MU-8/90911/NGC5194_90911.nc,../../2018-S1-MU-8/91112/NGC5194_91112.nc -o NGC5194_90911_91112.fits -w NGC5194_90911_91112.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 420 -y 600 -f 1 -r 3 -n 256 -0 1.1 -1 4.75 -2 2 -b -1 -e 0 file list=../../2018-S1-MU-8/90911/NGC5194_90911.nc,../../2018-S1-MU-8/91112/NGC5194_91112.nc DEBUG:5.5 sample_list=-1 Warning: sample list is not a multiple of 3 nsamples=1 Processing 2 SpecFiles: Opening SpecFile file ../../2018-S1-MU-8/90911/NGC5194_90911.nc file: ../../2018-S1-MU-8/90911/NGC5194_90911.nc nspec= 385449 nchan= 590 SpecFile version 6-mar-2021 X-range: -303.534 312.059 Y-range: -393.326 394.785 arcsec X-ramp: -220.134 228.659 Y-ramp: -309.926 311.385 arcsec MapSize: 615.593 x 788.111 arcsec 90911 NGC5194 DATE-OBS 2020-02-18T01:08:47 CF.n_cells= 7 delta=0.129412 cell=5.5 resol=11 oft_select=1 WARNING: code is not working for non-square sizesC-AXIS 2 starts at 799.778 C-AXIS 1 starts at -599.5 C-AXIS 0 starts at -418 P-AXIS 1 starts at -599.5 P-AXIS 0 starts at -418 P-AXIS 1 starts at -599.5 P-AXIS 0 starts at -418 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=385449 rms_cutoff=4 Warning: no pixels found for pixel 1 Opening SpecFile file ../../2018-S1-MU-8/91112/NGC5194_91112.nc file: ../../2018-S1-MU-8/91112/NGC5194_91112.nc nspec= 340024 nchan= 590 SpecFile version 6-mar-2021 X-range: -308.02 298.975 Y-range: -397.885 397.905 arcsec X-ramp: -224.62 215.575 Y-ramp: -314.485 314.505 arcsec MapSize: 606.995 x 795.79 arcsec rms_stats: n=340024 rms_cutoff=4 Warning: no pixels found for pixel 0 Warning: no pixels found for pixel 5 Cube Completed, 725473/725473 Spectra accepted = 1.000 Weighting Completed, fuzzy_edge=0 Weight at 0.000000 0.000000 is 67.659973 write to NGC5194_90911_91112.fits write weights to NGC5194_90911_91112.wt.fits STDERR **************************** Exit Code: 0 LMTOY>> Some NEMO post-processing ### nemo Debug Info: FITS file: Image size 153 219 590 ### Warning [fitsccd]: Setting map minimum from 0 to -5.79876 ### Warning [fitsccd]: Setting map maximum from 0 to 5.74136 ### nemo Debug Info: There were 11248350 blank values in the image (56.898559 %) ### nemo Debug Info: FITS file: Image size 153 219 ### Warning [fitsccd]: Setting map minimum from 0 to -1.59392 ### Warning [fitsccd]: Setting map maximum from 0 to 95.8092 ### nemo Debug Info: There were no blank values set in the image LMTOY>> STATS NGC5194_90911_91112.ccd centerbox robust ### Warning [ccdsub]: Sampling will be done ### Warning [ccdsub]: Attempting to fix the WCS ### nemo Debug Info: WCS Corner: 202.413 47.2777 799778 Number of points : 3515810 Min and Max : -5.798763 5.741362 Mean and dispersion : -0.004307 0.168156 Skewness and kurtosis : 0.103173 19.681311 Sum and Sum*Dx*Dy*Dz* : -15140.986815 -35.903321 Points per beam (map) : 1 N Robust : 3395733 Mean Robust : -0.006136 Sigma Robust : 0.127726 Median Robust : -0.006578 1546390/5062200 out-of-range points discarded LMTOY>> STATS NGC5194_90911_91112.wt.ccd centerbox robust ### Warning [ccdsub]: Sampling will be done ### Warning [ccdsub]: Attempting to fix the WCS ### nemo Debug Info: WCS Corner: 202.413 47.2777 0 Number of points : 6826 Min and Max : -0.943725 79.938065 Mean and dispersion : 47.106310 25.568816 Skewness and kurtosis : -0.809482 -0.922835 Sum and Sum*Dx*Dy* : 321547.672537 -0.750526 Points per beam (map) : 1 N Robust : 6826 Mean Robust : 47.106310 Sigma Robust : 25.568816 Median Robust : 64.345860 1754/8580 out-of-range points discarded ### nemo Debug Info: Keeping 153*219*590 cube ### Warning [ccdfits]: Replacing header from NGC5194_90911_91112.wt.fits SLABS: [[113,363],[563,813]] == 113,363,563,813 ### Warning [ccdslice]: axis=1 not fully supported yet ### nemo Debug Info: Axis: 590 0 799778 -1015.92 ### nemo Debug Info: Axis min/max: 799778 201400 ### nemo Debug Info: slab 113 363 -> 676 429 ### nemo Debug Info: slab 563 813 -> 233 -13 ### nemo Debug Info: Total planes: 495 ### Warning [ccdslice]: Code not converted to fix reference pixel value ### Fatal error [ccdslice]: 591: illegal plane in z, max is 590 /lma1/teuben/lmtoy/examples/lmtoy_functions.sh: line 169: 2317174 Exit 255 ccdslice $s_on.ccd - zslabs=$zslabs zscale=1000 2317175 Segmentation fault (core dumped) | ccdmom - - mom=-2 2317176 Segmentation fault (core dumped) | ccdmath - $s_on.wt3.ccd "ifne(%1,0,1/(%1*%1),0)" ### Fatal error [ccdfits]: Cannot process image select=0 /lma1/teuben/lmtoy/examples/lmtoy_functions.sh: line 169: 2317190 Segmentation fault (core dumped) ccdmath $s_on.wt2.ccd,$s_on.wt3.ccd $s_on.wtr.ccd %2/%1 ### Fatal error [ccdfits]: Cannot process image select=0 ### Warning [ccdfits]: Replacing header from NGC5194_90911_91112.fits QAC_STATS: NGC5194_90911_91112-full -0.00681114 0.161993 -5.79876 5.74136 -58036.2 -0.0591619 ### Warning [ccdsub]: Sampling will be done ### Warning [ccdsub]: Attempting to fix the WCS ### nemo Debug Info: WCS Corner: 202.413 47.2777 799778 QAC_STATS: NGC5194_90911_91112-cent -0.00430654 0.168156 -5.79876 5.74136 -15141 -0.0367413 ### nemo Debug Info: FITS file: Image size 153 219 590 ### Warning [fitsccd]: Setting map minimum from 0 to -0.0717913 ### Warning [fitsccd]: Setting map maximum from 0 to 0.61395 ### nemo Debug Info: There were no blank values set in the image spectab : # 76 109 590 min/mean/sig/max -0.478672 -0.00565754 0.116066 0.333408 -0.00011581 0.164564 1.00257 specstab: # 76 109 590 min/mean/sig/max -0.0463833 -0.00711429 0.0128377 0.0318878 -7.3077e-07 0.00439339 0.24199 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: NGC5194_90911_91112.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: NGC5194_90911_91112.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: NGC5194_90911_91112.mom2.fits INFO: Auto-setting vmin to -8.532e+00 [aplpy.core] INFO: Auto-setting vmax to 9.199e+01 [aplpy.core] INFO: Auto-setting vmin to -8.601e+00 [aplpy.core] INFO: Auto-setting vmax to 9.225e+01 [aplpy.core] Writing NGC5194_90911_91112.wt.png INFO: Auto-setting vmin to -1.086e+01 [aplpy.core] INFO: Auto-setting vmax to 1.205e+02 [aplpy.core] INFO: Auto-setting vmin to -1.034e+01 [aplpy.core] INFO: Auto-setting vmax to 1.147e+02 [aplpy.core] Writing NGC5194_90911_91112.wt2.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: NGC5194_90911_91112.wt3.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: NGC5194_90911_91112.wtn.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: NGC5194_90911_91112.wtr.fits 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 -1.734e+04 [aplpy.core] INFO: Auto-setting vmax to 2.726e+04 [aplpy.core] INFO: Auto-setting vmin to -1.777e+04 [aplpy.core] INFO: Auto-setting vmax to 2.761e+04 [aplpy.core] Writing NGC5194_90911_91112.mom0.png LMTOY>> Created NGC5194_90911_91112.nf.fits and NGC5194_90911_91112.nfs.fits LMTOY>> ADMIT post-processing LMTOY>> lmtoy_admit: 31-oct-2021 /lma1/teuben/lmtoy/examples/lmtoy_admit.sh: line 33: export: `NGC5194_90911_91112.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 ### (1/1) : processing NGC5194_90911_91112.nfs.fits NGC5194_90911_91112.nfs.fits [153, 219, 590] NGC5194 202.4696 47.19517 0.0007997778 0.074 /lma1/teuben/lmtoy/admit/admit/test/admit1.py --basename x NGC5194_90911_91112.nfs.fits 90.820u 3.550s 1:49.17 86.4% 0+0k 9968+511976io 0pf+0w Logfile: NGC5194_90911_91112.nfs.fits.log LMTOY>> lmtoy_admit: 31-oct-2021 /lma1/teuben/lmtoy/examples/lmtoy_admit.sh: line 33: export: `NGC5194_90911_91112.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 Found 33 Xvfb 1346223 Sl Xvfb 1345275 Sl Xvfb 1344686 Sl Xvfb 1343197 Sl Xvfb ### (1/1) : processing NGC5194_90911_91112.nf.fits NGC5194_90911_91112.nf.fits [153, 219, 590] NGC5194 202.4696 47.19517 0.0007997778 0.074 /lma1/teuben/lmtoy/admit/admit/test/admit1.py --basename x NGC5194_90911_91112.nf.fits 65.731u 2.519s 1:19.82 85.4% 0+0k 312+418760io 0pf+0w Logfile: NGC5194_90911_91112.nf.fits.log LMTOY>> Created NGC5194_90911_91112.fits and NGC5194_90911_91112.wt.fits LMTOY>> Parameter file used: 2018-S1-MU-8/90911/lmtoy_90911.rc LMTOY>> Making summary index.html: Making index.html for obsnum=90911_91112 NGC5194_90911_91112_? NGC5194_90911_91112_?_specviews NGC5194_90911_91112_?_specpoint Writing index.html Writing index_pipeline.html cp: cannot stat 'NGC5194_90911_91112_?_specviews.1.png': No such file or directory LMTOY>> Created NGC5194_90911_91112.fits and NGC5194_90911_91112.wt.fits LMTOY>> Parameter file used: 2018-S1-MU-8/90911/lmtoy_90911.rc