LMTOY>> seq_pipeline: 2-feb-2022
LMTOY>> READING lmtoy_functions 24-dec-2021 via /lma1/teuben/lmtoy/examples/seq_pipeline.sh
Working directory ./2018-S1-MU-8/90911
LMTOY>> Hang on, creating a bootstrap lmtoy_90911.rc from path=/n/lma1/lmt/data_lmt/
#
# version=2-feb-2022
# ifproc="/n/lma1/lmt/data_lmt//ifproc/ifproc_2020-02-18_090911_00_0001.nc"
date_obs="2020-02-18T01:08:47"
# skytime=3985.9 sec
# inttime=3070.28 sec
obsnum="90911"
calobsnum="90910"
obspgm="Map"
obsgoal="Science"
ProjectId="2018-S1-MU-8"
# SkyOff=720 0
# HPBW=12 arcsec
# XYLength=420 600 arcsec
# XYRamp=48 48 arcsec
# XYoff=0 0 arcsec
# XYstep=1 0.5
numbands=1
vlsr=463 # km/s
skyfreq=115.10133326844131 # GHz
restfreq=115.271204 # Ghz
src="NGC5194"
resolution=11 # arcsec
cell=5.5 # arcsec
x_extent=420 # arcsec
y_extent=600 # arcsec
instrument="SEQ"
#
LMTOY>> this is your startup lmtoy_90911.rc file:
# seq_pipeline: 2-feb-2022
# DATE: 2022-02-03T22:00:24.606632054
# obsnum=90911
# Using ifproc=/n/lma1/lmt/data_lmt//ifproc/ifproc_2020-02-18_090911_00_0001.nc
# path=/n/lma1/lmt/data_lmt/
#
# version=2-feb-2022
# ifproc="/n/lma1/lmt/data_lmt//ifproc/ifproc_2020-02-18_090911_00_0001.nc"
date_obs="2020-02-18T01:08:47"
# skytime=3985.9 sec
# inttime=3070.28 sec
obsnum="90911"
calobsnum="90910"
obspgm="Map"
obsgoal="Science"
ProjectId="2018-S1-MU-8"
# SkyOff=720 0
# HPBW=12 arcsec
# XYLength=420 600 arcsec
# XYRamp=48 48 arcsec
# XYoff=0 0 arcsec
# XYstep=1 0.5
numbands=1
vlsr=463 # km/s
skyfreq=115.10133326844131 # GHz
restfreq=115.271204 # Ghz
src="NGC5194"
resolution=11 # arcsec
cell=5.5 # arcsec
x_extent=420 # arcsec
y_extent=600 # arcsec
instrument="SEQ"
#
# based on vlsr=463, dv=100, dw=250
b_order=0
b_regions=[[113,363],[563,813]]
l_regions=[[363,563]]
slice=[113,813]
v_range=363,563
pix_list=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15
rmax=3
otf_a=1.1
otf_b=4.75
otf_c=2
sample=-1
otf_cal=0
edge=0
LMTOY>> Sleeping for 5 seconds, you can abort, edit lmtoy_90911.rc, then continuing
LMTOY>> process_otf_map2 in 2 seconds
{'--b_order': '0',
'--b_regions': '[[200,380],[580,670]]',
'--bank': '0',
'--eliminate_list': '0',
'--help': False,
'--l_regions': '[400,600]',
'--obsnum': '90911',
'--output': 'NGC5194_90911.nc',
'--path': '/n/lma1/lmt/data_lmt/',
'--pix_list': '0,2,3,4,5,6,7,8,9,10,11,12,13,14,15',
'--restfreq': None,
'--sample': None,
'--save_tsys': False,
'--slice': '[200,800]',
'--stype': '2',
'--tsys': '250.0',
'--use_cal': True,
'--use_otf_cal': False,
'--x_axis': 'VLSR'}
program process_otf_map options
bank = 0
tsys = 250.0
b_order = 0
output = NGC5194_90911.nc
use_cal = True
eliminate_list = [0]
stype = 2
b_regions = [[200, 380], [580, 670]]
output_file_name = NGC5194_90911.nc
x_axis = VLSR
use_otf_cal = False
slice = [200, 800]
pix_list = [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
l_regions = [400, 600]
data_path = /n/lma1/lmt/data_lmt/
path = /n/lma1/lmt/data_lmt/
obsnum = 90911
2020-02-18T01:08:47 begin /n/lma1/lmt/data_lmt/ifproc/ifproc_2020-02-18_090911_00_0001.nc
2020-02-18T02:15:13 end /n/lma1/lmt/data_lmt/ifproc/ifproc_2020-02-18_090911_00_0001.nc
BufPos 1 17.9 sec 90911
BufPos 0 49.0 sec 90911
BufPos 1 17.8 sec 90911
BufPos 0 49.7 sec 90911
BufPos 1 17.0 sec 90911
BufPos 0 49.9 sec 90911
BufPos 1 18.2 sec 90911
BufPos 0 49.6 sec 90911
BufPos 1 18.5 sec 90911
BufPos 0 49.6 sec 90911
BufPos 1 18.6 sec 90911
BufPos 0 49.7 sec 90911
BufPos 1 17.4 sec 90911
BufPos 0 49.3 sec 90911
BufPos 1 17.5 sec 90911
BufPos 0 49.8 sec 90911
BufPos 1 18.6 sec 90911
BufPos 0 49.4 sec 90911
BufPos 1 17.5 sec 90911
BufPos 0 49.1 sec 90911
BufPos 1 16.9 sec 90911
BufPos 0 49.6 sec 90911
BufPos 1 19.4 sec 90911
BufPos 0 49.2 sec 90911
BufPos 1 17.7 sec 90911
BufPos 0 49.8 sec 90911
BufPos 1 19.1 sec 90911
BufPos 0 50.0 sec 90911
BufPos 1 17.4 sec 90911
BufPos 0 49.6 sec 90911
BufPos 1 17.8 sec 90911
BufPos 0 49.8 sec 90911
BufPos 1 17.8 sec 90911
BufPos 0 49.0 sec 90911
BufPos 1 17.6 sec 90911
BufPos 0 49.3 sec 90911
BufPos 1 17.3 sec 90911
BufPos 0 49.2 sec 90911
BufPos 1 18.2 sec 90911
BufPos 0 49.8 sec 90911
BufPos 1 17.6 sec 90911
BufPos 0 49.7 sec 90911
BufPos 1 17.4 sec 90911
BufPos 0 49.8 sec 90911
BufPos 1 17.8 sec 90911
BufPos 0 49.3 sec 90911
BufPos 1 17.8 sec 90911
BufPos 0 50.0 sec 90911
BufPos 1 18.4 sec 90911
BufPos 0 49.6 sec 90911
BufPos 1 18.5 sec 90911
BufPos 0 49.5 sec 90911
BufPos 1 17.5 sec 90911
BufPos 0 49.5 sec 90911
BufPos 1 17.6 sec 90911
BufPos 0 50.2 sec 90911
BufPos 1 18.5 sec 90911
BufPos 0 50.2 sec 90911
BufPos 1 18.5 sec 90911
BufPos 0 50.1 sec 90911
BufPos 1 18.7 sec 90911
BufPos 0 50.6 sec 90911
BufPos 1 18.7 sec 90911
BufPos 0 49.9 sec 90911
BufPos 1 17.2 sec 90911
BufPos 0 50.5 sec 90911
BufPos 1 17.8 sec 90911
BufPos 0 50.0 sec 90911
BufPos 1 18.5 sec 90911
BufPos 0 49.8 sec 90911
BufPos 1 19.2 sec 90911
BufPos 0 50.1 sec 90911
BufPos 1 18.0 sec 90911
BufPos 0 50.2 sec 90911
BufPos 1 19.5 sec 90911
BufPos 0 49.9 sec 90911
BufPos 1 18.3 sec 90911
BufPos 0 49.8 sec 90911
BufPos 1 19.2 sec 90911
BufPos 0 49.5 sec 90911
BufPos 1 17.6 sec 90911
BufPos 0 49.8 sec 90911
BufPos 1 18.3 sec 90911
BufPos 0 49.6 sec 90911
BufPos 1 17.7 sec 90911
BufPos 0 49.7 sec 90911
BufPos 1 18.2 sec 90911
BufPos 0 49.7 sec 90911
BufPos 1 17.3 sec 90911
BufPos 0 50.0 sec 90911
BufPos 1 18.2 sec 90911
BufPos 0 51.1 sec 90911
BufPos 1 16.9 sec 90911
BufPos 0 49.3 sec 90911
BufPos 1 17.2 sec 90911
BufPos 0 50.0 sec 90911
BufPos 1 17.0 sec 90911
BufPos 0 49.8 sec 90911
BufPos 1 17.5 sec 90911
BufPos 0 49.6 sec 90911
BufPos 1 17.9 sec 90911
BufPos 0 49.5 sec 90911
BufPos 1 16.9 sec 90911
BufPos 0 49.6 sec 90911
BufPos 1 18.4 sec 90911
BufPos 0 50.3 sec 90911
BufPos 1 18.5 sec 90911
BufPos 0 50.6 sec 90911
BufPos 1 17.9 sec 90911
BufPos 0 51.3 sec 90911
BufPos 1 16.9 sec 90911
BufPos 0 50.6 sec 90911
BufPos 1 18.2 sec 90911
BufPos 0 49.9 sec 90911
BufPos 1 18.1 sec 90911
BufPos 0 50.0 sec 90911
BufPos 1 17.5 sec 90911
BufPos 0 26.5 sec 90911
BufPos 1 12.0 sec 90911
before read npix
from pixels npix = 16
from xlen npix = 16
Map Parameters: Ra Continuous
HPBW= 12.0 XLength= 420.0 YLength= 600.0 XStep= 1.00 YStep= 0.50
/n/lma1/lmt/data_lmt/ifproc/ifproc_2020-02-18_090911_00_0001.nc does not have bs parameters
90911 is a Map observation
get chop
'Data.Msip1mm.BeamChopperActPos'
no chop
2020-02-18T01:08:23 begin /n/lma1/lmt/data_lmt/ifproc/ifproc_2020-02-18_090910_00_0001.nc
2020-02-18T01:08:30 end /n/lma1/lmt/data_lmt/ifproc/ifproc_2020-02-18_090910_00_0001.nc
BufPos 3 4.5 sec 90910
BufPos 2 2.6 sec 90910
before read npix
from pixels npix = 16
from xlen npix = 16
/n/lma1/lmt/data_lmt/ifproc/ifproc_2020-02-18_090910_00_0001.nc does not have map parameters
/n/lma1/lmt/data_lmt/ifproc/ifproc_2020-02-18_090910_00_0001.nc does not have bs parameters
90910 is a Cal observation
get chop cal
'Data.Msip1mm.BeamChopperActPos'
no chop cal
read_roach /n/lma1/lmt/data_lmt/spectrometer/roach0/roach0_90911_0_1_NGC5194_2020-02-18_060841.nc nspec,nchan=132084,2048
r:0 inp:0 pix:0 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_90911_0_1_NGC5194_2020-02-18_060841.nc nspec,nchan=132316,2048
r:1 inp:0 pix:4 time_offset:-0.030000
r:1 inp:1 pix:5 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_90911_0_1_NGC5194_2020-02-18_060841.nc nspec,nchan=132640,2048
r:2 inp:0 pix:8 time_offset:-0.030000
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_90911_0_1_NGC5194_2020-02-18_060841.nc nspec,nchan=132904,2048
r:3 inp:0 pix:12 time_offset:-0.030000
r:3 inp:1 pix:13 time_offset:-0.030000
r:3 inp:2 pix:14 time_offset:-0.030000
r:3 inp:3 pix:15 time_offset:-0.030000
RESTFREQ 115.271 GHz
read_roach /n/lma1/lmt/data_lmt/spectrometer/roach0/roach0_90910_0_1_NGC5194_2020-02-18_060822.nc nspec,nchan=232,2048
r:0 inp:0 pix:0 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_90910_0_1_NGC5194_2020-02-18_060823.nc nspec,nchan=236,2048
r:1 inp:0 pix:4 time_offset:-0.030000
r:1 inp:1 pix:5 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_90910_0_1_NGC5194_2020-02-18_060823.nc nspec,nchan=240,2048
r:2 inp:0 pix:8 time_offset:-0.030000
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_90910_0_1_NGC5194_2020-02-18_060823.nc nspec,nchan=248,2048
r:3 inp:0 pix:12 time_offset:-0.030000
r:3 inp:1 pix:13 time_offset:-0.030000
r:3 inp:2 pix:14 time_offset:-0.030000
r:3 inp:3 pix:15 time_offset:-0.030000
TSYS[0] = 257.833 +/- 16.7771 (2048 channels)
TSYS[2] = 218.589 +/- 13.8186 (2048 channels)
TSYS[3] = 209.611 +/- 12.3329 (2048 channels)
TSYS[4] = 224.189 +/- 15.9483 (2048 channels)
TSYS[5] = 217.622 +/- 14.3344 (2048 channels)
TSYS[6] = 250.724 +/- 20.2376 (2048 channels)
TSYS[7] = 217.779 +/- 13.503 (2048 channels)
TSYS[8] = 208.746 +/- 13.3191 (2048 channels)
TSYS[9] = 220.078 +/- 12.0222 (2048 channels)
TSYS[10] = 215.084 +/- 13.0186 (2048 channels)Traceback (most recent call last):
File "/lma1/teuben/lmtoy/SpectralLineReduction/lmtslr/ifproc/ifproc.py", line 536, 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 667, 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: divide by zero encountered in true_divide
self.tsys_spectrum = 280 * sky_spectrum / (hot_spectrum -
/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: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[11] = 216.84 +/- 13.7669 (2048 channels)
TSYS[12] = 202.833 +/- 11.6843 (2048 channels)
TSYS[13] = 244.095 +/- 12.3134 (2048 channels)
TSYS[14] = 227.456 +/- 12.7194 (2048 channels)
TSYS[15] = 227.513 +/- 14.6906 (2048 channels)
Spectral Band velocity range: -576.795 1502.8 km/s
Total Number of OTF Spectra = 385449
NSPEC: 385449
NCHAN: 590
FAST_NC: True
Looping over 15 pixel list [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]:
Processing 1 CAL's for Tsys
Pix Nspec Mean Std MAD_std Min Max RMS_max Warnings
TSYS[0] slice: 257.08 (5.22686) minmax: 249.202 269.378
0 25699 0.022 1.373 1.360 -7.897 8.940 1.357 1.836 *M 1.3
TSYS[2] slice: 220.526 (3.52672) minmax: 213.859 227.291
2 25699 -0.100 1.296 1.201 -9.516 7.483 1.191 2.193 *M 3.3
TSYS[3] slice: 208.749 (3.19341) minmax: 202.97 215.456
3 25699 -0.042 1.142 1.114 -7.690 6.695 1.114 1.761 *M 2.2
TSYS[4] slice: 225.146 (4.58657) minmax: 217.026 235.398
4 25695 0.014 1.218 1.198 -7.375 7.483 1.196 2.043 *M 2.3
TSYS[5] slice: 217.586 (3.5062) minmax: 211.509 224.945
5 25695 -0.043 1.174 1.161 -8.471 6.680 1.160 2.036 *M 2.3
TSYS[6] slice: 250.683 (5.31041) minmax: 241.202 260.932
6 25695 -0.047 1.406 1.347 -10.791 8.534 1.368 2.856 *M 4.2
TSYS[7] slice: 218.013 (3.91629) minmax: 210.936 226.053
7 25695 -0.035 1.174 1.156 -8.099 6.259 1.152 1.801 *M 1.9
TSYS[8] slice: 208.831 (3.86701) minmax: 202.084 216.587
8 25695 -0.012 1.112 1.102 -7.196 6.668 1.118 2.036 *M 2.8
TSYS[9] slice: 219.754 (3.55822) minmax: 213.565 227.771
9 25695 -0.054 1.203 1.174 -8.363 6.355 1.175 1.999 *M 2.6
TSYS[10] slice: 214.634 (3.82335) minmax: 207.856 222.456
10 25695 -0.091 1.297 1.165 -11.226 7.241 1.165 2.148 *M 3.5
TSYS[11] slice: 216.839 (4.01409) minmax: 209.805 224.984
11 25695 -0.028 1.184 1.157 -8.025 7.313 1.163 2.057 *M 2.8
TSYS[12] slice: 202.221 (2.94791) minmax: 196.94 209.374
12 25698 -0.002 1.076 1.067 -6.366 6.838 1.064 1.446 *M 1.3
TSYS[13] slice: 243.527 (3.90396) minmax: 236.639 252.284
13 25698 -0.084 1.398 1.324 -10.089 8.798 1.342 3.100 *M 5.1
TSYS[14] slice: 226.638 (3.32687) minmax: 220.841 234.252
14 25698 -0.056 1.300 1.220 -10.685 7.704 1.211 2.000 *M 2.2
TSYS[15] slice: 226.878 (3.93238) minmax: 220.271 235.276
15 25698 -0.016 1.241 1.212 -8.713 8.023 1.231 2.287 *M 3.3
CPU TIME: 193.406 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': 'NGC5194_90911.nc',
'--pix_list': '0,2,3,4,5,6,7,8,9,10,11,12,13,14,15',
'--plot_range': '-1,3',
'--plots': 'NGC5194_90911_specviews',
'--rms_cut': '-4',
'--show_pixel': None,
'--skip_tsys': False}
SLR Plots initialized with 1 method=NGC5194_90911_specviews
Max sequence=25699
Plots saving in NGC5194_90911_specviews.1.png
Plots saving in NGC5194_90911_specviews.2.png
Plots saving in NGC5194_90911_specviews.3.png
Plots saving in NGC5194_90911_specviews.4.png
Plots saving in NGC5194_90911_specviews.5.png
NEW TSYS PIC
SHAPE (1, 15, 590)
PIXEL: 0 [ 0 1 2 ... 25696 25697 25698]
PIXEL: 2 [25699 25700 25701 ... 51395 51396 51397]
PIXEL: 3 [51398 51399 51400 ... 77094 77095 77096]
PIXEL: 4 [ 77097 77098 77099 ... 102789 102790 102791]
PIXEL: 5 [102792 102793 102794 ... 128484 128485 128486]
PIXEL: 6 [128487 128488 128489 ... 154179 154180 154181]
PIXEL: 7 [154182 154183 154184 ... 179874 179875 179876]
PIXEL: 8 [179877 179878 179879 ... 205569 205570 205571]
PIXEL: 9 [205572 205573 205574 ... 231264 231265 231266]
PIXEL: 10 [231267 231268 231269 ... 256959 256960 256961]
PIXEL: 11 [256962 256963 256964 ... 282654 282655 282656]
PIXEL: 12 [282657 282658 282659 ... 308352 308353 308354]
PIXEL: 13 [308355 308356 308357 ... 334050 334051 334052]
PIXEL: 14 [334053 334054 334055 ... 359748 359749 359750]
PIXEL: 15 [359751 359752 359753 ... 385446 385447 385448]
Plots saving in NGC5194_90911_specviews.6.png
/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=NGC5194_90911_specpoint,png,1
MAD: 0 1.3451263 0.06383157966586372 1.6004525899113187
MAD: 2 1.1504134 0.0550410644168721 1.3705776516417927
MAD: 3 1.0898638 0.05176872411015718 1.2969386736012734
MAD: 4 1.175205 0.05521621371441217 1.3960698471519601
MAD: 5 1.1365587 0.05429133351862286 1.3537239859986248
MAD: 6 1.3084797 0.06282557582974051 1.559781970028862
MAD: 7 1.1346782 0.053486813233655735 1.3486254975253822
MAD: 8 1.091265 0.051930087691039205 1.2989853139141811
MAD: 9 1.1455125 0.05484364588473056 1.3648870452012147
MAD: 10 1.12184 0.052889962398345106 1.3333998497459683
MAD: 11 1.1309632 0.05373955137238662 1.3459214117807452
MAD: 12 1.0577605 0.04949231346200767 1.2557297309140707
MAD: 13 1.2699555 0.060842465140488834 1.5133253764234667
MAD: 14 1.1852347 0.05632631738529937 1.410539935411864
MAD: 15 1.1886694 0.05670913613249594 1.415505987660477
Plots saving in NGC5194_90911_specpoint.1.png
/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=NGC5194_90911_specpoint,png,2
MAD: 0 1.3451263 0.06383157966586372 1.6004525899113187
MAD: 2 1.1504134 0.0550410644168721 1.3705776516417927
MAD: 3 1.0898638 0.05176872411015718 1.2969386736012734
MAD: 4 1.175205 0.05521621371441217 1.3960698471519601
MAD: 5 1.1365587 0.05429133351862286 1.3537239859986248
MAD: 6 1.3084797 0.06282557582974051 1.559781970028862
MAD: 7 1.1346782 0.053486813233655735 1.3486254975253822
MAD: 8 1.091265 0.051930087691039205 1.2989853139141811
MAD: 9 1.1455125 0.05484364588473056 1.3648870452012147
MAD: 10 1.12184 0.052889962398345106 1.3333998497459683
MAD: 11 1.1309632 0.05373955137238662 1.3459214117807452
MAD: 12 1.0577605 0.04949231346200767 1.2557297309140707
MAD: 13 1.2699555 0.060842465140488834 1.5133253764234667
MAD: 14 1.1852347 0.05632631738529937 1.410539935411864
MAD: 15 1.1886694 0.05670913613249594 1.415505987660477
Plots saving in NGC5194_90911_specpoint.2.png
LMTOY>> make_spec_fits (waterfall)
pix [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
Min nsamp 25695
Binning [1, 1]
FITS file will be 25695 x 590 x 15
Written waterfall cube to NGC5194_90911.wf.fits
pix [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
Min nsamp 25695
Binning [10, 1]
FITS file will be 2569 x 590 x 15
New shape: (15, 590, 2569)
Written waterfall cube to NGC5194_90911.wf10.fits
LMTOY>> grid_data
{'--cell': '6.25',
'--edge': '0',
'--help': False,
'--input': 'NGC5194_90911.nc',
'--n_samples': '256',
'--noise_sigma': '1',
'--otf_a': '1.1',
'--otf_b': '4.75',
'--otf_c': '2',
'--otf_select': '1',
'--output': 'NGC5194_90911.fits',
'--pix_list': '0,2,3,4,5,6,7,8,9,10,11,12,13,14,15',
'--program_path': 'spec_driver_fits',
'--resolution': '12.5',
'--rmax': '3',
'--rms_cut': '-4',
'--sample': '-1',
'--weight': 'NGC5194_90911.wt.fits',
'--x_extent': '450',
'--y_extent': '450'}
STDOUT ****************************
spec_driver_fits LMTSLR 26-jan-2022
CMD: spec_driver_fits -i NGC5194_90911.nc -o NGC5194_90911.fits -w NGC5194_90911.wt.fits -l 12.5 -c 6.25 -u [0,2,3,4,5,6,7,8,9,10,11,12,13,14,15] -z -4 -s 1 -x 450 -y 450 -f 1 -r 3 -n 256 -0 1.1 -1 4.75 -2 2 -b -1 -e 0
file list=NGC5194_90911.nc
DEBUG:6.25
sample_list=-1
Warning: sample list is not a multiple of 3
nsamples=1
Processing 1 SpecFiles:
Opening SpecFile file NGC5194_90911.nc
file: 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=0.147059 cell=6.25 resol=12.5 oft_select=1
C-AXIS 2 starts at 799.778
C-AXIS 1 starts at -450
C-AXIS 0 starts at -450
P-AXIS 1 starts at -450
P-AXIS 0 starts at -450
P-AXIS 1 starts at -450
P-AXIS 0 starts at -450
WARNING fuzzy_edge=0
pixel: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
used?: 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1
rms_stats: n=385449 rms_cutoff=-4
Cube Completed, 363823/385449 Spectra accepted = 0.944
Weighting Completed, fuzzy_edge=0
Weight at 0.000000 0.000000 is 42.174683
write to NGC5194_90911.fits
write weights to NGC5194_90911.wt.fits
STDERR ****************************
Exit Code: 0
LMTOY>> Some NEMO post-processing
### nemo Debug Info: FITS file: Image size 145 145 590
### Warning [fitsccd]: Setting map minimum from 0 to -179.565
### Warning [fitsccd]: Setting map maximum from 0 to 200.885
### nemo Debug Info: There were 5052170 blank values in the image (40.727705 %)
### nemo Debug Info: FITS file: Image size 145 145
### Warning [fitsccd]: Setting map minimum from 0 to -2.52244
### Warning [fitsccd]: Setting map maximum from 0 to 81.0589
### nemo Debug Info: There were no blank values set in the image
LMTOY>> STATS NGC5194_90911.ccd centerbox robust
### Warning [ccdsub]: Sampling will be done
### Warning [ccdsub]: Attempting to fix the WCS
### nemo Debug Info: WCS Corner: 202.409 47.2559 799778
Number of points : 3230840
Min and Max : -0.913018 1.625757
Mean and dispersion : 0.004089 0.145578
Skewness and kurtosis : 0.235779 1.042701
Sum and Sum*Dx*Dy*Dz* : 13210.233471 40.450642
Points per beam (map) : 1
N Robust : 3195807
Mean Robust : 0.002160
Sigma Robust : 0.137300
Median Robust : 0.001502
0/3230840 out-of-range points discarded
LMTOY>> STATS NGC5194_90911.wt.ccd centerbox robust
### Warning [ccdsub]: Sampling will be done
### Warning [ccdsub]: Attempting to fix the WCS
### nemo Debug Info: WCS Corner: 202.409 47.2559 0
Number of points : 5476
Min and Max : 24.623919 81.058891
Mean and dispersion : 43.863988 5.190493
Skewness and kurtosis : 2.467412 16.472818
Sum and Sum*Dx*Dy* : 240199.199892 -0.723980
Points per beam (map) : 1
N Robust : 5077
Mean Robust : 43.590044
Sigma Robust : 1.758496
Median Robust : 43.656441
0/5476 out-of-range points discarded
### nemo Debug Info: Keeping 145*145*590 cube
### Warning [ccdfits]: Replacing header from NGC5194_90911.wt.fits
SLABS: [[200,380],[580,670]] == 200,380,580,670
### 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 200 380 -> 590 413
### nemo Debug Info: slab 580 670 -> 216 127
### nemo Debug Info: Total planes: 268
### Warning [ccdslice]: Code not converted to fix reference pixel value
### Warning [ccdfits]: Replacing header from NGC5194_90911.wt.fits
### Warning [ccdfits]: Replacing header from NGC5194_90911.wt.fits
### Warning [ccdfits]: Replacing header from NGC5194_90911.fits
[0;31mQAC_STATS: NGC5194_90911-full 0.000760582 0.604464 -179.565 200.885 5592.24 0.00492973[0m
### Warning [ccdsub]: Sampling will be done
### Warning [ccdsub]: Attempting to fix the WCS
### nemo Debug Info: WCS Corner: 202.409 47.2559 799778
[0;31mQAC_STATS: NGC5194_90911-cent 0.00408879 0.145578 -0.913018 1.62576 13210.2 0.0357614[0m
### nemo Debug Info: FITS file: Image size 145 145 590
### Warning [fitsccd]: Setting map minimum from 0 to -0.075473
### Warning [fitsccd]: Setting map maximum from 0 to 0.515486
### nemo Debug Info: There were no blank values set in the image
spectab : # 72 72 590 min/mean/sig/max -0.424669 0.0365227 0.161384 0.508153 0.000488968 0.190097 0.832916
specstab: # 72 72 590 min/mean/sig/max -0.0376224 0.0382324 0.070353 0.226232 -1.14949e-06 0.00547034 0.0549815
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.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.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.mom2.fits
INFO: Auto-setting vmin to -8.074e+00 [aplpy.core]
INFO: Auto-setting vmax to 7.956e+01 [aplpy.core]
INFO: Auto-setting vmin to -7.921e+00 [aplpy.core]
INFO: Auto-setting vmax to 7.846e+01 [aplpy.core]
Writing NGC5194_90911.wt.png
INFO: Auto-setting vmin to -9.162e+00 [aplpy.core]
INFO: Auto-setting vmax to 1.017e+02 [aplpy.core]
INFO: Auto-setting vmin to -9.024e+00 [aplpy.core]
INFO: Auto-setting vmax to 1.002e+02 [aplpy.core]
Writing NGC5194_90911.wt2.png
INFO: Auto-setting vmin to -1.314e+02 [aplpy.core]
INFO: Auto-setting vmax to 1.458e+03 [aplpy.core]
INFO: Auto-setting vmin to -8.337e+02 [aplpy.core]
INFO: Auto-setting vmax to 9.254e+03 [aplpy.core]
Writing NGC5194_90911.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: NGC5194_90911.wtn.fits
INFO: Auto-setting vmin to -1.187e-01 [aplpy.core]
INFO: Auto-setting vmax to 1.317e+00 [aplpy.core]
INFO: Auto-setting vmin to -1.198e-01 [aplpy.core]
INFO: Auto-setting vmax to 1.330e+00 [aplpy.core]
Writing NGC5194_90911.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 -1.401e+04 [aplpy.core]
INFO: Auto-setting vmax to 3.061e+04 [aplpy.core]
INFO: Auto-setting vmin to -1.391e+04 [aplpy.core]
INFO: Auto-setting vmax to 3.070e+04 [aplpy.core]
Writing NGC5194_90911.mom0.png
LMTOY>> Created NGC5194_90911.nf.fits and NGC5194_90911.nfs.fits
LMTOY>> ADMIT post-processing
LMTOY>> lmtoy_admit: 31-oct-2021
/lma1/teuben/lmtoy/examples/lmtoy_admit.sh: line 33: export: `NGC5194_90911.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
1341515 Sl Xvfb
1261803 Sl Xvfb
1260405 Sl Xvfb
1258093 Sl Xvfb
### (1/1) : processing NGC5194_90911.nfs.fits
NGC5194_90911.nfs.fits [145, 145, 590] NGC5194 202.4696 47.19517 0.0007997778 0.046
/lma1/teuben/lmtoy/admit/admit/test/admit1.py --basename x NGC5194_90911.nfs.fits
91.866u 2.807s 1:47.29 88.2% 0+0k 1000+333968io 1pf+0w
Logfile: NGC5194_90911.nfs.fits.log
LMTOY>> lmtoy_admit: 31-oct-2021
/lma1/teuben/lmtoy/examples/lmtoy_admit.sh: line 33: export: `NGC5194_90911.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 NGC5194_90911.nf.fits
NGC5194_90911.nf.fits [145, 145, 590] NGC5194 202.4696 47.19517 0.0007997778 0.046
/lma1/teuben/lmtoy/admit/admit/test/admit1.py --basename x NGC5194_90911.nf.fits
62.120u 2.390s 1:16.16 84.7% 0+0k 312+257424io 0pf+0w
Logfile: NGC5194_90911.nf.fits.log
LMTOY>> Created NGC5194_90911.fits and NGC5194_90911.wt.fits
LMTOY>> Parameter file used: lmtoy_90911.rc
LMTOY>> Making summary index.html:
Making index.html for obsnum=90911
NGC5194_90911_?
NGC5194_90911_?_specviews
NGC5194_90911_?_specpoint
Writing index.html
Writing index_pipeline.html
cp: cannot stat 'NGC5194_90911_?_specviews.1.png': No such file or directory