Individual lines

Checking the lines for some sources


In [26]:
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from astropy.constants import c
from astropy.convolution import Gaussian1DKernel, convolve

import sys , os
sys.path.append("../../src/lines")

import lineTools as lt


### working dir. and files
wd = "/home/stephane/Science/RadioGalaxy/ALMA/absorptions/analysis/a/"
os.chdir(wd)

datadir   = "dataSpecAll/"
dbline    = "lineAll.db"
transfile = "splatalogue.csv"
dirplot   = "plots/"

In [27]:
def plotSource(lines, vel, amp , vx):
    "Overplot the different candidate lines"
#    
    plt.figure(figsize=(8.0,4.5))
    style = ["k-","r--", "b.-"]
    plt.xlim(vx[0],vx[1])

    
    for lindex in range(len(lines)):
        v = vel[lindex]
        a = amp[lindex]
        s = style[lindex]
        plt.step(v, a,  s , linewidth = 1.0 , label = lines[lindex][0])
    
    plt.xlabel ("v (km/s)")
    plt.ylabel(r"$S^*$")
    plt.legend()
    
    plt.show()

In [28]:
def getData(dataid, z, freqtrans):
    al = lt.analysisLines(dbline)
    cmdsql = "select filedata FROM dataset WHERE dataid = '%d'"%(dataid)
    resdb = al.query(cmdsql)
    
    pl = lt.plotLines("fake", "fake", "fake")
    datafile = datadir + resdb[0][0]
    
    freq , amp = pl.extractData(datafile)
    amp = amp / np.mean(amp)
    freq = freq * (1. + z)
    dv = c.value * 1e-3 *  (freq - freqtrans) / freqtrans
    
    return(dv , amp)

Source J2148


In [29]:
source = "J2148+0657"
z = 0.8983000
lines = []
line1 = ("HCO+v=0", 178.37506 , 4762)
lines.append(line1)
line1 = ("C18O", 439.08877 , 2041)
lines.append(line1)


velline = []
ampline = []

for l in lines:
    dv , amp = getData(l[2], z , l[1])
    amp = amp / np.mean(amp) 
    ampline.append(amp)
    velline.append(dv)
    
plotSource(lines, velline, ampline, [-200., 100.])



In [30]:
## fine tuning..

al = lt.analysisLines(dbline)
resLines = al.findSpeciesFineTuningSource(source , z, -32., -31., flag = False, outputline = 10)


------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 93.959127
Frequency at rest: 178.362611
Frequency offset:
0.0184424124104 GHz 0.0190385161227 GHz
    Species        Chemical Name    ... Lovas/AST Intensity    EU_K   
--------------- ------------------- ... ------------------- ----------
        HCO+v=0           Formylium ...                  --   12.84094
        HCO+v=0           Formylium ...                  --   12.84094
        HCO+v=0           Formylium ...                  --   12.84094
            ...                 ... ...                 ...        ...
        HOCH2CN Hydroxyacetonitrile ...                  -- 1896.43979
cis-CH2OHCHOv=3      Glycolaldehyde ...                  -- 2098.95534
cis-CH2OHCHOv=3      Glycolaldehyde ...                  -- 2098.95534
Length = 96 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 92.789206
Frequency at rest: 176.141750
Frequency offset:
0.0182096972833 GHz 0.0188014602822 GHz
     Species          Chemical Name     ... Lovas/AST Intensity    EU_K   
----------------- --------------------- ... ------------------- ----------
   O217O-sym,v2=1                 Ozone ...                  --        0.0
       CHD(OH)CHO        Glycolaldehyde ...                  --   16.29788
       CH3CODvt=0          Acetaldehyde ...                  --   20.80636
              ...                   ... ...                 ...        ...
        CH2F2v4=1       Difluoromethane ...                  -- 2660.48649
        CH2F2v4=1       Difluoromethane ...                  -- 2660.48662
aG'g-CH3CHOHCH2OH 1,2-propanediol, aG'g ...                  -- 2965.07571
Length = 298 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 92.754049
Frequency at rest: 176.075011
Frequency offset:
0.0182050967534 GHz 0.0187943365771 GHz
    Species      Chemical Name   ... Lovas/AST Intensity    EU_K   
--------------- ---------------- ... ------------------- ----------
             S3         Thiozone ...                  --   20.27428
         C3H6O2   Hydroxyacetone ...                  --   33.37956
CH2OHCOCH2OHv=0 Dihydroxyacetone ...                  --   42.73773
            ...              ... ...                 ...        ...
   CHOCHOHCH2OH   Glyceraldehyde ...                  -- 1617.64683
   CHOCHOHCH2OH   Glyceraldehyde ...                  -- 1617.64683
cis-CH2OHCHOv=3   Glycolaldehyde ...                  -- 2527.25586
Length = 168 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 229.984549
Frequency at rest: 436.579669
Frequency offset:
0.045144367951 GHz 0.0466007367661 GHz
Species    Chemical Name   ... Lovas/AST Intensity    EU_K   
-------- ----------------- ... ------------------- ----------
a-C2H5SH Ethanethiol, anti ...                  --   99.91558
a-C2H5SH Ethanethiol, anti ...                  --   99.91558
   H2C2S       Ethenthione ...                  --  540.50141
HCCCH2OH Propargyl Alcohol ...                  -- 1515.04996
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 231.290951
Frequency at rest: 439.059612
Frequency offset:
0.0454005185548 GHz 0.046865447139 GHz
  Species    Chemical Name  ... Lovas/AST Intensity    EU_K   
------------ -------------- ... ------------------- ----------
  CH3OCHOv=0 Methyl Formate ...                  --  154.80276
  CH3OCHOv=0 Methyl Formate ...                  --  154.80362
CH2CHCNv11=1  Vinyl Cyanide ...                  --  520.49838
         ...            ... ...                 ...        ...
        C3H8        Propane ...                  -- 1548.31581
       CH2CN    Cyanomethyl ...                  -- 1823.31585
       CH2CN    Cyanomethyl ...                  -- 1823.31585
Length = 20 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 231.284115
Frequency at rest: 439.046636
Frequency offset:
0.0453986015528 GHz 0.046864061991 GHz
   Species     Chemical Name  ... Lovas/AST Intensity    EU_K   
------------- --------------- ... ------------------- ----------
         C18O Carbon Monoxide ...                  --     52.684
         C18O Carbon Monoxide ...                  --     52.684
         C18O Carbon Monoxide ...                  --     52.684
          ...             ... ...                 ...        ...
HNO3v5=1/v9=2     Nitric acid ...                  -- 2447.95312
HNO3v5=1/v9=2     Nitric acid ...                  -- 2447.95312
HNO3v5=1/v9=2     Nitric acid ...                  -- 2447.95312
Length = 67 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 231.275814
Frequency at rest: 439.030878
Frequency offset:
0.0453973554819 GHz 0.0468623799966 GHz
   Species    Chemical Name  ... Lovas/AST Intensity    EU_K   
------------- -------------- ... ------------------- ----------
         D2CO   Formaldehyde ...                  --  100.62946
      CH3OCH3 Dimethyl ether ...                  --  130.90144
  CH3CH2CNv=0  Ethyl Cyanide ...                  --  167.64357
          ...            ... ...                 ...        ...
HNO3v5=1/v9=2    Nitric acid ...                  -- 2447.95259
HNO3v5=1/v9=2    Nitric acid ...                  -- 2447.95259
         D2CO   Formaldehyde ...                  -- 3017.09251
Length = 35 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 230.575130
Frequency at rest: 437.700769
Frequency offset:
0.0452601993499 GHz 0.0467204035431 GHz
     Species       Chemical Name   ... Lovas/AST Intensity    EU_K   
----------------- ---------------- ... ------------------- ----------
          CH3OCH3   Dimethyl ether ...                  --  300.21956
          CH3OCH3   Dimethyl ether ...                  --  300.22294
CH2OHCOCH2OHv28=1 Dihydroxyacetone ...                  -- 1504.88991
CH2OHCOCH2OHv28=1 Dihydroxyacetone ...                  -- 1504.88991
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 230.540951
Frequency at rest: 437.635887
Frequency offset:
0.0452533942481 GHz 0.0467134780057 GHz
     Species           Chemical Name      ... Lovas/AST Intensity    EU_K   
------------------ ---------------------- ... ------------------- ----------
               HO3           HOOO radical ...                  --   51.75851
               HO3           HOOO radical ...                  --   51.75854
               HO3           HOOO radical ...                  --   51.75855
               ...                    ... ...                 ...        ...
          HNO3v9=1            Nitric acid ...                  -- 1247.04318
            O81BrO        Bromine dioxide ...                  -- 1552.53145
g'G'g-CH3CHOHCH2OH 1,2-propanediol, g'G'g ...                  -- 2083.75946
Length = 9 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 230.538509
Frequency at rest: 437.631252
Frequency offset:
0.0452529150958 GHz 0.0467129831942 GHz
    Species       Chemical Name   ... Lovas/AST Intensity    EU_K   
---------------- ---------------- ... ------------------- ----------
H2NCH2COOH-IIv=0          Glycine ...                  --  230.88583
           HDCCO           Ketene ...                  --  261.11205
          O35ClO Chlorine dioxide ...                  --   431.1155
             ...              ... ...                 ...        ...
        HNO3v6=1      Nitric acid ...                  -- 1300.34199
       c-H13COOH      Formic acid ...                  --   4384.536
       c-H13COOH      Formic acid ...                  --   4384.536
Length = 14 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 243.470532
Frequency at rest: 462.180111
Frequency offset:
0.0477918656404 GHz 0.049333340963 GHz
     Species        Chemical Name    ... Lovas/AST Intensity    EU_K   
----------------- ------------------ ... ------------------- ----------
         i-C3H7CN iso-propyl cyanide ...                  --  335.01414
         i-C3H7CN iso-propyl cyanide ...                  --  335.01414
      aa-(C2H5)2O      Diethyl ether ...                  --  419.20607
              ...                ... ...                 ...        ...
CH2OHCOCH2OHv29=1   Dihydroxyacetone ...                  --  768.99763
          CH3C15N     Methyl Cyanide ...                  -- 1505.63369
             C3H8            Propane ...                  -- 2794.48487
Length = 9 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 244.157055
Frequency at rest: 463.483338
Frequency offset:
0.0479270091754 GHz 0.0494724480367 GHz
   Species     Chemical Name  ... Lovas/AST Intensity    EU_K   
-------------- -------------- ... ------------------- ----------
O218O-sym,v2=1          Ozone ...                  --        0.0
    O218O-asym          Ozone ...                  --        0.0
       HON18OO    Nitric acid ...                  --  285.19667
           ...            ... ...                 ...        ...
      34SO2v=0 Sulfur Dioxide ...                  -- 3200.04146
         H2CCO         Ketene ...                  -- 9611.09581
         H2CCO         Ketene ...                  -- 9611.09581
Length = 41 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 244.641430
Frequency at rest: 464.402827
Frequency offset:
0.0480217054608 GHz 0.0495705947686 GHz
 Species     Chemical Name    ... Lovas/AST Intensity    EU_K   
---------- ------------------ ... ------------------- ----------
        S4        Tetrasulfur ...                  --  129.86776
    NH2CHO          Formamide ...                  --  270.74952
    NH2CHO          Formamide ...                  --  270.74952
       ...                ... ...                 ...        ...
13CH3CH2CN      Ethyl Cyanide ...                  -- 1282.08748
     CH2OO Methylene peroxide ...                  -- 1311.32631
    C6H5OH             Phenol ...                  -- 1354.69561
Length = 25 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 114.149021
Frequency at rest: 216.689087
Frequency offset:
0.0224086237227 GHz 0.0231295037117 GHz
   Species     Chemical Name  ... Lovas/AST Intensity    EU_K   
------------- --------------- ... ------------------- ----------
         13CN Cyanide Radical ...                  --   15.64246
         13CN Cyanide Radical ...                  --   15.64246
         13CN Cyanide Radical ...                  --   15.64254
          ...             ... ...                 ...        ...
HNO3v5=1/v9=2     Nitric acid ...                  -- 3084.31248
HNO3v5=1/v9=2     Nitric acid ...                  -- 3084.31248
HNO3v5=1/v9=2     Nitric acid ...                  -- 3084.31248
Length = 139 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 114.164646
Frequency at rest: 216.718748
Frequency offset:
0.0224105405284 GHz 0.0231326697353 GHz
   Species        Chemical Name    ... Lovas/AST Intensity    EU_K   
-------------- ------------------- ... ------------------- ----------
        O37ClO    Chlorine dioxide ...                  --   65.89679
       HOCH2CN Hydroxyacetonitrile ...                  --  111.78304
NH2CH2CH2OHv=0        Aminoethanol ...                  --  116.30262
           ...                 ... ...                 ...        ...
      HNO3v9=1         Nitric acid ...                  -- 2800.76977
      HNO3v9=1         Nitric acid ...                  -- 2800.76977
      HNO3v9=1         Nitric acid ...                  -- 2800.76977
Length = 60 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 103.837505
Frequency at rest: 197.114736
Frequency offset:
0.0203818568059 GHz 0.0210401275129 GHz
Species    Chemical Name   ... Lovas/AST Intensity    EU_K   
-------- ----------------- ... ------------------- ----------
  C3H6O2    Hydroxyacetone ...                  --   34.12967
HCCCH2OH Propargyl Alcohol ...                  --   68.35039
 HON18OO       Nitric acid ...                  --   73.72214
     ...               ... ...                 ...        ...
HNO3v6=1       Nitric acid ...                  -- 3159.76995
HNO3v6=1       Nitric acid ...                  -- 3159.76995
HNO3v6=1       Nitric acid ...                  -- 3159.76996
Length = 52 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 103.825787
Frequency at rest: 197.092491
Frequency offset:
0.0203780229982 GHz 0.0210377531472 GHz
   Species       Chemical Name    ... Lovas/AST Intensity    EU_K   
------------- ------------------- ... ------------------- ----------
a-s-CH2DCH2OH <i>anti</i>-Ethanol ...                  --   19.20045
        HOONO  Peroxynitrous acid ...                  --   29.75134
        HOONO  Peroxynitrous acid ...                  --   29.75145
          ...                 ... ...                 ...        ...
         HNO3         Nitric acid ...                  -- 2852.18133
         HNO3         Nitric acid ...                  -- 2852.18133
         HNO3         Nitric acid ...                  -- 2852.18134
Length = 203 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 101.985943
Frequency at rest: 193.599916
Frequency offset:
0.0200176403689 GHz 0.0206649538165 GHz
    Species        Chemical Name    ... Lovas/AST Intensity    EU_K   
---------------- ------------------ ... ------------------- ----------
          SO2v=0     Sulfur dioxide ...                  --    41.9902
          SO2v=0     Sulfur dioxide ...                  --    41.9902
          SO2v=0     Sulfur dioxide ...                  --   41.99063
             ...                ... ...                 ...        ...
H2NCH2COOH-IIv=1            Glycine ...                  -- 2377.99046
H2NCH2COOH-IIv=1            Glycine ...                  -- 2377.99046
           CH2OO Methylene peroxide ...                  -- 3796.44763
Length = 151 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 101.970318
Frequency at rest: 193.570255
Frequency offset:
0.0200153402021 GHz 0.0206617877929 GHz
    Species       Chemical Name    ... Lovas/AST Intensity    EU_K   
--------------- ------------------ ... ------------------- ----------
O218O-asym,v2=1              Ozone ...                  --        0.0
           HNO3        Nitric acid ...                  --    22.5195
           HNO3        Nitric acid ...                  --   22.51951
            ...                ... ...                 ...        ...
  HNO3v5=1/v9=2        Nitric acid ...                  -- 1337.68029
  HNO3v5=1/v9=2        Nitric acid ...                  -- 1337.68029
      t-HC(O)SH Monothiformic acid ...                  -- 1425.42174
Length = 78 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 101.740818
Frequency at rest: 193.134595
Frequency offset:
0.0199695239336 GHz 0.0206152852381 GHz
     Species          Chemical Name     ... Lovas/AST Intensity    EU_K   
----------------- --------------------- ... ------------------- ----------
 CH3CH2CH2CN-anti         Butyronitrile ...                  --   13.72346
           C3H6O2        Hydroxyacetone ...                  --   34.93222
gG'a-CH3CHOHCH2OH 1,2-propanediol, gG'a ...                  --   37.40789
              ...                   ... ...                 ...        ...
         HNO3v9=1           Nitric acid ...                  -- 2472.01351
         HNO3v9=1           Nitric acid ...                  -- 2472.01351
         HNO3v9=1           Nitric acid ...                  -- 2472.01351
Length = 102 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 101.727146
Frequency at rest: 193.108641
Frequency offset:
0.0199672237668 GHz 0.0206125149421 GHz
    Species             Chemical Name        ... Lovas/AST Intensity    EU_K   
---------------- --------------------------- ... ------------------- ----------
      H&epsilon; Hydrogen Recombination Line ...                  --        0.0
CH3CH2CH2CN-anti               Butyronitrile ...                  --    12.4502
   Na13CN/NaN13C              Sodium Cyanide ...                  --   65.71718
             ...                         ... ...                 ...        ...
           HOONO          Peroxynitrous acid ...                  -- 3719.84955
           HOONO          Peroxynitrous acid ...                  -- 3719.84955
           HOONO          Peroxynitrous acid ...                  -- 3719.84955
Length = 96 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 100.053318
Frequency at rest: 189.931214
Frequency offset:
0.019639045632 GHz 0.0202733546883 GHz
    Species      Chemical Name   ... Lovas/AST Intensity     EU_K   
--------------- ---------------- ... ------------------- -----------
H2NCH2COOH-Iv=2          Glycine ...                  --    41.88964
H2NCH2COOH-Iv=2          Glycine ...                  --    41.88964
H2NCH2COOH-Iv=0          Glycine ...                  --    41.88965
            ...              ... ...                 ...         ...
           17OD Hydroxyl radical ...                  -- 13364.52935
           17OD Hydroxyl radical ...                  -- 13364.52966
           17OD Hydroxyl radical ...                  -- 13364.53003
Length = 66 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 93.959127
Frequency at rest: 178.362611
Frequency offset:
0.0184424124104 GHz 0.0190385161227 GHz
    Species        Chemical Name    ... Lovas/AST Intensity    EU_K   
--------------- ------------------- ... ------------------- ----------
        HCO+v=0           Formylium ...                  --   12.84094
        HCO+v=0           Formylium ...                  --   12.84094
        HCO+v=0           Formylium ...                  --   12.84094
            ...                 ... ...                 ...        ...
        HOCH2CN Hydroxyacetonitrile ...                  -- 1896.43979
cis-CH2OHCHOv=3      Glycolaldehyde ...                  -- 2098.95534
cis-CH2OHCHOv=3      Glycolaldehyde ...                  -- 2098.95534
Length = 96 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 92.789206
Frequency at rest: 176.141750
Frequency offset:
0.0182096972833 GHz 0.0188014602822 GHz
     Species          Chemical Name     ... Lovas/AST Intensity    EU_K   
----------------- --------------------- ... ------------------- ----------
   O217O-sym,v2=1                 Ozone ...                  --        0.0
       CHD(OH)CHO        Glycolaldehyde ...                  --   16.29788
       CH3CODvt=0          Acetaldehyde ...                  --   20.80636
              ...                   ... ...                 ...        ...
        CH2F2v4=1       Difluoromethane ...                  -- 2660.48649
        CH2F2v4=1       Difluoromethane ...                  -- 2660.48662
aG'g-CH3CHOHCH2OH 1,2-propanediol, aG'g ...                  -- 2965.07571
Length = 298 rows
------
Source: J2148+0657
Redshift: 0.898300
Frequency redshifted: 92.754049
Frequency at rest: 176.075011
Frequency offset:
0.0182050967534 GHz 0.0187943365771 GHz
    Species      Chemical Name   ... Lovas/AST Intensity    EU_K   
--------------- ---------------- ... ------------------- ----------
             S3         Thiozone ...                  --   20.27428
         C3H6O2   Hydroxyacetone ...                  --   33.37956
CH2OHCOCH2OHv=0 Dihydroxyacetone ...                  --   42.73773
            ...              ... ...                 ...        ...
   CHOCHOHCH2OH   Glyceraldehyde ...                  -- 1617.64683
   CHOCHOHCH2OH   Glyceraldehyde ...                  -- 1617.64683
cis-CH2OHCHOv=3   Glycolaldehyde ...                  -- 2527.25586
Length = 168 rows