old_contents: import os
  import sys
  import copy
  import numpy as np
  import itertools
  import argparse
  
  from fermipy.utils import init_matplotlib_backend
  
  init_matplotlib_backend()
  
  from fermipy.batch import check_log
  from fermipy.gtanalysis import GTAnalysis
  from haloanalysis.fit_funcs import fit_halo_scan
  from astropy.table import Table
      
  def main():
          
      usage = "usage: %(prog)s [config file]"
      description = "Run fermipy analysis chain."
      parser = argparse.ArgumentParser(usage=usage,description=description)
  
      parser.add_argument('--config', default = 'sample_config.yaml')
      parser.add_argument('--source', default = None)
  
      args = parser.parse_args()
      gta = GTAnalysis(args.config,logging={'verbosity' : 3},
                       fileio={'workdir_regex' : ['\.xml$|\.npy$']})
  
      logfile = os.path.join(gta.outdir,'run-region-analysis.log')
      if not check_log(logfile)=='Successful':
          print('Region analysis incomplete.  Exiting.')
          sys.exit(1)
          
      gta.setup()
      tab = Table.read('/u/gl/mdwood/fermi/ext_analysis/v20/std_psf0123_joint2a_stdmodel/table_std_psf0123_joint2a_stdmodel_cat.fits')
  
      src_name = gta.config['selection']['target']
      codename = src_name.lower().replace(' ','_')
      row = tab[tab['codename'] == codename][0]
  
      if row['fit_ext_ts_ext'] < 9.0:
          print('Source not extended.  Exiting.')
          sys.exit(0)
  
      ext_model = row['fit_ext_model']
      idx = row['fit_idx_ext']
      model = { 'SpatialModel' : 'PointSource', 'Index' : min(np.abs(row['fit_ext_index']),4.0) }
      
      gta.load_roi('fit%i_ext_%s_roi'%(idx,ext_model),reload_sources=True)
      
      gta.tsmap('fit%i_ext_nosource'%idx, outfile='fit%i_ext_nosource'%idx,
                model=model, exclude=[src_name],
                make_plots=True)
  
      gta.tsmap('fit%i_ext'%idx, outfile='fit%i_ext'%idx,
                model=model, 
                make_plots=True)
  
  if __name__ == '__main__':
  
      main()
  
new_contents: import os
  import sys
  import copy
  import numpy as np
  import itertools
  import argparse
  
  from fermipy.utils import init_matplotlib_backend
  
  init_matplotlib_backend()
  
  from fermipy.batch import check_log
  from fermipy.gtanalysis import GTAnalysis
  from haloanalysis.fit_funcs import fit_halo_scan
  from astropy.table import Table
      
  def main():
          
      usage = "usage: %(prog)s [config file]"
      description = "Run fermipy analysis chain."
      parser = argparse.ArgumentParser(usage=usage,description=description)
  
      parser.add_argument('--config', default = 'sample_config.yaml')
      parser.add_argument('--source', default = None)
  
      args = parser.parse_args()
      gta = GTAnalysis(args.config,logging={'verbosity' : 3},
                       fileio={'workdir_regex' : ['\.xml$|\.npy$']})
  
      logfile = os.path.join(gta.outdir,'run-region-analysis.log')
      if not check_log(logfile)=='Successful':
          print('Region analysis incomplete.  Exiting.')
          sys.exit(1)
          
      gta.setup()
      tab = Table.read('/u/gl/mdwood/fermi/ext_analysis/v20/std_psf0123_joint2a_stdmodel/table_std_psf0123_joint2a_stdmodel_cat.fits')
  
      src_name = gta.config['selection']['target']
      codename = src_name.lower().replace(' ','_')
      row = tab[tab['codename'] == codename][0]
  
      if row['fit_ext_ts_ext'] < 9.0:
          print('Source not extended.  Exiting.')
          sys.exit(0)
  
      ext_model = row['fit_ext_model']
      idx = row['fit_idx_ext']
      model = { 'SpatialModel' : 'PointSource', 'Index' : min(np.abs(row['fit_ext_index']),4.0) }
      
      gta.load_roi('fit%i_ext_%s_roi'%(idx,ext_model),reload_sources=True)
      
      gta.tsmap('fit_ext_nosource', outfile='fit_ext_nosource_tsmap',
                model=model, exclude=[src_name],
                make_plots=True)
  
      gta.tsmap('fit_ext', outfile='fit_ext_tsmap',
                model=model, 
                make_plots=True)
  
  if __name__ == '__main__':
  
      main()
  
subject: tweak TS map script