old_contents: #!/usr/bin/env python
  
  """
  Run CIAO's celldetect tool
  """
  
  import argparse
  import os
  import sys
  import numpy as np
  
  
  from chandra_suli import find_files
  from chandra_suli.run_command import CommandRunner
  from chandra_suli import logging_system
  
  if __name__=="__main__":
  
      parser = argparse.ArgumentParser(description="Check to see if transient candidates are actually hot pixels")
  
      parser.add_argument("--masterfile",help="Name of file containing master list of all potential transients",
                          required=True, type=str)
      parser.add_argument("--ranks",help="Ranks in file that you want to run",nargs="+",required=True,type=int)
      parser.add_argument("--data_dir", help="Path to directory containing data of all obsids", required=True,
                          type=str)
      parser.add_argument("--outdir",help="Directory where output files will go",required=True, type=str)
  
      # Get logger for this command
  
      logger = logging_system.get_logger(os.path.basename(sys.argv[0]))
  
      # Instance the command runner
  
      runner = CommandRunner(logger)
  
      args = parser.parse_args()
  
      # Get data from master list
      master_data = np.array(np.recfromtxt(args.masterfile, names=True), ndmin=1)
  
      for rank in args.ranks:
  
          # index of object in question will be one less than the rank (first source is index 0, etc)
          idx = rank - 1
  
          obsid = master_data['Obsid'][idx]
          ccd = master_data['CCD'][idx]
          candidate = master_data['Candidate'][idx]
          tstart = master_data['Tstart'][idx]
          tstop = master_data['Tstop'][idx]
          obsid_dir = os.path.join(args.data_dir,str(obsid))
  
          evtfile = find_files.find_files(obsid_dir, 'ccd_%s_%s_filtered.fits' %(ccd,obsid))[0]
          regfile = find_files.find_files(obsid_dir, 'ccd_%s_%s_filtered_candidate_%s.reg' %(ccd,obsid,candidate))[0]
  
          regfile_name = os.path.splitext(os.path.basename(regfile))[0]
          outfile = "%s_celldetect.fits" %regfile_name
          outfile_path = os.path.join(args.outdir,outfile)
  
          cmd_line = 'ftcopy \"%s[regfilter(\'%s\') && (TIME >= %s) && (TIME <= %s)]\" %s clobber=yes '\
                     %(evtfile, regfile, tstart, tstop, outfile_path)
  
          runner.run(cmd_line)
  
  
  
new_contents: #!/usr/bin/env python
  
  """
  Run CIAO's celldetect tool
  """
  
  import argparse
  import os
  import sys
  import numpy as np
  
  
  from chandra_suli import find_files
  from chandra_suli.run_command import CommandRunner
  from chandra_suli import logging_system
  
  if __name__=="__main__":
  
      parser = argparse.ArgumentParser(description="Check to see if transient candidates are actually hot pixels")
  
      parser.add_argument("--masterfile",help="Name of file containing master list of all potential transients",
                          required=True, type=str)
      parser.add_argument("--ranks",help="Ranks in file that you want to run",nargs="+",required=True,type=int)
      parser.add_argument("--data_dir", help="Path to directory containing data of all obsids", required=True,
                          type=str)
      parser.add_argument("--outdir",help="Directory where output files will go",required=True, type=str)
  
      # Get logger for this command
  
      logger = logging_system.get_logger(os.path.basename(sys.argv[0]))
  
      # Instance the command runner
  
      runner = CommandRunner(logger)
  
      args = parser.parse_args()
  
      # Get data from master list
      master_data = np.array(np.recfromtxt(args.masterfile, names=True), ndmin=1)
  
      for rank in args.ranks:
  
          # index of object in question will be one less than the rank (first source is index 0, etc)
          idx = rank - 1
  
          obsid = master_data['Obsid'][idx]
          ccd = master_data['CCD'][idx]
          candidate = master_data['Candidate'][idx]
          tstart = master_data['Tstart'][idx]
          tstop = master_data['Tstop'][idx]
          obsid_dir = os.path.join(args.data_dir,str(obsid))
  
          evtfile = find_files.find_files(obsid_dir, 'ccd_%s_%s_filtered.fits' %(ccd,obsid))[0]
          regfile = find_files.find_files(obsid_dir, 'ccd_%s_%s_filtered_candidate_%s.reg' %(ccd,obsid,candidate))[0]
  
          regfile_name = os.path.splitext(os.path.basename(regfile))[0]
          newreg = "%s_reg.fits" %regfile_name
          newreg_path = os.path.join(args.outdir,newreg)
  
          cmd_line = 'ftcopy \"%s[regfilter(\'%s\') && (TIME >= %s) && (TIME <= %s)]\" %s clobber=yes '\
                     %(evtfile, regfile, tstart, tstop, newreg_path)
  
          runner.run(cmd_line)
  
          celldetect_file = '%s_celldetect.fits' %regfile_name
          celldetect_path = os.path.join(args.outdir, celldetect_file)
  
          cmd_line = 'celldetect %s %s clobber=yes' %(newreg_path, celldetect_path)
          runner.run(cmd_line)
  
  
  
  
subject: Copy region and run celldetect