Documentation

This is documentation for the suite of programs I am writing.

Jan 8 2019 - first big add ; added onto it from time to time...
Jan 12 2020 - biggest revision to the documentation with the addition/removal of functions

################################## LEVEL 0 ####################################

Base level - calling/processing of data

>>>>>>>>>> Lv0_dirs <<<<<<<<<<

  Functions:

  ##### global_par
  -- Defining global variables for the directories
  -- has BASE_DIR, NICER_DATADIR, NICERSOFT_DATADIR, and NGC300

>>>>>>>>>> Lv0_fits2dict <<<<<<<<<<

  Functions:

  ##### fits2dict(fits_file,ext,par_list)

  -- 'Converts' a FITS file to a Python dictionary, with a list of the original
  FITS table's columns, of the user's choosing. Can use this for ANY FITS file,
  but is meant for mkf/orb files in $OBSID_pipe folders from NICER, or event files
  (be it from NICER-data or NICERsoft_outputs or any other mission which has this format)

  fits_file - path to the FITS file
  ext - which extension number; 1 for EVENTS, 2 for GTI, 3 for PPS_TREND
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI)

  TEST:
  eventfile = "/Volumes/Samsung_T5/NICERsoft_outputs/1034070101_pipe/cleanfilt.evt"
  print(fits2dict(eventfile,1,['TIME','RAWX']))
  print(fits2dict(eventfile,2,['START','STOP']))

>>>>>>>>>> Lv0_gunzip <<<<<<<<<<

  Functions:

  ##### unzip_all(obsdir)

  -- Does a recursive scan through the directory and unzips all files which have not yet been unzipped

  obsdir - directory of all the observation files

  TEST:
  unzip_all(Lv0_dirs.NICER_DATADIR+'1034070101')

>>>>>>>>>> Lv0_nicer_housekeeping <<<<<<<<<<

  Functions:

  ##### get_att(eventfile,par_list)

  -- Getting data from the .att FITS file! Just provide a path to the event file.
  I can also input the NICERsoft-output event files because this script will
  just search for the ObsID and trawl through the NICER-data folder.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI)

  ##### get_cat(eventfile,par_list)

  -- Getting data from the .cat FITS file! Just provide a path to the event file.
  I can also input the NICERsoft-output event files because this script will
  just search for the ObsID and trawl through the NICER-data folder.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI)

  ##### get_mkf(eventfile,par_list)

  -- Getting data from the .mkf FITS file! Just provide a path to the event file.
  I can also input the NICERsoft-output event files because this script will
  just search for the ObsID and trawl through the NICER-data folder.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI)

  ##### get_orb(eventfile,par_list)

  -- Getting data from the .orb FITS file! Just provide a path to the event file.
  I can also input the NICERsoft-output event files because this script will
  just search for the ObsID and trawl through the NICER-data folder.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI)

  ##### get_hk(eventfile,mpu_no,par_list)

  -- Getting data from the .hk FITS file! Just provide a path to the event file.
  I can also input the NICERsoft-output event files because this script will
  just search for the ObsID and trawl through the NICER-data folder.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  mpu_no - MPU number, from 0 to 6 inclusive. For the 7 MPUs.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI)

  ##### get_uf(eventfile,mpu_no,ext,par_list)

  -- Getting data from the .uf FITS file! Just provide a path to the event file.
  I can also input the NICERsoft-output event files because this script will
  just search for the ObsID and trawl through the NICER-data folder.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  mpu_no - MPU number, from 0 to 6 inclusive. For the 7 MPUs.
  ext - which extension number; 1 for EVENTS, 2 for GTI, 3 for PPS_TREND
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI)

  ##### get_ufa(eventfile,mpu_no,ext,par_list)

  -- Getting data from the .ufa FITS file! Just provide a path to the event file.
  I can also input the NICERsoft-output event files because this script will
  just search for the ObsID and trawl through the NICER-data folder.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  mpu_no - MPU number, from 0 to 6 inclusive. For the 7 MPUs.
           MPU number 7 corresponds to the COMBINED file!
  ext - which extension number; 1 for EVENTS, 2 for GTI
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI)

  TEST:
  eventfile = '/Volumes/Samsung_T5/NICER-data/1034070101/xti/event_cl/ni1034070101_0mpu7_cl.evt'

  print(get_att(eventfile,['TIME','QPARAM']))
  print(get_cat(eventfile,['FILENAME','FORMAT']))
  print(get_mkf(eventfile,['TIME','NICER_SAA','ANG_DIST']))
  print(get_orb(eventfile,['TIME','Vx','Vy']))
  print(get_hk(eventfile,'3',['TIME','GIT_HASH']))
  print(get_uf(eventfile,'2',1,['TIME','RAWX','DEADTIME']))
  print(get_ufa(eventfile,'7',1,['TIME','MPU_UNDER_COUNT','PI_RATIO']))

>>>>>>>>>> Lv0_nicerl2 <<<<<<<<<<

  Functions:

  ##### nicerl2(obsdir,nicerl2_flags)

  -- Running nicerl2 to do initial filtering of the ufa file!

  obsdir - NICER data directory containing all the data files (e.g., path_to_NICER_dir/1034070101)
  nicerl2_flags - a LIST of input flags for nicerl2

  TEST:
  obsid = '1034070101'
  obsdir = Lv0_dirs.NICER_DATADIR + obsid
  nicerl2(obsdir,['clobber=YES'])

>>>>>>>>>> Lv0_psrpipe <<<<<<<<<<

  Functions:

  ##### psrpipe(eventfile,flags)

  -- Running psrpipe on the observation, to make more cuts! I decided not to
  put in pre-determined options for fully flexibility. Though standard flags
  would be ['--emin','0.3','--emax','12.0','--shrinkelvcut'], though there are
  others. Check out "psrpipe.py -h"! Also made sure that I moved $OBSID_pipe from
  the working directory to where NICERSOFT_DATADIR is, though I need to temporarily
  store the output folder in the working directory.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  flags - a LIST of input flags for psrpipe

  TEST:
  obsid = '1034070101'
  eventfile = Lv0_dirs.NICER_DATADIR + obsid + '/xti/event_cl/ni' + obsid+'_0mpu7_cl.evt'
  psrpipe(eventfile,['--emin','0.3','--emax','12.0'])

>>>>>>>>>> Lv0_scp <<<<<<<<<<

  Functions:

  ##### scp(obsid)

  -- To securely copy the files from ciri onto /Volumes/Samsung_T5/NICER-data/

  obsid - Observation ID of the object of interest (10-digit str)

  TEST:
  for i in range(11,25):
      scp('10600601' + str(i)) WORKED.

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################################## LEVEL 1 #####################################

>>>>>>>>>> Lv1_barycorr <<<<<<<<<<

  Functions:

  ##### get_ra_dec(eventfile)

  -- Obtain the RA_OBJ and DEC_OBJ corresponding to the observation!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.

  ##### read_par(parfile)

  -- Function that reads a par file. In particular, for the purposes of barycorr,
  it will return POSEPOCH, RAJ, DECJ, PMRA, and PMDEC.

  Step 1: Read par file line by line, where each line is stored as a string in the 'contents' array
  Step 2a: For PSRJ, RAJ, DECJ, PMRA, and PMDEC, those lines are teased out
  Step 2b: The corresponding strings are split up without whitespace
  Step 3: Extract the values accordingly

  parfile - path of the .par file

  ##### barycorr(eventfile,outfile,refframe,orbit_file,parfile,output_folder)

  -- General function to perform the barycenter corrections for an event file

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  refframe - reference frame for barycenter corrections (usually ICRS)
  parfile - name of the .par file

  TEST:
  obsid = '1911212213'
  eventfile = Lv0_dirs.NICER_DATADIR + 'rxj0209/rxj0209kgfilt.evt'
  outfile = Lv0_dirs.NICER_DATADIR + 'rxj0209/rxj0209kgfilt_bary.evt'
  orbitfile = Lv0_dirs.NICER_DATADIR + 'rxj0209/rxj0209.orb'
  parfile = ''
  output_folder = Lv0_dirs.NICER_DATADIR + 'rxj0209/'
  refframe = 'ICRS'

  barycorr(eventfile,outfile,refframe,orbitfile,parfile,output_folder)

>>>>>>>>>> Lv1_data_bin <<<<<<<<<<

  Functions:

  ##### binning_t(eventfile,par_list,tbin_size,t1,t2)

  -- Binning routine for when I truncate the data by JUST time interval.
  Got to make sure I have TIME and PI called!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  t1 - lower time boundary
  t2 - upper time boundary

  ##### binning_E(eventfile,par_list,tbin_size,Ebin_size,E1,E2)

  -- Binning routine for when I truncate the data by JUST energy range.
  Got to make sure I have TIME and PI called!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  Ebin_size - the size of the energy bins (in keV!)
  >> e.g., Ebin_size = 0.1 means bin by 0.1keV
  >> e.g., Ebin_size = 0.05 means bin by 0.05keV
  E1 - lower energy boundary
  E2 - upper energy boundary

  ##### binning_tE(eventfile,par_list,tbin_size,Ebin_size,t1,t2,E1,E2)

  -- Binning routine for when I truncated the data by BOTH time interval AND energy range.
  Got to make sure I have TIME and PI called!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  Ebin_size - the size of the energy bins (in keV!)
  >> e.g., Ebin_size = 0.1 means bin by 0.1keV
  >> e.g., Ebin_size = 0.05 means bin by 0.05keV
  t1 - lower time boundary
  t2 - upper time boundary
  E1 - lower energy boundary
  E2 - upper energy boundary

  TEST:
  obsid = '1034070101'
  eventfile = Lv0_dirs.NICER_DATADIR + obsid + '/xti/event_cl/ni' + obsid + '_0mpu7_cl_bary.evt'
  par_list = ['TIME','PI','PI_RATIO']
  t1 = 0
  t2 = 300
  E1 = 0.3
  E2 = 6

  tbin_size = 1
  Ebin_size = 0.05

  tbins,summed_data = binning_t(eventfile,par_list,tbin_size,t1,t2)
  #print(len(tbins),len(summed_data))
  tbins,summed_t_data,Ebins,summed_E_data = binning_E(eventfile,par_list,tbin_size,Ebin_size,E1,E2)
  #print(len(tbins),len(summed_t_data),len(Ebins),len(summed_E_data))
  tbins,summed_t_data,Ebins,summed_E_data = binning_tE(eventfile,par_list,tbin_size,Ebin_size,t1,t2,E1,E2)
  #print(len(tbins),len(summed_t_data),len(Ebins),len(summed_E_data))

>>>>>>>>>> Lv1_data_filter <<<<<<<<<<

  Functions:

  ##### filter_time(eventfile,par_list,t1,t2)

  -- Obtain the time stamps that fall in a desired time interval.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  t1 - time value for the lower boundary (in s)
  t2 - time value for the upper boundary (in s)

  ##### filter_energy(eventfile,par_list,E1,E2)

  -- Obtain the time stamps and the corresponding energy value (of the photon)
  in a desired energy range.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  E1 - energy value for the lower boundary (in keV)
  E2 - energy value for the upper boundary (in keV)

  ##### filter_data(eventfile,par_list,t1,t2,E1,E2)

  -- Truncate the data such that you get counts in a given time interval and
  energy range.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  t1 - time value for the lower boundary (in s)
  t2 - time value for the upper boundary (in s)
  E1 - energy value for the lower boundary (in keV)
  E2 - energy value for the upper boundary (in keV)

  TEST:
  obsid = '1034070101'
  eventfile = Lv0_dirs.NICER_DATADIR + obsid + '/xti/event_cl/ni' + obsid + '_0mpu7_cl_bary.evt'
  par_list = ['TIME','PI','PI_RATIO']
  t1 = 0
  t2 = 300
  E1 = 0.3
  E2 = 6

  tcut = filter_time(eventfile,par_list,t1,t2)
  #print(len(tcut))
  tcut,E_cut = filter_energy(eventfile,par_list,E1,E2)
  #print(len(tcut),len(E_cut))
  tcut,E_cut = filter_data(eventfile,par_list,t1,t2,E1,E2)
  #print(len(tcut),len(E_cut))

>>>>>>>>>> Lv1_ngc300_binning <<<<<<<<<<

  Functions:

  ##### get_binned_data(counts_dict,err_dict)

  -- Given the dictionaries where the data (counts and uncertainty) are already
  binned, put them into lists!

  counts_dict - dictionary where the keys are MJD values, and the entries correspond
  to the counts/rate for a given MJD
  err_dict - dictionary where the keys are MJD values, and the entries correspond
  to the UNCERTAINTY in the counts/rate for a given MJD

  ##### binned_text()

  -- Given the MJDs, binned counts, and associated uncertainties, put them into a text file

  No arguments because I'll put all the bands in here

>>>>>>>>>> Lv1_ngc300_mathgrp_pha <<<<<<<<<<

  Functions:

  ##### mathpha(bin_size,filetype)

  -- Function that takes in a bin size, and does MATHPHA on the set of pha files.
  The file names are already saved in the binned .ffphot files. The function
  will output pha files of the format 'MJD_binsize_' + filetype + '_cl50.pha'!

  bin_size - bin size in days
  filetype - either 'bgsub' or 'bg' or 'cl'!

  ##### grppha(bin_size,filetype)

  -- Function that takes in a bin size, and does GRPPHA on a set of pha files.
  The input file names will be "$MJD_$binsize_bgsub_cl50.pha". The function
  will output pha files of the format 'grp_$MJD_$binsize_$filetype_cl50.pha'!

  bin_size - bin size in days
  filetype - either 'bgsub' or 'bg' or 'cl'!

  TEST:
  #mathpha(bin_size,'bgsub')
  grppha(bin_size,'bgsub')
  #bg_mathpha(bin_size)
  #bg_grppha(bin_size)

>>>>>>>>>> Lv1_spectra_txt <<<<<<<<<<

>>>>>>>>>> Lv1_spectral_renorm <<<<<<<<<<

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################################## LEVEL 2 #####################################

>>>>>>>>>> Lv2_average_ps_methods <<<<<<<<<<

  Functions:

  ##### do_demodulate(eventfile,segment_length,mode,par_file)

  -- Do orbital demodulation on the original events.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the segments
  par_file - orbital parameter file for input into binary_psr
  mode - "all", "t" or "E" ; basically to tell the function where to access files to run do_demodulate

  ##### do_nicerfits2presto(eventfile,tbin,segment_length)

  -- Using nicerfits2presto.py to bin the data, and to convert into PRESTO-readable format.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  tbin - size of the bins in time
  segment_length - length of the individual segments for combining power spectra

  ##### edit_inf(eventfile,tbin,segment_length)

  -- Editing the .inf file, as it seems like accelsearch uses some information from the .inf file!
  Mainly need to edit the "Number of bins in the time series".
  This is only for when we make segments by time though!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  tbin - size of the bins in time
  segment_length - length of the individual segments

  ##### edit_binary(eventfile,tbin,segment_length)

  -- To pad the binary file so that it will be as long as the desired segment length.
  The value to pad with for each time bin, is the average count rate in THAT segment!
  Jul 10: Do zero-padding instead... so that number of counts is consistent!
  Again, this is only for when we make segments by time!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  tbin - size of the bins in time
  segment_length - length of the individual segments

  ##### realfft(eventfile,segment_length)

  -- Performing PRESTO's realfft on the binned data (.dat)

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the individual segments

  ##### presto_dat(eventfile,segment_length,demod)

  -- Obtain the dat files that were generated from PRESTO

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the segments
  demod - whether we're dealing with demodulated data or not!

  ##### presto_fft(eventfile,segment_length,demod)

  -- Obtain the FFT files that were generated from PRESTO

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the segments
  demod - whether we're dealing with demodulated data or not!

  ##### segment_threshold(eventfile,segment_length,demod,tbin_size,threshold)

  -- Using the .dat files, rebin them into 1s bins, to weed out the segments below
  some desired threshold. Will return a *list* of *indices*! This is so that I
  can filter out the *sorted* array of .dat and .fft files that are below threshold!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the segments
  demod - whether we're dealing with demodulated data or not!
  tbin_size - size of the time bin
  threshold - if data is under threshold (in percentage), then don't use the segment!

  ##### average_ps(eventfile,segment_length,demod,tbin_size,threshold,starting_freq,W)

  -- Given the full list of .dat and .fft files, and the indices where the PRESTO-binned
  data is beyond some threshold, return the averaged power spectrum!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the segments
  demod - whether we're dealing with demodulated data or not!
  tbin_size - size of the time bin
  threshold - if data is under threshold (in percentage), then don't use the segment!
  W - number of consecutive frequency bins to AVERAGE over

  ##### noise_hist(eventfile,segment_length,demod,tbin_size,threshold,starting_freq,W)

  -- Given the average spectrum for an ObsID, return the histogram of powers, such
  that you have N(>P). This is for powers corresponding to frequencies larger
  than some starting frequency (perhaps to avoid red noise).

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the segments
  demod - whether we're dealing with demodulated data or not!
  tbin_size - size of the time bin
  threshold - if data is under threshold (in percentage), then don't use the segment!
  starting_freq - frequency to start constructing the histogram of powers from
  W - number of consecutive frequency bins to AVERAGE over

  TEST:
  eventfile = Lv0_dirs.NICERSOFT_DATADIR + '1034070101_pipe/ni1034070101_nicersoft_bary.evt'
  mode = 't'
  segment_length = 100
  par_file = Lv0_dirs.NICERSOFT_DATADIR + 'J1231-1411.par'
  do_demodulate(eventfile,segment_length,mode,par_file)

>>>>>>>>>> Lv2_color <<<<<<<<<<

  Functions:

  ##### soft_counts(E_bound,pi_data)

  -- Will get an array of PI values from the data, where each entry = 1 count.
  So construct an array of ones of equal length, then where E >= E_bound, set to 0.
  This will give an array where 0 = harder X-rays, 1 = softer X-rays, so when
  doing the binning, will get just soft counts.

  E_bound - boundary energy considered (in keV)
  pi_data - array of PI values

  ##### hard_counts(E_bound,pi_data)

  -- Will get an array of PI values from the data, where each entry = 1 count.
  So construct an array of ones of equal length, then where E < E_bound, set to 0.
  This will give an array where 0 = harder X-rays, 1 = softer X-rays, so when
  doing the binning, will get just soft counts.

  E_bound - boundary energy considered (in keV)
  pi_data - array of PI values

  ##### get_color(eventfile,par_list,E_bound,tbin_size)

  -- Calculating the color - hard/soft and (hard-soft)/(hard+soft)

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  E_bound - boundary energy considered (in keV)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!

  ##### get_color_t(eventfile,par_list,E_bound,tbin_size,t1,t2)

  -- Calculating the color - hard/soft and (hard-soft)/(hard+soft)

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  E_bound - boundary energy considered (in keV)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  t1 - lower time boundary
  t2 - upper time boundary

  ##### plotting(eventfile,par_list,E_bound,tbin_size,mode)

  -- Plotting the hardness ratio/color diagrams.

  t_bins,color,color_diff = get_color(eventfile,par_list,E_bound,tbin_size)

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  E_bound - boundary energy considered (in keV)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  mode - whether we want to show or save the plot.

  ##### plotting_t(eventfile,par_list,E_bound,tbin_size,t1,t2,mode)

  -- Plotting the hardness ratio/color diagrams.

  t_bins,color,color_diff = get_color_t(eventfile,par_list,E_bound,tbin_size)

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  E_bound - boundary energy considered (in keV)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  t1 - lower time boundary
  t2 - upper time boundary
  mode - whether we want to show or save the plot.

  TEST:
  eventfile = '/Volumes/Samsung_T5/NICERsoft_outputs/1034070101_pipe/cleanfilt.evt'

  plotting(eventfile,['TIME','PI','PI_FAST'],3,1,'save')
  plotting_t(eventfile,['TIME','PI','PI_FAST'],3,1,200,400,'save')

>>>>>>>>>> Lv2_efsearch <<<<<<<<<<

  Functions:

  ##### efsearch(eventfile,n_segments,dper,nphase,nbint,nper,dres,outfile_root,plot_efsearch)

  Performing FTOOLS' efsearch!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  n_segments - no. of segments to break the epoch folding search into
  dper - value for period used in the folding; input represents center of range of trial periods
  nphase - no. of phases in the folded light curve(s) ; "INDEF" uses the default value
  nbint - the number of newbins per interval used in the analysis
  nper - no. of periods over which the search is carried out
  dres - period resolution is the spacing between two contiguous periods in the search
         "INDEF" uses default value of half the Fourier resolution in the interval
  outfile_root - prefix for the end file name
  plot_efsearch - 'yes' or 'no' to plot the results from efsearch; do "exit" for the next plot!

  TEST:

  out_baryfile = Lv0_dirs.NICER_DATADIR + 'rxj0209/rxj0209kgfilt_bary.evt'

  n_segments = 10 #number of segments to break the epoch folding search into
  dper = 9.3 #Value for the period  used  in the folding. In 'efsearch' the
  #input period represents the centre of the range of the trial periods.
  nphase = 32 #Number of phases in the folded light curve(s). Typing 'INDEF'
  #forces the task to use the default value (see parameter "nbdf").
  nbint = int((T/(dper/nphase))/n_segments) # The number of newbins per interval used in the analysis. The
  #"nbint" together with the NEWBIN duration determines the length in time of an interval
  #and therefore the total number of intervals within the start and stop time over which the
  #analysis will be carried out. Typing 'INDEF' forces the task to use the default value
  #(see parameter "nbdf"). NOTE: By pressing return "nbint" is set to the value found in the
  #parameter file used in a previous run."
  nper = 128 #The number of periods over which the search is carried out
  dres = 1E-4 # The period resolution is the spacing between two contiguous periods in the search.
  #'INDEF' uses the default value of: half the Fourier resolution in the interval (e.g., P^2/T(i)/2 ; T(i) is interval duration)
  outfile_root = "testefsearch"
  plot_efsearch = 'no' #to plot the results from efsearch ; do "exit" to see the next plot!

  Lv2_efsearch.efsearch(out_baryfile,n_segments,dper,nphase,nbint,nper,dres,outfile_root,plot_efsearch)

>>>>>>>>>> Lv2_lc <<<<<<<<<<

  Functions:

  ##### whole(eventfile,par_list,tbin_size,mode)

  -- Plot the entire raw time series without any cuts to the data.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  mode - whether we want to show or save the plot.

  ##### partial_t(eventfile,par_list,tbin_size,t1,t2,mode)

  -- Plot the time series for a desired time interval.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  t1 - lower time boundary
  t2 - upper time boundary
  mode - whether we want to show or save the plot

  ##### partial_E(eventfile,par_list,tbin_size,E1,E2,mode)

  -- Plot the time series for a desired energy range.
  [Though I don't think this will be used much. Count/s vs energy is pointless,
  since we're not folding in response matrix information here to get the flux.
  So we're just doing a count/s vs time with an energy cut to the data.]

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means by in 0.05s
  E1 - lower energy boundary
  E2 - upper energy boundary

  ##### partial_tE(eventfile,par_list,tbin_size,t1,t2,E1,E2,mode)

  -- Plot the time series for a desired time interval and desired energy range.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means by in 0.05s
  t1 - lower time boundary
  t2 - upper time boundary
  E1 - lower energy boundary
  E2 - upper energy boundary

  TEST:
  eventfile = '/Volumes/Samsung_T5/NICERsoft_outputs/1034070101_pipe/cleanfilt.evt'

  whole(eventfile,['TIME','PI','PI_FAST'],1,'save')
  partial_t(eventfile,['TIME','PI','PI_FAST'],1,0,400,'save')
  partial_E(eventfile,['TIME','PI','PI_FAST'],1,0.3,6,'save')
  partial_tE(eventfile,['TIME','PI','PI_FAST'],1,0,200,0.3,6,'save')

>>>>>>>>>> Lv2_merged_pulse_methods <<<<<<<<<<

  Functions:

  ##### niextract_gti_energy(merging,data_id,PI1,PI2)

  -- Using niextract-events to get segmented data based on the energy range

  merging - True/False - whether to use merged data
  data_id - 10-digit ObsID or 6-digit ID for the merged event file
  PI1 - lower bound of PI (not energy in keV!) desired for the energy range
  PI2 - upper bound of PI (not energy in keV!) desired for the energy range

  ##### do_demodulate(merging,data_id,par_file,E_trunc,PI1,PI2)

  -- Using do_demodulate in binary_psr.py in Scott Ransom's PRESTO Python library to
  demodulate the time series for the merged event file!

  merging - True/False - whether to use merged data
  data_id - 10-digit ObsID or 6-digit ID for the merged event file
  par_file - orbital parameter file for input into binary_psr
  E_trunc - True/False - whether to do energy truncation
  PI1 - lower bound of PI (not energy in keV!) desired for the energy range
  PI2 - upper bound of PI (not energy in keV!) desired for the energy range

  ##### pulse_profile(merging,data_id,E_trunc,PI1,PI2,pulse_pars,no_phase_bins)

  -- Extracts the time series from the demodulated merged event file, and creates
  the pulse profile from Lv2_phase.py!

  merging - True/False - whether to use merged data
  data_id - 10-digit ObsID or 6-digit ID for the merged event file
  E_trunc - True/False - whether to do energy truncation
  PI1 - lower bound of PI (not energy in keV!) desired for the energy range
  PI2 - upper bound of PI (not energy in keV!) desired for the energy range
  pulse_pars - parameters corresponding to the pulse
  no_phase_bins - number of phase bins desired

  ##### plot_pf(merging,data_id,E_trunc,PI1,PI2,pulse_pars,no_phase_bins)

  -- Extracts the time series from the demodulated merged event file, and creates
  the pulse profile from Lv2_phase.py!

  merging - True/False - whether to use merged data
  data_id - 10-digit ObsID or 6-digit ID for the merged event file
  E_trunc - True/False - whether to do energy truncation
  PI1 - lower bound of PI (not energy in keV!) desired for the energy range
  PI2 - upper bound of PI (not energy in keV!) desired for the energy range
  pulse_pars - parameters corresponding to the pulse
  no_phase_bins - number of phase bins desired

  TEST:
  merging = False
  data_id = '1013010105'
  E_trunc = False
  PI1 = 30
  PI2 = 1200
  pulse_pars = [29.639575,-3.77535E-10,1.1147E-20]
  no_phase_bins = 50
  plot_pf(merging,data_id,E_trunc,PI1,PI2,pulse_pars,no_phase_bins)

>>>>>>>>>> Lv2_merging_events <<<<<<<<<<

  Functions:

  ##### merging(obsids)

  -- Given a list of ObsIDs, create a file which merges all the rows in the EVENTS
  extension of the FITS files!

  obsids - list (or array) of ObsIDs

  ##### merging_GTIs(obsids,merged_id)

  -- Given a list of ObsIDs and the merged_id, create the final event file, which
  already has all the rows in the EVENTS extension of the FITS files, BUT also
  including the GTI extension of the FITS files!

  obsids - list (or array) of ObsIDs
  merged_id - 6-digit ID for the merged event file

  TEST:
  obsids = ['2060060363','2060060364','2060060365']
  merged_id = '000013'
  merging(obsids)
  merging_GTIs(obsids,merged_id)

>>>>>>>>>> Lv2_mkdir <<<<<<<<<<

  Functions:

  ##### makedir(dir)

  Creating a folder if it does not exist in the directory.

  dir - desired directory (provide FULL path!)

  TEST:
  makedir('/Volumes/Samsung_T5/hahaha')

>>>>>>>>>> Lv2_ngc300_color <<<<<<<<<<

  Functions:

  ##### get_color(bin_size,band1,band2)

  -- Obtain colors and the corresponding uncertainties. Will NOT use values where
  either the counts/rate from band1 OR band2 are negative! Allowed band values are
  "soft1, soft2, A, B, C, D, and inband."

  bin_size - binning size desired (1 day or 10 days, for example)
  band1 - energy band 1
  band2 - energy band 2

>>>>>>>>>> Lv2_phase <<<<<<<<<<

  Functions:

  ##### pulse_profile(f_pulse,times,counts,shift,no_phase_bins)

  -- Calculating the pulse profile for the observation. Goes from 0 to 2!

  f_pulse - the frequency of the pulse
  times - the array of time values
  counts - the array of counts values
  shift - how much to shift the pulse by in the phase axis.
  It only affects how it is presented.
  no_phase_bins - number of phase bins desired

  ##### pulse_folding(t,T,T0,f,fdot,fdotdot,no_phase_bins)

  -- Calculating the pulse profile by also incorporating \dot{f} corrections!
  Goes from 0 to 2.

  t - array of time values
  T - sum of all the GTIs
  T0 - reference epoch in MJD
  f - pulse/folding Frequency
  fdot - frequency derivative
  fdotdot - second derivative of frequency
  no_phase_bins - number of phase bins desired (recommended 20!)

  Returns the pulse profile in counts/s/phase bin vs phase. The number of counts
  is divided by the exposure time (calculated through total sum of the GTIs)

  Also added a "TIMEZERO" manually in the script since it'd be inconvenient to call the eventfile here.

  ##### whole(eventfile,par_list,tbin_size,pulse_pars,shift,no_phase_bins,mode)

  -- Plot the entire raw pulse profile without any cuts to the data.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  pulse_pars - parameters corresponding to the pulse
  shift - how much to shift the pulse by in the phase axis.
  It only affects how the pulse profile is 'displaced'.
  no_phase_bins - number of phase bins desired
  mode - whether we want to show or save the plot.

  pulse_pars will have [f,fdot,fdotdot]

  ##### partial_t(eventfile,par_list,tbin_size,pulse_pars,shift,no_phase_bins,t1,t2,mode)

  -- Plot the pulse profile for a desired time interval.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  pulse_pars - parameters corresponding to the pulse
  shift - how much to shift the pulse by in the phase axis.
  It only affects how it is presented.
  no_phase_bins - number of phase bins desired
  t1 - lower time boundary
  t2 - upper time boundary
  mode - whether we want to show or save the plot

  pulse_pars will have [f,fdot,fdotdot]

  ##### partial_E(eventfile,par_list,tbin_size,Ebin_size,pulse_pars,shift,no_phase_bins,E1,E2,mode)

  -- Plot the pulse profile for a desired energy range.
  [Though I don't think this will be used much. Count/s vs energy is pointless,
  since we're not folding in response matrix information here to get the flux.
  So we're just doing a count/s vs time with an energy cut to the data.]
  INTERJECTION: This caveat is for the spectrum, NOT the pulse profile!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means by in 0.05s
  Ebin_size - the size of the energy bins (in keV!)
  >> e.g., Ebin_size = 0.1 means bin by 0.1keV
  >> e.g., Ebin_size = 0.01 means bin by 0.01keV!
  pulse_pars - parameters corresponding to the pulse
  shift - how much to shift the pulse by in the phase axis.
  It only affects how it is presented.
  no_phase_bins - number of phase bins desired
  E1 - lower energy boundary
  E2 - upper energy boundary

  pulse_pars will have [f,fdot,fdotdot]

  ##### partial_tE(eventfile,par_list,tbin_size,Ebin_size,pulse_pars,shift,no_phase_bins,t1,t2,E1,E2,mode)

  -- Plot the pulse profile for a desired time interval and desired energy range.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means by in 0.05s
  Ebin_size - the size of the energy bins (in keV!)
  >> e.g., Ebin_size = 0.1 means bin by 0.1keV
  >> e.g., Ebin_size = 0.01 means bin by 0.01keV!
  pulse_pars - parameters corresponding to the pulse
  shift - how much to shift the pulse by in the phase axis.
  It only affects how it is presented.
  no_phase_bins - number of phase bins desired
  t1 - lower time boundary
  t2 - upper time boundary
  E1 - lower energy boundary
  E2 - upper energy boundary
  mode - whether we want to show or save the plot

  pulse_pars will have [f,fdot,fdotdot]

  ##### partial_subplots_E(eventfile,par_list,tbin_size,Ebin_size,f_pulse,shift,no_phase_bins,subplot_Es,E1,E2,mode)

  -- Plot the pulse profile for a desired energy range.
  [Though I don't think this will be used much. Count/s vs energy is pointless,
  since we're not folding in response matrix information here to get the flux.
  So we're just doing a count/s vs time with an energy cut to the data.]
  INTERJECTION: This caveat is for the spectrum, NOT the pulse profile!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means by in 0.05s
  Ebin_size - the size of the energy bins (in keV!)
  >> e.g., Ebin_size = 0.1 means bin by 0.1keV
  >> e.g., Ebin_size = 0.01 means bin by 0.01keV!
  f_pulse - the frequency of the pulse
  shift - how much to shift the pulse by in the phase axis.
  It only affects how it is presented.
  no_phase_bins - number of phase bins desired
  subplot_Es - list of tuples defining energy boundaries for pulse profiles
  E1 - lower energy boundary
  E2 - upper energy boundary

  TEST:
  eventfile = '/Volumes/Samsung_T5/NICERsoft_outputs/1034070101_pipe/ni1034070101_nicersoft_bary.evt'

  whole(eventfile,['TIME','PI','PI_FAST'],0.01,[0.20801275,0,0],0.4,21,'show')
  partial_t(eventfile,['TIME','PI','PI_FAST'],1,[0.2081,0,0],0.4,21,0,400,'show')
  partial_E(eventfile,['TIME','PI','PI_FAST'],1,0.05,[0.2081,0,0],0.4,21,0.3,12,'show')
  partial_tE(eventfile,['TIME','PI','PI_FAST'],1,0.05,[0.2081,0,0],0.4,21,0,400,0.3,12,'show')

>>>>>>>>>> Lv2_preprocess <<<<<<<<<<

  Functions:

  ##### preprocess(obsdir,nicerl2_flags,psrpipe_flags,refframe,orbitfile,parfile,nicer_datafile,nicer_output,nicersoft_datafile,nicersoft_output,nicersoft_folder)

  -- Preprocessing the NICER data for use in PRESTO, so running gunzip, psrpipe, and barycorr.

  obsdir - NICER data directory containing all the data files (e.g., path_to_NICER_dir/1034070101)
  nicerl2_flags - a LIST of input flags for nicerl2
  psrpipe_flags - a LIST of input flags for psrpipe
  refframe - reference frame for barycenter corrections (usually ICRS)
  orbitfile - orbit file (from the NICER data directory) for the barycenter corrections
  parfile - .par file if any
  nicer_datafile - event file from the original NICER data directory
  nicer_output - output/barycenter-corrected event file from the original NICER data directory
  nicersoft_datafile - event file (usually cleanfilt.evt) from the NICERsoft data directory
  nicersoft_output - output/barycenter-corrected event file from the NICERsoft data directory
  nicersoft_folder - output folder for the NICERsoft data

  Functions:

  TEST:
  obsdir = Lv0_dirs.NICER_DATADIR + '1034070101/'
  nicerl2_flags = ['clobber=YES']
  psrpipe_flags = ['--emin','0.3','--emax','12.0'] #for psrpipe in Lv0_psrpipe
  refframe = 'ICRS' #for barycorr in Lv1_barycorr
  orbitfile = obsdir + '/auxil/ni1034070101.orb'
  parfile = ''

  nicer_datafile = obsdir + 'xti/event_cl/ni1034070101_0mpu7_cl.evt'
  nicer_output = obsdir + 'xti/event_cl/ni1034070101_0mpu7_cl_bary.evt'
  nicersoft_datafile = Lv0_dirs.NICERSOFT_DATADIR + '1034070101_pipe/cleanfilt.evt'
  nicersoft_output = Lv0_dirs.NICERSOFT_DATADIR + '1034070101_pipe/ni1034070101_nicersoft_bary.evt'
  nicersoft_folder = Lv0_dirs.NICERSOFT_DATADIR + '1034070101_pipe/'

  preprocess(obsdir,nicerl2_flags,psrpipe_flags,refframe,orbitfile,parfile,nicer_datafile,nicer_output,nicersoft_datafile,nicersoft_output,nicersoft_folder)

>>>>>>>>>> Lv2_presto_subroutines <<<<<<<<<<

  Functions:

  ##### get_gti_file(eventfile,segment_length)

  -- Creating the individual .gti files for my data segments!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the individual segments for combining power spectra

  ##### niextract_gti_time(eventfile,segment_length)

  -- Using niextract-events to get segmented data based on the [segment_length]-length
  GTIs that were created above!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the individual segments for combining power spectra

  ##### niextract_gti_energy(eventfile,PI1,PI2)

  -- Using niextract-events to get segmented data based on the energy range

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  PI1 - lower bound of PI (not energy in keV!) desired for the energy range
  PI2 - upper bound of PI (not energy in keV!) desired for the energy range

  ##### niextract_gti_time_energy(eventfile,segment_length,PI1,PI2)

  -- Using niextract-events to get segmented data based on [segment_length]-length
  GTIs that were created above, AND energy range!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the individual segments for combining power spectra
  PI1 - lower bound of PI (not energy in keV!) desired for the energy range
  PI2 - upper bound of PI (not energy in keV!) desired for the energy range

  ##### do_nicerfits2presto(eventfile,tbin,segment_length)

  -- Using nicerfits2presto.py to bin the data, and to convert into PRESTO-readable format.
  I can always move files to different folders to prevent repeats (especially for large files)

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  tbin - size of the bins in time
  segment_length - length of the individual segments for combining power spectra

  ##### edit_inf(eventfile,tbin,segment_length)

  -- Editing the .inf file, as it seems like accelsearch uses some information from the .inf file!
  Mainly need to edit the "Number of bins in the time series".
  This is only for when we make segments by time though!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  tbin - size of the bins in time
  segment_length - length of the individual segments

  ##### edit_binary(eventfile,tbin,segment_length)

  -- To pad the binary file so that it will be as long as the desired segment length.
  The value to pad with for each time bin, is the average count rate in THAT segment!
  Jul 10: Do zero-padding instead... so that number of counts is consistent!
  Again, this is only for when we make segments by time!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  tbin - size of the bins in time
  segment_length - length of the individual segments

  ##### realfft(eventfile,segment_length,mode)

  -- Performing PRESTO's realfft on the binned data (.dat)

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the individual segments
  mode - "all", "t" or "E" ; basically to tell the function where to access files to run realfft for

  ##### accelsearch(eventfile,segment_length,mode,flags)

  -- Performing PRESTO's accelsearch on the FFT data (.fft)

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  segment_length - length of the individual segments
  mode - "all", "t" or "E" ; basically to tell the function where to access files to run accelsearch for
  flags - a LIST of input flags for accelsearch

  ##### prepfold(eventfile,mode,zmax)

  -- Performing PRESTO's prepfold on the pulsation candidates.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  mode - "all", "t" or "E" ; basically to tell the function where to access files to run prepfold for
  zmax - maximum acceleration

  ##### ps2pdf(eventfile,mode)

  == Converting from .ps to .pdf

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  mode - "all", "t" or "E" ; basically to tell the function where to access files to run ps2pdf for

  TEST:
  eventfile = Lv0_dirs.NICERSOFT_DATADIR + '1034070101_pipe/ni1034070101_nicersoft_bary.evt'
  mode = 't'
  segment_length = 100
  PI1 = 100
  PI2 = 1000
  zmax=100

  tbin = 0.025

  accelsearch_flags = ['-numharm','4','-zmax','100','-photon','-flo','1','-fhi','1000']

  get_gti_file(eventfile,segment_length)
  niextract_gti_time(eventfile,segment_length)
  niextract_gti_energy(eventfile,PI1,PI2)
  niextract_gti_time_energy(eventfile,segment_length,PI1,PI2)
  do_nicerfits2presto(eventfile,tbin,segment_length)
  edit_inf(eventfile,tbin,segment_length)
  edit_binary(eventfile,tbin,segment_length)
  realfft(eventfile,segment_length,mode)
  accelsearch(eventfile,segment_length,mode,accelsearch_flags)
  prepfold(eventfile,mode,zmax)
  ps2pdf(eventfile,mode)

>>>>>>>>>> Lv2_ps_method <<<<<<<<<<

  Functions:

  ##### padding(counts)

  -- For use in the function manual. Recall: The optimal number of bins is 2^n,
  n being some natural number. We pad 0s onto the original data set, where
  the number of 0s to pad is determined by the difference between the optimal
  number of bins and the length of the data set (where the former should be
  greater than the latter!)

  counts - array of counts from the binned data

  ##### oversample(factor,counts)

  -- Perform oversampling on the data. Return the padded array of counts.

  factor - N-times oversampling; factor = 5 means 5x oversampling
  counts - array of counts from the binned data

  ##### pdgm(times,counts,xlims,vlines,toplot,oversampling)

  -- Generating the power spectrum through the signal.periodogram method.

  times - array of binned times
  counts - array of counts from the binned data
  xlims - a list or array: first entry = True/False as to whether to impose an
  xlim; second and third entry correspond to the desired x-limits of the plot
  vlines - a list or array: first entry = True/False as to whether to draw
  a vertical line in the plot; second entry is the equation for the vertical line
  toplot - whether to show the plot or not
  oversampling - whether to perform oversampling. Array will consist of
  [True/False, oversampling factor]

  ##### manual(times,counts,xlims,vlines,toplot,oversampling)

  -- Generating the power spectrum through the manual FFT method.

  times - array of binned times
  counts - array of counts from the binned data
  xlims - a list or array: first entry = True/False as to whether to impose an
  xlim; second and third entry correspond to the desired x-limits of the plot
  vlines - a list or array: first entry = True/False as to whether to draw
  a vertical line in the plot; second entry is the equation for the vertical line
  toplot - whether to show the plot or not
  oversampling - whether to perform oversampling. Array will consist of
  [True/False, oversampling factor]

>>>>>>>>>> Lv2_ps <<<<<<<<<<

  Functions:

  ##### whole(eventfile,par_list,tbin_size,mode,ps_type,oversampling,xlims,vlines)

  -- Plot the entire power spectrum without any cuts to the data.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  mode - whether we want to show or save the plot.
  ps_type - obtain power spectrum through the periodogram method ('period') or
  the manual FFT way ('manual') or both ('both')
  oversampling - whether to perform oversampling. Array will consist of
  [True/False, oversampling factor]
  xlims - a list or array: first entry = True/False as to whether to impose an
  xlim; second and third entry correspond to the desired x-limits of the plot
  vlines - a list or array: first entry = True/False as to whether to draw
  a vertical line in the plot; second entry is the equation for the vertical line

  ##### partial_t(eventfile,par_list,tbin_size,t1,t2,mode,ps_type,oversampling,xlims,vlines)

  -- Plot the power spectrum for a desired time interval.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  t1 - lower time boundary
  t2 - upper time boundary
  mode - whether we want to show or save the plot.
  ps_type - obtain power spectrum through the periodogram method ('period') or
  the manual FFT way ('manual') or both ('both')
  oversampling - whether to perform oversampling. Array will consist of
  [True/False, oversampling factor]
  xlims - a list or array: first entry = True/False as to whether to impose an
  xlim; second and third entry correspond to the desired x-limits of the plot
  vlines - a list or array: first entry = True/False as to whether to draw
  a vertical line in the plot; second entry is the equation for the vertical line

  ##### partial_E(eventfile,par_list,tbin_size,Ebin_size,E1,E2,mode,ps_type,oversampling,xlims,vlines)

  -- Plot the time series for a desired energy range.
  [Though I don't think this will be used much. Count/s vs energy is pointless,
  since we're not folding in response matrix information here to get the flux.
  So we're just doing a count/s vs time with an energy cut to the data.]

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means by in 0.05s
  Ebin_size - the size of the energy bins (in keV!)
  >> e.g., Ebin_size = 0.1 means bin by 0.1keV
  >> e.g., Ebin_size = 0.01 means bin by 0.01keV!
  E1 - lower energy boundary
  E2 - upper energy boundary
  mode - whether we want to show or save the plot.
  ps_type - obtain power spectrum through the periodogram method ('period') or
  the manual FFT way ('manual') or both ('both')
  oversampling - whether to perform oversampling. Array will consist of
  [True/False, oversampling factor]
  xlims - a list or array: first entry = True/False as to whether to impose an
  xlim; second and third entry correspond to the desired x-limits of the plot
  vlines - a list or array: first entry = True/False as to whether to draw
  a vertical line in the plot; second entry is the equation for the vertical line

  ##### partial_tE(eventfile,par_list,tbin_size,Ebin_size,t1,t2,E1,E2,mode,ps_type,oversampling,xlims,vlines)

  -- Plot the time series for a desired time interval and desired energy range.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means by in 0.05s
  Ebin_size - the size of the energy bins (in keV!)
  >> e.g., Ebin_size = 0.1 means bin by 0.1keV
  >> e.g., Ebin_size = 0.01 means bin by 0.01keV!
  t1 - lower time boundary
  t2 - upper time boundary
  E1 - lower energy boundary
  E2 - upper energy boundary
  mode - whether we want to show or save the plot.
  ps_type - obtain power spectrum through the periodogram method ('period') or
  the manual FFT way ('manual') or both ('both')
  oversampling - whether to perform oversampling. Array will consist of
  [True/False, oversampling factor]
  xlims - a list or array: first entry = True/False as to whether to impose an
  xlim; second and third entry correspond to the desired x-limits of the plot
  vlines - a list or array: first entry = True/False as to whether to draw
  a vertical line in the plot; second entry is the equation for the vertical line

  TEST:
  eventfile = '/Volumes/Samsung_T5/NICERsoft_outputs/1034070101_pipe/ni1034070101_nicersoft_bary.evt'
  whole(eventfile,['TIME','PI','PI_FAST'],0.1,'show','both',[True,5],[False,0,1],[True,0.2081])
  partial_t(eventfile,['TIME','PI','PI_FAST'],0.1,0,100,'show','both',[False,5],[False,0,1],[True,0.2081])
  partial_E(eventfile,['TIME','PI','PI_FAST'],0.1,0.05,3,8,'show','both',[False,5],[False,0,1],[True,0.2081])
  partial_tE(eventfile,['TIME','PI','PI_FAST'],0.1,0.05,0,100,3,8,'show','both',[False,5],[False,0,1],[True,0.2081])


################################################################################
################################################################################
################################################################################

################################## LEVEL 3 #####################################

>>>>>>>>>> Lv3_analyze_xspec_pars <<<<<<<<<<

 Functions:

  ##### model_par(model)

  -- Given the model, return a list of associated Parameters

  model - name of the model used

  ##### xspec_par(model,E1,E2)

  -- From the model.txt files, obtain the XSPEC parameter fit values

  model - name of the model used
  E1 - lower bound for energy (4-digit PI string)
  E2 - upper bound for energy (4-digit PI string)

  ##### plot_ufspectra(model,MJDs,E1,E2)

  -- Plotting the outputs from ufspectra!

  model - name of the model used
  MJDs - list of MJDs used
  E1 - lower bound for energy (4-digit PI string)
  E2 - upper bound for energy (4-digit PI string)

  ##### plot_rrcl(model,MJDs,E1,E2,plottype)

  -- To plot either of ratio, residual, chi, or lumin

  model - name of the model used
  MJDs - list of MJDs used
  E1 - lower bound for energy (4-digit PI string)
  E2 - upper bound for energy (4-digit PI string)
  plottype - either of 'ratio','resid','chi', or 'lumin'

  ##### plot_HID(MJDs)

  -- Plot the soft color-intensity diagram for a given set of MJDs

  MJDs - list of MJDs used

  ##### lumin_plus_par(model,MJDs,E1,E2)

  -- Plot luminosity against a spectral parameter
  11/17: Need to be able to generalize such that I can use this function for >1 model!

  model - name of the model used
  MJDs - list of MJDs used
  E1 - lower bound for energy (4-digit PI string)
  E2 - upper bound for energy (4-digit PI string)

  TEST:
  E1 = '0040'
  E2 = '0500'
  absorption = 'tbnew'
  models = ['-powerlaw','-bbodyrad','-ezdiskbb','-diskbb']
  MJDs_25 = ['58239','58244','58249','58254','58259','58264','58269','58274',
              '58289','58309','58314','58324','58329','58334','58339','58389',
              '58399','58449','58454','58459','58464','58484','58489','58504',
              '58509']
  MJDs_23 = ['58239','58244','58249','58254','58259','58264','58269','58274',
              '58289','58309','58314','58324','58329','58334','58339','58389',
              '58449','58454','58464','58484','58489','58504','58509']
  MJDs_21 = ['58239','58244','58249','58254','58259','58264','58269','58274',
              '58309','58314','58324','58329','58334','58339','58389','58449',
              '58454','58484','58489','58504','58509']

  #for i in range(len(models)):
  #    plot_rrcl(absorption+models[i],MJDs_25,E1,E2,'ratio')
  #plot_rrcl(absorption+'-powerlaw-bbodyrad',MJDs_21,E1,E2,'ratio')
  #plot_rrcl(absorption+'-powerlaw-bbodyrad',MJDs_21,E1,E2,'resid')
  #plot_rrcl(absorption+'-powerlaw-bbodyrad',MJDs_21,E1,E2,'chi')
  #plot_rrcl(absorption+'-powerlaw-bbodyrad',MJDs_21,E1,E2,'lumin')
  plot_ufspectra(absorption+'-powerlaw',MJDs_21,E1,E2)
  #xspec_par('tbnew-powerlaw',E1,E2)

>>>>>>>>>> Lv3_average_ps_main <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_B1957+20_merged <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_calc_deadtime <<<<<<<<<<

  Functions:

  ##### deadtime(obsid,mpu_no,par_list)

  -- Calculate the accumulated deadtime for a given observation ID

  obsid - Observation ID of the object of interest (10-digit str)
  mpu_no - Will be '7' for the combined file
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)

  ##### exposure(obsid,bary,par_list)

  -- Get the on-source, exposure time

  obsid - Observation ID of the object of interest (10-digit str)
  bary - Whether the data is barycentered. True/False
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)

  TEST:
  print(deadtime('1050390148','7',['TIME','DEADTIME']))
  print(exposure('1050390148',True,['TIME','DEADTIME','PI','PI_FAST']))

>>>>>>>>>> Lv3_detection_level <<<<<<<<<<

  Functions:

  ##### max_acc(zmax,T,f0)

  -- To obtain the maximum acceleration 'detectable' by PRESTO.

  zmax - (expected) maximum number of Fourier bins that the pulsar frequency
  f0 drifts
  T - observation duration (s)
  f0 - pulsar's frequency (Hz)

  ##### N_trials(tbin,T)

  -- To obtain the number of trials used in the FFT. Divided by two to get number
  of trials f >= 0!

  tbin- size of the bins in time
  T - observation duration (s) or segment length (s)

  ##### single_trial_prob(significance,N)

  -- To obtain the single trial probability required for a statistically significant
  "significance" detection, with N trials.

  significance - the number of 'sigmas' desired for detection
  N - number of trials

  ##### signal_significance(M,W,Pthreshold)

  -- Calculating the significance of a particular signal in the power spectrum,
  given M (number of segments), W (number of consecutive bins summed), and
  Pthreshold (the power [Leahy-normalized] of the signal).

  M - number of segments
  W - number of consecutive bins summed
  Pthreshold - the power of the signal (Leahy-normalized)

  ##### power_for_sigma(significance,N,M,W)

  -- Given some probability (that is, desired significance), what is the corresponding
  power needed in the power spectrum to claim statistical significance? Use the
  inverse survival function for this!

  significance - the number of 'sigmas' desired for detection
  N - number of trials
  M - number of segments
  W - number of consecutive bins summed

  TEST:
  print(max_acc(200,200,230))
  sig_sig = signal_significance(43,5000,2.02697)
  sig_sig = signal_significance(43,5000,2.01199)
  print(power_for_sigma(5,4000,1,1))
  single_trial_prob(2,4e6)
  single_trial_prob(1,4e6)

>>>>>>>>>> Lv3_diagnostics_display <<<<<<<<<<

  Functions:

  ##### display_all(eventfile,diag_var,lc_t,lc_counts,diag_t,diag_counts,filetype)

  -- To display the plots for desired time interval. Whether to save or show the
  plots is determined in Lv3_diagnostics.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  diag_var - the diagnostic variable we are looking at
  lc_t - array corresponding to time values for the light curve
  lc_counts - array corresponding to counts for the light curve
  diag_t - array corresponding to times for the diagnostic variable
  diag_counts - array corresponding to counts for the diagnostic variable
  filetype = '.att', '.mkf', '.cl' or ['.hk',mpuno]

  ##### display_t(eventfile,diag_var,t1,t2,lc_t,lc_counts,diag_t,diag_counts,filetype)

  -- To display the plots for desired time interval. Whether to save or show the
  plots is determined in Lv3_diagnostics.

  obsid - Observation ID of the object of interest (10-digit str)
  diag_var - the diagnostic variable we are looking at
  t1 - lower time boundary
  t2 - upper time boundary
  lc_t - array corresponding to time values for the light curve
  lc_counts - array corresponding to counts for the light curve
  diag_t - array corresponding to times for the diagnostic variable
  diag_counts - array corresponding to counts for the diagnostic variable
  filetype = '.att', '.mkf', '.cl' or ['.hk',mpuno]

>>>>>>>>>> Lv3_diagnostics <<<<<<<<<<

  Functions:

  ##### diag_all(eventfile,par_list,tbin_size,mode,diag_vars)

  Get the diagnostic plots for a desired time interval.
  [Likely too large a range in time (and energy) to be sufficiently useful for
  diagnosis.]

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  mode - whether we want to show or save the plot.
  diag_vars - a dictionary where each key = 'att','mkf','hk', or 'cl', and
  diag_vars[key] provides the list of variables to loop over.

  ##### diag_t(eventfile,par_list,tbin_size,t1,t2,mode,diag_vars)

  Get the diagnostic plots for a desired time interval.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  t1 - lower time boundary
  t2 - upper time boundary
  mode - whether we want to show or save the plot.
  diag_vars - a dictionary where each key = 'att','mkf','hk', or 'cl', and
  diag_vars[key] provides the list of variables to loop over.

>>>>>>>>>> Lv3_duty_cycle <<<<<<<<<<

  Functions:

  ##### duty_cycle(eventfile,tbin,segment_length,duty_cycle_bin,threshold)

  -- To determine the percentage of "data used"/total amount of data. Have two
  types of values:
  1) % of bins (of size duty_cycle_bin) with data over the ENTIRE observation
  2) % of bins with data over the GTIs

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  tbin - size of the bins in time
  segment_length - length of the individual segments
  duty_cycle_bin - binning used to calculate the duty cycle
  threshold - if amount of data in the segment is more than threshold IN PERCENTAGE, use the data

  ##### duty_cycle_dist(eventfile,tbin,segment_length,duty_cycle_bin,threshold)

  -- To get the distribution of duty cycles over all segments, given an ObsID and
  a desired segment length!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  tbin - size of the bins in time
  segment_length - length of the individual segments
  duty_cycle_bin - binning used to calculate the duty cycle
  threshold - if amount of data in the segment is more than threshold IN PERCENTAGE, use the data

  ##### duty_cycle_tE(eventfile,tbin,segment_length,PI1,PI2,duty_cycle_bin,threshold)

  -- To determine the percentage of "data used"/total amount of data. Have two
  types of values:
  1) % of bins (of size duty_cycle_bin) with data over the ENTIRE observation
  2) % of bins with data over the GTIs

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  tbin - size of the bins in time
  segment_length - length of the individual segments
  PI1 - lower energy boundary (in units of PI)
  PI2 - upper energy boundary (in units of PI)
  duty_cycle_bin - binning used to calculate the duty cycle
  threshold - if amount of data in the segment is more than threshold IN PERCENTAGE, use the data

  ##### duty_cycle_tE_dist(eventfile,tbin,segment_length,PI1,PI2,duty_cycle_bin,threshold)

  -- To get the distribution of duty cycles over all segments, given an ObsID and
  a desired segment length!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  tbin - size of the bins in time
  PI1 - lower energy boundary (in units of PI)
  PI2 - upper energy boundary (in units of PI)
  segment_length - length of the individual segments
  duty_cycle_bin - binning used to calculate the duty cycle
  threshold - if amount of data in the segment is more than threshold IN PERCENTAGE, use the data

  ##### compare_segment_lengths(eventfile,tbin,segment_lengths,duty_cycle_bin)

  -- To get the distribution of duty cycles over all segments, given an ObsID and
  a desired segment length! Compare through different thresholds!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  tbin - size of the bins in time
  segment_lengths - array of length of the individual segments
  duty_cycle_bin - binning used to calculate the duty cycle

  TEST:
  eventfile = Lv0_dirs.NICERSOFT_DATADIR + '1034070101_pipe/ni1034070101_nicersoft_bary.evt'
  #duty_cycle(eventfile,0.00025,100,1,10)
  ### REMEMBER, tbin is NOT from Lv3_average_segments, but it's from nicerfits2presto!

  duty_cycle_tE(eventfile,0.00025,100,30,200,1,10)

>>>>>>>>>> Lv3_E_boundary <<<<<<<<<<

  Functions:

  ##### E_bound(eventfile,par_list,E1,E2,cut_type,bound)

  -- Gives the energy bound corresponding to either a custom cut or a median cut.
  Could add more cuts in the future!

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  E1 - energy value for the lower boundary (in keV)
  E2 - energy value for the upper boundary (in keV)
  cut_type - 'manual' or 'median'
  bound - boundary energy for when cut_type = 'manual'

  TEST:
  obsid = '1034070101'
  eventfile = Lv0_dirs.NICER_DATADIR + obsid + '/xti/event_cl/ni' + obsid + '_0mpu7_cl_bary.evt'
  print(E_bound(eventfile,['PI','TIME','PI_FAST'],0.0,20,'median',2.7))

>>>>>>>>>> Lv3_holistic_CenX3 <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_J1231-1411_changeW <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_main <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_merged_pulsed_profile <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_ngc300_plots <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_orbsol <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_plot_at2018cow_v2 <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_plot_at2018cow <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_presto_candidates <<<<<<<<<<

  Functions:

  ##### get_candidates(obsid,name_par_list,zmax,f1,f2)

  -- Getting pulsation candidates within some frequency range. If I want the full
  frequency range, just do f1 = 0, f2 = some large number.

  obsid - Observation ID of the object of interest (10-digit str)
  name_par_list - list of parameters specifying parameters like GTI number and/or energy range
  zmax - maximum acceleration
  f1 - lower limit of frequency range
  f2 - upper limit of frequency range

  name_par_list should be [GTI_true,E_true,GTIno,segment_length,PI1,PI2]

  TEST:
  get_candidates('1200250101',[True,False,0,64,0,0],100,0,100)

>>>>>>>>>> Lv3_presto_main <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_pulsations <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_pulsedfrac <<<<<<<<<<

  Functions:

  ##### pf_all(eventfile,par_list,tbin_size,f_pulse,shift,no_phase_bins,mode)

  -- Obtaining the pulsed fraction from the entire raw pulse profile without
  any cuts to the data.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  f_pulse - the frequency of the pulse
  shift - how much to shift the pulse by in the phase axis.
  It only affects how the pulse profile is 'displaced'.
  no_phase_bins - number of phase bins desired
  mode - whether we want to show or save the plot.

  ##### pf_t(eventfile,par_list,tbin_size,f_pulse,shift,no_phase_bins,t1,t2,mode)

  -- Obtain the pulsed fraction from the pulse profile for a desired time interval.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means bin by 0.05s!
  f_pulse - the frequency of the pulse
  shift - how much to shift the pulse by in the phase axis.
  It only affects how it is presented.
  no_phase_bins - number of phase bins desired
  t1 - lower time boundary
  t2 - upper time boundary
  mode - whether we want to show or save the plot

  ##### pf_E(eventfile,par_list,tbin_size,Ebin_size,f_pulse,shift,no_phase_bins,E1,E2,mode)

  -- Obtain the pulsed fraction from the pulse profile for a desired energy range.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means by in 0.05s
  Ebin_size - the size of the energy bins (in keV!)
  >> e.g., Ebin_size = 0.1 means bin by 0.1keV
  >> e.g., Ebin_size = 0.01 means bin by 0.01keV!
  f_pulse - the frequency of the pulse
  shift - how much to shift the pulse by in the phase axis.
  It only affects how it is presented.
  no_phase_bins - number of phase bins desired
  E1 - lower energy boundary
  E2 - upper energy boundary

  ##### pf_tE(eventfile,par_list,tbin_size,Ebin_size,f_pulse,shift,no_phase_bins,t1,t2,E1,E2,mode)

  -- Obtain the pulsed fraction from a desired time interval and desired energy range.

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  par_list - A list of parameters we'd like to extract from the FITS file
  (e.g., from eventcl, PI_FAST, TIME, PI,)
  tbin_size - the size of the time bins (in seconds!)
  >> e.g., tbin_size = 2 means bin by 2s
  >> e.g., tbin_size = 0.05 means by in 0.05s
  Ebin_size - the size of the energy bins (in keV!)
  >> e.g., Ebin_size = 0.1 means bin by 0.1keV
  >> e.g., Ebin_size = 0.01 means bin by 0.01keV!
  f_pulse - the frequency of the pulse
  shift - how much to shift the pulse by in the phase axis.
  It only affects how it is presented.
  no_phase_bins - number of phase bins desired
  t1 - lower time boundary
  t2 - upper time boundary
  E1 - lower energy boundary
  E2 - upper energy boundary
  mode - whether we want to show or save the plot

  TEST:
  eventfile = Lv0_dirs.NICERSOFT_DATADIR + '1034070101_pipe/ni1034070101_nicersoft_bary.evt'
  print(pf_tE(eventfile,['TIME','PI','PI_FAST'],0.01,0.05,[0.20801725,0,0],0.4,50,0,500,1,6,'show'))

>>>>>>>>>> Lv3_quicklook <<<<<<<<<<

  ##### nicerql(eventfile,extra_nicerql_args)

  -- Probably the second step in the process, but this is to generate the psrpipe
  diagnostic plots, to see if there are any obvious red flags in the data.

  Will just really need eventfile ; orb file and mkf file is assumed to be in the SAME folder

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  extra_nicerql_args - extra arguments to the nicerql script

  ##### filtering(eventfile,outfile,maskdet,eventflags)

  -- Function that will filter out bad detectors and impose eventflag restrictions.
  Will expect to add to this function over time...

  eventfile - path to the event file. Will extract ObsID from this for the NICER files.
  outfile - output file from the filtering
  maskdet - list of DET_IDs to mask
  eventflags - NICER event flags to filter out (e.g., in the format '(EVENT_FLAGS==bx1x000)')

>>>>>>>>>> Lv3_swift <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_TBOs <<<<<<<<<<

  Functions:

>>>>>>>>>> Lv3_Z2_stat <<<<<<<<<<

  -- Update later! Still need to upgrade this to use 'eventfile'