Detailed Usage#

C/C++ executable binary: cali#

./cali param.txt

Here param.txt is the parameter file passed to cali. The parameter file looks like:

# parameter file
# lines beginning with '#' are regarded as comments and are neglected

FileCont      data/ngc5548_cont.txt
#FileLine      data/ngc5548_line.txt

#NMcmc         10000

#PTol         0.1

#FixedScale     0
#FixedShift     0

#ScaleRangeLow  0.5
#ScaleRangeUp   1.5

#ShiftRangeLow  -1.0
#ShiftRangeUp   1.0

#FixedSyserr     1
#FixedErrorScale  1

#SyserrRangeLow  0.0
#SyserrRangeUp   0.1

#ErrscaleRangeLow  0.1
#ErrscaleRangeUp   2.0

#FlagNorm  0

#SigmaRangeLow  1.0e-4
#SigmaRangeUp  1.0

#TauRangeLow  1.0
#TauRangeUp  1.0e4

#FixedCodes  1,3

#FixedScaleCodes 1,3

In the parameter file, except for the option FileCont, all the rest options are optional. If they are not specified, cali will use the default values as shown above. The meaning of the above options are

Option	Example	Type	Meaning
FileCont	data/ngc5548_cont.txt		file name of continuum light curve
FileLine	data/ngc5548_line.txt	optional	file name of line light curves, can be multiple lines, use comma (,) to separate, e.g., data/ngc5548_line1.txt, data/ngc5548_line2.txt
NMcmc	10000	optional	number of mcmc steps
PTol	0.1	optional	tolerance of log likelihood in MCMC samling
FixedScale	0	optional	1: fix scale factor (=1); 0: not
FixedShift	0	optional	1: fix shift factor (=0); 0: not
ScaleRangeLow	0.5	optional	lower limit of scale factor
ScaleRangeUp	1.5	optional	upper limit of scale factor
ShiftRangeLow	-1.0	optional	lower limit of shift factor
ShiftRangeUp	1.0	optional	upper limit of shift factor
FixedSyserr	1	optional	1: fix systematic error (=0); 0: not
FixedErrorScale	1	optional	1: fix error scale (=1); 0: not
SyserrRangeLow	0.0	optional	lower limit of systematic error
SyserrRangeUp	0.1	optional	upper limit of systematic error
ErrscaleRangeLow	0.1	optional	lower limit of error scale
ErrscaleRangeUp	2.0	optional	upper limit of error scale
SigmaRangeLow	1.0e-4	optional	lower limit of DRW sigma
SigmaRangeUp	1.0	optional	upper limit of DRW sigma
TauRangeLow	1.0	optional	lower limit of DRW tau
TauRangeUp	1.0e4	optional	upper limit of DRW tau
FixedCodes	1,3	optional	codes to be fixed can be multiple codes, use comma (,) to separate, e.g., 1,3 this will fix 1st and 3rd code (counting from 0)
FixedScaleCodes	1,3	optional	codes need to fix the scale can be multiple codes, use comma (,) to separate, e.g., 1,3 this will fix 1st and 3rd code (=1) (counting from 0)
FlagNorm	1	optional	whether do normalization before intercalibrating 1: yes; 0: no

Here FlagNorm specifies whether mica2 does normalization to the light curves of each data codes by their means before intercalibrating. This is necessary when there are large offsets between data codes. However, when the data has large variability and the time span of data code(s) is short, the means might be seriously biased. In this case, doing normalization is not helpful to intercalibration. One may first mannually align the data and turn off FlagNorm option.

After running cali, there is a Python script plot_for_cali.py that can used to generate plots, which generates a PDF file named PyCALI_results.pdf and draw a matplotlib figure window to show intercalibrated light curves.

Please also refer to Frequently Asked Questions for more details not covered here.

Python module: pycali#

An example for using pycali in a Python script is

import pycali
import matplotlib.pyplot as plt
import numpy as np

#######################################################
# setup configurations, there are two ways:
# 1) load from a param file
#    cfg = pycali.Config("param.txt")
# 2) direct call setup()
#
cfg = pycali.Config()

# except for the argument "fcont", the rest arguments are optional.
# e.g.,  cfg.setup(fcont="data/ngc5548_cont.txt")
#
cfg.setup(
          fcont="data/ngc5548_cont.txt",     # fcont is a string
          fline=["data/ngc5548_line.txt"],   # fline is a list, include multiple lines
          nmcmc=10000, ptol=0.1,
          scale_range_low=0.5, scale_range_up=2.0,
          shift_range_low=-1.0, shift_range_up=1.0,
          syserr_range_low=0.0, syserr_range_up=0.2,
          errscale_range_low=0.5, errscale_range_up=2.0,
          sigma_range_low=1.0e-4, sigma_range_up=1.0,
          tau_range_low=1.0, tau_range_up=1.0e4,
          fixed_scale=False, fixed_shift=False,
          fixed_syserr=True, fixed_error_scale=True,
          fixed_codes=[],
          fixed_scalecodes=[],
          flag_norm=True,
          )
cfg.print_cfg()

######################################################
# do intercalibration
#
cali = pycali.Cali(cfg)  # create an instance
cali.mcmc()              # do mcmc
cali.get_best_params()   # calculate the best parameters
cali.output()            # print output
cali.recon()             # do reconstruction

# plot results to PyCALI_results.pdf
pycali.plot_results(cfg)

# a simple plot
pycali.simple_plot(cfg)

Please also refer to Frequently Asked Questions for more details not covered here.

Detailed Usage

Contents

Detailed Usage#

C/C++ executable binary: cali#

Python module: pycali#