Problems with enrico_lc

[ErickR100]

Hi

I try to generate the Mrk421 light curve with time intervals in a text file, but when executing enrico_lc with the configuration file, I get the following error:

['/home/erick/enrico/bin/enrico_lc', 'mrk421.conf']
[Message]: work on the config file mrk421.conf
{'out': '/home/erick/Escritorio/Mkn421_intt/datos', 'verbose': 'yes', 'clobber': 'yes', 'Submit': 'no', 'target': {'name': 'Mrk421', 'ra': 166.113808, 'dec': 38.20883287, 'redshift': 0.031, 'ebl_model': 4, 'spectrum': 'PowerLaw', 'fit_tau': 'no'}, 'space': {'xref': 166.113808, 'yref': 38.20883287, 'rad': 15.0, 'binsz': 0.1, 'coordsys': 'CEL', 'proj': 'AIT', 'phibins': 0}, 'file': {'spacecraft': 'sc.fits', 'event': 'fotones.dat', 'xml': '/home/erick/Escritorio/Mkn421_intt/datos/Mrk421_PowerLaw_model.xml', 'tag': 'LAT_Analysis', 'parent_config': ''}, 'time': {'tmin': 0.0, 'tmax': 0.0, 'file': '/home/erick/Escritorio/Mkn421_intt/tiempo.dat', 'type': 'MET'}, 'energy': {'emin': 100.0, 'emax': 300000.0, 'enumbins_per_decade': 10, 'decorrelation_energy': 'no'}, 'event': {'irfs': 'CALDB', 'evclass': 128, 'evtype': 3}, 'analysis': {'zmax': 90.0, 'likelihood': 'binned', 'EnergyDispersion': 'yes', 'ComputeDiffrsp': 'yes', 'roicut': 'no', 'evtroicuts': 'yes', 'evttimecuts': 'yes', 'filter': '(DATA_QUAL>0)&&(LAT_CONFIG==1)', 'keep_all_srcmaps': 'no'}, 'environ': {'FERMI_DATA_DIR': '', 'FERMI_CATALOG_DIR': '', 'FERMI_CATALOG': '', 'FERMI_DIFFUSE_DIR': '', 'FERMI_PREPROCESSED_DIR': ''}, 'fitting': {'optimizer': 'MINUIT', 'ftol': 1e-06, 'min_source_TS': 1.0}, 'model': {'diffuse_gal_dir': '', 'diffuse_iso_dir': '', 'diffuse_gal': '', 'diffuse_iso': '', 'min_significance_catalog': 4.0, 'min_significance_free': 25.0, 'max_radius': 5.0, 'max_roi': 10.0, 'parameters_noise': 0.0}, 'Spectrum': {'FitsGeneration': 'yes', 'ResultPlots': 'yes', 'ResultParentPlots': 'no', 'FrozenSpectralIndex': 0.0}, 'UpperLimit': {'SpectralIndex': 2.0, 'Method': 'Profile', 'envelope': 'no', 'TSlimit': 25.0, 'cl': 0.95}, 'LightCurve': {'FitsGeneration': 'yes', 'NLCbin': 1, 'SpectralIndex': 2.0, 'MakeConfFile': 'yes', 'BayesianBlocks': 'no', 'ComputeVarIndex': 'yes', 'TSLightCurve': 9.0, 'DiagnosticPlots': 'yes', 'DiagnosticParentPlots': 'no'}, 'BayesianBlocks': {'FitsGeneration': 'yes', 'p0': 0.01, 'SpectralIndex': 1.8, 'MakeConfFile': 'yes', 'TSLightCurve': 9.0, 'DiagnosticPlots': 'yes', 'DiagnosticParentPlots': 'no'}, 'FoldedLC': {'NLCbin': 10, 'epoch': 0.0, 'Period': 0.0}, 'AppLC': {'FitsGeneration': 'yes', 'index': 2.0, 'rad': 1.0, 'NLCbin': 10, 'binsFromData': 'no', 'emin': -1.0, 'emax': -1.0}, 'Ebin': {'FitsGeneration': 'yes', 'NumEnergyBins': 0, 'TSEnergyBins': 9.0, 'DistEbins': 'logE'}, 'TSMap': {'Re-Fit': 'no', 'npix': 10, 'RemoveTarget': 'yes', 'method': 'row'}, 'findsrc': {'FitsGeneration': 'yes', 'Refit': 'yes'}, 'srcprob': {'FitsGeneration': 'yes', 'rad': 1.0, 'srclist': '', 'numberPhoton': 10}, 'Contours': {'parname1': 'Prefactor', 'parname2': 'Index'}, 'ComponentAnalysis': {'EUnBinned': -1.0, 'FrontBack': 'no', 'PSF': 'no', 'EDISP': 'no', 'FGL4': 'no'}}
reusing /home/erick/Escritorio/Mkn421_intt/datos/Mrk421_LAT_Analysis_EvtCoarse.fits as event file to speed-up the analysis
use /home/erick/Escritorio/Mkn421_intt/tiempo.dat
[LightCurve]: Running LC with 9.0 bins

Traceback (most recent call last):
File "/home/erick/enrico/bin/enrico_lc", line 26, in
liste = np.genfromtxt(sys.argv[1],dtype="str",unpack=True)
File "/home/erick/anaconda3/envs/fermi/lib/python3.7/site-packages/numpy/lib/npyio.py", line 2122, in genfromtxt
raise ValueError(errmsg)
ValueError: Some errors were detected !
Line #9 (got 1 columns instead of 3)
Line #20 (got 1 columns instead of 3)
Line #29 (got 1 columns instead of 3)
Line #37 (got 1 columns instead of 3)
Line #43 (got 1 columns instead of 3)
Line #49 (got 1 columns instead of 3)
Line #54 (got 1 columns instead of 3)
Line #70 (got 1 columns instead of 3)
Line #79 (got 1 columns instead of 3)
Line #85 (got 1 columns instead of 3)
Line #101 (got 1 columns instead of 3)
Line #111 (got 1 columns instead of 3)
Line #123 (got 1 columns instead of 3)
Line #142 (got 1 columns instead of 3)
Line #158 (got 1 columns instead of 3)
Line #166 (got 1 columns instead of 3)
Line #181 (got 1 columns instead of 3)
Line #195 (got 1 columns instead of 3)
Line #206 (got 1 columns instead of 3)
Line #212 (got 1 columns instead of 3)
Line #222 (got 1 columns instead of 3)
Line #226 (got 1 columns instead of 3)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/erick/enrico/bin/enrico_lc", line 32, in
run_over_conffile(sys.argv[1])
File "/home/erick/enrico/bin/enrico_lc", line 20, in run_over_conffile
lc.MakeLC()
File "/home/erick/enrico/enrico/lightcurve.py", line 225, in MakeLC
self._MakeTimeBins()
File "/home/erick/enrico/enrico/lightcurve.py", line 119, in _MakeTimeBins
for i in range(self.Nbin):
TypeError: 'float' object cannot be interpreted as an integer

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

I have the following in my config file:

[time]
tmin = 441763203
tmax = 454809603
file = "/home/erick/Escritorio/Mkn421_intt/tiempo.dat"
type = MET

[LightCurve]
#Generates fits files or not?
FitsGeneration = yes
#Number of points for the LC
NLCbin = 1
#Index for the power law. Left free to vary if 0
SpectralIndex = 2.0
MakeConfFile = yes
#Bayesian blocks
BayesianBlocks = no
#Compute Variability index as in the 2FGL.
ComputeVarIndex = yes
#Compute an UL if the TS of the sources is <TSLightCurve
TSLightCurve = 9.0
#Generates control plots
DiagnosticPlots = yes
# Plot (update) the parent config related plots during time bin production
DiagnosticParentPlots = no

[davidsanchez]

Hi
how your /tiempo.dat looks like?
best

[ErickR100]

It is as follows
############################################################################################################################################################################################################

441763203 446860803
446860804 449539203
449539205 450748803
450748806 451353603
451353607 451699203
451699208 451785603
451785609 451807203
451807200 451828803
451828801 454420803

[davidsanchez]

With the # ? not sur this is well read.

[ErickR100]

Without the # signs, only the 2 columns with the first the start time and the second the end time

[davidsanchez]

ok. I'll have a deeper look asap

[ErickR100]

Thank you so much

[davidsanchez]

Could you give me the full config file please?

[davidsanchez]

Could you try the fix I made ?thanks

[ErickR100]

Default config and validation file for Enrico.

Besides providing default options it is also used

to check the user config file.

Options without default options here must be

specified in the user config file

Folder where the output will be stored

out = /home/erick/Escritorio/Mkn421_intt/datos

verbosity

verbose = yes
#Overwrite existing output files. Use with caution
clobber = yes
#Submit the job to a cluster?
Submit = no

[target]
name = Mrk421
ra = 166.113808
dec = 38.20883287
redshift = 0.031
ebl_model = 4
spectrum = PowerLaw
# 0=Kneiske, 1=Primack05, 2=Kneiske_HighUV, 3=Stecker05, 4=Franceschini, 5=Finke, 6=Gilmore, 10=Dominguez11
# full list http://www-glast.stanford.edu/cgi-bin/viewcvs/celestialSources/eblAtten/eblAtten/EblAtten.h?view=markup
fit_tau = no

[space]
xref = 166.113808
yref = 38.20883287
rad = 15.0
binsz = 0.1
coordsys = CEL
proj = AIT
phibins = 0

[file]
spacecraft = sc.fits
event = fotones.dat
xml = /home/erick/Escritorio/Mkn421_intt/datos/Mrk421_PowerLaw_model.xml
tag = LAT_Analysis
# keep track of the parent config during nested operations (e.g. energy/time bins)
parent_config = ""

[time]
tmin = 441763203.0
tmax = 454809603.0
file = "/home/erick/Escritorio/Mkn421_intt/tiempo.txt"
type ='MET'

[energy]
emin = 100.0
emax = 300000.0
enumbins_per_decade = 10
decorrelation_energy = no

[event]
irfs = CALDB
evclass = 128
evtype = 3

[analysis]
zmax = 100
# General analysis options
likelihood = unbinned
# Correct energy dispersion?
EnergyDispersion = yes
ComputeDiffrsp = yes
roicut = no
# cuts applied during the first coarse bin selection:
evtroicuts = yes
evttimecuts = yes
filter = (DATA_QUAL>0)&&(LAT_CONFIG==1)
# should we keep the srcmaps for all sources in the srcMap file?
# this should speed up future fits, at the cost of disk space.
keep_all_srcmaps = no

[environ]
# Analysis environment configuration
# Can also be done via shell environment variables
FERMI_DATA_DIR = ""
FERMI_CATALOG_DIR = ""
FERMI_CATALOG = ""
FERMI_DIFFUSE_DIR = ""
FERMI_PREPROCESSED_DIR = ""

[fitting]
optimizer = MINUIT
ftol = 1e-06
# if source_ts < min_source_TS in the fit, the source is removed from the model
min_source_TS = 1.0

[model]
# The following options determine the xml model
diffuse_gal_dir = ""
diffuse_iso_dir = ""
diffuse_gal = ""
diffuse_iso = ""
# user points sources for diffuse catalog sources
# freeze spectral parameters for weak and far away sources:
min_significance_catalog = 4.0
min_significance_free = 25.0
max_radius = 5.0
# Add all source in a radius of analyse ROI + this radius
max_roi = 10.0
# Add gaussian noise to the spectral parameters of free sources (may help during the fit)
parameters_noise = 0.0

[Spectrum]
#Generates fits files or not?
FitsGeneration = yes
#Generates plots (SED, model map)
ResultPlots = yes
# Plot (update) the parent config related plots during energy bin production
ResultParentPlots = no
#Freeze the spectral index of the source. Has no implication if 0 (Left free to vary)
FrozenSpectralIndex = 0.0

[UpperLimit]
#Assumed Spectral index
SpectralIndex = 2.0
# UL method could be Profile or Integral (provided by the fermi collaboration).
#Poisson is base on the Feldman-Cousins method for low signal. Only 95 % yet available
Method = Profile
envelope = no
#Compute an UL if the TS of the sources is <TSlimit
TSlimit = 25.0
# Confidence level for the Ul computation
cl = 0.95

[LightCurve]
#Generates fits files or not?
FitsGeneration = yes
#Number of points for the LC
NLCbin = 1
#Index for the power law. Left free to vary if 0
SpectralIndex = 2.0
MakeConfFile = yes
#Bayesian blocks
BayesianBlocks = no
#Compute Variability index as in the 2FGL.
ComputeVarIndex = yes
#Compute an UL if the TS of the sources is <TSLightCurve
TSLightCurve = 9.0
#Generates control plots
DiagnosticPlots = yes
# Plot (update) the parent config related plots during time bin production
DiagnosticParentPlots = no

[BayesianBlocks]
#Generates fits files or not?
FitsGeneration = yes
#False alarm probability
p0 = 0.01
#Index for the power law. Left free to vary if 0
SpectralIndex = 1.8
MakeConfFile = yes
#Compute an UL if the TS of the sources is <TSLightCurve
TSLightCurve = 9.0
#Generates control plots
DiagnosticPlots = yes
# Plot (update) the parent config related plots during time bin production
DiagnosticParentPlots = no

[FoldedLC]
#Number of bins for the orbitally folded LC
NLCbin = 10
#Epoch of phase=0 in MJD, equal to tmin is 0
epoch = 0.0
#Orbital period in days
Period = 0.0

[AppLC]
#Generates fits files or not?
FitsGeneration = yes
#Spectral index for the exposure calculation
index = 2.0
#Apperture radius
rad = 1.0
#Number of bins
NLCbin = 10
#bin form data or frozen bin size
binsFromData = no
#minimum energy for the apperture lightcurve, if -1 use the one define in energy section
emin = -1.0
emax = -1.0

[Ebin]
#Generates fits files or not?
FitsGeneration = yes
NumEnergyBins = 0
#Compute an UL if the TS of the sources is <TSEnergyBins
TSEnergyBins = 9.0
# How to generate the Ebins
# - logE: log scaled bins
# - TS: similar TS per bin
# - mix: half-way between log and TS.
# - [ E1, E2, E3, E4, ..., EN ]: custom binning.
# - default is logE
DistEbins = logE

[TSMap]
#Re-fit before computing the TS map
Re-Fit = no
#Numbers of pixel in x and y
npix = 10
#Remove or not the target from the model
RemoveTarget = yes
#Generate the TS map pixel by pixel or by grouping the pixels by row.
#(reduce the numbers of jobs but each job is longer)
method = row

[findsrc]
#Generates fits files or not?
FitsGeneration = yes
#Reoptimize before
Refit = yes

[srcprob]
#Generates fits files or not?
FitsGeneration = yes
#radius for the computation
rad = 1.0
# list of sources
srclist = ""
# number of photons to print
numberPhoton = 10

[Contours]
parname1 = Prefactor
parname2 = Index

[ComponentAnalysis]
# EUnBinned to the energy (MeV) where
# binned and unbinned analysis should be split
# disabled if -1
EUnBinned = -1.0
# Divide the analysis in FrontBack classes
FrontBack = no
# Divide the analysis in PSF classes
PSF = no
# Divide the analysis in EDISP classes
EDISP = no
# Divide the analysis in EDISP classes
FGL4 = no

[ErickR100]

Could you try the fix I made ?thanks
Sorry, but what solution?

[davidsanchez]

I made a push . could you update your enrico?

[Sahakyan86]

Hi,

I had a similar issue but the new version is fine.

[davidsanchez]

great.

[ErickR100]

thank you so much, everything works very well