version for Pass 8 release

bin/enrico_gui

@@ -19,12 +19,4 @@ except:
 
 gui=gui.EnricoGui(infile)
 
-## Message
-win = gtk.Window(gtk.WINDOW_TOPLEVEL)
-button = gtk.Button("The gui is in development. Use with caution")
-button.connect_object("clicked", gtk.Widget.destroy, win)
-win.add(button)
-button.show()
-win.show()
-
 gtk.main()

doc/source/_templates/layout.html

@@ -0,0 +1,22 @@
+{% extends "!layout.html" %}
+
+
+{% block rootrellink %}
+        <li><a href="{{ pathto('index') }}">home</a>|&nbsp;</li>
+        <li><a href="{{ pathto('search') }}">search</a>|&nbsp;</li>
+       <li><a href="{{ pathto('contents') }}">documentation </a> &raquo;</li>
+{% endblock %}
+
+
+{% block relbar1 %}
+
+<div style="background-color: white; text-align: left; padding: 10px 10px 15px 15px">
+<a href="{{ pathto('index') }}"><img src="{{
+pathto("_static/banner.png", 1) }}" border="0" alt="sampledoc"/></a>
+</div>
+{{ super() }}
+{% endblock %}
+
+{# put the sidebar before the body #}
+{% block sidebar1 %}{{ sidebar() }}{% endblock %}
+{% block sidebar2 %}{% endblock %}

doc/source/configfile.rst

@@ -31,7 +31,12 @@ Note :
  * Coordinate are in degrees.
  * Available models are 'PowerLaw', 'PowerLaw2', 'LogParabola', 'PLExpCutoff'
 
-The parameter `spectrum` is used for the generation of the sky model. Of course, you can change the model describing the spectrum of any sources (by hand...). All the models supported by the ST are described `here <http://fermi.gsfc.nasa.gov/ssc/data/analysis/documentation/Cicerone/Cicerone_Likelihood/Model_Selection.html>`_. For now, the supported models by `enrico` are PowerLaw, PowerLaw2, LogParabola, PLExpCutoff, Generic. `Generic` is for the non-supported models. By supported, we mean that enrico can produce a xml file with such model and has some optional features. It is completely possible to run an analyze with enrico and a non-supported model.
+The parameter `spectrum` is used for the generation of the sky model. Of course, you can change the model describing the spectrum of any sources (by hand...). All the models supported by the ST are described `here <http://fermi.gsfc.nasa.gov/ssc/data/analysis/documentation/Cicerone/Cicerone_Likelihood/Model_Selection.html>`_. For now, the supported models by `enrico` are PowerLaw, PowerLaw2, LogParabola, PLExpCutoff, Generic. `Generic` is for the non-supported models. By supported, we mean that enrico can produce a xml file with such model and has some optional features. It is completely possible to run an analyse with enrico and a non-supported model. For extragalactic sources, absorption by the extragalactic background light can be taken into account. This feature is disable if z=0:
+
+ * redshift has to be provided
+ * ebl_model is a id of a model - the number is defined in the ST. 0=Kneiske, 1=Primack05, 2=Kneiske_HighUV, 3=Stecker05, 4=Franceschini, 5=Finke, 6=Gilmore
+ * the EBL absorption can be scaled by a parameter which can be fitted if fit_tau = yes
+
 
 .. code-block:: ini
 
@@ -40,6 +45,9 @@ The parameter `spectrum` is used for the generation of the sky model. Of course,
       ra = 238.92935
       dec = 11.190102
       spectrum = PowerLaw2
+      redshift = 0.5
+      ebl_model = 4
+      fit_tau = no
 
 Space
 -----
@@ -136,16 +144,29 @@ Convtype is use to select either the front (0), back (1) or both (-1) events. If
    [analysis]
       # General analysis options
       likelihood = binned
-      evclass = 2
       zmax = 100.0
       roicut = no
       filter = DATA_QUAL==1&&LAT_CONFIG==1&&ABS(ROCK_ANGLE)<52
-      irfs = P7REP_SOURCE_V15
-      # if convtype =0 or 1, an ::FRONT of ::BACK is happend at the end of the irfs string automatically
-      convtype = -1
 
 
-fitting
+Events and IRFs
+--------
+
+This part is used to defined how enrico should select the event and which IRFs to use. You can defined the event class and evtype. By default IRFS are automatically selected using the  evclass and evtype (see ST documentation), irfs default value is then CALDB.
+
+event class (PSF, edisp, etc..) can be selected through this skim. For more information, please see XXX
+
+Currently supported irfs with this system are the PASS8_R2 irfs.
+
+.. code-block:: ini
+
+   [event]
+      irfs = CALDB
+      evclass = 128
+      evtype = 3
+
+
+Fitting
 -------
 
 Option for the minimizer. You can use MINUIT, NEWMINUIT, DRMGB, etc. ftol is the tolerance that the minimizer should reach.
@@ -157,7 +178,7 @@ Option for the minimizer. You can use MINUIT, NEWMINUIT, DRMGB, etc. ftol is the
       ftol = 1e-06
 
 
-model
+Model
 -----
 
 This section is about the sky model generation. If you have set correctly you environment variables, then enrico is able to find the galactic and extragalactic model. If you want to use other model, you can specify here, their names and locations.
@@ -216,8 +237,8 @@ UpperLimit
 
 This section allows to set up the upper limit computation. During the
 computation, the spectral index of the source (it is assumed that a POWERLAW or
-POWERLAW2 model is used) is frozen to `SpectralIndex`. Two methods can be used,
-Profile of Integral, see the Fermi web site for more informations.
+POWERLAW2 model is used) is frozen to `SpectralIndex`. 3 methods can be used,
+Profile or Integral (see the Fermi web site for more informations) and Poisson .base on the Feldman-Cousins method for low signal (Only 95 % yet available)
 
 An upper limit, at the confidence level `cl`, is computed if the TS is below TSlimit. This hold only for `enrico_sed`
 
@@ -235,8 +256,9 @@ An upper limit, at the confidence level `cl`, is computed if the TS is below TSl
       # Confidence level for the Ul computation
       cl = 0.95
 
-LightCurve
-----------
+LightCurve : running the analyse in time bins
+----------------------------------------
+
 
 Option for enrico_lc which run an entire analysis in time bins and produce all the fits files needed to use gtlike.
 
@@ -288,8 +310,8 @@ This section is devoted to the folded LC. This is designed for binary system ana
       Period = 10
 
 
-Ebin
-----
+Ebin : running the analyse in energy bins
+--------------------------------
 
  * FitsGeneration, if yes, enrico will make all the steps before running gtlike and generated all the fits files needed. If the files have already been generated, change FitsGeneration to no and enrico will only run gtlike
 
@@ -310,8 +332,8 @@ Ebin
 
 Option for enrico_tsmap
 
-TSMap
------
+TSMap : creating a TS map
+--------------------------------
 
 This section is used to configured `enrico_tsmap` and `enrico_plot_tsmap` 
 
@@ -354,7 +376,7 @@ For the entire row 49 :
 
 
 
-Finding the position of a source
+Findsrc : Finding the position of a source
 --------------------------------
 
 This section is used to configured `enrico_findsrc`. It run the tool gtfindsource and update the file Roi_model.reg with the fitted position in red.
@@ -371,3 +393,31 @@ This section is used to configured `enrico_findsrc`. It run the tool gtfindsourc
       #Reoptimize before
       Refit = option('yes', 'no', default='yes')
 
+srcprob : Get the highest energy event
+--------------------------------
+
+This section is used to configured `enrico_srcprob`.
+
+This part get the highest energy events that can bee associated to the sources in the lit. The probability to be a source event is also computed (using unbinned analyse). The source list has to be an ascii text.
+
+.. code-block:: ini
+   [srcprob]
+      #Generates fits files or not?
+      FitsGeneration = option('yes', 'no', default='yes')
+      #radius for the computation
+      rad = float(default=1)
+      # list of sources 
+      srclist = string(default="")
+      # number of photons to print
+      numberPhoton = integer(default=10)
+
+Contours : Compute confidence contour
+--------------------------------
+
+This section is used to configured `enrico_contour`. It is possible to compute the 1, 2 and 3 sigma contour of the 2 parameters given here.
+
+.. code-block:: ini
+   [Contours]
+      parname1 = string(default="Prefactor")
+      parname2 = string(default="Index")
+

doc/source/script.rst

@@ -18,6 +18,14 @@ Options:
 
  * vmax is used to defined the max of the color scale
 
+
+
+.. figure::  _static/Maps.png
+   :align:   center
+
+   Maps of  PG 1553+113, from top to bottom: counts map, model map, residuals map.
+
+
 Plot TS Maps
 ------------------
 
@@ -32,3 +40,28 @@ Options:
  * vmax is used to defined the max of the color scale
 
  * stretch can be linear (default), log, sqrt, arcsinh or power
+
+
+.. figure::  _static/TSMaps.png
+   :align:   center
+
+   TS Map of PG 1553+113.
+
+Convert Time
+------------------
+
+The script ConvertTime.py convert a given time to another units
+
+Type can be : MJD, JD, MET or ISO
+
+.. code-block:: ini
+
+  python ConvertTime.py  type value
+
+Here are some examples:
+
+.. code-block:: ini
+
+    python  ConvertTime.py  MJD 56101
+    python  ConvertTime.py  ISO 2012-02-05
+    python  ConvertTime.py  ISO 2012-02-05 16:15:18

doc/source/team.rst

@@ -0,0 +1,11 @@
+.. _team:
+
+Enrico Developers
+=================
+
+Enrico was initially written by David Sanchez and Christoph Deil in 2011.
+
+You can find up to date lists of contributors
+`here <https://github.com/gammapy/enrico/graphs/contributors>`_
+or
+`here <http://www.ohloh.net/p/enrico/contributors/summary>`_.

doc/source/tools.rst

@@ -25,3 +25,4 @@ ScienceTools are described `here <http://fermi.gsfc.nasa.gov/ssc/data/analysis/s
 * ``enrico_plot_tsmap`` : plot the TS Map resulting from enrico_tsmap
 * ``enrico_scan`` : make a profile likelihood for each free parameter of the target
 * ``enrico_findsrc`` : run gtfindsource
+* ``enrico_contour`` : make a confidence contour of 2 parameters

doc/source/tutorial.rst

@@ -118,12 +118,18 @@ and store it into a xml file which will be used for the analysis.
    Use the catalog :  /CATALOG_PATH/gll_psc_v06.fit
    Add  12  sources in the ROI of  10.0  degrees
    3  sources have free parameters inside  3.0  degrees
+   Iso model file  /gpfs/LAPP-DATA/hess/sanchez/Fermi/Soft/ScienceTools//IExternal/diffuseModels/v5r0/iso_P8R2_SOURCE_V6_v06.txt
+   Galactic model file  /gpfs/LAPP-DATA/hess/sanchez/Fermi/Soft/ScienceTools//IExternal/diffuseModels/v5r0/gll_iem_v06.fits
+
    write the Xml file in  ~/myanalysis/PG155+113_PowerLaw2_model.xml
 
 .. note:: 
    Note that you give options for this step simply by mentioning
    the config file. For the `enrico_xml` tool, the relevant options
    are in the [space], [target] section.  The out file is given by [file]/xml.
+
+   The Iso model can be guess using the evclass and evtype given in the config file. 
+   If the file does not excist the default one is used
 
 Get data
 --------
@@ -247,19 +253,48 @@ An upper limits is calculated if the Test Statistic (TS) of the source is below
  * bins in energy, use the option [Ebin]/TSEnergyBins. 
  * `enrico_lc`, use the option [LightCurve]/TSLightCurve. 
 
-Two methods are available :
+3 methods are available :
 
  * The profile method, which look for a decrease of a certain amount of the likelihood function
  * The integral method which compute the integral of the  likelihood function as a function of a parameter to set the UL
+ * The Poisson method based on Feldman-Cousins method for low signal
 
-Both implementations are provided by the ScienceTools and used by enrico.
+The first 2 implementations are provided by the ScienceTools and used by enrico.
 
 
 .. note:: 
    For upper limits, most of the relevant options are in the [UpperLimits]
    section
 
 
+
+Results
+------------
+
+At the end of `enrico_sed`, a file with the extension `.results`  is created. After is an example for a POWERLAW model:
+
+
+ * Index : Value of the spectral index (for POWERLAW)
+ * Scale : Value of the scale parameter (MeV, for POWERLAW)
+ * Optimizer : optimizer used in the fit
+ * Emin : Value of the energy min (MeV)
+ * Emax : Value of the energy max (MeV)
+ * tmax : Value of the time max (MET)
+ * dScale : Error of the scale parameter (MeV, for POWERLAW)
+ * TS : Value of the Test statistic 
+ * ModelType : Spectral model fitted
+ * SrcName : Name of the target
+ * Flux : fitted integral flux (ph/cm2/s)
+ * Npred : Number of predicted photons
+ * log_like : Value of the loglikehihood
+ * dIndex : Error of the spectral index (for POWERLAW)
+ * dFlux : Error fitted integral flux (ph/cm2/s)
+ * dPrefactor : Error Prefactor parameter (ph/MeV/cm2/s)
+ * tmin : Value of the time min (MET)
+ * Prefactor : Value Prefactor parameter (ph/MeV/cm2/s)
+
+Summaries of the LC and Ebin computations are also given in a ascii file at the end of `enrico_plot_sed` and `enrico_plot_lc`
+
 Plot results
 ------------
 
@@ -347,7 +382,22 @@ These maps are use to visualize the ROI and check and see any misfitted sources.
 Make Profile likelihood
 -----------------------
 
-The tool `enrico_scan` allows to make profile likelihood of the free parameters of the target. Each plot is save under the `scan` folder. Fits files must have been generated before.
+The tool `enrico_scan` allows to make a profile likelihood of the free parameters of the target. Each plot is save under the `scan` folder. Fits files must have been generated before.
+
+Make Confidence contour
+-----------------------
+
+The tool `enrico_contour` allows to make a contour of 2  free parameters of the target. Each plot is save under the `contour` folder. Fits files must have been generated before.
+
+Get the highest energy events
+-----------------------
+
+The tool `enrico_srcprob' compute the highest energy photons that can be associated to a list of sources (provided in an ascii file). The probability of the photons to be associated to the sources is also computed
+
+Refine source position
+-----------------------
+
+The tool `enrico_findsrc' is based on gtfindsource and find the best position of a source
 
 Check different models
 ----------------------

enrico/RunGTlike.py

@@ -7,9 +7,9 @@
 from enrico.fitmaker import FitMaker
 
 
-def Analysis(folder, config, tag="", convtyp='-1', verbose = 1):
+def Analysis(folder, config, tag="" ,verbose = 1):
     """ run an analysis"""
-    Obs = Observation(folder, config, convtyp, tag=tag)
+    Obs = Observation(folder, config, tag=tag)
     if verbose:
         utils._log('SUMMARY: ' + tag)
         Obs.printSum()
@@ -25,8 +25,9 @@ def GenAnalysisObjects(config, verbose = 1, xmlfile =""):
     folder = config['out']
     if SummedLike == 'yes':
         # Create two obs instances
-        FitRunnerfront = Analysis(folder, config, tag="FRONT", convtyp=0, verbose = verbose)
-        FitRunnerback = Analysis(folder, config, tag="BACK", convtyp=1, verbose = verbose)
+        sys.exit("not yet working")
+        FitRunnerfront = Analysis(folder, config, tag="FRONT", verbose = verbose)
+        FitRunnerback = Analysis(folder, config, tag="BACK", verbose = verbose)
         if not(xmlfile ==""):
             FitRunnerfront.obs.xmlfile = xmlfile
             FitRunnerback.obs.xmlfile = xmlfile
@@ -38,12 +39,11 @@ def GenAnalysisObjects(config, verbose = 1, xmlfile =""):
         Fit.addComponent(FitF)
         FitRunner = FitRunnerback
     else:
-        convtype = config['analysis']['convtype']
         # Create one obs instance
-        FitRunner = Analysis(folder, config, tag="", convtyp=convtype, verbose = verbose)
-        if not(xmlfile ==""):
-            FitRunner.obs.xmlfile = xmlfile
-        Fit = FitRunner.CreateLikeObject()
+        FitRunner = Analysis(folder, config, tag="", verbose = verbose)
+    if not(xmlfile ==""):
+        FitRunner.obs.xmlfile = xmlfile
+    Fit = FitRunner.CreateLikeObject()
     return FitRunner,Fit
 
 def run(infile):
@@ -57,9 +57,6 @@ def run(infile):
     FitRunner.PerformFit(Fit)
 
     Result = FitRunner.GetAndPrintResults(Fit)#Get and dump the target specific results
-    if config['verbose'] == 'yes' :
-        utils.GetFluxes(Fit,FitRunner.obs.Emin,FitRunner.obs.Emax) #print the flux of all the sources
-
     utils.DumpResult(Result, config)
 
     #plot the SED and model map if possible and asked