Iftach Sadeh / ctools

Commit 9afc4de28fcd628c59acf45ccf57b727dfaa1133

Authored by Michael Mayer
1 parent 794678a8

Modify csspec to work on binned input, too. Added test case and slighlty updated… 

… ctcubemask for this purpose
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Showing 4 changed files with 144 additions and 183 deletions
cscripts/csspec.py
  View file @9afc4de
... ... @@ -43,7 +43,7 @@ class csspec(ctools.cscript):
43 43 self.version = "1.0.0"
44 44  
45 45 # Initialise some members
46   - self.obs = None
  46 + self.obs = gammalib.GObservations()
47 47 self.fits = None
48 48  
49 49 # Initialise some members
... ... @@ -106,7 +106,7 @@ class csspec(ctools.cscript):
106 106 pars.append(gammalib.GApplicationPar("outfile","f","a","spectrum.fits","","","Output file name"))
107 107 pars.append(gammalib.GApplicationPar("expcube","f","a","NONE","","","Exposure cube file (only needed for stacked analysis)"))
108 108 pars.append(gammalib.GApplicationPar("psfcube","f","a","NONE","","","PSF cube file (only needed for stacked analysis)"))
109   - pars.append(gammalib.GApplicationPar("bkgcube","s","a","NONE","","","Background cube file (only needed for stacked analysis)"))
  109 + pars.append(gammalib.GApplicationPar("bkgcube","f","a","NONE","","","Background cube file (only needed for stacked analysis)"))
110 110 pars.append(gammalib.GApplicationPar("caldb","s","a","prod2","","","Calibration database"))
111 111 pars.append(gammalib.GApplicationPar("irf","s","a","South_50h","","","Instrument response function"))
112 112 pars.append(gammalib.GApplicationPar("edisp","b","h","no","","","Apply energy dispersion?"))
... ... @@ -114,16 +114,6 @@ class csspec(ctools.cscript):
114 114 pars.append(gammalib.GApplicationPar("emax","r","h","100.0","","","Upper energy limit for spectral points(TeV)"))
115 115 pars.append(gammalib.GApplicationPar("enumbins","i","a","20","","","Number of spectral points"))
116 116 pars.append(gammalib.GApplicationPar("ebinalg","s", "h","LOG","FILE|LIN|LOG","", "Algorithm for defining energy bins"))
117   - pars.append(gammalib.GApplicationPar("binned","b","a","no","yes|no","","Use binned analysis in each energy bin"))
118   - pars.append(gammalib.GApplicationPar("nebins","i","h","5","","","Number of energy bins per spectral point"))
119   - pars.append(gammalib.GApplicationPar("coordsys","s","a","CEL","CEL|GAL","","Coordinate System"))
120   - pars.append(gammalib.GApplicationPar("proj","s","a","CAR","AIT|AZP|CAR|MER|MOL|STG|TAN","","Projection method"))
121   - pars.append(gammalib.GApplicationPar("xref","r","a","83.63","0","360","First coordinate of image center in degrees (RA or galactic l)"))
122   - pars.append(gammalib.GApplicationPar("yref","r","a","22.01","-90","90","Second coordinate of image center in degrees (DEC or galactic b)"))
123   - pars.append(gammalib.GApplicationPar("nxpix","i","a","200","","","Size of the X axis in pixels"))
124   - pars.append(gammalib.GApplicationPar("nypix","i","a","200","","","Size of the Y axis in pixels"))
125   - pars.append(gammalib.GApplicationPar("binsz","r","a","0.02","","","Pixel size (deg/pixel)"))
126   - pars.append(gammalib.GApplicationPar("anumbins","i","h","200","","","Angular separation bins for PSF cube in binned mode"))
127 117 pars.append(gammalib.GApplicationPar("calc_ts","b","h","yes","yes|no","","Compute TS value in each bin"))
128 118 pars.append(gammalib.GApplicationPar("calc_ulim","b","h","yes","yes|no","","Compute upper limit in each bin"))
129 119 pars.append(gammalib.GApplicationPar("fix_srcs","b","h","yes","yes|no","","Fix other skymodel parameters"))
... ... @@ -139,10 +129,18 @@ class csspec(ctools.cscript):
139 129 """
140 130 Get parameters from parfile and setup the observation.
141 131 """
  132 +
142 133 # Set observation if not done before
143 134 if self.obs == None or self.obs.size() == 0:
144 135 self.require_inobs("csspec::get_parameters()")
145 136 self.obs = self.get_observations()
  137 +
  138 + # Check if we have one binned cta observation, i.e. if we are in binned mode
  139 + self.m_binned_mode = False
  140 + if self.obs.size() == 1:
  141 + if self.obs[0].classname() == "GCTAObservation":
  142 + if self.obs[0].eventtype() == "CountsCube":
  143 + self.m_binned_mode = True
146 144  
147 145 # Set models if we have none
148 146 if self.obs.models().size() == 0:
... ... @@ -151,25 +149,44 @@ class csspec(ctools.cscript):
151 149 # Get source name
152 150 self.m_srcname = self["srcname"].string()
153 151  
154   - # Get ebounds
155   - self.m_ebounds = self.create_ebounds()
156   -
157   - # Get binning flag
158   - self.m_binned = self["binned"].boolean()
159   -
  152 + # Get ebounds
  153 + if self.m_binned_mode:
  154 +
  155 + # Extract cube ebounds
  156 + cube_ebounds = self.obs[0].events().ebounds()
  157 +
  158 + # Read user parameters
  159 + self.m_enumbins = self["enumbins"].integer()
  160 + self.m_emin = self["emin"].real() - 1e-6 #rounding tolerance
  161 + self.m_emax = self["emax"].real() + 1e-6 #rounding tolerance
  162 +
  163 + # Compute number of energy layers used for one spectral bin
  164 + n_layers = cube_ebounds.size() / self.m_enumbins
  165 +
  166 + # Don't allow zero layers
  167 + if n_layers == 0:
  168 + n_layers = 1
  169 +
  170 + # Create new ebounds object and fill it
  171 + self.m_ebounds = gammalib.GEbounds()
  172 + for i in range(cube_ebounds.size())[::n_layers]:
  173 + if i + n_layers > cube_ebounds.size():
  174 + break
  175 +
  176 + # Get new emin and emax of bin
  177 + emin = cube_ebounds.emin(i)
  178 + emax = cube_ebounds.emax(i + n_layers - 1)
  179 +
  180 + # Append energy bin if within user range
  181 + if self.m_emin <= emin.TeV() and self.m_emax >= emax.TeV():
  182 + self.m_ebounds.append(emin, emax)
  183 +
  184 + # Unbinned mode
  185 + else:
  186 + self.m_ebounds = self.create_ebounds()
  187 +
160 188 # Get edisp flag
161 189 self.m_edisp = self["edisp"].boolean()
162   -
163   - if self.m_binned:
164   - self.m_xref = self["xref"].real()
165   - self.m_yref = self["yref"].real()
166   - self.m_nxpix = self["nxpix"].integer()
167   - self.m_nypix = self["nypix"].integer()
168   - self.m_binsz = self["binsz"].real()
169   - self.m_coordsys = self["coordsys"].string()
170   - self.m_proj = self["proj"].string()
171   - self.m_ebins = self["nebins"].integer()
172   - self.m_anumbins = self["anumbins"].integer()
173 190  
174 191 # Read other parameters
175 192 self.m_outfile = self["outfile"].filename()
... ... @@ -286,7 +303,8 @@ class csspec(ctools.cscript):
286 303 # Write header
287 304 if self.logTerse():
288 305 self.log("\n")
289   - self.log.header1("Generate spectrum")
  306 + self.log.header1("Generate spectrum")
  307 + self.log(str(self.m_ebounds))
290 308  
291 309 # Initialise FITS Table with extension "SPECTRUM"
292 310 table = gammalib.GFitsBinTable(self.m_ebounds.size())
... ... @@ -334,8 +352,8 @@ class csspec(ctools.cscript):
334 352 energy_low[i] = (elogmean - emin).TeV()
335 353 energy_high[i] = (emax - elogmean).TeV()
336 354  
337   - # unbinned analysis
338   - if not self.m_binned:
  355 + # use ctselect for unbinned analysis
  356 + if not self.m_binned_mode:
339 357  
340 358 # Log information
341 359 if self.logExplicit():
... ... @@ -355,121 +373,32 @@ class csspec(ctools.cscript):
355 373 # Retrieve observation
356 374 obs = select.obs()
357 375  
358   - # Binned analysis
  376 + # use ctcubemask for binned analysis
359 377 else:
360 378  
361 379 # Header
362 380 if self.logTerse():
363   - self.log.header3("Binning events")
364   -
365   - # Bin events
366   - bin = ctools.ctbin(self.obs)
367   - bin["usepnt"] = False
368   - bin["ebinalg"] = "LOG"
369   - bin["xref"] = self.m_xref
370   - bin["yref"] = self.m_yref
371   - bin["binsz"] = self.m_binsz
372   - bin["nxpix"] = self.m_nxpix
373   - bin["nypix"] = self.m_nypix
374   - bin["enumbins"] = self.m_ebins
375   - bin["emin"] = emin.TeV()
376   - bin["emax"] = emax.TeV()
377   - bin["coordsys"] = self.m_coordsys
378   - bin["proj"] = self.m_proj
379   - bin.run()
380   -
381   - # Header
382   - if self.logTerse():
383   - self.log.header3("Creating exposure cube")
384   -
385   - # Create exposure cube
386   - expcube = ctools.ctexpcube(self.obs)
387   - expcube["incube"] = "NONE"
388   - expcube["usepnt"] = False
389   - expcube["ebinalg"] = "LOG"
390   - expcube["edisp"] = self.m_edisp
391   - expcube["xref"] = self.m_xref
392   - expcube["yref"] = self.m_yref
393   - expcube["binsz"] = self.m_binsz
394   - expcube["nxpix"] = self.m_nxpix
395   - expcube["nypix"] = self.m_nypix
396   - expcube["enumbins"] = self.m_ebins
397   - expcube["emin"] = emin.TeV()
398   - expcube["emax"] = emax.TeV()
399   - expcube["coordsys"] = self.m_coordsys
400   - expcube["proj"] = self.m_proj
401   - expcube.run()
402   -
403   - # Header
404   - if self.logTerse():
405   - self.log.header3("Creating PSF cube")
406   -
407   - # Create psf cube
408   - psfcube = ctools.ctpsfcube(self.obs)
409   - psfcube["incube"] = "NONE"
410   - psfcube["usepnt"] = False
411   - psfcube["ebinalg"] = "LOG"
412   - psfcube["edisp"] = self.m_edisp
413   - psfcube["xref"] = self.m_xref
414   - psfcube["yref"] = self.m_yref
415   - psfcube["binsz"] = self.m_binsz*20.0 # Slow Psf variation
416   - psfcube["nxpix"] = self.m_nxpix/20+1
417   - psfcube["nypix"] = self.m_nypix/20+1
418   - psfcube["enumbins"] = self.m_ebins
419   - psfcube["anumbins"] = self.m_anumbins
420   - psfcube["emin"] = emin.TeV()
421   - psfcube["emax"] = emax.TeV()
422   - psfcube["coordsys"] = self.m_coordsys
423   - psfcube["proj"] = self.m_proj
424   - psfcube.run()
425   -
426   - # Header
427   - if self.logTerse():
428   - self.log.header3("Creating background cube")
429   -
430   - # Create background cube
431   - bkgcube = ctools.ctbkgcube(self.obs)
432   - bkgcube["incube"] = "NONE"
433   - bkgcube["usepnt"] = False
434   - bkgcube["ebinalg"] = "LOG"
435   - bkgcube["xref"] = self.m_xref
436   - bkgcube["yref"] = self.m_yref
437   - bkgcube["binsz"] = self.m_binsz
438   - bkgcube["nxpix"] = self.m_nxpix
439   - bkgcube["nypix"] = self.m_nypix
440   - bkgcube["enumbins"] = self.m_ebins
441   - bkgcube["emin"] = emin.TeV()
442   - bkgcube["emax"] = emax.TeV()
443   - bkgcube["coordsys"] = self.m_coordsys
444   - bkgcube["proj"] = self.m_proj
445   - bkgcube.run()
  381 + self.log.header3("Selecting events")
446 382  
  383 + cubemask = ctools.ctcubemask(self.obs)
  384 + cubemask["regfile"] = "NONE"
  385 + cubemask["ra"] = "UNDEFINED"
  386 + cubemask["dec"] = "UNDEFINED"
  387 + cubemask["rad"] = "UNDEFINED"
  388 + cubemask["emin"] = emin.TeV()
  389 + cubemask["emax"] = emax.TeV()
  390 + cubemask.run()
  391 +
447 392 # Set new binned observation
448   - obs = bin.obs()
449   -
450   - # Set precomputed binned response
451   - obs[0].response(expcube.expcube(), psfcube.psfcube(), bkgcube.bkgcube())
452   -
453   - # Get new models
454   - models = bkgcube.models()
455   -
456   - # Fix background models if required
457   - if self.m_fix_bkg:
458   - for model in models:
459   - if not model.classname() == "GModelSky":
460   - for par in model:
461   - par.fix()
462   -
463   - # Set new models to binned observation
464   - obs.models(models)
  393 + obs = cubemask.obs()
465 394  
466 395 # Header
467 396 if self.logTerse():
468 397 self.log.header3("Performing fit")
469 398  
470 399 # Likelihood
471   - like = ctools.ctlike(obs)
472   - like["edisp"].boolean(self.m_edisp)
  400 + like = ctools.ctlike(obs)
  401 + like["edisp"] = self.m_edisp
473 402 like.run()
474 403  
475 404 # Skip bin if no event was present
... ... @@ -518,9 +447,9 @@ class csspec(ctools.cscript):
518 447 if self.m_calc_ts:
519 448 TS = source.ts()
520 449  
521   - # Compute Npred value
  450 + # Compute Npred value (only works for unbinned analysis)
522 451 Npred = 0.0
523   - if not self.m_binned:
  452 + if not self.m_binned_mode:
524 453 for observation in like.obs():
525 454 Npred += observation.npred(source)
526 455  
... ... @@ -529,8 +458,8 @@ class csspec(ctools.cscript):
529 458  
530 459 # Compute flux error
531 460 parvalue = source.spectral()[0].value()
532   - rel_error = source.spectral()[0].error()/parvalue
533   - e_flux = fitted_flux*rel_error
  461 + rel_error = source.spectral()[0].error() / parvalue
  462 + e_flux = fitted_flux * rel_error
534 463  
535 464 # Set values for storage
536 465 TSvalues[i] = TS
... ...
src/ctcubemask/ctcubemask.cpp
  View file @9afc4de
... ... @@ -349,6 +349,10 @@ void ctcubemask::save(void)
349 349 ***************************************************************************/
350 350 void ctcubemask::get_parameters(void)
351 351 {
  352 + // Initialise selection flags
  353 + m_select_energy = true;
  354 + m_select_roi = true;
  355 +
352 356 // If there are no observations in container then load them via user
353 357 // parameters
354 358 if (m_obs.size() == 0) {
... ... @@ -373,13 +377,36 @@ void ctcubemask::get_parameters(void)
373 377 m_regfile = (*this)["regfile"].filename();
374 378 m_usepnt = (*this)["usepnt"].boolean();
375 379 if (!m_usepnt) {
376   - m_ra = (*this)["ra"].real();
377   - m_dec = (*this)["dec"].real();
  380 +
  381 + // Check RA/DEC parameters for validity to read
  382 + if ((*this)["ra"].is_valid() && (*this)["dec"].is_valid()) {
  383 + m_ra = (*this)["ra"].real();
  384 + m_dec = (*this)["dec"].real();
  385 + m_select_roi = true;
  386 + }
  387 + else {
  388 + m_select_roi = false;
  389 + }
  390 + }
  391 +
  392 + // Check if radius is vaild for a RoI selection
  393 + if (m_select_roi && (*this)["rad"].is_valid()) {
  394 + m_rad = (*this)["rad"].real();
378 395 }
379   - m_rad = (*this)["rad"].real();
380   - m_emin = (*this)["emin"].real();
381   - m_emax = (*this)["emax"].real();
382   -
  396 + else {
  397 + m_select_roi = false;
  398 + }
  399 +
  400 + // Check for sanity of energy selection parameters
  401 + if ((*this)["emin"].is_valid() && (*this)["emax"].is_valid()) {
  402 + m_emin = (*this)["emin"].real();
  403 + m_emax = (*this)["emax"].real();
  404 + m_select_energy = true;
  405 + }
  406 + else {
  407 + m_select_energy = false;
  408 + }
  409 +
383 410 // Optionally read ahead parameters so that they get correctly
384 411 // dumped into the log file
385 412 if (read_ahead()) {
... ... @@ -410,6 +437,12 @@ void ctcubemask::apply_mask(GCTAObservation* obs)
410 437 GSkyMap map = cube->map();
411 438 const GEbounds& ebounds = cube->ebounds();
412 439  
  440 + // If no energy selection is required set energy boundaries to cube boundaries
  441 + if (!m_select_energy) {
  442 + m_emin = ebounds.emin().TeV();
  443 + m_emax = ebounds.emax().TeV();
  444 + }
  445 +
413 446 // Initialise energy selection
414 447 int n_ebin = ebounds.size();
415 448 int e_idx1 = 0;
... ... @@ -455,24 +488,26 @@ void ctcubemask::apply_mask(GCTAObservation* obs)
455 488 }
456 489  
457 490 // Set all pixels inside selected energy bands but outside ROI
458   - // to -1.0
459   - GSkyRegionCircle roi(m_ra, m_dec, m_rad);
460   - for (int i = e_idx1; i <= e_idx2; ++i) {
461   - for (int pixel = 0; pixel < npix; ++pixel) {
462   - GSkyDir dir = map.inx2dir(pixel);
463   - if (!roi.contains(dir)) {
464   - map(pixel,i) = -1.0;
  491 + // to -1.0 if requested
  492 + if (m_select_roi) {
  493 + GSkyRegionCircle roi(m_ra, m_dec, m_rad);
  494 + for (int i = e_idx1; i <= e_idx2; ++i) {
  495 + for (int pixel = 0; pixel < npix; ++pixel) {
  496 + GSkyDir dir = map.inx2dir(pixel);
  497 + if (!roi.contains(dir)) {
  498 + map(pixel,i) = -1.0;
  499 + }
465 500 }
466 501 }
467   - }
468 502  
469   - // Log selected energy band
470   - if (logTerse()) {
471   - log << gammalib::parformat("Selected ROI");
472   - log << "RA=" << m_ra << " deg, ";
473   - log << "DEC=" << m_dec << " deg, ";
474   - log << "Radius=" << m_rad << " deg";
475   - log << std::endl;
  503 + // Log selected energy band
  504 + if (logTerse()) {
  505 + log << gammalib::parformat("Selected ROI");
  506 + log << "RA=" << m_ra << " deg, ";
  507 + log << "DEC=" << m_dec << " deg, ";
  508 + log << "Radius=" << m_rad << " deg";
  509 + log << std::endl;
  510 + }
476 511 }
477 512  
478 513 // Set all pixels inside selected energy bands and inside exclusion
... ... @@ -538,6 +573,8 @@ void ctcubemask::init_members(void)
538 573 // Initialise protected members
539 574 m_obs.clear();
540 575 m_infiles.clear();
  576 + m_select_energy = true;
  577 + m_select_roi = true;
541 578  
542 579 // Return
543 580 return;
... ... @@ -565,6 +602,8 @@ void ctcubemask::copy_members(const ctcubemask&amp; app)
565 602 // Copy protected members
566 603 m_obs = app.m_obs;
567 604 m_infiles = app.m_infiles;
  605 + m_select_energy = app.m_select_energy;
  606 + m_select_roi = app.m_select_roi;
568 607  
569 608 // Return
570 609 return;
... ...
src/ctcubemask/ctcubemask.hpp
  View file @9afc4de
... ... @@ -92,6 +92,8 @@ protected:
92 92 // Protected members
93 93 GObservations m_obs; //!< Observations container
94 94 std::vector<std::string> m_infiles; //!< Input event filenames
  95 + bool m_select_energy; //!< Perform energy selection
  96 + bool m_select_roi; //!< Perform ROI selection
95 97 };
96 98  
97 99  
... ...
test/test_cscripts.sh.in
  View file @9afc4de
... ... @@ -36,7 +36,7 @@ $ECHO &quot;*****************&quot;
36 36 #
37 37 # Remove any existing result files
38 38 # ================================
39   -rm -rf *.fits *.xml *.dat
  39 +rm -rf spectrum*.fits lightcurve*.fits resmap*.fits obs.xml *.dat
40 40  
41 41  
42 42 #
... ... @@ -209,7 +209,6 @@ chmod +x @abs_top_srcdir@/cscripts/csspec.py
209 209 srcname="Crab" \
210 210 emin=0.1 \
211 211 emax=100.0 \
212   - binned=no \
213 212 outfile="spectrum.fits" > csspec.log
214 213 $ECHO -n "."
215 214 if [ -s "spectrum.fits" ]
... ... @@ -228,30 +227,22 @@ $ECHO &quot; ok&quot;
228 227 $ECHO -n "Test csspec (binned): "
229 228 chmod +x @abs_top_srcdir@/cscripts/csspec.py
230 229 @abs_top_srcdir@/cscripts/csspec.py \
231   - inobs="data/crab_events.fits" \
232   - inmodel="data/crab.xml" \
233   - caldb="irf" \
234   - irf="cta_dummy_irf" \
235   - enumbins=3 \
236   - srcname="Crab" \
  230 + inobs="cntmap2.fits" \
  231 + expcube="expcube2.fits" \
  232 + psfcube="psfcube2.fits" \
  233 + bkgcube="bkgcube2.fits" \
  234 + inmodel="bkgcube2.xml" \
  235 + enumbins=2 \
237 236 emin=0.1 \
238 237 emax=100.0 \
239   - binned=yes \
240   - nxpix=10 \
241   - nypix=10 \
242   - binsz=0.1 \
243   - nebins=2 \
244   - coordsys="CEL" \
245   - xref=83.63 \
246   - yref=22.01 \
247   - proj="CAR" \
248   - outfile="spectrum.fits" > csspec.log
  238 + srcname="Crab" \
  239 + outfile="spectrum_binned.fits" > csspec.log
249 240 $ECHO -n "."
250   -if [ -s "spectrum.fits" ]
  241 +if [ -s "spectrum_binned.fits" ]
251 242 then
252 243 $ECHO -n "."
253 244 else
254   - $ECHO " spectrum.fits file is not valid"
  245 + $ECHO " spectrum_binned.fits file is not valid"
255 246 exit 1
256 247 fi
257 248 $ECHO " ok"
... ... @@ -309,13 +300,13 @@ chmod +x @abs_top_srcdir@/cscripts/cslightcrv.py
309 300 nxpix=10 \
310 301 nypix=10 \
311 302 binsz=0.1 \
312   - outfile="lightcurve.fits" > cslightcrv.log
  303 + outfile="lightcurve_binned.fits" > cslightcrv.log
313 304 $ECHO -n "."
314   -if [ -s "lightcurve.fits" ]
  305 +if [ -s "lightcurve_binned.fits" ]
315 306 then
316 307 $ECHO -n "."
317 308 else
318   - $ECHO " lightcurve.fits file is not valid"
  309 + $ECHO " lightcurve_binned.fits file is not valid"
319 310 exit 1
320 311 fi
321 312 $ECHO " ok"
... ...