EllipSect 3.2.2__tar.gz → 3.4.0__tar.gz

{EllipSect-3.2.2 → EllipSect-3.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: EllipSect
-Version: 3.2.2
+Version: 3.4.0
 Summary: A surface brightness analysis tool for GALFIT output.
 Home-page: https://github.com/canorve/EllipSect
 Author: Christopher Añorve
@@ -19,8 +19,18 @@ Classifier: Natural Language :: Spanish
 Classifier: Natural Language :: English
 Classifier: Topic :: Scientific/Engineering :: Astronomy
 Description-Content-Type: text/x-rst; charset=UTF-8
-Provides-Extra: testing
 License-File: LICENSE.txt
+Requires-Dist: importlib-metadata
+Requires-Dist: sphinx>=3.2.1
+Requires-Dist: numpy>=1.20.3
+Requires-Dist: astropy>=5.1
+Requires-Dist: scipy>=1.5.2
+Requires-Dist: matplotlib>=3.5.2
+Requires-Dist: mgefit>=5.0.13
+Provides-Extra: testing
+Requires-Dist: setuptools; extra == "testing"
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
 
 .. contents::
    :depth: 3

{EllipSect-3.2.2 → EllipSect-3.4.0}/docs/howto.rst

@@ -23,14 +23,26 @@ The options are:
 
 ::
 
-    ellipsect [GALFIT_File] [--logx] [-q AxisRatio] [-pa PositionAngle] [--comp] [--pix] [--ranx/y Value] [--grid] [--dpi Value] [--noplot] [--phot] [--sbout] [--noplot] [--minlevel Value] [--sectors Value] [--object Name] [--filter Name] [--snr] [--help] [--checkimg] [--noned] [--distmod Value] [--magcor Value] [--scalekpc Value][--sbdim Value] [--model ModelImage] [--keep] [--ned XmlFile] [--gradsky ] [--randsky ] [--skyinit Value] [--skyRadmax Value][--skynum Value] [--skybox Value] [--skywidth Value] [--fwhm Value] [--galax ]
+   
+      
+    ellipsect [-h] [-lx] [-cp] [-px] [-g] [-sb] [-np] [-ph] [-ci] [-nn] [-gsky] [-rsky] [-snr]
+                 [-re] [-r90] [-r95] [-k] [-gx] [-asp] [-t] [-q AXISRAT] [-pa POSANGLE]
+                 [-rx RANX RANX] [-ry RANY RANY] [-dpi DOTSINCH] [-ml MINLEVEL] [-sc SECTORS]
+                 [-ob OBJECT] [-f FILTER] [-dm DISTMOD] [-mc MAGCOR] [-sk SCALEKPC] [-sd SBDIM]
+                 [-md MODEL] [-sky SKY] [-ned NED] [-ri RADINIT] [-srm SKYRADMAX] [-skb SKYBOX]
+                 [-skn SKYNUM] [-skw SKYWIDTH] [-distm DISTMAX] [-fw FWHM] [-br BRIGHTNESS]
+                 [-co CONTRAST] [-cm CMAP] [-nc NUMCOMP] [-ae AEXT] [-hc HCONST] [-om OMEGAM]
+                 [-ov OMEGAV]
+                 GalFile
+
+
 
 Below is an explanation of each parameter:
 
 **Main input parameters**
 -------------------------
 
-**GALFIT_File**: GALFIT output file (e.g. galfit.01). This **must** be
+**GalFile**: GALFIT output file (e.g. galfit.01). This **must** be
 the last GALFIT run. In other words, if there are two files: galfit.01
 and galfit.02, the one you need is galfit.02
 
@@ -63,6 +75,11 @@ profiles.
 
 **galax**: Only the galaxy surface brightness is plotted.
 
+**effrad** Draw a vertical line indicating the effective radius
+**rad90**  Draw a vertical line indicating the 90% of total light
+**rad95**  Draw a vertical line indicating the 95% of total light
+
+
 **Photometric output options**
 ------------------------------
 

{EllipSect-3.2.2 → EllipSect-3.4.0}/src/EllipSect.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: EllipSect
-Version: 3.2.2
+Version: 3.4.0
 Summary: A surface brightness analysis tool for GALFIT output.
 Home-page: https://github.com/canorve/EllipSect
 Author: Christopher Añorve
@@ -19,8 +19,18 @@ Classifier: Natural Language :: Spanish
 Classifier: Natural Language :: English
 Classifier: Topic :: Scientific/Engineering :: Astronomy
 Description-Content-Type: text/x-rst; charset=UTF-8
-Provides-Extra: testing
 License-File: LICENSE.txt
+Requires-Dist: importlib-metadata
+Requires-Dist: sphinx>=3.2.1
+Requires-Dist: numpy>=1.20.3
+Requires-Dist: astropy>=5.1
+Requires-Dist: scipy>=1.5.2
+Requires-Dist: matplotlib>=3.5.2
+Requires-Dist: mgefit>=5.0.13
+Provides-Extra: testing
+Requires-Dist: setuptools; extra == "testing"
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
 
 .. contents::
    :depth: 3

{EllipSect-3.2.2 → EllipSect-3.4.0}/src/ellipsect/inout/plots.py

@@ -23,7 +23,8 @@ from ellipsect.sectors.num import Interpol
 from ellipsect.inout.prt import  PrintFilesGax
 from ellipsect.inout.prt import PrintFilesComps
 
-
+from ellipsect.inout.galfit  import conver2Sersic 
+from ellipsect.inout.galfit  import GetReff 
 
 def PlotSB(xradq,ysbq,ysberrq,xradm,ysbm,ysberrm,ellconf,scale):
     """  Produces final best-fitting plot  """
@@ -58,7 +59,7 @@ def PlotSB(xradq,ysbq,ysberrq,xradm,ysbm,ysberrm,ellconf,scale):
     # ULISES begin
     axsec = plt.subplot(gs[0])
 
-    axsec.set_ylabel("Surface Brightness (mag/'')")
+    axsec.set_ylabel(r"Surface Brightness $(mag\; arcsec^{-2})$")
     # ULISES end
 
     axsec.errorbar(xradq, ysbq,yerr=ysberrq,fmt='o-',capsize=2,color='red',markersize=0.7,label="galaxy",linewidth=2)
@@ -97,9 +98,24 @@ def PlotSB(xradq,ysbq,ysberrq,xradm,ysbm,ysberrm,ellconf,scale):
     #begin psf fwhm 
     if ellconf.flagfwhm: 
         xpos = ellconf.fwhm*scale
-        axsec.axvline(x=xpos,  linestyle='--', color='k', linewidth=2)
+        axsec.axvline(x=xpos,  linestyle='--', color='k', label='FWHM', linewidth=2)
     # end 
 
+    #effective radius 
+    if ellconf.flagrep: 
+        xre = ellconf.rep*scale
+        axsec.axvline(x=xre,  linestyle='--', color='r', label='Re', linewidth=1.5)
+ 
+    #90% of total light radius 
+    if ellconf.flagr90p: 
+        xr90 = ellconf.r90p*scale
+        axsec.axvline(x = xr90,  linestyle='--', color='b', label='R90', linewidth=1.5)
+ 
+    #95%  of total light radius 
+    if ellconf.flagr95p: 
+        xr95 = ellconf.r95p*scale
+        axsec.axvline(x = xr95,  linestyle='--', color='c', label='R95', linewidth=1.5)
+ 
 
     # ULISES begin
     axsec.axes.xaxis.set_ticklabels([])
@@ -109,6 +125,8 @@ def PlotSB(xradq,ysbq,ysberrq,xradm,ysbm,ysberrm,ellconf,scale):
     axsec.yaxis.set_minor_locator(AutoMinorLocator())
     axsec.yaxis.set_major_locator(AutoLocator())
 
+    if ellconf.title:
+        plt.title(ellconf.namefile, fontsize=10)
 
     # ULISES begin
     # Residual plot
@@ -136,7 +154,7 @@ def PlotSB(xradq,ysbq,ysberrq,xradm,ysbm,ysberrm,ellconf,scale):
         axred.errorbar(xradq, residual, yerr=err,fmt='.',capsize=2,color='k')
 
     axred.axhline(y=0,ls='dashed', color='k')
-    axred.set_xlabel('Radius (arcsec)')
+    axred.set_xlabel('Radius $(arcsec)$')
     axred.set_ylabel('Residual (%)')
     axred.set_ylim(-2,2)
     # ULISES end
@@ -373,7 +391,6 @@ class ShowCube:
         data[mask] = 1 # avoids problems in log
      
         fig, (ax1, ax2, ax3) = plt.subplots(figsize=(14, 5), nrows = 1, ncols = 3)
-        fig.subplots_adjust(left=0.04, right=0.98, bottom=0.02, top=0.98)
 
         im = ax1.imshow(newdata, origin ='lower', interpolation='nearest', norm 
                     = colors.LogNorm(vmin=modmin, vmax=modmax), cmap = cmap)
@@ -422,6 +439,7 @@ class ShowCube:
         ax3.set_title('Residual')
 
 
+        fig.subplots_adjust(left=0.04, right=0.98, bottom=0.02, top=0.98)
         plt.savefig(namepng, dpi = dpival)
     
 
@@ -430,6 +448,11 @@ class ShowCube:
 
 def PlotMul(ellconf, galhead, galcomps, mgegal, mgemod, mgecom):
 
+
+    
+    comps = conver2Sersic(galcomps) #to compute Re
+
+
     fignum = 1
 
     minrad = np.min(mgegal.rad)
@@ -459,19 +482,29 @@ def PlotMul(ellconf, galhead, galcomps, mgegal, mgemod, mgecom):
 
     plt.clf()
 
+
+    if ellconf.title:
+        plt.title(ellconf.namefile, fontsize=10)
+
+
+
     fig, axsec = plt.subplots(nrows, 2, sharex=True, sharey='col', num=fignum)
     fig.subplots_adjust(hspace=0.01)
 
 
+
+
+
+
     if ellconf.flagpix:
         axpix = axsec[0,0].twiny()
         axpix2 = axsec[0,1].twiny()
 
-    fig.text(0.04, 0.5, "Surface Brightness (mag/'')", va='center', rotation='vertical')
+    fig.text(0.04, 0.5, r"Surface Brightness $(mag\; arcsec^{-2})$", va='center', rotation='vertical')
     fig.text(0.96, 0.5, 'error ', va='center', rotation='vertical')
 
-    axsec[-1, 0].set_xlabel("radius ('')")
-    axsec[-1, 1].set_xlabel("radius ('')")
+    axsec[-1, 0].set_xlabel("radius $(arcsec)$")
+    axsec[-1, 1].set_xlabel("radius $(arcsec)$")
 
     if ellconf.flaglogx == True:
         axsec[-1, 0].xaxis.set_major_locator(LogLocator(base=10.0, numticks=15))
@@ -549,6 +582,30 @@ def PlotMul(ellconf, galhead, galcomps, mgegal, mgemod, mgecom):
         # end 
 
 
+        #effective radius 
+        if ellconf.flagrep: 
+            eff = 0.5
+            xre, tempmag = GetReff().GetReSer(galhead, comps, eff, txtangsky)
+
+            xre = xre*galhead.scale
+            axsec[row, 0].axvline(x=xre,  linestyle='--', color='r', label='Re', linewidth=1.5)
+     
+        #90% radius 
+        if ellconf.flagr90p: 
+            eff = 0.9
+            xr90, tempmag = GetReff().GetReSer(galhead, comps, eff, txtangsky)
+
+            xr90 = xr90*galhead.scale
+            axsec[row, 0].axvline(x = xr90,  linestyle='--', color='b', label='R90', linewidth=1.5)
+ 
+        #95% radius 
+        if ellconf.flagr95p: 
+            eff = 0.95
+            xr95, tempmag = GetReff().GetReSer(galhead, comps, eff, txtangsky)
+
+            xr95 = xr95*galhead.scale
+            axsec[row, 0].axvline(x = xr95,  linestyle='--', color='c', label='R95', linewidth=1.5)
+ 
 
 
 

{EllipSect-3.2.2 → EllipSect-3.4.0}/src/ellipsect/inout/prt.py

@@ -391,6 +391,12 @@ def printPhot(ellconf, galhead, galcomps, dataned, datatidal, sectgalax):
     lineout = "# All photometric quantities are computed for filter {} (use -filter option to change it) \n".format(ellconf.band)
     OUTPHOT.write(lineout)
 
+
+
+    lineout = '# Cosmology: hconst = {}, omega m = {}, omega lambda= {}'.format(ellconf.hconst,ellconf.omegam,ellconf.omegav) 
+    OUTPHOT.write(lineout)
+
+
     lineout = "# Magnitudes are not corrected by K-Correction \n"
     OUTPHOT.write(lineout)
 

{EllipSect-3.2.2 → EllipSect-3.4.0}/src/ellipsect/inout/read.py

@@ -68,7 +68,15 @@ def InitParsing():
     parser.add_argument("-gsky","--gradsky", action="store_true", help="computes sky using the gradient method")
     parser.add_argument("-rsky","--randsky", action="store_true", help="computes sky using random boxes")
     parser.add_argument("-snr","--snr", action="store_true", help="Creates Signal to Noise image if phot is activated")
-    parser.add_argument("-chi","--chisqr", action="store_true", help="Creates Chi-square image if phot is activated")
+    #parser.add_argument("-chi","--chisqr", action="store_true", help="Creates Chi-square image if phot is activated")
+
+
+    parser.add_argument("-re","--effrad", action="store_true", help="Draw a vertical line indicating the effective radius")
+
+    parser.add_argument("-r90","--rad90", action="store_true", help="Draw a vertical line indicating the 90%% of total light")
+
+    parser.add_argument("-r95","--rad95", action="store_true", help="Draw a vertical line indicating the 95%% of total light")
+
 
     parser.add_argument("-k","--keep", action="store_true", help="use existing file to compute subcomponents")
     parser.add_argument("-gx","--galax", action="store_true", help="only the galaxy surface brightness is shown in the plot")
@@ -78,7 +86,11 @@ def InitParsing():
             + "Default mode removes top %%80 and bottom %%20 sky pixels "
     parser.add_argument("-asp","--allskypx", action="store_true", 
                         help=linehelp)
- 
+
+
+
+    parser.add_argument("-t","--title", action="store_true", help="put title on plots")
+
     #options with arguments
     #parser.add_argument("-cn","--center",nargs=2,action="store", type=float, help="galaxy's center ")
 
@@ -87,8 +99,8 @@ def InitParsing():
     parser.add_argument("-rx","--ranx",nargs=2, type=float, help="provide a range for x-axis: xmin - xmax ")
     parser.add_argument("-ry","--rany", nargs=2,type=float, help="provide a range for y-axis: ymin - ymax  ")
     parser.add_argument("-dpi","--dotsinch", type=int, help="dots per inch used for images files ")
-    parser.add_argument("-ml","--minlevel", type=float, help="parameter given directly to sectors_photometry. ")
-    parser.add_argument("-sc","--sectors", type=int, help="parameter given directly to sectors_photometry. Divide elipse in 'sectors'")
+    parser.add_argument("-ml","--minlevel", type=float, help="parameter given to sectors_photometry. ")
+    parser.add_argument("-sc","--sectors", type=int, help="parameter given to sectors_photometry. It divides the ellipse in 'sectors'")
     parser.add_argument("-ob","--object",  help="used for 'phot' to search in NED")
     parser.add_argument("-f","--filter",  help="used for 'phot' to indicate band for NED  ")
     parser.add_argument("-dm","--distmod", type=float, help="Introduce Distance Modulus  ")
@@ -130,7 +142,15 @@ def InitParsing():
     parser.add_argument("-ae","--aext", type=float, 
                         help="Surface brightness correction for plots only ", default=0)
  
-
+    parser.add_argument("-hc","--hconst", type=float, 
+                        help="hubble constant to download xml file from NED ", default=67.8)
+ 
+    parser.add_argument("-om","--omegam", type=float, 
+                        help="omega matter value to download xml file from NED ", default=.308)
+ 
+    parser.add_argument("-ov","--omegav", type=float, 
+                        help="omega lambda value to download xml file from NED ", default=0.692)
+ 
 
     # every new parameter added here must be
     # also added in function PassArgs() in ellipsect/sectors/sect.py
@@ -490,37 +510,45 @@ def prefixNames(ellconf, outimage):
     numstr = gal_ext[1] 
     numstr = numstr[1:]
 
+    if ellconf.numcomp:
+        precomp = "-nc" + str(ellconf.numcomp)
+    else:
+        precomp = ""
+
+
+
+
     if numstr.isnumeric():
 
         # names for the different png
-        ellconf.namepng = ellconf.namefile + '-' + numstr + ".png"
-        ellconf.namesec = ellconf.namefile + '-' + numstr + "-gal.png"
-        ellconf.namemod = ellconf.namefile + '-' + numstr + "-mod.png"
-        ellconf.namemul = ellconf.namefile + '-' + numstr + "-mul.png"
-        ellconf.namesub = ellconf.namefile + '-' + numstr + "-comp.fits"
+        ellconf.namepng = ellconf.namefile + '-g' + numstr + precomp + "-splot.png"
+        ellconf.namesec = ellconf.namefile + '-g' + numstr + precomp + "-gal.png"
+        ellconf.namemod = ellconf.namefile + '-g' + numstr + precomp + "-mod.png"
+        ellconf.namemul = ellconf.namefile + '-g' + numstr + precomp + "-mplot.png"
+        ellconf.namesub = ellconf.namefile + '-g' + numstr + precomp + "-comp.fits"
 
-        ellconf.namesig = ellconf.namefile + '-' + numstr + "-sig.fits"
+        ellconf.namesig = ellconf.namefile + '-g' + numstr + precomp + "-sig.fits"
 
 
-        ellconf.sboutput = ellconf.namefile + '-' + numstr + "-sbout"
-        ellconf.output = ellconf.namefile + '-' + numstr + "-out.txt"
+        ellconf.sboutput = ellconf.namefile + '-g' + numstr + precomp + "-sbout"
+        ellconf.output = ellconf.namefile + '-g' + numstr + precomp +  "-out.txt"
 
-        ellconf.namened = ellconf.namefile + '-' + numstr + "-ned.xml"
+        ellconf.namened = ellconf.namefile + '-g' + numstr + precomp + "-ned.xml"
 
-        ellconf.namesnr = ellconf.namefile + '-' + numstr + "-snr.fits"
-        ellconf.namecheck = ellconf.namefile + '-' + numstr + "-check.fits"
-        ellconf.namering = ellconf.namefile + '-' + numstr + "-ring.fits"
-        ellconf.nameringmask = ellconf.namefile + '-' + numstr + "-ringmask.fits"
-        ellconf.namecube = ellconf.namefile + '-' + numstr + "-cub.png"
-        ellconf.namechi = ellconf.namefile + '-' + numstr + "-chi.fits"
+        ellconf.namesnr = ellconf.namefile + '-g' + numstr + precomp + "-snr.fits"
+        ellconf.namecheck = ellconf.namefile + '-g' + numstr + precomp + "-check.fits"
+        ellconf.namering = ellconf.namefile + '-g' + numstr + precomp + "-ring.fits"
+        ellconf.nameringmask = ellconf.namefile + '-g' + numstr + precomp + "-ringmask.fits"
+        ellconf.namecube = ellconf.namefile + '-g' + numstr + precomp + "-cub.png"
+        ellconf.namechi = ellconf.namefile + '-g' + numstr + precomp + "-chi.fits"
 
     else:
 
         # names for the different png
-        ellconf.namepng = ellconf.namefile + ".png"
+        ellconf.namepng = ellconf.namefile + "-splot.png"
         ellconf.namesec = ellconf.namefile + "-gal.png"
         ellconf.namemod = ellconf.namefile + "-mod.png"
-        ellconf.namemul = ellconf.namefile + "-mul.png"
+        ellconf.namemul = ellconf.namefile + "-mplot.png"
         ellconf.namesub = ellconf.namefile + "-comp.fits"
 
         ellconf.namesig = ellconf.namefile + "-sig.fits"

{EllipSect-3.2.2 → EllipSect-3.4.0}/src/ellipsect/lib/clas.py

@@ -42,7 +42,7 @@ class EllipSectConfig:
     flagband=False
     flagweb=False # to check connection to ned
     flagsnr = False
-    flagchi = False
+    #flagchi = False
 
     flagcheck=False
     flagned=False
@@ -74,6 +74,9 @@ class EllipSectConfig:
 
     flagfwhm = False
 
+    flagrep = False
+    flagr90p = False
+    flagr95p = False
     #flagcent = False 
 
     flagrmsky=True
@@ -97,7 +100,7 @@ class EllipSectConfig:
     minlevel=0
     sectors=19
 
-
+    title = False
 
     #input file
     galfile= "galfit.01"
@@ -153,6 +156,10 @@ class EllipSectConfig:
 
     fwhm = 2
 
+    rep = 0
+    r90p = 0
+    r95p = 0
+
     distmax = 10
 
     brightness = 0 
@@ -176,6 +183,11 @@ class EllipSectConfig:
 
     Aext = 0  # surface brightness correction for plots
 
+    hconst = 67.8 
+    omegam  = 0.308
+    omegav = 0.692
+
+
 
 #class to comunicate externally:
 class PhotAPI:
@@ -237,6 +249,11 @@ class PhotAPI:
     inputimage="galaxy.fits"
     Aext = 0
 
+    hconst = 67.8 
+    omegam  = 0.308
+    omegav = 0.692
+
+
     # from gradsky
     gradskymean = 0
     gradskystd = 0

{EllipSect-3.2.2 → EllipSect-3.4.0}/src/ellipsect/phot/ned.py

@@ -43,6 +43,8 @@ def NED(ellconf):
 
     nedweb="https://ned.ipac.caltech.edu/cgi-bin/nph-objsearch?extend=no&of=xml_all&objname="
 
+
+
     if ellconf.flagnedfile:
         filened = ellconf.nedfile
     else:
@@ -56,8 +58,8 @@ def NED(ellconf):
         Scalekpc=ellconf.InScale
         SbDim=ellconf.InSbDim
     else:
-        #checar si el archivo existe para no hacer conexion a internet
         if(not(os.path.isfile(filened))):
+        #verifica si el archivo existe para no hacer conexion a internet
 
             if ellconf.flagnedfile:
                 print("can't find user's ned {} file ".format(filened))
@@ -65,10 +67,18 @@ def NED(ellconf):
             else:
                 # command for wget
                 #wget -O NED_51.xml "https://ned.ipac.caltech.edu/cgi-bin/nph-objsearch?extend=no&of=xml_all&objname=m+51"
-                wgetcmd = 'wget -O {} "{}{}"'.format(filened,nedweb,objname)
+
+                #https://ned.ipac.caltech.edu/cgi-bin/nph-objsearch?extend=no&of=xml_all&objname=ngc+6166&hconst=67.8&omegam=0.308&omegav=0.692
+
+
+                wgetcmd = 'wget -O {} "{}{}&hconst={:.1f}\&omegam={:.3f}\&omegav={:.3f}"'.format(
+                            filened,nedweb,objname,ellconf.hconst,ellconf.omegam,ellconf.omegav)
 
                 print("Running: ",wgetcmd)
 
+                print('Cosmology: hconst = {}, omega m= {}, omega lambda= {}'.format(ellconf.hconst,ellconf.omegam,ellconf.omegav)) 
+
+
                 errwg = sp.run([wgetcmd], shell=True, stdout=sp.PIPE,stderr=sp.PIPE, universal_newlines=True)
 
                 if errwg.returncode != 0:

{EllipSect-3.2.2 → EllipSect-3.4.0}/src/ellipsect/phot/tidal.py

@@ -179,28 +179,33 @@ def Tidal(datatidal, ellconf, dataimg, galhead, galcomps, sectgalax, rmin):
     # creation of the Chi-square image 
     ##################################
 
-    if ellconf.flagchi:
-        header['TypeIMG'] = ('CHI-SQR', 'Chi-Square image')
-        hdu[0].header  = header
+    #if ellconf.flagchi:
 
+    header['TypeIMG'] = ('CHI-SQR', 'Chi-Square image')
+    hdu[0].header  = header
 
-        maskchi = immask == True # big image coordinates
 
+    maskchi = immask == True # big image coordinates
 
-        if imgal.shape == imsigma.shape:
-            dataimg.imchi = (imgal - immodel)**2 / imsigma**2
-            if maskchi.any():
-                dataimg.imchi[maskchi] = 0
-        else:
-            print("WARNING: Chi-square image can not be computed" +
-                    "because galaxy and sigma images have different shapes")
-            dataimg.imchi = np.ones(imgal.shape)
-        
-        hdu[0].data = dataimg.imchi
 
-        hdu.writeto(ellconf.namechi, overwrite=True)
-        print("Chi square image created.. ", ellconf.namechi)
+    if imgal.shape == imsigma.shape:
+        dataimg.imchi = (imgal - immodel)**2 / imsigma**2
+        if maskchi.any():
+            dataimg.imchi[maskchi] = 0
+    else:
+        print("WARNING: Chi-square image can not be computed" +
+                "because galaxy and sigma images have different shapes")
+        dataimg.imchi = np.ones(imgal.shape)
+    
+    hdu[0].data = dataimg.imchi
+
+    hdu.writeto(ellconf.namechi, overwrite=True)
+    print("Chi square image created.. ", ellconf.namechi)
+
 
+    ##################################
+    # end of the Chi-square image 
+    ##################################
 
 
 
@@ -433,10 +438,10 @@ def ExtractEllip(imagemat, idn, x, y, R, theta, ell, xmin, xmax, ymin, ymax):
     "It returns the area of ellipse with idn values. "
 
 
-    xmin = np.int(xmin)
-    xmax = np.int(xmax)
-    ymin = np.int(ymin)
-    ymax = np.int(ymax)
+    xmin = int(xmin)
+    xmax = int(xmax)
+    ymin = int(ymin)
+    ymax = int(ymax)
 
     q = (1 - ell)
     bim = q * R

{EllipSect-3.2.2 → EllipSect-3.4.0}/src/ellipsect/sectors/sect.py

@@ -35,7 +35,11 @@ from ellipsect.lib.clas import EllipSectConfig
 
 from ellipsect.inout.galfit  import Galfit 
 from ellipsect.inout.galfit  import numComps
+from ellipsect.inout.galfit  import conver2Sersic 
 from ellipsect.inout.galfit  import readDataImg
+from ellipsect.inout.galfit  import GetReff 
+
+from ellipsect.inout.gfits import GetFits
 
 from ellipsect.inout.prt import printEllinfo
 
@@ -81,7 +85,10 @@ def SectorsGalfit(args):
     prefixNames(ellconf, galhead.outimage)
 
     if os.path.isfile(galhead.sigimage):
-        ellconf.namesig = galhead.sigimage #using existing sigma file
+        #ellconf.namesig = galhead.sigimage #using existing sigma file
+        GetFits(galhead.sigimage, ellconf.namesig, galhead.xmin, galhead.xmax, 
+                galhead.ymin, galhead.ymax)
+
 
 
 
@@ -107,7 +114,11 @@ def SectorsGalfit(args):
     dataimg.img = dataimg.img - ellconf.skylevel
     dataimg.model = dataimg.model - ellconf.skylevel
 
-    plotCube(ellconf, galhead, galcomps) #plots the cube image
+
+
+    comps = conver2Sersic(galcomps) 
+
+    plotCube(ellconf, galhead, comps) #plots the cube image
 
 
     #   numsectors=19 default
@@ -137,6 +148,23 @@ def SectorsGalfit(args):
     skyCall(ellconf, galhead, galcomps)
 
 
+    #computing fraction of light radius
+    if ellconf.flagrep:
+        eff = 0.5
+        ellconf.rep, tempmag = GetReff().GetReSer(galhead, comps, eff, ellconf.parg)
+
+    if ellconf.flagr90p:
+        eff = 0.9
+        ellconf.r90p, tempmag = GetReff().GetReSer(galhead, comps, eff, ellconf.parg)
+
+    if ellconf.flagr95p:
+        eff = 0.95
+        ellconf.r95p, tempmag = GetReff().GetReSer(galhead, comps, eff, ellconf.parg)
+
+
+
+
+
 
     print("creating plots..")
 
@@ -389,8 +417,8 @@ def SectPhotComp(ellconf, dataimg, galcomps, n_sectors=19, minlevel=0):
 
             subim = subimgs[i]
 
-            eps = 1 - galcomps.AxRat[n]
-            angsec = 90 - galcomps.PosAng[n]
+            #eps = 1 - galcomps.AxRat[n]   #removed because it must follow the axrat of galaxy
+            #angsec = 90 - galcomps.PosAng[n] #same but for angle
 
 
             if ellconf.flagcheck:
@@ -537,6 +565,14 @@ def PassVars(photapi, ellconf, galhead, galcomps):
     photapi.kser = galcomps.kser.copy()
 
 
+    photapi.hconst = ellconf.hconst 
+
+    photapi.omegam = ellconf.omegam 
+
+    photapi.omegav = ellconf.omegav
+
+
+
 
 
 def PassArgs(args):
@@ -605,9 +641,12 @@ def PassArgs(args):
     if args.allskypx:
         ellconf.flagrmsky=False
 
-    if args.chisqr:
-        ellconf.flagchi = True
+    #if args.chisqr:
+    #    ellconf.flagchi = True
  
+    if args.title:
+        ellconf.title = args.title
+
 
     #options with arguments
 
@@ -728,6 +767,29 @@ def PassArgs(args):
         ellconf.Aext = args.aext
 
 
+    if args.hconst:
+        ellconf.hconst = args.hconst
+
+    if args.omegam:
+        ellconf.omegam = args.omegam
+
+    if args.omegav:
+        ellconf.omegav = args.omegav
+
+
+
+    if args.effrad:
+        ellconf.flagrep = True
+
+
+    if args.rad90:
+        ellconf.flagr90p = True
+
+
+    if args.rad95:
+        ellconf.flagr95p = True
+
+
 
 
     return ellconf

{EllipSect-3.2.2 → EllipSect-3.4.0}/tests/test_ellipsect.py

@@ -39,8 +39,8 @@ def test_files():
 
     path="tests/"
 
-    filepng = "imgblock-01.png"
-    filemulpng = "imgblock-01-mul.png"
+    filepng = "imgblock-g01-nc1-splot.png"
+    filemulpng = "imgblock-g01-nc1-mplot.png"
 
     filepng = path+filepng
     filemulpng = path+filemulpng
@@ -78,15 +78,17 @@ def test_comp():
 
     path="tests/"
 
-    filepng = "imgblock-01.png"
-    filemulpng = "imgblock-01-mul.png"
+    filepng = "imgblock-g01-nc1-splot.png"
+    filemulpng = "imgblock-g01-nc1-mplot.png"
+
+
 
     filepng = path+filepng
     filemulpng = path+filemulpng
 
 
 
-    filecomp = "imgblock-01-comp.fits"
+    filecomp = "imgblock-g01-nc1-comp.fits"
 
     filecomp= path+filecomp
 
@@ -128,22 +130,24 @@ def test_phot():
 
     path="tests/"
 
-    filephot = "imgblock-01-out.txt"
+    filephot = "imgblock-g01-nc1-out.txt"
     filephot= path+filephot
 
-    filecomp = "imgblock-01-comp.fits"
+    filecomp = "imgblock-g01-nc1-comp.fits"
     filecomp= path+filecomp
 
-    filepng = "imgblock-01.png"
-    filemulpng = "imgblock-01-mul.png"
+    filepng = "imgblock-g01-nc1-splot.png"
+    filemulpng = "imgblock-g01-nc1-mplot.png"
+
 
-    filesig = "imgblock-01-sig.fits"
+
+    filesig = "imgblock-g01-nc1-sig.fits"
     filesig= path+filesig
 
-    filecheck = "imgblock-01-check.fits"
+    filecheck = "imgblock-g01-nc1-check.fits"
     filecheck= path+filecheck
 
-    filecube = "imgblock-01-cub.png"
+    filecube = "imgblock-g01-nc1-cub.png"
     filecube = path+filecube
 
 
@@ -259,30 +263,36 @@ def test_gsky():
 
     path="tests/"
 
-    filephot = "imgblock-01-out.txt"
+
+    filephot = "imgblock-g01-nc1-out.txt"
     filephot= path+filephot
 
-    filecomp = "imgblock-01-comp.fits"
+    filecomp = "imgblock-g01-nc1-comp.fits"
     filecomp= path+filecomp
 
-    filepng = "imgblock-01.png"
-    filemulpng = "imgblock-01-mul.png"
+    filepng = "imgblock-g01-nc1-splot.png"
+    filemulpng = "imgblock-g01-nc1-mplot.png"
 
-    filesig = "imgblock-01-sig.fits"
+    filesig = "imgblock-g01-nc1-sig.fits"
     filesig= path+filesig
 
-    filecheck = "imgblock-01-check.fits"
+    filecheck = "imgblock-g01-nc1-check.fits"
     filecheck= path+filecheck
 
-    filecube = "imgblock-01-cub.png"
+    filecube = "imgblock-g01-nc1-cub.png"
     filecube = path+filecube
 
-    filersky = "imgblock-01-ring.fits"
+    filersky = "imgblock-g01-nc1-ring.fits"
     filersky = path + filersky
 
-    filermsky = "imgblock-01-ringmask.fits"
+    filermsky = "imgblock-g01-nc1-ringmask.fits"
     filermsky = path + filermsky
 
+    filechi = "imgblock-g01-nc1-chi.fits"
+    filechi = path + filechi
+
+
+
 
 
     filepng = path+filepng
@@ -374,30 +384,37 @@ def test_rsky():
 
     path="tests/"
 
-    filephot = "imgblock-01-out.txt"
+    filephot = "imgblock-g01-nc1-out.txt"
     filephot= path+filephot
 
-    filecomp = "imgblock-01-comp.fits"
+    filecomp = "imgblock-g01-nc1-comp.fits"
     filecomp= path+filecomp
 
-    filepng = "imgblock.01-png"
-    filemulpng = "imgblock-01-mul.png"
+    filepng = "imgblock-g01-nc1-splot.png"
+    filemulpng = "imgblock-g01-nc1-mplot.png"
 
-    filesig = "imgblock-01-sig.fits"
+    filesig = "imgblock-g01-nc1-sig.fits"
     filesig= path+filesig
 
-    filecheck = "imgblock-01-check.fits"
+    filecheck = "imgblock-g01-nc1-check.fits"
     filecheck= path+filecheck
 
-    filecube = "imgblock-01-cub.png"
+    filecube = "imgblock-g01-nc1-cub.png"
     filecube = path+filecube
 
-    filersky = "imgblock-01-ring.fits"
+    filersky = "imgblock-g01-nc1-ring.fits"
     filersky = path + filersky
 
-    filermsky = "imgblock-01-ringmask.fits"
+    filermsky = "imgblock-g01-nc1-ringmask.fits"
     filermsky = path + filermsky
 
+    filechi = "imgblock-g01-nc1-chi.fits"
+    filechi = path + filechi
+
+
+
+
+
 
 
     filepng = path+filepng
@@ -491,30 +508,35 @@ def test_freepar():
 
     path="tests/"
 
-    filephot = "imgblock-01-out.txt"
+    filephot = "imgblock-g01-nc1-out.txt"
     filephot= path+filephot
 
-    filecomp = "imgblock-01-comp.fits"
+    filecomp = "imgblock-g01-nc1-comp.fits"
     filecomp= path+filecomp
 
-    filepng = "imgblock-01.png"
-    filemulpng = "imgblock-mul.png"
+    filepng = "imgblock-g01-nc1-splot.png"
+    filemulpng = "imgblock-g01-nc1-mplot.png"
 
-    filesig = "imgblock-01-sig.fits"
+    filesig = "imgblock-g01-nc1-sig.fits"
     filesig= path+filesig
 
-    filecheck = "imgblock-01-check.fits"
+    filecheck = "imgblock-g01-nc1-check.fits"
     filecheck= path+filecheck
 
-    filecube = "imgblock-01-cub.png"
+    filecube = "imgblock-g01-nc1-cub.png"
     filecube = path+filecube
 
-    filersky = "imgblock-01-ring.fits"
+    filersky = "imgblock-g01-nc1-ring.fits"
     filersky = path + filersky
 
-    filermsky = "imgblock-01-ringmask.fits"
+    filermsky = "imgblock-g01-nc1-ringmask.fits"
     filermsky = path + filermsky
 
+    filechi = "imgblock-g01-nc1-chi.fits"
+    filechi = path + filechi
+
+
+
 
 
     filepng = path+filepng
@@ -624,30 +646,33 @@ def test_img_size():
 
     path="tests/"
 
-    filephot = "imgblock-01-out.txt"
+    filephot = "imgblock-g01-nc1-out.txt"
     filephot= path+filephot
 
-    filecomp = "imgblock-01-comp.fits"
+    filecomp = "imgblock-g01-nc1-comp.fits"
     filecomp= path+filecomp
 
-    filepng = "imgblock-01.png"
-    filemulpng = "imgblock-01-mul.png"
+    filepng = "imgblock-g01-nc1-splot.png"
+    filemulpng = "imgblock-g01-nc1-mplot.png"
 
-    filesig = "imgblock-01-sig.fits"
+    filesig = "imgblock-g01-nc1-sig.fits"
     filesig= path+filesig
 
-    filecheck = "imgblock-01-check.fits"
+    filecheck = "imgblock-g01-nc1-check.fits"
     filecheck= path+filecheck
 
-    filecube = "imgblock-01-cub.png"
+    filecube = "imgblock-g01-nc1-cub.png"
     filecube = path+filecube
 
-    filersky = "imgblock-01-ring.fits"
+    filersky = "imgblock-g01-nc1-ring.fits"
     filersky = path + filersky
 
-    filermsky = "imgblock-01-ringmask.fits"
+    filermsky = "imgblock-g01-nc1-ringmask.fits"
     filermsky = path + filermsky
 
+    filechi = "imgblock-g01-nc1-chi.fits"
+    filechi = path + filechi
+
 
     tempmask="tempmask.fits"
     filetempmask = tempmask 
@@ -684,7 +709,9 @@ def test_img_size():
     if os.path.isfile(filetempmask):
         os.remove(filetempmask)
  
-
+    if os.path.isfile(filechi):
+        os.remove(filechi)
+ 
 
     from ellipsect.inout.galfit  import Galfit 
     from ellipsect.sectors.sect  import PassArgs 
@@ -761,7 +788,9 @@ def test_img_size():
     if os.path.isfile(filetempmask):
         os.remove(filetempmask)
  
-
+    if os.path.isfile(filechi):
+        os.remove(filechi)
+