Merge branch 'master' of gitlab.mpcdf.mpg.de:MPIBP-Hummer/BioEM

* 'master' of gitlab.mpcdf.mpg.de:MPIBP-Hummer/BioEM:
  Delete Compare_LogP
  Delete COORDREAD
  Delete QUATERNION_LIST_5000_Orient
  Delete QUATERNION_LIST_1700_Orient
  Delete CTF_PSF_Manual.eps
  Fig Manual cor
  Fixing Norm in B prior

Manual/ModComp.eps

 %!PS-Adobe-2.0 EPSF-2.0
 %%Title: ModComp.eps
 %%Creator: gnuplot 4.2 patchlevel 3 
-%%CreationDate: Wed Jun  8 14:14:44 2016
+%%CreationDate: Tue Jun 14 16:31:31 2016
 %%DocumentFonts: (atend)
 %%BoundingBox: 50 50 410 554
 %%EndComments
@@ -48,7 +48,7 @@ SDict begin [
   /Author (Pilar Cossio,MBP, ,)
 %  /Producer (gnuplot)
 %  /Keywords ()
-  /CreationDate (Wed Jun  8 14:14:44 2016)
+  /CreationDate (Tue Jun 14 16:31:31 2016)
   /DOCINFO pdfmark
 end
 } ifelse
@@ -566,26 +566,26 @@ LTb
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@@ -884,9 +884,9 @@ LT3
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@@ -905,24 +905,24 @@ LT3
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 stroke

Tutorial_BioEM/MODEL_COMPARISION/Compare_LogP

-   0  -70910.9000  -70904.7000      -6.2000      -6.2000
-   1  -70625.1000  -70607.9000     -17.2000     -23.4000
-   2  -70838.0000  -70812.7000     -25.3000     -48.7000
-   3  -70742.2000  -70751.8000       9.6000     -39.1000
-   4  -70582.3000  -70691.6000     109.3000      70.2000
-   5  -70756.7000  -70823.8000      67.1000     137.3000
-   6  -70565.9000  -70556.2000      -9.7000     127.6000
-   7  -70737.6000  -70742.0000       4.4000     132.0000
-   8  -70312.2000  -70464.9000     152.7000     284.7000
-   9  -70880.0000  -70880.4000       0.4000     285.1000
-  10  -70645.1000  -70645.5000       0.4000     285.5000
-  11  -70816.3000  -70814.3000      -2.0000     283.5000
-  12  -70759.3000  -70755.2000      -4.1000     279.4000
-  13  -70636.6000  -70638.0000       1.4000     280.8000
-  14  -70567.5000  -70638.3000      70.8000     351.6000
-  15  -70593.5000  -70579.6000     -13.9000     337.7000
-  16  -70785.1000  -70800.9000      15.8000     353.5000
-  17  -70548.2000  -70585.2000      37.0000     390.5000
-  18  -70856.3000  -70876.7000      20.4000     410.9000
-  19  -70764.9000  -70763.5000      -1.4000     409.5000

param.cpp

@@ -1313,9 +1313,13 @@ int bioem_param::CalculateRefCTF()
   // ********** Calculating normalized volumen element *********
 
   if(!printModel){
-    param_device.volu = voluang * (myfloat_t) param_device.GridSpaceCenter * pixelSize * (myfloat_t) param_device.GridSpaceCenter * pixelSize
-      * gridCTF_phase * gridCTF_amp * gridEnvelop / ((2.f * (myfloat_t) param_device.maxDisplaceCenter+1.)) / (2.f * (myfloat_t) (param_device.maxDisplaceCenter + 1.)) / ((myfloat_t) numberGridPointsCTF_amp * gridCTF_amp )
-      / ((myfloat_t) numberGridPointsCTF_phase * gridCTF_phase) / ((myfloat_t) numberGridPointsEnvelop * gridEnvelop ) / sqrt(2 * M_PI ) / param_device.sigmaPriorbctf ;
+  // All priors (uniform or not) normalized to 1
+  // The volume is the grid-spacing of the parameter / normalization
+  // the order is angles, displacement, ctf amplitud (all uniform) then env b & phase (non uniform) the sqrt(2) cancel out (see SI)
+    param_device.volu = voluang * 
+		 (myfloat_t) param_device.GridSpaceCenter * pixelSize * (myfloat_t) param_device.GridSpaceCenter * pixelSize / ((2.f * (myfloat_t) param_device.maxDisplaceCenter+1.)) / (2.f * (myfloat_t) (param_device.maxDisplaceCenter + 1.)) 
+                / (myfloat_t) numberGridPointsCTF_amp 
+		* gridEnvelop * gridCTF_phase / M_PI  / param_device.sigmaPriorbctf /  param_device.sigmaPriordefo ; 
 
     //  cout << "VOLU " << param_device.volu  << " " << gridCTF_amp << "\n";
     // *** Number of total pixels***