Expand environment variable in egs++ applications

HEN_HOUSE/user_codes/cavity/cavity.cpp

@@ -2822,6 +2822,7 @@ int Cavity_Application::initScoring() {
                 if( err3 ) egsFatal(
                   "\n\n***  Wrong/missing 'muen file' input for a "
                   "HVL calculation\n    This is a fatal error\n\n");
+                muen_file = egsExpandPath(muen_file);
                 ifstream muen_data(muen_file.c_str());
                 if( !muen_data ){
                     egsFatal(

HEN_HOUSE/user_codes/egs_cbct/egs_cbct.cpp

@@ -1145,15 +1145,19 @@ int EGS_CBCT::initScoring() {
             if( err3 ) egsFatal(
               "\n\n***  Wrong/missing 'muen file' input for a "
               "kerma calculation\n    This is a fatal error\n\n");
+            muen_file = egsExpandPath(muen_file);
             ifstream muen_data(muen_file.c_str());
             if( !muen_data.is_open() ){
                 egsFatal(
               "\n\n***  Failed to open muen file %s\n"
                   "     This is a fatal error\n",muen_file.c_str());
             }
             else{
-              egsInformation("\nUsing E*muen file %s for air-kerma calculation\n",
-                             muen_file.c_str());
+                egsInformation(
+                "\n\n=============== Kerma Scoring ===============\n"
+                    "E*muen/rho file: %s\n"
+                    "=============================================\n",
+                    muen_file.c_str());
             }
             int ndat; muen_data >> ndat;
             if( ndat < 2 || muen_data.fail() ) egsFatal(
@@ -1403,7 +1407,7 @@ void EGS_CBCT::initOutput() {
             scan_type = blank;
         }
         else{
-          blank_scan = b_scan;
+          blank_scan = egsExpandPath(b_scan);
         }
         /*
           If no scan file name entry, a warning is issued.
@@ -1417,7 +1421,7 @@ void EGS_CBCT::initOutput() {
               "       This is not a proper CBCT calculation.\n\n");
         }
         else{
-          real_scan = the_scan;
+          real_scan = egsExpandPath(the_scan);
         }
         /* check what scans are requested by the user
            real => real scan simulation

HEN_HOUSE/user_codes/egs_cbct/example_w5br.egsinp

@@ -31,8 +31,8 @@
 #
 #  Projections at other angles can be obtained by modifying input block
 #  :cbct setup: below. One can define the projection angle and angular
-#  :interval. Negative values of the latter indicate rotation is done
-#  :counter-clockwise around the indicated axis.
+#  interval. Negative values of the latter indicate rotation is done
+#  counter-clockwise around the indicated axis.
 #
 #  BEWARE:
 #
@@ -43,8 +43,6 @@
 #  - media information in PEGS4 data file 521icru.pegs4dat distributed
 #    with EGSnrc.
 #
-#  - Replace $EGS_HOME string below with the actual value!!!
-#
 #  - If the detector resolution is changed, one must recalculate the blank
 #    scan
 #
@@ -183,7 +181,7 @@
               rotation = 0 1.570796326794896619 0
            :stop transformation:
             # Uses file provided in the distribution
-            muen file = /home/mainegra/egsnrc_mp/egs_fac/muen_air.data
+            muen file = $HEN_HOUSE/user_codes/egs_fac/examples/muen_air.data
         :stop planar scoring:
 
 :stop scoring options:
@@ -197,13 +195,13 @@
         ###############################################
         # Use the 2 lines below to produce a blank scan
         ###############################################
-        #scan file = /home/mainegra/egsnrc_mp/egs_cbct/blank_coll_64.scan
+        #scan file = $EGS_HOME/egs_cbct/blank_coll_64.scan
 	#scan type = blank
         ###############################################
         # Use the 3 lines below to produce real scans
         ###############################################
-        scan file = /home/mainegra/egsnrc_mp/egs_cbct/scan_w5br_coll_64.scan
-        blank scan = /home/mainegra/egsnrc_mp/egs_cbct/blank_coll_64.scan
+        scan file  = $EGS_HOME/egs_cbct/scan_w5br_coll_64.scan
+        blank scan = $EGS_HOME/egs_cbct/blank_coll_64.scan
 	scan type = scatter
         ###############################################
     :stop scan output:
@@ -286,18 +284,20 @@
 
 
 ########
-# For fast computation one can use KN for Compton scattering. However,
-# in realistic phantoms this may cause a 3% discrepancy.
+# For fast computation one can assume scattering from free electrons.
+# However, in realistic phantoms this may cause a 3% discrepancy.
 ########
 :start MC transport parameter:
 
   Global ECUT = 1
 
-  Photon cross sections = xcom  # epdl (or xcom)
+  Photon cross sections    = xcom  # epdl (or xcom)
 
   Bound Compton scattering = off
+
+  Rayleigh scattering      = off
 
-  Rayleigh scattering=  on
+  Atomic relaxations       = off
 
 :stop MC transport parameter:
 

HEN_HOUSE/user_codes/egs_fac/egs_fac.cpp

@@ -955,9 +955,17 @@ int EGS_FACApplication::initScoring() {
         int err3 = options->getInput("muen file",muen_file);
         if( err3 ) egsFatal("\n\n***  Wrong/missing 'muen file' input\n"
              "     This is a fatal error\n\n");
+        muen_file = egsExpandPath(muen_file);
         ifstream muen_data(muen_file.c_str());
         if( !muen_data ) egsFatal("\n\n***  Failed to open muen file %s\n"
                  "     This is a fatal error\n",muen_file.c_str());
+        else{
+            egsInformation(
+                "\n\n=============== Kerma Scoring ===============\n"
+                    "E*muen/rho file: %s\n"
+                    "=============================================\n\n",
+                    muen_file.c_str());
+        }
         int ndat; muen_data >> ndat;
         if( ndat < 2 || muen_data.fail() ) egsFatal(
                    "\n\n*** Failed to read muen dfata file\n");

HEN_HOUSE/user_codes/egs_fac/examples/example_mees_250kV.egsinp

@@ -29,8 +29,7 @@
 #
 #  An example input file for egs_fac.
 #
-#  NOTE: Substitute every instance of $HEN_HOUSE for its actual value in this
-#  file! It is essential to use 'Bound Compton Scattering = norej'. See the MC
+#  NOTE: It is essential to use 'Bound Compton Scattering = norej'. See the MC
 #  transport parameter input section for more info. See comments accompanying
 #  the various inputs for more details.
 #
@@ -803,7 +802,7 @@
     # ignores them (except for the first and last energy, which define the
     # energy interval).
     #
-    muen file = $HEN_HOUSE/user_codes/egs_fac/muen_air.data
+    muen file = $HEN_HOUSE/user_codes/egs_fac/examples/muen_air.data
 
 :stop scoring options:
 
@@ -852,4 +851,4 @@
   Bound Compton Scattering = norej
   Photon cross sections = xcom  # (could also be epdl or si)
 
-:stop MC transport parameter:
+:stop MC transport parameter:

HEN_HOUSE/user_codes/egs_fac/examples/mxr-320-250kVp_tube.egsinp

@@ -163,9 +163,16 @@ AIRICRU512
 
  :Stop MC Transport Parameter:
  #########################
+ #
+ # User-defined entries
+ #
+ #########################
  :Start user inputs:
 
-  # phsp output directory = /home/mainegra/egsnrc_mp/phsp/
+  # Enter here a custom location for phase-space file output
+  # For instance users might want to direct the output to a
+  # device with enough disk space!
+  # phsp output directory = enter_user_defined_location
 
  :Stop user inputs:
  #########################

HEN_HOUSE/user_codes/egs_kerma/egs_kerma.cpp

@@ -1312,36 +1312,23 @@ int EGS_KermaApplication::initScoring() {
         }
 
         string emuen_file;
-        int errKmuen = options->getInput("emuen file",emuen_file);
+        int errKmuen = options->getInput("emuen file", emuen_file);
         if (errKmuen) {
             // Handle legacy option
-            errKmuen = options->getInput("muen file",emuen_file);
+            errKmuen = options->getInput("muen file", emuen_file);
             if (errKmuen)
                 egsFatal(
                     "\n\n***  Wrong/missing 'emuen file' input for a "
                     "Kerma calculation\n    This is a fatal error\n\n");
         }
-        //Check for environment variable at beginning of file name
-        std::size_t p1= emuen_file.find_first_of("$");
-        if (p1 != emuen_file.npos) {
-            string str = emuen_file;
-            std::size_t p2 = str.find_first_of("/");
-            string envvar = str.substr(p1+1,p2-1);
-            //egsInformation(" Found env var: %s\n",envvar.c_str());
-            char  *envloc = getenv(envvar.c_str());
-            //egsInformation(" %s points to: %s\n",envvar.c_str(),envloc);
-            emuen_file.replace(p1,p2+1,envloc);
-            //egsInformation("\n-> Kerma calculated using E*muen/rho file : %s\n\n",emuen_file.c_str());
 
-        }
-
-        //emuen_file = egsExpandPath(emuen_file);
+        emuen_file = egsExpandPath(emuen_file);
 
         ifstream muen_data(emuen_file.c_str());
         if (!muen_data) {
             egsFatal(
                 "\n\n***  Failed to open emuen file %s\n"
-                "     This is a fatal error\n",emuen_file.c_str());
+                "     This is a fatal error\n", emuen_file.c_str());
         }
         else {
             egsInformation(

HEN_HOUSE/user_codes/egs_kerma/example_40keV_SDD_1m_FD.egsinp

@@ -218,10 +218,8 @@
     :stop fluence scoring:
 
     ### E*muen file (could also be E*mutr): absolute or relative file path
-    #emuen file = emuen_icru90_1.5MeV.data
     ### Use absolute path when submitting parallel jobs!!!
-    ### $EGS_HOME replaced with its value now
-    emuen file = $EGS_HOME/egs_kerma/emuen_rho_air_1keV-1.5MeV.data
+    emuen file = $EGS_HOME/egs_kerma/emuen_icru90_1.5MeV.data
 
     ### geometry for forced-detection (if omitted, score ONLY when reaching scoring region)
     Default FD geometry = sphere