Expand environment variable in file names for C++ apps

HEN_HOUSE/egs++/egs_functions.cpp

@@ -205,6 +205,79 @@ string egsJoinPath(const string &first, const string &second) {
     return result;
 }
 
+/* Expand first environment variable found anywhere in string aname
+
+   - Checks for Unix or Windows style environment variable
+   - Expands environment variable in aname appending folder
+     separator if missing
+   - Replaces backslashes with slashes
+   - Checks for duplicate slashes in aname
+*/
+string egsExpandPath(const string &aname) {
+    string str = aname;
+    string c   = "%$";
+    // Check for FIRST environment variable anywhere in aname
+    size_t p1= str.npos;
+    int i = 0;
+    while (i < c.size()) {
+        p1= str.find_first_of(c[i++]);
+        if (p1 != str.npos) {
+            break;
+        }
+    }
+    string fs = "%/\\";
+    i = 0;
+    size_t p2 = str.npos;
+    while (p1 != str.npos && i < fs.size()) {
+        p2 = str.find_first_of(fs[i++],p1+1);
+        if (p2 != str.npos) {
+            break;
+        }
+    }
+    // Did we find an environment variable?
+    if (p1 != str.npos && p2 != str.npos) {
+        string envvar = str.substr(p1+1, p2-(p1+1));
+        char  *envval = getenv(envvar.c_str());
+        // Check that env var is defined
+        string envloc = envval ? string(envval) : string();
+        if (!envloc.empty()) {
+            // Append missing separator
+            size_t last = envloc.find_last_of("/\\");
+            if (last != envloc.size()-1) {
+                if (envloc[last] == __egs_fs) {
+                    envloc.append("\\");
+                }
+                else {
+                    envloc.append("/");
+                }
+            }
+            str.replace(p1, p2-p1+1,envloc);
+        }
+        else {
+            if (str[p1] == '$') {
+                egsWarning("\n\n *** egs++ egsExpandPath: Undefined environment variable $%s \n\n", envvar.c_str());
+            }
+            else {
+                egsWarning("\n\n *** egs++ egsExpandPath: Undefined environment variable %%%s%% \n\n", envvar.c_str());
+            }
+        }
+    }
+    // Replace back slashes with slashes
+    size_t found = str.find("\\");
+    while (found != str.npos) {
+        str.replace(found,1,"/");
+        found = str.find("\\");
+    }
+    // Remove duplicated slashes
+    found = str.find("//");
+    while (found != str.npos) {
+        str.replace(found,2,"/");
+        found = str.find("//");
+    }
+
+    return str;
+}
+
 string egsStripPath(const string &aname) {
     int j;
     for (j=aname.size()-1; j>=0; j--) {

HEN_HOUSE/egs++/egs_functions.h

@@ -199,6 +199,16 @@ string EGS_EXPORT egsJoinPath(const string &first, const string &second);
  */
 string EGS_EXPORT egsStripPath(const string &fname);
 
+/*! \brief Expands first environment variable found in a file name.
+ *
+ *  Looks for first Unix or Windows environment variable and expands
+ *  it into its value. Missing folder separator is added, duplicated
+ *  separators are removed. Final file name uses slashes as separators.
+ *
+ * \ingroup egspp_main
+ */
+string EGS_EXPORT egsExpandPath(const string &fname);
+
 /*! \brief Get the name of the host the program is running on.
  *
  * \ingroup egspp_main

HEN_HOUSE/egs++/egs_spectra.cpp

@@ -1873,6 +1873,8 @@ EGS_BaseSpectrum *EGS_BaseSpectrum::createSpectrum(EGS_Input *input) {
     else if (inp->compare(stype,"tabulated spectrum")) {
         string spec_file;
         err = inp->getInput("spectrum file",spec_file);
+        // Expands FIRST environment variable found in spec_file
+        spec_file = egsExpandPath(spec_file);
         if (!err) {
             ifstream sdata(spec_file.c_str());
             if (!sdata) egsWarning("%s failed to open spectrum file %s\n",

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