Merge #600: expand environment variables in egs++

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