Merge pull request #291 from ABRG-Models/dev/tools_class_to_namespace

morph::Tools refactor
ABRG-Models · Nov 26, 2024 · 4855bdf · 4855bdf
2 parents f05dfa7 + 7b4a515
commit 4855bdf
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Showing 37 changed files with 490 additions and 507 deletions.
diff --git a/buildtools/process_colourmap.cpp b/buildtools/process_colourmap.cpp
@@ -19,8 +19,8 @@ int main (int argc, char** argv)
 
     // Obtain name from fpath
     std::string name = fpath;
-    morph::Tools::stripUnixPath (name);
-    morph::Tools::stripFileSuffix (name);
+    morph::tools::stripUnixPath (name);
+    morph::tools::stripFileSuffix (name);
     if (name.empty()) {
         std::cerr << "No name.\n";
         return -1;
@@ -53,7 +53,7 @@ int main (int argc, char** argv)
     unsigned int lastline = nlines - 1;
     for (std::string line; std::getline(ifile, line);) {
         // Process line into csv
-        std::vector<std::string> tokens = morph::Tools::stringToVector (line, (commas ? "," : " "));
+        std::vector<std::string> tokens = morph::tools::stringToVector (line, (commas ? "," : " "));
         if (tokens.size() != 3) {
             std::cerr << "text format error: != 3 values in line '" << line << "', (got "<< tokens.size() << ")\n";
             return -1;

diff --git a/buildtools/process_colourtables.cpp b/buildtools/process_colourtables.cpp
@@ -21,9 +21,9 @@ int main ()
 {
     ctabletype tt = ctabletype::unknown;
     // First get a directory listing and make sure we're in the Crameri folder
-    if (morph::Tools::fileExists ("+README_ScientificColourMaps.pdf")) {
+    if (morph::tools::fileExists ("+README_ScientificColourMaps.pdf")) {
         tt = ctabletype::Crameri;
-    } else if (morph::Tools::fileExists ("CET-C1.csv")) {
+    } else if (morph::tools::fileExists ("CET-C1.csv")) {
         tt = ctabletype::CET;
     } else {
         std::cerr << "Run this program within the Crameri OR CET colour table directories\n";
@@ -35,7 +35,7 @@ int main ()
     std::vector<std::string> table_files;
     std::string basedir = "./";
     std::string subdir = "";
-    morph::Tools::readDirectoryTree (dirs, basedir, subdir);
+    morph::tools::readDirectoryTree (dirs, basedir, subdir);
     if (tt == ctabletype::Crameri) {
         for (auto dir : dirs) {
             std::cerr << "Got file " << dir << std::endl;
@@ -90,14 +90,14 @@ int main ()
 
         // Obtain name from fpath
         std::string name = fpath;
-        morph::Tools::stripUnixPath (name);
-        morph::Tools::stripFileSuffix (name);
+        morph::tools::stripUnixPath (name);
+        morph::tools::stripFileSuffix (name);
         if (name.empty()) {
             std::cerr << "No name.\n";
             return -1;
         }
         std::string name_lower = name;
-        morph::Tools::toLowerCase (name_lower);
+        morph::tools::toLowerCase (name_lower);
 
         std::ifstream ifile (fpath, std::ios::in);
         if (!ifile.is_open()) {
@@ -135,7 +135,7 @@ int main ()
         unsigned int lastline = nlines - 1;
         for (std::string line; std::getline(ifile, line);) {
             // Process line into csv
-            std::vector<std::string> tokens = morph::Tools::stringToVector (line, (commas ? "," : " "));
+            std::vector<std::string> tokens = morph::tools::stringToVector (line, (commas ? "," : " "));
             if (tokens.size() != 3) {
                 std::cerr << "text format error: != 3 values in line '" << line << "', (got "<< tokens.size() << ")\n";
                 return -1;

diff --git a/examples/Ermentrout2009/erm.cpp b/examples/Ermentrout2009/erm.cpp
@@ -104,9 +104,9 @@ int main (int argc, char **argv)
     bool do_autoscale = conf.getBool ("autoscale", false);
 
     // Now create a log directory if necessary, and exit on any failures.
-    if (morph::Tools::dirExists (logpath) == false) {
-        morph::Tools::createDir (logpath);
-        if (morph::Tools::dirExists (logpath) == false) {
+    if (morph::tools::dirExists (logpath) == false) {
+        morph::tools::createDir (logpath);
+        if (morph::tools::dirExists (logpath) == false) {
             std::cerr << "Failed to create the logpath directory "
                       << logpath << " which does not exist.\n";
             return 1;
@@ -115,8 +115,8 @@ int main (int argc, char **argv)
         // Directory DOES exist. See if it contains a previous run and
         // exit without overwriting to avoid confusion.
         if (overwrite_logs == false
-            && (morph::Tools::fileExists (logpath + "/params.json") == true
-                || morph::Tools::fileExists (logpath + "/positions.h5") == true)) {
+            && (morph::tools::fileExists (logpath + "/params.json") == true
+                || morph::tools::fileExists (logpath + "/positions.h5") == true)) {
             std::cerr << "Seems like a previous simulation was logged in " << logpath << ".\n"
                       << "Please clean it out manually, choose another directory or set\n"
                       << "overwrite_logs to true in your parameters config JSON file.\n";
@@ -261,7 +261,7 @@ int main (int argc, char **argv)
 
     // Add simulation runtime information to the config, before saving it out as params.json
     conf.set ("float_width", (unsigned int)sizeof(FLT));
-    std::string tnow = morph::Tools::timeNow();
+    std::string tnow = morph::tools::timeNow();
     conf.set ("sim_ran_at_time", tnow.substr(0,tnow.size()-1));
     conf.set ("final_step", RD.stepCount);
     conf.set ("hextohex_d", RD.hextohex_d);

diff --git a/examples/LotkaVolterra/lv.cpp b/examples/LotkaVolterra/lv.cpp
@@ -111,9 +111,9 @@ int main (int argc, char **argv)
         // Using json filename as logpath
         std::string justfile = paramsfile;
         // Remove trailing .json and leading directories
-        std::vector<std::string> pth = morph::Tools::stringToVector (justfile, "/");
+        std::vector<std::string> pth = morph::tools::stringToVector (justfile, "/");
         justfile = pth.back();
-        morph::Tools::searchReplace (".json", "", justfile);
+        morph::tools::searchReplace (".json", "", justfile);
         // Use logbase as the subdirectory into which this should go
         logbase = conf.getString ("logbase", "logs/");
         if (logbase.back() != '/') { logbase += '/'; }
@@ -217,9 +217,9 @@ int main (int argc, char **argv)
      * Now create a log directory if necessary, and exit on any
      * failures.
      */
-    if (morph::Tools::dirExists (logpath) == false) {
-        morph::Tools::createDir (logpath);
-        if (morph::Tools::dirExists (logpath) == false) {
+    if (morph::tools::dirExists (logpath) == false) {
+        morph::tools::createDir (logpath);
+        if (morph::tools::dirExists (logpath) == false) {
             std::cerr << "Failed to create the logpath directory "
                       << logpath << " which does not exist.\n";
             return 1;
@@ -228,8 +228,8 @@ int main (int argc, char **argv)
         // Directory DOES exist. See if it contains a previous run and
         // exit without overwriting to avoid confusion.
         if (overwrite_logs == false
-            && (morph::Tools::fileExists (logpath + "/params.json") == true
-                || morph::Tools::fileExists (logpath + "/positions.h5") == true)) {
+            && (morph::tools::fileExists (logpath + "/params.json") == true
+                || morph::tools::fileExists (logpath + "/positions.h5") == true)) {
             std::cerr << "Seems like a previous simulation was logged in " << logpath << ".\n"
                       << "Please clean it out manually, choose another directory or set\n"
                       << "overwrite_logs to true in your parameters config JSON file.\n";
@@ -319,7 +319,7 @@ int main (int argc, char **argv)
     // results were computed with single precision, if 8, then double
     // precision was used. Also save various parameters from the RD system.
     conf.set ("float_width", (unsigned int)sizeof(FLT));
-    std::string tnow = morph::Tools::timeNow();
+    std::string tnow = morph::tools::timeNow();
     conf.set ("sim_ran_at_time", tnow.substr(0,tnow.size()-1));
     conf.set ("hextohex_d", RD.hextohex_d);
     conf.set ("dt", RD.get_dt());

diff --git a/examples/SimpsonGoodhill/sg.cpp b/examples/SimpsonGoodhill/sg.cpp
@@ -220,7 +220,7 @@ int main (int argc, char **argv)
     } else {
         // Create an empty/default json file
         paramsfile = "./sg.json";
-        morph::Tools::copyStringToFile ("{}\n", paramsfile);
+        morph::tools::copyStringToFile ("{}\n", paramsfile);
     }
 
     morph::Config conf(paramsfile);

diff --git a/examples/schnakenberg/schnak_whisk.cpp b/examples/schnakenberg/schnak_whisk.cpp
@@ -79,7 +79,6 @@ using morph::scale;
 using morph::vec;
 #endif
 using morph::Config;
-using morph::Tools;
 using std::string;
 using std::stringstream;
 using std::cerr;
@@ -133,9 +132,9 @@ int main (int argc, char **argv)
         // Using json filename as logpath
         string justfile = paramsfile;
         // Remove trailing .json and leading directories
-        vector<string> pth = Tools::stringToVector (justfile, "/");
+        vector<string> pth = morph::tools::stringToVector (justfile, "/");
         justfile = pth.back();
-        Tools::searchReplace (".json", "", justfile);
+        morph::tools::searchReplace (".json", "", justfile);
         // Use logbase as the subdirectory into which this should go
         logbase = conf.getString ("logbase", "logs/");
         if (logbase.back() != '/') {
@@ -237,9 +236,9 @@ int main (int argc, char **argv)
      * Now create a log directory if necessary, and exit on any
      * failures.
      */
-    if (Tools::dirExists (logpath) == false) {
-        Tools::createDir (logpath);
-        if (Tools::dirExists (logpath) == false) {
+    if (morph::tools::dirExists (logpath) == false) {
+        morph::tools::createDir (logpath);
+        if (morph::tools::dirExists (logpath) == false) {
             cerr << "Failed to create the logpath directory "
                  << logpath << " which does not exist."<< endl;
             return 1;
@@ -248,8 +247,8 @@ int main (int argc, char **argv)
         // Directory DOES exist. See if it contains a previous run and
         // exit without overwriting to avoid confusion.
         if (overwrite_logs == false
-            && (Tools::fileExists (logpath + "/params.json") == true
-                || Tools::fileExists (logpath + "/positions.h5") == true)) {
+            && (morph::tools::fileExists (logpath + "/params.json") == true
+                || morph::tools::fileExists (logpath + "/positions.h5") == true)) {
             cerr << "Seems like a previous simulation was logged in " << logpath << ".\n"
                  << "Please clean it out manually, choose another directory or set\n"
                  << "overwrite_logs to true in your parameters config JSON file." << endl;
@@ -347,7 +346,7 @@ int main (int argc, char **argv)
     // results were computed with single precision, if 8, then double
     // precision was used. Also save various parameters from the RD system.
     conf.set ("float_width", (unsigned int)sizeof(FLT));
-    string tnow = Tools::timeNow();
+    string tnow = morph::tools::timeNow();
     conf.set ("sim_ran_at_time", tnow.substr(0,tnow.size()-1));
     conf.set ("hextohex_d", RD.hextohex_d);
     conf.set ("D_A", RD.D_A);

diff --git a/examples/schnakenberg/schnakenberg.cpp b/examples/schnakenberg/schnakenberg.cpp
@@ -79,7 +79,6 @@ using morph::scale;
 using morph::vec;
 #endif
 using morph::Config;
-using morph::Tools;
 using std::string;
 using std::stringstream;
 using std::cerr;
@@ -133,9 +132,9 @@ int main (int argc, char **argv)
         // Using json filename as logpath
         string justfile = paramsfile;
         // Remove trailing .json and leading directories
-        vector<string> pth = Tools::stringToVector (justfile, "/");
+        vector<string> pth = morph::tools::stringToVector (justfile, "/");
         justfile = pth.back();
-        Tools::searchReplace (".json", "", justfile);
+        morph::tools::searchReplace (".json", "", justfile);
         // Use logbase as the subdirectory into which this should go
         logbase = conf.getString ("logbase", "logs/");
         if (logbase.back() != '/') {
@@ -239,9 +238,9 @@ int main (int argc, char **argv)
      * Now create a log directory if necessary, and exit on any
      * failures.
      */
-    if (Tools::dirExists (logpath) == false) {
-        Tools::createDir (logpath);
-        if (Tools::dirExists (logpath) == false) {
+    if (morph::tools::dirExists (logpath) == false) {
+        morph::tools::createDir (logpath);
+        if (morph::tools::dirExists (logpath) == false) {
             cerr << "Failed to create the logpath directory "
                  << logpath << " which does not exist."<< endl;
             return 1;
@@ -250,8 +249,8 @@ int main (int argc, char **argv)
         // Directory DOES exist. See if it contains a previous run and
         // exit without overwriting to avoid confusion.
         if (overwrite_logs == false
-            && (Tools::fileExists (logpath + "/params.json") == true
-                || Tools::fileExists (logpath + "/positions.h5") == true)) {
+            && (morph::tools::fileExists (logpath + "/params.json") == true
+                || morph::tools::fileExists (logpath + "/positions.h5") == true)) {
             cerr << "Seems like a previous simulation was logged in " << logpath << ".\n"
                  << "Please clean it out manually, choose another directory or set\n"
                  << "overwrite_logs to true in your parameters config JSON file." << endl;
@@ -355,7 +354,7 @@ int main (int argc, char **argv)
     // results were computed with single precision, if 8, then double
     // precision was used. Also save various parameters from the RD system.
     conf.set ("float_width", (unsigned int)sizeof(FLT));
-    string tnow = Tools::timeNow();
+    string tnow = morph::tools::timeNow();
     conf.set ("sim_ran_at_time", tnow.substr(0,tnow.size()-1));
     conf.set ("hextohex_d", RD.hextohex_d);
     conf.set ("D_A", RD.D_A);

diff --git a/morph/ColourMap.h b/morph/ColourMap.h
@@ -578,7 +578,7 @@ namespace morph {
         {
             ColourMapType cmt = morph::ColourMapType::Plasma;
             std::string _s = s;
-            morph::Tools::toLowerCase (_s);
+            morph::tools::toLowerCase (_s);
             if (_s == "fixed") {
                 cmt = morph::ColourMapType::Fixed;
             } else if (_s == "trichrome") {

diff --git a/morph/Config.h b/morph/Config.h
@@ -279,7 +279,7 @@ namespace morph {
                 if ((pos = arg.find ("-co:")) == 0) {
                     std::string arg_ss = arg.substr (4);
                     // Split arg based on '='
-                    std::vector<std::string> co = morph::Tools::stringToVector (arg_ss, std::string("="));
+                    std::vector<std::string> co = morph::tools::stringToVector (arg_ss, std::string("="));
                     if (co.size() >= 2) {
                         std::cout << "Override parameter '" << co[0] << "' with value '" << co[1] << "'\n";
                         //...so stick with using a map

diff --git a/morph/HdfData.h b/morph/HdfData.h
@@ -719,7 +719,7 @@ namespace morph {
          */
         void process_groups (const char* path)
         {
-            std::vector<std::string> pbits = morph::Tools::stringToVector (path, "/");
+            std::vector<std::string> pbits = morph::tools::stringToVector (path, "/");
             unsigned int numgroups = pbits.size() - 1;
             if (numgroups > 1) { // There's always the first, empty (root) group
                 std::string groupstr("");

diff --git a/morph/RD_Base.h b/morph/RD_Base.h
@@ -164,7 +164,7 @@ namespace morph {
         void setLogpath (const std::string p) {
             this->logpath = p;
             // Ensure log directory exists
-            morph::Tools::createDir (this->logpath);
+            morph::tools::createDir (this->logpath);
         }
 
         /*!

diff --git a/morph/Random.h b/morph/Random.h
@@ -44,7 +44,7 @@
  * exponential).
  *
  * See tests/testRandom.cpp for a variety of usage examples. Here is a single, simple
- * example to replace the old (and now removed) morph::Tools::randDouble():
+ * example:
  *
  * \code
  * #include <morph/Random.h>

diff --git a/morph/ReadCurves.h b/morph/ReadCurves.h
@@ -366,9 +366,9 @@ namespace morph
                 // Extract the length of the line in mm from the layer name
                 // _x33_mm means .33 mm
                 std::string mm(g_id);
-                morph::Tools::searchReplace ("x", ".", mm);
-                morph::Tools::searchReplace ("_", "", mm);
-                morph::Tools::searchReplace ("m", "", mm);
+                morph::tools::searchReplace ("x", ".", mm);
+                morph::tools::searchReplace ("_", "", mm);
+                morph::tools::searchReplace ("m", "", mm);
                 float mmf = std::atof (mm.c_str());
                 // dl is the length of the scale bar line
                 float dl = 0.0f;
@@ -404,7 +404,7 @@ namespace morph
                     std::stringstream ss;
                     ss << s.substr(p0, p1-p0);
                     std::string ccs = ss.str();
-                    if (morph::Tools::containsOnlyWhitespace (ccs)) {
+                    if (morph::tools::containsOnlyWhitespace (ccs)) {
                         // Do nothing
                     } else {
                         ss >> n;
@@ -516,7 +516,7 @@ namespace morph
                 {
                     p2 = d.find_first_of (svgCmds, p1+1);
                     std::string lCmd = d.substr (p1+1, p2-p1-1);
-                    if (morph::Tools::containsOnlyWhitespace (lCmd)) {
+                    if (morph::tools::containsOnlyWhitespace (lCmd)) {
                         p3 = lCmd.size()-1;
                     } else {
                         std::vector<float> v = this->splitSvgCmdString (lCmd, cmd, 10000, p3);
@@ -542,7 +542,7 @@ namespace morph
                 {
                     p2 = d.find_first_of (svgCmds, p1+1);
                     std::string lCmd = d.substr (p1+1, p2-p1-1);
-                    if (morph::Tools::containsOnlyWhitespace (lCmd)) {
+                    if (morph::tools::containsOnlyWhitespace (lCmd)) {
                         p3 = lCmd.size()-1;
                     } else {
                         std::vector<float> v = this->splitSvgCmdString (lCmd, cmd, 10000, p3);
@@ -568,7 +568,7 @@ namespace morph
                 {
                     p2 = d.find_first_of (svgCmds, p1+1);
                     std::string lCmd = d.substr (p1+1, p2-p1-1);
-                    if (morph::Tools::containsOnlyWhitespace (lCmd)) {
+                    if (morph::tools::containsOnlyWhitespace (lCmd)) {
                         p3 = lCmd.size()-1;
                     } else {
                         std::vector<float> v = this->splitSvgCmdString (lCmd, cmd, 10000, p3);
@@ -599,7 +599,7 @@ namespace morph
                 {
                     p2 = d.find_first_of (svgCmds, p1+1);
                     std::string mCmd = d.substr (p1+1, p2-p1-1);
-                    if (morph::Tools::containsOnlyWhitespace (mCmd)) {
+                    if (morph::tools::containsOnlyWhitespace (mCmd)) {
                         p3 = mCmd.size()-1;
                     } else {
                         std::vector<float> v = this->splitSvgCmdString (mCmd, cmd, 10000, p3);
@@ -639,7 +639,7 @@ namespace morph
                 {
                     p2 = d.find_first_of (svgCmds, p1+1);
                     std::string cCmd = d.substr (p1+1, p2-p1-1); // cCmd may be either a single command (6 params) or a great long line.
-                    if (morph::Tools::containsOnlyWhitespace (cCmd)) {
+                    if (morph::tools::containsOnlyWhitespace (cCmd)) {
                         p3 = cCmd.size()-1;
                     } else {
                         std::vector<float> v = this->splitSvgCmdString (cCmd, cmd, 6, p3);
@@ -669,7 +669,7 @@ namespace morph
                 {
                     p2 = d.find_first_of (svgCmds, p1+1);
                     std::string sCmd = d.substr (p1+1, p2-p1-1);
-                    if (morph::Tools::containsOnlyWhitespace (sCmd)) {
+                    if (morph::tools::containsOnlyWhitespace (sCmd)) {
                         p3 = sCmd.size()-1;
                     } else {
                         std::vector<float> v = this->splitSvgCmdString (sCmd, cmd, 4, p3);

diff --git a/morph/RecurrentNetworkModel.h b/morph/RecurrentNetworkModel.h
@@ -257,7 +257,7 @@ namespace morph {
 
                 // setup log file
                 this->logpath = logpath;
-                morph::Tools::createDir (logpath);
+                morph::tools::createDir (logpath);
                 { std::stringstream ss; ss << logpath << "/log.txt"; logfile.open(ss.str());}
                 logfile<<"Hello."<<std::endl;