Add usage of command line.

src/main.cxx

@@ -1,24 +1,66 @@
 #include "config/config.h"
+#include <vector>
 #define EIGEN_USE_MKL_ALL
 
-#include <iostream>
-#include <algorithm>
-
-
-#include <complex>
-
-#include "common/ceMatchedFilterHandling.h"
-#include "MatlabReader.h"
+#include "src/common/fileHelper.h"
 #include "startReconstructions.h"
 #include "log/log.h"
 
-int main()
+/* 0 is data path.
+    1 is dataRef path.
+    2 is output path.
+    3 is config file path.
+*/
+
+int main(int argc, char *argv[])
 {
     auto defaultLogger = getLogger("Main");
     spdlog::set_default_logger(defaultLogger);
+    int argNum = 4; 
+    std::vector<std::string> args(argNum);
+    args[0] = "";
+    args[1] = "";
+    args[2] = Recon::DEFAULT_OUTPUT_PATH;
+    args[3] = Recon::DEFAULT_CONFIG_PATH;
+    argc = argc <= argNum? argc-1 : argNum;
+    for (int i = 0; i < argc; i++)
+    {
+        args[i] = argv[i+1];
+    }
+
+    if(args[0].empty())
+    {
+        RECON_INFO("No reconstruction data.");
+        return 0;
+    }
+    std::string configPath = Recon::fixPathSlash(args[3]);
+    Recon::initalizeConfig(configPath);
+    if( args[1].empty() && Recon::transParams::runTransmissionReco)
+    {
+        RECON_INFO("Running transmission reconstruction, but no refrence data.");
+        return 0;
+    }
+
+    std::string outPutPath = args[2];
+    std::string directoryPath = outPutPath;
+    if(Recon::endsWithMat(outPutPath))
+    {
+       directoryPath =  Recon::getPath(outPutPath);
+    }
+    else
+    {
+        outPutPath = Recon::fixPathSlash(outPutPath) + Recon::DEFAULT_OUTPUT_FILENAME;
+    }
+    if(!Recon::isDirectory(directoryPath))
+    {
+        RECON_INFO("Output directory is not valid.");
+        return 0;
+    }
+    
+    std::string dataPath = Recon::fixPathSlash(args[0]);
+    std::string dataRefPath = Recon::fixPathSlash(args[1]);
     RECON_INFO("start");
-    Recon::initalizeConfig();
-    Recon::startReconstructions();
+    Recon::startReconstructions(dataPath, dataRefPath, outPutPath);
     SPDLOG_INFO("finish");
     return 0;
 }