merge with code documentation

src/BoundingBox.hpp

@@ -1,5 +1,9 @@
 #pragma once
 
+/*
+* Class representing analyzed bound box
+*/
+
 class BoundingBox
 {
 public:

src/HydroDataReader.hpp

@@ -6,6 +6,10 @@
 #include "csv.hpp"
 #include "types.hpp"
 
+/*
+Class for paring discharge data.
+*/
+
 class HydroDataReader
 {
 public:

src/RasterInfo.hpp

@@ -7,6 +7,12 @@
 
 namespace fs = std::filesystem;
 
+/*
+*
+* Utility class for extracting infromation about satellite imagery
+*
+*/
+
 class RasterInfo
 {
 public:
@@ -22,13 +28,18 @@ class RasterInfo
   Polarization pol;
   Date date;
 };
-
+/*
+* 
+* This class contains methods to retrevie acquistiion date and polarization for input satellite imagery filebuf*
+*
+*/
 class RasterInfoExtractor
 {
 public:
   virtual RasterInfo extractFromPath(std::string filepath) = 0;
 };
 
+//Extractor for file preprocessed using Hyp3
 class AsfExtractor : public RasterInfoExtractor
 {
 public:
@@ -52,7 +63,7 @@ class AsfExtractor : public RasterInfoExtractor
     return RasterInfo(filepath, resultPol, resultDate);
   }
 };
-
+//Extractor for locally processed imagery files (date + polarization) 
 class StdExtractor : public RasterInfoExtractor
 {
 public:

src/XYPair.hpp

@@ -1,5 +1,11 @@
 #pragma once
 
+/* 
+* 
+* Utility script for representing coordinates in the algorothm
+*
+*/
+
 class XYPair
 {
 public:

src/analyze_dir.cpp

@@ -17,6 +17,11 @@
 #include <sys/wait.h>
 #include <thread>
 
+/*
+* Utility function that contains main() . This script can is used additionaly to analyze and prepare input data for the floodsar 
+* algorithm.
+*/
+
 namespace fs = std::filesystem;
 
 void
@@ -75,6 +80,7 @@ main(int argc, char** argv)
 
     std::ifstream proj4file(proj4Path);
 
+	//get polarization and date info from imagery filenames
     RasterInfo extractedInfo = extractor->extractFromPath(filepath.string());
 
     std::getline(proj4file, extractedInfo.proj4);

src/clustering.hpp

@@ -3,9 +3,23 @@
 #include <random>
 #include <fstream>
 
+/*
+* The 2D algorithm that performs clustering on two SAR polarizations at the same time.
+
+@param vectorVH is a cross polarization
+@param vectorVV is a co-polarization
+@param numClasses is a number of flooded classes
+@param maxiter is a maximum number of iteration to find clusters
+@param frac is a fraction of pixels that algorithms analyzes in order to find cluster centroids.
+
+*/
 const std::string kmeansInputFilename = "KMEANS_INPUT";
 const int kmeansMinimumPoints = 100;
-
+/*
+*
+* Function performs k-means clustering for floodSar
+*
+*/
 void
 performClustering(std::vector<double>& vectorVH,
     std::vector<double>& vectorVV,
@@ -159,7 +173,14 @@ performClustering(std::vector<double>& vectorVH,
         ofsPoints << clusterAssignments[i] << "\n";
     }
 }
-
+/*
+Function that returns a vector with classes list
+*
+* @params clusersFilePath is a prefix for filenemame that stores flood mapping results
+* @params classesNum is a number of flood classes
+* @params is a strategy how to pick flood classes. Only applicable to 2D algorithm. Possible values: vh, vv, sum.
+* 
+*/
 std::vector<unsigned int>
 createFloodClassesList(std::string clustersFilePath,
                        unsigned int classesNum,
@@ -202,6 +223,12 @@ createFloodClassesList(std::string clustersFilePath,
 
 
 void
+/*
+Function to calculate flooder Areas
+@params floodedAreas is a vector that is filled in during function invocation. 
+@params numberofClasses iz  total number of classes analyzed by k-means
+@params floodClassesNum is a number of flood classes to calculate area
+*/
 calculateFloodedAreasFromKMeansOutput(
   std::vector<unsigned int>& floodedAreas, // vector to fill
   unsigned int numberOfClasses,

src/csv.hpp

@@ -3,6 +3,10 @@
 #include <string>
 #include <vector>
 
+/*
+* Class for reading a CSV file with discharge data. See exammple -> discharge.csv file 
+*/
+
 class CSVRow
 {
 public:

src/main.cpp

@@ -19,6 +19,10 @@
 #include "utils.hpp"
 #include "clustering.hpp"
 
+/*
+* Main function file
+*/
+
 namespace fs = std::filesystem;
 
 

src/mapper.cpp

@@ -19,6 +19,11 @@
 
 namespace fs = std::filesystem;
 
+/*
+*
+* This is a postprocessing script for transforming floodSar results to rasters. 
+*
+*/
 int
 main(int argc, char** argv)
 {
@@ -34,6 +39,7 @@ main(int argc, char** argv)
     "a,auto",
     "automatically use best k-means results");
 
+//default values for 1D algorithm
   int numAllClassess = 2;
   int numFloodClasses = 1;
   int aa;
@@ -67,12 +73,12 @@ main(int argc, char** argv)
     // base algoritm mapping.
     floodClasses.push_back(1);
     std::string pol = userInput["base"].as<std::string>();
-    // bedzie VV albo VH
+    // either VV or VH
 
     pointsFile = "./.floodsar-cache/1d_output/" + pol;
     mapDirectory = "./mapped/base_algo_pol_" + pol + "/";
   } else {
-    // improved algo mapping.
+    // 2D algroithm
     if (userInput.count("auto")) 
        {
         std::ifstream bestClassStream(".floodsar-cache/kmeans_outputs/best.txt");
@@ -167,6 +173,7 @@ main(int argc, char** argv)
         std::cout << "Its time to stop. \n";
         break;
       }
+	  //mapPath contains reults raster for particular date
       mapPath = mapDirectory + dates[dateIndex] + ".tif";
       std::filesystem::copy_file(rasterToClassify, mapPath);
 

src/polarization.hpp

@@ -2,6 +2,13 @@
 
 #include <iostream>
 
+/*
+*
+* Utility scripts for converting strings to polarization and vice versa.
+*
+*/
+
+
 enum class Polarization
 {
   VH,

src/rasters.hpp

@@ -7,6 +7,13 @@
 #include <thread>
 #include <fstream>
 
+
+/*
+* Gets the bounding box of Sentintel Imagery raster
+* @param raster is retreived from GDAL
+*
+*/
+
 BoundingBox
 getRasterBoundingBox(GDALDataset* raster)
 {
@@ -41,6 +48,13 @@ getRasterBoundingBox(GDALDataset* raster)
   return boundingBox;
 }
 
+/*
+* The functions crops satellite imagery in smaller region of interes
+* @param zoneBbox defines area of interest
+* @param info is a georeference info GDAL
+* @param epsgCode is projection code applied in satelltie imagery*
+*/
+
 void
 cropToZone(BoundingBox zoneBBox, RasterInfo info, std::string epsgCode)
 {
@@ -68,6 +82,13 @@ cropToZone(BoundingBox zoneBBox, RasterInfo info, std::string epsgCode)
   std::system(command.c_str());
 }
 
+/* The function reduces geographcially raster to the area of interest in order to save memory.
+*
+* @param rasterPaths is a vector of raster information  (RasterInfo) of analyzed satellite imageries
+* @param aoiDataset is a pointer to imagery data
+* @param epsgCode is a cartographic projection code used in imagery (assumed equal to every imagery)
+*
+*/
 void
 cropRastersToAreaOfInterest(std::vector<RasterInfo>& rasterPaths,
                             GDALDataset* aoiDataset,
@@ -97,6 +118,7 @@ cropRastersToAreaOfInterest(std::vector<RasterInfo>& rasterPaths,
   }
 }
 
+//get imagery projection info
 void
 getProjectionInfo(std::string rasterPath, std::string proj4filePath)
 {
@@ -120,8 +142,7 @@ printProjCrs(RasterInfo info)
   std::system(command.c_str());
 }
 
-// returns absolute paths to all images that will take part in calculating the
-// result
+// returns absolute paths to all images that will take part in calculating the result...
 std::vector<RasterInfo>
 readRasterDirectory(std::string dirname,
                     std::string fileExtension,
@@ -183,6 +204,7 @@ mosaicRasters(const std::string targetPath,
   std::system(command.c_str());
 }
 
+//if two rasters with the same are present then mosaicing is performed...
 void
 performMosaicking(std::vector<RasterInfo>& rasterInfos,
                   std::vector<RasterInfo>& outputVector)
@@ -226,6 +248,7 @@ performMosaicking(std::vector<RasterInfo>& rasterInfos,
   }
 }
 
+//prefrom reprojection using GDAL (gdalwarp) 
 std::string
 performReprojection(RasterInfo& info, std::string epsgCode)
 {
@@ -248,7 +271,7 @@ performReprojection(RasterInfo& info, std::string epsgCode)
 
   return filename;
 }
-
+//in case of different projection of a raster file..
 void
 reprojectIfNeeded(std::vector<RasterInfo>& rasters, std::string epsgCode)
 {
@@ -301,6 +324,7 @@ getPixelValuesFromRaster(GDALDataset* raster,
   CPLFree(buffer);
 }
 
+// Method to calculae flooder area basing on threshold in 1D algorithm
 unsigned int
 calcFloodedArea(GDALDataset* raster, double threshold)
 {

src/utils.hpp

@@ -12,7 +12,7 @@ struct ClassifiedCentroid
   double vv;
   unsigned int cl;
 };
-
+//simple utilites to compare value of centroids by polariztion (vh,vv or sum).
 struct compareByVH
 {
   inline bool operator()(const ClassifiedCentroid& c1,
@@ -105,6 +105,7 @@ calcCorrelationCoeff(std::vector<unsigned int>& floodedAreaVals,
   return corr;
 }
 
+//Converts hydrological date format to standard date format yyyymmdd
 Date
 hydrologicalToNormalDate(std::string_view year,
                          std::string_view month,
@@ -156,6 +157,7 @@ hydrologicalToNormalDate(std::string_view year,
   return out;
 }
 
+//utility function that prints obsElevationMaps to console
 void
 printMap(const std::map<std::string, double>& m)
 {
@@ -165,6 +167,7 @@ printMap(const std::map<std::string, double>& m)
   std::cout << '\n';
 }
 
+//creates neccasary local files 
 void
 createCacheDirectoryIfNotExists()
 {