cleanup

.gitignore

@@ -7,3 +7,4 @@ vri*
 *.tar.gz
 bin*
 test*
+*.pyc

cpp/ansicolor.h

@@ -0,0 +1,27 @@
+#pragma once
+#ifndef HEADER_ANSICOLOR_H
+#define HEADER_ANSICOLOR_H
+#define KNRM "\x1B[0m" //normal
+#define KBLK "\x1B[30m" //black
+#define KRED "\x1B[31m" //red
+#define KGRN "\x1B[32m" //green
+#define KYEL "\x1B[33m" //yellow
+#define KBLU "\x1B[34m" //blue
+#define KMAG "\x1B[35m" //magenta
+#define KCYN "\x1B[36m" //cyan
+#define KWHT "\x1B[37m" //white
+#define KBLD "\x1B[1m" //bold
+#define KRES "\x1B[0m" //reset
+#define KITA "\x1B[3m" //italics
+#define KUND "\x1B[4m" //underline
+#define KSTR "\x1B[9m" //strikethrough
+#define KINV "\x1B[7m" //inverseON
+#define BBLK "\x1B[30m" //black
+#define BRED "\x1B[31m" //red
+#define BGRN "\x1B[32m" //green
+#define BYEL "\x1B[33m" //yellow
+#define BBLU "\x1B[34m" //blue
+#define BMAG "\x1B[35m" //magenta
+#define BCYN "\x1B[36m" //cyan
+#define BWHT "\x1B[37m" //white
+#endif

cpp/misc.h

@@ -0,0 +1,212 @@
+#ifndef _MISC_H_
+#define _MISC_H_
+//---------------------------------------------------------------------------//
+// misc.h: helper functions //
+// date: 20190124 //
+//---------------------------------------------------------------------------//
+
+/* shorthand for for loops from 0 to N */
+#define for0(i,n) for(i = 0; i < n; i++)
+
+#define STR_MAX 16384
+
+#include<map>
+#include<set>
+#include<cmath>
+#include<queue>
+#include<vector>
+#include<string>
+#include<sstream>
+#include<fstream>
+#include<iostream>
+#include<limits.h>
+#include<memory.h>
+#include<pthread.h>
+#include<algorithm>
+#include"ansicolor.h"
+
+#include <algorithm>
+#include <cctype>
+#include <locale>
+
+
+using namespace std;
+
+#include <stdio.h> /* defines FILENAME_MAX */
+#ifdef WINDOWS
+#include <direct.h>
+#define _cwd _getcwd
+#else
+#include <unistd.h>
+#define _cwd getcwd
+#endif
+
+void rewind(ifstream &a);
+
+#define str string
+string cwd();
+
+/* split a string (a-la python) */
+vector<string> split(string s, char delim);
+vector<string> split(string s); // comma
+vector<string> split_special(string s); // comma with possible commas inside quotation marks!
+string join(const char * delim, vector<string> s);
+
+template<class T> std::ostream& operator << (std::ostream& os, const std::vector<T>& v){
+  os << "[";
+  for (typename std::vector<T>::const_iterator ii = v.begin(); ii != v.end(); ++ii){
+    os << " '" << *ii << "'";
+  }
+  os << "]";
+  return os;
+}
+
+template<class T> std::ostream& operator << (std::ostream& os, const std::set<T>& v){
+  os << "{";
+  for (typename std::set<T>::const_iterator ii = v.begin(); ii != v.end(); ++ii){
+    os << " " << *ii;
+  }
+  os << "}";
+  return os;
+}
+
+template<class A, class B> std::ostream& operator << (std::ostream& os, const std::map<A, B>& v){
+  os << "{" << endl;
+  for (typename std::map<A, B>::const_iterator ii = v.begin(); ii != v.end(); ++ii){
+    os << ii->first << ":" << ii->second << ","; //endl;
+  }
+  os << "}" << endl;
+  return os;
+}
+
+void err(string msg);
+
+void err(const char * msg);
+
+/* allocate memory */
+inline void * alloc(size_t nb){
+  void * d = malloc(nb);
+  if(!d){
+    printf("%zu\n", nb);
+    err("failed to allocate memory");
+  }
+  memset(d, '\0', nb);
+  return d;
+}
+
+
+//a trim from start (in place)
+static inline void ltrim(std::string &s){
+  s.erase(s.begin(), std::find_if(s.begin(), s.end(), [](int ch){
+    return !std::isspace(ch);
+  }
+  ));
+}
+
+// trim from end (in place)
+static inline void rtrim(std::string &s){
+  s.erase(std::find_if(s.rbegin(), s.rend(), [](int ch){
+    return !std::isspace(ch);
+  }
+  ).base(), s.end());
+}
+
+// trim from both ends (in place)
+static inline void trim(std::string &s){
+  ltrim(s);
+  rtrim(s);
+}
+
+// trim from start (copying): not implemented properly
+static inline std::string ltrim_copy(std::string s){
+  ltrim(s);
+  return s;
+}
+
+// trim from end (copying): not implemented properly
+static inline std::string rtrim_copy(std::string s){
+  rtrim(s);
+  return s;
+}
+
+// trim from both ends (copying): not implemented properly
+static inline std::string trim_copy(std::string s){
+  trim(s);
+  return s;
+}
+
+static inline void trim(std::string &s, char delim){
+  str ret("");
+  int end = s.size() - 1; 
+  int start = 0;
+  while(s[start] == delim) start += 1;
+  while(s[end] == delim) end -= 1;
+  s = s.substr(start, 1 + end - start);
+}
+
+#define strip trim
+
+/* convert to lower case */
+static void inline lower(std::string & s){
+  std::transform(s.begin(), s.end(), s.begin(), ::tolower);
+}
+
+static inline std::string lower_copy(std::string &s){
+  string r(s);
+  std::transform(r.begin(), r.end(), r.begin(), ::tolower);
+  return r;
+}
+
+/* get size of file pointer */
+size_t size(FILE * f);
+size_t fsize(string fn);
+
+// in-memory reader (writer to be implemented)
+// note this should be able to modulate between available protocols (like ifstream, ofstream, etc. , fwrite, fread, if available)
+
+FILE * wopen(string fn);
+
+class f_idx{
+  public: // float, index tuple object
+  float d;
+  unsigned int idx;
+  f_idx(float d_ = 0., unsigned int idx_ = 0){
+    d = d_;
+    idx = idx_;
+  }
+  f_idx(const f_idx &a){
+    d = a.d;
+    idx = a.idx;
+  }
+};
+
+bool operator<(const f_idx& a, const f_idx&b);
+
+// read header file
+void hread(str hfn, size_t & nrow, size_t & ncol, size_t & nband);
+void hwrite(str hfn, size_t nrow, size_t ncol, size_t nband);
+
+float * falloc(size_t nf);
+
+// read binary file
+float * bread(str bfn, size_t nrow, size_t ncol, size_t nband);
+
+extern  pthread_mutex_t print_mutex;
+void cprint(str s);
+/*
+  pthread_mutex_lock(&print_mutex);
+  cout << s << endl;
+  pthread_mutex_unlock(&print_mutex);
+*/
+
+int hsv_to_rgb(float *r, float *g, float *b, float h, float s, float v);
+
+str hdr_fn(str fn);
+
+/* get size of file pointer */
+size_t size(FILE * f);
+size_t fsize(string fn);
+bool exists(str fn);
+
+
+#endif

run

@@ -20,24 +20,26 @@ bin/fast_cluster data/mS2.bin 10
 
 rm data/*.png
 
-bin/class_recode data/mS2.bin_fastclust.bin
-bin/class_recode data/mS2.bin_kmeans.bin
+class_recode data/mS2.bin_fastclust.bin
+class_recode data/mS2.bin_kmeans.bin
 
 mv data/mS2.bin_fastclust.bin_recode.bin data/mS2.bin_fastclust.bin
 mv data/mS2.bin_kmeans.bin_recode.bin data/mS2.bin_kmeans.bin
 
-bin/class_count data/mS2.bin_fastclust.bin
-bin/class_count data/mS2.bin_kmeans.bin
+class_count data/mS2.bin_fastclust.bin
+class_count data/mS2.bin_kmeans.bin
 
-bin/class_wheel data/mS2.bin_fastclust.bin
-bin/class_wheel data/mS2.bin_kmeans.bin
+class_wheel data/mS2.bin_fastclust.bin
+class_wheel data/mS2.bin_kmeans.bin
 
 
-bin/read_multispectral data/mS2.bin_fastclust.bin_wheel.bin 1
-bin/read_multispectral data/mS2.bin_kmeans.bin_wheel.bin 1
+read_multi data/mS2.bin_fastclust.bin_wheel.bin 1
+read_multi data/mS2.bin_kmeans.bin_wheel.bin 1
 
+class_match_onto data/mS2.bin_fastclust.bin data/mS2.bin_kmeans.bin data/fastclust_onto_kmeans.bin
+class_wheel data/fastclust_onto_kmeans.bin
+read_multi data/fastclust_onto_kmeans.bin_wheel.bin 1
 
-bin/class_match_onto data/mS2.bin_fastclust.bin data/mS2.bin_kmeans.bin match.bin
 exit
 
 
@@ -53,9 +55,9 @@ bin/class_wheel data/mS2.bin_kmeans.bin
 bin/class_wheel data/mS2.bin_fastclust.bin_match.bin
 
 rm data/*.png
-bin/read_multispectral data/mS2.bin_fastclust.bin_match.bin_wheel.bin 1
-#bin/read_multispectral data/mS2.bin_kmeans.bin_match.bin_wheel.bin 1 
-#bin/read_multispectral data/mS2.bin_fastclust.bin_wheel.bin 1 
-bin/read_multispectral data/mS2.bin_kmeans.bin_wheel.bin 1
+bin/read_multi data/mS2.bin_fastclust.bin_match.bin_wheel.bin 1
+#bin/read_multi data/mS2.bin_kmeans.bin_match.bin_wheel.bin 1 
+#bin/read_multi data/mS2.bin_fastclust.bin_wheel.bin 1 
+bin/read_multi data/mS2.bin_kmeans.bin_wheel.bin 1