Merge branch 'dev' into pointreg_test

isis/src/CMakeLists.txt

@@ -1,5 +1,5 @@
 #===============================================================================
-set(CORE_LIST base database control qisis system socet)
+set(CORE_LIST base database control qisis system socet dev)
 
 get_subdirectory_list(${CMAKE_CURRENT_LIST_DIR} modules)
 

isis/src/base/apps/bandnorm/bandnorm.cpp

@@ -0,0 +1,173 @@
+// system include files go first
+#include <string>
+#include <iostream>
+#include <iomanip>
+#include <vector>
+#include <algorithm>
+
+// Isis specific include files go next
+#include "ProcessByLine.h"
+#include "SpecialPixel.h"
+#include "IException.h"
+#include "Pvl.h"
+#include "TextFile.h"
+#include "Statistics.h"
+
+#include "bandnorm.h"
+
+using namespace std;
+
+namespace Isis {
+
+  static vector<int> band;
+  static vector<double> average;
+  static vector<double> normalizer;
+
+  // function prototypes
+  static void getStats(Buffer &in);
+  static void normalize(Buffer &in, Buffer &out);
+  static void Tokenize(const QString &str,
+                vector<QString> & tokens,
+                const QString &delimiters = " ");
+
+  void bandnorm(UserInterface &ui) {
+    Cube icube(ui.GetFileName("FROM"), "r");
+    bandnorm(&icube, ui);
+  }
+
+
+  void bandnorm(Cube *icube, UserInterface &ui) {
+    // We will be processing by line
+    ProcessByLine p;
+
+    // Now get the statistics for each band or the entire cube
+    QString avg = ui.GetString("AVERAGE");
+    p.SetInputCube(icube);
+    p.StartProcess(getStats);
+    if(avg == "BAND") {
+      int b = 0;
+      Statistics stats;
+      for(int i = 0; i < (int)average.size(); i++) {
+        if(b == band[i]) {
+          stats.AddData(&average[i], (unsigned int)1);
+        }
+        else {
+          normalizer.push_back(stats.Average());
+          b++;
+          stats.Reset();
+        }
+      }
+      normalizer.push_back(stats.Average());
+    }
+    else if(avg == "PENCIL") {
+      TextFile pencil;
+      pencil.Open(ui.GetFileName("SPECTRUM"));
+      std::cout << pencil.LineCount() << " " << icube->bandCount() << std::endl;
+      if(pencil.LineCount() - 1 < icube->bandCount()) {
+        QString msg = "The spectral pencil file [" + ui.GetAsString("SPECTRUM") +
+                      "] does not contain enough data for all bands.";
+        throw IException(IException::User, msg, _FILEINFO_);
+      }
+      QString st;
+      int column = -1;
+      vector<QString> tokens;
+      pencil.GetLine(st);     //Takes care of title line
+      Tokenize(st, tokens, ", \"-+");
+      if(ui.GetAsString("METHOD") == "number") {
+        column = ui.GetInteger("NUMBER");
+      }
+      else {
+        for(unsigned i = 0; i < tokens.size(); i++) {
+          if(tokens[i] == ui.GetString("NAME")) {
+            column = i;
+        break;
+          }
+        }
+      }
+      if(column < 0  || (unsigned)column > tokens.size()) {
+        QString msg = "The column specified in file [" + ui.GetFileName("SPECTRUM")
+                      + "] was not found.";
+        throw IException(IException::User, msg, _FILEINFO_);
+      }
+      // Add the correct column of data to normalizer
+      for(int i = 0; i < icube->bandCount(); i++) {
+        tokens.clear();
+        pencil.GetLine(st);
+        Tokenize(st, tokens, ", \"");
+        std::cout << "col: " << column << std::endl;
+        std::cout << Isis::IString(tokens[column]).ToDouble() << std::endl;
+        normalizer.push_back(Isis::IString(tokens[column]).ToDouble());
+      }
+    }
+    else {  // avg == "CUBE"
+      Statistics stats;
+      for(int i = 0; i < (int)average.size(); i++) {
+        stats.AddData(&average[i], (unsigned int)1);
+      }
+      for(int b = 0; b < icube->bandCount(); b++) {
+        normalizer.push_back(stats.Average());
+      }
+    }
+
+    // Setup the output file and apply the correction
+    p.SetOutputCube(ui.GetFileName("TO"), ui.GetOutputAttribute("TO"), icube->sampleCount(), icube->lineCount(), icube->bandCount());
+    p.StartProcess(normalize);
+
+    // Cleanup
+    p.EndProcess();
+    normalizer.clear();
+    band.clear();
+    average.clear();
+  }
+
+  //**********************************************************
+  // Get statistics on a band or entire cube
+  //**********************************************************
+  void getStats(Buffer &in) {
+    Statistics stats;
+    stats.AddData(in.DoubleBuffer(), in.size());
+    average.push_back(stats.Average());
+    band.push_back(in.Band() - 1);
+  }
+
+  // Apply coefficients
+  void normalize(Buffer &in, Buffer &out) {
+    int index = in.Band() - 1;
+    double coeff = normalizer[index];
+
+    // Now loop and apply the coefficents
+    for(int i = 0; i < in.size(); i++) {
+      if(IsSpecial(in[i])) {
+        out[i] = in[i];
+      }
+      else {
+        out[i] = Null;
+        if(coeff != 0.0 && IsValidPixel(coeff)) {
+          out[i] = in[i] / coeff;
+        }
+      }
+    }
+  }
+
+  // Tokenizer
+  void Tokenize(const QString &strQStr,
+                vector<QString> & tokens,
+                const QString &delimitersQStr) {
+    IString str = strQStr;
+    IString delimiters = delimitersQStr;
+
+    //Skip delimiters at the beginning
+    string::size_type lastPos = str.find_first_not_of(delimiters, 0);
+    // Find first "non-delimiter".
+    string::size_type pos     = str.find_first_of(delimiters, lastPos);
+
+    while(string::npos != pos  ||  string::npos != lastPos) {
+      // Found a token, add it to the vector
+      tokens.push_back(str.substr(lastPos, pos - lastPos).c_str());
+      // Skip delimiters
+      lastPos = str.find_first_not_of(delimiters, pos);
+      // Find next "non-delimiter"
+      pos = str.find_first_of(delimiters, lastPos);
+    }
+  }
+}

isis/src/base/apps/bandnorm/bandnorm.h

@@ -0,0 +1,12 @@
+#ifndef bandnorm_h 
+#define bandnorm_h
+
+#include "UserInterface.h"
+#include "Cube.h"
+
+namespace Isis {
+  extern void bandnorm(Cube *icube, UserInterface &ui);
+  extern void bandnorm(UserInterface &ui);
+}
+
+#endif

isis/src/base/apps/bandnorm/main.cpp

@@ -1,165 +1,11 @@
 #include "Isis.h"
 
-// system include files go first
-#include <string>
-#include <iostream>
-#include <iomanip>
-#include <vector>
-#include <algorithm>
+#include "Application.h"
+#include "bandnorm.h"
 
-// Isis specific include files go next
-#include "ProcessByLine.h"
-#include "SpecialPixel.h"
-#include "IException.h"
-#include "Pvl.h"
-#include "TextFile.h"
-#include "Statistics.h"
-
-using namespace std;
 using namespace Isis;
 
-static vector<int> band;
-static vector<double> average;
-static vector<double> normalizer;
-
-// function prototypes
-void getStats(Buffer &in);
-void normalize(Buffer &in, Buffer &out);
-void Tokenize(const QString &str,
-              vector<QString> & tokens,
-              const QString &delimiters = " ");
-
 void IsisMain() {
-  // We will be processing by line
-  ProcessByLine p;
-
-  // Setup the input cube
   UserInterface &ui = Application::GetUserInterface();
-  Cube *icube = p.SetInputCube("FROM");
-
-  // Now get the statistics for each band or the entire cube
-  QString avg = ui.GetString("AVERAGE");
-  p.StartProcess(getStats);
-  if(avg == "BAND") {
-    int b = 0;
-    Statistics stats;
-    for(int i = 0; i < (int)average.size(); i++) {
-      if(b == band[i]) {
-        stats.AddData(&average[i], (unsigned int)1);
-      }
-      else {
-        normalizer.push_back(stats.Average());
-        b++;
-        stats.Reset();
-      }
-    }
-    normalizer.push_back(stats.Average());
-  }
-  else if(avg == "PENCIL") {
-    TextFile pencil;
-    pencil.Open(ui.GetFileName("SPECTRUM"));
-    if(pencil.LineCount() - 1 < icube->bandCount()) {
-      QString msg = "The spectral pencil file [" + ui.GetAsString("SPECTRUM") +
-                    "] does not contain enough data for all bands.";
-      throw IException(IException::User, msg, _FILEINFO_);
-    }
-    QString st;
-    int column = -1;
-    vector<QString> tokens;
-    pencil.GetLine(st);     //Takes care of title line
-    Tokenize(st, tokens, ", \"-+");
-    if(ui.GetAsString("METHOD") == "number") {
-      column = ui.GetInteger("NUMBER");
-    }
-    else {
-      for(unsigned i = 0; i < tokens.size(); i++) {
-        if(tokens[i] == ui.GetString("NAME")) {
-          column = i;
-          break;
-        }
-      }
-    }
-    if(column < 0  || (unsigned)column > tokens.size()) {
-      QString msg = "The column specified in file [" + ui.GetFileName("SPECTRUM")
-                    + "] was not found.";
-      throw IException(IException::User, msg, _FILEINFO_);
-    }
-    // Add the correct column of data to normalizer
-    for(int i = 0; i < icube->bandCount(); i++) {
-      tokens.clear();
-      pencil.GetLine(st);
-      Tokenize(st, tokens, ", \"");
-      normalizer.push_back(Isis::IString(tokens[column]).ToDouble());
-    }
-  }
-  else {  // avg == "CUBE"
-    Statistics stats;
-    for(int i = 0; i < (int)average.size(); i++) {
-      stats.AddData(&average[i], (unsigned int)1);
-    }
-    for(int b = 0; b < icube->bandCount(); b++) {
-      normalizer.push_back(stats.Average());
-    }
-  }
-
-  // Setup the output file and apply the correction
-  p.SetOutputCube("TO");
-  p.StartProcess(normalize);
-
-  // Cleanup
-  p.EndProcess();
-  normalizer.clear();
-  band.clear();
-  average.clear();
-}
-
-//**********************************************************
-// Get statistics on a band or entire cube
-//**********************************************************
-void getStats(Buffer &in) {
-  Statistics stats;
-  stats.AddData(in.DoubleBuffer(), in.size());
-  average.push_back(stats.Average());
-  band.push_back(in.Band() - 1);
-}
-
-// Apply coefficients
-void normalize(Buffer &in, Buffer &out) {
-  int index = in.Band() - 1;
-  double coeff = normalizer[index];
-
-  // Now loop and apply the coefficents
-  for(int i = 0; i < in.size(); i++) {
-    if(IsSpecial(in[i])) {
-      out[i] = in[i];
-    }
-    else {
-      out[i] = Null;
-      if(coeff != 0.0 && IsValidPixel(coeff)) {
-        out[i] = in[i] / coeff;
-      }
-    }
-  }
-}
-
-// Tokenizer
-void Tokenize(const QString &strQStr,
-              vector<QString> & tokens,
-              const QString &delimitersQStr) {
-  IString str = strQStr;
-  IString delimiters = delimitersQStr;
-
-  //Skip delimiters at the beginning
-  string::size_type lastPos = str.find_first_not_of(delimiters, 0);
-  // Find first "non-delimiter".
-  string::size_type pos     = str.find_first_of(delimiters, lastPos);
-
-  while(string::npos != pos  ||  string::npos != lastPos) {
-    // Found a token, add it to the vector
-    tokens.push_back(str.substr(lastPos, pos - lastPos).c_str());
-    // Skip delimiters
-    lastPos = str.find_first_not_of(delimiters, pos);
-    // Find next "non-delimiter"
-    pos = str.find_first_of(delimiters, lastPos);
-  }
-}
+  bandnorm(ui);
+}