Revert "stretch app conversion"

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

@@ -1,26 +1,84 @@
 #include "Isis.h"
-
-#include "Application.h"
-#include "UserInterface.h"
-
-#include "stretch_app.h"
+#include "TextFile.h"
+#include "Statistics.h"
+#include "ProcessByLine.h"
+#include "SpecialPixel.h"
+#include "Stretch.h"
+#include "PvlGroup.h"
+#include "PvlKeyword.h"
 
 using namespace std;
 using namespace Isis;
 
+void stretch(Buffer &in, Buffer &out);
+Stretch str;
+Statistics stats;
+
 void IsisMain() {
+  ProcessByLine p;
+  Cube *inCube = p.SetInputCube("FROM");
+
   UserInterface &ui = Application::GetUserInterface();
-  Pvl results;
-  try{
-      stretch(ui, &results);
+
+  QString pairs;
+
+  // first just get the pairs from where ever and worry about
+  // whether they are dn values or %'s later
+  if(ui.GetBoolean("READFILE")) {
+    FileName pairsFileName = ui.GetFileName("INPUTFILE");
+    TextFile pairsFile;
+    pairsFile.SetComment("#");
+    pairsFile.Open(pairsFileName.expanded());
+
+    // concat all non-comment lines into one string (pairs)
+    QString line = "";
+    while(pairsFile.GetLine(line, true)) {
+      pairs += " " + line;
+    }
+    pairs += line;
   }
-  catch(...){
-      for (int resultIndex = 0; resultIndex < results.groups(); resultIndex++) {
-          Application::Log(results.group(resultIndex));
-      }
-      throw;
+  else {
+    if(ui.WasEntered("PAIRS"))
+      pairs = ui.GetString("PAIRS");
+  }
+
+  if(ui.GetBoolean("USEPERCENTAGES")) {
+    str.Parse(pairs, inCube->histogram());
   }
-  for (int resultIndex = 0; resultIndex < results.groups(); resultIndex++) {
-      Application::Log(results.group(resultIndex));
+  else
+    str.Parse(pairs);
+
+  // Setup new mappings for special pixels if necessary
+  if(ui.WasEntered("NULL"))
+    str.SetNull(StringToPixel(ui.GetString("NULL")));
+  if(ui.WasEntered("LIS"))
+    str.SetLis(StringToPixel(ui.GetString("LIS")));
+  if(ui.WasEntered("LRS"))
+    str.SetLrs(StringToPixel(ui.GetString("LRS")));
+  if(ui.WasEntered("HIS"))
+    str.SetHis(StringToPixel(ui.GetString("HIS")));
+  if(ui.WasEntered("HRS"))
+    str.SetHrs(StringToPixel(ui.GetString("HRS")));
+
+  p.SetOutputCube("TO");
+
+  // Start the processing
+  p.StartProcess(stretch);
+  p.EndProcess();
+
+  PvlKeyword dnPairs = PvlKeyword("StretchPairs");
+  dnPairs.addValue(str.Text());
+
+  PvlGroup results = PvlGroup("Results");
+  results.addKeyword(dnPairs);
+
+  Application::Log(results);
+
+}
+
+// Line processing routine
+void stretch(Buffer &in, Buffer &out) {
+  for(int i = 0; i < in.size(); i++) {
+    out[i] = str.Map(in[i]);
   }
 }

isis/src/base/objs/Process/Process.cpp

@@ -263,7 +263,7 @@ namespace Isis {
    *
    * @throws Isis::iException::Message
    */
-  Isis::Cube *Process::SetOutputCube(const QString &parameter, UserInterface *ui) {
+  Isis::Cube *Process::SetOutputCube(const QString &parameter) {
     // Make sure we have an input cube to get a default size from
     if(InputCubes.size() == 0) {
       QString message = "No input images have been selected ... therefore";
@@ -274,7 +274,7 @@ namespace Isis {
     int nl = InputCubes[0]->lineCount();
     int ns = InputCubes[0]->sampleCount();
     int nb = InputCubes[0]->bandCount();
-    return SetOutputCube(parameter, ns, nl, nb, ui);
+    return SetOutputCube(parameter, ns, nl, nb);
   }
 
   /**
@@ -300,24 +300,16 @@ namespace Isis {
    * @throws Isis::iException::Message
    */
   Isis::Cube *Process::SetOutputCube(const QString &parameter, const int ns,
-                                     const int nl, const int nb, UserInterface *ui) {
+                                     const int nl, const int nb) {
     // Make sure we have good dimensions
     if((ns <= 0) || (nl <= 0) || (nb <= 0)) {
       ostringstream message;
       message << "Invalid cube size specifications [ns=" << ns << ",nl=" << nl
               << ",nb=" << nb << "]";
       throw IException(IException::Programmer, message.str().c_str(), _FILEINFO_);
     }
-    QString fname;
-    Isis::CubeAttributeOutput atts;
-    if(ui==nullptr){
-        fname = Application::GetUserInterface().GetFileName(parameter);
-        atts = Application::GetUserInterface().GetOutputAttribute(parameter);
-    }
-    else{
-        fname = ui->GetFileName(parameter);
-        atts = ui->GetOutputAttribute(parameter);
-    }
+    QString fname = Application::GetUserInterface().GetFileName(parameter);
+    Isis::CubeAttributeOutput &atts = Application::GetUserInterface().GetOutputAttribute(parameter);
     return SetOutputCube(fname, atts, ns, nl, nb);
   }
 
@@ -416,7 +408,7 @@ namespace Isis {
 
       // Allocate the cube
       cube->create(fname);
-
+      
       // Transfer labels from the first input cube
       if((p_propagateLabels) && (InputCubes.size() > 0)) {
         Isis::PvlObject &incube =

isis/src/base/objs/Process/Process.h

@@ -240,9 +240,9 @@ namespace Isis {
       virtual void SetInputCube(Isis::Cube *inCube);
 
 
-      virtual Isis::Cube *SetOutputCube(const QString &parameter, UserInterface *ui=nullptr);
+      virtual Isis::Cube *SetOutputCube(const QString &parameter);
       virtual Isis::Cube *SetOutputCube(const QString &parameter, const int nsamps,
-                                const int nlines, const int nbands = 1, UserInterface *ui=nullptr);
+                                const int nlines, const int nbands = 1);
       virtual Isis::Cube *SetOutputCube(const QString &fname,
                                 const Isis::CubeAttributeOutput &att,
                                 const int nsamps, const int nlines,

isis/src/base/objs/ProcessImport/ProcessImport.cpp

@@ -1273,21 +1273,26 @@ namespace Isis {
    *
    * @throws Isis::iException::Message "Unsupported pixel type."
    */
-  Isis::Cube *ProcessImport::SetOutputCube(const QString &parameter, UserInterface *ui) {
-    CubeAttributeOutput att;
-    if (!ui) {
-      att = Application::GetUserInterface().GetOutputAttribute(parameter);
-    }
-    else {
-      att = ui->GetOutputAttribute(parameter);
-    }
+  Isis::Cube *ProcessImport::SetOutputCube(const QString &parameter) {
+    CubeAttributeOutput &att =
+      Application::GetUserInterface().GetOutputAttribute(parameter);
 
     SetAttributes(att);
 
     return Process::SetOutputCube(Application::GetUserInterface().GetFileName(parameter), att, p_ns, p_nl, p_nb);
   }
 
 
+  /**
+   * Create the output file.
+   *
+  */
+  Isis::Cube *ProcessImport::SetOutputCube(const QString &parameter, UserInterface &ui){
+    CubeAttributeOutput &att = ui.GetOutputAttribute(parameter);
+    SetAttributes(att);
+    return Isis::Process::SetOutputCube(ui.GetFileName(parameter), att, p_ns, p_nl, p_nb);
+  }
+
   /**
    * Create the output file. Note that all the appropiate calls to at least
    * SetDimensions should be invoked prior to calling this method.

isis/src/base/objs/ProcessImport/ProcessImport.h

@@ -199,7 +199,8 @@ namespace Isis {
       // ProcessImport objects and child objects
 
       using Isis::Process::SetOutputCube;  // make parent functions visable
-      Isis::Cube *SetOutputCube(const QString &parameter, UserInterface *ui=nullptr);
+      Isis::Cube *SetOutputCube(const QString &parameter);
+      Isis::Cube *SetOutputCube(const QString &parameter, UserInterface &ui);
       virtual Isis::Cube *SetOutputCube(const QString &fname,
                                 Isis::CubeAttributeOutput &att);
 

isis/src/newhorizons/apps/leisa2isis/leisa2isis.cpp

@@ -250,7 +250,7 @@ namespace Isis {
       PvlGroup extensionLabel = importFits.fitsImageLabel(5);
       importFits.SetOrganization(ProcessImport::BIL);
       importFits.setProcessFileStructure(5);
-      Cube *output = importFits.SetOutputCube("ERRORMAP", &ui);
+      Cube *output = importFits.SetOutputCube("ERRORMAP", ui);
 
       // Save the input FITS label in the Cube original labels
       Pvl origLabel;
@@ -269,7 +269,7 @@ namespace Isis {
       PvlGroup extensionLabel = importFits.fitsImageLabel(6);
       importFits.SetOrganization(ProcessImport::BIL);
       importFits.setProcessFileStructure(6);
-      Cube *output = importFits.SetOutputCube("QUALITY", &ui);
+      Cube *output = importFits.SetOutputCube("QUALITY", ui);
 
       // Save the input FITS label in the Cube original labels
       Pvl origLabel;