Update eisstitch to place DNs into an output cube

isis/src/clipper/apps/eisstitch/eisstitch.cpp

@@ -14,6 +14,9 @@ find files of those names at the top level of this repository. **/
 #include "IException.h"
 #include "iTime.h"
 
+#include "CubeAttribute.h"
+#include "EisStitchFunctor.h"
+#include "ProcessByBrick.h"
 #include "Pvl.h"
 #include "PvlKeyword.h"
 #include "Table.h"
@@ -24,6 +27,7 @@ find files of those names at the top level of this repository. **/
 #include <iostream>
 #include <fstream>
 #include <istream>
+#include <cmath>
 
 #include "eisstitch.h"
 #include <QDebug>
@@ -72,14 +76,14 @@ namespace Isis {
       throw IException(IException::User, msg, _FILEINFO_);
     }
 
-    std::vector<struct eisTiming> eisTime = {};
+    std::vector<struct eisTiming> eisTimes = {};
 
     for (auto file : fileList) {
-      Pvl cubeLabel(file.expanded());
+      Pvl inputCubeLabel = Pvl(file.expanded());
 
       PvlGroup instGroup;
       try {
-        instGroup = cubeLabel.findGroup("Instrument", PvlObject::FindOptions::Traverse);
+        instGroup = inputCubeLabel.findGroup("Instrument", PvlObject::FindOptions::Traverse);
       }
       catch(IException &e) {
         QString msg = "Unable to find instrument group in [" + file.name() + "]";
@@ -88,7 +92,7 @@ namespace Isis {
 
       PvlGroup dimGroup;
       try {
-        dimGroup = cubeLabel.findGroup("Dimensions", PvlObject::FindOptions::Traverse);
+        dimGroup = inputCubeLabel.findGroup("Dimensions", PvlObject::FindOptions::Traverse);
       }
       catch(IException &e) {
         QString msg = "Unable to find instrument group in [" + file.name() + "]";
@@ -99,14 +103,16 @@ namespace Isis {
       int lines = dimGroup.findKeyword("Lines");
       double exposureDuration = instGroup.findKeyword("LineExposureDuration");
       exposureDuration /= 1000;
-      eisTime.push_back(eisTiming(time.Et(), lines, exposureDuration));
+      eisTimes.push_back(eisTiming(time.Et(), lines, exposureDuration));
     }
 
-    sort(eisTime.begin(), eisTime.end(), compareByStartTime);
+    // Likely need to re-order the cubes in the fileList if the eisTimes
+    // are moved around
+    sort(eisTimes.begin(), eisTimes.end(), compareByStartTime);
 
     // Check for overlap
-    for (int i = 0; i < eisTime.size() - 1; i++) {
-      if (eisTime[i].stop > eisTime[i + 1].start) {
+    for (int i = 0; i < eisTimes.size() - 1; i++) {
+      if (eisTimes[i].stop > eisTimes[i + 1].start) {
         QString msg = "Image " + QString(i + 1) + " and " + QString(i + 2) + " in the image list have " + 
         "overlapping times.";
         throw IException(IException::User, msg, _FILEINFO_);
@@ -125,14 +131,75 @@ namespace Isis {
 
     Table timesTable("LineScanTimes", timesRecord);
 
-    int currentLine = 1;
-    for (auto time : eisTime) {
-      timesRecord[0] = time.start;
-      timesRecord[1] = time.exposureDuration;
-      timesRecord[2] = currentLine;
-      currentLine += time.lines;
+    int lineCount = 1;
+    for (int i = 0; i < eisTimes.size(); i++) {
+      timesRecord[0] = eisTimes[i].start;
+      timesRecord[1] = eisTimes[i].exposureDuration;
+      timesRecord[2] = lineCount;
+      lineCount += eisTimes[i].lines;
       timesTable += timesRecord;
+
+      if (i < eisTimes.size() - 1) {
+        double imageTotalTime = eisTimes[i].start + (eisTimes[i].exposureDuration * eisTimes[i].lines);
+        if ( std::abs(imageTotalTime - eisTimes[i + 1].start) > std::numeric_limits<double>::epsilon()) {
+          double remainingTime = eisTimes[i + 1].start - imageTotalTime;
+          int blankLines = int(remainingTime / eisTimes[i].exposureDuration);
+          lineCount += blankLines;
+        }
+      }
+    }
+
+    Pvl firstCubeLabel(fileList[0].expanded());
+    PvlGroup dimGroup;
+    try {
+      dimGroup = firstCubeLabel.findGroup("Dimensions", PvlObject::FindOptions::Traverse);
+    }
+    catch(IException &e) {
+      QString msg = "Unable to find instrument group in [" + fileList[0].name() + "]";
+      throw IException(e, IException::User, msg, _FILEINFO_); 
     }
-    cout << Table::toString(timesTable, ",") << endl;
+    int outLines = lineCount - 1;
+    int outSamples = dimGroup["Samples"];
+
+    ProcessByBrick process;
+    process.PropagateLabels(false);
+    process.PropagateTables(false);
+    process.PropagatePolygons(false);
+    process.PropagateOriginalLabel(false);
+    process.SetInputCube(fileList[0].expanded(),  CubeAttributeInput());
+
+    QString outCubeFile = ui.GetCubeName("TO");
+    Cube *outCube = process.SetOutputCube(outCubeFile, CubeAttributeOutput(outCubeFile),
+                          outSamples, outLines, 1);
+    process.ClearInputCubes();
+    Brick cubeBrick = Brick(outCube->sampleCount(), 1, 1, outCube->pixelType());
+
+    int writeLine = 1;
+
+    for (int i = 0; i < fileList.size(); i++) {
+
+      Cube *inputCube = process.SetInputCube(fileList[i].expanded(), CubeAttributeInput());
+
+      for (int line = 1; line < inputCube->lineCount() + 1; line++) {
+        cubeBrick.SetBasePosition(1, line, 1);
+        inputCube->read(cubeBrick);
+        cubeBrick.SetBasePosition(1, writeLine, 1);
+        outCube->write(cubeBrick);
+        writeLine++;
+      }
+
+      if (i < fileList.size() - 1) {
+        int expectedLines = (int)timesTable[i + 1][2] - 1;
+        while(writeLine != expectedLines) {
+          writeLine++;
+        }
+      }
+
+      process.ClearInputCubes();
+    }
+
+    // Still need to write the Time table and other label data
+
+    process.EndProcess();
   }
 }