EIS Stitch

CHANGELOG.md

@@ -49,6 +49,7 @@ ctest FunctionalTestJigsawApollo to validate this output. [#5710](https://github
 - Added CSM State output capability for jigsaw. [#5609](https://github.com/DOI-USGS/ISIS3/issues/5609)
 - Added ShowDeprecated option to show or hide warnings in IsisPreferences. [#5611](https://github.com/DOI-USGS/ISIS3/issues/5611)
 - Added SpiceQL integration to replace cspice calls. [#5545](https://github.com/DOI-USGS/ISIS3/pull/5545)
+- Added initial `eisstitch` app [#5591](https://github.com/DOI-USGS/ISIS3/pull/5591)
 
 ### Changed
 - Removed Arm dependency on xalan-c, as it does not build for now on conda-forge. This requires turning off doc building on Arm. Also changed some variables to avoid name clashes on Arm with clang 16. [#5802](https://github.com/DOI-USGS/ISIS3/pull/5802)

isis/src/clipper/apps/eisstitch/assets/IN/eis_cubes.lis

@@ -0,0 +1,3 @@
+/Path/to/eis_images/capture_1.cub
+/Path/to/eis_images/capture_2.cub
+/Path/to/eis_images/capture_3.cub

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

@@ -0,0 +1,321 @@
+/** This is free and unencumbered software released into the public domain.
+
+The authors of ISIS do not claim copyright on the contents of this file.
+For more details about the LICENSE terms and the AUTHORS, you will
+find files of those names at the top level of this repository. **/
+
+/* SPDX-License-Identifier: CC0-1.0 */
+
+#include "Application.h"
+#include "Cube.h"
+
+#include "FileName.h"
+#include "FileList.h"
+#include "IException.h"
+#include "iTime.h"
+
+#include "CubeAttribute.h"
+#include "ProcessByBrick.h"
+#include "Pvl.h"
+#include "PvlKeyword.h"
+#include "Table.h"
+#include "TableField.h"
+#include "TableRecord.h"
+#include "UserInterface.h"
+
+#include <iostream>
+#include <fstream>
+#include <istream>
+#include <cmath>
+
+#include "eisstitch.h"
+#include <QDebug>
+#include <QPair>
+#include <QString>
+#include <QVector>
+
+using namespace std;
+
+// This will eventually change to account for the pushbroom
+// framelets but is just a linescanner for now
+struct eisTiming {
+  double start;
+  int line_start;
+  int lines;
+  double exposureDuration;
+  // Should be the start + (lineCounts * exposureTimes)
+  double stop;
+
+  eisTiming(double start, int line_start, int lines, double exposureDuration) : 
+            start(start), line_start(line_start), lines(lines), exposureDuration(exposureDuration) 
+  {
+    stop = start + (lines * exposureDuration);
+  }
+};
+
+bool compareByStartTime(const eisTiming &time1, const eisTiming &time2) {
+  return time1.start < time2.start;
+}
+
+namespace Isis {
+
+  void eisstitch(UserInterface &ui) {
+    // Get the list of names of input cubes to stitch together
+    FileList fileList;
+    ui = Application::GetUserInterface();
+    try {
+      fileList.read(ui.GetFileName("FROMLIST"));
+    }
+    catch(IException &e) {
+      QString msg = "Unable to read [" + ui.GetFileName("FROMLIST") + "]";
+      IException(e, IException::User, msg, _FILEINFO_);
+    }
+    if (fileList.size() < 1) {
+      QString msg = "The list file[" + ui.GetFileName("FROMLIST") +
+                    " does not contain any filenames";
+      throw IException(IException::User, msg, _FILEINFO_);
+    }
+
+    std::vector<struct eisTiming> eisTimes = {};
+    QString filterName = "";
+    int naifFrameCode = 0;
+    int detectorOffset = -1;
+
+    for (FileName file : fileList) {
+      Pvl inputCubeLabel = Pvl(file.expanded());
+
+      PvlGroup instGroup;
+      try {
+        instGroup = inputCubeLabel.findGroup("Instrument", PvlObject::FindOptions::Traverse);
+      }
+      catch(IException &e) {
+        QString msg = "Unable to find instrument group in [" + file.name() + "]";
+        throw IException(e, IException::User, msg, _FILEINFO_); 
+      }
+
+      if (instGroup.findKeyword("SpacecraftName")[0] != "Europa Clipper" &&
+          !instGroup.findKeyword("InstrumentId")[0].contains("EIS")) {
+        QString msg = "Cube " + file.name() + " is not a Clipper EIS image. Either update the "
+                      "image or remove it so the other images can be stitched.";
+        throw IException(IException::User, msg, _FILEINFO_);
+      }
+
+      if (detectorOffset == -1) {
+        detectorOffset = instGroup.findKeyword("DetectorOffset");
+      }
+      else {
+        if (detectorOffset != toInt(instGroup.findKeyword("DetectorOffset"))) {
+          QString msg = "DetectorOffset [" + instGroup.findKeyword("DetectorOffset")[0] + "] from image [" + file.name() + "] does "
+                        "not match recorded detector offset " + toString(detectorOffset);
+          throw IException(IException::User, msg, _FILEINFO_);
+        }
+      }
+
+      PvlGroup kernelGroup;
+      try {
+        kernelGroup = inputCubeLabel.findGroup("Kernels", PvlObject::FindOptions::Traverse);
+      }
+      catch(IException &e) {
+        QString msg = "Unable to find kernels group in [" + file.name() + "]";
+        throw IException(e, IException::User, msg, _FILEINFO_); 
+      }
+
+      if (naifFrameCode == 0) {
+        naifFrameCode = kernelGroup.findKeyword("NaifFrameCode");
+      }
+      else {
+        if (naifFrameCode != toInt(kernelGroup.findKeyword("NaifFrameCode"))) {
+          QString msg = "NaifFrameCode [" + kernelGroup.findKeyword("NaifFrameCode")[0] + "] from image [" + file.name() + "] does "
+                        "not match recorded frame code " + toString(naifFrameCode);
+          throw IException(IException::User, msg, _FILEINFO_); 
+        }
+      }
+
+      PvlGroup bandBinGroup;
+      try {
+        bandBinGroup = inputCubeLabel.findGroup("BandBin", PvlObject::FindOptions::Traverse);
+      }
+      catch(IException &e) {
+        QString msg = "Unable to find kernels group in [" + file.name() + "]";
+        throw IException(e, IException::User, msg, _FILEINFO_); 
+      }
+
+      if (filterName == "") {
+        filterName = bandBinGroup.findKeyword("FilterName")[0];
+      }
+      else {
+        if (filterName != bandBinGroup.findKeyword("FilterName")[0]) {
+          QString msg = "FilterName [" + kernelGroup.findKeyword("FilterName")[0] + "] from image [" + file.name() + "] does "
+                        "not match recorded filter name " + filterName;
+          throw IException(IException::User, msg, _FILEINFO_); 
+        }
+      }
+
+      PvlGroup dimGroup;
+      try {
+        dimGroup = inputCubeLabel.findGroup("Dimensions", PvlObject::FindOptions::Traverse);
+      }
+      catch(IException &e) {
+        QString msg = "Unable to find instrument group in [" + file.name() + "]";
+        throw IException(e, IException::User, msg, _FILEINFO_); 
+      }
+      Table timesTable("LineScanTimes", file.expanded());
+
+      if(timesTable.Records() <= 0) {
+        QString msg = "Table [LineScanTimes] in [";
+        msg += file.expanded() + "] must not be empty";
+        throw IException(IException::Unknown, msg, _FILEINFO_);
+      }
+
+      for(int i = 0; i < timesTable.Records(); i++) {
+        double startTime = (double)timesTable[i][0];
+        int line_start = timesTable[i][2];
+        int lines = int(dimGroup.findKeyword("Lines")) - (line_start - 1);
+        double exposureDuration = timesTable[i][1];
+        eisTimes.push_back(eisTiming(startTime, line_start, lines, exposureDuration));
+      }
+    }
+
+    // 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 < 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_);
+      }
+    }
+
+    // Assume the images don't know about each other
+    TableField ephTimeField("EphemerisTime", TableField::Double);
+    TableField expTimeField("ExposureTime", TableField::Double);
+    TableField lineStartField("LineStart", TableField::Integer);
+
+    TableRecord timesRecord;
+    timesRecord += ephTimeField;
+    timesRecord += expTimeField;
+    timesRecord += lineStartField;
+
+    Table timesTable("LineScanTimes", timesRecord);
+
+    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_); 
+    }
+    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
+    outCube->write(timesTable);
+
+    Pvl *outLabel = outCube->label();
+    PvlObject &outputIsisObject = outLabel->findObject("IsisCube");
+
+    Pvl inputCubeLabel = Pvl(fileList[0].expanded());
+    PvlGroup inputInstGroup;
+    try {
+      inputInstGroup = inputCubeLabel.findGroup("Instrument", PvlObject::FindOptions::Traverse);
+    }
+    catch(IException &e) {
+      QString msg = "Unable to find instrument group in [" + fileList[0].name() + "]";
+      throw IException(e, IException::User, msg, _FILEINFO_); 
+    }
+
+    PvlGroup instGroup("Instrument");
+    instGroup.addKeyword(PvlKeyword("SpacecraftName", inputInstGroup["SpacecraftName"]));
+    instGroup.addKeyword(PvlKeyword("InstrumentId", inputInstGroup["InstrumentId"]));
+    instGroup.addKeyword(PvlKeyword("TargetName", inputInstGroup["TargetName"]));
+    instGroup.addKeyword(PvlKeyword("StartTime", inputInstGroup["StartTime"]));
+    instGroup.addKeyword(PvlKeyword("DetectorOffset", inputInstGroup["DetectorOffset"]));
+    outputIsisObject.addGroup(instGroup);
+
+
+    PvlGroup inputKernelsGroup;
+    try {
+      inputKernelsGroup = inputCubeLabel.findGroup("Kernels", PvlObject::FindOptions::Traverse);
+    }
+    catch(IException &e) {
+      QString msg = "Unable to find instrument group in [" + fileList[0].name() + "]";
+      throw IException(e, IException::User, msg, _FILEINFO_); 
+    }
+
+    PvlGroup kernelsGroup("Kernels");
+    kernelsGroup.addKeyword(PvlKeyword("NaifFrameCode", inputKernelsGroup["NaifFrameCode"]));
+    outputIsisObject.addGroup(kernelsGroup);
+
+    PvlGroup bandBinGroup;
+    try {
+      bandBinGroup = inputCubeLabel.findGroup("BandBin", PvlObject::FindOptions::Traverse);
+    }
+    catch(IException &e) {
+      QString msg = "Unable to find instrument group in [" + fileList[0].name() + "]";
+      throw IException(e, IException::User, msg, _FILEINFO_); 
+    }
+    outputIsisObject.addGroup(bandBinGroup);
+
+    process.EndProcess();
+  }
+}

isis/src/clipper/apps/eisstitch/eisstitch.h

@@ -0,0 +1,18 @@
+#ifndef eis2isis_h
+#define eis2isis_h
+
+/** This is free and unencumbered software released into the public domain.
+
+The authors of ISIS do not claim copyright on the contents of this file.
+For more details about the LICENSE terms and the AUTHORS, you will
+find files of those names at the top level of this repository. **/
+
+/* SPDX-License-Identifier: CC0-1.0 */
+
+#include "UserInterface.h"
+
+namespace Isis {
+  extern void eisstitch(UserInterface &ui);
+}
+
+#endif