Unverified Commit e64f1566 authored by Alessandro Frigeri's avatar Alessandro Frigeri Committed by GitHub
Browse files

Refactor of the pixel2map application and add geospatial vector file output (#5606) 

* added README.md

* added pixel2map '23 mods

* updated the 2023 code to the current dev branch

* Started the refactoring

* Added app functional test

* updated files for refactoring

* removed call to UserInterface in new cpp code

* refactored started working

* First functional test working

* Removed unused headers

* code reviewed with Kelvin

* fixed Functional Test - started UnitTest

* added the unit test cpp file in the tests folder

* added new test, fixed code in case of 360 crossing

* cleanup for PR

* updated CHANGELOG and docs

* updated institution info

* removed commented-out lines in header

* removed README.md

* pixel2map definition re-inserted into Isis namespace (which was deleted during code cleanup)

* change on testCube path reverted
parent 0dff5234

.zenodo.json

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Original line number Original line Diff line number Diff line
@@ -166,6 +166,11 @@ 
      "affiliation": "United States Geological Survey, Astro Geology Science Center",

      "affiliation": "United States Geological Survey, Astro Geology Science Center",

      "name": "Fergason, Robin"

      "name": "Fergason, Robin"

    },

    },

    {

      "affiliation": "Italian National Institute for Astrophysics (INAF), Istituto di Astrofisica e Planetologia Spaziali (IAPS), Rome, Italy",

      "name": "Frigeri, Alessandro",

      "orcid": "0000-0002-9140-3977"   

    },

    {

    {

      "name": "Gaddis, Lisa"

      "name": "Gaddis, Lisa"

    },

    },

CHANGELOG.md

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@@ -35,8 +35,16 @@ release. 




## [Unreleased]

## [Unreleased]





### Fixed

### Added

- Added TOVECT output parameter which generate a geospatial CSV file with a VRT metadata sidecar file [#5571](https://github.com/DOI-USGS/ISIS3/issues/5571)  

- Added Vectorize to ProcessGroundPolygon library

- Added gtest files for the app and unit test 





### Changed

- Refactored the pixel2map app

- Updated pixel2map documentation



### Fixed

- Fixed a bug in kaguyasp2isis that doesn't work for data with a detached label.

- Fixed a bug in kaguyasp2isis that doesn't work for data with a detached label.





## [8.3.0] - 2024-08-16

## [8.3.0] - 2024-08-16

isis/src/base/apps/pixel2map/main.cpp

+16 −385
Original line number Original line Diff line number Diff line 
#define GUIHELPERS

#define GUIHELPERS



#include "Isis.h"

#include "Isis.h"





#include <QDebug>

#include "Application.h"

#include <QList>

#include <QPointF>

#include <QString>



#include "Camera.h"

#include "Cube.h"

#include "CubeAttribute.h"

#include "FileList.h"

#include "IException.h"

#include "PixelFOV.h"

#include "ProcessByBrick.h"

#include "ProcessGroundPolygons.h"

#include "ProcessRubberSheet.h"

#include "ProjectionFactory.h"

#include "Pvl.h"

#include "PvlGroup.h"

#include "Target.h"





#include "pixel2map.h"

#include "pixel2map.h"





#include "UserInterface.h"



using namespace std;

using namespace std;

using namespace Isis;

using namespace Isis;





void PrintMap();

void PrintMap();

void rasterizePixel(Isis::Buffer &in);





map <QString, void *> GuiHelpers() {

// Check for docs for GUI helpers -> KEEP and move it to pixel2map.cpp 

  std::map <QString, void *> GuiHelpers() {

  map <QString, void *> helper;

  map <QString, void *> helper;

  helper ["PrintMap"] = (void *) PrintMap;

  helper ["PrintMap"] = (void *) PrintMap;

  return helper;

  return helper;

}

}





// Global variables

ProcessGroundPolygons g_processGroundPolygons;

Camera *g_incam;

int g_numIFOVs = 0;





void IsisMain() {

void IsisMain() {



  g_incam = NULL;



  // Get the map projection file provided by the user

  UserInterface &ui = Application::GetUserInterface();

  UserInterface &ui = Application::GetUserInterface();

  Pvl userMap;

  Pvl appLog;

  userMap.read(ui.GetFileName("MAP"));

  pixel2map(ui, &appLog);

  PvlGroup &userGrp = userMap.findGroup("Mapping", Pvl::Traverse);



  FileList list;

  if (ui.GetString("FROMTYPE") == "FROM") {

    // GetAsString will capture the entire string, including attributes

    list.push_back(FileName(ui.GetAsString("FROM")));

  }

  else {

    try {

      list.read(ui.GetFileName("FROMLIST"));

    }

    catch (IException &e) {

      throw IException(e);

    }

  }



  if (ui.GetString("FOVRANGE") == "INSTANTANEOUS") {

    g_numIFOVs = 1;

  }

  else {

    g_numIFOVs = ui.GetInteger("NUMIFOV");

  }



  double newminlat, newmaxlat, newminlon, newmaxlon;

  double minlat = 90;

  double maxlat = -90;

  double minlon = 360.0;

  double maxlon = 0;

  PvlGroup camGrp;

  QString lastBandString;



  // Get the combined lat/lon range for all input cubes

  int bands = 1;

  for (int i = 0; i < list.size(); i++) {



    // Open the input cube and get the camera

    CubeAttributeInput atts0(list[i]);

    Cube icube;

    if(atts0.bands().size() != 0) {

      vector<QString> lame = atts0.bands();

      icube.setVirtualBands(lame);

    }

    icube.open( list[i].toString() );

    bands = icube.bandCount();

    g_incam = icube.camera();



    // Make sure it is not the sky

    if (g_incam->target()->isSky()) {

      QString msg = "The image [" + list[i].toString() +

                    "] is targeting the sky, use skymap instead.";

      throw IException(IException::User, msg, _FILEINFO_);

    }



    // Make sure all the bands for all the files match

    if (i >= 1 && atts0.bandsString() != lastBandString) {

      QString msg = "The Band numbers for all the files do not match.";

      throw IException(IException::User, msg, _FILEINFO_);

    }

    else {

      lastBandString = atts0.bandsString();

    }



    // Get the mapping group

    Pvl camMap;

    g_incam->BasicMapping(camMap);

    camGrp = camMap.findGroup("Mapping");



    g_incam->GroundRange(newminlat, newmaxlat, newminlon, newmaxlon, userMap);

    //set min lat/lon

    if (newminlat < minlat) {

      minlat = newminlat;

    }

    if (newminlon < minlon) {

      minlon = newminlon;

    }



    //set max lat/lon

    if (newmaxlat > maxlat) {

      maxlat = newmaxlat;

    }

    if (newmaxlon > maxlon) {

      maxlon = newmaxlon;

    }



    // The camera will be deleted when the Cube is deleted so NULL g_incam

    g_incam = NULL;

  } //end for list.size



  camGrp.addKeyword(PvlKeyword("MinimumLatitude", toString(minlat)), Pvl::Replace);

  camGrp.addKeyword(PvlKeyword("MaximumLatitude", toString(maxlat)), Pvl::Replace);

  camGrp.addKeyword(PvlKeyword("MinimumLongitude", toString(minlon)), Pvl::Replace);

  camGrp.addKeyword(PvlKeyword("MaximumLongitude", toString(maxlon)), Pvl::Replace);





  // We want to delete the keywords we just added if the user wants the range

  // out of the mapfile, otherwise they will replace any keywords not in the

  // mapfile

  if (ui.GetString("DEFAULTRANGE") == "MAP") {

    camGrp.deleteKeyword("MinimumLatitude");

    camGrp.deleteKeyword("MaximumLatitude");

    camGrp.deleteKeyword("MinimumLongitude");

    camGrp.deleteKeyword("MaximumLongitude");

  }



  // Otherwise, remove the keywords from the map file so the camera keywords

  // will be propogated correctly

  else {

    while (userGrp.hasKeyword("MinimumLatitude")) {

      userGrp.deleteKeyword("MinimumLatitude");

    }

    while (userGrp.hasKeyword("MinimumLongitude")) {

      userGrp.deleteKeyword("MinimumLongitude");

    }

    while (userGrp.hasKeyword("MaximumLatitude")) {

      userGrp.deleteKeyword("MaximumLatitude");

    }

    while (userGrp.hasKeyword("MaximumLongitude")) {

      userGrp.deleteKeyword("MaximumLongitude");

    }

  }



  // If the user decided to enter a ground range then override

  if (ui.WasEntered("MINLON")) {

    userGrp.addKeyword(PvlKeyword("MinimumLongitude",

                                  toString(ui.GetDouble("MINLON"))), Pvl::Replace);

  }



  if (ui.WasEntered("MAXLON")) {

    userGrp.addKeyword(PvlKeyword("MaximumLongitude",

                                  toString(ui.GetDouble("MAXLON"))), Pvl::Replace);

  }



  if (ui.WasEntered("MINLAT")) {

    userGrp.addKeyword(PvlKeyword("MinimumLatitude",

                                  toString(ui.GetDouble("MINLAT"))), Pvl::Replace);

  }



  if (ui.WasEntered("MAXLAT")) {

    userGrp.addKeyword(PvlKeyword("MaximumLatitude",

                                  toString(ui.GetDouble("MAXLAT"))), Pvl::Replace);

  }



  // If they want the res. from the mapfile, delete it from the camera so

  // nothing gets overriden

  if (ui.GetString("PIXRES") == "MAP") {

    camGrp.deleteKeyword("PixelResolution");

  }

  // Otherwise, delete any resolution keywords from the mapfile so the camera

  // info is propogated over

  else if (ui.GetString("PIXRES") == "CAMERA") {

    if (userGrp.hasKeyword("Scale")) {

      userGrp.deleteKeyword("Scale");

    }

    if (userGrp.hasKeyword("PixelResolution")) {

      userGrp.deleteKeyword("PixelResolution");

    }

  }

  

  

  // Copy any defaults that are not in the user map from the camera map file

  if( ui.WasEntered("TO") && ui.IsInteractive() ) {

  for (int k = 0; k < camGrp.keywords(); k++) {

    Application::GuiLog(appLog);

    if (!userGrp.hasKeyword(camGrp[k].name())) {

      userGrp += camGrp[k];

  }

  }

  }



  // If the user decided to enter a resolution then override

  if (ui.GetString("PIXRES") == "MPP") {

    userGrp.addKeyword(PvlKeyword("PixelResolution",

                                  toString(ui.GetDouble("RESOLUTION"))),

                       Pvl::Replace);

    if (userGrp.hasKeyword("Scale")) {

      userGrp.deleteKeyword("Scale");

    }

  }

  else if (ui.GetString("PIXRES") == "PPD") {

    userGrp.addKeyword(PvlKeyword("Scale",

                                  toString(ui.GetDouble("RESOLUTION"))),

                       Pvl::Replace);

    if (userGrp.hasKeyword("PixelResolution")) {

      userGrp.deleteKeyword("PixelResolution");

    }

  }



  // See if the user want us to handle the longitude seam

  if (ui.GetString("DEFAULTRANGE") == "CAMERA" || ui.GetString("DEFAULTRANGE") == "MINIMIZE") {



    // Open the last cube and use its camera

    CubeAttributeInput atts0( list.back() );

    Cube icube;

    if(atts0.bands().size() != 0) {

      vector<QString> lame = atts0.bands();

      icube.setVirtualBands(lame);

    }

    icube.open( list.back().toString() );

    g_incam = icube.camera();



    if (g_incam->IntersectsLongitudeDomain(userMap)) {

      if (ui.GetString("LONSEAM") == "AUTO") {

        if ((int) userGrp["LongitudeDomain"] == 360) {

          userGrp.addKeyword(PvlKeyword("LongitudeDomain", toString(180)),

                             Pvl::Replace);

          if (g_incam->IntersectsLongitudeDomain(userMap)) {

            // Its looks like a global image so switch back to the

            // users preference

            userGrp.addKeyword(PvlKeyword("LongitudeDomain", toString(360)),

                               Pvl::Replace);

          }

        }

        else {

          userGrp.addKeyword(PvlKeyword("LongitudeDomain", toString(360)),

                             Pvl::Replace);

          if (g_incam->IntersectsLongitudeDomain(userMap)) {

            // Its looks like a global image so switch back to the

            // users preference

            userGrp.addKeyword(PvlKeyword("LongitudeDomain", toString(180)),

                               Pvl::Replace);

          }

        }

        // Make the target info match the new longitude domain

        double minlat, maxlat, minlon, maxlon;

        g_incam->GroundRange(minlat, maxlat, minlon, maxlon, userMap);

        if (!ui.WasEntered("MINLAT")) {

          userGrp.addKeyword(PvlKeyword("MinimumLatitude", toString(minlat)), Pvl::Replace);

        }

        if (!ui.WasEntered("MAXLAT")) {

          userGrp.addKeyword(PvlKeyword("MaximumLatitude", toString(maxlat)), Pvl::Replace);

        }

        if (!ui.WasEntered("MINLON")) {

          userGrp.addKeyword(PvlKeyword("MinimumLongitude", toString(minlon)), Pvl::Replace);

        }

        if (!ui.WasEntered("MAXLON")) {

          userGrp.addKeyword(PvlKeyword("MaximumLongitude", toString(maxlon)), Pvl::Replace);

        }

      }



      else if (ui.GetString("LONSEAM") == "ERROR") {

        QString msg = "The image [" + ui.GetCubeName("FROM") + "] crosses the " +

                     "longitude seam";

        throw IException(IException::User, msg, _FILEINFO_);

      }

    }



    // The camera will be deleted when the Cube is deleted so NULL g_incam

    g_incam = NULL;

  }





  Pvl pvl;

  pvl.addGroup(userGrp);



  // If there is only one input cube, we need to attach an AlphaCube to the outputs.

  if (list.size() == 1) {

    Cube parent(list[0].toString());

    if (!parent.hasGroup("AlphaCube")) {

      PvlGroup alpha("AlphaCube");

      alpha += PvlKeyword("AlphaSamples", toString(parent.sampleCount()));

      alpha += PvlKeyword("AlphaLines", toString(parent.lineCount()));

      alpha += PvlKeyword("AlphaStartingSample", toString(0.5));

      alpha += PvlKeyword("AlphaStartingLine", toString(0.5));

      alpha += PvlKeyword("AlphaEndingSample", toString(parent.sampleCount() + 0.5));

      alpha += PvlKeyword("AlphaEndingLine", toString(parent.lineCount() + 0.5));

      alpha += PvlKeyword("BetaSamples", toString(parent.sampleCount()));

      alpha += PvlKeyword("BetaLines", toString(parent.lineCount()));

      pvl.addGroup(alpha);

    }

  }



  g_processGroundPolygons.SetStatCubes("TO", pvl, bands);



  bool useCenter = true;

  if (ui.GetString("METHOD") == "CENTER") {

    useCenter = true;

  }

  else if (ui.GetString("METHOD") == " WHOLEPIXEL") {

    useCenter = false;

  }

 

  g_processGroundPolygons.SetIntersectAlgorithm(useCenter);



  for (int f = 0; f < list.size(); f++) {



    Cube cube(list[f].toString(), "r");

    // Loop through the input cube and get the all pixels values for all bands

    ProcessByBrick processBrick;

    processBrick.Progress()->SetText("Working on file:  " + list[f].toString());

    processBrick.SetBrickSize(1, 1, bands);

    // Recall list[f] is a FileName, which stores the attributes

    CubeAttributeInput atts0(list[f]);

    Cube *icube = processBrick.SetInputCube(list[f].toString(), atts0, 0);

    g_incam = icube->camera();



    processBrick.StartProcess(rasterizePixel);

    processBrick.EndProcess();

  }

  

  // When there is only one input cube, we want to propagate IsisCube labels to output cubes

  if (list.size() == 1) {

    // Note that polygons and original labels are not propagated

    g_processGroundPolygons.PropagateLabels(list[0].toString());

    // Tell Process which tables we want to propagate

    QList<QString> tablesToPropagate;

    tablesToPropagate << "InstrumentPointing" << "InstrumentPosition" << "BodyRotation"

        << "SunPosition";

    g_processGroundPolygons.PropagateTables(list[0].toString(), tablesToPropagate);

  }

  g_processGroundPolygons.EndProcess();



  // WARNING: rasterizePixel() method alters the current state of the camera.

  // If any code is added after this point, you must call setImage to return

  // to original camera state before rasterization.

    

    

}

}
@@ -366,56 +36,17 @@ void IsisMain() { 
  * Helper function to print out mapfile to session log

  * Helper function to print out mapfile to session log

  */

  */

void PrintMap() {

void PrintMap() {

//removed in the refactoring process 

UserInterface &ui = Application::GetUserInterface();

UserInterface &ui = Application::GetUserInterface();





  // Get mapping group from map file

  // Get mapping group from map file

  Pvl userMap;

  Pvl userMap(ui.GetFileName("MAP"));

  userMap.read(ui.GetFileName("MAP"));

  PvlGroup &userGrp = userMap.findGroup("Mapping", Pvl::Traverse);

  PvlGroup &userGrp = userMap.findGroup("Mapping", Pvl::Traverse);





  //Write map file out to the log

  //Write map file out to the log

//

  Isis::Application::GuiLog(userGrp);

  Isis::Application::GuiLog(userGrp);

}

} // PrintMap







/**

  * This method uses the ProcessGroundPolygons object to rasterize each 

  * pixel in the given buffer. 

  *  

  * @param in Input ProcessByBrick buffer. 

  */

void rasterizePixel(Isis::Buffer &in) {



  std::vector<double>lat, lon;

  std::vector<double>dns;



  for (int i = 0; i < in.size(); i++) {

    dns.push_back(in[i]);

  }

  

  

  int l = in.Line();

  int s = in.Sample();

  // TODO: This needs to be done for each band for band dependant instruments

  // Note: This can slow this down a lot



  // Get the IFOVs in lat/lon space

  PixelFOV fov;

  QList< QList< QPointF > > fovVertices = fov.latLonVertices(*g_incam, l, s, g_numIFOVs);



  // loop through each ifov list

  for (int ifov = 0; ifov < fovVertices.size(); ifov++) {

    // we need at least 3 vertices for a polygon

    if (fovVertices[ifov].size() > 3) {

      //  Get lat/lon for each vertex of the ifov

      for (int point = 0; point < fovVertices[ifov].size(); point++) {

        lat.push_back(fovVertices[ifov][point].x());

        lon.push_back(fovVertices[ifov][point].y());

      }

      // rasterize this ifov and clear vectors for next ifov

      g_processGroundPolygons.Rasterize(lat, lon, dns);

      lat.clear();

      lon.clear();

    }

  }

}

isis/src/base/apps/pixel2map/pixel2map.cpp

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isis/src/base/apps/pixel2map/pixel2map.h

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#ifndef pixel2map_h

#ifndef pixel2map_h

#define pixel2map_h

#define pixel2map_h





#include <QDebug>

#include <QList>

#include <QPointF>

#include <QString>



#include "Camera.h"

#include "Cube.h"

#include "FileList.h"

#include "PixelFOV.h"

#include "ProcessByBrick.h"

#include "ProcessGroundPolygons.h"

#include "Pvl.h"

#include "Target.h"



#include "Transform.h"

#include "Transform.h"





/**

#include "geos/geom/Geometry.h"

 * @author 2008-02-13 Stacy Alley

#include "geos/io/WKTWriter.h"

 *



 * @internal 

#include "UserInterface.h"

 *   @history 2013-07-30 Stuart C. Sides & Tracie Sucharski Renamed from vim2map

 */

class pixel2map : public Isis::Transform {

  private:

    Isis::Camera *p_incam;

    Isis::Projection *p_outmap;





  public:

    // constructor

    pixel2map(const int inputSamples, const int inputLines, Isis::Camera *incam,

             const int outputSamples, const int outputLines, Isis::Projection *outmap,

             bool trim);





    // destructor

namespace Isis {

    ~pixel2map() {};

	

	

extern void pixel2map(UserInterface &ui, Pvl *log=nullptr);





};

} 





#endif
 
#endif