Unverified Commit f8d013a9 authored by Kristin's avatar Kristin Committed by GitHub
Browse files

Update to CaSSIS Exported PDS4 images and Mosaicking program (#3402) 

* Update date and other metadata

* Added changes to tgo-related applications and PEP4 to update PDS4 exported labels for CaSSIS based on requests

* Updated tgocassisrdrgen to add PSA schema

* Add function on cube to return actual min/max lat/lons based on DNs and updated PEP4 to format a couple of specific output map values with a trailing .0. Also update PEP4 to use the new function on Cube to calculate min/max lat/lons

* Fixed description order, updated geom schema details to pass validation, propagate Archive group to mosaic output needed for PDS4 export

* Update to PEP4

* Update tgocassisrdrgen

* Cleanup before commit

* More cleanup add header file history entries

* Clean up PEP4 before commit

* Updates to address review comments
parent fae3b9e1

isis/src/base/objs/Cube/Cube.cpp

+93 −0
Original line number Diff line number Diff line
@@ -49,6 +49,7 @@ 
#include "Projection.h"

#include "SpecialPixel.h"

#include "Statistics.h"

#include "TProjection.h"



using namespace std;
@@ -2133,6 +2134,98 @@ namespace Isis { 
  }





/**

 * Returns the latitude and longitude range for the Cube. More accurate than the minimum and 

 * maximum latitude and longitude from the mapping group. 

 * 

 * @param[out] minLatitude minimum latitude present in the cube

 * @param[out] maxLatitude maximum latitude present in the cube

 * @param[out] minLongitude minimum longitude present in the cube

 * @param[out] maxLongitude maximum longitude present in the cube

 */

  void Cube::latLonRange(double &minLatitude, double &maxLatitude, double &minLongitude, double &

                         maxLongitude) {

    Camera *cam;

    TProjection *proj;



    bool isGood = false;

    bool useProj = true;



    if (hasGroup("Instrument")) {

      useProj = false;

    }



    // setup camera or projection

    if (useProj) {

     try {

       proj = (TProjection *) projection();

     }

     catch(IException &e) {

       QString msg = "Cannot calculate lat/lon range without a camera or projection";

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

     }

    }

    else {

      try {

        cam = camera();

      }

      catch(IException &e) {

        QString msg = "Unable to create camera when calculating a lat/lon range.";

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

      }

    }



    // Iterate over all samp/line combos in cube

    minLatitude = 99999;

    minLongitude = 99999;

    maxLatitude = -99999;

    maxLongitude = -99999;



    for (int sample = 0.5; sample < sampleCount() + 0.5; sample++) {

    // Checks to see if the point is in outer space

      for (int line = 0.5; line < lineCount() + 0.5; line++) {

        if (useProj) {

          isGood = proj->SetWorld(sample, line);

        }

        else {

          isGood = cam->SetImage(sample, line);

        }

      

        double lat, lon;

        if (isGood) {

          if (useProj) {

            lat = proj->UniversalLatitude();

            lon = proj->UniversalLongitude();

          }

          else {

            lat = cam->UniversalLatitude(); 

            lon = cam->UniversalLongitude(); 

          }

        

          // update mix/max lat/lons

          if (lat < minLatitude) {

            minLatitude = lat;

          }

          else if (lat > maxLatitude) {

            maxLatitude = lat;

          }

          

          if (lon < minLongitude) {

            minLongitude = lon;

          }

          else if (lon > maxLongitude) {

            maxLongitude = lon; 

          }

        }

      }

    }

    if ( (minLatitude == 99999) || (minLongitude == 99999) || (maxLatitude == -99999) || 

    (maxLongitude == -99999) ) {

      QString msg = "Unable to calculate a minimum or maximum latitutde or longitude.";

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

    }

  }

  

  /**

   * Write the Pvl labels to the cube's label file. Excess data in the attached

   *   labels is set to 0.

isis/src/base/objs/Cube/Cube.h

+3 −0
Original line number Diff line number Diff line
@@ -165,6 +165,7 @@ namespace Isis { 
   *   @history 2018-01-18 Summer Stapleton - Updated error message in ::create() to address when

   *                           an IsisPreference file cannot be found. Fixes #5145.

   *   @history 2018-11-16 Jesse Mapel - Made several methods virtual for mocking.

   *   @history 2019-06-15 Kristin Berry - Added latLonRange method to return the valid lat/lon rage of the cube. The values in the mapping group are not sufficiently accurate for some purposes. 

   */

  class Cube {

    public:
@@ -301,6 +302,8 @@ namespace Isis { 
      bool hasGroup(const QString &group) const;

      bool hasTable(const QString &name);

      void putGroup(const PvlGroup &group);

      void latLonRange(double &minLatitude, double &maxLatitude, double &minLongitude, 

                       double &maxLongitude); 



    private:

      void applyVirtualBandsToLabel();

isis/src/base/objs/ProcessExportPds4/ProcessExportPds4.cpp

+207 −57
Original line number Diff line number Diff line
@@ -273,7 +273,7 @@ namespace Isis { 
      PvlToXmlTranslationManager targXlator(*inputLabel, translationFileName.expanded());

      targXlator.Auto(*m_domDoc);



      // move target to just below Observing_System. 

      // Move target to just below Observing_System. 

      QDomElement targetIdNode = obsAreaNode.firstChildElement("Target_Identification");

      obsAreaNode.insertAfter(targetIdNode, obsAreaNode.firstChildElement("Observing_System"));

    }
@@ -304,12 +304,19 @@ namespace Isis { 
          if (startTime.text() == "") {

            startTime.setAttribute("xsi:nil", "true");

          }

          else {

            QString timeValue = startTime.text();

            PvlToXmlTranslationManager::resetElementValue(startTime, timeValue + "Z");

          }



          QDomElement stopTime  = timeNode.firstChildElement("stop_date_time"); 

          if (stopTime.text() == "") {

            stopTime.setAttribute("xsi:nil", "true");

          }



          else {

            QString timeValue = stopTime.text();

            PvlToXmlTranslationManager::resetElementValue(stopTime, timeValue + "Z");

          }

          QStringList xmlPath;

          xmlPath << "Product_Observational"

            << "Observation_Area"
@@ -779,6 +786,15 @@ namespace Isis { 
    

  }



 /**

  * Sets the description string which describes the pixel vales in 

  * File_Area_Observational 

  *  

  * @param description Description of pixel values to use.

  */

  void ProcessExportPds4::setPixelDescription(QString description) {

    m_pixelDescription = description;

  }



  /**

   * Create and internalize an image output label from the input
@@ -882,36 +898,139 @@ namespace Isis { 
        elementArrayElement.appendChild(offsetElement);

      }



      // Add the Special_Constants class to define ISIS special pixel values: 



      // Assume 32-bit/Real for CaSSIS

      // Add the Special_Constants class to define ISIS special pixel values if pixel type is

      QDomElement specialConstantElement = m_domDoc->createElement("Special_Constants"); 

      arrayImageElement.insertAfter(specialConstantElement,

                                    arrayImageElement.lastChildElement("Axis_Array"));



      QDomElement nullElement = m_domDoc->createElement("missing_constant");

      PvlToXmlTranslationManager::setElementValue(nullElement, QString::number(NULL8, 'g', 18)); //toString(NULL8));

      switch (p_pixelType) {

        case Real: 

          { QDomElement nullElement = m_domDoc->createElement("missing_constant");

          PvlToXmlTranslationManager::setElementValue(nullElement, QString::number(NULL4, 'g', 18));

          specialConstantElement.appendChild(nullElement);

        

          QDomElement highInstrumentSatElement = m_domDoc->createElement("high_instrument_saturation");

          PvlToXmlTranslationManager::setElementValue(highInstrumentSatElement, QString::number(HIGH_INSTR_SAT4, 'g', 18));

          specialConstantElement.appendChild(highInstrumentSatElement);



          QDomElement highRepresentationSatElement = m_domDoc->createElement("high_representation_saturation");

          PvlToXmlTranslationManager::setElementValue(highRepresentationSatElement, QString::number(HIGH_REPR_SAT4, 'g', 18));

          specialConstantElement.appendChild(highRepresentationSatElement);



          QDomElement lowInstrumentSatElement = m_domDoc->createElement("low_instrument_saturation");

          PvlToXmlTranslationManager::setElementValue(lowInstrumentSatElement, QString::number(LOW_INSTR_SAT4, 'g', 18));

          specialConstantElement.appendChild(lowInstrumentSatElement);



          QDomElement lowRepresentationSatElement = m_domDoc->createElement("low_representation_saturation");

          PvlToXmlTranslationManager::setElementValue(lowRepresentationSatElement, QString::number(LOW_REPR_SAT4, 'g', 18));

          specialConstantElement.appendChild(lowRepresentationSatElement); 

          break;}



        case UnsignedByte:

          { QDomElement nullElement = m_domDoc->createElement("missing_constant");

          PvlToXmlTranslationManager::setElementValue(nullElement, QString::number(NULL1, 'g', 18));

          specialConstantElement.appendChild(nullElement);

        

          QDomElement highInstrumentSatElement = m_domDoc->createElement("high_instrument_saturation");

          PvlToXmlTranslationManager::setElementValue(highInstrumentSatElement, QString::number(HIGH_INSTR_SAT1, 'g', 18));

          specialConstantElement.appendChild(highInstrumentSatElement);



          QDomElement highRepresentationSatElement = m_domDoc->createElement("high_representation_saturation");

          PvlToXmlTranslationManager::setElementValue(highRepresentationSatElement, QString::number(HIGH_REPR_SAT1, 'g', 18));

          specialConstantElement.appendChild(highRepresentationSatElement);



          QDomElement lowInstrumentSatElement = m_domDoc->createElement("low_instrument_saturation");

          PvlToXmlTranslationManager::setElementValue(lowInstrumentSatElement, QString::number(LOW_INSTR_SAT1, 'g', 18));

          specialConstantElement.appendChild(lowInstrumentSatElement);



          QDomElement lowRepresentationSatElement = m_domDoc->createElement("low_representation_saturation");

          PvlToXmlTranslationManager::setElementValue(lowRepresentationSatElement, QString::number(LOW_REPR_SAT1, 'g', 18));

          specialConstantElement.appendChild(lowRepresentationSatElement);

          break; }



        case SignedWord:

          { QDomElement nullElement = m_domDoc->createElement("missing_constant");

          PvlToXmlTranslationManager::setElementValue(nullElement, QString::number(NULL2, 'g', 18));

          specialConstantElement.appendChild(nullElement);

        

          QDomElement highInstrumentSatElement = m_domDoc->createElement("high_instrument_saturation");

      PvlToXmlTranslationManager::setElementValue(highInstrumentSatElement, QString::number(HIGH_INSTR_SAT8, 'g', 18));

          PvlToXmlTranslationManager::setElementValue(highInstrumentSatElement, QString::number(HIGH_INSTR_SAT2, 'g', 18));

          specialConstantElement.appendChild(highInstrumentSatElement);



          QDomElement highRepresentationSatElement = m_domDoc->createElement("high_representation_saturation");

      PvlToXmlTranslationManager::setElementValue(highRepresentationSatElement, QString::number(HIGH_REPR_SAT8, 'g', 18));

          PvlToXmlTranslationManager::setElementValue(highRepresentationSatElement, QString::number(HIGH_REPR_SAT2, 'g', 18));

          specialConstantElement.appendChild(highRepresentationSatElement);



          QDomElement lowInstrumentSatElement = m_domDoc->createElement("low_instrument_saturation");

      PvlToXmlTranslationManager::setElementValue(lowInstrumentSatElement, QString::number(LOW_INSTR_SAT8, 'g', 18));

          PvlToXmlTranslationManager::setElementValue(lowInstrumentSatElement, QString::number(LOW_INSTR_SAT2, 'g', 18));

          specialConstantElement.appendChild(lowInstrumentSatElement);



          QDomElement lowRepresentationSatElement = m_domDoc->createElement("low_representation_saturation");

      PvlToXmlTranslationManager::setElementValue(lowRepresentationSatElement, QString::number(LOW_REPR_SAT8, 'g', 18));

          PvlToXmlTranslationManager::setElementValue(lowRepresentationSatElement, QString::number(LOW_REPR_SAT2, 'g', 18));

          specialConstantElement.appendChild(lowRepresentationSatElement); 

          break; }



        case UnsignedWord:

          { QDomElement nullElement = m_domDoc->createElement("missing_constant");

          PvlToXmlTranslationManager::setElementValue(nullElement, QString::number(NULLU2, 'g', 18));

          specialConstantElement.appendChild(nullElement);

        

          QDomElement highInstrumentSatElement = m_domDoc->createElement("high_instrument_saturation");

          PvlToXmlTranslationManager::setElementValue(highInstrumentSatElement, QString::number(HIGH_INSTR_SATU2, 'g', 18));

          specialConstantElement.appendChild(highInstrumentSatElement);



          QDomElement highRepresentationSatElement = m_domDoc->createElement("high_representation_saturation");

          PvlToXmlTranslationManager::setElementValue(highRepresentationSatElement, QString::number(HIGH_REPR_SATU2, 'g', 18));

          specialConstantElement.appendChild(highRepresentationSatElement);



          QDomElement lowInstrumentSatElement = m_domDoc->createElement("low_instrument_saturation");

          PvlToXmlTranslationManager::setElementValue(lowInstrumentSatElement, QString::number(LOW_INSTR_SATU2, 'g', 18));

          specialConstantElement.appendChild(lowInstrumentSatElement);



          QDomElement lowRepresentationSatElement = m_domDoc->createElement("low_representation_saturation");

          PvlToXmlTranslationManager::setElementValue(lowRepresentationSatElement, QString::number(LOW_REPR_SATU2, 'g', 18));

          specialConstantElement.appendChild(lowRepresentationSatElement); 

          break; }



        case None: break;

      }







      if (!m_pixelDescription.isEmpty()) {

        QDomElement descriptionElement = m_domDoc->createElement("description"); 

        PvlToXmlTranslationManager::setElementValue(descriptionElement,

                                                    m_pixelDescription);

        arrayImageElement.insertAfter(descriptionElement, arrayImageElement.lastChildElement());

      }

    }

  }





  /**

   * Adds necessary information to the xml header for a pds4 class for schema which lack 

   * schematron files (.sch) 

   * 

   * @param xsd Schema filename without path

   * @param xmlns The xml namespace used 

   * @param xmlnsURI Full URL to the xml namespace URI. Also used as the location of the sch and xsd

   */

  void ProcessExportPds4::addSchema(QString xsd, QString xmlns, QString xmlnsURI) {

    // Add xmlns

    QDomElement root = m_domDoc->documentElement();

    root.setAttribute(xmlns, xmlnsURI);



    // Add to xsi:schemaLocation

    m_schemaLocation += " "; 

    m_schemaLocation += xmlnsURI;

    m_schemaLocation += " ";

    m_schemaLocation += xmlnsURI;

    m_schemaLocation += "/";

    m_schemaLocation += xsd;

    root.setAttribute("xsi:schemaLocation", m_schemaLocation);

  }





  /**

   * Adds necessary information to the xml header for a pds4 class. 

   *
@@ -933,17 +1052,7 @@ namespace Isis { 
    m_domDoc->insertAfter(header, m_domDoc->firstChild());



    // Add xmlns

    QDomElement root = m_domDoc->documentElement();

    root.setAttribute(xmlns, xmlnsURI);



    // Add to xsi:schemaLocation

    m_schemaLocation += " "; 

    m_schemaLocation += xmlnsURI;

    m_schemaLocation += " ";

    m_schemaLocation += xmlnsURI;

    m_schemaLocation += "/";

    m_schemaLocation += xsd;

    root.setAttribute("xsi:schemaLocation", m_schemaLocation);

    addSchema(xsd, xmlns, xmlnsURI);

  }
@@ -1126,13 +1235,14 @@ namespace Isis { 
      }

    }



    // Add the EASTERNMOST AND WESTERNMOST LONGITUDE keywords

    PvlKeyword &isisLonDir = inputMapping.findKeyword("LongitudeDirection");

    QString lonDir = isisLonDir[0];

    lonDir = lonDir.toUpper();

    if (inputMapping.hasKeyword("MaximumLongitude") && inputMapping.hasKeyword("MinimumLongitude")) {

      double maxLon = inputMapping.findKeyword("MaximumLongitude");

      double minLon = inputMapping.findKeyword("MinimumLongitude");

    

    // Add Lat/Lon range

    double maxLon, minLon, maxLat, minLat; 

    InputCubes[0]->latLonRange(minLat, maxLat, minLon, maxLon); 

    

    xmlPath.clear();

    xmlPath << "Product_Observational"

            << "Observation_Area"
@@ -1143,14 +1253,55 @@ namespace Isis { 
    QDomElement boundingCoordElement = getElement(xmlPath, baseElement);

    QDomElement eastElement = boundingCoordElement.firstChildElement("cart:east_bounding_coordinate");

    QDomElement westElement = boundingCoordElement.firstChildElement("cart:west_bounding_coordinate");

    QDomElement northElement = boundingCoordElement.firstChildElement("cart:north_bounding_coordinate");

    QDomElement southElement = boundingCoordElement.firstChildElement("cart:south_bounding_coordinate");



      // translation files currently handles Positive West case where east = min, west = max

    // Translation files currently handles Positive West case where east = min, west = max

    // so if positive east, swap min/max

    if(QString::compare(lonDir, "PositiveEast", Qt::CaseInsensitive) == 0) {

      // west min, east max

      PvlToXmlTranslationManager::resetElementValue(eastElement, toString(maxLon), "deg");

      PvlToXmlTranslationManager::resetElementValue(westElement, toString(minLon), "deg");

    }

    else {

      PvlToXmlTranslationManager::resetElementValue(eastElement, toString(minLon), "deg");

      PvlToXmlTranslationManager::resetElementValue(westElement, toString(maxLon), "deg");

    }



    PvlToXmlTranslationManager::resetElementValue(northElement, toString(maxLat), "deg");

    PvlToXmlTranslationManager::resetElementValue(southElement, toString(minLat), "deg");



    // longitude_of_central_meridian and latitude_of_projection_origin need to be converted to floats.

    xmlPath.clear();

    xmlPath << "Product_Observational"

            << "Observation_Area" 

            << "Discipline_Area"

            << "cart:Cartography" 

            << "cart:Spatial_Reference_Information"

            << "cart:Horizontal_Coordinate_System_Definition"

            << "cart:Planar"

            << "cart:Map_Projection";



    // The following is necessary because the full xmlPath differs depending on the projection used.

    QDomElement projectionElement = getElement(xmlPath, baseElement);

    QDomElement tempElement = projectionElement.firstChildElement();

    QDomElement nameElement = tempElement.nextSiblingElement();



    QDomElement longitudeElement = nameElement.firstChildElement("cart:longitude_of_central_meridian"); 

    QDomElement originElement = nameElement.firstChildElement("cart:latitude_of_projection_origin");



    double longitudeElementValue = longitudeElement.text().toDouble(); 

    double originElementValue = originElement.text().toDouble(); 



    // Only update the ouput formatting if there are no digits after the decimal point. 

    if (!longitudeElement.text().contains('.')) {

      QString toset1 = QString::number(longitudeElementValue, 'f', 1); 

      PvlToXmlTranslationManager::resetElementValue(longitudeElement, toset1, "deg"); 

    }



    if (!originElement.text().contains('.')) {

      QString toset2 = QString::number(originElementValue, 'f', 1); 

      PvlToXmlTranslationManager::resetElementValue(originElement, toset2, "deg");

    }

  }
@@ -1373,7 +1524,6 @@ namespace Isis { 
        }

      }

    }



    return transMap; 

  }

isis/src/base/objs/ProcessExportPds4/ProcessExportPds4.h

+8 −2
Original line number Diff line number Diff line
@@ -78,6 +78,9 @@ namespace Isis { 
   *   @history 2019-03-01 Kristin Berry - Added ability to set version_id and title, added

   *                           Special_Constants to define ISIS special pixel values, fixed east/west

   *                           bounding coordinates swap bug. Fixes git issue #2635.

   *   @history 2019-06-15 Kristin Berry - Added a new addSchema() function for cases in which a

   *                           schematron file is not available and added setPixelDescription to

   *                           set a pixel description for the output image. 

   */



  class ProcessExportPds4: public Isis::ProcessExport {
@@ -115,11 +118,13 @@ namespace Isis { 
      void setTitle(QString title);

      void setSchemaLocation(QString schema);

      void setImageType(ImageType imageType);



      void setPixelDescription(QString description); 

      static void translateUnits(QDomDocument &label,

                                 QString transMapFile = "$base/translations/pds4ExportUnits.pvl");

      void reorder();

      void addSchema(QString sch, QString xsd, QString xmlns, QString xmlnsURI);

      void addSchema(QString xsd, QString xmlns, QString xmlnsURI);



    protected:

      void identificationArea();

      void standardInstrument();
@@ -139,6 +144,7 @@ namespace Isis { 
      QString m_versionId;                  //!< QString with specified version id.

      QString m_title;                      //!< QString with specified title. 

      ImageType m_imageType;                //!< Type of image data to be written.

      QString m_pixelDescription;           //!< Description of pixel values.



  };

}

isis/src/base/objs/iTime/iTime.cpp

+6 −7
Original line number Diff line number Diff line
@@ -350,15 +350,14 @@ namespace Isis { 
   *

   * @return string

   */

  QString iTime::SecondString() const {

  QString iTime::SecondString(int precision) const {

    ostringstream osec;

    osec.setf(ios::fixed);

    osec << setprecision(8) << Second();

    osec << setprecision(precision) << Second();

    QString sSeconds(osec.str().c_str());

    sSeconds = sSeconds.remove(QRegExp("(\\.0*|0*)$"));



    if(sSeconds.isEmpty()) sSeconds = "0";



    return sSeconds;

  }
@@ -416,7 +415,7 @@ namespace Isis { 
   *

   * @return string The internalized time, in UTC format

   */

  QString iTime::UTC() const {

  QString iTime::UTC(int precision) const {

    QString utc = YearString() + "-" ;

    if(Month() < 10) utc += "0" + MonthString() + "-";

    else utc += MonthString() + "-";
@@ -430,8 +429,8 @@ namespace Isis { 
    if(Minute() < 10) utc += "0" + MinuteString() + ":";

    else utc += MinuteString() + ":";



    if(Second() < 10) utc += "0" + SecondString();

    else utc += SecondString();

    if(Second() < 10) utc += "0" + SecondString(precision);

    else utc += SecondString(precision);

    

    return utc;

  }