Unverified Commit 625b7f0e authored by Cordell Michaud's avatar Cordell Michaud Committed by GitHub
Browse files

Update lrowacphomap with versioned defaults for PHOALGO and PHOPARCUBE parameters (#5452) 



* Update lrowacphomap.xml with PHOALGO and PHOPARCUBE defaults

* Add test cases for lrowacphomap PHOALGO and PHOPARCUBE defaults

* Add handling for lrowacphomap PHOALGO and PHOPARCUBE defaults

* Add CHANGELOG.md entry for lrowacphomap defaults update

* Fix error during parCube setVirtualBands call

* Move lrowacphomap defaults update changelog entry to the Unreleased section

---------

Co-authored-by: default avatarAustin Sanders <arsanders@usgs.gov>
parent dce1406b

CHANGELOG.md

+3 −0
Original line number Diff line number Diff line
@@ -44,6 +44,9 @@ release. 
- Fixed a bug in QVIEW's Stretch tool where the default min/max type was not an available option [#5289](https://github.com/DOI-USGS/ISIS3/issues/5289)

- Fixed a bug in QVIEW where images would double load if loaded from the commandline [#5505](https://github.com/DOI-USGS/ISIS3/pull/5505)



### Added

- Added versioned default values to lrowacphomap's PHOALGO and PHOPARCUBE parameters and updated lrowacphomap to handle them properly. [#5452](https://github.com/DOI-USGS/ISIS3/pull/5452)



## [8.2.0] - 2024-04-18



### Changed

isis/src/lro/apps/lrowacphomap/lrowacphomap.cpp

+97 −37
Original line number Diff line number Diff line 
#include <string>

#include "lrowacphomap.h"



#include <memory>

#include <vector>



#include <QList>

#include <QString>



#include "Buffer.h"

#include "Cube.h"

#include "CubeAttribute.h"

#include "FileName.h"

#include "HapkeLRO.h"

#include "HapkeLROC.h"

#include "IException.h"

#include "PhotometricFunction.h"

#include "ProcessByBrick.h"

#include "Pvl.h"

#include "PvlGroup.h"

#include "SpecialPixel.h"



#include "lrowacphomap.h"



using namespace std;

using namespace Isis;



#include "UserInterface.h"



namespace Isis {

  /**

   * @brief Apply Hapke photometric correction to a WAC cube.

   * 

   * This is the programmatic interface to the lrowacphomap application.

   * 

   * @author 2021-08-02 Cordell Michaud

   * 

   * @internal

   *   @history 2021-08-02 Cordell Michaud - Code adapted from lrowacphomap by Kris Becker

   *   @history 2024-04-02 Cordell Michaud - Changed icube to be a regular Cube object rather than 

   *                           a pointer

   * 

   * @param ui the user interface to parse parameters from

  */

  Pvl lrowacphomap(UserInterface &ui) {

    // Set up the input cube

    Cube *icube = new Cube();

    Cube icube;

    CubeAttributeInput inAtt = ui.GetInputAttribute("FROM");

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

      icube->setVirtualBands(inAtt.bands());

      icube.setVirtualBands(inAtt.bands());

    }

    icube->open(ui.GetCubeName("FROM"));

    icube.open(ui.GetCubeName("FROM"));



    Pvl log = lrowacphomap(icube, ui);

    Pvl log = lrowacphomap(&icube, ui);



    delete icube;

    icube = NULL;

    icube.close();



    return log;

  }



  /**

   * @brief Apply Hapke photometric correction to a WAC cube.

   * 

   * This is the programmatic interface to the lrowacphomap application.

   * 

   * @author 2021-08-02 Cordell Michaud

   * 

   * @internal

   *   @history 2021-08-02 Cordell Michaud - Code adapted from lrowacphomap by Kris Becker

   *   @history 2024-04-02 Cordell Michaud - Converted phoLro and phoLroc to smart pointers and 

   *                           added handling for new PHOALGO and PHOPARCUBE defaults

   * 

   * @param icube the input cube to apply Hapke photometric correction to

   * @param ui the user interface to parse parameters from

  */

  Pvl lrowacphomap(Cube *icube, UserInterface &ui) {

    Pvl log;



    HapkeLRO *phoLro = NULL;

    HapkeLROC *phoLroc = NULL;

    std::shared_ptr<HapkeLRO> phoLro;

    std::shared_ptr<HapkeLROC> phoLroc;

    QString algoName;



    bool normalized;
@@ -54,13 +88,14 @@ namespace Isis { 


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

      if (icube->bandCount() != 1) {

        string msg = "Invalid Image: The backplane option can only be used with a single image band at a time.";

        QString msg = "Invalid Image: The backplane option can only be used with a single image "

                      "band at a time.";

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

      }



      CubeAttributeInput backplaneCai = ui.GetInputAttribute("BACKPLANE");



      vector<QString> bands = backplaneCai.bands();

      std::vector<QString> bands = backplaneCai.bands();



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

        bands.clear();
@@ -71,7 +106,7 @@ namespace Isis { 
        bands.push_back("5");

      }

      else if (bands.size() != 5) {

        string msg = "Invalid Backplane: The backplane must be exactly 5 bands";

        QString msg = "Invalid Backplane: The backplane must be exactly 5 bands";

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

      }
@@ -91,13 +126,37 @@ namespace Isis { 
    }



    // Get the name of the parameter files

    Pvl par(ui.GetFileName("PHOALGO"));

    Cube *parCube = new Cube();

    CubeAttributeInput parCubeAtt = ui.GetInputAttribute("PHOPARCUBE");

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

      parCube->setVirtualBands(parCubeAtt.bands());

    QString algoFile = ui.GetAsString("PHOALGO");

    FileName algoFileName(algoFile);

    if (algoFileName.isVersioned()) {

      algoFileName = algoFileName.highestVersion();

    }

    if (!algoFileName.fileExists()) {

      QString msg = algoFileName.expanded() + " does not exist.";

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

    }

    Pvl par(algoFileName.expanded());



    QString parCubeFile = ui.GetCubeName("PHOPARCUBE");

    FileName parCubeFileName(parCubeFile);

    if (parCubeFileName.isVersioned()) {

      parCubeFileName = parCubeFileName.highestVersion();

    }

    if (!parCubeFileName.fileExists()) {

      QString msg = parCubeFileName.expanded() + " does not exist.";

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

    }

    CubeAttributeInput parCubeAtt(parCubeFileName);

    Cube parCube(parCubeFileName);

    std::vector<QString> parCubeBandsVector = parCubeAtt.bands();

    QList<QString> parCubeBands;

    parCubeBands.reserve(parCubeBandsVector.size());

    for (const QString &band : parCubeBandsVector) {

      parCubeBands.push_back(band);

    }

    if (parCubeBands.size() != 0) {

      parCube.setVirtualBands(parCubeBands);

    }

    parCube->open(ui.GetCubeName("PHOPARCUBE"));



    p.SetBrickSize(128, 128, icube->bandCount());
@@ -107,7 +166,7 @@ namespace Isis { 
    normalized = ui.GetBoolean("NORMALIZED");



    if (algoName == "HAPKELRO") {

      phoLro = new HapkeLRO(par, *icube, !useBackplane, parCube);

      phoLro = std::make_shared<HapkeLRO>(par, *icube, !useBackplane, &parCube);

      phoLro->setMinimumPhaseAngle(ui.GetDouble("MINPHASE"));

      phoLro->setMaximumPhaseAngle(ui.GetDouble("MAXPHASE"));

      phoLro->setMinimumEmissionAngle(ui.GetDouble("MINEMISSION"));
@@ -118,7 +177,7 @@ namespace Isis { 
      phoLro->setNormalized(normalized);

    }

    else if (algoName == "HAPKELROC") {

      phoLroc = new HapkeLROC(par, *icube, !useBackplane, parCube);

      phoLroc = std::make_shared<HapkeLROC>(par, *icube, !useBackplane, &parCube);

      phoLroc->setMinimumPhaseAngle(ui.GetDouble("MINPHASE"));

      phoLroc->setMaximumPhaseAngle(ui.GetDouble("MAXPHASE"));

      phoLroc->setMinimumEmissionAngle(ui.GetDouble("MINEMISSION"));
@@ -147,11 +206,13 @@ namespace Isis { 
    * 

    * @internal

    *   @history 2021-07-19 Cordell Michaud - Code adapted from lrowacphomap by Kris Becker

    *   @history 2024-04-02 Cordell Michaud - Changed to capture phoLro and phoLroc by value

    *

    * @param in Buffer containing input data

    * @param out Buffer of photometrically corrected data

    */

    auto phoCal = [&phoLro, &phoLroc, algoName, useDem, photometryOnly](Buffer &in, Buffer &out) -> void {

    auto phoCal = [phoLro, phoLroc, algoName, useDem, photometryOnly](

        Buffer &in, Buffer &out) -> void {

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

        //  Don't correct special pixels

        if (IsSpecial(in[i])) {
@@ -189,12 +250,13 @@ namespace Isis { 
    * 

    * @internal

    *   @history 2021-07-19 Cordell Michaud - Code adapted from lrowacphomap by Kris Becker

    *   @history 2024-04-02 Cordell Michaud - Changed to capture phoLro and phoLroc by value

    *

    * @param in Buffer containing input data

    * @param out Buffer of photometrically corrected data

    */

    auto phoCalWithBackplane = [&phoLro, &phoLroc, algoName, photometryOnly](std::vector<Isis::Buffer *> &in, std::vector<Isis::Buffer *> &out) -> void {



    auto phoCalWithBackplane = [phoLro, phoLroc, algoName, photometryOnly](

        std::vector<Buffer *> &in, std::vector<Buffer *> &out) -> void {

      Buffer &image = *in[0];

      Buffer &phase = *in[1];

      Buffer &emission = *in[2];
@@ -208,17 +270,20 @@ namespace Isis { 
        if (IsSpecial(image[i])) {

          calibrated[i] = image[i];

        }

        else if (IsSpecial(phase[i]) || IsSpecial(emission[i]) || IsSpecial(incidence[i]) || IsSpecial(lat[i]) || IsSpecial(lon[i])) {

        else if (IsSpecial(phase[i]) || IsSpecial(emission[i]) || IsSpecial(incidence[i]) 

                 || IsSpecial(lat[i]) || IsSpecial(lon[i])) {

          calibrated[i] = Isis::Null;

        }

        else {

          // Get correction and test for validity

          double ph = Null;

          if (algoName == "HAPKELRO") {

            ph = phoLro->photometry(incidence[i], emission[i], phase[i], lat[i], lon[i], image.Band(i));

            ph = phoLro->photometry(incidence[i], emission[i], phase[i], lat[i], lon[i], 

                                    image.Band(i));

          }

          else if (algoName == "HAPKELROC") {

            ph = phoLroc->photometry(incidence[i], emission[i], phase[i], lat[i], lon[i], image.Band(i));

            ph = phoLroc->photometry(incidence[i], emission[i], phase[i], lat[i], lon[i], 

                                     image.Band(i));

          }



          if (!photometryOnly) {
@@ -253,11 +318,6 @@ namespace Isis { 
    ocube->putGroup(photo);

    log.addGroup(photo);



    delete phoLro;

    phoLro = NULL;

    delete phoLroc;

    phoLroc = NULL;



    return log;

  }

}
 
 No newline at end of file

isis/src/lro/apps/lrowacphomap/lrowacphomap.xml

+7 −0
Original line number Diff line number Diff line
@@ -272,6 +272,10 @@ 
    <change name="Cordell Michaud" date="2022-05-10">

      Refactored lrowacphomap for testability and added functional tests.

    </change>

    <change name="Cordell Michaud" date="2024-04-02">

      Added new default for PHOALGO.

      Added new default for PHOPARCUBE.

    </change>

  </history>



  <category>
@@ -326,6 +330,8 @@ 
      <parameter name="PHOALGO">

        <type>filename</type>

        <fileMode>input</fileMode>

        <defaultPath>$lro/calibration</defaultPath>

        <default><item>$lro/calibration/WAC_hapke_full.????.pvl</item></default>

        <brief>

          Pvl file

        </brief>
@@ -353,6 +359,7 @@ 
      <parameter name="PHOPARCUBE">

        <type>cube</type>

        <fileMode>input</fileMode>

        <default><item>$lro/calibration/WAC_global_7bands_1x1_wbhs70NS_const_each_pole.????.cub</item></default>

        <brief>

          Parameter cube

        </brief>

isis/tests/FunctionalTestsLrowacphomap.cpp

+94 −6
Original line number Diff line number Diff line 
#include <memory>

#include <ostream>



#include <QString>

#include <QTemporaryDir>

#include <QVector>



#include "Cube.h"

#include "FileName.h"

#include "Histogram.h"

#include "Pvl.h"

#include "PvlGroup.h"

#include "IException.h"

#include "TestUtilities.h"



#include "lrowacphomap.h"

#include "UserInterface.h"



#include "gtest/gtest.h"



#include "lrowacphomap.h"



using namespace Isis;



static QString APP_XML = FileName("$ISISROOT/bin/xml/lrowacphomap.xml").expanded();
@@ -34,7 +41,8 @@ TEST(Lrowacphomap, FunctionalTestLrowacphomapWithBack) { 
    lrowacphomap(options);

  }

  catch(IException &e) {

    FAIL() << "Call to lrowacphomap failed, unable to apply photometric correction to input cube: " << e.what() << std::endl;

    FAIL() << "Call to lrowacphomap failed, unable to apply photometric correction to input cube: " 

           << e.what() << std::endl;

  }



  double expectedAvg = 58.565850201775;
@@ -76,7 +84,8 @@ TEST(Lrowacphomap, FunctionalTestLrowacphomapNoBack) { 
    lrowacphomap(options);

  }

  catch(IException &e) {

    FAIL() << "Call to lrowacphomap failed, unable to apply photometric correction to input cube: " << e.what() << std::endl;

    FAIL() << "Call to lrowacphomap failed, unable to apply photometric correction to input cube: " 

           << e.what() << std::endl;

  }



  double expectedAvg = 58.159470616532;
@@ -97,3 +106,82 @@ TEST(Lrowacphomap, FunctionalTestLrowacphomapNoBack) { 
  EXPECT_NEAR(hist->Maximum(), expectedMax, 0.001);

  EXPECT_NEAR(hist->Sum(), expectedSum, 0.001);

}



TEST(Lrowacphomap, FunctionalTestLrowacphomapDefaultAlgoAndParCubeWithBack) {

  QTemporaryDir tempDir;

  ASSERT_TRUE(tempDir.isValid());



  QString outCubeFileName = tempDir.path() + "/outTemp.cub";

  QString testCubeFileName = "data/lrowacphomap/M1181493219CE.vis.odd.reduced.cub";

  QString backplaneFileName = "data/lrowacphomap/back.reduced.cub";



  QVector<QString> args = {"from=" + testCubeFileName + "+1",

                           "to=" + outCubeFileName,

                           "backplane=" + backplaneFileName};

  UserInterface options(APP_XML, args);



  try {

    lrowacphomap(options);

  }

  catch(IException &e) {

    FAIL() << "Call to lrowacphomap failed, unable to apply photometric correction to input cube: " 

           << e.what() << std::endl;

  }



  double expectedAvg = 57.150192172911;

  double expectedStdDev = 19.201699528246;

  double expectedMedian = 55.0376024164;

  double expectedMin = 20.151010513306;

  double expectedMax = 157.08757019043;

  double expectedSum = 192367.54685402;



  Cube outCube(outCubeFileName);



  std::unique_ptr<Histogram> hist(outCube.histogram());



  EXPECT_NEAR(hist->Average(), expectedAvg, 0.001);

  EXPECT_NEAR(hist->StandardDeviation(), expectedStdDev, 0.001);

  EXPECT_NEAR(hist->Median(), expectedMedian, 0.001);

  EXPECT_NEAR(hist->Minimum(), expectedMin, 0.001);

  EXPECT_NEAR(hist->Maximum(), expectedMax, 0.001);

  EXPECT_NEAR(hist->Sum(), expectedSum, 0.001);

}



TEST(Lrowacphomap, FunctionalTestLrowacphomapDefaultAlgoAndParCubeNoBack) {

  QTemporaryDir tempDir;

  ASSERT_TRUE(tempDir.isValid());



  QString outCubeFileName = tempDir.path() + "/outTemp.cub";

  QString testCubeFileName = "data/lrowacphomap/M1181493219CE.vis.odd.reduced.cub";



  QVector<QString> args = {"from=" + testCubeFileName + "+1",

                           "to=" + outCubeFileName,

                           "usedem=true"};

  UserInterface options(APP_XML, args);



  try {

    lrowacphomap(options);

  }

  catch(IException &e) {

    FAIL() << "Call to lrowacphomap failed, unable to apply photometric correction to input cube: " 

           << e.what() << std::endl;

  }



  double expectedAvg = 56.750011832815;

  double expectedStdDev = 18.44290433699;

  double expectedMedian = 55.263128187622;

  double expectedMin = 22.274614334106;

  double expectedMax = 152.65106201172;

  double expectedSum = 191020.53982925;



  Cube outCube(outCubeFileName);



  std::unique_ptr<Histogram> hist(outCube.histogram());



  EXPECT_NEAR(hist->Average(), expectedAvg, 0.001);

  EXPECT_NEAR(hist->StandardDeviation(), expectedStdDev, 0.001);

  EXPECT_NEAR(hist->Median(), expectedMedian, 0.001);

  EXPECT_NEAR(hist->Minimum(), expectedMin, 0.001);

  EXPECT_NEAR(hist->Maximum(), expectedMax, 0.001);

  EXPECT_NEAR(hist->Sum(), expectedSum, 0.001);

}