8.0.2 Release Prep (#5364)

* Cnetthinner application bug fix resolving divide by zero in CnetManager.cpp. (#5356) * Bug fix for a divide by zero in CnetManager.cpp. Additionally, the cnetthinner app has been converted to a callable function and Makefile tests converted to gtests. Addresses #5354. * Updated CHANGELOG.md. Addresses #5354. * Minor change to cnetthinner.xml. Addresses #5354. * Update photomet's MinnaertEmpirical model to handle PVL input in photemplate format. Fixes #3621. (#5175) * Update photomet's MinnaertEmpirical model to handle PVL input in photemplate format * Updated CHANGELOG * Dawn Target Translation Fix (#5294) * Fixes dawn target translation for CERES images * Added Changelog entry * CSM Camera Qview Try Catches (#5295) * Fix errors when using CSM camera in qview * Added Changelog entry * Fixes CSV parsing in shadowtau (#5316) * Fixes CSV parsing in shadowtau * Addressed PR feedback * Error Report Fix for Program Launcher (#5331) * Removed line that gets class, it is derived from the code * Added more detailed error around itime not finding the leapsecond kernel * Added changelog entry * Updated trimfilter to correctly use high/low filters (#5340) * Added high/low filters to trimfilter * Updated changelog * Updated changelog --------- Co-authored-by: acpaquette <[email protected]> * corrected calibration inclusion filter (needed ,) (#5357) * corrected calibration inclusion filter (needed ,) * changelog entry downloadIsisData fix * Updated changelog * Updated changelog * Cnetthinner application bug fix resolving divide by zero in CnetManager.cpp. (#5356) * Bug fix for a divide by zero in CnetManager.cpp. Additionally, the cnetthinner app has been converted to a callable function and Makefile tests converted to gtests. Addresses #5354. * Updated CHANGELOG.md. Addresses #5354. * Minor change to cnetthinner.xml. Addresses #5354. * The cnetedit application has been refactored to be callable; Makefile tests have been removed and replaced by gtests (#5348) * The cnetedit application has been refactored to be callable; Makefile tests have been migrated to gtest format. Addresses #5346. * Removed extraneous variables from FunctionalTestsCnetedit.cpp. Addresses #5346. * Updated gtests; replace cubes with labels. Addresses #5346. * Per review cleaned up sloppy spacing; made global variables static in cnetedit.cpp to avoid issues when linking libisis. Addresses #5346. * The cnetdiff application has been refactored to be callable; Makefile tests have been removed and replaced by gtests. (#5323) * The cnetedit applciation has been refactored to be callable; Makefile tests have been removed and replace by gtests. Addresses #5322. * Moved CHANGELOG.md entry for cnetdiff changes from "Added" section to "Changed" section per reviewer suggestion. Addresses #5322. * Reverted back to original ControlNetDiff source and header files per reviewer suggestion. Addresses #5322. * Changes to cnetdiff.cpp and main.cpp to use the addLogGroup method to add PvlGroups to Pvl. Per reviewer suggestion. Addresses #5322. * Put back line erroneously removed in CHANGELOG.md, per review. Addresses #5322. * Version ticks * Updated changelog * Updated changelog --------- Co-authored-by: kledmundson <[email protected]> Co-authored-by: Christine Kim <[email protected]> Co-authored-by: acpaquette <[email protected]> Co-authored-by: Jacob Cain <[email protected]>
DOI-USGS · Dec 6, 2023 · a8c2c49 · a8c2c49
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -35,6 +35,20 @@ release.
 
 ## [Unreleased]
 
+## [8.0.2] - 2023-12-05
+### Changed
+- Cnetedit has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5346](https://github.com/USGS-Astrogeology/ISIS3/issues/5346), 
+- Cnetdiff has been refactored to be callable; old Makefile tests have been removed and replaced by gtests. Issue: [#5322](https://github.com/USGS-Astrogeology/ISIS3/issues/5322), 
+### Fixed
+- Bug fix for Cnetthinner app resolving divide by zero in CnetManager.cpp. Issue: [#5354](https://github.com/USGS-Astrogeology/ISIS3/issues/5354), 
+- Updated photomet MinnaertEmpirical model to support photemplate-style PVL format [#3621](https://github.com/DOI-USGS/ISIS3/issues/3621)
+- Fixed target name translation for any dawn images with target "4 CERES" [#5294](https://github.com/DOI-USGS/ISIS3/pull/5294)
+- Fixed exception pop ups in qview when viewing images created using the CSM Camera [#5259](https://github.com/DOI-USGS/ISIS3/pull/5295/files)
+- Fixed shadowtau input file parseing errors when using example file [#5316](https://github.com/DOI-USGS/ISIS3/pull/5316)
+- Fixed ProgramLauncher failing while reporting errors from launched programs [#5331](https://github.com/DOI-USGS/ISIS3/pull/5331)
+- Fixed high/low filter functionality in trimfilter [#5311](https://github.com/DOI-USGS/ISIS3/issues/5311)
+- Fixed downloadIsisData script excluding needed files in the calibration folder [#5272](https://github.com/DOI-USGS/ISIS3/issues/5272)
+
 ## [8.0.1] - 2023-08-23
 
 ### Fixed

diff --git a/code.json b/code.json
@@ -44,6 +44,50 @@
       "metadataLastUpdated": "2023-02-27"
     }
   }, {
+    "name": "ISIS3",
+    "organization": "U.S. Geological Survey",
+    "description": "GitHub code repository for the Integrated Software for Imagers and Spectrometers (ISIS)",
+    "version": "8.0.2",
+    "status": "Production",
+
+    "permissions": {
+      "usageType": "openSource",
+      "licenses": [
+        {
+          "name": "Public Domain, CC0-1.0",
+          "URL": "https://code.usgs.gov/DOI-USGS/isis/-/raw/8.0.2/LICENSE.md"
+        }
+      ]
+    },
+
+    "homepageURL": "https://isis.astrogeology.usgs.gov",
+    "downloadURL": "https://code.usgs.gov/astrogeology/isis/-/archive/8.0.2/isis-8.0.2.zip",
+    "disclaimerURL": "https://code.usgs.gov/astrogeology/isis/-/raw/8.0.2/DISCLAIMER.md",
+    "repositoryURL": "https://code.usgs.gov/astrogeology/isis.git",
+    "vcs": "git",
+
+    "laborHours": 0,
+
+    "tags": [
+      "Planetary",
+      "Remote Sensing",
+      "Photogrammetry",
+      "Data Processing"
+    ],
+
+    "languages": [
+      "C++"
+    ],
+
+    "contact": {
+      "name": "Austin Sanders",
+      "email": "[email protected]"
+    },
+
+    "date": {
+      "metadataLastUpdated": "2023-12-05"
+    }
+  },{
     "name": "ISIS3",
     "organization": "U.S. Geological Survey",
     "description": "GitHub code repository for the Integrated Software for Imagers and Spectrometers (ISIS)",

diff --git a/isis/CMakeLists.txt b/isis/CMakeLists.txt
@@ -34,7 +34,7 @@ set(PACKAGE            "ISIS")
 set(PACKAGE_NAME       "USGS ISIS")
 
 # Version number
-set(VERSION            "8.0.1")
+set(VERSION            "8.0.2")
 string(REPLACE "." ";" VERSION_LIST ${VERSION})
 list(GET VERSION_LIST 0 VERSION_MAJOR)
 list(GET VERSION_LIST 1 VERSION_MINOR)

diff --git a/isis/scripts/downloadIsisData b/isis/scripts/downloadIsisData
@@ -17,7 +17,7 @@ import re
 
 # priority is: lowest index is highest priority 
 filter_list = [
-        '+ calibration/**' # we generally want everything in calibration 
+        '+ calibration/**', # we generally want everything in calibration 
         '- source/',
         '- /a_older_versions/',
         '- /former_versions/',

diff --git a/isis/src/base/apps/mosrange/tsts/Makefile b/isis/src/base/apps/mosrange/tsts/Makefile
diff --git a/isis/src/base/apps/shadowtau/main.cpp b/isis/src/base/apps/shadowtau/main.cpp
@@ -250,17 +250,45 @@ void IsisMain() {
   // rejected if there aren't enough words or if any of them don't make
   // sense as the corresponding parameter.
   FileName sInFileName(sInFile);
-  TextFile infile(sInFileName.expanded());
+  // Try with the default ',' delimiter, if that only produces one row
+  // item, try with spaces
+  CSVReader inFile(sInFileName.expanded());
+  if (inFile.getRow(0).dim() <= 1) {
+    inFile = CSVReader(sInFileName.expanded(), false, 0, ' ');
+  }
+
+  if (inFile.getRow(0).dim() <= 1) {
+    QString msg = "File [" + sInFileName.expanded() + "] either has only one line item or is not delimited by a ',' or ' '.";
+    throw IException(IException::User, msg, _FILEINFO_);
+  }
+
   QString infileString;
-  while (infile.GetLine(infileString)) {
-    QStringList tokens = infileString.split(QRegExp("[ ,]"));
-
-    QString imgId = tokens.takeFirst();
-    double inc    = toDouble(tokens.takeFirst());
-    double ema    = toDouble(tokens.takeFirst());
-    double phase  = toDouble(tokens.takeFirst());
-    double pflat  = toDouble(tokens.takeFirst());
-    double pshad  = toDouble(tokens.takeFirst());
+  for (int i = 0; i < inFile.rows(); i++) {
+    CSVReader::CSVAxis row = inFile.getRow(i);
+
+    if (row.dim1() < 6) {
+      continue;
+    }
+
+    QString imgId = row[0];
+    std::vector<double> angles = {};
+    for (int j = 1; j < row.dim(); j++) {
+      try {
+        angles.push_back(toDouble(row[j]));
+      }
+      catch (IException &e) {
+        QString msg = "Unable to convert (" + toString(i) + ", " + toString(j) + 
+        ") element [" + row[j] + "] to double. You may want to check for excess delimiters." + 
+        "Current delimiter is set to '" + inFile.getDelimiter() + "'";
+        throw IException(IException::User, msg, _FILEINFO_);
+      }
+    }
+
+    double inc    = angles[0];
+    double ema    = angles[1];
+    double phase  = angles[2];
+    double pflat  = angles[3];
+    double pshad  = angles[4];
 
     // checking validity
     if (!imgId.length() || (inc < 0 || inc >= 89.9) || (ema < 0 || ema >= 89.9) ||

diff --git a/isis/src/base/apps/trimfilter/main.cpp b/isis/src/base/apps/trimfilter/main.cpp
@@ -27,6 +27,13 @@ void IsisMain() {
   double low = -DBL_MAX;
   double high = DBL_MAX;
   int minimum;
+
+  if(ui.WasEntered("LOW")) {
+    low = ui.GetDouble("LOW");
+  }
+  if(ui.WasEntered("HIGH")) {
+    high = ui.GetDouble("HIGH");
+  }
   if(ui.GetString("MINOPT") == "PERCENTAGE") {
     int size = lines * samples;
     double perc = ui.GetDouble("MINIMUM") / 100;
@@ -35,6 +42,7 @@ void IsisMain() {
   else {
     minimum = (int) ui.GetDouble("MINIMUM");
   }
+
   p.SetFilterParameters(samples, lines, low, high, minimum);
 
   // Process each line

diff --git a/isis/src/base/objs/MinnaertEmpirical/MinnaertEmpirical.cpp b/isis/src/base/objs/MinnaertEmpirical/MinnaertEmpirical.cpp
@@ -74,7 +74,7 @@ namespace Isis {
     * phase curve values that exist between the given phase angles. The values
     * in the phase angle list are limited to values that are >=0 and <=180.
     *
-    * @param phaselist  List of phase angles to interpolate
+    * @param phasestrlist  List of phase angles to interpolate
     */
   void MinnaertEmpirical::SetPhotoPhaseList(QString phasestrlist) {
     double phaseangle;
@@ -92,14 +92,46 @@ namespace Isis {
     }
   }
 
+  /**
+    * Set the empirical Minnaert function phase angle list.  This is the list
+    * of phase angles that Minnaert K values and phase curve list values will
+    * be provided for. A spline curve will be used to interpolate K values and
+    * phase curve values that exist between the given phase angles. The values
+    * in the phase angle list are limited to values that are >=0 and <=180.
+    *
+    * @param phaselist  PvlKeyword containing phase angles to interpolate
+    */
+  void MinnaertEmpirical::SetPhotoPhaseList(PvlKeyword phaseList) {
+
+    // If the format is Keyword="1,2,3,4,5" rather than Keyword = (1,2,3,4,5) 
+    if (phaseList.size() == 1) {
+      SetPhotoPhaseList(QString(phaseList));
+      return;
+    }
+
+    double phaseAngle;
+    p_photoPhaseList.clear();
+
+    for (int i=0; i< phaseList.size(); i++) {
+      phaseAngle = phaseList[i].toDouble();
+
+      if (phaseAngle < 0.0 || phaseAngle > 180.0) {
+        QString msg = "Invalid value of empirical Minnaert phase angle list value [" +
+                          toString(phaseAngle) + "]";
+        throw IException(IException::User, msg, _FILEINFO_);
+      }
+      p_photoPhaseList.push_back(phaseAngle);
+    }
+  }
+
   /**
     * Set the empirical Minnaert function K exponent list.  This is used to
     * govern the limb-darkening in the Minnaert photometric function.  Values
     * of the Minnaert exponent generally fall in the range from 0.5 ("lunar-like",
     * almost no limb darkening) to 1.0 (Lambert function).  This
     * parameter is limited to values that are >=0.
     *
-    * @param klist  List of Minnaert function exponents to interpolate
+    * @param kstrlist  List of Minnaert function exponents to interpolate
     */
   void MinnaertEmpirical::SetPhotoKList(QString kstrlist) {
     double kvalue;
@@ -117,6 +149,29 @@ namespace Isis {
     }
   }
 
+  /**
+    * Set the empirical Minnaert function K exponent list.  This is used to
+    * govern the limb-darkening in the Minnaert photometric function.  Values
+    * of the Minnaert exponent generally fall in the range from 0.5 ("lunar-like",
+    * almost no limb darkening) to 1.0 (Lambert function).  This
+    * parameter is limited to values that are >=0.
+    *
+    * @param kstrList  PvkKeyword containing List of Minnaert function exponents to interpolate
+    */
+  void MinnaertEmpirical::SetPhotoKList(PvlKeyword kstrList) {
+
+    // If the format is Keyword="1,2,3,4,5" rather than Keyword = (1,2,3,4,5) 
+    if (kstrList.size() == 1) {
+      SetPhotoKList(QString(kstrList));
+      return;
+    }
+
+    p_photoKList.clear();
+    for (int i=0; i<kstrList.size(); i++) {
+      p_photoKList.push_back(kstrList[i].toDouble());
+    }
+  }
+
   /**
     * Set the empirical Minnaert function phase curve list.  This list provides
     * the brightness values that correspond to the limb-darkening values in the
@@ -135,6 +190,28 @@ namespace Isis {
     }
   }
 
+  /**
+    * Set the empirical Minnaert function phase curve list.  This list provides
+    * the brightness values that correspond to the limb-darkening values in the
+    * empirical Minnaert photometric function.
+    *
+    * @param phasecurvelist  PvlKeyword containing list of brightness values corresponding 
+    * to Minnaert function exponents
+    */
+  void MinnaertEmpirical::SetPhotoPhaseCurveList(PvlKeyword photocurvestrList) {
+
+    // If the format is Keyword="1,2,3,4,5" rather than Keyword = (1,2,3,4,5) 
+    if (photocurvestrList.size() == 1) {
+      SetPhotoPhaseCurveList(QString(photocurvestrList));
+      return;
+    }
+
+    p_photoPhaseCurveList.clear();
+    for (int i=0; i<photocurvestrList.size(); i++) {
+      p_photoPhaseCurveList.push_back(photocurvestrList[i].toDouble());
+    }
+  }
+
   double MinnaertEmpirical::PhotoModelAlgorithm(double phase, double incidence,
                                        double emission) {
     static double pht_minnaert_empirical;

diff --git a/isis/src/base/objs/MinnaertEmpirical/MinnaertEmpirical.h b/isis/src/base/objs/MinnaertEmpirical/MinnaertEmpirical.h
@@ -46,8 +46,11 @@ namespace Isis {
       virtual ~MinnaertEmpirical();
 
       void SetPhotoPhaseList(QString phasestrlist);
+      void SetPhotoPhaseList(PvlKeyword phaselist);
       void SetPhotoKList(QString kstrlist);
+      void SetPhotoKList(PvlKeyword kstrlist);
       void SetPhotoPhaseCurveList(QString phasecurvestrlist);
+      void SetPhotoPhaseCurveList(PvlKeyword phasecurvestrlist);
 
       //! Return photometric phase angle list
 //      inline std::vector<double> PhotoPhaseList() const {

diff --git a/isis/src/base/objs/MinnaertEmpirical/MinnaertEmpirical.truth b/isis/src/base/objs/MinnaertEmpirical/MinnaertEmpirical.truth
@@ -26,3 +26,27 @@ Albedo = 0.008174
 Test phase=180.0, incidence=90.0, emission=90.0 ...
 Albedo = 0
 
+Object = PhotometricModel
+  Group = Algorithm
+    Name           = MinnaertEmpirical
+    PhaseList      = (0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120,
+                      130, 140)
+    KList          = (0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1,
+                      1.2, 1.3, 1.4)
+    PhaseCurveList = (0, 0.3, 0.6, 0.9, 1.2, 1.5, 1.8, 2.1, 2.4, 2.7, 3, 3.3,
+                      3.6, 3.9, 4.2)
+  End_Group
+End_Object
+End
+
+Test phase=0.0, incidence=0.0, emission=0.0 ...
+Albedo = 0
+Test phase=38.0, incidence=11.0, emission=20.0 ...
+Albedo = 1.1765
+Test phase=65.0, incidence=45.0, emission=30.0 ...
+Albedo = 1.63706
+Test phase=127.0, incidence=52.0, emission=33.0 ...
+Albedo = 1.96227
+Test phase=180.0, incidence=90.0, emission=90.0 ...
+Albedo = 0
+
diff --git a/isis/src/base/objs/MinnaertEmpirical/unitTest.cpp b/isis/src/base/objs/MinnaertEmpirical/unitTest.cpp
@@ -68,5 +68,64 @@ int main() {
     e.print();
   }
 
+  // Test Keyword = (1,2,3,4,5) format for input
+  // 
+  // The actual numbers used for this test are not relevant -- this test's primary purpose is to 
+  // ensure that this format of input is usable for the calculations done by the class without the 
+  // program error-ing out. 
+  PvlGroup algOtherFormat("Algorithm");
+  algOtherFormat += PvlKeyword("Name", "MinnaertEmpirical");
+
+  PvlKeyword phaseList("PhaseList");
+  PvlKeyword kList("KList"); 
+  PvlKeyword phaseCurveList("PhaseCurveList");
+
+  for (int i=0; i < 15; i++) {
+    phaseList += QString::number(i*10);
+    kList += QString::number(i*0.1); 
+    phaseCurveList += QString::number(i*0.3);
+  }
+
+  algOtherFormat += phaseList; 
+  algOtherFormat += kList; 
+  algOtherFormat += phaseCurveList; 
+
+  PvlObject photometricModel("PhotometricModel");
+  photometricModel.addGroup(algOtherFormat);
+
+  Pvl pvlOtherFormat;
+  pvlOtherFormat.addObject(photometricModel);
+  std::cout << pvlOtherFormat << std::endl << std::endl;
+
+  try {
+    PhotoModel *pm = PhotoModelFactory::Create(pvlOtherFormat);
+
+    std::vector<double>phaselist = pm->PhotoPhaseList();
+
+    std::cout << "Test phase=0.0, incidence=0.0, emission=0.0 ..." <<
+              std::endl;
+    std::cout << "Albedo = " << pm->CalcSurfAlbedo(0.0, 0.0, 0.0) <<
+              std::endl;
+    std::cout << "Test phase=38.0, incidence=11.0, emission=20.0 ..." <<
+              std::endl;
+    std::cout << "Albedo = " << pm->CalcSurfAlbedo(38.0, 11.0, 20.0) <<
+              std::endl;
+    std::cout << "Test phase=65.0, incidence=45.0, emission=30.0 ..." <<
+              std::endl;
+    std::cout << "Albedo = " << pm->CalcSurfAlbedo(65.0, 45.0, 30.0) <<
+              std::endl;
+    std::cout << "Test phase=127.0, incidence=52.0, emission=33.0 ..." <<
+              std::endl;
+    std::cout << "Albedo = " << pm->CalcSurfAlbedo(127.0, 52.0, 33.0) <<
+              std::endl;
+    std::cout << "Test phase=180.0, incidence=90.0, emission=90.0 ..." <<
+              std::endl;
+    std::cout << "Albedo = " << pm->CalcSurfAlbedo(180.0, 90.0, 90.0) <<
+              std::endl << std::endl;
+  }
+  catch(IException &e) {
+    e.print();
+  }
+
   return 0;
 }