Lro lidar infrastructure updated to fix ambiguity with global variabl…

…e proj and merge of dev into branch (#3145)

* Updated the cmake version to 3.10

* Adding configurations for gtest

* Tweaking things for gtest

* Got gtest working and made a small example test

* Updated the cmake version to be 3.10 or greater

* Added test file discovery support and seperated the main into another file

* Added more tests for FileName

* Updated with the new testing guidelines and added new tests.

* Added gmock

* PixelTest (#536)

* initial Pixel test

* Add more test cases for Pixel

* testing parameterization in Pixel test

* testing function parameterization

* parameterize static vs object methods

* basic PixelTests implementation

* clean up and more static tests

* update PixelTests with float/dbl expects

* Refactored stats to a functions

* Modified to have cubeit remove mosaic pixel tracking info from labels. Fixes #5533

* Update cubeit.xml

Fixed a typo

* Fixes conda channels in Jenkinsfile & adds a MacOS node (#633)

* Merged dev and cleaned up header conflicts

* Update for #619.

* Fix libtiff dependency (#636) (#644)

* Upgrade libtiff to 4.0.10 (#636)

* Switch libtiff to 4.0.9 or higher to remove geotiff conflict

* Moved ISIS3 conda-build recipe from ISIS3_deps repository (#650)

* Fixed warning in Pixel unit tests

* Removing build numbers from external libraries (#660)

* Moved ISIS3 conda-build recipe from ISIS3_deps repository

* Un-pinned non-astro build numbers

* Removing build numbers from external libraries in the environment and meta.yeml files

* Final merging

* Added pixel type attribute to the output image of program shadow. Fixes #5187 (#659)

* Removed bolding of some text to decrease distraction.

* Fixed some typos.

* Reworded documentation.

* Added section for Environment and PreferemcesSetup in the Getting Started Section. (#663)

* Updated .gitmodules to use https rather than ssh (#673)

* Added build type release to conda recipe (#676)

* Updates README with Discourse (#690)

* Updates README with Discourse

* Update README.md

* Update README.md

* Added fix to Spice Server to accept clients with version nums >=3.5.*.* (#780)

* Fixed error when trying to export a compressed image using pds2hideal. Fixes #5525. (#2059)

* Added capability to export a compressed image with tables missing RECORD_BYTES keyword. Added test for compressed image.

* Changed names of test output cubes.

* Adding explanatory comments to the meta.yaml file (#2358)

* Adding explanatory comments to the recipes/meta.yaml

* Replacing accidentally erased line

* Added option to sort the output for consistent order in testing and added a test case

* Cleaned up commented out lines in LidarData.h and .cpp

* Added additional documentation for LidarData, LidarControlPoint, and lrolola2isis

* Multisegment DSK support for Bullet engine (#2791)

* Merged multisegment DSKs for Bullet

* basic tests

* removed original tests

* Minor updates to download sizes and some text. (#2790)

* Removed debug lines from LidarData.cpp and old comments from the lrolola2isis twoImage test

* Added an additional comment about the Test format to LidarData.cpp

* Phocube will export RA and declination planes even if the point is not on the planet. Fixes #4446 (#657)

* Made it so that RA and Dec are added last.

* Updated code to be up to standards.

* Added RA and dec test.

* Updated history comment.

* Renamed test.

* Fixed typo in documentation

* Refactored code so that RA and dec are placed in the correct bands instead of moving them to the last two bands.

* Updated documentation, test now checks cube label.

* Fixed SummingMode keyword being set in tgocassis2isis  (#2847)

* Adding Expanded keyword to cassis label and modifying SummingMode keyword

* Updating the window count value

* Adding capacity to handle imports without Expanded tag

* Setting tgocassismos to have tracking turned-on (#2856)

* Adding parameter "tracking=true" to tgocassismos call to automos

* Adding documentation

* Fixing indentation in documentation

* Updates to tgocassisrdrgen and ProcessExportPds4 to add content to exported CaSSIS Label. (#2858)

* Add 32-bit ISIS Special Pixel Constants to ProcessExportPds4

* Add ability to set title and version id in exported PDS4 produce in tgocassisrdrgen and ProcessExportPds4 API

* Fix bug that occurs when exporting mosaics with Archive groups and fixed min/max lat/lon to east/west bounding box positive east flip bug

* Added docs.

* Update schema to most recent versions and comment-out schema that isn't used (temporarily) in tgocassisrdrgen.

* Adds Issue Templates to Issues (#664)

* Adds issue templates

* Verbage update

* Updates issue template for questions (#3131)

Removed a newline in the header that I believe was causing the automatic template detection to fail.

* Added gtest for ID and split TestUtilities into a cpp and h file to fix duplicate symbol error when building. (#2824)

Code reviewed and tested

* tgocassisrdrgen exported label re-order.  (#3135)

* Add 32-bit ISIS Special Pixel Constants to ProcessExportPds4

* Add ability to set title and version id in exported PDS4 produce in tgocassisrdrgen and ProcessExportPds4 API

* Fix bug that occurs when exporting mosaics with Archive groups and fixed min/max lat/lon to east/west bounding box positive east flip bug

* Added docs.

* Update schema to most recent versions and comment-out schema that isn't used (temporarily) in tgocassisrdrgen.

* Added reorder function to ProcessExportPds4 to reorder xml files generated in the wrong order for PDS4 and added cassis-specific schema

* Update label generated by tgocassisrdrgen from additional feedback (#3137)

* Add 32-bit ISIS Special Pixel Constants to ProcessExportPds4

* Add ability to set title and version id in exported PDS4 produce in tgocassisrdrgen and ProcessExportPds4 API

* Fix bug that occurs when exporting mosaics with Archive groups and fixed min/max lat/lon to east/west bounding box positive east flip bug

* Added docs.

* Update schema to most recent versions and comment-out schema that isn't used (temporarily) in tgocassisrdrgen.

* Added reorder function to ProcessExportPds4 to reorder xml files generated in the wrong order for PDS4 and added cassis-specific schema

* Add StopTime to tgocassismos's Mosaic PVL group, as it is required for PDS4 export. Also, fix time formatting and east_azimuth units

* Remove comment

* Changed global variable proj back to projection to avoid build ambiguity errors with the std::proj

.github/ISSUE_TEMPLATE/1_Bug_report.md

@@ -0,0 +1,19 @@
+---
+name: 🐛 Bug Report
+about: Report errors and problems
+
+---
+
+**ISIS version(s) affected**: x.y.z
+
+**Description**  
+<!-- A clear and concise description of the problem. -->
+
+**How to reproduce**  
+<!-- Code and/or config needed to reproduce the problem. -->
+
+**Possible Solution**  
+<!--- Optional: only if you have suggestions on a fix/reason for the bug -->
+
+**Additional context**  
+<!-- Optional: any other context about the problem: log messages, screenshots, etc. -->

.github/ISSUE_TEMPLATE/2_Feature_request.md

@@ -0,0 +1,13 @@
+---
+name: 🚀 Feature Request
+about: RFC and ideas for new features and improvements
+
+---
+
+**Description**  
+<!-- A clear and concise description of the new feature. -->
+
+**Example**  
+<!-- A simple example of the new feature in action (include code, links to necessary data, etc.)
+     If the new feature changes an existing feature, include a simple before/after comparison. -->
+

.github/ISSUE_TEMPLATE/3_Support_question.md

@@ -0,0 +1,11 @@
+---
+name: ⛔ Support Question
+about: See https://astrodiscuss.usgs.gov for questions about using ISIS3 and other Astrogeology Science Center software.
+
+---
+
+We use GitHub issues only to discuss about ISIS3 bugs and new features. For
+questions about using ISIS3 or other ASC software, please use
+any of the support alternatives: https://astrodiscuss.usgs.gov or https://gitter.im/USGS-Astrogeology/IAA
+
+Thanks!

.github/ISSUE_TEMPLATE/4_Documentation_issue.md

@@ -0,0 +1,13 @@
+---
+name: ⛔ Documentation Issue
+about: Report issues or problems with documentation.
+
+---
+
+**Description**
+<!-- A clear and concise description of the problem. -->
+
+**Suggested Edit**
+<!--- Optional: only if you have suggestions on a fix for the documentation -->
+
+Thanks!

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

@@ -410,7 +410,7 @@ void phocube(Buffer &out) {
         }
         if (latitude) {
           if (noCamera) {
-            out[index] = proj->UniversalLatitude();
+            out[index] = projection->UniversalLatitude();
           }
           else {
             out[index] = cam->UniversalLatitude();
@@ -419,7 +419,7 @@ void phocube(Buffer &out) {
         }
         if (longitude) {
           if (noCamera) {
-            out[index] = proj->UniversalLongitude();
+            out[index] = projection->UniversalLongitude();
           }
           else {
             out[index] = cam->UniversalLongitude();
@@ -428,7 +428,7 @@ void phocube(Buffer &out) {
         }
         if (pixelResolution) {
           if (noCamera) {
-            out[index] = proj->Resolution();
+            out[index] = projection->Resolution();
           }
           else {
             out[index] = cam->PixelResolution();

isis/src/base/apps/phocube/phocube.xml

@@ -305,6 +305,11 @@ xsi:noNamespaceSchemaLocation=
     <change name="Kaitlyn Lee" date="2019-02-15">
       Allowed RA and DEC to be exported regardless if the pixel is off body. Fixes #4446.
     </change>
+    <change name="Debbie A. Cook" date="2019-03-06">
+      Changed global variable name proj to projection, as Jesse Maple had done for the 
+      Piecewise branch, due to a conflict with the std complex library and includes used in 
+      piecewise branch.  References #5343.
+    </change>
   </history>
 
   <category>

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

@@ -235,7 +235,6 @@ namespace Isis {
             QString timeValue = stopTime.text();
             PvlToXmlTranslationManager::resetElementValue(stopTime, timeValue + "Z");
           }
-
         }
 
         QDomElement obsSysNode = obsAreaNode.firstChildElement("Observing_System");
@@ -277,26 +276,116 @@ namespace Isis {
       // move target to just below Observing_System. 
       QDomElement targetIdNode = obsAreaNode.firstChildElement("Target_Identification");
       obsAreaNode.insertAfter(targetIdNode, obsAreaNode.firstChildElement("Observing_System"));
-
     }
     else if (inputLabel->findObject("IsisCube").hasGroup("Mapping")) {
 
       translationFileName = "$base/translations/pds4ExportTargetFromMapping.trn"; 
       PvlToXmlTranslationManager targXlator(*inputLabel, translationFileName.expanded());
       targXlator.Auto(*m_domDoc);
-
     }
     else {
       throw IException(IException::Unknown, "Unable to find a target in input cube.", _FILEINFO_);
     }
   }
 
 
+ /**
+   * This method reorders the existing m_domDoc to follow PDS4 standards and fixes time formatting
+   * if needed.
+   */
+  void ProcessExportPds4::reorder() {
+      QDomElement obsAreaNode = m_domDoc->documentElement().firstChildElement("Observation_Area");
+      if ( !obsAreaNode.isNull() ) {
+
+        // fix times
+        QDomElement timeNode = obsAreaNode.firstChildElement("Time_Coordinates");
+        if (!timeNode.isNull()) {
+          QDomElement startTime = timeNode.firstChildElement("start_date_time");
+          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"
+            << "Discipline_Area"
+            << "geom:Geometry"
+            << "geom:Geometry_Orbiter"
+            << "geom:geometry_reference_time_utc";
+
+          QDomElement baseElement = m_domDoc->documentElement();
+          QDomElement geomRefTime = getElement(xmlPath, baseElement);
+          if (geomRefTime.text() == "") {
+            geomRefTime.setAttribute("xsi:nil", "true");
+          }
+          else {
+            QString timeValue = geomRefTime.text();
+            PvlToXmlTranslationManager::resetElementValue(geomRefTime, timeValue + "Z");
+          }
+        xmlPath.clear();
+          xmlPath << "Product_Observational"
+            << "Observation_Area"
+            << "Discipline_Area"
+            << "geom:Geometry"
+            << "geom:Image_Display_Geometry"
+            << "geom:Object_Orientation_North_East"
+            << "geom:east_azimuth";
+          QDomElement eastAzimuth = getElement(xmlPath, baseElement);
+          if (eastAzimuth.text() != "") {
+            PvlToXmlTranslationManager::resetElementValue(eastAzimuth, eastAzimuth.text(), "deg");
+          }
+        }
+
+        QDomElement investigationAreaNode = obsAreaNode.firstChildElement("Investigation_Area");
+        obsAreaNode.insertAfter(investigationAreaNode, obsAreaNode.firstChildElement("Time_Coordinates"));
+
+        QDomElement obsSystemNode = obsAreaNode.firstChildElement("Observing_System");
+        obsAreaNode.insertAfter(obsSystemNode, obsAreaNode.firstChildElement("Investigation_Area"));
+
+        QDomElement targetIdNode = obsAreaNode.firstChildElement("Target_Identification");
+        obsAreaNode.insertAfter(targetIdNode, obsAreaNode.firstChildElement("Observing_System"));
+
+        QDomElement missionAreaNode = obsAreaNode.firstChildElement("Mission_Area");
+        obsAreaNode.insertAfter(missionAreaNode, obsAreaNode.firstChildElement("Target_Identification"));
+
+        QDomElement disciplineAreaNode = obsAreaNode.firstChildElement("Discipline_Area");
+        obsAreaNode.insertAfter(disciplineAreaNode, obsAreaNode.firstChildElement("Mission_Area"));
+      }
+
+      QDomElement identificationAreaNode = m_domDoc->documentElement().firstChildElement("Identification_Area");
+      if ( !identificationAreaNode.isNull() ) {
+        QDomElement aliasListNode = identificationAreaNode.firstChildElement("Alias_List");
+        identificationAreaNode.insertAfter(aliasListNode, identificationAreaNode.firstChildElement("product_class"));
+      }
+
+      QDomElement fileAreaObservationalNode = m_domDoc->documentElement().firstChildElement("File_Area_Observational");
+      QDomElement array2DImageNode = fileAreaObservationalNode.firstChildElement("Array_2D_Image");
+      if ( !array2DImageNode.isNull() ) {
+        QDomElement descriptionNode = array2DImageNode.firstChildElement("description");
+        array2DImageNode.insertAfter(descriptionNode, array2DImageNode.firstChildElement("axis_index_order"));
+      }
+  }
+
   /**
    * Allows mission specific programs to set logical_identifier 
    * required for PDS4 labels. This value is added to the xml file 
    * by the identificationArea() method. 
    *  
+   * The input value will be converted to all-lowercase if not already 
+   * in line with PDS4 requirements.  
+   *  
    * The input string should be colon separated string with 6 
    * identifiers: 
    *  
@@ -318,7 +407,25 @@ namespace Isis {
    *            compliant labels.
    */
   void ProcessExportPds4::setLogicalId(QString lid) {
-    m_lid = lid;
+    m_lid = lid.toLower();
+  }
+
+
+  /**
+   * Allows mission specific programs to set version_id
+   * required for PDS4 labels. This value is added to the xml file 
+   * by the identificationArea() method. 
+   *  
+   * The input string should be colon separated string with 6 
+   * identifiers: 
+   *  
+   * @author 2019-03-01 Kristin Berry
+   * 
+   * @param versiondId The version_id value required for PDS4 
+   *            compliant labels.
+   */
+   void ProcessExportPds4::setVersionId(QString versionId) {
+    m_versionId = versionId;
   }
 
 

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

@@ -118,7 +118,7 @@ namespace Isis {
 
       static void translateUnits(QDomDocument &label,
                                  QString transMapFile = "$base/translations/pds4ExportUnits.pvl");
-
+      void reorder();
       void addSchema(QString sch, QString xsd, QString xmlns, QString xmlnsURI) ;
     protected:
       void identificationArea();

isis/src/tgo/apps/tgocassismos/main.cpp

@@ -13,7 +13,7 @@
 #include "ProgramLauncher.h"
 #include "TProjection.h"
 #include "UserInterface.h"
-
+#include "iTime.h"
 
 using namespace std;
 using namespace Isis;
@@ -170,6 +170,8 @@ void IsisMain() {
     QString instrumentId;
     QString spacecraftName;
     QString observationId;
+    QString stopTime;
+    QString exposureDuration;
 
     for (int i = 0; i < (int)cubeList.size(); i++) {
       // himos used original label here.
@@ -184,17 +186,27 @@ void IsisMain() {
         observationId =  archiveGroup["ObservationId"][0];
         startTime =      instGroup["StartTime"][0];
         startClock =     instGroup["SpacecraftClockStartCount"][0];
+        stopTime   =     instGroup["StartTime"][0]; 
+        exposureDuration  = instGroup["ExposureDuration"][0]; 
       }
       else {
-        QString testStartTime = instGroup["StartTime"][0];
-        if (testStartTime < startTime) {
-          startTime = testStartTime;
+        iTime testStartTime = iTime(instGroup["StartTime"][0]);
+        iTime testStopTime = iTime(instGroup["StartTime"][0]);
+        if (testStartTime < iTime(startTime)) {
+          startTime = testStartTime.UTC();
           startClock = instGroup["SpacecraftClockStartCount"][0];
         }
+        if (testStopTime > iTime(stopTime)) {
+          stopTime = testStopTime.UTC();
+        }
       }
     }
 
-    // Get the blob of original labels from first image in list
+   iTime stopTimeValue = iTime(stopTime);
+   stopTimeValue = stopTimeValue + exposureDuration.toDouble(); 
+   stopTime = stopTimeValue.UTC(); 
+
+   // Get the blob of original labels from first image in list
    // Pvl *org = cubeList[0]->label();
 
     //close all cubes
@@ -230,6 +242,7 @@ void IsisMain() {
     mos += PvlKeyword("InstrumentId", instrumentId);
     mos += PvlKeyword("ObservationId ", observationId);
     mos += PvlKeyword("StartTime ", startTime);
+    mos += PvlKeyword("StopTime ", stopTime);
     mos += PvlKeyword("SpacecraftClockStartCount ", startClock);
     mos += PvlKeyword("IncidenceAngle ", toString(incidenceAngle), "degrees");
     mos += PvlKeyword("EmissionAngle ", toString(emissionAngle), "degrees");

isis/src/tgo/apps/tgocassismos/tgocassismos.xml

@@ -54,6 +54,10 @@
       Added the "tracking=true" parameter to tgocassismos' call to automos resulting in automatic
       tracking cube creation. 
     </change>
+    <change name="Kristin Berry" date="2019-03-01">
+      Added the StopTime keyword to the output Mosaic PVL group, as stop_date_time is required for 
+      PDS4 export. 
+    </change>
   </history>
 
   <groups>

isis/src/tgo/apps/tgocassisrdrgen/main.cpp

@@ -109,6 +109,10 @@ void IsisMain() {
                     "xmlns",
                     "http://psa.esa.int/psa/em16/cas/v1");*/
 
+  process.addSchema("CASSIS_1010.sch", 
+                    "CASSIS_1010.xsd",
+                    "xmlns:cassis",
+                    "local");
   // Add geometry schema for mosaics
   if (label->findObject("IsisCube").hasGroup("Mosaic")) {
     process.addSchema("PDS4_GEOM_1B00_1610.sch", 
@@ -117,7 +121,6 @@ void IsisMain() {
                       "https://pds.jpl.nasa.gov/datastandards/schema/released/geom/v1");
   }
 
-
  /*
   * Add additional pds label data here
   */
@@ -135,6 +138,7 @@ void IsisMain() {
   cubeLab.Auto(pdsLabel);
 
   ProcessExportPds4::translateUnits(pdsLabel);
+  process.reorder(); 
 
   QString outFile = ui.GetFileName("TO");