Port changes from Dev to 3.X for 3.11 release (#3723)

* Fix for QMOS not updating lat/lon ranges correctly.  (#3714)

* qqqqqqmoooooosssssss

* added doc string

* Hand ported #3716 from dev to 3.10

* Adds the ability to save and restore a greyscale stretch to/from a Cube (#3717)

* Update meta.yaml to rename conda package to isis from isis3

* Initial stretch attempt

* Now will write a single stretch with a name and type to the cube

* Stretch updated to inherit from Blob, re-loading a saved stretch works but only if Linear right now

* Clean up Stretch class

* Completely move stretchTypes into stretch class, and some minor cleanup

* Fixed combo-box not updating bug and more cleanup

* Further cleanup of propagated earlier changes with types and names being removed from unnecessary classes

* Removed added unneeded member variables from StretchType

* Cleanup StretchTool class

* Update enter-text dialogs to drop down selection options

* Wrapped some long strings

* Initial commit to address most of review comments

* Removed buttons in case of RGB stretch and add a 'Color' PvlKeyword to Stretch output

Co-authored-by: Stuart Sides <[email protected]>

* Pinned opencv

* Ported #3713 to ISIS3

* Fixes ddd2isis to support updated uvflat files (#3719)

* Fixes ddd2isis to support updated uvflat files

* Added history comment

* Ticked to 3.11_RC1

* changed kaguyatc2isis outputcube call

Co-authored-by: Kelvin Rodriguez <[email protected]>
Co-authored-by: Kristin <[email protected]>
Co-authored-by: Stuart Sides <[email protected]>
Co-authored-by: acpaquette <[email protected]>

environment.yml

@@ -38,7 +38,7 @@ dependencies:
   - ninja==1.7.2
   - conda-forge/label/gcc7::nn
   - openblas==0.2.19
-  - opencv
+  - opencv==3.2.0
   - openssl==1.0.2n
   - pcl==1.8.1
   - pip==9.0.1

environment_gcc4.yml

@@ -40,7 +40,7 @@ dependencies:
   - ninja==1.7.2
   - nn==1.86.0
   - openblas==0.2.19
-  - opencv
+  - opencv==3.2.0
   - openssl==1.0.2n
   - pcl==1.8.1
   - pip==9.0.1

isis/CMakeLists.txt

@@ -33,15 +33,15 @@ set(PACKAGE            "ISIS")
 set(PACKAGE_NAME       "USGS ISIS")
 
 # Version number
-set(VERSION            "3.10.0")
+set(VERSION            "3.11.0")
 set(PACKAGE_VERSION    ${VERSION})
 
 # Full name and version number
 set(PACKAGE_STRING     "${PACKAGE_NAME} ${VERSION}")
 
 # Other release information
 string(TIMESTAMP VERSION_DATE "%Y-%m-%d" UTC)
-set(RELEASE_STAGE             "stable") # (alpha, beta, stable)
+set(RELEASE_STAGE             "beta") # (alpha, beta, stable)
 
 # Define to the address where bug reports for this package should be sent.
 set(PACKAGE_BUGREPORT  "https://github.com/USGS-Astrogeology/ISIS3/issues")

isis/src/base/apps/ddd2isis/ddd2isis.xml

@@ -41,6 +41,10 @@
       bands. Removed the internal default of the output parameter set to None so
       that an output file is now requried. Fixes #703.
     </change>
+    <change name="Adam Paquette" date="2020-02-28">
+      Updated the dataTypes QMap with a new mapping (32, 4) to handle ingesting
+      the updated uvflat files from malin. Fixes #3715.
+    </change>
   </history>
 
   <category>

isis/src/base/apps/ddd2isis/main.cpp

@@ -100,6 +100,7 @@ void IsisMain() {
   dataTypes.insert(1450903360, 8);
   dataTypes.insert(8, 1);
   dataTypes.insert(16, 2);
+  dataTypes.insert(32, 4);
   dataTypes.insert(48, 2);
 
   // Read bytes 16-19 to get the bit type
@@ -130,6 +131,12 @@ void IsisMain() {
      nOffset = 1024;
   }
 
+  if (dataTypeBytes == 0) {
+    string msg = "The value totalBandBits [" + to_string(totalBandBits) + "] does not map " +
+                  "to any byte size in the dataTypes table.";
+    throw IException(IException::Programmer, msg, _FILEINFO_);
+  }
+
   fin.close();
 
   PvlGroup results("FileInfo");

isis/src/base/apps/ddd2isis/tsts/badBandBit/Makefile

@@ -0,0 +1,24 @@
+APPNAME = ddd2isis
+
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+	# TEST: Throws an error when trying to open the file
+	if [ `$(APPNAME) \
+                FROM=$(INPUT)/bad_flat.ddd \
+                TO=$(OUTPUT)/bad_flat.cub \
+                2> $(OUTPUT)/temp.txt > /dev/null` ]; \
+                then true; \
+                fi;
+	
+	# TEST: Throws an error when trying to read from a cub instead of ddd
+	if [ `$(APPNAME) \
+                FROM=$(INPUT)/bad_flat.cub \
+                TO=$(OUTPUT)/bad_flat.cub \
+                2>> $(OUTPUT)/temp.txt > /dev/null` ]; \
+                then true; \
+                fi;
+
+        # Removes input file path up until input
+	$(SED) 's+\[.*/input+[input+' $(OUTPUT)/temp.txt > $(OUTPUT)/errorTruth.txt;
+	$(RM) $(OUTPUT)/temp.txt

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

@@ -121,7 +121,7 @@ void IsisMain() {
     Kernel lk, pck, targetSpk, fk, ik, sclk, spk, iak, dem, exk;
     QList< priority_queue<Kernel> > ck;
     lk        = baseKernels.leapSecond(lab);
-    pck       = baseKernels.targetAttitudeShape(lab);
+    pck       = ckKernels.targetAttitudeShape(lab);
     targetSpk = baseKernels.targetPosition(lab);
     ik        = baseKernels.instrument(lab);
     sclk      = baseKernels.spacecraftClock(lab);
@@ -175,7 +175,7 @@ void IsisMain() {
                        _FILEINFO_);
     }
     else if (ui.WasEntered("CK")) {
-      // if user entered ck 
+      // if user entered ck
       // empty ck queue list found in system
       while (ck.size()) {
         ck.pop_back();
@@ -189,7 +189,7 @@ void IsisMain() {
 
     // while the first queue is not empty, loop through it until tryKernels() succeeds
     while (ck.at(0).size() != 0 && !kernelSuccess) {
-      // create an empty kernel 
+      // create an empty kernel
       Kernel realCkKernel;
       QStringList ckKernelList;
 
@@ -213,13 +213,13 @@ void IsisMain() {
             Kernel topPriority = ck.at(i).top();
             ckKernelList.append(topPriority.kernels());
             // set the type to equal the type of the to priority of the first
-            //queue 
-            realCkKernel.setType(topPriority.type()); 
+            //queue
+            realCkKernel.setType(topPriority.type());
           }
         }
 
       }
-      // pop the top priority ck off only the first queue so that the next 
+      // pop the top priority ck off only the first queue so that the next
       // iteration will test the next highest priority of the first queue with
       // the top priority of each of the other queues.
       ck[0].pop();
@@ -244,14 +244,14 @@ void IsisMain() {
 }
 
 /**
- * If the user entered the parameter param, then kernel is replaced by the 
+ * If the user entered the parameter param, then kernel is replaced by the
  * user's values and quality is reset to 0. Otherwise, the kernels loaded by the
  * KernelDb class will be kept.
  *
  * @param param Name of the kernel input parameter
- *  
- * @param kernel Kernel object to be overwritten if the specified user parameter 
- *               was entered. 
+ *
+ * @param kernel Kernel object to be overwritten if the specified user parameter
+ *               was entered.
  */
 void getUserEnteredKernel(const QString &param, Kernel &kernel) {
   UserInterface &ui = Application::GetUserInterface();
@@ -264,10 +264,10 @@ void getUserEnteredKernel(const QString &param, Kernel &kernel) {
   }
 }
 
-/** 
+/**
   * This fuction now also adds any ShapeModel information specified in a
   * preferences file to the Kernels group.
- */  
+ */
 bool tryKernels(Cube *icube, Process &p,
                 Kernel lk, Kernel pck,
                 Kernel targetSpk, Kernel ck,

isis/src/base/apps/spiceinit/spiceinit.xml

@@ -90,9 +90,9 @@
        not have their paths expanded.  This is to allow variables like $msg/ to work correctly.
     </p>
     <p>
-      The spiceinit program will also add the RayTraceEngine, OnError, and Tolerance keywords to the Kernels 
-      group if specified in the IsisPreferences file. If included, these keywords specify the ray-tracing engine to use and how to use it for shapemodels. 
-      Please see the IsisPreferences file for more details. 
+      The spiceinit program will also add the RayTraceEngine, OnError, and Tolerance keywords to the Kernels
+      group if specified in the IsisPreferences file. If included, these keywords specify the ray-tracing engine to use and how to use it for shapemodels.
+      Please see the IsisPreferences file for more details.
 
     </p>
     <p><b>Troubleshooting:</b> If spiceinit is failing with the error
@@ -279,17 +279,22 @@
     </change>
     <change name="Kristin Berry" date="2017-06-06">
       Updated spiceinit to retain ShapeModel-related keywords set by the ShapeModelFactory and add them to the kernel
-      group. Like other keywords in the kernels group, if they are present at the beginning of a spiceinit run (if we are re-spiceiniting) 
-      they are removed. 
+      group. Like other keywords in the kernels group, if they are present at the beginning of a spiceinit run (if we are re-spiceiniting)
+      they are removed.
     </change>
     <change name="Kristin Berry" date="2017-08-06">
-      Updated spiceinit to remove code dealing with the CubeSupported Pvl Keyword, from the ShapeModel group in the IsisPreferences file, 
+      Updated spiceinit to remove code dealing with the CubeSupported Pvl Keyword, from the ShapeModel group in the IsisPreferences file,
       which has been removed.
     </change>
     <change name="Christopher Combs" date="2018-01-11">
       Made change to camera construction error throw for better reporting on uninstantiated cameras.
       Fixes #5163.
     </change>
+    <change name="Jesse Mapel" date="2020-02-26">
+      Changed PCK selection to use the same qualities as CK so that target body parameters
+      derived from bundle adjustment can be used alongside CKs derived from bundle adjustment.
+      Fixes #3669.
+    </change>
   </history>
 
   <oldName>

isis/src/base/objs/Stretch/Stretch.cpp

@@ -38,7 +38,7 @@ namespace Isis {
    * Constructs a Stretch object with default mapping of special pixel values to
    * themselves.
    */
-  Stretch::Stretch() {
+  Stretch::Stretch() : Blob("ImageStretch", "Stretch") {
     p_null = Isis::NULL8;
     p_lis = Isis::LOW_INSTR_SAT8;
     p_lrs = Isis::LOW_REPR_SAT8;
@@ -47,8 +47,29 @@ namespace Isis {
     p_minimum = p_lrs;
     p_maximum = p_hrs;
     p_pairs = 0;
+    p_type = "None";
   }
 
+
+  /**
+   * Constructs a Stretch object with default mapping of special pixel values to
+   * themselves and a provided name. 
+   *  
+   * @param name Name to use for Stretch 
+   */
+  Stretch::Stretch(QString name) : Blob(name, "Stretch") {
+    p_null = Isis::NULL8;
+    p_lis = Isis::LOW_INSTR_SAT8;
+    p_lrs = Isis::LOW_REPR_SAT8;
+    p_his = Isis::HIGH_INSTR_SAT8;
+    p_hrs = Isis::HIGH_REPR_SAT8;
+    p_minimum = p_lrs;
+    p_maximum = p_hrs;
+    p_pairs = 0;
+    p_type = "None";
+  }
+
+
   /**
    * Adds a stretch pair to the list of pairs. Note that all input pairs must be
    * in ascending order.
@@ -410,6 +431,89 @@ namespace Isis {
     this->p_output = other.p_output;
   }
 
+
+  /**
+   * Read saved Stretch data from a Cube into this object. 
+   *  
+   * This is called by Blob::Read() and is the actual data reading function 
+   * ultimately called when running something like cube->read(stretch);  
+   * 
+   * @param is input stream containing the saved Stretch information
+   */
+  void Stretch::ReadData(std::istream &is) {
+    // Set the Stretch Type
+     p_type = p_blobPvl["StretchType"][0];
+
+     // Read in the Stretch Pairs
+     streampos sbyte = p_startByte - 1;
+     is.seekg(sbyte, std::ios::beg);
+     if (!is.good()) {
+       QString msg = "Error preparing to read data from " + p_type +
+                    " [" + p_blobName + "]";
+       throw IException(IException::Io, msg, _FILEINFO_);
+     }
+
+     char *buf = new char[p_nbytes+1];
+     memset(buf, 0, p_nbytes + 1);
+
+     is.read(buf, p_nbytes);
+
+     // Read buffer data into a QString so we can call Parse()
+     std::string stringFromBuffer(buf);
+     QString qStringFromBuffer = QString::fromStdString(stringFromBuffer);
+     Parse(qStringFromBuffer);
+
+     delete [] buf;
+
+     if (!is.good()) {
+       QString msg = "Error reading data from " + p_type + " [" +
+                    p_blobName + "]";
+       throw IException(IException::Io, msg, _FILEINFO_);
+     }
+   }
+
+
+  /**
+   * Get the Type of Stretch. This is only used by the AdvancedStretchTool.
+   * 
+   * @return QString Type of Stretch. 
+   */
+  QString Stretch::getType(){
+    return p_type;
+  }
+
+
+  /**
+   * Set the Type of Stretch. This is only used by the AdvancedStretchTool.
+   *  
+   * @param stretchType The type of stretch.  
+   */
+  void Stretch::setType(QString stretchType){
+    // check to see if valid input
+    p_type = stretchType;
+  }
+
+
+  /**
+   *  Initializes for writing stretch to cube blob
+   */
+  void Stretch::WriteInit() {
+    p_nbytes = Text().toStdString().size(); 
+  }
+
+
+  /**
+   * Writes the stretch information to a cube. 
+   *  
+   * This is called by Blob::write() and is ultimately the function 
+   * called when running something like cube->write(stretch);  
+   *  
+   * @param os output stream to write the stretch data to.
+   */
+  void Stretch::WriteData(std::fstream &os) {
+    os.write(Text().toStdString().c_str(), p_nbytes);
+  }
+
 } // end namespace isis
 
 

isis/src/base/objs/Stretch/Stretch.h

@@ -26,6 +26,7 @@
 #include <string>
 #include "Pvl.h"
 #include "Histogram.h"
+#include "Blob.h"
 
 namespace Isis {
   /**
@@ -67,9 +68,10 @@ namespace Isis {
    *               Created second Parse method for handling pairs where the
    *               input side is a perentage.  Fixed Input and Output getters
    *               to check both sides of boundry condition for valid data
-   *
+   *  @history 2020-02-27 Kristin Berry - Updated to inherit from Blob so Stretches can be
+   *               saved and restored from cubes. 
    */
-  class Stretch {
+  class Stretch : public Isis::Blob {
     private:
       std::vector<double> p_input;   //!< Array for input side of stretch pairs
       std::vector<double> p_output;  //!< Array for output side of stretch pairs
@@ -88,10 +90,13 @@ namespace Isis {
       double p_minimum; //!<By default this value is set to p_lrs
       double p_maximum; //!<By default this value is set to p_hrs
 
+      QString p_type; //! Type of stretch. This is only currently used in the AdvancedStretchTool.
+
       std::pair<double, double> NextPair(QString &pairs);
 
     public:
       Stretch();
+      Stretch(QString name);
 
       //! Destroys the Stretch object
       ~Stretch() {};
@@ -177,6 +182,9 @@ namespace Isis {
         return p_pairs;
       };
 
+      QString getType(); 
+      void setType(QString type); 
+
       double Input(const int index) const;
       double Output(const int index) const;
 
@@ -188,6 +196,11 @@ namespace Isis {
       };
 
       void CopyPairs(const Stretch &other);
+
+    protected:
+      void WriteInit();
+      void ReadData(std::istream &is);
+      void WriteData(std::fstream &os);
   };
 };