Adds initial directory structure for appdata in source and update fro…

…m dev (#3724) * Update meta.yaml to rename conda package to isis from isis3 * Used CK quality for PCK selection in spiceinit (#3716) * Changed PCK to use CK quality in spiceinit * Added spiceinit history for change * 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]> * Updated kaguyatc2isis to allow ingestion of data provided by JAXA online archive (#3713) * Updated to allow ingestion of data provided by JAXA online archive * Listed SLN-L-TC-5-MORNING-MAP-V4.0 as a supported format. * Added tests + testing data * Replaced several label parsing tests with cube attribute tests. * Fixes ddd2isis to support updated uvflat files (#3719) * Fixes ddd2isis to support updated uvflat files * Added history comment * Changed version numbers for 4.1 RC (#3722) * Add directory structure for appdata in source Co-authored-by: Jesse Mapel <[email protected]> Co-authored-by: Stuart Sides <[email protected]> Co-authored-by: AustinSanders <[email protected]> Co-authored-by: acpaquette <[email protected]>
DOI-USGS · Mar 3, 2020 · ce5cd2f · ce5cd2f
1 parent 79e652e
commit ce5cd2f
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diff --git a/isis/CMakeLists.txt b/isis/CMakeLists.txt
@@ -33,7 +33,7 @@ set(PACKAGE            "ISIS")
 set(PACKAGE_NAME       "USGS ISIS")
 
 # Version number
-set(VERSION            "4.0.0")
+set(VERSION            "4.1.0")
 set(PACKAGE_VERSION    ${VERSION})
 
 # Full name and version number

diff --git a/isis/appdata/autoreg/DELETEME.txt b/isis/appdata/autoreg/DELETEME.txt
diff --git a/isis/appdata/images/icons/DELETEME.txt b/isis/appdata/images/icons/DELETEME.txt
diff --git a/isis/appdata/images/targets/DELETEME.txt b/isis/appdata/images/targets/DELETEME.txt
diff --git a/isis/appdata/labels/DELETEME.txt b/isis/appdata/labels/DELETEME.txt
diff --git a/isis/appdata/maps/DELETEME.txt b/isis/appdata/maps/DELETEME.txt
diff --git a/isis/appdata/serialnumbers/DELETEME.txt b/isis/appdata/serialnumbers/DELETEME.txt
diff --git a/isis/src/base/apps/ddd2isis/ddd2isis.xml b/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>

diff --git a/isis/src/base/apps/ddd2isis/main.cpp b/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");

diff --git a/isis/src/base/apps/ddd2isis/tsts/badBandBit/Makefile b/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
diff --git a/isis/src/base/apps/spiceinit/spiceinit.cpp b/isis/src/base/apps/spiceinit/spiceinit.cpp
@@ -23,7 +23,7 @@
 
 using namespace std;
 
-namespace Isis { 
+namespace Isis {
 
   void getUserEnteredKernel(UserInterface &ui, const QString &param, Kernel &kernel);
   bool tryKernels(Cube *icube, Process &p, UserInterface &ui, Pvl *log,
@@ -42,16 +42,16 @@ namespace Isis {
    * @param ui The Application UI
    * @param(out) log The Pvl that attempted kernel sets will be logged to
    */
-  void spiceinit(UserInterface &ui, Pvl *log) { 
+  void spiceinit(UserInterface &ui, Pvl *log) {
     // Open the input cube
     Process p;
-    
+
     CubeAttributeInput cai;
     Cube *icube = p.SetInputCube(ui.GetFileName("FROM"), cai, ReadWrite);
     spiceinit(icube, ui, log);
     p.EndProcess();
   }
- 
+
 
   /**
    * Spiceinit a Cube
@@ -76,7 +76,7 @@ namespace Isis {
       QString msg = "At least one SPK quality must be selected";
       throw IException(IException::User, msg, _FILEINFO_);
     }
-    
+
     // Make sure it is not projected
     Projection *proj = NULL;
     try {
@@ -92,7 +92,7 @@ namespace Isis {
     }
 
     Pvl lab = *icube->label();
-    
+
     // if cube has existing polygon delete it
     if (icube->label()->hasObject("Polygon")) {
       icube->label()->deleteObject("Polygon");
@@ -144,15 +144,15 @@ namespace Isis {
       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);
       iak       = baseKernels.instrumentAddendum(lab);
       fk        = ckKernels.frame(lab);
       ck        = ckKernels.spacecraftPointing(lab);
       spk       = spkKernels.spacecraftPosition(lab);
-      
+
       if (ui.GetBoolean("CKNADIR")) {
         // Only add nadir if no spacecraft pointing found, so we will set (priority) type to 0.
         QStringList nadirCk;
@@ -198,7 +198,7 @@ namespace Isis {
                          _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();
@@ -209,10 +209,10 @@ namespace Isis {
         emptyKernelQueue.push(Kernel());
         ck.push_back(emptyKernelQueue);
       }
-      
+
       // 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;
 
@@ -236,13 +236,13 @@ namespace Isis {
               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();
@@ -267,14 +267,14 @@ namespace Isis {
   }
 
   /**
-   * 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(UserInterface &ui, const QString &param, Kernel &kernel) {
     if (ui.WasEntered(param)) {
@@ -395,7 +395,7 @@ namespace Isis {
     // Get rid of old keywords from previously inited cubes
     if (currentKernels.hasKeyword("Source"))
       currentKernels.deleteKeyword("Source");
-    
+
     if (currentKernels.hasKeyword("SpacecraftPointing"))
       currentKernels.deleteKeyword("SpacecraftPointing");
 
@@ -450,7 +450,7 @@ namespace Isis {
       try {
         cam = icube->camera();
         currentKernels = icube->group("Kernels");
-        
+
         PvlKeyword source("Source");
 
         if (cam->isUsingAle()) {
@@ -461,11 +461,11 @@ namespace Isis {
         }
 
         currentKernels += source;
-        icube->putGroup(currentKernels);   
+        icube->putGroup(currentKernels);
         if (log){
           log->addGroup(currentKernels);
-        } 
-          
+        }
+
       }
       catch(IException &e) {
         Pvl errPvl = e.toPvl();
@@ -665,7 +665,7 @@ namespace Isis {
         continue;
       }
     }
-    
+
     if (log) {
       log->addGroup(logGrp);
     }

diff --git a/isis/src/base/apps/spiceinit/spiceinit.xml b/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>

diff --git a/isis/src/base/objs/Stretch/Stretch.cpp b/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