App Fixes For GeoTiffs

CHANGELOG.md

@@ -70,6 +70,7 @@ ctest FunctionalTestJigsawApollo to validate this output. [#5710](https://github
 - Changed 'jigsaw' attribute type to account for Linux compiler changes [#5904](https://github.com/DOI-USGS/ISIS3/pull/5904)
 - Updated GDAL to 3.12 and QT to 6.X [#5909](https://github.com/DOI-USGS/ISIS3/pull/5909)
 - Updated cmake configs to accommodate new cspice release [#5886](https://github.com/DOI-USGS/ISIS3/pull/5886)
+- Changed `PVL` class to read data from GDAL metadata directly [#5824](https://github.com/DOI-USGS/ISIS3/pull/5824)
 
 ### Fixed
 - Fixed Chandrayaan-2 TMC2 serial numbers by setting InstrumentId to CH2_TMC_FORE/NADIR/AFT based on the filename sensor [#5871](https://github.com/DOI-USGS/ISIS3/issues/5871)

isis/CMakeLists.txt

@@ -302,7 +302,7 @@ find_package(GSL       2.2.1   REQUIRED)
 find_package(HDF5      1.8.15  REQUIRED)
 find_package(Jama      125     REQUIRED)
 find_package(NN                REQUIRED)
-find_package(OpenCV    4.12.0  REQUIRED)
+find_package(OpenCV    4.9.0   REQUIRED CONFIG)
 find_package(PCL               REQUIRED)
 find_package(Protobuf          REQUIRED CONFIG)
 find_package(PROJ              REQUIRED CONFIG)
@@ -396,6 +396,9 @@ endforeach()
 # add target based linkages to ALLLIBS variable
 list(APPEND ALLLIBS pantor::inja sensorutilities protobuf::libprotobuf embree GDAL::GDAL Bullet::Bullet_double CSPICE::cspice)
 
+list(APPEND ALLLIBS ${OpenCV_LIBS})
+list(APPEND ALLINCDIRS ${OpenCV_INCLUDE_DIRS})
+
 # Sometimes we add the same lib more than once (especially with LIBDIRS)
 list(REMOVE_DUPLICATES ALLLIBDIRS)
 list(REMOVE_DUPLICATES ALLLIBS)

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

@@ -17,14 +17,7 @@ void IsisMain() {
   QString file = ui.GetCubeName("FROM");
 
   // Extract label from file
-  Pvl label;
-  try {
-    label = Pvl(file);
-  }
-  catch (...) {
-    Cube cube(file);
-    label = *cube.label();
-  }
+  Pvl label(file);
 
   // Output to file if entered
   if(ui.WasEntered("TO")) {

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

@@ -77,6 +77,12 @@ namespace Isis {
 
     raw += "  <label>\n";
     stringstream str;
+    // Force BandSequential format as a hack to avoid issues 
+    // opening/operating on GTiff formated data
+    PvlObject& core = cubeLabel.findObject("IsisCube").findObject("Core");
+    if (core.findKeyword("Format")[0] == "GTiff") {
+      core.findKeyword("Format") = "BandSequential";
+    }
     str << cubeLabel;
     raw += QString(QByteArray(str.str().c_str()).toHex().constData()) + "\n";
 

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

@@ -154,14 +154,7 @@ void helperButtonGetTableList() {
 
   UserInterface &ui = Application::GetUserInterface();
   QString currentFile = ui.GetCubeName("FROM");
-  Pvl label;
-  try {
-    label = Pvl(FileName(currentFile).expanded());
-  }
-  catch (...) {
-    Cube cube(FileName(currentFile).expanded());
-    label = *cube.label();
-  }
+  const Pvl label(FileName(currentFile).expanded());
 
   // Check to see if the "FILE" parameter has changed since last press
   if (currentFile != g_previousFile) {

isis/src/base/objs/Cube/Cube.cpp

@@ -499,7 +499,10 @@ namespace Isis {
         imageFile = imageFile.addExtension("cub");
       }
       else if (format() == Format::GTiff) {
-        imageFile = imageFile.addExtension("tiff");
+        if (imageFile.extension() != "tif" &&
+            imageFile.extension() != "tiff") {
+          imageFile = imageFile.addExtension("tif");
+        }
       }
       else {
         QString msg = "Unknown format type [" + toString(format()) + "]";
@@ -533,14 +536,15 @@ namespace Isis {
       core.addGroup(ptype);
     }
     else if (labelsAttached() == LabelAttachment::ExternalLabel) {
+      imageFile = imageFile.addExtension("ecub");
       if (!m_dataFileName) {
         if (format() == Bsq || format() == Tile) {
-          imageFile = imageFile.addExtension("cub");
+          imageFile = imageFile.setExtension("cub");
 
           Pvl dnLabel;
           PvlObject isiscube("IsisCube");
           PvlObject dnCore(core);
-          PvlKeyword fileFormat("Format", toString(format()));
+          PvlKeyword fileFormat("Format", CubeAttributeOutput::toString(format()));
 
           dnCore.addKeyword(fileFormat);
           dnCore.addGroup(dims);
@@ -552,13 +556,11 @@ namespace Isis {
           Cube dnCube;
           dnCube.fromLabel(imageFile, dnLabel, "rw");
           dnCube.close();
-
-          m_dataFileName = new FileName(imageFile);
         }
         else if (format() ==  Format::GTiff) {
-          imageFile = imageFile.setExtension("tiff");
-          m_dataFileName = new FileName(imageFile);
+          imageFile = imageFile.setExtension("tif");
         }
+        m_dataFileName = new FileName(imageFile);
 
         imageFile = imageFile.setExtension("ecub");
         FileName labelFileName(imageFile);
@@ -808,27 +810,26 @@ namespace Isis {
 
     QString msg = "Failed to open [" + cubeFileName + "]";
     IException exceptions(IException::Io, msg, _FILEINFO_);
-    if (!isOpen()) {
-      try {
-        openCube(cubeFileName, access);
-      }
-      catch (IException &e) {
-        cleanUp(false);
-        exceptions.append(e);
-      }
+
+    GDALDriverH hDriver = GDALIdentifyDriver(FileName(cubeFileName).expanded().toStdString().c_str(), nullptr);
+    bool openWithGdal = false;
+    if (hDriver != nullptr) {
+      GDALDriver* poDriver = (GDALDriver*)hDriver;
+      QString driverDescription = poDriver->GetDescription();
+      openWithGdal = (!driverDescription.contains("ISIS"));
     }
 
-    if (!isOpen()) {
-      try {
+    try{
+      if (openWithGdal) {
         openGdal(cubeFileName, access);
       }
-      catch(IException &e) {
-        cleanUp(false);
-        exceptions.append(e);
+      else {
+        openCube(cubeFileName, access);
       }
     }
-
-    if (!isOpen()) {
+    catch(IException &e) {
+      cleanUp(false);
+      exceptions.append(e);
       throw exceptions;
     }
 
@@ -942,7 +943,9 @@ namespace Isis {
           realDataFileLabel(), true);
     }
     else if (m_format == GTiff) {
-      m_dataFile->close();
+      if (m_dataFile) {
+        m_dataFile->close();
+      }
       m_geodataSet = GDALDataset::FromHandle(GDALOpen(m_dataFileName->expanded().toStdString().c_str(), eAccess));
       if (!m_geodataSet) {
         QString msg = "Opening GDALDataset from [" + m_dataFileName->name() + "] failed with access [" + QString::number(eAccess) +"]";
@@ -975,145 +978,8 @@ namespace Isis {
     m_dataFileName = new FileName(*m_labelFileName);
 
     initCoreFromGdal(m_labelFileName->expanded());
-    GDALDataset *dataset = GDALDataset::FromHandle(GDALOpen(m_dataFileName->expanded().toStdString().c_str(), GA_ReadOnly));
-    if (!dataset) {
-      QString msg = "Failed opening GDALDataset from [" + m_dataFileName->name() + "]";
-      cleanUp(false);
-      throw IException(IException::Programmer, msg, _FILEINFO_);
-    }
-
-    CPLStringList metadata = CPLStringList(dataset->GetMetadata("USGS"), false);
-
-    m_label = new Pvl();
-    if (metadata[0] != nullptr) {
-      for (int i = 0; i < metadata.size(); i++) {
-        const char *metadataItem = CPLParseNameValue(metadata[i], nullptr);
-        nlohmann::ordered_json metadataAsJson = nlohmann::ordered_json::parse(metadataItem);
-        Pvl pvl;
-        Pvl::readObject(pvl, metadataAsJson);
-        for (int i = 0; i < pvl.objects(); i++) {
-          m_label->addObject(pvl.object(i));
-        }
-        for (int i = 0; i < pvl.groups(); i++) {
-          m_label->addGroup(pvl.group(i));
-        }
-      }
-    }
-    else {
-      // Setup the PVL
-      PvlObject isiscube("IsisCube");
-      PvlObject core("Core");
-
-      // Create the size of the core
-      PvlGroup dims("Dimensions");
-      dims += PvlKeyword("Samples", toString(m_samples));
-      dims += PvlKeyword("Lines", toString(m_lines));
-      dims += PvlKeyword("Bands", toString(m_bands));
-
-      // Create the pixel type
-      PvlGroup ptype("Pixels");
-      ptype += PvlKeyword("Type", PixelTypeName(m_pixelType));
-
-      // And the byte ordering
-      ptype += PvlKeyword("ByteOrder", ByteOrderName(m_byteOrder));
-      ptype += PvlKeyword("Base", toString(m_base));
-      ptype += PvlKeyword("Multiplier", toString(m_multiplier));
-
-      core += PvlKeyword("StartByte", toString(m_labelBytes + 1));
-
-      core.addGroup(dims);
-      core.addGroup(ptype);
 
-      isiscube.addObject(core);
-
-      m_label->addObject(isiscube);
-    }
-
-    if (dataset->GetSpatialRef() && !(m_label->findObject("IsisCube").hasGroup("Mapping"))) {
-      char ** projStr = new char*[1];
-      const OGRSpatialReference &oSRS = *dataset->GetSpatialRef();
-      oSRS.exportToProj4(projStr);
-      QString qProjStr = QString::fromStdString(std::string(projStr[0]) + " +type=crs");
-      delete[] projStr[0];
-      delete[] projStr;
-
-      char ** projJsonStr = new char*[1];
-      oSRS.exportToPROJJSON(projJsonStr, nullptr);
-      nlohmann::json projJson = nlohmann::json::parse(projJsonStr[0]);
-      CPLFree(projJsonStr);
-
-      PvlGroup mappingGroup("Mapping");
-      mappingGroup.addKeyword(PvlKeyword("ProjectionName", "IProj"));
-      mappingGroup.addKeyword(PvlKeyword("EquatorialRadius", toString(oSRS.GetSemiMajor()), "meters"));
-      mappingGroup.addKeyword(PvlKeyword("PolarRadius", toString(oSRS.GetSemiMinor()), "meters"));
-
-      if (projJson.contains("base_crs")) {
-        projJson = projJson["base_crs"];
-      }
-
-      std::string direction = projJson["coordinate_system"]["axis"][1]["direction"];
-      if (direction == "east") {
-        mappingGroup.addKeyword(PvlKeyword("LongitudeDirection", "PositiveEast"));
-      }
-      else if (direction == "west") {
-        mappingGroup.addKeyword(PvlKeyword("LongitudeDirection", "PositiveWest"));
-      }
-      else {
-        QString msg = "Unknown direction [" + QString::fromStdString(direction) + "]";
-        throw IException(IException::Programmer, msg, _FILEINFO_);
-      }
-
-      if (oSRS.GetSemiMajor() == oSRS.GetSemiMinor()) {
-        mappingGroup.addKeyword(PvlKeyword("LatitudeType", "Planetocentric"));
-      }
-      else {
-        mappingGroup.addKeyword(PvlKeyword("LatitudeType", "Planetographic"));
-      }
-
-      mappingGroup.addKeyword(PvlKeyword("LongitudeDomain", "180"));
-      mappingGroup.addKeyword(PvlKeyword("ProjStr", qProjStr));
-
-      // Read the GeoTransform and get the elements we care about
-      double *padfTransform = new double[6];
-      dataset->GetGeoTransform(padfTransform);
-      if (abs(padfTransform[1]) != abs(padfTransform[5])) {
-        delete[] padfTransform;
-        QString msg = "Vertical and horizontal resolution do not match";
-        throw IException(IException::Io, msg, _FILEINFO_);
-      }
-
-      double dfScale;
-      double dfRes;
-      double upperLeftX;
-      double upperLeftY;
-      dfRes = padfTransform[1] * oSRS.GetLinearUnits();
-      upperLeftX = padfTransform[0];
-      upperLeftY = padfTransform[3];
-      if (oSRS.IsProjected()) {
-        const double dfDegToMeter = oSRS.GetSemiMajor() * M_PI / 180.0;
-        dfScale = dfDegToMeter / dfRes;
-        mappingGroup.addKeyword(PvlKeyword("PixelResolution", toString(dfRes), "meters/pixel"));
-      }
-      else if (oSRS.IsGeographic()) {
-        dfScale = 1.0 / dfRes;
-        mappingGroup.addKeyword(PvlKeyword("PixelResolution", toString(dfRes), "degrees/pixel"));
-      }
-      else {
-        QString msg = "Gdal spatial reference is not Geographic or Projected";
-        throw IException(IException::Io, msg, _FILEINFO_);
-      }
-      mappingGroup.addKeyword(PvlKeyword("Scale", toString(dfScale), "pixels/degree"));
-      mappingGroup.addKeyword(PvlKeyword("UpperLeftCornerX", toString(upperLeftX)));
-      mappingGroup.addKeyword(PvlKeyword("UpperLeftCornerY", toString(upperLeftY)));
-      delete[] padfTransform;
-
-      PvlObject &isiscube = m_label->findObject("IsisCube");
-      if (isiscube.hasGroup("Mapping")) {
-        isiscube.deleteGroup("Mapping");
-      }
-      isiscube.addGroup(mappingGroup);
-    }
-    GDALClose(dataset);
+    m_label = new Pvl(m_dataFileName->expanded());
 
     GDALAccess eAccess = GA_ReadOnly;
     if (access == "rw") {
@@ -1374,7 +1240,9 @@ namespace Isis {
       // maxbyte = position after the cube DN data and labels
       streampos maxbyte = (streampos) m_labelBytes;
 
-      maxbyte += (streampos) m_ioHandler->getDataSize();
+      if (labelsAttached() != ExternalLabel) {
+        maxbyte += (streampos) m_ioHandler->getDataSize();
+      }
 
       // If EOF is too early, allocate space up to where we want the blob
       if (endByte < maxbyte) {
@@ -2406,6 +2274,16 @@ namespace Isis {
    * @return bool True if the BLOB was found
    */
   bool Cube::hasBlob(const QString &name, const QString &type) {
+    if (gdalDataset()) {
+      string key = type.toStdString() + "_" + name.toStdString();
+      const char *jsonblobStr = gdalDataset()->GetMetadataItem(key.c_str(), "USGS");
+
+      if (jsonblobStr) {
+        return true;
+      }
+      return false;
+    }
+
     for(int o = 0; o < label()->objects(); o++) {
       PvlObject &obj = label()->object(o);
       if (obj.isNamed(type)) {
@@ -2585,10 +2463,6 @@ namespace Isis {
 
 
   GDALDataset *Cube::gdalDataset() const {
-    if (!m_geodataSet) {
-      QString msg = "No GDALDataset has been constructed";
-      throw IException(IException::Programmer, msg, _FILEINFO_);
-    }
     return m_geodataSet;
   }
 

isis/src/base/objs/CubeAttribute/CubeAttribute.h

@@ -527,6 +527,7 @@ namespace Isis {
 
       using CubeAttribute<CubeAttributeOutput>::toString;
 
+      static QString toString(Cube::Format);
 
     private:
       bool isByteOrder(QString attribute) const;
@@ -535,8 +536,6 @@ namespace Isis {
       bool isPixelType(QString attribute) const;
       bool isRange(QString attribute) const;
 
-      static QString toString(Cube::Format);
-
       /**
        * @brief Output cube range tracker
        *

isis/src/base/objs/CubeManager/CubeManager.truth

@@ -50,5 +50,4 @@ Setting number of open cubes > 60 percent of system open file limit
 
 Attempting to open a file that does not exist:
   **I/O ERROR** Failed to open [dne.cub].
-**PROGRAMMER ERROR** Gdal failed to open [dne.cub].
 **I/O ERROR** Unable to open [dne.cub].

isis/src/base/objs/ProcessMapMosaic/ProcessMapMosaic.cpp

@@ -508,8 +508,7 @@ namespace Isis {
       double xmin, double xmax, double ymin, double ymax,
       double slat, double elat, double slon, double elon, int nbands,
       CubeAttributeOutput &oAtt, const QString &mosaicFile, bool latlonflag) {
-    Cube cube(inputFile);
-    Pvl fileLab = *cube.label();
+    Pvl fileLab(inputFile);
     PvlGroup &mapping = fileLab.findGroup("Mapping", Pvl::Traverse);
 
     // All mosaicking programs use only the upper left x and y to determine where to