GTiff Reading and Writing

environment.yml

@@ -6,8 +6,8 @@ dependencies:
   - ale =0.10.0,<1
   - aom
   - armadillo
-  - boost >=1.78.0,<1.79
-  - boost-cpp >=1.78.0,<1.79
+  - boost >=1.76.0,<1.82
+  - boost-cpp >=1.76.0,<1.82
   - blas
   - usgs-astrogeology::bullet
   - bz2file
@@ -23,6 +23,7 @@ dependencies:
   - ffmpeg
   - geos >=3.12, <3.13
   - geotiff
+  - gdal >=3.5 ,<3.9.0a0
   - gmp
   - graphviz
   - conda-forge::gsl >=2.6, <2.7
@@ -35,10 +36,10 @@ dependencies:
   - kalasiris
   - krb5
   - libgdal >=3.7,<3.8
-  - libopencv >=4.7,<4.8
+  - libopencv >=4.5,<4.8
   - libpng >=1.6.34,<1.7
   - libprotobuf
-  - libtiff >=4.5,<4.6
+  - libtiff >=4.5,<4.8
   - libxml2
   - make
   - mesalib
@@ -48,17 +49,17 @@ dependencies:
   - nlohmann_json=3.11.2
   - ninja >=1.7.2,<1.8
   - nn
-  - opencv >=4.7,<4.8
+  - opencv >=4.5,<4.8
   - openssl >=3.1.2,<3.2
   - pcl >=1.13,<1.14
   - plio
   - protobuf
-  - python >=3.10
-  - python_abi >=3.10
+  - python >=3.9
+  - python_abi >=3.9
   - pytest
   - rclone
   - qhull
-  - qt-main>=5.15.8, <5.16
+  - qt-main>=5.15, <5.16
   - qwt <6.3.0
   - sqlite >=3.46.0,<3.47
   - suitesparse <7.7.0

isis/CMakeLists.txt

@@ -267,6 +267,7 @@ find_package(CSM       3.0.3.3 REQUIRED)
 find_package(CSPICE    65      REQUIRED)
 find_package(Eigen             REQUIRED)
 find_package(Embree    3.13.0  REQUIRED)
+find_package(GDAL              REQUIRED CONFIG)
 find_package(GeoTIFF   2       REQUIRED)
 SET(GSL_ROOT_DIR $ENV{CONDA_PREFIX})
 find_package(GSL       2.2.1   REQUIRED)
@@ -353,7 +354,7 @@ foreach (_variableName ${_variableNames})
 endforeach()
 
 # add target based linkages to ALLLIBS variable
-list(APPEND ALLLIBS pantor::inja sensorutilities protobuf::libprotobuf embree)
+list(APPEND ALLLIBS pantor::inja sensorutilities protobuf::libprotobuf embree GDAL::GDAL)
 
 # Sometimes we add the same lib more than once (especially with LIBDIRS)
 list(REMOVE_DUPLICATES ALLLIBDIRS)

isis/src/apollo/apps/apollopanstitcher/apollopanstitcher.cpp

@@ -715,11 +715,11 @@ namespace Isis {
     att.setFileFormat( panC[0]->format() );
     att.setByteOrder(  panC[0]->byteOrder() );
     att.setPixelType(  panC[0]->pixelType() );
-    if (panC[0]->labelsAttached()) {
-      att.setLabelAttachment(AttachedLabel);
+    if (panC[0]->labelsAttached() == Cube::AttachedLabel) {
+      att.setLabelAttachment(Cube::AttachedLabel);
     }
     else {
-      att.setLabelAttachment(DetachedLabel);
+      att.setLabelAttachment(Cube::DetachedLabel);
     }
 
     //define an output cube

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

@@ -26,8 +26,8 @@ void IsisMain() {
   }
 
   // Extract history from file
-  Blob historyBlob("IsisCube", "History", fromfile.expanded());
-  History hist(historyBlob);
+  Cube cube(fromfile);
+  History hist = cube.readHistory();
   Pvl pvl = hist.ReturnHist();
 
   // Print full history

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

@@ -17,7 +17,8 @@ void IsisMain() {
   QString file = ui.GetCubeName("FROM");
 
   // Extract label from file
-  Pvl label(file);
+  Cube cube(file);
+  Pvl label = *cube.label();
 
   // Output to file if entered
   if(ui.WasEntered("TO")) {

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

@@ -22,9 +22,10 @@ void IsisMain() {
   UserInterface &ui = Application::GetUserInterface();
   QString file = ui.GetCubeName("FROM");
 
-  Pvl fromLabel(file);
+  Cube fromCube(file);
+  Pvl fromLabel = *(fromCube.label());
   if ( fromLabel.hasObject("OriginalLabel") ) {
-    OriginalLabel origLab(file);
+    OriginalLabel origLab = fromCube.readOriginalLabel();
     Pvl pvl = origLab.ReturnLabels();
     if (ui.IsInteractive()) {
       Application::GuiLog(pvl);

isis/src/base/apps/crop/crop.cpp

@@ -140,7 +140,7 @@ namespace Isis {
       }
 
       // Read the table into a table object
-      Table table(obj["Name"], from);
+      Table table = cube->readTable(obj["Name"]);
 
       // We are not going to bother with line/sample associations; they apply
       //   only to the alpha cube at this time. I'm leaving this code here for the

isis/src/base/apps/noproj/noproj.cpp

@@ -191,7 +191,7 @@ namespace Isis {
     CubeAttributeOutput cao;
 
     // Can we do a regular label? Didn't work on 12-15-2006
-    cao.setLabelAttachment(Isis::DetachedLabel);
+    cao.setLabelAttachment(Cube::DetachedLabel);
     FileName matchCubeFile = FileName::createTempFile("$Temporary/match.cub");
     QString matchCubeFileNoExt = matchCubeFile.path() + "/" + matchCubeFile.baseName();
 

isis/src/base/apps/shadow/ShadowFunctor.cpp

@@ -394,7 +394,7 @@ namespace Isis {
 
 
           Portal portal(3, 3, m_inputDem->pixelType(), -0.5, -0.5);
-          portal.SetPosition(sample, line, input.Band());
+          portal.SetPosition(sample + 1, line + 1, input.Band());
 
           if (!portal.CopyOverlapFrom(input)) {
             m_inputDem->read(portal);

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

@@ -263,7 +263,6 @@ namespace Isis {
       }
     }
     icube->deleteGroup("CsmInfo");
-
     p.WriteHistory(*icube);
     p.EndProcess();
   }
@@ -592,7 +591,6 @@ namespace Isis {
       icube->putGroup(originalKernels);
       return false;
     }
-
     return true;
   }
 

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

@@ -27,7 +27,8 @@ void IsisMain() {
   UserInterface &ui = Application::GetUserInterface();
   FileName file = ui.GetCubeName("FROM");
   QString tableName = ui.GetString("NAME");
-  Table table(tableName, file.expanded());
+  Cube fromCube(file);
+  Table table = fromCube.readTable(tableName);
 
   // Set the character to separate the entries
   QString delimit;

isis/src/base/objs/Blob/Blob.cpp

@@ -9,6 +9,8 @@ find files of those names at the top level of this repository. **/
 #include <cstring>
 #include <fstream>
 #include <sstream>
+#include <filesystem>
+#include <gdal_priv.h>
 
 #include <QDebug>
 
@@ -17,7 +19,11 @@ find files of those names at the top level of this repository. **/
 #include "Message.h"
 #include "Pvl.h"
 
+namespace fs = std::filesystem;
+using json = nlohmann::json;
+using ordered_json = nlohmann::ordered_json;
 using namespace std;
+
 namespace Isis {
   /**
    * Constructs a Blob object using a name and type.
@@ -244,6 +250,33 @@ namespace Isis {
     }
   }
 
+  void Blob::ReadGdal(GDALDataset *dataset) {
+    try {
+      std::string key = QString(p_type + "_" + p_blobName).toStdString();
+      const char *jsonblobStr = dataset->GetMetadataItem(key.c_str(), "USGS");
+      if (jsonblobStr == nullptr) {
+        QString msg = "The key [" + QString::fromStdString(key) + "] does not exist on the geodata set.";
+        throw IException( IException::Io, msg, _FILEINFO_);
+      }
+      ordered_json jsonblob = ordered_json::parse(jsonblobStr);
+      std::string blobData = jsonblob[key]["Data"];
+      jsonblob[key].erase("Data");
+
+      Pvl pvl;
+      Pvl::readObject(pvl, jsonblob);
+
+      p_blobName = QString::fromStdString(jsonblob[key]["Name"]);
+      p_type = QString::fromStdString(jsonblob[key]["_container_name"]);
+
+      Find(pvl);
+      ReadData(blobData);
+    }
+    catch(exception &e) { 
+      QString msg = "Failed to read blob [" + p_blobName + "]: " + e.what();
+      throw IException(IException::Io, msg, _FILEINFO_);
+    }
+  }
+
   /**
    * This method reads Pvl values from a specified file.
    *
@@ -255,7 +288,7 @@ namespace Isis {
   void Blob::Read(const QString &file, const std::vector<PvlKeyword> keywords) {
     // Expand the filename
     QString temp(FileName(file).expanded());
-
+    
     // Get the pvl
     Pvl pvl;
     try {
@@ -405,6 +438,46 @@ namespace Isis {
     p_buffer = buffer;
   }
 
+  void Blob::WriteGdal(GDALDataset *dataset) {
+    try {
+      WriteInit();
+      Pvl pvl;
+      pvl.addObject(p_blobPvl);
+      ostringstream os;
+      os << pvl << endl;
+      os.seekp(0, std::ios::end);
+
+      stringstream stream;
+      WriteData(stream);
+      PvlObject &blobObj = pvl.findObject(p_type);
+
+      blobObj["Bytes"] = toString(p_nbytes);
+      blobObj["StartByte"] = toString(1);
+      if(blobObj.hasKeyword("Data")) { 
+        blobObj["Data"] = QString::fromStdString(stream.str()); 
+      }
+      else { 
+        blobObj += PvlKeyword("Data", QString::fromStdString(stream.str()));
+      }
+
+      if(blobObj.hasKeyword("Name")) { 
+        blobObj["Name"] = p_blobName; 
+      }
+      else { 
+        blobObj += PvlKeyword("Name", p_blobName);
+      }
+
+      // update metadata
+      string jsonblobstr = pvl.toJson().dump();
+      string key = this->Type().toStdString() + "_" + this->Name().toStdString();
+      dataset->SetMetadataItem(key.c_str(), jsonblobstr.c_str(), "USGS");
+    }
+    catch(exception &e) {
+      cout << "Failed to write blob [" + p_blobName + "]: " << e.what() << endl;
+    }
+  }
+
+
   /**
    * Write the blob data out to a file.
    *
@@ -415,7 +488,7 @@ namespace Isis {
    * @throws IException::Io - Error creating file
    */
   void Blob::Write(const QString &file) {
-    // Determine the size of the label and write it out
+    // Determine the size of the label and write it out   
     try {
       WriteInit();
       Pvl pvl;
@@ -456,6 +529,7 @@ namespace Isis {
     }
   }
 
+
   /**
    * Write the blob data out to a Pvl object.
    * @param pvl The pvl object to update
@@ -464,10 +538,10 @@ namespace Isis {
    * the name of the file
    */
   void Blob::Write(Pvl &pvl, std::fstream &stm,
-                   const QString &detachedFileName, bool overwrite) {
+                   const QString &detachedFileName, bool overwrite, bool inline_data) {
+
     // Handle 64-bit I/O
     WriteInit();
-
     // Find out where they wanted to write the blob
     streampos sbyte = stm.tellp();
     sbyte += 1;
@@ -482,11 +556,9 @@ namespace Isis {
       p_blobPvl += PvlKeyword("^" + p_type, detachedFileName);
     }
 
-
     p_blobPvl["StartByte"] = toString((BigInt)sbyte);
     p_blobPvl["Bytes"] = toString(p_nbytes);
 
-
     // See if the blob is already in the file
     bool found = false;
     if (overwrite) {
@@ -570,6 +642,54 @@ namespace Isis {
   }
 
 
+  /**
+   * Writes blob data to a stream
+   *
+   * @param stream Output steam blob data will be written to
+   *
+   * @throws IException::Io - Error writing data to stream
+   */
+  void Blob::WriteData(std::stringstream &stream) {
+    stream << std::hex;
+    int copy;
+    for (int i = 0; i < p_nbytes; ++i) {
+      memcpy(&copy, &p_buffer[i], 1);
+      stream << std::setw(2) << std::setfill('0') << copy;
+    }
+
+    if (!stream.good()) {
+      QString msg = "Error writing data to " + p_type + " [" + p_blobName + "]";
+      throw IException(IException::Io, msg, _FILEINFO_);
+    }
+  }
+
+
+  /**
+   * Writes blob data to a stream
+   *
+   * @param stream Output steam blob data will be written to
+   *
+   * @throws IException::Io - Error writing data to stream
+   */
+  void Blob::ReadData(string &hexdata) {
+    // Read the binary data
+    if (p_buffer != NULL) delete [] p_buffer;
+    p_buffer = new char[p_nbytes];
+
+    // Loop through the hex string and bytes, hex is two characters at a time 
+    for (size_t i=0,j=0; i < p_nbytes; i++,j+=2) { 
+        string byteString = hexdata.substr(j, 2);
+
+        int byteValue = static_cast<int>( 
+            stoi(byteString, nullptr, 16));
+
+        // Add the byte to the byte array 
+        p_buffer[i] = byteValue;
+    }
+  }
+
+
+
   /**
    * Checks pvl object and returns whether or not it is a Blob
    *