GTiff Reading and Writing

environment.yml

@@ -5,8 +5,8 @@ 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
@@ -22,6 +22,7 @@ dependencies:
   - ffmpeg
   - geos >=3.12, <3.13
   - geotiff
+  - gdal >=3.5 ,<3.9.0a0
   - gmp
   - graphviz
   - conda-forge::gsl >=2.6, <2.7
@@ -34,10 +35,10 @@ 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
@@ -47,17 +48,17 @@ 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

@@ -26,9 +26,17 @@ void IsisMain() {
   }
 
   // Extract history from file
-  Blob historyBlob("IsisCube", "History", fromfile.expanded());
-  History hist(historyBlob);
-  Pvl pvl = hist.ReturnHist();
+  Pvl pvl;
+  try {
+    Blob historyBlob("IsisCube", "History", fromfile.expanded());
+    History hist(historyBlob);
+    pvl = hist.ReturnHist();
+  }
+  catch (...) {
+    Cube cube(fromfile);
+    History hist = cube.readHistory();
+    pvl = hist.ReturnHist();
+  }
 
   // Print full history
   if(mode == "FULL") {

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

@@ -17,7 +17,14 @@ void IsisMain() {
   QString file = ui.GetCubeName("FROM");
 
   // Extract label from file
-  Pvl label(file);
+  Pvl label;
+  try {
+    label = Pvl(file);
+  }
+  catch (...) {
+    Cube cube(file);
+    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 +27,14 @@ void IsisMain() {
   UserInterface &ui = Application::GetUserInterface();
   FileName file = ui.GetCubeName("FROM");
   QString tableName = ui.GetString("NAME");
-  Table table(tableName, file.expanded());
+  Table table(tableName);
+  try {
+    table = Table(tableName, file.expanded());
+  }
+  catch (...) {
+    Cube fromCube(file);
+    table = fromCube.readTable(tableName);
+  }
 
   // Set the character to separate the entries
   QString delimit;
@@ -147,7 +154,14 @@ void helperButtonGetTableList() {
 
   UserInterface &ui = Application::GetUserInterface();
   QString currentFile = ui.GetCubeName("FROM");
-  const Pvl label(FileName(currentFile).expanded());
+  Pvl label;
+  try {
+    label = Pvl(FileName(currentFile).expanded());
+  }
+  catch (...) {
+    Cube cube(FileName(currentFile).expanded());
+    label = *cube.label();
+  }
 
   // Check to see if the "FILE" parameter has changed since last press
   if (currentFile != g_previousFile) {