CARTAvis · confluence · Mar 22, 2023 · Sep 8, 2022 · Sep 8, 2022 · Sep 10, 2022
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * Added support to keep previously generated moment images ([#1202](https://github.com/CARTAvis/carta-backend/issues/1202)).
 * Added pugixml as a third-party library with the option PUGIXML_COMPACT enabled ([#1217](https://github.com/CARTAvis/carta-backend/issues/1217)).
 * Added automatically generated documentation with Doxygen ([#1215](https://github.com/CARTAvis/carta-backend/issues/1215)).
+* Added support for loading swapped-axes image cubes ([#1178](https://github.com/CARTAvis/carta-backend/issues/1178)).
 
 ### Changed
 * Removed CASA CRTF parser for performance and annotation region support ([#1219](https://github.com/CARTAvis/carta-backend/issues/1219)).

diff --git a/carta-protobuf b/carta-protobuf
diff --git a/src/FileList/FileExtInfoLoader.cc b/src/FileList/FileExtInfoLoader.cc
diff --git a/src/FileList/FileExtInfoLoader.h b/src/FileList/FileExtInfoLoader.h
@@ -50,8 +50,9 @@ class FileExtInfoLoader {
 
     // Computed entries
     void AddDataTypeEntry(CARTA::FileInfoExtended& extended_info, casacore::DataType data_type);
-    void AddShapeEntries(CARTA::FileInfoExtended& extended_info, const casacore::IPosition& shape, int chan_axis, int depth_axis,
-        int stokes_axis, const std::vector<int>& render_axes);
+    void AddShapeEntries(CARTA::FileInfoExtended& extended_info, const casacore::IPosition& shape, const std::vector<int>& spatial_axes,
+        int spectral_axis, int stokes_axis, const std::vector<int>& render_axes, int depth_axis,
+        casacore::Vector<casacore::String>& axes_names);
     void AddInitialComputedEntries(const std::string& hdu, CARTA::FileInfoExtended& extended_info, const std::string& filename,
         const std::vector<int>& render_axes, CompressedFits* compressed_fits = nullptr);
     void AddComputedEntries(CARTA::FileInfoExtended& extended_info, casacore::ImageInterface<float>* image,
@@ -66,7 +67,7 @@ class FileExtInfoLoader {
     std::string MakeAngleString(const std::string& type, double val, const std::string& unit);
 
     // Convert Quantities and return formatted string
-    std::string ConvertCoordsToDeg(const casacore::Quantity& coord0, const casacore::Quantity& coord1);
+    std::string ConvertCoordsToDeg(const std::string& type, const casacore::Quantity& coord);
     std::string ConvertIncrementToArcsec(const casacore::Quantity& inc0, const casacore::Quantity& inc1);
 
     void GetCoordNames(std::string& ctype1, std::string& ctype2, std::string& radesys, std::string& coord_name1, std::string& coord_name2,

diff --git a/src/Frame/Frame.cc b/src/Frame/Frame.cc
@@ -68,18 +68,16 @@ Frame::Frame(uint32_t session_id, std::shared_ptr<FileLoader> loader, const std:
 
     // Get shape and axis values from the loader
     std::string log_message;
-    if (!_loader->FindCoordinateAxes(_image_shape, _spectral_axis, _z_axis, _stokes_axis, log_message)) {
+    std::vector<int> spatial_axes, render_axes;
+    if (!_loader->FindCoordinateAxes(_image_shape, spatial_axes, _spectral_axis, _stokes_axis, render_axes, _z_axis, log_message)) {
         _open_image_error = fmt::format("Cannot determine file shape. {}", log_message);
         spdlog::error("Session {}: {}", session_id, _open_image_error);
         _valid = false;
         return;
     }
 
-    // Determine which axes are rendered, e.g. for pV images
-    std::vector<int> render_axes = _loader->GetRenderAxes();
     _x_axis = render_axes[0];
     _y_axis = render_axes[1];
-
     _width = _image_shape(_x_axis);
     _height = _image_shape(_y_axis);
     _depth = (_z_axis >= 0 ? _image_shape(_z_axis) : 1);

diff --git a/src/Frame/Frame.h b/src/Frame/Frame.h
@@ -279,7 +279,8 @@ class Frame {
 
     // Shape and axis info: X, Y, Z, Stokes
     casacore::IPosition _image_shape;
-    int _x_axis, _y_axis, _z_axis, _spectral_axis, _stokes_axis;
+    int _x_axis, _y_axis, _z_axis; // X and Y are render axes, Z is depth axis (non-render axis) that is not stokes (if any)
+    int _spectral_axis, _stokes_axis;
     int _z_index, _stokes_index; // current index
     size_t _width, _height, _depth, _num_stokes;
 

diff --git a/src/ImageData/FileLoader.cc b/src/ImageData/FileLoader.cc
@@ -175,9 +175,11 @@ std::shared_ptr<casacore::CoordinateSystem> FileLoader::GetCoordinateSystem(cons
     return std::make_shared<casacore::CoordinateSystem>();
 }
 
-bool FileLoader::FindCoordinateAxes(casacore::IPosition& shape, int& spectral_axis, int& z_axis, int& stokes_axis, std::string& message) {
+bool FileLoader::FindCoordinateAxes(casacore::IPosition& shape, std::vector<int>& spatial_axes, int& spectral_axis, int& stokes_axis,
+    std::vector<int>& render_axes, int& z_axis, std::string& message) {
     // Return image shape and axes for image. Spectral axis may or may not be z axis.
     // All parameters are return values.
+    spatial_axes.assign(2, -1);
     spectral_axis = -1;
     z_axis = -1;
     stokes_axis = -1;
@@ -201,15 +203,33 @@ bool FileLoader::FindCoordinateAxes(casacore::IPosition& shape, int& spectral_ax
         return false;
     }
 
-    // Determine which axes will be rendered
-    std::vector<int> render_axes = GetRenderAxes();
+    // Get spectral and stokes axis
+    spectral_axis = _coord_sys->spectralAxisNumber();
+    stokes_axis = _coord_sys->polarizationAxisNumber();
+
+    // Set render axes are the first two axes that are not stokes
+    render_axes.resize(0);
+    for (int i = 0; i < _num_dims && render_axes.size() < 2; ++i) {
+        if (i != stokes_axis) {
+            render_axes.push_back(i);
+        }
+    }
+
     _width = shape(render_axes[0]);
     _height = shape(render_axes[1]);
     _image_plane_size = _width * _height;
 
-    // Spectral and stokes axis
-    spectral_axis = _coord_sys->spectralAxisNumber();
-    stokes_axis = _coord_sys->polarizationAxisNumber();
+    // Find spatial axes
+    if (_coord_sys->hasDirectionCoordinate()) {
+        auto tmp_axes = _coord_sys->directionAxesNumbers();
+        spatial_axes[0] = tmp_axes[0];
+        spatial_axes[1] = tmp_axes[1];
+    } else if (_coord_sys->hasLinearCoordinate()) {
+        auto tmp_axes = _coord_sys->linearAxesNumbers();
+        for (int i = 0; i < casacore::min(tmp_axes.size(), 2); ++i) { // Assume the first two linear axes are spatial axes, if any
+            spatial_axes[i] = tmp_axes[i];
+        }
+    }
 
     // 2D image
     if (_num_dims == 2) {
@@ -282,59 +302,6 @@ bool FileLoader::FindCoordinateAxes(casacore::IPosition& shape, int& spectral_ax
     return true;
 }
 
-std::vector<int> FileLoader::GetRenderAxes() {
-    // Determine which axes will be rendered
-    std::vector<int> axes;
-
-    if (!_render_axes.empty()) {
-        axes = _render_axes;
-        return axes;
-    }
-
-    // Default unless PV image
-    axes.assign({0, 1});
-
-    if (_image_shape.size() > 2) {
-        // Normally, use direction axes
-        if (_coord_sys->hasDirectionCoordinate()) {
-            casacore::Vector<casacore::Int> dir_axes = _coord_sys->directionAxesNumbers();
-            axes[0] = dir_axes[0];
-            axes[1] = dir_axes[1];
-        } else if (_coord_sys->hasLinearCoordinate()) {
-            // Check for PV image: usually [Linear, Spectral] axes but could be reversed
-            // Returns -1 if no spectral axis
-            int spectral_axis = _coord_sys->spectralAxisNumber();
-
-            if (spectral_axis >= 0) {
-                // Find valid (not -1) linear axes
-                std::vector<int> valid_axes;
-                if (spectral_axis == 0) { // reversed
-                    valid_axes.push_back(spectral_axis);
-                }
-
-                casacore::Vector<casacore::Int> lin_axes = _coord_sys->linearAxesNumbers();
-                for (auto axis : lin_axes) {
-                    if (axis >= 0) {
-                        valid_axes.push_back(axis);
-                    }
-                }
-
-                if (spectral_axis > 0) { // not reversed
-                    valid_axes.push_back(spectral_axis);
-                }
-
-                // One linear + spectral axis = pV image
-                if (valid_axes.size() == 2) {
-                    axes = valid_axes;
-                }
-            }
-        }
-    }
-
-    _render_axes = axes;
-    return axes;
-}
-
 bool FileLoader::GetSlice(casacore::Array<float>& data, const StokesSlicer& stokes_slicer) {
     StokesSource stokes_source = stokes_slicer.stokes_source;
     casacore::Slicer slicer = stokes_slicer.slicer;

diff --git a/src/ImageData/FileLoader.h b/src/ImageData/FileLoader.h
@@ -23,8 +23,6 @@
 
 namespace carta {
 
-class Frame;
-
 struct StokesSlicer {
     StokesSource stokes_source;
     casacore::Slicer slicer;
@@ -78,8 +76,8 @@ class FileLoader {
     // Image shape and coordinate system axes
     casacore::IPosition GetShape();
     std::shared_ptr<casacore::CoordinateSystem> GetCoordinateSystem(const StokesSource& stokes_source = StokesSource());
-    bool FindCoordinateAxes(casacore::IPosition& shape, int& spectral_axis, int& z_axis, int& stokes_axis, std::string& message);
-    std::vector<int> GetRenderAxes(); // Determine axes used for image raster data
+    bool FindCoordinateAxes(casacore::IPosition& shape, std::vector<int>& spatial_axes, int& spectral_axis, int& stokes_axis,
+        std::vector<int>& render_axes, int& z_axis, std::string& message);
 
     // Slice image data (with mask applied)
     bool GetSlice(casacore::Array<float>& data, const StokesSlicer& stokes_slicer);
@@ -152,7 +150,6 @@ class FileLoader {
     size_t _num_dims, _image_plane_size;
     size_t _width, _height, _depth, _num_stokes;
     int _z_axis, _stokes_axis;
-    std::vector<int> _render_axes;
     std::shared_ptr<casacore::CoordinateSystem> _coord_sys;
     bool _has_pixel_mask;
     casacore::DataType _data_type;

diff --git a/src/ImageData/StokesFilesConnector.cc b/src/ImageData/StokesFilesConnector.cc
@@ -300,20 +300,23 @@ bool StokesFilesConnector::StokesFilesValid(std::string& err, int& stokes_axis)
     }
 
     casacore::IPosition ref_shape(0);
+    std::vector<int> ref_spatial_axes, ref_render_axes;
     int ref_spectral_axis = -1;
     int ref_z_axis = -1;
     int ref_stokes_axis = -1;
     int ref_index = 0;
 
     for (auto& loader : _loaders) {
         casacore::IPosition shape;
+        std::vector<int> spatial_axes, render_axes;
         int spectral_axis;
         int z_axis;
 
         if (ref_index == 0) {
-            loader.second->FindCoordinateAxes(ref_shape, ref_spectral_axis, ref_z_axis, ref_stokes_axis, err);
+            loader.second->FindCoordinateAxes(
+                ref_shape, ref_spatial_axes, ref_spectral_axis, ref_stokes_axis, ref_render_axes, ref_z_axis, err);
         } else {
-            loader.second->FindCoordinateAxes(shape, spectral_axis, z_axis, stokes_axis, err);
+            loader.second->FindCoordinateAxes(shape, spatial_axes, spectral_axis, stokes_axis, render_axes, z_axis, err);
             if ((ref_shape.nelements() != shape.nelements()) || (ref_shape != shape) || (ref_spectral_axis != spectral_axis) ||
                 (ref_stokes_axis != stokes_axis)) {
                 err = "Image shapes or axes are not consistent!";

diff --git a/test/TestFileInfo.cc b/test/TestFileInfo.cc
@@ -115,7 +115,7 @@ class FileExtInfoLoaderTest : public ::testing::Test {
             } else if (computed_entries.name() == "HDU") {
                 CheckHeaderEntry(computed_entries, "0", CARTA::EntryType::STRING);
             } else if (computed_entries.name() == "Shape") {
-                CheckHeaderEntry(computed_entries, "[6, 6, 5, 1]", CARTA::EntryType::STRING);
+                CheckHeaderEntry(computed_entries, "[6, 6, 5, 1] (RA, DEC, FREQ, STOKES)", CARTA::EntryType::STRING);
             } else if (computed_entries.name() == "Number of channels") {
                 CheckHeaderEntry(computed_entries, "5", CARTA::EntryType::INT, 5);
             } else if (computed_entries.name() == "Number of polarizations") {
+3 −0		docs/src/changelog.rst.txt
+45 −0		docs/src/defs.rst.txt
+2 −2		docs/src/index.rst
+15 −0		shared/defs.proto