Initial implementation of multispectral isds

CMakeLists.txt

@@ -21,6 +21,7 @@ set(CMAKE_CXX_STANDARD 11)
 option(ALE_BUILD_LOAD "If the C++ Python load interface should be built." ON)
 option(ALE_USE_EXTERNAL_JSON "If an external nlohmann JSON library should be used" ON)
 option(ALE_USE_EXTERNAL_EIGEN "If an external EIGEN library should be used" ON)
+option(ALE_USE_EXTERNAL_HIGHFIVE "If an external HIGHFIVE library should be used" ON)
 
 # Third Party Dependencies
 if(ALE_USE_EXTERNAL_JSON)
@@ -39,6 +40,12 @@ else()
     ${CMAKE_CURRENT_SOURCE_DIR}/eigen)
 endif()
 
+if(ALE_USE_EXTERNAL_HIGHFIVE)
+  find_package(HDF5 COMPONENTS C CXX)
+  find_package(highfive REQUIRED)
+endif()
+
+
 if(ALE_BUILD_LOAD)
   # If there is an Anaconda environment activated, search that for Python first
   if(EXISTS $ENV{CONDA_PREFIX})
@@ -141,4 +148,4 @@ if(ALE_BUILD_DOCS)
   add_subdirectory ("docs")
 else()
   message(STATUS "Skipping Docs")
-endif()
+endif()

environment.yml

@@ -1,13 +1,13 @@
 name: ale
 channels:
   - conda-forge
-  - default
 
 dependencies:
   - cmake>=3.15
   - pytest
   - eigen
   - gdal 
+  - highfive
   - jupyter
   - nlohmann_json
   - numpy
@@ -23,3 +23,5 @@ dependencies:
   - networkx
   - breathe
   - brotli
+  - h5py
+  - pip

include/ale/Isd.h

@@ -5,6 +5,7 @@
 #include <vector>
 #include <map>
 
+#include <highfive/highfive.hpp>
 #include <nlohmann/json.hpp>
 
 #include "ale/Distortion.h"
@@ -68,6 +69,63 @@ namespace ale {
     Orientations inst_pointing;
     Orientations body_rotation;
   };
+
+
+  class MultiSpectralIsd {
+    public:
+
+    MultiSpectralIsd(HighFive::File);
+
+    std::vector<std::string> usgscsm_name_model;
+    std::vector<std::string> name_platform;
+    std::vector<std::string> image_id;
+    std::vector<std::string> name_sensor;
+
+    std::vector<double> semi_major;
+    std::vector<double> semi_minor;
+
+    std::vector<double> detector_sample_summing;
+    std::vector<double> detector_line_summing;
+
+    std::vector<double> focal_length;
+    std::vector<double> focal_uncertainty;
+
+    std::vector<double> detector_center_line;
+    std::vector<double> detector_center_sample;
+
+    // should probably be ints
+    std::vector<double> starting_detector_line;
+    std::vector<double> starting_detector_sample;
+
+    std::vector<std::vector<double>> focal2pixel_line;
+    std::vector<std::vector<double>> focal2pixel_sample;
+
+    // maybe change
+    std::vector<DistortionType> distortion_model;
+    std::vector<std::vector<double>> distortion_coefficients;
+
+    std::vector<unsigned int> image_lines;
+    std::vector<unsigned int> image_samples;
+
+    std::vector<double> max_reference_height;
+    std::vector<double> min_reference_height;
+
+    std::vector<std::vector<std::vector<double>>> line_scan_rate;
+
+    std::vector<double> starting_ephemeris_time;
+    std::vector<double> center_ephemeris_time;
+
+    std::vector<nlohmann::json> naif_keywords;
+
+    std::vector<PositionInterpolation> interpMethod;
+
+    std::vector<States> inst_pos;
+    std::vector<States> sun_pos;
+
+    std::vector<Orientations> inst_pointing;
+    std::vector<Orientations> body_rotation;
+  };
 }
 
+
 #endif

include/ale/Util.h

@@ -1,6 +1,7 @@
 #ifndef ALE_UTIL_H
 #define ALE_UTIL_H
 
+#include <highfive/highfive.hpp>
 #include <string>
 #include <nlohmann/json.hpp>
 
@@ -25,6 +26,17 @@ namespace ale {
     return positions;
   }
 
+  template<typename T>
+  std::vector<std::vector<T>> getMultiSpectralArray(HighFive::DataSet ds){
+    std::vector<std::vector<T>> data;
+    try {
+      ds.read(data);
+    } catch (...) {
+      throw std::runtime_error("Could not parse the hdf5 dataset");
+    }
+    return data;
+  }
+
 
   PositionInterpolation getInterpolationMethod(nlohmann::json isd);
   double getMinHeight(nlohmann::json isd);
@@ -65,9 +77,43 @@ namespace ale {
 
   States getInstrumentPosition(nlohmann::json isd);
   States getSunPosition(nlohmann::json isd);
-
   Orientations getBodyRotation(nlohmann::json isd);
   Orientations getInstrumentPointing(nlohmann::json isd);
+
+
+  std::vector<std::string> getSensorModelName(HighFive::File hdf5);
+  std::vector<std::string> getImageId(HighFive::File hdf5);
+  std::vector<std::string> getPlatformName(HighFive::File hdf5);
+  std::vector<std::string> getSensorName(HighFive::File hdf5);
+  std::vector<unsigned int> getTotalLines(HighFive::File hdf5);
+  std::vector<unsigned int> getTotalSamples(HighFive::File hdf5);
+  std::vector<double> getStartingTime(HighFive::File hdf5);
+  std::vector<double> getCenterTime(HighFive::File hdf5);
+  std::vector<std::vector<std::vector<double>>> getLineScanRate(HighFive::File hdf5);
+  std::vector<double> getSampleSumming(HighFive::File hdf5);
+  std::vector<double> getLineSumming(HighFive::File hdf5);
+  std::vector<double> getFocalLength(HighFive::File hdf5);
+  std::vector<double> getFocalLengthUncertainty(HighFive::File hdf5);
+  std::vector<std::vector<double>> getFocal2PixelLines(HighFive::File hdf5);
+  std::vector<std::vector<double>> getFocal2PixelSamples(HighFive::File hdf5);
+  std::vector<double> getDetectorCenterLine(HighFive::File hdf5);
+  std::vector<double> getDetectorCenterSample(HighFive::File hdf5);
+  std::vector<double> getDetectorStartingLine(HighFive::File hdf5);
+  std::vector<double> getDetectorStartingSample(HighFive::File hdf5);
+  std::vector<double> getMinHeight(HighFive::File hdf5);
+  std::vector<double> getMaxHeight(HighFive::File hdf5);
+  std::vector<double> getSemiMajorRadius(HighFive::File hdf5);
+  std::vector<double> getSemiMinorRadius(HighFive::File hdf5);
+  std::vector<DistortionType> getDistortionModel(HighFive::File hdf5);
+  std::vector<std::vector<double>> getDistortionCoeffs(HighFive::File hdf5);
+  std::vector<PositionInterpolation> getInterpolationMethod(HighFive::File hdf5);
+  std::vector<Orientations> getBodyRotation(HighFive::File hdf5);
+  std::vector<std::vector<Vec3d>> getVec3dArray(HighFive::DataSet ds);
+  std::vector<std::vector<Rotation>> getQuatArray(HighFive::DataSet ds);
+
+  std::vector<States> getInstrumentPosition(HighFive::File hdf5);
+  std::vector<States> getSunPosition(HighFive::File hdf5);
+  std::vector<Orientations> getInstrumentPointing(HighFive::File hdf5);
 }
 
 #endif