Loading Science Data into Sensors (#86)

* Science data implementation using PCL Octree kNN for spatial search Signed-off-by: Mabel Zhang <[email protected]> Co-authored-by: Louise Poubel <[email protected]>
osrf · Nov 2, 2021 · d43fc5e · d43fc5e
1 parent 3f58752
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diff --git a/README.md b/README.md
@@ -7,6 +7,11 @@ This repository contains packages for simulating the MBARI Tethys.
 Make sure you have [ignition-fortress](https://ignitionrobotics.org/docs/fortress) and
 [colcon](https://colcon.readthedocs.io/en/released/), on Ubuntu Focal or higher.
 
+Install dependencies
+```
+sudo apt-get install libpcl-dev
+```
+
 Clone this repository then run
 ```
 colcon build
@@ -328,3 +333,19 @@ Make sure to use
 quick on
 ```
 to let the system finish loading, before issuing control commands.
+
+# Science data
+
+Science data can be read from a csv file with the following recognized field
+names in the first line of the file:
+```
+elapsed_time_second
+northings_meter
+eastings_meter
+depth_meter
+sea_water_temperature_degC
+sea_water_salinity_psu
+mass_concentration_of_chlorophyll_in_sea_water_ugram_per_liter
+eastward_sea_water_velocity_meter_per_sec
+northward_sea_water_velocity_meter_per_sec
+```
diff --git a/docker/tests/Dockerfile b/docker/tests/Dockerfile
@@ -46,6 +46,11 @@ RUN apt-get -qq update && apt-get -q -y install \
   python3-colcon-common-extensions \
   ignition-fortress
 
+# Install PCL
+RUN apt-get update \
+ && apt-get install -y \
+        libpcl-dev
+
 # Clean up apt
 RUN rm -rf /var/lib/apt/lists/* \
   && apt-get -qq clean

diff --git a/lrauv_ignition_plugins/CMakeLists.txt b/lrauv_ignition_plugins/CMakeLists.txt
@@ -25,28 +25,34 @@ set(IGN_UTILS_VER ${ignition-utils1_VERSION_MAJOR})
 
 find_package (Eigen3 3.3 REQUIRED)
 
+find_package(PCL 1.2 REQUIRED)
+
 # Build protobuf messages
 add_subdirectory(proto)
 
 #============================================================================
 # Plugins
 
 # add_lrauv_plugin (<plugin_name>
-#              [PROTO])
+#              [PROTO] [PCL] [PRIVATE_LINK_LIBS])
 #
 # Configure and install plugins.
 #
 # <plugin_name> Required. Name of the plugin library, which matches source file.
 #
-# [PROTO]: Optional. If included, plugin will be linked against custom protobuf messages.
+# [PROTO]: Optional. If included, plugin will be linked against custom protobuf
+# messages.
+#
+# [PCL]: Optional. If included, plugin will be linked against PCL.
 #
 # [PRIVATE_LINK_LIBS]: Specify a list of libraries to be privately linked.
 function(add_lrauv_plugin PLUGIN)
-  set(options PROTO)
+  set(options PROTO PCL)
   set(oneValueArgs)
   set(multiValueArgs PRIVATE_LINK_LIBS)
 
-  cmake_parse_arguments(add_lrauv_plugin "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+  cmake_parse_arguments(add_lrauv_plugin
+    "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
 
   add_library(${PLUGIN} SHARED src/${PLUGIN}.cc)
   set_property(TARGET ${PLUGIN} PROPERTY CXX_STANDARD 17)
@@ -69,6 +75,14 @@ function(add_lrauv_plugin PLUGIN)
 
   endif()
 
+  # Include PCL
+  if (add_lrauv_plugin_PCL)
+
+    target_include_directories(${PLUGIN}
+      PUBLIC ${PCL_INCLUDE_DIRS})
+
+  endif()
+
   install(
     TARGETS ${PLUGIN}
     DESTINATION lib)
@@ -79,8 +93,10 @@ add_lrauv_plugin(BuoyancyEnginePlugin)
 add_lrauv_plugin(HydrodynamicsPlugin)
 add_lrauv_plugin(JointPositionPlugin)
 add_lrauv_plugin(ScienceSensorsSystem
+  PCL
   PRIVATE_LINK_LIBS
-    ignition-sensors${IGN_SENSORS_VER}::ignition-sensors${IGN_SENSORS_VER})
+    ignition-sensors${IGN_SENSORS_VER}::ignition-sensors${IGN_SENSORS_VER}
+    ${PCL_LIBRARIES})
 add_lrauv_plugin(TethysCommPlugin PROTO)
 add_lrauv_plugin(ThrusterPlugin)
 add_lrauv_plugin(TimeAnalysisPlugin)
@@ -167,6 +183,7 @@ endif()
 
 install(
   DIRECTORY
+    data
     launch
     models
     worlds

diff --git a/lrauv_ignition_plugins/data/2003080103_mb_l3_las.csv b/lrauv_ignition_plugins/data/2003080103_mb_l3_las.csv
diff --git a/lrauv_ignition_plugins/hooks/hook.dsv.in b/lrauv_ignition_plugins/hooks/hook.dsv.in
@@ -3,6 +3,7 @@ prepend-non-duplicate;IGN_LAUNCH_PLUGIN_PATH;@CMAKE_INSTALL_PREFIX@/lib
 
 prepend-non-duplicate;IGN_GAZEBO_RESOURCE_PATH;@CMAKE_INSTALL_PREFIX@/share/@PROJECT_NAME@/worlds
 prepend-non-duplicate;IGN_GAZEBO_RESOURCE_PATH;@CMAKE_INSTALL_PREFIX@/share/@PROJECT_NAME@/models
+prepend-non-duplicate;IGN_GAZEBO_RESOURCE_PATH;@CMAKE_INSTALL_PREFIX@/share/@PROJECT_NAME@/data
 prepend-non-duplicate;IGN_GAZEBO_SYSTEM_PLUGIN_PATH;@CMAKE_INSTALL_PREFIX@/lib
 
 prepend-non-duplicate;LD_LIBRARY_PATH;@CMAKE_INSTALL_PREFIX@/lib
diff --git a/lrauv_ignition_plugins/src/BuoyancyEnginePlugin.hh b/lrauv_ignition_plugins/src/BuoyancyEnginePlugin.hh
@@ -71,7 +71,7 @@ namespace tethys
         const ignition::gazebo::UpdateInfo &_info,
         ignition::gazebo::EntityComponentManager &_ecm);
 
-    /// Inherits documentation from parent class
+    /// \brief Private data pointer
     private: std::unique_ptr<BuoyancyEnginePrivateData> dataPtr;
   };
 }

diff --git a/lrauv_ignition_plugins/src/HydrodynamicsPlugin.cc b/lrauv_ignition_plugins/src/HydrodynamicsPlugin.cc
@@ -152,8 +152,8 @@ double SdfParamDouble(
 
 
 HydrodynamicsPlugin::HydrodynamicsPlugin()
+  : dataPtr(std::make_unique<HydrodynamicsPrivateData>())
 {
-  this->dataPtr = std::make_unique<HydrodynamicsPrivateData>();
 }
 
 void HydrodynamicsPlugin::Configure(

diff --git a/lrauv_ignition_plugins/src/JointPositionPlugin.hh b/lrauv_ignition_plugins/src/JointPositionPlugin.hh
@@ -55,9 +55,9 @@ namespace tethys
         const ignition::gazebo::UpdateInfo &_info,
         ignition::gazebo::EntityComponentManager &_ecm);
 
-    /// Inherits documentation from parent class
+    /// \brief Private data pointer
     private: std::unique_ptr<TethysJointPrivateData> dataPtr;
   };
 }
 
-#endif
+#endif