Merge dev into master for 1.1 release (#190)

* Updated ISD and tests (#87) * updated tests + RIP TestyMcTestFace * keys updated * Probably should not hard code .cpps in the CMakeLists.txt for GTest * updated specs to mimic synthetic json * appveyor assumed broken from standup, disabling until fixed * eulers are now quats * merge from jay's changes * merge markers * renamed quats as per Jessie's reccomendation * only appends sensor_orientation to missing params * stupid markers * updated test ISD * changes as per some comments * updated as per comments * defaults are all 0 * #pragma once to C style header guard * stragler change * missed some params * missed another * moving things around * patched segfault error + added detector center as defined in json schema (#94) * patched segfault error + added detector center as defined in the swagger schema * verbose travi * Fixed optical distortion and pixel to focal transforms. (#115) * Update to use quaternions in test to match new ISD * Fixes #121 * Fix 1 remaining failing omega rotation test * Updates token to be in quotes * Still trying to get the builds working. * Updates to force upload * Adds newline * Update for formatting * Trying to force travis to deploy with labels I am editing this on the repo in order to get Travis to do its thing - I can not do this via a PR. * Update .travis.yml * Update meta.yaml to try and force a dev tag on the builds to get labels to work. * Update meta.yaml * Update .travis.yml * test x scaling for reset model state * test FL500 conversion * test FL500 conversion * Add tests to include * commit to force run of tests on mac with debug output * switch to using tolerances from dev * 0.5 pixel offset * try moving set of filename into setup * initialize differently test * more debug output * Add matrix to debug output * Even more debug output from matrix calculation * Add missing quaternion component to state string * cleanup debug output now that problem is fixed * fix added spacing * Adds in check for PR for upload * echo to check travis env * fixes equality check for PR * Clean up some spacing (non-functional) in UsgsAstroFrameModel * Fixed canModelBeConstructedFromISD throwing an exception when the metadata file doesn't exist. (#134) * fixed can be converted error * Added not constructible test for frame plugin * Removed old LS ISD header (#137) * Update some of the tests that set a new state value to use a function in the fixture, rather than repeating code * Windows Build (#139) * adds win build * Windows build * Updates submodules * Refactoring to move to one plugin and removed unused classes. (#138) * merge * changed varrs * reset test * First iteration * it compiles, although renaming this is still neccessary * added source * cleaned up, tests still need to pass * post merge clean up * validation updated, validation tests are now passing * Addressed comments from Jesse * last Jesse comment, convertISDToModelState doesn't check if pointer is invalid anymore as the sensor model should except * model_name -> m_modelName for frame getState * copy paste error in FrameSensorModel * Resolve merge conflicts with FrameIsdTest vs. SimpleFrameIsdTest names * Fix hopefully last merge problem * Conda build on win (#143) * Conda build on win * Trying a straight build first * Unneeded csmapi * Now trying to upload build * Trying a build and upload * Trying syntax change * trying ps * Update .appveyor.yml * Update .appveyor.yml * Update .appveyor.yml * Update .appveyor.yml * Update .appveyor.yml * Update .appveyor.yml * Update .appveyor.yml * Update .appveyor.yml * Update .appveyor.yml * Update .appveyor.yml * Update .appveyor.yml * Update meta.yaml * Update bld.bat This is a test to see where appveyor is failing. * Update bld.bat * Update bld.bat * Update meta.yaml * Update .appveyor.yml * Update .appveyor.yml * Update .appveyor.yml * Update .appveyor.yml * Adds if/else into appveyor (#146) * Adds if/else into appveyor * Update .appveyor.yml * Updates to use gcc7 * Update .travis.yml * Update .appveyor.yml * Fixed Line Scan construction and condensed plugin tests (#145) * First pass at test LS ISD * Initial LS plugin test base * fixed a test in frame plugin tests * Initial LS plugin test suite * Moved to single plugin test file * Added some new plugin tests * Fixed LS construction * Re-updated submodules * Reverted gtest * removed debuf prints left in and made getModelName functional (#148) * Changed line scan sensor model to new ISD spec (#149) * Changed line scan sensor model to new ISD spec * Updated LS to the proper spec * Changed model_name to name_model * Updated tests to use new name_ format in ISD * Updated LS test data to new spec * Fixed typo in ls test ISD * Moved framer to new ISD format. Added bad debug statements. * Updated LS to new spec * Fixed focal length epsilon name * Fixes 142 for framer * Removes unused state keyword counter * Updates Ls * Updates for parametercov and ref point * Adds sensor and platform names * Updates with collection identifier * updates for vector parameters in state * Added model state test for framer (#152) * Adds current param value and referencePt * unsupported pushed in * fixed nan issue (#153) * fixed nan issue * left in for loop * Removed switch statement for ls distortion: (#150) * Updated build recipe to use release and sha hash * Copied distortion inversion from ISIS3 Distortion Map (#161) * Fixed ground to image and image to ground not giving inverse results. (#162) * Copied distortion inversion from ISIS3 Distortion Map * mid-testing commit to fix LS i2g and g2i inconsistency * Fixed ground to image taking excessive iterations. Added simple line scan test and test stubs * Added more comments and replaced some hard coded tolerances * Added debug output to ground to image error message. (#168) * Initial steps to modularize losToEcf in UsgsAstroLsSensorModel * Try changing line endings * Re-converted line endings to dos * Modularize some of computeViewingPixel * Cleanup * Reconvert to dos line endings * Reformat member variables in header and switch more to use const pass-by-reference parameters to be consistent with rest of code * Updates in response to code review (part 1) * Update calculateRotationMatrixFromQuaternions -- removed invert parameter. Now, will always return the matrix that rotates the in the same direction as the quaternions. * Updates the version number in the meta. (#159) * Updates the version number in the meta. * Update meta.yaml * Build to hash This should be using the short hash now. * Update meta.yaml * Update meta.yaml * Finish Modularizing computeViewingPixel (#170) * Finishing modularization of UsgsAstroLsSensorModel::computeViewingPixel * Fixes per request * Removing ISIS references in variable names while I'm here * Example for LS testing (#171) * Removed odd height gradient descent search from image to ground when not intersecting. * Added first off body test. * Added angular velocity line scan test * Added failing, copy paste tests * Commented out line scan pan tests until 0 velocity bug is addressed * Removed extraneous focal epsilon from LS test ISDs * Extracts distortion models from the Line Scanner and Framer cameras into its own function set (#172) * Moved transverse distortion from line scanner into new file * Updated fixtures for distortion tests * Forgot a semicolon * Extracted radial destortion, and built associated tests * Removed invertDistortion commented code from Linescanner * Reconstructed distortion functions return results * Incorperated invertDistortion function * Corrected spelling, and removed commented out functions * Renamed all dpoint variables to distortionPoint * Removed computeUndistortedFocalPlaneCoordinates function * Renamed distortionPoint to undistortedPoint and distortedPoint where applicable * Fixed typo * Removed doc string parameters * Further extracted transverse destortion out of the Framer * Pulled losToEcf shared functions out into Utilities class (#174) * Initial steps to pull common camera model or math utility functions into a separate Utilities file. * dos2unix line endings again * ../include/usgscsm/UsgsAstroLsSensorModel.h * updates to modularized functions * dos2unix UsgsAstroFrameSensorModel * Forgot to actually add the Utilities class * Keep needed to unix2dos to re-fix line ending caracters * We have some dos line ending and some unix line endings in our code * Copied unit conversion from framer to ls (#177) * Makes GTest fully optional (#175) * removes unused setup.py (#178) * Refactored ISD parsing into utilities and added warnings (#179) * Added utility ISD parsing functions * ISD Parsing Test stub * Added ISD parsing method tests * Added ISD Parsing utilities to Framer * Replaced framer ISD parsing * added check for warning output to bad fram ISD test * Added a bit more testing * Removed ground to image 10m errormessage (#180) * Fixed state being written out and read in differently (#183) * Fixed state being written out and read in differently * Fixed canModelBeConstructedFromState * Updated README (#154) * Updated README * Added BAE license and removed open source license * Gtests for Utilities.cpp (#181) * Finishing modularization of UsgsAstroLsSensorModel::computeViewingPixel * Fixes per request * Removing ISIS references in variable names while I'm here * Beginning to implement tests for modularization changes in LS sensor model class * Adding tests for Utilities as well as a few minor modifications * Making suggested changes and adding test for caculateAttitudeCorrection * Fixing vector size * Updated LS ISD parsing code to match Framer (#186) * updated LS ISD parsing to match style in framer * reverted the 1 to 0 * Fixed attitude test, removed all cerr lines * removed image flip flag * added tests * Fixed computeDistortedFocalPlaneCoordinates test (#187) * Distortion Integration (#184) * Moved transverse distortion from line scanner into new file * Extracted radial destortion, and built associated tests * Reconstructed distortion functions return results * Corrected spelling, and removed commented out functions * Renamed all dpoint variables to distortionPoint * Removed computeUndistortedFocalPlaneCoordinates function * Renamed distortionPoint to undistortedPoint and distortedPoint where applicable * Removed doc string parameters * Added combined new distortion model * Half way through redefining parameters * Major update to distortion and coefficient storage * More debugging * More debugging * More debugging * debugging * debugging * Removed debugging messages and set the output value for remove distortion * Brought changes inline with dev * Updated isd parsing to handle either radial or transverse * Added Distortion Parse function * Split apply and remove distortion, and added the distortion type to each model state * Removed cmath * Removing prints, and other fixes * Updated how coefficients are parsed * Reverted notebook * Function namespace and parameter clean up * More function and parameter clean up * Reverted old code and updated distortion defaults * Small changes for distortion * Updated utilities and fixed failing test * Final LS tests and release prep (#188) * Added image locus tests * Pan LS tests now pass * updated release date in plugin * Forgot to update plugin release date test
DOI-USGS · Feb 22, 2019 · a3d433c · a3d433c
1 parent 9bcdc97
commit a3d433c
Show file tree

Hide file tree

Showing 27 changed files with 2,755 additions and 1,464 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,9 +1,9 @@
 cmake_minimum_required(VERSION 3.10)
 project(usgscsm VERSION 0.0.1 DESCRIPTION "usgscsm library")
 
+include(GoogleTest)
 include(cmake/gtest.cmake)
 include(GNUInstallDirs)
-include(GoogleTest)
 
 set(CMAKE_CXX_STANDARD 11)
 
@@ -18,15 +18,17 @@ else()
 			    PATH_SUFFIXES "csm"
 			    PATHS $ENV{CONDA_PREFIX}/include/)
   find_library(CSM_LIBRARY csmapi PATHS $ENV{CONDA_PREFIX}/lib)
-  
+
   message("--Found CSM Library: ${CSM_LIBRARY}")
   message("--Found CSM Include Directory: ${CSM_INCLUDE_DIR}")
 endif(BUILD_CSM)
 
 add_library(usgscsm SHARED
             src/UsgsAstroPlugin.cpp
             src/UsgsAstroFrameSensorModel.cpp
-            src/UsgsAstroLsSensorModel.cpp)
+            src/UsgsAstroLsSensorModel.cpp
+            src/Distortion.cpp
+	    src/Utilities.cpp)
 
 set_target_properties(usgscsm PROPERTIES
     VERSION ${PROJECT_VERSION}
@@ -42,12 +44,8 @@ target_include_directories(usgscsm
                            ${CSM_INCLUDE_DIR}
 )
 
-# Setup for GoogleTest
-find_package (Threads)
-
 target_link_libraries(usgscsm
-                      ${CSM_LIBRARY}
-                      gtest ${CMAKE_THREAD_LIBS_INIT})
+                      ${CSM_LIBRARY})
 
 if(WIN32)
   install(TARGETS usgscsm RUNTIME DESTINATION ${CMAKE_INSTALL_LIBDIR})
@@ -60,6 +58,12 @@ install(DIRECTORY ${USGSCSM_INCLUDE_DIRS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR
 # Optional build or link against CSM
 option (BUILD_TESTS "Build tests" ON)
 if(BUILD_TESTS)
+
+  # Setup for GoogleTest
+  find_package (Threads)
+
+  target_link_libraries(usgscsm
+                        gtest ${CMAKE_THREAD_LIBS_INIT})
   include(CTest)
   enable_testing()
   add_subdirectory(tests)

diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
@@ -1,100 +1,66 @@
 # CSM-CameraModel
 
-ISD Specification: https://github.com/USGS-Astrogeology/pfeffernusse/blob/master/swagger.yaml
-
-## Setting up dependencies with conda (RECOMMENDED)
-
-Install conda if you do not already have it.
-```bash
-wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-bash miniconda.sh -b
-```
-> You can add a `-p <install-prefix>` to choose where to install miniconda. By default, it will install it to `$HOME/miniconda3`.
-
-### Setting up conda for bash
-Copy and paste the following into a terminal running the `bash` shell:
-```bash
-echo -e "\n\n# Adding miniconda3 to PATH" >> $HOME/.bashrc && \
-echo -e "export PATH=$HOME/miniconda3/bin:\$PATH" >> $HOME/.bashrc && \
-source $HOME/.bashrc && \
-which conda
-```
-> *For more information: [bash installation](https://conda.io/docs/user-guide/install/linux.html "Reference to bash conda install")*
-
-### Setting up conda for tcsh
-Copy and paste the following into a terminal running the `tcsh` shell:
-```tcsh
-echo  "\n\n# Setting up miniconda3 for tcsh" >> $HOME/.cshrc && \
-echo  "source $HOME/miniconda3/etc/profile.d/conda.csh > /dev/null" >> $HOME/.cshrc && \
-source $HOME/.cshrc && \
-which conda
-```
-> *For more information: [tcsh installation](https://github.com/ESMValGroup/ESMValTool/issues/301 "Reference to tcsh conda install")*
-
-### Creating an isolated conda environment
-Run the following commands to create a self-contained dev environment for CSM-CameraModel (type `y` to confirm creation):
-```bash
-conda create -n csmdev -c usgs-astrogeology cmake libcsm
-```
-> *For more information: [conda environments](https://conda.io/docs/user-guide/tasks/manage-environments.html)*
-
-### Activating the environment
-After creating the `csmdev` environment and installing cmake and libcsm into it, we need to activate it. Right now, cmake, libcsm, and their dependencies are isolated to a conda environment and we need to tell conda that we want to use it. The activation command depends on your shell.
-* **bash**: `source activate csmdev`
-* **tcsh**: `conda activate csmdev`
-> *You can add these to the end of your $HOME/.bashrc or $HOME/.cshrc if you want the `csmdev` environment to be active in every new terminal.*
+Community Sensor Model (CSM) compliant sensor models created by USGS Astrogeology
+Science Center.
 
-## Building CSM-CameraModel
-After you've set up conda, you can build CSM-CameraModel:
-
-1. Fork `USGS-Astrogeology/CSM-CameraModel` if you don't already have a fork.
-2. Clone your fork of `CSM-CameraModel` *with `--recursive` option to get the gtest submodule*.
-```bash
-git clone --recursive git@github.com:<your-username>/CSM-CameraModel.git
-cd CSM-CameraModel
-git remote add upstream git@github.com:USGS-Astrogeology/CSM-CameraModel.git
-```
-3. Sync your fork with `upstream` and ensure the gtest submodule is init'd if your fork is old.
-```bash
-git pull upstream master
-git submodule update --init --recursive
-git push -u origin master
-```
-4. `mkdir build && cd build`
-5. `cmake .. && make`
-6. `ctest`
+CSM-CameraModel contains two different sensor models. The first, is a generic
+framing camera model written from scratch. The second is a generic line scan
+camera model based on code from BAE Systems Information and Electronic Systems
+Integration Inc.
+
+## Using CSM-CameraModel
+
+This library is a CSM plugin library that is intended to be dynamically loaded
+at run time along side the
+[CSM API library](https://github.com/USGS-Astrogeology/csm).
+
+Once, the library is loaded, it can be accessed through the CSM Plugin interface.
+For an example of how to do through the CSM c++ interface see the SensorModelFactory
+class in [SensorUtils](https://github.com/USGS-Astrogeology/SensorUtils).
+For an example of how to do this through the CSM Python bindings see this
+[notebook](http://nbviewer.jupyter.org/gist/thareUSGS/4c0eb72799edc33ff4816b2587027148).
+
+From the CSM Plugin interface, a generic framing camera model
+(USGS_ASTRO_FRAME_SENSOR_MODEL) or generic line scan camera model
+(USGS_ASTRO_LINE_SCANNER_SENSOR_MODEL) can be instantiated from suitable Image
+Support Data (ISD). Under the CSM standard, each plugin library can define its
+own ISD format. This library uses an auxiliary JSON formatted file that must be
+next to the image file passed to the CSM::ISD class. We provide an OpenAPI
+server for generating these,
+[pfeffernusse](https://github.com/USGS-Astrogeology/pfeffernusse). The swagger
+specification is located on
+[swaggerhub](https://app.swaggerhub.com/apis/USGS-Astro/pfeffernusse2/0.1.4-oas3).
 
 ---
 
-## Building without a package manager
-To build:
-
-1. Install [libcsmapi](https://github.com/sminster/csm "CSM API")
-    > You can install this with an `INSTDIR` of your choice, or let it default (see [libcsmapi README](https://github.com/sminster/csm/blob/master/README))
-```bash
-mkdir $HOME/csmenv
-cd $HOME
-git clone git@github.com:sminster/csm.git
-cd csm
-make -f Makefile.linux64 all install clean INSTDIR="$csmenv"
-```
-2. Install cmake >= 3.10
-```bash
-cd $HOME
-wget https://cmake.org/files/v3.12/cmake-3.12.0-Linux-x86_64.tar.gz
-tar xzf cmake-3.12.0-Linux-x86_64.tar.gz
-rsync -azv cmake-3.12.0-Linux-x86_64/ $HOME/csmenv/
-echo -e "\n#Prepending csm env to path\nsetenv PATH "$HOME/csmenv/bin:$PATH" >> $HOME/.cshrc
-source $HOME/.cshrc
-```
-3. Fork and clone down this repo and its submodules (gtest)
-```bash
-git clone --recursive git@github.com:<username>/CSM-CameraModel.git
-cd CSM-CameraModel
-git remote add upstream git@github.com:USGS-Astrogeology/CSM-CameraModel.git
-git pull upstream master
-git submodule update --init --recursive
-git push -u origin master
-```
-4. `mkdir build` && `cd build`
-5. `cmake -DCSM_INCLUDE_DIR="${csmenv}/include/csm -DCSM_LIBRARY="${csmenv}/lib/libcsmapi.so .. && make`
+## Build Requirements
+
+* cmake 3.10 or newer
+* GNU-compatible Make
+* a c++11 compliant compiler
+
+This repository has all of its external c++ dependencies included in it. The
+excellent header-only JSON library
+[JSON for Modern C++](https://github.com/nlohmann/json) is included directly in
+the source code. The other two dependencies, the CSM API library, and gtest
+are included as git submodules. When you clone this library make sure you add
+the `--recursive` flag to your `git clone` command. Alaterntively, you can run
+`git submodule update --init --recursive` after cloning. The library can also be
+compiled against an installed versions of the CSM API by setting the BUILD_CSM
+flag to OFF during cmake configuration.
+
+## Building CSM-CameraModel
+
+CSM-CameraModel uses a standard cmake build system. To compile the library, and
+tests use the following commands:
+
+1. `mkdir build && cd build`
+2. `cmake .. && cmake --build .`
+
+## Testing CSM-CameraModel
+
+All of the tests for CSM-CameraModel are written in the googletests framework
+and are run via ctest. To run all of the tests simply run `ctest` in the build.
+
+All of the tests are purposefully written to use generic data that values have
+been hand validated for. This data can be found under `tests/data`.
diff --git a/include/usgscsm/Distortion.h b/include/usgscsm/Distortion.h
@@ -0,0 +1,30 @@
+#ifndef Distortion_h
+#define Distortion_h
+
+#include <vector>
+#include <math.h>
+#include <tuple>
+#include <iostream>
+
+enum DistortionType {
+  RADIAL,
+  TRANSVERSE
+};
+
+// Transverse Distortion
+void distortionJacobian(double x, double y, double *jacobian,
+                        const std::vector<double> opticalDistCoeffs);
+
+void computeTransverseDistortion(double ux, double uy, double &dx, double &dy,
+                                 const std::vector<double> opticalDistCoeffs);
+
+void removeDistortion(double dx, double dy, double &ux, double &uy,
+                      const std::vector<double> opticalDistCoeffs,
+                      DistortionType distortionType,
+                      const double tolerance = 1.0E-6);
+
+void applyDistortion(double ux, double uy, double &dx, double &dy,
+                     const std::vector<double> opticalDistCoeffs,
+                     DistortionType distortionType,
+                     const double desiredPrecision = 0, const double tolerance = 1.0E-6);
+#endif
diff --git a/include/usgscsm/UsgsAstroFrameSensorModel.h b/include/usgscsm/UsgsAstroFrameSensorModel.h
@@ -8,6 +8,12 @@
 #include <gtest/gtest.h>
 #include "RasterGM.h"
 #include "CorrelationModel.h"
+#include "Distortion.h"
+#include "Utilities.h"
+
+#include <json.hpp>
+using json = nlohmann::json;
+
 
 #include <json.hpp>
 using json = nlohmann::json;
@@ -320,12 +326,6 @@ class UsgsAstroFrameSensorModel : public csm::RasterGM {
     FRIEND_TEST(FrameSensorModel, setFocalPlane_AlternatingOnes);
     FRIEND_TEST(FrameSensorModel, distortMe_AlternatingOnes);
 
-    virtual bool setFocalPlane(double dx,double dy,double &undistortedX,double &undistortedY) const;
-    virtual void distortionFunction(double ux, double uy, double &dx, double &dy) const;
-    virtual void distortionJacobian(double x, double y, double &Jxx,
-                                    double &Jxy, double &Jyx, double &Jyy) const;
-
-
 
   private:
     // Input parameters
@@ -335,8 +335,8 @@ class UsgsAstroFrameSensorModel : public csm::RasterGM {
     std::vector<double> m_currentParameterCovariance;
     std::vector<csm::param::Type> m_parameterType;
     std::vector<double> m_noAdjustments;
-    std::vector<double> m_odtX;
-    std::vector<double> m_odtY;
+    DistortionType m_distortionType;
+    std::vector<double> m_opticalDistCoeffs;
     std::vector<double> m_transX;
     std::vector<double> m_transY;
     std::vector<double> m_spacecraftVelocity;
@@ -356,6 +356,10 @@ class UsgsAstroFrameSensorModel : public csm::RasterGM {
     double m_startingDetectorLine;
     std::string m_targetName;
     std::string m_modelName;
+    std::string m_sensorName;
+    std::string m_platformName;
+    std::string m_imageIdentifier;
+    std::string m_collectionIdentifier;
     double m_ifov;
     std::string m_instrumentID;
     double m_focalLengthEpsilon;
@@ -369,6 +373,8 @@ class UsgsAstroFrameSensorModel : public csm::RasterGM {
     int m_nSamples;
     int m_nParameters;
 
+    csm::EcefCoord m_referencePointXyz;
+
     json _state;
     static const int         _NUM_STATE_KEYWORDS;
     static const int         NUM_PARAMETERS;