diff --git a/.github/workflows/build_test.sh b/.github/workflows/build_test.sh index 774e4fbd8..f5c6ae9c4 100755 --- a/.github/workflows/build_test.sh +++ b/.github/workflows/build_test.sh @@ -169,6 +169,11 @@ tar xfv StereoPipelineTest.tar > /dev/null 2>&1 # this is verbose if [ 1 -eq 0 ]; then # Inspect all tests. Update the failed ones (each 'gold' is overwritten with 'run'). # Make the new 'run' directory the new 'gold'. Do not keep the 'run' directories. + # Go to the directory having StereoPipelineTest as a subdirectory + if [ ! -d "StereoPipelineTest" ]; then + echo "Error: Directory: StereoPipelineTest does not exist" + exit 1 + fi for f in StereoPipelineTest/ss*/run; do g=${f/run/gold} /bin/rm -rfv $g diff --git a/NEWS.rst b/NEWS.rst index 1dcaf2380..a5935b0b7 100644 --- a/NEWS.rst +++ b/NEWS.rst @@ -9,7 +9,12 @@ New camera support: * Added the ability to use the CSM camera model with ASTER images (:numref:`aster_csm`). +New external library support: + * Migrated to PDAL 2.6.0 from libLAS for LAS input/output (in ``pointlas``, + ``point2dem``, and ``pc_align``), as libLAS is no longer developed. + jitter_solve (:numref:`jitter_solve`): + * Added an example for ASTER cameras (:numref:`jitter_aster`). * Added the option ``--weight-image``, to weigh observations based on geographic location of triangulated points (:numref:`limit_ip`). * Can use anchor points with frame cameras. @@ -17,7 +22,6 @@ jitter_solve (:numref:`jitter_solve`): images have different sizes but want to ensure the same point density. * Added the option ``--anchor-weight-image`` that is used to limit where anchor points are placed. - * Added an example for ASTER cameras (:numref:`jitter_aster`). * Can handle a linescan and frame camera rig (almost parallel rays) (:numref:`jitter_no_baseline`). * The roll and yaw constraints no longer assume linescan camera positions and @@ -91,10 +95,13 @@ sfs (:numref:`sfs`): image_calc (:numref:`image_calc`): * Added the ability to create a random image. + +isis + * Expanded the ``jigsaw`` documentation (:numref:`jigsaw`). This is the + ISIS bundle adjustment tool. misc: - * Using PDAL 2.4.2 instead of libLAS for LAS input/output (in ``pointlas``, - ``point2dem``, and ``pc_align``). libLAS is no longer developed. + * Upgraded to GDAL 3.8.0, PROJ 9.3.0, Boost 1.82.0. * Fixed a couple of runtime errors when using conda packages on OSX. * Eliminated a procedure for cleaning the name of an input path that was replacing two slashes with one slash, resulting in inconsistencies. diff --git a/docs/bundle_adjustment.rst b/docs/bundle_adjustment.rst index 405491832..ab8b5b801 100644 --- a/docs/bundle_adjustment.rst +++ b/docs/bundle_adjustment.rst @@ -92,36 +92,50 @@ and its effect on decreasing the stereo triangulation error. Illustration of the triangulation error (intersection error) map (:numref:`triangulation_error`) for a pair of images before (left) and after - (right) using Stereo Pipeline's ``bundle_adjust``. Red and black - colors suggest higher error. + (right) using Stereo Pipeline's ``bundle_adjust``. Red and black colors + suggest higher error. It can be seen that the triangulation error is much + reduced, so the resulting cameras are more self-consistent. -Running ``parallel_stereo`` without using bundle-adjusted camera models:: +Start by running ``parallel_stereo`` without using bundle-adjusted camera +models:: parallel_stereo AS15-M-1134.cub AS15-M-1135.cub run_noadjust/run -Performing bundle adjustment:: +Create a DEM and triangulation error image as in :numref:`point2dem`. - bundle_adjust AS15-M-1134.cub AS15-M-1135.cub -o run_ba/run +Run bundle adjustment:: -Here only camera orientations are refined. How to optimize the -intrinsics (if applicable) is discussed further down + bundle_adjust --camera-weight 0 \ + --tri-weight 0.1 --tri-robust-threshold 0.1 \ + AS15-M-1134.cub AS15-M-1135.cub -o run_ba/run + +Here only camera positions and orientations are refined. How to optimize the +camera intrinsics (if applicable) is discussed further down (:numref:`floatingintrinsics`). -Running ``parallel_stereo`` while using the bundle-adjusted camera models:: +Run ``parallel_stereo`` while using the bundle-adjusted camera models:: parallel_stereo AS15-M-1134.cub AS15-M-1135.cub run_adjust/run \ --bundle-adjust-prefix run_ba/run -A comparison of the two ways of doing stereo is shown in +This should be followed, as before, by creation of an DEM and a +triangulation error image. + +A comparison of the results given these two ways of doing stereo is shown in :numref:`asp-ba-example`. -Bundle adjustment aims to make the cameras more self-consistent but -offers no guarantees about their absolute positions (unless GCP are -used), in fact, the cameras can move away a lot sometimes. The options -``--rotation-weight``, ``--translation-weight``, and -``--camera-weight`` can be used to constrain how much the cameras can -move during bundle adjustment. Note that large values for these may -impact the ability to make the cameras self-consistent. +Bundle adjustment aims to make the cameras more self-consistent but offers no +guarantees about their absolute positions (unless GCP are used), in fact, the +cameras can move away a lot sometimes. The options ``--tri-weight``, +``--rotation-weight``, ``--translation-weight``, and ``--camera-weight`` can be +used to constrain how much the cameras can move during bundle adjustment. Note +that large values for these may impact the ability to make the cameras +self-consistent. + +This program can constrain the triangulated points, and hence the cameras, +relative to a DEM. This option only works when the cameras are already +rather well-aligned to this DEM and only fine-level adjustments are needed. +That is discussed in :numref:`heights_from_dem`. ASP also offers the tool ``parallel_bundle_adjust`` which can create match files using multiple processes spread over multiple machines @@ -964,11 +978,13 @@ can be first shifted up with ``image_calc``. Various such weight images can be merged with ``dem_mosaic`` (:numref:`dem_mosaic`) or the values manipulated with ``image_calc``. +.. _jigsaw: + Bundle adjustment using ISIS ---------------------------- In what follows we describe how to do bundle adjustment using ISIS's -tool-chain. It also serves to describe bundle adjustment in more detail, +toolchain. It also serves to describe bundle adjustment in more detail, which is applicable to other bundle adjustment tools as well, including Stereo Pipeline's own tool. @@ -1000,22 +1016,26 @@ measurement is looking at the same feature. A feature observation in bundle adjustment, from :cite:`moore09` -Bundle Adjustment in ISIS is performed with the ``jigsaw`` executable. +Bundle adjustment in ISIS is performed with the ``jigsaw`` executable. It generally follows the method described in :cite:`triggs00` and determines the best camera parameters that minimize the projection error given by -:math:`{\bf \epsilon} = -\sum_k\sum_j(I_k-I(C_j, X_k))^2` where :math:`I_k` are the tie points on -the image plane, :math:`C_j` are the camera parameters, and :math:`X_k` -are the 3D positions associated with features :math:`I_k`. -:math:`I(C_j, X_k)` is an image formation model (i.e. forward -projection) for a given camera and 3D point. To recap, it projects the -3D point, :math:`X_k`, into the camera with parameters :math:`C_j`. This -produces a predicted image location for the 3D point that is compared -against the observed location, :math:`I_k`. It then reduces this error -with the Levenberg-Marquardt algorithm (LMA). Speed is improved by using -sparse methods as described in :cite:`hartley04`, -:cite:`konolige:sparsesparse`, and :cite:`cholmod`. + +.. math:: + + {\bf \epsilon} = \sum_k\sum_j(I_k-I(C_j, X_k))^2 + +where :math:`I_k` are the tie points on the image plane, :math:`C_j` are the +camera parameters, and :math:`X_k` are the 3D positions associated with features +:math:`I_k`. :math:`I(C_j, X_k)` is an image formation model (i.e. forward +projection) for a given camera and 3D point. To recap, it projects the 3D point, +:math:`X_k`, into the camera with parameters :math:`C_j`. + +This produces a predicted image location for the 3D point that is compared +against the observed location, :math:`I_k`. It then reduces this error with the +Levenberg-Marquardt algorithm (LMA). Speed is improved by using sparse methods +as described in :cite:`hartley04`, :cite:`konolige:sparsesparse`, and +:cite:`cholmod`. Even though the arithmetic for bundle adjustment sounds clever, there are faults with the base implementation. Imagine a case where all @@ -1031,25 +1051,32 @@ have correct scale and translation. ISIS attempts to fix this problem by adding two additional cost functions to bundle adjustment. First of which is -:math:`{\bf \epsilon} = -\sum_j(C_j^{initial}-C_j)^2`. This constrains camera parameters to stay -relatively close to their initial values. Second, a small handful of 3D -ground control points can be chosen by hand and added to the error -metric as :math:`{\bf \epsilon} = \sum_k(X_k^{gcp}-X_k)^2` to constrain -these points to known locations in the planetary coordinate frame. A -physical example of a ground control point could be the location of a -lander that has a well known location. GCPs could also be hand-picked -points against a highly regarded and prior existing map such as the -THEMIS Global Mosaic or the LRO-WAC Global Mosaic. - -Like other iterative optimization methods, there are several conditions -that will cause bundle adjustment to terminate. When updates to -parameters become insignificantly small or when the error, -:math:`{\bf \epsilon}`, becomes insignificantly small, then the -algorithm has converged and the result is most likely as good as it will -get. However, the algorithm will also terminate when the number of -iterations becomes too large in which case bundle adjustment may or may -not have finished refining the parameters of the cameras. + +.. math:: + + {\bf \epsilon} = \sum_j(C_j^{initial}-C_j)^2. + +This constrains camera parameters to stay relatively close to their initial +values. Second, a small handful of 3D ground control points can be chosen by +hand and added to the error metric as + +.. math:: + + {\bf \epsilon} = \sum_k(X_k^{gcp}-X_k)^2 + +to constrain these points to known locations in the planetary coordinate frame. +A physical example of a ground control point could be the location of a lander +that has a well known location. GCPs could also be hand-picked points against a +highly regarded and prior existing map such as the THEMIS Global Mosaic or the +LRO-WAC Global Mosaic. + +Like other iterative optimization methods, there are several conditions that +will cause bundle adjustment to terminate. When updates to parameters become +insignificantly small or when the error, :math:`{\bf \epsilon}`, becomes +insignificantly small, then the algorithm has converged and the result is most +likely as good as it will get. However, the algorithm will also terminate when +the number of iterations becomes too large in which case bundle adjustment may +or may not have finished refining the parameters of the cameras. .. _ba_example: @@ -1062,30 +1089,38 @@ This tutorial for ISIS's bundle adjustment tools is taken from nor the authors of Stereo Pipeline. They were created by USGS and their documentation is available at :cite:`isis:documentation`. -What follows is an example of bundle adjustment using two MOC images of -Hrad Vallis. We use images E02/01461 and M01/00115, the same as used in -:numref:`moc_tutorial`. These images are -available from NASA's PDS (the ISIS ``mocproc`` program will operate on -either the IMQ or IMG format files, we use the ``.imq`` below in the -example). For reference, the following ISIS commands are how to convert -the MOC images to ISIS cubes. +What follows is an example of bundle adjustment using two MOC images of Hrad +Vallis. We use images E02/01461 and M01/00115, the same as used in +:numref:`moc_tutorial`. These images are available from NASA's PDS (the ISIS +``mocproc`` program will operate on either the IMQ or IMG format files, we use +the ``.imq`` below in the example). + +Ensure that ISIS and its supporting data is installed, per :numref:`isis_start`, +and that ``ISISROOT`` and ``ISIS3DATA`` are set. The string ``ISIS>`` is not +part of the shell commands below, it is just suggestive of the fact that we operate +in an ISIS environment. + +Fetch the MOC images anc convert them to ISIS cubes. :: - ISIS> mocproc from=e0201461.imq to=e0201461.cub mapping=no - ISIS> mocproc from=m0100115.imq to=m0100115.cub mapping=no - -Note that the resulting images are not map-projected. Bundle adjustment -requires the ability to project arbitrary 3D points into the camera -frame. The process of map-projecting an image dissociates the camera -model from the image. Map-projecting can be perceived as the generation -of a new infinitely large camera sensor that may be parallel to the -surface, a conic shape, or something more complex. That makes it -extremely hard to project a random point into the camera's original -model. The math would follow the transformation from projection into the -camera frame, then projected back down to surface that ISIS uses, then -finally up into the infinitely large sensor. ``Jigsaw`` does not support -this and thus does not operate on map-projected images. + ISIS> mocproc from=E0201461.imq to=E0201461.cub mapping=no + ISIS> mocproc from=M0100115.imq to=M0100115.cub mapping=no + +Note that the resulting images are not map-projected. That because bundle +adjustment requires the ability to project arbitrary 3D points into the camera +frame. The process of map-projecting an image dissociates the camera model from +the image. Map-projecting can be perceived as the generation of a new infinitely +large camera sensor that may be parallel to the surface, a conic shape, or +something more complex. That makes it extremely hard to project a random point +into the camera's original model. The math would follow the transformation from +projection into the camera frame, then projected back down to surface that ISIS +uses, then finally up into the infinitely large sensor. ``Jigsaw`` does not +support this and thus does not operate on map-projected images. + +ASP's ``bundle_adjust`` program, however, can create and match features +on mapprojected images, and then project those into the original images +(:numref:`mapip`). Before we can dive into creating our tie-point measurements we must finish prepping these images. The following commands will add a vector @@ -1095,9 +1130,9 @@ files. :: - ISIS> footprintinit from=e0201461.cub - ISIS> footprintinit from=m0100115.cub - ISIS> echo *cub | xargs -n1 echo > cube.lis + ISIS> footprintinit from=E0201461.cub + ISIS> footprintinit from=M0100115.cub + ISIS> ls *.cub > cube.lis ISIS> findimageoverlaps from=cube.lis overlaplist=overlap.lis At this point, we are ready to start generating our measurements. This @@ -1126,26 +1161,43 @@ an overlap region. The last two are the spacing in meters between control points. Those values were specifically chosen for this pair so that about 30 measurements would be produced from ``autoseed``. Having more control points just makes for more work later on in this process. -Run ``autoseed`` with the following instruction. +Run ``autoseed`` as follows. + +:: + ISIS> autoseed fromlist=cube.lis overlaplist=overlap.lis \ + onet=control.net deffile=autoseed.def networkid=moc \ + pointid=vallis???? description=hrad_vallis + +Note the option ``pointid=vallis????``. It must be used verbatim. This command +will create ids that will look like ``vallis0001``, ``valis0002``, potentially +up to ``vallis9999``. The number of question marks will control hom many +measurements are created. See `autoseed +`_'s +manual page for more details. + +Inspect this control network with +`qnet `_. Type "qnet" in a terminal, with +no options. A couple of windows will pop up. From the *File* menu of the +``qnet`` window, click on *Open control network and cube list*. Open the +file ``cube.lis``. From the same dialog, open ``control.net``. + +Click on ``vallis0001`` in the Control Network Navigator window, then click on +``view cubes``. This will show the illustration below. + .. figure:: images/qnet/Qnet_AfterAutoseed_400px.png - :name: after_autoseed] + :name: after_autoseed :alt: Autoseed visualization A visualization of the features laid out by ``autoseed`` in ``qnet``. Note that the marks do not cover the same features between images. This is due to the poor initial SPICE data for MOC images. -:: - - ISIS> autoseed fromlist=cube.lis overlaplist=overlap.lis \ - onet=control.net deffile=autoseed.def networkid=moc \ - pointid=???? description=hrad_vallis - -The next step is to perform auto registration of these features between -the two images using ``pointreg``. This program also requires a settings -file that describes how to do the automatic search. Copy the text box -below into a *autoRegTemplate.def* file. +The next step is to perform auto registration of these features between the two +images using `pointreg +`_. +This program also requires a settings file that describes how to do the +automatic search. Copy the text box below into a *autoRegTemplate.def* file. :: @@ -1184,15 +1236,14 @@ to match automatically. Here are the arguments to use in this example of ISIS> pointreg fromlist=cube.lis cnet=control.net \ onet=control_pointreg.net deffile=autoRegTemplate.def -The third step is to manually edit the control and verify the -measurements in ``qnet``. Type ``qnet`` in the terminal and then open -*cube.lis* and lastly *control_pointreg.net*. From the Control Network -Navigator window, click on the first point listed as *0001*. That opens -a third window called the Qnet Tool. That window will allow you to play -a flip animation that shows alignment of the feature between the two -images. Correcting a measurement is performed by left clicking in the -right image, then clicking *Save Measure*, and finally finishing by -clicking *Save Point*. +The third step is to manually edit the control and verify the measurements in +``qnet``. Type ``qnet`` in the terminal and then open *cube.lis*, followed by +*control_pointreg.net*. From the Control Network Navigator window, click, as +before, on the first point, *vallis0001*. That opens a third window called the +Qnet Tool. That window will allow you to play a flip animation that shows +alignment of the feature between the two images. Correcting a measurement is +performed by left clicking in the right image, then clicking *Save Measure*, and +finally finishing by clicking *Save Point*. In this tutorial, measurement *0025* ended up being incorrect. Your number may vary if you used different settings than the above or if MOC @@ -1221,7 +1272,7 @@ a line-scan camera. The *radius=yes* means that the radius of the 3D features can be solved for. Using no will force the points to use height values from another source, usually LOLA or MOLA. -The above command will spew out a bunch of diagnostic information from +The above command will print out diagnostic information from every iteration of the optimization algorithm. The most important feature to look at is the *sigma0* value. It represents the mean of pixel errors in the control network. In our run, the initial error was @@ -1230,11 +1281,23 @@ pixel errors in the control network. In our run, the initial error was Producing a DEM using the newly created camera corrections is the same as covered in the Tutorial. When using ``jigsaw``, it modifies a copy of the spice data that is stored internally to the cube file. -Thus when we want to create a DEM using the correct camera geometry, no -extra information needs to be given to ``parallel_stereo`` since it is already -contained in the file. In the event a mistake has been made, -``spiceinit`` will overwrite the spice data inside a cube file and -provide the original uncorrected camera pointing. Hence, the stereo -command does not change:: + +Thus, when we want to create a DEM using the correct camera geometry, no extra +information needs to be given to ``parallel_stereo`` since it is already +contained in the file. + +In the event a mistake has been made, ``spiceinit`` will overwrite the spice +data inside a cube file and provide the original uncorrected camera pointing. +It can be invoked on each cub file as:: + + ISIS> spiceinit from=image.cub + +Hence, the same ``stereo`` command is used, whether the cubes have been modified +or not:: ISIS> parallel_stereo E0201461.cub M0100115.cub bundled/bundled + +See :numref:`nextsteps` for how how to improve the quality of stereo +correlation results (at the expense of speed), how to create a DEM, +etc. + diff --git a/docs/tools/bundle_adjust.rst b/docs/tools/bundle_adjust.rst index d6febf661..82070e89a 100644 --- a/docs/tools/bundle_adjust.rst +++ b/docs/tools/bundle_adjust.rst @@ -6,9 +6,10 @@ bundle_adjust The ``bundle_adjust`` program performs bundle adjustment on a given set of images and cameras. An introduction to bundle adjustment, and some advanced usage, including solving for intrinsics, can be found in -:numref:`bundle_adjustment`. If it is desired to process a large -number of images, consider using ``parallel_bundle_adjust`` -(:numref:`parallel_bundle_adjust`). +:numref:`bundle_adjustment`. + +If it is desired to process a large number of images, consider using +``parallel_bundle_adjust`` (:numref:`parallel_bundle_adjust`). This tool solves a least squares problem (:numref:`how_ba_works`). It uses Google's `Ceres Solver `_.