PC Align

Last month we had a new release of Ames Stereo Pipeline, version 2.3! We’ve performed a lot of bug fixing and implementing new features. But my two new prized features in ASP are pc_align and lronac2mosaic. Today I’d like to only introduce pc_align, a utility for registering DEMs, LIDAR points, and ASP point clouds to each other. All you have to do is specify an input, a reference, and an approximate estimate for how bad you think the misplacement is.

Does that sound like magic? Under the hood, pc_align is performing an implementation of the iterative closest point algorithm (ICP). Specifically we are using internally libpointmatcher library from ETH. What ICP does is iteratively attempt to match every point of the input with the nearest neighbor in the reference point cloud. ICP then solves for a transform that would globally reduce the distances between the current set of matches. Then it repeats itself and performs a new round of matching input to reference and then again solves for another global step. Repeat, repeat, repeat until we no longer see any improvements in the sum of distances between matches.

This means that failure cases for PC_align are when the reference set is too coarse to describe the features seen in the input. An example would be having a HiRISE DEM and then only having a single orbit of MOLA that intersects. A single line of MOLA does nothing to constrain the DEM about the axis of the shot line. The 300 meter post spacing might also not be detailed enough to constrain a DEM that is looking at small features such as dunes on a mostly flat plane. What is required is a large feature that both the DEM and the LIDAR source can resolve.

CTX to HRSC example

Enough about how it works. Examples! I’m going to be uncreative and just process CTX and Gale Crater because they’re fast to process and easy to find. I’ve processed the CTX images P21_009149_1752_XI_04S222W, P21_009294_1752_XI_04S222W, P22_009650_1772_XI_02S222W, and P22_009716_1773_XI_02S223W using stereo options “–alignment affineepipolar –subpixel-mode 1”. This means correlation happens in 15 minutes and then triangulation takes an hour because ISIS subroutines are not thread safe. I’ve plotted these two DEMs on top of a DLR HRSC product, H1927_0000_DT4.IMG. It is important to note that this version of the DLR DEM is referenced against the Mars ellipsoid and not the Aeroid. If your data is referenced against the Aeroid, you’ll need to use dem_geoid to temporarily remove it for processing with pc_align who only understand ellipsoidal datums.

In the above picture, the two ASP created DEMs stick out like sore thumbs and are misplaced by some 200 meters. This is due to pointing information for MRO and subsequently CTX being imperfect (how much can you ask for anyway?). You could run jigsaw and that is the gold standard solution, but that takes a lot of manual effort. So instead let’s use pc_align with the commands shown next.

> pc_align --max-displacement 200 H1927_0000_DT4.tif P22-PC.tif \
        --save-transformed-source-points  -o P22_align/P22_align \
> point2dem --t_srs "+proj=sinu +lon_0=138 +x_0=0 +y_0=0 \
        +a=3396000 +b=3396000 +units=m +no_defs" \
        --nodata -32767 P22_align/P22_align-trans_source.tif

There are 3 important observations to make from the command line above. (1) We are using the max displacement option to set the upper bound of how bad we think we are, 200 meters. (2) I’m feeding the ASP PC file as the input source instead of ASP’s DEM. This is because in (3) with the save transformed source points we’ll be writing out another PC file. PC align can only export PC files so we always have to perform another round of point2dem. It is possible to run stereo -> point2dem -> PC Align -> point2dem, but it means you are unneccesarily resampling your data once. Using the PC file directly from stereo saves us from potential aliasing and removes a point2dem call.

Here’s the final result where both CTX DEMs are plotted on top of the HRSC DEM. Everything looks really good except for that left edge. This might be because the DEM was rendered with incorrect geometry and the output DEM is subtly warped from a perfect solution.

Another cool feature that pc_align author Oleg Alexandrov added was recording the beginning and ending matching errors in CSV files. They’re found with the names <prefix>-{beg,end}_errors.csv. You can load those up in QGIS and plot theirs errors to visualize that pc_align uniformly reduced matching error across the map. (Thanks Ross for showing me how to do this!)


Quite a few MOLA shots can be found inside the CTX footprints. Above is a plot of all MOLA PEDR data for Gale crater. I was able to download this information in CSV format from the MOLA PEDR Query tool from Washington University St. Louis. Conveniently PC_align can read CSV files, just not in the format provided by this tool. PC_align is expecting the data to be in format long, lat, elevation against ellipsoid. What is provide is lat, long, elevation against aeroid, and then radius. So I had to manually edit the CSV in Excel to be in the correct order and create my elevation values by subtracting 3396190 (this number was wrong in first draft) from the radius column. The other added bit of information needed with CSV files is that you’ll need to define the datum to use. If you don’t, pc_align will assume you’re using WGS84.

> pc_align --max-displacement 200 P22-PC.tif mola.csv\
        -o P22_mola/P22_mola --datum D_MARS --save-inv-trans \
> point2dem --t_srs "+proj=sinu +lon_0=138 +x_0=0 +y_0=0 \
        +a=3396000 +b=3396000 +units=m +no_defs" \
        --nodata -32767 P22_mola/P22_mola-trans_reference.tif

Two things to notice in these commands, the inputs are backwards from before and I’m saving the inverse transform.  You can keep things in the same order as when I was aligning to HRSC,  it is just that things will run very slowly. For performance reasons, the denser source should be considered the reference and then you must request the reference to be transformed to the source. You’ll likely routinely be using this inverse form with LIDAR sources.

In the end I was able to reduce alignment error for my CTX DEMs from being over 50 meters to being less than 15 meters against MOLA and from over 100 meter to 40 meters error against HRSC. A result I’m quite happy with for a single night processing at home. You can see my final composited MOLA registered CTX DEMs on the left. The ASP team will have more information about pc_align in LPSC abstract form next year. We also hope that you try out pc_align and find it worth regular use in your research.


I goofed in the MOLA example! Using D_MARS implies a datum that is a sphere with 3396190 meter radius. I subtracted the wrong number from MOLA’s radius measurement before (the value 3396000). That probably had some effect on the registration result shown in the pictures, but this mistake is smaller than the shot spacing of MOLA. Meaning the horizontal registration is fine, but my output DTMs are 190 meters higher than they should have been. FYI, D_MOON implies a datum that is a sphere with radius 1737400 meters.

Code to Semi Global Matching

I’ve received a few emails asking me for the code to my implementation of Semi Global Matching. So here it is in the state that I last touched it. This is my icky dev code and I have no plans for maintaining it. In another month I’ll probably forget how it works. Before you look at the code, take to heart that this is not a full implementation of what Hirschmuller described in his papers. I didn’t implement 16-path integration or the mutual information cost metric.

TestSemiGlobalMatching is my main function. I developed inside a GTest framework while I was writing this code. [source]

The core of the algorithm is inside the following header and source file links, titled SemiGlobalMatching. As you can see it is all in VW-ese. Most of the math looks Eigen-like and there’s a lot of STL in action that I hope you can still read along. [header] [source]

Also, I haven’t forgotten that I promised to write another article on what I thought was a cool correlator idea. I’m still working on that code base so that I can show off cool urban 3D reconstruction using the satellite imagery I have of NASA Ames Research Center and Mountain View. (I think I have Google’s HQ in the shot.)

Update 3/3/2014

Someone emailed me to figure out what is the MOC imagery that the code keeps referring to? In this case MOC stands for the Mars Orbital Camera on board the 1996 Mars Global Surveyor mission. The stereo pair is epipolar rectified images of Hrad Vallis that I use regularly and represent a classical problem for me when performing satellite stereo correlation. A copy of the input imagery is now available here [epi-L.tif][epi-R.tif].

Super Ball Bot


A Super Ball Bot for Titan

At the Intelligent Robotics Group (IRG), my projects are the few that are software only. All my other coworkers actually do work with robotics. Here is a link about fellow IRG’er, Vytas Sunspiral and Team’s research into tensegrity robots. Imagine a robot that is tightly packed in flight and unfolds just before landing and doesn’t need retrorockets or parachutes because it is a compliant structure.

I gave Vytas a lot a skepticism the first time he presented this idea. Now I am happy to eat my words.

Advances in LRO-NAC processing in ASP

Since I last wrote, we’ve hired a new full-time employee. His name is Scott and we assigned him the task of learning ASP and LROC. The first utilities he’ll be contributing back to ASP are lronacjitreg and lronac2mosaic.py. The first utility is very similar to the ISIS utility with a similar name designed for HiRISE. The second utility, lronac2mosaic.py, uses the first tool and can take LRO-NAC EDR imagery and make a non-projected image mosaic. What lronac2mosaic.py does internally is ‘noproj’ and then ‘handmos’ the images together. There is an offset between the images due to model imperfections. Finding the correct offset so the combined images are seamless is the task of lronacjitreg. All of this just a streamed line version of what I wrote in a past blog post.

Previously users and our team only had the option to run all 4 combinations of the 4 LRO-NAC input files through ASP and then glue them together afterwards. Now with the use of lronac2mosaic, we can feed whole LRO-NAC observations into ASP and receive the full DTM in one go. No messy mosaicking of 4 files.

I’ve used Scott’s program successfully to recreate most DTMs that ASU has made via SOCET SET. Using my home server, I’ve been able to recreate 77 of their DTMs to date. We’ve been fixing bugs as we hit them. One of the biggest was in our search range guessing code. The next upcoming release of ASP will have the fruits of that labor. Previously ASP had a bad habit of ignoring elevation maximas in the image as it thought those IP measurements were noise. Now we should have a better track record of getting measurements for the entire image.

One of the major criticisms I’m expecting from the large dump of LRO-NAC DTMs we expect to deliver next year is what is the quality of the placement of our DTMs in comparison to LOLA. Another engineer we have on staff, Oleg, has just the solution for this. He has developed an iterative closest point (ICP) program called pc_align which will be in the next release. This is built on top of ETHZ Autonomous System Lab’s libpointmatcher and has the ability to take DTMs and align them to other DTMs or LIDAR data. This enables us to create well-aligned products that have height values agreeing within tens of meters with LOLA. Our rough testing shows us having a CE90 of 4 meters against LOLA after performing our corrections.

We’re not ready for the big production run yet. One problem still plaguing our process is that we can see the CCD boundaries in our output DTMs. We believe most of this problem is due to the fact that the angle between line of sight of the left and right CCDs changes with every observation. ISIS however only has one number programmed into it, the number provided by the FK. Scott is actively developing an automated system to determine this angle and to make a custom FK for every LRO-NAC observation. The second problem we’re tracking is that areas of high slope are missing from our DEMs. This is partially because we didn’t use Bayes EM for our test runs but it also seems like our disparity filtering is overly aggressive or just wrong. We’ll get on to that. That’s all for now!

Mimicking Zero Gravity

I know I promised a different blog post than this one. However I’m a bit crammed for time lately. However I do have something quick to show …

This summer, my interns Abe Shultz and Benjamin Reinhardt rejuvenated an old gantry system that is used for mimicking zero gravity for small spacecraft. This is part of my work with the NASA SPHERES program. In this video I demonstrate the gantry responding to external forces applied on a wooden analog for SPHERE. In the future the real SPHERE will be loaded up and will use CO2 thrusters to move itself about the room with the gantry responding accordingly.

This test apparatus is one facility I plan to use to test out a new visual navigation system that my coworkers and I are developing. What I’m looking forward to is the vomit comet flight we have scheduled towards the end of the year. This is why I’ve left some of the software development of ASP with others.

Semi-Global Matching

My co-worker Oleg Alexandrov has been working on Ames Stereo Pipeline for a while now. He’s just about touched all parts of the code. This is crystal clear when you look at our logs on Github. One of things he ribs me most about in ASP is that he doesn’t like that we advertise ASP as using up-to-date stereo correlation algorithms. “Come ‘on Man! That’s just not true!” he tells me. Depending on whom you talk to, we’re using primo 90’s research[7] or something re-hashed from the 70’s[1]. Either way, it is clear, we haven’t been tracking along with the current research in our field when it comes to integer correlation. This blog post covers the first part of my own personal research to find a new correlator algorithm that would improve ASP in terms of both runtime and quality. In this post, I’ll be reviewing an algorithm called Semi-Global Matching.

Semi-Global Matching or SGM is a method developed by Heiko Hirschmueller from the DLR. He first wrote about this in his 2005 paper[2]. He then elaborated and proposed further improvements in [3][4]. The best paper to learn the method is probably his second paper[3]. In my opinion his first paper gets side tracked in using a Mutual Information (MI) cost metric when the interesting bit is just SGM. The most exciting bit about this work is that it comes from DLR and is an algorithm they have applied to aerial and satellite mapping. I believe this is the method that was used to create the wonderful HRSC DTMs that some how managed to overcome the weird JPEG artifacts in their raw imagery.

The Algorithm

Heiko might have sped over his SGM algorithm in his first paper because he didn’t view it as being as challenging to implement when compared to the MI cost metric. SGM shares a lot in common with scanline optimization stereo, which has had a lot of prior research but now-a-days is considered a dead end. Let’s review how that worked. Also, the images used for this testing are from the Middlebury Stereo dataset. More information about this data and stereo algorithms applied to them can be found in [8][9][10][11].

Scanline optimization stereo is essentially Viterbi decoding in my mind. We evaluate along an epipolar line. In the case of a rectified image, this is along the horizontal scanline. For each pixel along that scanline we evaluate each possible disparity result. The costs of each pixel along the scanline can then be stacked into a matrix. A scanline was highlighted in the above picture. The cost of each pixel (x-direction) versus each possible disparity value (y-direction) is shown in the picture below. The solution for the disparity along this scanline is then the path through this matrix/image that has minimum costs (dark areas). We also have to include some smoothness constraint otherwise our disparity result could follow the jagged jumps in this map that don’t represent reality.

Finding the minimum path is then an application of Linear Programming. We iterate through the matrix left to right and take a rolling sum. The cost of an element in the rolling sum vector for the current pixel and disparity combination is equal to the cost for the current location plus the lowest summed cost from the set of all possible disparities for the prior pixel location. Heiko applies some additional constraints in that he penalizes the cost when ever the disparity changes. He penalizes higher for multiple disparity value transitions than he does for 1. Penality for an increment of 1 in disparity is P1 and anything greater is P2. This entire paragraph can more elegantly be described in the following equation.

Applying this forward and backward for each scanline we can solve for a disparity map. Here’s an example.

Notice there’s a lot of tearing between the scanlines. The image looks as if we had tracking error on a VCR. We could fix this by using a larger kernel size. For the above, the kernel size was 1 x 1 px. Something more unique would insure matches that are constrained between lines. Another approach would be to insure some smoothness constraint across lines as opposed to just disparity transitions. Heiko’s solution to this issue is what makes SGM what it is. He opted to instead perform scanline optimization at multiple angles and then take the summed cost vector to determine the final disparity result. Note, that even though we evaluate the scanline along an angle, the disparity is still defined as going along the epipolar line (perfectly horizontal in this case). Each line direction produces results like the following:

The sum of their cost vectors and then taking the minimum produces a beautiful result like the following:

My Implementation and Results

All of the pictures above were created with my implementation of SGM. In my version, I only evaluate 8 line directions. So my results are noisier than what’s seen in Heiko’s original paper. Despite this, the end results are pretty impressive. Here’s line up of ASP result, my SGM result, Heiko’s result, and the ground truth result. ASP performs so badly because it has a large kernel size that can’t handle the sudden jumps in depth. ASP then blurs the disparity discontinuities.

Unfortunately I must mention the bad side of this method. There are several cons the first and weakest of arguments is the required CPU time. My implementation of this method takes about 23 seconds to evaluate this with 8 paths. 16 paths like the paper would have doubled the processing time. ASP chops through this image in seconds. Heiko says he got the processing time down to 1.3 seconds in 2005. So I’m doing something horribly wrong and could improve my implementation. However speed is always an issue, some ideas to address this issue are iSGM[5] and wSGM[6]. These are hierarchical methods of SGM and fancy maps to reduce the length required to integrate paths for cost evaluation.

A bigger issue is that SGM requires an absurd amount of memory. All costs for all pixels and all possible disparity values are evaluated up front in a big tensor that has a size of W * H * D * 1 byte. We also need a copy of this tensor for evaluating paths and another to store summing for all paths. Those are two allocations of memory that are W * H * D * 2 bytes. They need to be a higher data type to avoid integer rollover artifacts. This demo set is 450 x 375 px and I evaluated it across 64 possible disparities. Thus SGM required 51 MB. That doesn’t include the memory cost of just loading the images up and allocating space for the disparity result. Imagine tackling a satellite image where we we have a disparity range of 2000 pixels.

Another pesky complaint against SGM is how to figure out what the values should be for the two penalty arguments. Heiko never mentioned what he used; likely he tuned the values for each stereo pair to get best results. However these penalty values ultimately determine how this algorithm responds to occlusion and angled surfaces. What works for World View 1 in glacier regions (low frequencies) might not necessarily apply to World View 1 in the city (square wave patterns). In practice, we would want to have tuned parameters for each instrument we work on and for each type of terrain.

The final and most harsh criticism of SGM is that it can only be applied to 1D disparity searches and the range must be defined beforehand. 1D searches work for calibrated stereo rigs such as the imagery used in this post. However it is my opinion that real data always has imperfections and finding the true disparity requires searching in the Y direction still. Examples of this are linescan cameras that have jitter but the spacecraft ephemeris isn’t sampled high enough to capture such as MOC, HiRISE, and LROC. There’s also the case were the camera isn’t perfect such as the World View cameras where there is a subpixel misregistration of all 50 CCDs. They can’t be easily corrected for because we can’t have raw imagery. ASP also doesn’t have a perfect method for epipolar rectification of linescan cameras. We have a linear approximation with our affine method but the problem is nonlinear.

SGM is still an amazing algorithm that is incredibly useful. There are ton of papers out there that find it to be perfect for their applications. Beside the incredible detail it resolves, my other favorite bit about the algorithm is that its runtime is deterministic. It depends squarely on search range and there is no worst-case path versus best-case path that we have to deal with in ASP’s binary search approach. Despite this, SGM seems to be a non-ideal match for ASP. ASP hopes to address the generic correlation problem where we don’t always trust our camera information or our data. I want something that can still handle 2D searching. In my next post I’ll show off another promising algorithm that seems to address that concern along with runtime and memory requirements. Until then, have some music.

Update: Code is now available here.

Works Cited

[1]  Barnea, D. (1972). A Class of Algorithms for Fast Digital Image Registration. IEEE Transactions on Computers.
[2]  Hirschmuller, H. (2005). Accurate and Efficient Stereo Processing by Semi Global Matching and Mutual Information. CVPR .
[3]  Hirschmuller, H. (2008). Stereo Processing by Semiglobal Matching and Mutual Information. Pattern Analysis and Machine Intelligence .
[4]  Hirschmulller, H., Buder, M., & Ernst, I. (2012). Memory Efficient Semi-Global Matching. Remote Sensing and Spatial Information Sciences .
[5]  Klette, S. H. (2012). Iterative Semi-Global Matching for Robust Driver Assistance Systems. ACCV .
[6]  Spangenberg, R., Langner, T., & Rojas, R. (2013). Weighted Semi-Global Matching and Center-Symmetric Census Transform for Robust Driver Assistance. CAIP .
[7]  Sun, C. (1997). A Fast Stereo Matching Method. Digital Image Computing: Techniques and Application.
[8] Scharstein, D., Szeliski, R. (2002). A taxonomy and evaluation of dense two-frame stereo correspondence algorithms. International Journal of Computer Vision .
[9] Scharstein, D., Szeliski, R. (2003). High-accuracy stereo depth maps using structured light. CVPR .
[10] Scharstein, D., Pal, C. (2007). Learning conditional random fields for stereo. CVPR .
[11] Hirschmuller, H., Scharstein, D. (2007). Evaluation of cost functions for stereo matching. CVPR .