Trouble with LRO NAC Stereo #408
Replies: 12 comments 2 replies
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> stereo_gui M1106796038RE_crop.cal.echo.cub
M1112693469LE_crop.cal.echo.cub
Here there is no output prefix, as the third option, if you want to run
stereo from inside the gui, but your issues are likely not here.
/home/usr/miniconda3/envs/asp/bin/stereo_parse: symbol lookup error:
/home/usr/miniconda3/envs/asp/bin/../lib/libisis.so: undefined symbol:
_ZN3ale4loadENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_S5_b
I never saw this before. Your "libale" is missing. Normally conda should
fetch that. You can try the binary release (non-conda) from:
https://stereopipeline.readthedocs.io/en/latest/installation.html
When I try to run stereo_parallel on the GUI I get the message: "No valid
region for stereo is present. Regions can be selected with Control-Mouse in
each image." I can see that the region is the same, except one is upside
down. Does the orientation of the image make a difference?
No. Orientation does not make a difference. Did you select the same
visually similar images with Control-Mouse? It should draw a rectangle
around each as in the screenshot in the manual.
Let us know how it goes.
… Message ID: <NeoGeographyToolkit/StereoPipeline/repo-discussions/408@
github.com>
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I reinstalled ASP with the binary release, but I am still encountering some errors when running stereo. I also looked at the manual and I selected two sections that were as similar as possible. When running the stereo_gui command it now returns: "Done running stereo." But nothing appears in the run or result file. This is what appears in the terminal: $ stereo_gui M1106796038RE_crop.cal.echo.cub M1112693469LE_crop.cal.echo.cub \
Thank you so much for the reply, I hope this isn't too much of a hastle. |
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This is actually progress. Sorry for the gui noise, that is some Qt
thingie.
Now you are getting the error: Unknown unit for the ellipsoid radii in
M1106796038RE.json.
I will suggest you open up this .json file. I see in my own .json file text
like:
"radii": {
"semimajor": 1737.4,
"semiminor": 1737.4,
"unit": "km"
},
I wonder what you see. Apparently we do not allow any other unit except
meters and km.
This is the first time I see something else in there. I think the unit is
important, otherwise we cannot convert properly to meters.
You can also edit those files and convert the values and units to meters,
and that should let it run, I think.
…On Fri, Aug 4, 2023 at 1:11 PM FlashRisk ***@***.***> wrote:
I reinstalled ASP with the binary release, but I am still encountering
some errors when running stereo. I also looked at the manual and I selected
two sections that were as similar as possible. When running the stereo_gui
command it now returns: "Done running stereo." But nothing appears in the
run or result file. This is what appears in the terminal:
$ stereo_gui M1106796038RE_crop.cal.echo.cub
M1112693469LE_crop.cal.echo.cub \
M1106796038RE.json M1112693469LE.json
--alignment-method local_epipolar
--stereo-algorithm asp_mgm --subpixel-mode 2
run/run
--> Setting number of processing threads to: 4
Not a valid image: run/run. Using this as the output prefix.
Reading: M1106796038RE_crop.cal.echo.cub
Detected large image: M1106796038RE_crop.cal.echo.cub.
Will construct an image pyramid on disk.
Using existing subsampled image: M1106796038RE_crop.cal.echo_sub2.tif
Using existing subsampled image: M1106796038RE_crop.cal.echo_sub4.tif
Using existing subsampled image: M1106796038RE_crop.cal.echo_sub8.tif
Reading: M1112693469LE_crop.cal.echo.cub
Detected large image: M1112693469LE_crop.cal.echo.cub.
Will construct an image pyramid on disk.
Using existing subsampled image: M1112693469LE_crop.cal.echo_sub2.tif
Using existing subsampled image: M1112693469LE_crop.cal.echo_sub4.tif
Using existing subsampled image: M1112693469LE_crop.cal.echo_sub8.tif
qt.qpa.xcb: QXcbConnection: XCB error: 14 (BadIDChoice), sequence: 380,
resource id: 1, major code: 53 (CreatePixmap), minor code: 0
qt.qpa.xcb: QXcbConnection: XCB error: 9 (BadDrawable), sequence: 381,
resource id: 1, major code: 55 (CreateGC), minor code: 0
qt.qpa.xcb: QXcbConnection: XCB error: 9 (BadDrawable), sequence: 382,
resource id: 1, major code: 72 (PutImage), minor code: 0
qt.qpa.xcb: QXcbConnection: XCB error: 13 (BadGC), sequence: 383, resource
id: 71303177, major code: 60 (FreeGC), minor code: 0
qt.qpa.xcb: QXcbConnection: XCB error: 9 (BadDrawable), sequence: 384,
resource id: 1, major code: 139 (Unknown), minor code: 4
qt.qpa.xcb: QXcbConnection: XCB error: 4 (BadPixmap), sequence: 385,
resource id: 1, major code: 54 (FreePixmap), minor code: 0
qt.qpa.xcb: QXcbConnection: XCB error: 143 (Unknown), sequence: 386,
resource id: 71303178, major code: 139 (Unknown), minor code: 27
qt.qpa.xcb: QXcbConnection: XCB error: 143 (Unknown), sequence: 387,
resource id: 71303178, major code: 139 (Unknown), minor code: 7
qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 390,
resource id: 71303179, major code: 138 (Unknown), minor code: 23
qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 391,
resource id: 71303179, major code: 138 (Unknown), minor code: 23
qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 392,
resource id: 71303179, major code: 2 (ChangeWindowAttributes), minor code: 0
qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 393,
resource id: 71303179, major code: 2 (ChangeWindowAttributes), minor code: 0
src win for M1106796038RE_crop.cal.echo.cub: 562 945 3174 2868
src win for M1112693469LE_crop.cal.echo.cub: 362 743 3265 3095
qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 7591,
resource id: 71303179, major code: 2 (ChangeWindowAttributes), minor code: 0
qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 7592,
resource id: 71303179, major code: 2 (ChangeWindowAttributes), minor code: 0
Running:
/home/usr/Downloads/StereoPipeline-3.2.1-alpha-2023-08-04-x86_64-Linux/libexec/parallel_stereo
M1106796038RE_crop.cal.echo.cub M1112693469LE_crop.cal.echo.cub
M1106796038RE.json M1112693469LE.json --alignment-method local_epipolar
--stereo-algorithm asp_mgm --subpixel-mode 2 run/run --left-image-crop-win
562 945 3174 2868 --right-image-crop-win 362 743 3265 3095
--> Setting number of processing threads to: 4
Stereo file ./stereo.default could not be found. Will use default settings
and command line options only.
num_stereo_pairs,1
Will refine the disparity using the ASP subpixel-mode: 2.
Using session: csm
Loading camera model: M1106796038RE_crop.cal.echo.cub M1106796038RE.json
Unknown unit for the ellipsoid radii in M1106796038RE.json. The read value
is:
Traceback (most recent call last):
File
"/home/usr/Downloads/StereoPipeline-3.2.1-alpha-2023-08-04-x86_64-Linux/libexec/parallel_stereo",
line 898, in
settings = run_and_parse_output("stereo_parse", args, sep, opt.verbose)
File
"/home/usr/Downloads/StereoPipeline-3.2.1-alpha-2023-08-04-x86_64-Linux/libexec/asp_system_utils.py",
line 298, in run_and_parse_output
raise Exception('Failed executing: ' + " ".join(call))
Exception: Failed executing:
/home/usr/Downloads/StereoPipeline-3.2.1-alpha-2023-08-04-x86_64-Linux/libexec/stereo_parse
M1106796038RE_crop.cal.echo.cub M1112693469LE_crop.cal.echo.cub
M1106796038RE.json M1112693469LE.json --alignment-method local_epipolar
--stereo-algorithm asp_mgm --subpixel-mode 2 run/run --left-image-crop-win
562 945 3174 2868 --right-image-crop-win 362 743 3265 3095 --corr-seed-mode
1
qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 7789,
resource id: 71303179, major code: 2 (ChangeWindowAttributes), minor code: 0
qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 7790,
resource id: 71303179, major code: 2 (ChangeWindowAttributes), minor code: 0
$
Thank you so much for the reply, I hope this isn't too much of a hastle.
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So turns out there is not a variable that matches the ellipsoid radii name. The closest thing that I found was the following code: "naifkeywords": { I wonder if it has something to do with downloading the .json file from PILOT? Should I try downloading the .json file from somewhere else? Also thank you for replying so fast and offering such good advice. It's really appreciated. |
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Aha. I don't know what "PILOT" is, and I could not find any info online.
Maybe one needs to figure out what tools they use to create .json files.
ASP uses, what I thought until now, the ale library (
https://github.com/DOI-USGS/ale).
We have an example for LRO NAC at
https://stereopipeline.readthedocs.io/en/latest/examples/csm.html (section
on linescan cameras, with prior material there for context).
…On Mon, Aug 7, 2023 at 11:04 AM FlashRisk ***@***.***> wrote:
So turns out there is not a variable that matches the ellipsoid radii
name. The closest thing that I found was the following code:
"naifkeywords": {
"body_code": 301,
"body301_radii": [
1737.4,
1737.4,
1737.4
],
I wonder if it has something to do with downloading the .json file from
PILOT? Should I try downloading the .json file from somewhere else?
Also thank you for replying so fast and offering such good advice. It's
really appreciated.
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@FlashRisk The JSON labels on PILOT are provided as a convenience for users who might want to do advanced searching through PDS labels, but the JSON files themselves are not part of the PDS archive and aren't meant to be ingested by applications like ASP. Don't pass the JSON files to ASP. You don't need the information from the JSON files for ASP anyway because the labels are already embedded in the ISIS cubes that you've prepared. Also, ASP has a script that automates preprocessing of LROC NAC stereopairs, |
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So the confusion here is that JSON is just a way to organize information in a text file, like CSV or YAML. As @dpmayerUSGS points out, the PILOT files are to support searching, but the JSON files that you can give to ASP must contain Community Sensor Model information, they coincidentally are both JSON files, but have wildly different contents. The documentation Oleg points to describes how to create |
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Thank you @rbeyer @dpmayerUSGS and @oleg-alexandrov for the advice, it really helps. I haven't worked with .json files before and assumed they were a part of the PDS archive. However when using the both the stereo_gui and the parallel_stereo commands with just the .cub files I get the following error: Error: ERROR Unable to initialize camera model in Camera Factory. I don't know if this makes any difference, but for the preprocessing of the images I ran the following code: f=M1112693469LE I don't have local SPICE data and instead am using the ISIS SPICE Web Service as I don't have enough space on my computer for all of the kernels. I do have an external hard drive that I might be able to hook up if need be... Also, I haven't worked with the terminal, python, or C++ prior to this so I am a beginner when it comes to all this. If need be I can produce the CSM JSON files using gen_csm.py, but if there is an easier way to do it I would prefer to do that. Sorry if these are stupid questions. |
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I think what you may be seeing here is that while spiceinit can get away
with using web-based kernels, for creating the .cub file, that is not
enough for creating .json files. That needs local kernels (also setting
ISISDATA, ALESPICEROOT).
The lro data kernels seem to take up 270 GB on my hard drive, and that is
humongous.
The trick I use sometimes is to simply download all the kernels it is
complaining about, such as what you see earlier, with lro/kernels/pck/
moon_080317.tf. A list of these should be in the .cub file, I think, though
it may not be complete. So, several attempts may be needed, but it beats
waiting half a day to get the full set.
Also note the remark here:
https://stereopipeline.readthedocs.io/en/latest/examples/csm.html#creation-of-csm-cameras.
That if you get an error about your paths not being the same as the
hard-coded path /usgs/cpkgs/isis3/.
Sorry for all this pain. ISIS is a legacy system, and while it is also
being modernized, there's more to go.
…On Mon, Aug 7, 2023 at 12:09 PM FlashRisk ***@***.***> wrote:
Thank you @rbeyer <https://github.com/rbeyer> @dpmayerUSGS
<https://github.com/dpmayerUSGS> and @oleg-alexandrov
<https://github.com/oleg-alexandrov> for the advice, it really helps. I
haven't worked with .json files before and assumed they were a part of the
PDS archive. However when using the both the stereo_gui and the
parallel_stereo commands with just the .cub files I get the following error:
Error: *ERROR* Unable to initialize camera model in Camera Factory.
*I/O ERROR* Spice file does not exist
[/home/usr/miniconda3/envs/isis/lro/kernels/pck/moon_080317.tf].
I don't know if this makes any difference, but for the preprocessing of
the images I ran the following code:
f=M1112693469LE
lronac2isis from = ${f}.IMG to = ${f}.cub
spiceinit from = ${f}.cub shape = ellipsoid web = true
lronaccal from = ${f}.cub to = ${f}.cal.cub
I don't have local SPICE data and instead am using the ISIS SPICE Web
Service as I don't have enough space on my computer for all of the kernels.
I do have an external hard drive that I might be able to hook up if need
be...
Also, I haven't worked with the terminal, python, or C++ prior to this so
I am a beginner when it comes to all this. If need be I can produce the CSM
JSON files using gen_csm.py, but if there is an easier way to do it I would
prefer to do that.
Sorry if these are stupid questions.
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I was able to make some progress! Although I encountered a new error. The following is a portion of what the program returned: Performing IP matching with alignment. VW Error: RANSAC was unable to find a fit that matched the supplied data. Edit: I ran it a few more times with the error above happening a few more times. But occasionally the following error will occur: [ 2023-Aug-07 14:37:23 ] : Stage 1 --> LOW-RESOLUTION CORRELATION Traceback (most recent call last): (P.S. Sorry for all of the questions I am asking. I hope this isn't too much of a hastle.) |
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Glad to hear you made progress.
The error:
Matching forward
---> Obtained 5002 matches.
Matching backward
---> Obtained 4415 matches.
Matched 21 points.
Inlier cluster:
Triangulation error: 497.697 +- 473.934 meters
Removed 6 points in triangulation filtering.
Removed 0 points in stddev filtering.
Reduced matches to 15
* Writing match file: run/run-L-cropped__R-cropped.match
RANSAC was unable to find a fit that matched the supplied data.
is sign of the left and right images not being similar, as most interest
points failed to match. I will suggest you examine your images side by
side, and seeing if they are similar, if the shadows are in the same place,
etc.
Sometimes LRO NAC images are acquired with vastly different illumination,
and then it will fail.
If that's the case, you may need to fetch new data.
Another thing to watch for is convergence angle.
Here's a writeup of these issues:
https://stereopipeline.readthedocs.io/en/latest/examples/stereo_pairs.html
…On Mon, Aug 7, 2023 at 3:28 PM FlashRisk ***@***.***> wrote:
I was able to make some progress! Although I encountered a new error. The
following is a portion of what the program returned:
Performing IP matching with alignment.
Rough homography--> [****************************************] Complete!
Projected 18184 rays for rough homography.
Number of inliers: 18184.
Aligning right to left for IP capture using rough homography:
Matrix3x3((-0.911702,-0.0555786,0)(0.0624794,-0.904369,0)(-7.44586e-07,-2.15614e-08,1))
Looking for IP in left image...
Using 911 interest points per tile (1024^2 px).
Detecting IP
Removing IP near nodata with radius 4
Building descriptors
Found interest points: 5002
Recording interest points to file: run/run-L-cropped.vwip
Looking for IP in right image...
Using 944 interest points per tile (1024^2 px).
Detecting IP
Removing IP near nodata with radius 4
Building descriptors
Found interest points: 4415
--> Matching interest points using the epipolar line.
Uniqueness threshold: 0.8
Epipolar threshold: 3497.93
Matching forward
---> Obtained 5002 matches.
Matching backward
---> Obtained 4415 matches.
Matched 21 points.
Inlier cluster:
Triangulation error: 497.697 +- 473.934 meters
Removed 6 points in triangulation filtering.
Removed 0 points in stddev filtering.
Reduced matches to 15
* Writing match file: run/run-L-cropped__R-cropped.match
RANSAC was unable to find a fit that matched the supplied data.
VW Error: RANSAC was unable to find a fit that matched the supplied data.
Traceback (most recent call last):
File
"/home/usr/Downloads/StereoPipeline-3.2.1-alpha-2023-08-04-x86_64-Linux/libexec/parallel_stereo",
line 1090, in
normal_run('stereo_pprc', args, msg='%d: Preprocessing' % step)
File
"/home/usr/Downloads/StereoPipeline-3.2.1-alpha-2023-08-04-x86_64-Linux/libexec/parallel_stereo",
line 679, in normal_run
raise Exception('Stereo step ' + kw['msg'] + ' failed')
Exception: Stereo step 0: Preprocessing failed
qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 1846,
resource id: 71303179, major code: 2 (ChangeWindowAttributes), minor code: 0
qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 1847,
resource id: 71303179, major code: 2 (ChangeWindowAttributes), minor code: 0
$
(P.S. Sorry for all of the questions I am asking. I hope this isn't too
much of a hastle.)
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To add to the previous, if you are sure the images are very similar, you
can also consider selecting bigger areas in both clips, if you are using
the gui (ast it seems based on your log).
On Mon, Aug 7, 2023 at 3:38 PM Oleg Alexandrov ***@***.***>
wrote:
… Glad to hear you made progress.
The error:
Matching forward
---> Obtained 5002 matches.
Matching backward
---> Obtained 4415 matches.
Matched 21 points.
Inlier cluster:
Triangulation error: 497.697 +- 473.934 meters
Removed 6 points in triangulation filtering.
Removed 0 points in stddev filtering.
Reduced matches to 15
* Writing match file: run/run-L-cropped__R-cropped.match
RANSAC was unable to find a fit that matched the supplied data.
is sign of the left and right images not being similar, as most interest
points failed to match. I will suggest you examine your images side by
side, and seeing if they are similar, if the shadows are in the same place,
etc.
Sometimes LRO NAC images are acquired with vastly different illumination,
and then it will fail.
If that's the case, you may need to fetch new data.
Another thing to watch for is convergence angle.
Here's a writeup of these issues:
https://stereopipeline.readthedocs.io/en/latest/examples/stereo_pairs.html
On Mon, Aug 7, 2023 at 3:28 PM FlashRisk ***@***.***> wrote:
> I was able to make some progress! Although I encountered a new error. The
> following is a portion of what the program returned:
>
> Performing IP matching with alignment.
> Rough homography--> [****************************************] Complete!
> Projected 18184 rays for rough homography.
> Number of inliers: 18184.
> Aligning right to left for IP capture using rough homography:
> Matrix3x3((-0.911702,-0.0555786,0)(0.0624794,-0.904369,0)(-7.44586e-07,-2.15614e-08,1))
> Looking for IP in left image...
> Using 911 interest points per tile (1024^2 px).
> Detecting IP
> Removing IP near nodata with radius 4
> Building descriptors
> Found interest points: 5002
> Recording interest points to file: run/run-L-cropped.vwip
> Looking for IP in right image...
> Using 944 interest points per tile (1024^2 px).
> Detecting IP
> Removing IP near nodata with radius 4
> Building descriptors
> Found interest points: 4415
> --> Matching interest points using the epipolar line.
> Uniqueness threshold: 0.8
> Epipolar threshold: 3497.93
> Matching forward
> ---> Obtained 5002 matches.
> Matching backward
> ---> Obtained 4415 matches.
> Matched 21 points.
> Inlier cluster:
> Triangulation error: 497.697 +- 473.934 meters
> Removed 6 points in triangulation filtering.
> Removed 0 points in stddev filtering.
> Reduced matches to 15
> * Writing match file: run/run-L-cropped__R-cropped.match
> RANSAC was unable to find a fit that matched the supplied data.
>
> VW Error: RANSAC was unable to find a fit that matched the supplied data.
> Traceback (most recent call last):
> File
> "/home/usr/Downloads/StereoPipeline-3.2.1-alpha-2023-08-04-x86_64-Linux/libexec/parallel_stereo",
> line 1090, in
> normal_run('stereo_pprc', args, msg='%d: Preprocessing' % step)
> File
> "/home/usr/Downloads/StereoPipeline-3.2.1-alpha-2023-08-04-x86_64-Linux/libexec/parallel_stereo",
> line 679, in normal_run
> raise Exception('Stereo step ' + kw['msg'] + ' failed')
> Exception: Stereo step 0: Preprocessing failed
> qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 1846,
> resource id: 71303179, major code: 2 (ChangeWindowAttributes), minor code: 0
> qt.qpa.xcb: QXcbConnection: XCB error: 6 (BadCursor), sequence: 1847,
> resource id: 71303179, major code: 2 (ChangeWindowAttributes), minor code: 0
> $
>
> (P.S. Sorry for all of the questions I am asking. I hope this isn't too
> much of a hastle.)
>
> —
> Reply to this email directly, view it on GitHub
> <#408 (comment)>,
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>
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I was able to get a result! I used different data and that seemed to do the trick. Thank you so much @oleg-alexandrov. You were so helpful through all of my blunders. I will toy around with the different stereo algorithms and other parameters to get some improved results. |
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Glad to hear there is progress. I made the error message more informative, by stating, before these errors, that the user should check the images for similarity in illumination and overlap. This will be soon in the checked in code and for a future release. |
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I am currently having trouble getting a stereo image from LRO NAC images. I am downloading NAC images and JSON Labels from PILOT, then I am running the following code for each respective image:
f=file name(ex. M1112693469LE)
lronac2isis from = ${f}.IMG to = ${f}.cub
spiceinit from = ${f}.cub shape = ellipsoid web = true
lronaccal from = ${f}.cub to = ${f}.cal.cub
lronacecho from = ${f}.cal.cub to = ${f}.cal.echo.cub
(^These commands execute without a hitch.)
I then crop each cal.echo.cub file with qview. Finally, I run one of the 3 following code options:
1.
parallel_stereo M1114696273RE.cal.echo.cub
M1219484122LE.cal.echo.cub result/output
--alignment-method affineepipolar
stereo_gui M1106796038RE_crop.cal.echo.cub M1112693469LE_crop.cal.echo.cub
stereo_gui M1106796038RE_crop.cal.echo.cub M1112693469LE_crop.cal.echo.cub
M1106796038RE.json M1112693469LE.json
--alignment-method local_epipolar
--stereo-algorithm asp_mgm --subpixel-mode 9
run/run
When I run the first option I get the following error:
/home/usr/miniconda3/envs/asp/bin/stereo_parse: symbol lookup error: /home/usr/miniconda3/envs/asp/bin/../lib/libisis.so: undefined symbol: _ZN3ale4loadENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_S5_b
--> Setting number of processing threads to: 4
Stereo file ./stereo.default could not be found. Will use default settings and command line options only.
num_stereo_pairs,1
Using session: isis
Loading camera model: M1106796038RE_crop.cal.echo.cub
None
Traceback (most recent call last):
File "/home/usr/miniconda3/envs/asp/bin/parallel_stereo", line 897, in
settings = run_and_parse_output("stereo_parse", args, sep, opt.verbose)
File "/home/usr/miniconda3/envs/asp/libexec/asp_system_utils.py", line 294, in run_and_parse_output
raise Exception('Failed executing: ' + " ".join(call))
Exception: Failed executing: /home/usr/miniconda3/envs/asp/bin/stereo_parse M1106796038RE_crop.cal.echo.cub M1112693469LE_crop.cal.echo.cub result/output --alignment-method affineepipolar --corr-seed-mode 1
When I try to run stereo_parallel on the GUI I get the message: "No valid region for stereo is present. Regions can be selected with Control-Mouse in each image." I can see that the region is the same, except one is upside down. Does the orientation of the image make a difference?
Any help would be greatly appreciated. Thanks!
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