Computing neighbors errors

From @NguyenHuynh0594 on Thu Jun 22 2017 05:21:24 GMT+0000 (UTC)

For some reason, I ran into this problem while running this specific flight. This flight contains 176 images, all geotagged.

python /home/winwinnh/Desktop/OpenDroneMap/run.py --use-exif --time --dem --build-overviews --project-path pathtoproject

2017-06-22 00:01:41,792 Computing neighbors
/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/opensfm/dense.py:238: RuntimeWarning: invalid value encountered in arccos
return np.arccos(a.dot(b) / (np.linalg.norm(a) * np.linalg.norm(b)))
2017-06-22 00:01:51,553 Computing depthmap for image 2017_0524_164936_206_geotag.JPG
2017-06-22 00:02:30,196 Computing depthmap for image 2017_0524_164724_132_geotag.JPG
2017-06-22 00:03:07,329 Computing depthmap for image 2017_0524_164603_086_geotag.JPG
2017-06-22 00:03:45,525 Computing depthmap for image 2017_0524_164735_138_geotag.JPG
2017-06-22 00:04:23,963 Computing depthmap for image 2017_0524_165145_278_geotag.JPG
2017-06-22 00:05:04,032 Computing depthmap for image 2017_0524_164542_074_geotag.JPG
2017-06-22 00:05:45,810 Computing depthmap for image 2017_0524_165055_250_geotag.JPG
2017-06-22 00:06:26,299 Computing depthmap for image 2017_0524_164553_080_geotag.JPG
^CTraceback (most recent call last):
File “/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/bin/opensfm”, line 34, in
command.run(args)
File “/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/opensfm/commands/compute_depthmaps.py”, line 25, in run
dense.compute_depthmaps(data, graph, reconstructions[0])
File “/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/opensfm/dense.py”, line 31, in compute_depthmaps
parallel_run(compute_depthmap, arguments, processes)
File “/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/opensfm/dense.py”, line 47, in parallel_run
return [function(arg) for arg in arguments]
File “/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/opensfm/dense.py”, line 68, in compute_depthmap
depth, plane, score = de.compute_patch_match()
KeyboardInterrupt
Traceback (most recent call last):
File “/home/winwinnh/Desktop/OpenDroneMap/run.py”, line 46, in
plasm.execute(niter=1)
File “/home/winwinnh/Desktop/OpenDroneMap/scripts/opensfm.py”, line 128, in process
(context.pyopencv_path, context.opensfm_path, tree.opensfm))
File “/home/winwinnh/Desktop/OpenDroneMap/opendm/system.py”, line 26, in run
raise Exception(“Child was terminated by signal {}”.format(-retcode))
Exception: Child was terminated by signal 2


Copied from original issue: https://github.com/OpenDroneMap/OpenDroneMap/issues/609

From @dakotabenjamin on Thu Jun 22 2017 13:08:26 GMT+0000 (UTC)

It looks like it was just a warning. Can you try to run the thing through and see if you get a dense point cloud despite the warning?

From @NguyenHuynh0594 on Thu Jun 22 2017 17:42:17 GMT+0000 (UTC)

The process just stops every times.

[INFO] Resized 175 images
[INFO] Running ODM Resize Cell - Finished
[INFO] Running ODM OpenSfM Cell
[WARNING] Found a feature matching done progress file in: /media/winwinnh/Work_Storage/Job/Job_1/RED/FLIGHT_5_RED/opensfm/matching_done.txt
[WARNING] Found a valid OpenSfM tracks file in: /media/winwinnh/Work_Storage/Job/Job_1/RED/FLIGHT_5_RED/opensfm/tracks.csv
[WARNING] Found a valid OpenSfM reconstruction file in: /media/winwinnh/Work_Storage/Job/Job_1/RED/FLIGHT_5_RED/opensfm/reconstruction.json
[WARNING] Found a valid OpenSfM meshed reconstruction file in: /media/winwinnh/Work_Storage/Job/Job_1/RED/FLIGHT_5_RED/opensfm/reconstruction.meshed.json
[WARNING] Found a valid OpenSfM NVM reconstruction file in: /media/winwinnh/Work_Storage/Job/Job_1/RED/FLIGHT_5_RED/opensfm/reconstruction.nvm
[DEBUG] running PYTHONPATH=/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/install/lib/python2.7/dist-packages /home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/bin/opensfm undistort /media/winwinnh/Work_Storage/Job/Job_1/RED/FLIGHT_5_RED/opensfm
Traceback (most recent call last):
File “/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/bin/opensfm”, line 34, in
command.run(args)
File “/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/opensfm/commands/undistort.py”, line 23, in run
self.undistort_images(reconstructions[0], data)
File “/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/opensfm/commands/undistort.py”, line 28, in undistort_images
image = data.image_as_array(shot.id)
File “/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/opensfm/dataset.py”, line 65, in image_as_array
return cv2.imread(self.__image_file(image), IMREAD_COLOR)[:,:,::-1] # Turn BGR to RGB
File “/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/src/opensfm/opensfm/dataset.py”, line 57, in __image_file
return self.image_files[image]
KeyError: u’2017_0524_164553_080_geotag.JPG’
Traceback (most recent call last):
File “/home/winwinnh/Desktop/OpenDroneMap/run.py”, line 46, in
plasm.execute(niter=1)
File “/home/winwinnh/Desktop/OpenDroneMap/scripts/opensfm.py”, line 126, in process
(context.pyopencv_path, context.opensfm_path, tree.opensfm))
File “/home/winwinnh/Desktop/OpenDroneMap/opendm/system.py”, line 28, in run
raise Exception(“Child returned {}”.format(retcode))
Exception: Child returned 1
[email protected]:~/Desktop/OpenDroneMap$

From @dakotabenjamin on Thu Jun 22 2017 17:43:24 GMT+0000 (UTC)

Delete the opensfm folder and try again.

From @NguyenHuynh0594 on Thu Jun 22 2017 22:39:06 GMT+0000 (UTC)

It didn’t give that error after deleting opensfm then rerunning it. Also deleted this image cause I thought it was also the problem.

2017-06-22 00:06:26,299 Computing depthmap for image 2017_0524_164553_080_geotag.JPG

The program completed normally after that, except it did not create the orthophoto.tif, only png. The png however is pretty messed up.

[INFO] Running ODM Meshing Cell - Finished
[INFO] Running MVS Texturing Cell
[DEBUG] Writing MVS Textured file in: /media/winwinnh/Work_Storage/JOB/Job_1/RED/FLIGHT_5_RED/odm_texturing/odm_textured_model.obj
[DEBUG] running /home/winwinnh/Desktop/OpenDroneMap/SuperBuild/install/bin/texrecon /media/winwinnh/Work_Storage/JOB/Job_1/RED/FLIGHT_5_RED/opensfm/reconstruction.nvm /media/winwinnh/Work_Storage/JOB/Job_1/RED/FLIGHT_5_RED/odm_meshing/odm_mesh.ply /media/winwinnh/Work_Storage/JOB/Job_1/RED/FLIGHT_5_RED/odm_texturing/odm_textured_model -d gmi -o gauss_clamping -t none
/home/winwinnh/Desktop/OpenDroneMap/SuperBuild/install/bin/texrecon (built on Jun 19 2017, 01:29:30)
Load and prepare mesh:
PLY Loader: comment PCL generated
Reading PLY: 99987 verts… 199908 faces… done.
Generating texture views:
NVM: Loading file…
NVM: Number of views: 155
NVM: Number of features: 0
Loading 100%… done. (Took 12.092s)
Building adjacency graph:
Adding edges 100%… done. (Took 0.563s)
299751 total edges.
View selection:
Building BVH from 199908 faces… done. (Took: 373 ms)
Calculating face qualities 100%… done. (Took 8.584s)
Postprocessing face infos 100%… done. (Took 0.057s)
Maximum quality of a face within an image: 21107.9
Clamping qualities to 54.8859 within normalization.
Writing data cost file… done.
93591 faces have not been seen by a view.
Comp Iter Energy Runtime
0000 0 232052 0.005
0000 1 190052 0.14
0000 2 172870 0.269
0000 3 168730 0.398
0000 4 163491 0.526
0000 5 159771 0.655
0000 6 155958 0.784
0000 7 152373 0.913
0000 8 148780 1.042
0000 9 145036 1.171
0000 10 141882 1.3
0000 11 139464 1.433
0000 12 137220 1.568
0000 13 135216 1.705
0000 14 133659 1.839
0000 15 131885 1.972
0000 16 130568 2.105
0000 17 129711 2.238
0000 18 128429 2.371
0000 19 127737 2.504
0000 20 126805 2.634
0000 21 126111 2.764
0000 22 125629 2.893
0000 23 125085 3.023
0000 24 124517 3.152
0000 25 124194 3.281
0000 26 123902 3.412
0000 27 123275 3.541
0000 28 122861 3.67
0000 29 122712 3.798
0000 30 122332 3.928
0000 31 122112 4.056
0000 32 121927 4.185
0000 33 121846 4.313
0000 34 121701 4.442
0000 35 121683 4.57
0000 36 121488 4.699
0000 37 121319 4.829
0000 38 121123 4.969
0000 39 121073 5.109
0000 40 120946 5.241
0000 41 120973
0000 Increase of energy - stopping optimization
Took: 18.735s
Generating texture patches:
Running… done. (Took 2.564s)
3900 texture patches.
Running global seam leveling:
Create matrices for optimization… done.
Lhs dimensionality: 74741 x 74741
Calculating adjustments:
Color channel 0: CG took 100 iterations. Residual is 9.50446e-05
Color channel 1: CG took 100 iterations. Residual is 9.62947e-05
Color channel 2: CG took 102 iterations. Residual is 9.82383e-05
Took 0.221 seconds
Adjusting texture patches 100%… done. (Took 1.16s)
Running local seam leveling:
Blending texture patches 100%… done. (Took 13.6s)
Generating texture atlases:
Sorting texture patches… done.
Working on atlas 21 100%… done.
Finalizing texture atlases… done. (Took: 5.727s)
Building objmodel:
Saving model… done.
Whole texturing procedure took: 92.558s
[INFO] Running ODM Texturing Cell - Finished
[INFO] Running ODM Georeferencing Cell
[DEBUG] None
[WARNING] No coordinates file. Generating coordinates file: /media/winwinnh/Work_Storage/JOB/Job_1/RED/FLIGHT_5_RED/odm_georeferencing/coords.txt
[WARNING] Could not generate coordinates file. Ignore if there is a GCP file. Error: Error in OdmExtractUtm:
Image is missing GPS Latitude data
For more detailed information, see log file.

[WARNING] Georeferencing failed. Make sure your photos have geotags in the EXIF or you have provided a GCP file.
[WARNING] Found a valid georeferenced model in: /media/winwinnh/Work_Storage/JOB/Job_1/RED/FLIGHT_5_RED/odm_georeferencing/odm_georeferenced_model.ply
[INFO] Running ODM Georeferencing Cell - Finished
[INFO] Running ODM Orthophoto Cell
[DEBUG] running /home/winwinnh/Desktop/OpenDroneMap/build/bin/odm_orthophoto -inputFile /media/winwinnh/Work_Storage/JOB/Job_1/RED/FLIGHT_5_RED/odm_texturing/odm_textured_model.obj -logFile /media/winwinnh/Work_Storage/JOB/Job_1/RED/FLIGHT_5_RED/odm_orthophoto/odm_orthophoto_log.txt -outputFile /media/winwinnh/Work_Storage/JOB/Job_1/RED/FLIGHT_5_RED/odm_orthophoto/odm_orthophoto.png -resolution 20.0 -outputCornerFile /media/winwinnh/Work_Storage/JOB/Job_1/RED/FLIGHT_5_RED/odm_orthophoto/odm_orthophoto_corners.txt
[WARNING] No coordinates file. A georeferenced raster will not be created
[INFO] Running ODM OrthoPhoto Cell - Finished
[INFO] OpenDroneMap app finished - Thu Jun 22 17:25:17 2017
[email protected]:~/Desktop/OpenDroneMap$

From @dakotabenjamin on Fri Jun 23 2017 12:42:33 GMT+0000 (UTC)

Do your images ahve GPS in their EXIF? Otherwise you will need to either geotag them if you have the drone GPS track (most mission planning software has this functionality) or generate a GCP file.