{{ message }}
Cucim support for get_mask_edges and get_surface_distance#7008
Merged
wyli merged 13 commits intoOct 1, 2023
Conversation
Signed-off-by: John Zielke <john.zielke@snkeos.com>
Contributor
Author
Signed-off-by: John Zielke <john.zielke@snkeos.com>
7 tasks
Signed-off-by: John Zielke <john.zielke@snkeos.com>
Signed-off-by: John Zielke <john.zielke@snkeos.com>
Signed-off-by: John Zielke <john.zielke@snkeos.com>
Signed-off-by: John Zielke <john.zielke@snkeos.com>
Signed-off-by: John Zielke <john.zielke@snkeos.com>
Signed-off-by: John Zielke <john.zielke@snkeos.com>
Contributor
|
/build |
Contributor
|
/build |
Contributor
wyli
approved these changes
Oct 1, 2023
wyli
left a comment
Contributor
There was a problem hiding this comment.
Thanks, it looks good to me.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.

Description
Add support for cucim for
get_mask_edgesandget_surface_distance. This provides significant speedup in surface related metrics. Profiling on my system gave 3-20x speedups depending on the input shape:[---------------- (250, 250, 250) -----------------]
| cpu | cuda
1 threads: -----------------------------------------
random()>0.2 | 26400.8 | 1306.3
random()>0.5 | 26411.8 | 1399.1
random()>0.8 | 29993.2 | 1009.5
create_spherical_seg_3d | 623.8 | 45.0
Times are in milliseconds (ms).
[--------------- (100, 100, 100) ----------------]
| cpu | cuda
1 threads: ---------------------------------------
random()>0.2 | 1332.5 | 140.2
random()>0.5 | 1276.3 | 128.1
random()>0.8 | 1179.2 | 89.1
create_spherical_seg_3d | 111.7 | 44.0
Times are in milliseconds (ms).
[---------------- (50, 50, 50) ----------------]
| cpu | cuda
1 threads: -------------------------------------
random()>0.2 | 154.5 | 47.4
random()>0.5 | 166.7 | 39.3
random()>0.8 | 165.0 | 38.0
create_spherical_seg_3d | 77.2 | 44.4
Times are in milliseconds (ms).
where create_spherical_seg_3d uses the same function from test_hausdorff_distance, and binarizes random array using
random(shape)>ratio.Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.