From 8d006fb3fa30a6c20e78b431f60b974d3f34eff7 Mon Sep 17 00:00:00 2001 From: Seth Parker Date: Fri, 19 May 2023 11:46:46 -0400 Subject: [PATCH] (docs) Add more utils to the apps list --- docs/pages/apps-list.md | 38 +++++++++++++++++++++++++++++++++++++- 1 file changed, 37 insertions(+), 1 deletion(-) diff --git a/docs/pages/apps-list.md b/docs/pages/apps-list.md index a61c42ba4..ce9ceb48d 100644 --- a/docs/pages/apps-list.md +++ b/docs/pages/apps-list.md @@ -190,6 +190,43 @@ purposes. We occasionally upgrade the Volume Package (`.volpkg`) file format to support new features. This tool upgrades existing volume packages to the new format. +## vc_repair_pointsets +A [bug](https://github.com/educelab/volume-cartographer/issues/24) in certain +versions of VC resulted in ordered `.vcps` files where the z-values of points +were off by a few slices. This utility repairs these files by assigning new +z-indices to all points relative to the z-index of the first row: + +| row | old z | new z | +|-----|-------|-------| +| 0 | 400 | 400 | +| 1 | 400 | 401 | +| 2 | 401 | 402 | +| ... | ... | ... | +| 9 | 408 | 409 | +| 10 | 410 | 410 | +| 11 | 410 | 411 | + +The utility can be run from the command line: +```shell +# See what will be modified +vc_repair_pointsets -i pointset.vcps --verbose + +# Repair the pointset and save the result to a new file +vc_repair_pointsets -i pointset.vcps -o repaired.vcps + +# Backup and repair the pointset +cp pointset.vcps pointset.vcps.orig +vc_repair_pointsets -i pointset.vcps -o pointset.vcps +``` + +## vc_visualize_ppm +This file generates visualizations of the positions and normals saved in PPM +files. Files are saved as 32-bit, RGB TIFs: +```shell +# Generate surface_maps_normal.tif and surface_maps_pos.tif +vc_visualize_ppm --volpkg my-project.volpkg --ppm surface.ppm -o surface_maps_ +``` + ## Other utilities These are extra utilities available in the Volume Cartographer build directory when building from source. They are largely developer tools. @@ -207,7 +244,6 @@ vc_ppm_to_pointset vc_project_mesh vc_seg_to_pointmask vc_uv2mesh -vc_visualize_ppm vc_volume_bump vc_volume_client vc_volume_server