From 07ff129e6a305cbce4ae5e1c4b19055d4b3ba6ea Mon Sep 17 00:00:00 2001 From: "Adam L. Taylor" Date: Mon, 22 May 2023 17:05:53 -0400 Subject: [PATCH] Updated README.txt --- README.txt | 40 ++++++++++++++++++++++++++++++++++++++-- 1 file changed, 38 insertions(+), 2 deletions(-) diff --git a/README.txt b/README.txt index 90c9148..1fc00b8 100644 --- a/README.txt +++ b/README.txt @@ -1,4 +1,40 @@ -Freezing +Mouselight freezing/thawing code Code for lossy-compressing raw .tif tiles to .mj2 (freezing), and for -uncompressing .mj2 tiles back to .tifs (thawing). +uncompressing .mj2 tiles back to .tifs (thawing). This code works for +both raw tile folders and octree folders. Any ktx/ folder in +the root input folder will be ignored when freezing. + +To run tests, cd into the source code folder, start Matlab, then do + +modpath + +to add all the needed code to the Matlab path. + +After that, do + +test_all(); + +to run the tests. They take several hours to run. + +An example script to freeze a single sample (either raw tiles or +octree) is in + +freeze_2022_05_30.m + +An example of a thawing script is in + +thaw_2017_12_19_sample.m + +To run such a script on the Janelia cluster, ssh into +login1/login2/submit, then do e.g.: + +bsub -P mouselight \ + -n 1 \ + -oo freeze-2022-05-30-round-1.out.txt \ + -eo freeze-2022-05-30-round-1.err.txt \ + /misc/local/matlab-2019a/bin/matlab -batch "modpath; freeze_2022_05_30" + + +ALT +2022-05-22