Updated README.txt

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