Commit 8a68df9f authored by actb's avatar actb

updated readme.md

parent 9067871a
......@@ -34,7 +34,7 @@ open this link: <https://leverjs.net/download/>. click on the latest (windows --
you can download sample image data from the link as well, as well as a zip file of a recent git archive (better to see "INSTALLING FROM SOURCE" below)
Finally, (sort of optionally, you really will want this) **install the matlab 2017b runtime (v9.3)** so analysis and image import to work: https://www.mathworks.com/products/compiler/matlab-runtime.html. If you have matlab 2017b installed (including database toolkit) you can skip this step.
Finally, (sort of optionally, you really will want this) **install the matlab 2019b runtime (v9.7)** so analysis and image import to work: https://www.mathworks.com/products/compiler/matlab-runtime.html. If you have matlab 2019b installed (including database toolkit) you can skip this step.
<h1>INSTALLING FROM SOURCE</h1>
......@@ -46,7 +46,7 @@ Finally, (sort of optionally, you really will want this) **install the matlab 20
1. install python 2.7 (and make sure it's on your path!). from the node.js command prompt, type 'python' to be sure. NOTE I did not need to do this explicitly on the mac.
2. if you want to analyze the images, and you don't have **matlab 2017b runtime** installed, download and and run the mcr installer from here: https://www.mathworks.com/products/compiler/matlab-runtime.html
2. if you want to analyze the images, and you don't have **matlab 2019b runtime** installed, download and and run the mcr installer from here: https://www.mathworks.com/products/compiler/matlab-runtime.html
3. install git lfs support from https://git-lfs.github.com/
......@@ -102,7 +102,7 @@ some users have reported trouble with npm not installing electron (once on a Mac
<h3>notes</h3>
a. you will need to have matlab2017b installed, or the runtime. download the runtime from https://www.mathworks.com/products/compiler/matlab-runtime.html
a. you will need to have matlab2019b installed, or the runtime. download the runtime from https://www.mathworks.com/products/compiler/matlab-runtime.html
b. the software works on windows, unix and mac. for unix and mac, the matlab path in cmdloop.js is hardcoded (see CmdLoop.js.getMCRpath()). for mac, the path to the nodejs binary is also hardcoded in the importer (matlab/+Import/leverImport.m) as /usr/local/bin/node. this is because matlab on mac doesn't seem to pick up the system path variable...
......@@ -133,6 +133,34 @@ b. it is possible to open the .LEVER file directly using e.g. the DB Browser sql
c. to debug matlab process, edit config.js and set 'debugMatlab' to true. start the image window renderer program, pick your algorithms and select reseg all (or next). then start matlab. run matlabpollDB('\path\to\leverFile.LEVER'). Or, just run matlabPollDB and it usually finds the right LEVER file automagically (from lever.state tidbit left by CmdLoop.js).
<h1>interactive use</h1>
leverjs can be used interactively from any image analysis environment. MATLAB has the most helper code.
prerequisites,
(1) add to your path: hydra-image-processor/source/src/matlab and leverUtilities/src/matlab
(2) run AddSQLiteToPath();
now, some useful tidbits:
```
strDB='\path\to\your\leverFile.LEVER';
[conn,CONSTANTS,segParams]=openDB(strDB);
```
conn is the database connection to your lever file. it is used in almost all the MATLAB entry points.
segParams are the segmentation settings on your file. these need to be set first. if you want to debug
your segmentation (i.e. Segment.frameSegment()) be sure segParams.minimumRadius_um is set to a scalar
(not an ensemble segmentation).
```
% segment time t
cx=Segment.frameSegment(conn,t,CONSTANTS,segParams);
% write results into database for visualization - most useful for 3-d viewing
% be sure there are not already objects at time t in the database
Write.CreateCells(conn,cx);
```
<h1>scripting and image capture for visualization</h1>
see the scripting tab in the electron (stand-alone) image window for more details...there is now a matlab/+MovieMaker folder with two examples.
......
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