Commit 3d910476 authored by sp8646's avatar sp8646
Browse files

add readme

parent 6c560309
##Setup
### 1) create folder structure
- create local directory LOCAL_DIR
- clone code to LOCAL_DIR
- add folders data and results in LOCAL_DIR
so the final structure is
--LOCAL_DIR
|
-- data (contains the ground truth data sets)
|
-- code
|
-- results (synthetically degraded segmentation masks stored will be stored here)
### 2) create environment
- install packages from requirements
- install gurobi 9.1.1 (see help_gurobi.txt)
## run tracking
## Reproduce data sets
### 1) download data sets
- go to http://celltrackingchallenge.net
and download : Fluo-N2DH-SIM+ and FLuo-N3DH-SIM+ and unpack and save in data directory
### 2) run code
- run create_synth_segm_data.py to create synthetically
In the tracking step a solver (Gurobi) is used to solve integer linear programs
For academic purposes, Gurobi provides an academic license free of charge.
To run the tracking, Gurobi needs to be installed:
1) register at https://www.gurobi.com
if academia: select academic license
2)download gurobi optimizer version 9.1.1 from https://www.gurobi.com/downloads/gurobi-software/
3) move download to a local directory (LOCAL_DIR)
mv /../Downloads/gurobi9.1.1_linux64.tar.gz /LOCAL_DIR
4) change to local dir and unzip
tar xvfz gurobi9.1.1_linux64.tar.gz
5) add gurobi to path
export=$PATH:/LOCAL_DIR/gurobi911/linux/bin
6) get gurobi license key https://www.gurobi.com/downloads/end-user-license-agreement-academic/
7) copy license key to comand line
grbgetkey xxxx-xxxx-xxx
hit enter (select provided default directory to store license file)
8) run tracking
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