Commit 34657122 authored by pkda001's avatar pkda001

Updated install instructions.

parent a8eeaafc
......@@ -7,7 +7,11 @@ The closed-loop assistant (CLA) simulation framework (CLAsim) enables simulation
CLAsim is has only been tested on Ubuntu 16.04. This is the recommended platform. We hope to support other platforms soon.
#### Pulse
To install, go to the <a href="https://gitlab.kitware.com/physiology/engine">Pulse repository</a> and follow the instructions there. Be sure to follow the instructions for Ubuntu. *For Java, be sure to use the openjdk version.*
To install, go to the <a href="https://gitlab.kitware.com/physiology/engine">Pulse repository</a> and follow the instructions there. Be sure to follow the instructions for Ubuntu.
If you need to install or update cmake, be sure to use the install from source option.
*For Java, be sure to use the openjdk version.*
#### CLASim
1. Check out the CLAsim repository into a folder of your choice.
......@@ -18,8 +22,39 @@ To install, go to the <a href="https://gitlab.kitware.com/physiology/engine">Pul
# install libconfig++
$ sudo apt-get install libconfig++-dev
~~~
3. Find the paths for the libconfig.h++ and libconfig++.a and input them in clasim.cmake
a. For libconfig.h++
~~~bash
# find the path for libconfig.h++
$ dpkg -L libconfig++-dev | grep libconfig.h++
# output should be
$ <somepath>/libconfig.h++
# for example
$ /usr/include/libconfig.h++
~~~
b. For libconfig++.a
~~~bash
# find the path for libconfig++.a
$ dpkg -L libconfig++-dev | grep libconfig++.a
~~~
c. Go to clasim.cmake file which should be in <PathToCLAsim>
d. On line 6, which should looks like
~~~bash
find_path(CONFIG++_INCLUDE_DIR libconfig.h++ <libconfig.h++ location>)
~~~
replace `<libconfig.h++ location>` with the path (`<somepath>`) you found in step 3a.
3. Install CLASim with CMake
e. On line 7, which should look like
~~~bash
find_library(CONFIG++_LIBRARY NAMES libconfig++.a PATH <libconfig++.a location>)
~~~
replace `<libconfig++.a location>` with the path (`<somepath>`) you found in step 3b.
4. Install CLASim with CMake
~~~bash
# make sure you are in the CLAsim folder
$ cd <PathToCLAsim>
......@@ -34,7 +69,7 @@ To install, go to the <a href="https://gitlab.kitware.com/physiology/engine">Pul
$ make Install
~~~
4. Test that the CLASim executable installed properly.
5. Test that the CLASim executable installed properly.
~~~bash
# go to Pulse bin directory
# (CLAsim executable installs there)
......@@ -45,3 +80,16 @@ To install, go to the <a href="https://gitlab.kitware.com/physiology/engine">Pul
~~~
### Running Demo Examples
The repository comes with demo examples in `/simsrc/mcps2018`. The clasim.cmake file is already configured for `algo1` in this example. In the `resources` folder, you will find a `scenario.cfg` file. Here, you can adjust some of the simulation parameters.
Running step 5 above should run the simulation. The results will be generated in a `results` folder. The patient data will be in a `PulseSimEngine_<patient name>.txt` file.
## Coming Soon
We are working on the following:
- *Data visualization/interaction tools:* making the python scripts for plotting the data more flexible so others can use them to visualize/interact with data generated from the simulation.
- *Flexible output:* making it easier to specify where the results should go.
- *Flexible input:* making it easier to specify where the specific scenario file to use as well as making it easier to control more of the simulation from configuration files without the need to recompile.
- *Modulalar base code:* making the base code more modular so others can create and use their own models of devices and algorithms.
......@@ -24,7 +24,7 @@ configure_file(
${CMAKE_CURRENT_SOURCE_DIR}/simsrc/mcps2018/include/configure_clasim_paths.h
)
# set your simulation source directory
# *** set your simulation source directory
set(SIM_SRC_DIR simsrc/mcps2018/algo1)
# *** include your source files
......
......@@ -31,7 +31,9 @@ pump = {
simulation = {
patients = {
names = ["Hassan", "Gus", "ExtremeFemale"];
# enter patient names in an array form.
# valid patients are Hassan, Gus, ExtremeFemale
names = ["Hassan"];
}
time = {
run = 3600.0; # Time -> Seconds # How long should simulation run
......
# Configuration file for Heart Rate Scenario
## rate : Number of samples per second ## MAX: 50.0 Hz ## Type: double
monitor = {
input_period = 30.0; # in secs MUST be multiple of 0.02
output_period = 60.0; # in secs MUST be >= monitor.input_period
# and be multiple of 0.02
};
controller = {
period = 60.0; # in secs MUST be >= monitor.output_period
# and be multiple of 0.02
patientData = {
enabled = ["HeartRate", "BloodPressure", "BloodVolume"];
}
algorithm= {
wait_10 = 10.0; # Wait for 10 minutes
wait_5 = 5.0; # Wait for 5 minutes
}
};
pump = {
period = 60.0; # Intercommand delay -> to be used later
delay = 15.0; # in secs
};
simulation = {
patients = {
names = ["Hassan"];
}
time = {
run = 3600.0; # Time -> Seconds # How long should simulation run
injury_start = 50.0; # When should injury be introduced to patient
injury_stop = 700.0; # When should injury be stopped
}
path = "results"; # folder to store out sim output files -> to be used later
};
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