|
@@ -1 +1,47 @@
|
|
|
-# Instructions on use
|
|
|
|
|
|
|
+# Instructions
|
|
|
|
|
+
|
|
|
|
|
+## Install code
|
|
|
|
|
+
|
|
|
|
|
+Install with
|
|
|
|
|
+
|
|
|
|
|
+```bash
|
|
|
|
|
+git clone https://git0.fmf.uni-lj.si/studen/PBPK_public.git
|
|
|
|
|
+```
|
|
|
|
|
+
|
|
|
|
|
+Use [GIT][GITinstaller] for Windows. More instructions on the web page.
|
|
|
|
|
+
|
|
|
|
|
+## Dependencies
|
|
|
|
|
+
|
|
|
|
|
+On top of python, you'll need numpy and scipy. Install using pip
|
|
|
|
|
+
|
|
|
|
|
+```
|
|
|
|
|
+pip3 install numpy,scipy
|
|
|
|
|
+```
|
|
|
|
|
+
|
|
|
|
|
+Use windows terminal (ie. cmd.exe)
|
|
|
|
|
+
|
|
|
|
|
+## Use
|
|
|
|
|
+
|
|
|
|
|
+Follow `cDiazepam.json`. Basic instructions:
|
|
|
|
|
+- `runSolver.main(setup,model,parameters,jobDir,srcDir)`
|
|
|
|
|
+ This constructs a model from the model file, sets it up with parameters from parameters file, uses the setup to drive calculation which it stores in jobDir. If srcDir is not a string NONE, it takes the solution from srcDir and continues it until tmax in setup is reached.
|
|
|
|
|
+
|
|
|
|
|
+- `runSolver.loadSolutionFromDir(jobDir,True)`
|
|
|
|
|
+ Read solution from dir jobDir. Returns a dict with fields
|
|
|
|
|
+ t,sol,se,qt,sOut,lut,lutSE,setup,model,parameters,qt,sOut where:
|
|
|
|
|
+
|
|
|
|
|
+ - t is the sequence of time points
|
|
|
|
|
+ - sol is the list of solutions for each compartment at each time point
|
|
|
|
|
+ - se is the error
|
|
|
|
|
+ - lut is the look up table of named containers / indices pairs where index points to a list in solution, ie `['sol'][lut[containerName],j]` is the concentration of containerName at time point j
|
|
|
|
|
+ - lutSE is the lookup table of parameters
|
|
|
|
|
+ - setup is the parsed setup file
|
|
|
|
|
+ - parameters are the parsed parameters
|
|
|
|
|
+ - model is the model parse model
|
|
|
|
|
+
|
|
|
|
|
+
|
|
|
|
|
+
|
|
|
|
|
+
|
|
|
|
|
+
|
|
|
|
|
+[GITinstaller]: https://www.git-scm.com/download/win
|
|
|
|
|
+
|
