initial commit

Author: mjlaine

bin/eppesroutine.py

@@ -0,0 +1,112 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8; -*-
+
+# Eppes command line routine
+# Reads files defined in a conf file given as input argument with -c (default name is eppes.cfg).
+# Overwrites mufile, sigfile, wfile and nfile on output.
+
+import numpy as np
+import eppes
+# from eppes import config
+
+def main(*args):
+
+    # Read configuration
+    opts = eppes.config.parseargs(*args[1:])
+
+    # define bounds
+    if len(opts.boundsfile)>0:
+        bounds = np.loadtxt(opts.boundsfile)
+    else:
+        bounds = None
+
+    # load mu and sig from file
+    mu = np.loadtxt(opts.mufile)
+    sig = np.loadtxt(opts.sigfile)
+
+    if (mu.shape[0] != sig.shape[0]) | (mu.shape[0] != sig.shape[1]) :
+        print('mu and sig shapes do not match')
+        return 1
+
+    # sample only, no update
+    if opts.sampleonly == 1:
+        newsample = eppes.propose(opts.nsample,mu,sig,bounds=bounds)
+        if opts.lognor:
+            newsample = np.exp(newsample)
+        if opts.verbosity:
+            print(mu)
+            print(sig)
+            print(newsample)
+        np.savetxt(opts.sampleout,newsample)
+        return 0
+
+    # load W and N, current sample and the scores
+    w = np.loadtxt(opts.wfile)
+    n = np.loadtxt(opts.nfile)
+    oldsample = np.loadtxt(opts.samplein)
+    scores = np.loadtxt(opts.scorefile)
+    nsample = oldsample.shape[0]
+    if opts.lognor:
+        oldsample = np.log(oldsample)
+
+
+    eppes.tomatrix(scores)
+    if scores.shape[0] != nsample:
+        print('scores and sample do not match')
+        return 1
+    # turn scores into ranks
+    if opts.useranks:
+        scores = eppes.rankscores(scores)
+        if opts.verbosity:
+            print(scores)
+
+    if np.size(np.shape(scores)) > 1:
+        if np.shape(scores)[1] > 1:
+            scores = eppes.combinescores(scores,opts.combine_method)
+            eppes.tomatrix(scores)
+            if opts.verbosity:
+                print(scores)
+        
+    # resample and update parameters mu,w,sig,n
+    theta,wout = eppes.logresample(oldsample,scores)
+    mu,w,sig,n = eppes.eppesupdate(theta,mu,w,sig,n, maxsteprel=opts.maxsteprel)
+
+    # optionally, fix N and W
+    if opts.maxn>0:
+        n = min(n,opts.maxn)
+    if len(opts.w00file)>0:
+        w00 = np.loadtxt(opts.w00file)
+        if w.shape != sig.shape:
+            print('error in w00 shape, not using it')
+        else:
+            w = w + w00
+
+    # generate new sample, based on updated mu and sig
+    newsample = eppes.propose(opts.nsample,mu,sig,bounds=bounds)
+
+    if opts.lognor:
+        newsample = np.exp(newsample)
+    
+    if opts.verbosity:
+        print(mu)
+        print(sig)
+        print(newsample)
+        print(n)
+
+    # save all back to files (they are over written!)
+    np.savetxt(opts.sampleout,newsample)
+    np.savetxt(opts.mufile,mu)
+    np.savetxt(opts.sigfile,sig)
+    np.savetxt(opts.wfile,w)
+    np.savetxt(opts.nfile,np.array([n]))
+    if len(opts.winfofile)>0:
+        np.savetxt(opts.winfofile,wout)
+    return 0
+
+   
+if __name__ == "__main__":
+    import sys 
+    status = main(*sys.argv)
+    # need some nice way to pass failure to the caller
+    if status:
+        sys.exit("Some error happened during the call, status="+str(status))