From 4319f4e394c91677343467a9f53f8841e91fd24d Mon Sep 17 00:00:00 2001
From: Marco Cammarata <marcocamma@gmail.com>
Date: Fri, 27 Jan 2017 15:40:26 +0100
Subject: [PATCH] added errorbar weighting and filter for nans and inf

---
 xray/peaks.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/xray/peaks.py b/xray/peaks.py
index 3e8224a..a1f42ad 100644
--- a/xray/peaks.py
+++ b/xray/peaks.py
@@ -1,9 +1,21 @@
 import lmfit
 import numpy as np
+import logging as log
 
 pv = lmfit.models.PseudoVoigtModel()
 
-def fitPeak(x,y,autorange=False):
+def fitPeak(x,y,err=1,autorange=False):
+  if isinstance(err,np.ndarray):
+    if np.all(err==0):
+      err = 1
+      log.warn("Asked to fit peak but all errors are zero, forcing them to 1")
+    elif np.isfinite(err).sum() != len(err):
+      idx = np.isfinite(err)
+      x = x[idx]
+      y = y[idx]
+      err = err[idx]
+      log.warn("Asked to fit peak but some errorbars are infinite or nans,\
+                excluding those points")
   if autorange:
     # find fwhm
     idx = np.ravel(np.argwhere( y<y.max()/2 ))
@@ -16,5 +28,5 @@ def fitPeak(x,y,autorange=False):
     x = x[idx]
     y = y[idx]
   pars = pv.guess(y,x=x)
-  ret  = pv.fit(y,x=x,params=pars)
+  ret  = pv.fit(y,x=x,weights=1/err,params=pars)
   return ret