Updating for version 0.6.3

Fix #47

pyzebra/__init__.py

@@ -5,4 +5,4 @@ from pyzebra.h5 import *
 from pyzebra.utils import *
 from pyzebra.xtal import *
 
-__version__ = "0.6.1"
+__version__ = "0.6.3"

pyzebra/ccl_io.py

@@ -170,7 +170,7 @@ def parse_1D(fileobj, data_type):
             while len(counts) < s["n_points"]:
                 counts.extend(map(float, next(fileobj).split()))
             s["counts"] = np.array(counts)
-            s["counts_err"] = np.sqrt(s["counts"])
+            s["counts_err"] = np.sqrt(np.maximum(s["counts"], 1))
 
             if s["h"].is_integer() and s["k"].is_integer() and s["l"].is_integer():
                 s["h"], s["k"], s["l"] = map(int, (s["h"], s["k"], s["l"]))
@@ -208,7 +208,7 @@ def parse_1D(fileobj, data_type):
         for name in col_names:
             s[name] = np.array(s[name])
 
-        s["counts_err"] = np.sqrt(s["counts"])
+        s["counts_err"] = np.sqrt(np.maximum(s["counts"], 1))
 
         s["scan_motors"] = []
         for motor, step in zip(motors, steps):

pyzebra/ccl_process.py

@@ -131,7 +131,7 @@ def merge_scans(scan_into, scan_from):
 
     scan_into[scan_motor] = pos_tmp
     scan_into["counts"] = val_tmp / num_tmp
-    scan_into["counts_err"] = np.sqrt(err_tmp)
+    scan_into["counts_err"] = np.sqrt(err_tmp) / num_tmp
 
     scan_from["export"] = False
 
@@ -220,8 +220,7 @@ def fit_scan(scan, model_dict, fit_from=None, fit_to=None):
         else:
             model += _model
 
-    weights = [1 / y_err if y_err != 0 else 1 for y_err in y_err]
-    scan["fit"] = model.fit(y_fit, x=x_fit, weights=weights)
+    scan["fit"] = model.fit(y_fit, x=x_fit, weights=1 / y_err)
 
 
 def get_area(scan, area_method, lorentz):