clean up

SarthakJariwala · SarthakJariwala · commit d591cbc41703 · 2020-03-15T17:39:26.000-07:00
diff --git a/PythonGUI_apps/Lifetime_analysis/read_ph_phd.py b/PythonGUI_apps/Lifetime_analysis/read_ph_phd.py
@@ -14,56 +14,38 @@
 
 
 def read_picoharp_phd(datafile):
-    parser = picoharp_phd.PicoharpParser(datafile)
+    parser = picoharp.PicoharpParser(datafile)
     return parser
 
-def phd_to_csv(datafile):
-    parser = read_picoharp_phd(datafile)
-    name, ext = datafile.rsplit('.', 1)
-    
-    total_curves = parser.no_of_curves()
-    y = []
-    for i in range(total_curves):
-        res, curve = parser.get_curve(i)
-        time_window = int(numpy.floor(parser.get_time_window_in_ns(curve_no)))
-        curve = curve[0:time_window]
-        y.append(curve)
-
-parser = picoharp_phd.PicoharpParser(datafile)
-name, ext = datafile.rsplit('.', 1)
-
-#for i in range(parser.no_of_curves()):
+#def phd_to_csv(datafile, return_df = False):
+#    parser = read_picoharp_phd(datafile)
+#    name, ext = datafile.rsplit('.', 1)
 #    
-#    res, curve1 = parser.get_curve(0)
-#    res, curve2 = parser.get_curve(1)
-#    res, curve3 = parser.get_curve(2)
-#    res, curve4 = parser.get_curve(3)
-#    res, curve5 = parser.get_curve(4)
-##    res, curve2 = parser.get_curve(1)
-#    size = len(curve1)
-
-curve_no = 3
-
-res, curve1 = parser.get_curve(curve_no)
-time_window = int(numpy.floor(parser.get_time_window_in_ns(curve_no)))
-curve1 = curve1[0:time_window]
-size = len(curve1)
-X = numpy.arange(0, size*res, res, numpy.float)
-
-plt.figure()
-plt.plot(X,curve1)
-plt.yscale('log')
-plt.ylim([1,1e4])
-#csvname = '%s.csv' % name
-#csv = open(csvname, 'w')
-#
-#for x, y1, y2, y3, y4, y5 in zip(X, curve1, curve2, curve3, curve4, curve5):
-#    csv.write('%f,%d,%d,%d,%d,%d\n' % (x, y1, y2, y3,y4,y5))
-#
-#csv.close()
-#
-#print('Saved %s.' % csvname)
+#    total_curves = parser.no_of_curves()
+#    y = []
+#    for i in range(total_curves):
+#        res, curve = parser.get_curve(i)
+#        time_window = int(np.floor(parser.get_time_window_in_ns(curve_no)))
+#        curve = curve[0:time_window]
+#        y.append(curve)
+#    
+#    df = pd.DataFrame(y)
+#    df.T.to_csv(name+".csv", index=False, header=False)
+#    if return_df == True:
+#        return df.T
 
+def smooth(curve, boxwidth):
+    sm_curve = np.convolve(curve, np.ones(boxwidth)/boxwidth, mode="same")
+    return sm_curve
 
-#if __name__ == '__main__':
-#    main()
+def get_x_y(curve_no, parser, smooth_trace = False, boxwidth = 3):
+    
+    assert type(parser) == picoharp.PicoharpParser, 'must be picoharp parser'
+    res, curve = parser.get_curve(curve_no)
+    time_window = int(np.floor(parser.get_time_window_in_ns(curve_no)))
+    curve = curve[0:time_window]
+    size = len(curve)
+    x = np.arange(0, size*res, res, np.float)
+    if smooth_trace == True:
+        curve = smooth(curve, boxwidth=boxwidth)
+    return x,curve
