Updating Examples

Examples/KTaO3.py

@@ -2,6 +2,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from libhreels.calcHREELS import lambin, importMaterials
+import os
 
 ###### Define Strontium titanate film on Silver ####
 ## (Thickness is given in Angstroem as second parm)#
@@ -20,4 +21,9 @@ plt.xlabel('Energy Loss (cm$^{-1}$)')
 plt.title(thinFilm[0][0]['name'])
 plt.ylim(bottom=0.)
 plt.legend()
+
+plt.text(0.99, 0.01,os.path.basename(__file__), fontsize=10, ha='right', va='bottom', transform=plt.gcf().transFigure)
+output_filename = os.path.splitext(__file__)[0] + '.png'
+plt.savefig(output_filename)
+
 plt.show()
\ No newline at end of file

Examples/calcHREELS1.py

@@ -2,6 +2,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from libhreels import calcHREELS
+import os
 
 ###### Define Strontium titanate film on Silver ####
 ## (Thickness is given in Angstroem as second parm)#
@@ -20,4 +21,9 @@ plt.xlabel('Energy Loss (cm$^{-1}$)')
 plt.title(r'SrTiO$_3$')
 plt.ylim(bottom=0.)
 plt.legend()
+
+plt.text(0.99, 0.01,os.path.basename(__file__), fontsize=10, ha='right', va='bottom', transform=plt.gcf().transFigure)
+output_filename = os.path.splitext(__file__)[0] + '.png'
+plt.savefig(output_filename)
+
 plt.show()
\ No newline at end of file

Examples/calcHREELS3.py

@@ -2,12 +2,13 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from libhreels.calcHREELS import lambin, importMaterials
+import os
 
 # Experimental setup as dictionary:
 setup = {
     "e0": 4.0,          # Primary electron energy
     "theta": 60.,       # Scattering angle wrt surface normal
-    "phia": 2.0,
+    "phia": 0.33,
     "phib": 2.0,
     "temperature": 80.,# Sample temperature
     "debug": False
@@ -32,7 +33,7 @@ thinFilm = [[{'eps': 5.1295,
     20000.]]
 
 d = lambin(thinFilm, setup=setup, instrument=instrument)
-x = np.linspace(-100,1000,1100)
+x = np.linspace(-100,1000,2000)
 x,y = d.calcHREELS(x)
 
 ###### Plotting ###########################
@@ -42,4 +43,9 @@ plt.ylabel('Relative HREELS signal')
 plt.xlabel('Energy Loss (cm$^{-1}$)')
 plt.ylim(bottom=0.)
 plt.legend()
+
+plt.text(0.99, 0.01,os.path.basename(__file__), fontsize=10, ha='right', va='bottom', transform=plt.gcf().transFigure)
+output_filename = os.path.splitext(__file__)[0] + '.png'
+plt.savefig(output_filename)
+
 plt.show()
\ No newline at end of file

Examples/showHREELS1.py

 from libhreels import HREELS as hh
-import sys
+import os
 import matplotlib.pyplot as plt
 import numpy as np
 
-# datapath = ".\\data"
+# datapath = "./Examples/data"
 datapath = "./data"
 
 d2 = hh.HREELS('c1a02', datapath=datapath)
@@ -19,4 +19,9 @@ d2.plot(normalized=True, color='gray', factor = 1, label=None)
 d1.ax.set_ylim(bottom=0)
 d1.ax.set_xlim(left=-200,right=1300)
 plt.axvline(x=69,ymax=0.4, linestyle='dashed')
+
+plt.text(0.99, 0.01,os.path.basename(__file__), fontsize=10, ha='right', va='bottom', transform=plt.gcf().transFigure)
+output_filename = os.path.splitext(__file__)[0] + '.png'
+plt.savefig(output_filename)
+
 plt.show()
\ No newline at end of file

Examples/showHREELS2.py

 from libhreels import HREELS 
+import matplotlib.pyplot as plt
+import os
 
 d = './data'
 # d = './Examples/data'
@@ -10,4 +12,9 @@ xmin = 35
 d1 = HREELS.HREELS(file,d)
 d1.plotInfoAmp(factor=factor, xmin=xmin)
 d1.pickPeak()
+
+d1.fig.text(0.99, 0.01,os.path.basename(__file__), fontsize=10, ha='right', va='bottom', transform=plt.gcf().transFigure)
+output_filename = os.path.splitext(__file__)[0] + '.png'
+d1.fig.savefig(output_filename)
+
 d1.show()

libhreels/HREELS.py

@@ -402,9 +402,11 @@ class HREELS:
         ''' Set vertical marker with text label. Note that self.figure() needs to be 
         called before use.'''
         trans = offset(self.ax, 0, 30)
-        plt.plot([x,x],[ymin,y], lw=1, c='black', ls='dashed')
+        # plt.plot([x,x],[ymin,y], lw=1, c='black', ls='dashed')
+        self.ax.plot([x,x],[ymin,y], lw=1, c='black', ls='dashed')
         x = round(x)
-        plt.text(x,y,'%4i' % x, rotation=90, 
+        # plt.text(x,y,'%4i' % x, rotation=90, 
+        self.ax.text(x,y,'%4i' % x, rotation=90, 
         verticalalignment='bottom', horizontalalignment='center', transform=trans)
         return
 

libhreels/calcHREELS.py

@@ -11,21 +11,21 @@ libDir = os.path.dirname(os.path.realpath(__file__))
 setup = {
     "e0": 4.0,
     "theta": 60.,
-    "phia": 2.0,
+    "phia": 0.33,
     "phib": 2.0,
     "temperature": 298.,
     "debug": False
 }
 # Instrumental function describing elastic peak shape:
 instrument = {
-    "width": 19.,
+    "width": 18.,
     "intensity": 100000.,
-    "asym": 0.1,
-    "gauss": 0.8
+    "asym": 0.01,
+    "gauss": 0.88
 }
 
 	
-def importMaterials(string, path=libDir):
+def importMaterials(string='', path=libDir):
     file = os.path.join(myPath(path),'materials.json')
     with open(file) as json_file:
         materials = json.load(json_file)
@@ -33,6 +33,7 @@ def importMaterials(string, path=libDir):
             mat = materials[string]
         except:
             print('No data for material >>{}<< found in {} materials.json!!'.format(string, path))
+            print('Available materials:\n{}\n'.format(materials.keys()))
             mat = 'None'
     return mat