Updated setup file to compile ublocklu with boost and updated example…

… files

Polymode/Material.py

@@ -134,7 +134,7 @@ def convertwavelength(self, x, wlunits='um'):
 
 		return wl
 
-	def plot(self,wlrange=None, points=100):
+	def plot(self,wlrange=None, points=100, showdata=False):
 		'''
 		Plot the material refractive index
 		* wrange is the wavelength range

Polymode/mathlink/setup.py

@@ -17,14 +17,39 @@
 	print "Numpy doesn't support Cython!"
 
 def configuration(parent_package='', top_path=None):
+    from numpy.distutils.system_info import get_info, NotFoundError
 
     config = Configuration('mathlink', parent_package, top_path)
-    config.add_library('famos',sources=[join('amos','*f'), join('amos','mach','*f')])
-    #config.add_extension('amos', sources=['amos.cpp'], depends=['amos.h'], libraries=['famos', 'g2c'])
-    config.add_extension('bessel_ratios', sources=['bessel_ratios.cpp'], depends=['bessel_function_ratios.h'], libraries=['famos', 'gfortran'])
-
-	#C++ tridiagonal block solver
-    #config.add_extension('ublocklu', sources=['ublas_block_lu/ublocklu.cpp','ublas_block_lu/numimport.cpp'], libraries=[])
+
+    #Compile the amos library
+    config.add_library('famos',
+                    sources=[join('amos','*f'),
+                    join('amos','mach','*f')]
+                    )
+
+    config.add_extension('bessel_ratios',
+                    sources=['bessel_ratios.cpp'],
+                    depends=['bessel_function_ratios.h'],
+                    libraries=['famos', 'gfortran']
+                    )
+
+    #Get blas/lapack resources from numpy
+    lapack_opt = get_info('lapack_opt')
+
+    if not lapack_opt:
+        raise NotFoundError,'no lapack/blas resources found'
+
+    atlas_version = ([v[3:-3] for k,v in lapack_opt.get('define_macros',[]) \
+                      if k=='ATLAS_INFO']+[None])[0]
+
+    #C++ tridiagonal block solver
+    ublock_sources = ['ublas_block_lu/ublocklu.cpp','ublas_block_lu/numimport.cpp']
+    config.add_extension('ublocklu',
+                    sources=ublock_sources,
+                    include_dirs=['ublas_block_lu'],
+                    libraries=['atlas','lapack_atlas','boost_python-mt'],
+                    extra_info = lapack_opt
+                    )
 
     return config
 

examples/ex4_extra_materials.py

@@ -5,13 +5,21 @@
 Material.find_materials('ag')
 
 #Use supplied data from internal material databases
-ag_sopra = Material.Sopra('Ag')
 ag_fs = Material.FreeSnell('ag')
 
-for mat in [ag_sopra, ag_fs]:
+#Compare refractive index of some plastics
+pmma = Material.PMMA()
+pc = Material.Polycarbonate()
+ps = Material.Polystyrene()
+zeo = Material.Zeonex()
+
+#Plot the dispersion of the different materials 
+#This will give some errors as we are extrapolating
+#outside the valid region of wavelengths
+for mat in [pmma, pc, ps, zeo]:
 	print mat
-	mat.plot([0.4,1.0], showdata=True)
-Plotter.title("The refractive index of silver from different sources")
+	mat.plot([0.4,1.2], showdata=True)
+Plotter.title("The refractive index of different optical polymers")
 Plotter.show()
 
 #Example of a new material using Sellmeier coefficients
@@ -36,4 +44,3 @@ def strange_index(self, wavelength):
 #Example of a new material using interpolation of a Sopra formatted file
 #nm_sopra = Material.SopraFile( open('test.nk', 'r') )
 
-

examples/ex6_coordinates.py

@@ -18,11 +18,11 @@
 
 #Plot the point distribution
 subplot(221)
-scatter(x1,y1, 2)
+scatter(x1.ravel(), y1.ravel(), 2)
 axis('tight')
 
 subplot(222)
-scatter(x2,y2, 2)
+scatter(x2.ravel(), y2.ravel(), 2)
 axis('tight')
 
 #Example function