Changed cython folder to numcore subfolder

Changed setup.py
Implemented assertion to check if jacobi matrix is the same

desktop.ini

 [.ShellClassInfo]
-IconResource=C:\Users\Jan\Daten\FZ-Jlich\PYRAMID\pyramid.ico,0
+IconResource=C:\Users\Jan\PhD Thesis\Pyramid\icon.ico,0
 [ViewState]
 Mode=
 Vid=

pyramid/magdata.py

+# -*- coding: utf-8 -*-
+"""Load magnetization data from LLG files."""
+
+
+import numpy as np
+
+
+class MagData:
+    
+    '''An object storing magnetization data loaded from a LLG-file.'''
+    
+    def __init__(self, x_mag, y_mag, z_mag, res):  # TODO: electrostatic component!
+        '''Load magnetization in LLG-file format.
+        Arguments:
+            filename - the name of the file where the data are stored
+        Returns:
+            None
+        
+        '''
+        assert np.shape(x_mag) == np.shape(y_mag) == np.shape(z_mag), 'Dimensions do not match!'
+        
+        self.res = res
+        self.dim = np.shape(x_mag)
+        
+        
+        
+        
+        
+        scale = 1.0E-9 / 1.0E-2  #from cm to nm
+        data = np.genfromtxt(filename, skip_header=2)  
+        x_dim, y_dim, z_dim = np.genfromtxt(filename, dtype=int, 
+                                            skip_header=1, 
+                                            skip_footer=len(data[:, 0]))
+        res = (data[1, 0] - data[0, 0]) / scale
+        x_len, y_len, z_len = [data[-1, i]/scale+res/2 for i in range(3)]
+        x_mag, y_mag, z_mag = [data[:, i].reshape(z_dim, y_dim, x_dim) 
+                               for i in range(3,6)]
+        #Reshape in Python and Igor is different, 
+        #Python fills rows first, Igor columns!
+        self.filename = filename
+        self.res = res
+        self.dim = (z_dim, y_dim, x_dim)
+        self.length = (z_len, y_len, x_len)
+        self.magnitude = (z_mag, y_mag, x_mag)
+    
+    def __str__(self):
+        '''Return the filename of the loaded file.
+        Arguments:
+            None
+        Returns:
+            the name of the loaded file as a string
+            
+        '''
+        return self.filename
\ No newline at end of file

pyramid/cython/setup.py → pyramid/numcore/setup.py

-# -*- coding: utf-8 -*-
 """
 Created on Fri May 03 10:27:04 2013
 
@@ -8,8 +7,18 @@ Created on Fri May 03 10:27:04 2013
 #call with: python setup.py build_ext --inplace --compiler=mingw32
 
 import glob
+import numpy
 from distutils.core import setup
+from distutils.extension import Extension
 from Cython.Build import cythonize
+from Cython.Distutils import build_ext
+
+#setup(
+#    cmdclass = {'build_ext': build_ext},
+#    ext_modules = [Extension("multiply",
+#                             sources=["multiply.pyx", "c_multiply.c"],
+#                             include_dirs=[numpy.get_include()])],
+#)
 
 setup(
     name = 'Pyramex',
@@ -18,4 +27,4 @@ setup(
     author = 'Jan Caron',
     author_email = 'j.caron@fz-juelich.de',
     ext_modules = cythonize(glob.glob('*.pyx'))
-)
\ No newline at end of file
+)

pyramid/phasemap.py

@@ -129,7 +129,8 @@ def real_space(mag_data, method, b_0=1, jacobi=None):
     phase = np.zeros((y_dim, x_dim))
     
     # TODO: only iterate over pixels that have a magn. > threshold (first >0)
-    jacobi_fd = jacobi.copy()
+    if jacobi is not None:
+        jacobi_fd = jacobi.copy()
     h = 0.0001
     
     for j in range(y_dim):
@@ -146,8 +147,9 @@ def real_space(mag_data, method, b_0=1, jacobi=None):
                     
                     
     
-    jacobi_diff = jacobi_fd - jacobi
-    assert (np.abs(jacobi_diff) < 1.0E-8).all(), 'jacobi matrix is not the same'
+    if jacobi is not None:
+        jacobi_diff = jacobi_fd - jacobi
+        assert (np.abs(jacobi_diff) < 1.0E-8).all(), 'jacobi matrix is not the same'
     
     return phase
     

scripts/create_random_distribution.py

+# -*- coding: utf-8 -*-
+"""
+Created on Mon May 13 13:05:40 2013
+
+@author: Jan
+"""
+
+import random
+import numpy as np
+import matplotlib.pyplot as plt
+import pyramid.magcreator as mc
+import time
+import pdb, traceback, sys
+from numpy import pi
+
+
+def phase_from_mag():
+    
+    count = 10
+    dim = (128, 128)    
+    
+    random.seed(42)
+    
+    for i in range(count):
+        
+        x = random.rand
+    
+    
+if __name__ == "__main__":
+    try:
+        phase_from_mag()
+    except:
+        type, value, tb = sys.exc_info()
+        traceback.print_exc()
+        pdb.post_mortem(tb)
\ No newline at end of file

setup.py

@@ -18,8 +18,6 @@ setup(
     description = 'PYthon based Reconstruction Algorithm for MagnetIc Distributions',
     author = 'Jan Caron',
     author_email = 'j.caron@fz-juelich.de',
-    package_dir = {'': 'src'},
     packages = ['pyramid'],
-    ext_package = ['pyramex']
-    ext_modules = cythonize(glob.glob(os.path.join('pyramex','*.pyx')))
+    ext_modules = cythonize(glob.glob(os.path.join('pyramid','numcore','*.pyx')))
 )