From 90d038a639fe0623e69badb2a8eb2b00b44ed066 Mon Sep 17 00:00:00 2001
From: Jan Caron <caron@fz-juelich.de>
Date: Mon, 6 May 2013 17:00:34 +0200
Subject: [PATCH] Added initcython.py (import this befor importing .pyx files
to use Cython-Code)
---
scripts/get_jacobi.py | 2 ++
src/pyramex/.sconsign.dblite | Bin 2379 -> 0 bytes
src/pyramex/SConstruct | 12 +++++++++---
src/pyramex/initcython.py | 32 +++++++++++++++++++++++++++++++
src/pyramex/setup.py | 28 ++++-----------------------
src/pyramid/phasemap.py | 36 ++++++++++++++++++++++-------------
6 files changed, 70 insertions(+), 40 deletions(-)
delete mode 100644 src/pyramex/.sconsign.dblite
create mode 100644 src/pyramex/initcython.py
diff --git a/scripts/get_jacobi.py b/scripts/get_jacobi.py
index ad3091b..42de910 100644
--- a/scripts/get_jacobi.py
+++ b/scripts/get_jacobi.py
@@ -48,6 +48,8 @@ def phase_from_mag():
np.savetxt('../output/jacobi.npy', jacobi)
print 'Time for Real Space Approach with Jacobi-Matrix (Slab): ' + str(toc - tic)
+
+
return jacobi
diff --git a/src/pyramex/.sconsign.dblite b/src/pyramex/.sconsign.dblite
deleted file mode 100644
index 0e8ccb44f58bbb31c7780f36f464f52b6d17a122..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/src/pyramex/SConstruct b/src/pyramex/SConstruct
index dbcb3e9..7f4fe34 100644
--- a/src/pyramex/SConstruct
+++ b/src/pyramex/SConstruct
@@ -6,11 +6,17 @@ PYTHON_LIBPATH = distutils.sysconfig.get_python_lib()
PYTHON_INCPATH = distutils.sysconfig.get_python_inc()
PYTHON_LIBRARY = "python" + sys.version[:3]
-cythonBuilder = Builder(action ='cython $SOURCE',
+CythonBuilder = Builder(action ='cython $SOURCE',
suffix = '.c',
src_suffix = '.pyx')
+def PydBuilder(env,source):
+ cCode = env.Py2C(source)
+ env.SharedLibrary(target='karl.pyd', source=cCode, LIBPREFIX='')
+
env = Environment(ENV = os.environ,
- BUILDERS = {'Py2C':cythonBuilder})
+ BUILDERS = {'Py2C':CythonBuilder})
+
+env.AddMethod(CythonBuilder,'Cython')
-env.Py2C('c1.c', 'c1.pyx')
\ No newline at end of file
+env.Cython('c1')
\ No newline at end of file
diff --git a/src/pyramex/initcython.py b/src/pyramex/initcython.py
new file mode 100644
index 0000000..010a693
--- /dev/null
+++ b/src/pyramex/initcython.py
@@ -0,0 +1,32 @@
+# -*- coding: utf-8 -*-
+"""Script to initialize Cythons pyximport to ensure compatibility with MinGW compiler and NumPy."""
+
+
+import os
+import numpy
+import pyximport
+
+
+if os.name == 'nt':
+ if os.environ.has_key('CPATH'):
+ os.environ['CPATH'] = os.environ['CPATH'] + numpy.get_include()
+ else:
+ os.environ['CPATH'] = numpy.get_include()
+# # XXX: assuming that MinGW is installed in C:\MinGW (default)
+# # for PythonXY the default is C:\MinGW-xy
+# if os.environ.has_key('PATH'):
+# os.environ['PATH'] = os.environ['PATH'] + ';C:\MinGW\bin'
+# else:
+# os.environ['PATH'] = 'C:\MinGW\bin'
+
+ mingw_setup_args = { 'options': { 'build_ext': { 'compiler': 'mingw32' } } }
+ pyximport.install(setup_args=mingw_setup_args)
+
+
+elif os.name == 'posix':
+ if os.environ.has_key('CFLAGS'):
+ os.environ['CFLAGS'] = os.environ['CFLAGS'] + ' -I' + numpy.get_include()
+ else:
+ os.environ['CFLAGS'] = ' -I' + numpy.get_include()
+
+ pyximport.install()
\ No newline at end of file
diff --git a/src/pyramex/setup.py b/src/pyramex/setup.py
index b802b79..57ac98d 100644
--- a/src/pyramex/setup.py
+++ b/src/pyramex/setup.py
@@ -5,32 +5,12 @@ Created on Fri May 03 10:27:04 2013
@author: Jan
"""
-#from distutils.core import setup, Extension
-#
-#module1 = Extension('c1',
-# sources = ['c1.pyx'])
-#
-#setup (name = 'pyramex',
-# version = '1.0',
-# description = 'This is a demo package',
-# ext_modules = [module1])
-
-
+#call with: python setup.py build_ext --inplace --compiler=mingw32
from distutils.core import setup
-from distutils.extension import Extension
-from Cython.Distutils import build_ext
-
-def get_extensions():
- return [
- Extension('hello', ['hello.pyx']),
- Extension('c1', ['c1.pyx']),
- Extension('c2', ['c2.pyx']),
- Extension('c3', ['c3.pyx'])
- ]
+from Cython.Build import cythonize
setup(
- name = 'pyramex',
- cmdclass = {'build_ext': build_ext},
- ext_modules = get_extensions()
+ name = "My hello app",
+ ext_modules = cythonize('hello.pyx'), # accepts a glob pattern
)
\ No newline at end of file
diff --git a/src/pyramid/phasemap.py b/src/pyramid/phasemap.py
index 6096799..e828560 100644
--- a/src/pyramid/phasemap.py
+++ b/src/pyramid/phasemap.py
@@ -112,34 +112,44 @@ def real_space(mag_data, method, b_0=1, jacobi=None):
phi_sin = phi_pixel(method, yy_big, xx_big, res, b_0)
def phi_mag(i, j): # TODO: rename
- return (np.cos(beta[j,i])*phi_cos[y_dim-1-j:(2*y_dim-1)-j,
- x_dim-1-i:(2*x_dim-1)-i]
- -np.sin(beta[j,i])*phi_sin[y_dim-1-j:(2*y_dim-1)-j,
- x_dim-1-i:(2*x_dim-1)-i])
+ return (np.cos(beta[j,i])*phi_cos[y_dim-1-j:(2*y_dim-1)-j, x_dim-1-i:(2*x_dim-1)-i]
+ -np.sin(beta[j,i])*phi_sin[y_dim-1-j:(2*y_dim-1)-j, x_dim-1-i:(2*x_dim-1)-i])
def phi_mag_deriv(i, j): # TODO: rename
- return -(np.sin(beta[j,i])*phi_cos[y_dim-1-j:(2*y_dim-1)-j,
- x_dim-1-i:(2*x_dim-1)-i]
- +np.cos(beta[j,i])*phi_sin[y_dim-1-j:(2*y_dim-1)-j,
- x_dim-1-i:(2*x_dim-1)-i])
+ return -(np.sin(beta[j,i])*phi_cos[y_dim-1-j:(2*y_dim-1)-j, x_dim-1-i:(2*x_dim-1)-i]
+ +np.cos(beta[j,i])*phi_sin[y_dim-1-j:(2*y_dim-1)-j, x_dim-1-i:(2*x_dim-1)-i])
+
+ def phi_mag_fd(i, j, h): # TODO: rename
+ return ((np.cos(beta[j,i]+h) - np.cos(beta[j,i])) / h
+ * phi_cos[y_dim-1-j:(2*y_dim-1)-j, x_dim-1-i:(2*x_dim-1)-i]
+ -(np.sin(beta[j,i]+h) - np.sin(beta[j,i])) / h
+ * phi_sin[y_dim-1-j:(2*y_dim-1)-j, x_dim-1-i:(2*x_dim-1)-i])
'''CALCULATE THE PHASE'''
phase = np.zeros((y_dim, x_dim))
# TODO: only iterate over pixels that have a magn. > threshold (first >0)
+ jacobi_fd = jacobi.copy()
+ h = 0.0001
+
for j in range(y_dim):
for i in range(x_dim):
- if (mag[j, i] != 0 ):#or jacobi is not None): # TODO: same result with or without?
+ #if (mag[j,i] != 0 ):#or jacobi is not None): # TODO: same result with or without?
phi_mag_cache = phi_mag(i, j)
phase += mag[j,i] * phi_mag_cache
if jacobi is not None:
jacobi[:,i+x_dim*j] = phi_mag_cache.reshape(-1)
- jacobi[:,x_dim*y_dim+i+x_dim*j] = (mag[j,i]*phi_mag_deriv(i, j)).reshape(-1)
+ jacobi[:,x_dim*y_dim+i+x_dim*j] = (mag[j,i]*phi_mag_deriv(i,j)).reshape(-1)
+
+ jacobi_fd[:,i+x_dim*j] = phi_mag_cache.reshape(-1)
+ jacobi_fd[:,x_dim*y_dim+i+x_dim*j] = (mag[j,i]*phi_mag_fd(i,j,h)).reshape(-1)
+
+
- return phase
-
+ jacobi_diff = jacobi_fd - jacobi
+ assert (np.abs(jacobi_diff) < 1.0E-8).all(), 'jacobi matrix is not the same'
-
+ return phase
def phase_elec(mag_data, b_0=1, v_0=0, v_acc=30000):
--
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