From ca6649023c5bbc970a8f3af6a2b377a585f9ce94 Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Mon, 13 May 2013 15:53:48 +0200
Subject: [PATCH] Changed cython folder to numcore subfolder Changed setup.py
Implemented assertion to check if jacobi matrix is the same
---
desktop.ini | 2 +-
pyramid/magdata.py | 54 ++++++++++++++++++++
pyramid/numcore/__init__.py | 0
pyramid/{cython => numcore}/c1.pyx | 0
pyramid/{cython => numcore}/c2.pyx | 0
pyramid/{cython => numcore}/c3.pyx | 0
pyramid/{cython => numcore}/hello.pyx | 0
pyramid/{cython => numcore}/initpyximport.py | 0
pyramid/{cython => numcore}/setup.py | 13 ++++-
pyramid/phasemap.py | 8 +--
scripts/create_random_distribution.py | 35 +++++++++++++
setup.py | 4 +-
12 files changed, 107 insertions(+), 9 deletions(-)
create mode 100644 pyramid/magdata.py
create mode 100644 pyramid/numcore/__init__.py
rename pyramid/{cython => numcore}/c1.pyx (100%)
rename pyramid/{cython => numcore}/c2.pyx (100%)
rename pyramid/{cython => numcore}/c3.pyx (100%)
rename pyramid/{cython => numcore}/hello.pyx (100%)
rename pyramid/{cython => numcore}/initpyximport.py (100%)
rename pyramid/{cython => numcore}/setup.py (54%)
create mode 100644 scripts/create_random_distribution.py
diff --git a/desktop.ini b/desktop.ini
index 2d10ec1..85ecbcf 100644
--- a/desktop.ini
+++ b/desktop.ini
@@ -1,5 +1,5 @@
[.ShellClassInfo]
-IconResource=C:\Users\Jan\Daten\FZ-Jülich\PYRAMID\pyramid.ico,0
+IconResource=C:\Users\Jan\PhD Thesis\Pyramid\icon.ico,0
[ViewState]
Mode=
Vid=
diff --git a/pyramid/magdata.py b/pyramid/magdata.py
new file mode 100644
index 0000000..3d91b8d
--- /dev/null
+++ b/pyramid/magdata.py
@@ -0,0 +1,54 @@
+# -*- 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
diff --git a/pyramid/numcore/__init__.py b/pyramid/numcore/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/pyramid/cython/c1.pyx b/pyramid/numcore/c1.pyx
similarity index 100%
rename from pyramid/cython/c1.pyx
rename to pyramid/numcore/c1.pyx
diff --git a/pyramid/cython/c2.pyx b/pyramid/numcore/c2.pyx
similarity index 100%
rename from pyramid/cython/c2.pyx
rename to pyramid/numcore/c2.pyx
diff --git a/pyramid/cython/c3.pyx b/pyramid/numcore/c3.pyx
similarity index 100%
rename from pyramid/cython/c3.pyx
rename to pyramid/numcore/c3.pyx
diff --git a/pyramid/cython/hello.pyx b/pyramid/numcore/hello.pyx
similarity index 100%
rename from pyramid/cython/hello.pyx
rename to pyramid/numcore/hello.pyx
diff --git a/pyramid/cython/initpyximport.py b/pyramid/numcore/initpyximport.py
similarity index 100%
rename from pyramid/cython/initpyximport.py
rename to pyramid/numcore/initpyximport.py
diff --git a/pyramid/cython/setup.py b/pyramid/numcore/setup.py
similarity index 54%
rename from pyramid/cython/setup.py
rename to pyramid/numcore/setup.py
index b49dc9f..b31924c 100644
--- a/pyramid/cython/setup.py
+++ b/pyramid/numcore/setup.py
@@ -1,4 +1,3 @@
-# -*- 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
+)
diff --git a/pyramid/phasemap.py b/pyramid/phasemap.py
index e828560..60c639d 100644
--- a/pyramid/phasemap.py
+++ b/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
diff --git a/scripts/create_random_distribution.py b/scripts/create_random_distribution.py
new file mode 100644
index 0000000..1ac5c6b
--- /dev/null
+++ b/scripts/create_random_distribution.py
@@ -0,0 +1,35 @@
+# -*- 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
diff --git a/setup.py b/setup.py
index 27d813f..9b340f6 100644
--- a/setup.py
+++ b/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')))
)
--
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