scripts: Splitted the main in several smaller scripts

test: changed the dataloader TestCase
pyramex: first experiments with Cython and SCons
dataloader: changed the order in which the dimensions are saved,
        z_len is no longer part of the magnetization (this was the reason why
        we had to divide by res, which is equal to z_len for calculating coeff)
magcreator: shapes are now separate functions, mag_shape is now an argument for
        one unified create_hom_mag-function
phasemap: unification of the phasemap-functions in real space (just the pixel-
        field is calculated different now)

test/run_tests.py

+# -*- coding: utf-8 -*-
+"""
+Unittests for pyramid.
+"""
+
+import unittest
+import sys
+from test_dataloader import *
+from test_compliance import *
+
+
+def run():
+    
+    suite  = unittest.TestSuite()
+    loader = unittest.TestLoader()
+    runner = unittest.TextTestRunner(verbosity=2)
+    
+    suite.addTest(loader.loadTestsFromTestCase(TestCaseDataloader))
+    suite.addTest(loader.loadTestsFromTestCase(TestCaseCompliance))
+    runner.run(suite)
+    
+    #TODO: why that?
+#    result = runner.run(suite)
+#    if result.wasSuccessful():
+#        sys.exit(0)
+#    else:
+#        sys.exit(1)
+
+
+if __name__ == '__main__':
+    run()
+    
+    
+    
+    
+
+#if __name__ == '__main__':
+#    suite = unittest.TestLoader().loadTestsFromTestCase(TestSuite)
+#    unittest.TextTestRunner(verbosity=2).run(suite)
+
+
+
+''' GLORIPY VERSION '''
+##! /usr/bin/python
+#"""
+#Unittests for pyjurassic.
+#"""
+#
+#import unittest
+#import os
+#import sys
+#import tests
+#
+#
+#def main():
+#    all_tests = unittest.TestSuite()
+#    tl = unittest.defaultTestLoader
+#    if os.getenv("BOOST_TESTS_TO_RUN") is not None:
+#        return
+#    elif os.getenv("PYTHON_TESTS_TO_RUN") is None:
+#        all_tests.addTest(tl.loadTestsFromName("tests"))
+#    else:
+#        all_tests.addTest(tl.loadTestsFromName(os.getenv("PYTHON_TESTS_TO_RUN")))
+#
+#    runner = unittest.TextTestRunner(verbosity=2)
+#    res = runner.run(all_tests)
+#    if res.wasSuccessful():
+#        sys.exit(0)
+#    else:
+#        sys.exit(1)
+#
+#
+#if __name__ == '__main__':
+#    main()
\ No newline at end of file

test/test_compliance.py

+import os
+import unittest
+
+
+class TestCompliance(unittest.TestCase):
+    """
+    Class for checking compliance of pyjurassic.
+    """
+
+    def setUp(self):
+        # self.getPaths()
+        # self.data_dir = "test_jrp_data"
+        # self.src_ctl = "ctl.py"
+        # remove E201 to get a working version of str(- b)
+        # remove E203 to get a working version of a[:, :]
+        # remove E501 as 80 chars are not enough
+        self.ignores = ["E201", "E203", "E501"]
+        self.options = ["dummy_name", "--ignore", ",".join(self.ignores), "--repeat"]
+        self.options += ["--exclude", "collections_python27.py"]
+        try:
+            import pep8
+            self.pep8 = pep8
+        except ImportError:
+            self.pep8 = None
+            print("\nWARNING: You do not have package pep8!")
+
+    def countErrors(self):
+        """
+        Counts the relevant errors from the pep8 counter structure.
+        """
+        return sum([self.pep8.options.counters[key]
+                    for key in self.pep8.options.messages.keys()
+                    if key not in self.ignores])
+
+    def checkDirectory(self, dir_name):
+        """
+        Checks all python files in the supplied directory and subdirectories.
+        """
+        self.pep8.process_options(self.options)
+        self.pep8.input_dir(dir_name)
+        return self.countErrors()
+
+    def test_pep8(self):
+        """
+        Tests all directories containing python files for PEP8 compliance.
+        """
+        self.assertTrue(self.pep8 is not None,
+                        msg="Install Python pep8 module to fully execute testbench!")
+        errors = 0
+        for dir_name in ["test", os.environ["BUILDDIR"]]:
+            errors += self.checkDirectory(dir_name)
+        self.assertEqual(errors, 0)
+
+#    def test_variables(self):
+#        """
+#        Function for checking that all attributes are present.
+#        """
+#        try:
+#            import gloripy
+##            for name in ['X', 'Y', 'B',
+##                         'APR_VAL', 'APR_STD', 'FINAL_VAL', 'FINAL_STD',
+##                         'IG_VAL', 'TRUE_VAL',
+##                         'CARTESIAN', 'GEO', 'SPHERICAL',
+##                         'P', 'T', 'C']:
+##                self.assertTrue(hasattr(j, name), msg=str(name) + " is missing.")
+#        except ImportError:
+#            self.assertTrue(False, msg="could not import gloripy")
+
+#    def test_import(self):
+#        """
+#        Checks that all modules are importable.
+#        """
+#        module_list = ["gloripy",
+#                       "gloripy.pylevel0",
+#                      ]
+#        for module in module_list:
+#            try:
+#                exec("import " + module)
+#                importable = True
+#            except ImportError:
+#                importable = False
+#            self.assertTrue(importable, msg="importing " + module + " failed")

test/test_dataloader.py

@@ -7,23 +7,78 @@ Created on Wed Apr 24 07:10:28 2013
 # py.test
 
 import unittest
+import numpy as np
+import pyramid.dataloader as dl
+from numpy import pi
 
 
-class TestSuite(unittest.TestCase):
+# TODO: define test constants somewhere
+# TODO: proper error messages
+# TODO: Docstring
+
+
+class TestCaseDataloader(unittest.TestCase):
     
     def setUp(self):
-        pass
+        self.filename = 'test_dataloader/test_data.txt'
+        self.mag_data = dl.MagDataLLG(self.filename)
     
     def tearDown(self):
-        pass
+        self.filename = None
+        self.mag_data = None
+        
+    def test_filename(self):
+        self.assertEqual(self.mag_data.filename, self.filename)
+        
+    def test_resolution(self):
+        self.assertEqual(self.mag_data.res, 10.0)
+        
+    def test_dimensions(self):
+        self.assertEqual(self.mag_data.dim, (1, 3, 5))
     
-    def test(self):
-        self.assertTrue(True)
+    def test_length(self):
+        self.assertEqual(self.mag_data.length, (10.0, 30.0, 50.0))
         
-    def test_almost(self):
-        self.assertAlmostEqual(0, 0.01, places=1)
+    def test_magnitude(self):
+        test_shape = (1, 3, 5)
+        test_array = np.zeros(test_shape)
+        z_mag = self.mag_data.magnitude[0]
+        y_mag = self.mag_data.magnitude[1]
+        x_mag = self.mag_data.magnitude[2]
+        self.assertEqual(z_mag.shape, test_shape)
+        self.assertEqual(y_mag.shape, test_shape)
+        self.assertEqual(x_mag.shape, test_shape)
+        np.testing.assert_array_equal(z_mag, test_array, 'Testmessage')
+        test_array[:,1,1:4] = np.cos(pi/4)
+        np.testing.assert_array_almost_equal(y_mag, test_array, err_msg='y failure')
+        np.testing.assert_array_almost_equal(x_mag, test_array, err_msg='x failure')
         
         
+        
+        
+        
+    
+#mc.create_hom_mag((3,5),10.0,pi/4,mc.slab,((1,2),(1,3)),'test.txt',plot_mag_distr=True)   
+#        '{:7.6e}'
+#        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).mean(0) 
+#                               *z_len 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 = (x_dim, y_dim, z_dim)
+#        self.length = (x_len, y_len, z_len)
+#        self.magnitude = (x_mag, y_mag, z_mag)
+#        self.assertAlmostEqual(0, 0.01, places=1)
+#        mc.create_hom_mag((10,10),10.0,0,mc.slab,((4,4),(5,5)),'test.txt')
+        
 if __name__ == '__main__':
-    suite = unittest.TestLoader().loadTestsFromTestCase(TestSuite)
+    suite = unittest.TestLoader().loadTestsFromTestCase(TestCaseDataloader)
     unittest.TextTestRunner(verbosity=2).run(suite)
\ No newline at end of file

test/test_dataloader/test_data.txt

+LLGFileCreator2D: test_data
+    5    3    1
+5.000000e-07   5.000000e-07   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
+1.500000e-06   5.000000e-07   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
+2.500000e-06   5.000000e-07   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
+3.500000e-06   5.000000e-07   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
+4.500000e-06   5.000000e-07   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
+5.000000e-07   1.500000e-06   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
+1.500000e-06   1.500000e-06   5.000000e-07   7.071068e-01   7.071068e-01   0.000000e+00
+2.500000e-06   1.500000e-06   5.000000e-07   7.071068e-01   7.071068e-01   0.000000e+00
+3.500000e-06   1.500000e-06   5.000000e-07   7.071068e-01   7.071068e-01   0.000000e+00
+4.500000e-06   1.500000e-06   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
+5.000000e-07   2.500000e-06   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
+1.500000e-06   2.500000e-06   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
+2.500000e-06   2.500000e-06   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
+3.500000e-06   2.500000e-06   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
+4.500000e-06   2.500000e-06   5.000000e-07   0.000000e+00   0.000000e+00   0.000000e+00
\ No newline at end of file

test/testsuite.py

-# -*- coding: utf-8 -*-
-"""
-Created on Wed Apr 24 07:10:28 2013
-
-@author: Jan
-"""
-# py.test
-
-import unittest
-
-
-class TestSuite(unittest.TestCase):
-    
-    def setUp(self):
-        pass
-    
-    def tearDown(self):
-        pass
-    
-    def test(self):
-        self.assertTrue(True)
-        
-    def test_almost(self):
-        self.assertAlmostEqual(0, 0.01, places=1)
-        
-        
-if __name__ == '__main__':
-    suite = unittest.TestLoader().loadTestsFromTestCase(TestSuite)
-    unittest.TextTestRunner(verbosity=2).run(suite)
\ No newline at end of file