create_random_slabs: Added script to create a random slab distribution

test_compliance: Added PEP8 TestCase

pyramid/analytic.py

@@ -17,8 +17,8 @@ def phase_mag_slab(dim, res, beta, center, width, b_0):
     x0 = res * (center[2] + 0.5)
     # Ly, Lx have to be odd, because the slab borders should not lie in the
     # center of a pixel (so L/2 can't be an integer)
-    Ly = res * ( width[1] + (width[1]+1)%2) 
-    Lx = res * ( width[2] + (width[2]+1)%2)   
+    Ly = res * (width[1] + (width[1]+1)%2) 
+    Lx = res * (width[2] + (width[2]+1)%2)   
     
     '''COMPUTATION MAGNETIC PHASE SHIFT (REAL SPACE) SLAB'''
 

pyramid/test/test_compliance.py

 # -*- coding: utf-8 -*-
 """Testcase for the magcreator module."""
 
-
+import datetime
+import sys
 import os
 import unittest
+import pep8
 
 
 class TestCaseCompliance(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()
-
+        pass
+    
+    def tearDown(self):
+        pass
+    
+    
+    def get_files_to_check(self, rootdir):
+        filepaths = []
+        for root, dirs, files in os.walk(rootdir):
+            for filename in files:
+                if filename.endswith('.py'):
+                    filepaths.append(os.path.join(root,filename))
+        return filepaths
+    
     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 "./":
-            errors += self.checkDirectory(dir_name)
-        self.assertEqual(errors, 0)
-
+        # TODO: Docstring
+        files = self.get_files_to_check('..')  # search in pyramid package   
+        ignores = ('E226',)# 'E201', 'E203')        
+        pep8.MAX_LINE_LENGTH = 99
+        pep8style = pep8.StyleGuide(quiet=False)
+        pep8style.options.ignore = ignores
+        
+        stdout_buffer = sys.stdout
+        with open(os.path.join('..','..','output','pep8_log.txt'), 'w') as sys.stdout:
+            print '<<< PEP8 LOGFILE >>>' 
+            print 'RUN:', datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
+            print 'IGNORED RULES:', ignores
+            print 'MAX LINE LENGTH:', pep8.MAX_LINE_LENGTH          
+            print '\nERRORS AND WARNINGS:'
+            result= pep8style.check_files(files)
+            if result.total_errors == 0:
+                print 'No Warnings or Errors detected!'
+        sys.stdout = stdout_buffer
+        
+        error_message = 'Found %s Errors and Warnings!' % result.total_errors
+        self.assertEqual(result.total_errors, 0, error_message)
+    
 
 if __name__ == '__main__':
     suite = unittest.TestLoader().loadTestsFromTestCase(TestCaseCompliance)
-    unittest.TextTestRunner(verbosity=2).run(suite)
-
-#    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")
+    unittest.TextTestRunner(verbosity=2).run(suite)
\ No newline at end of file

scripts/compare_method_errors.py

@@ -28,8 +28,8 @@ def phase_from_mag():
     # Input parameters:
     b_0     =  1    # in T
     res     = 10.0  # in nm
-    beta    = pi/4#np.linspace(0, 2*pi, endpoint=False, num=72)
-    padding = range(26)
+    betas    = pi/4#np.linspace(0, 2*pi, endpoint=False, num=72)
+    paddings = range(26)
     dim = (1, 100, 100)  # in px (z, y, x)    
     # Create magnetic shape:
     geometry = 'slab'        
@@ -48,25 +48,25 @@ def phase_from_mag():
     mag_data = MagData(res, mc.create_mag_dist(mag_shape, beta))    
     projection = pj.simple_axis_projection(mag_data)
    
-#    '''FOURIER'''
-#    #padding
-#    RMS = np.zeros(len(padding))
-#    duration = np.zeros(len(padding))
-#    for i in range(len(padding)):
-#        print 'padding =', padding[i]
-#        start_time = time.time()
-#        phase_num  = pm.phase_mag_fourier(res, projection, b_0, padding[i])
-#        duration[i] = time.time() - start_time
-#        phase_diff = phase_ana - phase_num
-#        RMS[i]  = np.std(phase_diff)
-#    
-#    fig = plt.figure()
-#    fig.add_subplot(111)    
-#    plt.plot(padding, RMS)
-#    
-#    fig = plt.figure()
-#    fig.add_subplot(111)    
-#    plt.plot(padding, duration)
+    '''FOURIER'''
+    #padding
+    RMS = np.zeros(len(paddings))
+    duration = np.zeros(len(paddings))
+    for (i, padding) in enumerate(paddings):
+        print 'padding =', padding[i]
+        start_time = time.time()
+        phase_num  = pm.phase_mag_fourier(res, projection, b_0, padding[i])
+        duration[i] = time.time() - start_time
+        phase_diff = phase_ana - phase_num
+        RMS[i]  = np.std(phase_diff)
+    
+    fig = plt.figure()
+    fig.add_subplot(111)
+    plt.plot(padding, RMS)
+    
+    fig = plt.figure()
+    fig.add_subplot(111)    
+    plt.plot(padding, duration)
     
     
     '''REAL SLAB '''

scripts/create_random_distribution.py → scripts/create_random_pixels.py

@@ -14,7 +14,7 @@ import pyramid.holoimage as hi
 from pyramid.phasemap import PhaseMap
 
 
-def create_random_distribution():
+def create_random_pixels():
     '''Calculate, display and save a random magnetic distribution to file.
     Arguments:
         None
@@ -40,7 +40,7 @@ def create_random_distribution():
     magnitude = mc.create_mag_dist_comb(mag_shape_list, beta_list, magnitude_list) 
     mag_data = MagData(res, magnitude)
     mag_data.quiver_plot()
-    mag_data.save_to_llg('../output/mag_dist_random_pixel.txt')
+    mag_data.save_to_llg('../output/mag_dist_random_pixels.txt')
     projection = pj.simple_axis_projection(mag_data)
     phase_map  = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))    
     hi.display(hi.holo_image(phase_map, 10))
@@ -48,7 +48,7 @@ def create_random_distribution():
     
 if __name__ == "__main__":
     try:
-        create_random_distribution()
+        create_random_pixels()
     except:
         type, value, tb = sys.exc_info()
         traceback.print_exc()

scripts/create_random_slabs.py

+# -*- coding: utf-8 -*-
+"""Create random magnetic distributions."""
+
+import random as rnd
+import pdb, traceback, sys
+import numpy as np
+from numpy import pi
+
+import pyramid.magcreator as mc
+from pyramid.magdata import MagData
+import pyramid.phasemapper as pm
+import pyramid.projector as pj
+import pyramid.holoimage as hi
+from pyramid.phasemap import PhaseMap
+
+
+def create_random_slabs():
+    '''Calculate, display and save a random magnetic distribution to file.
+    Arguments:
+        None
+    Returns:
+        None
+    
+    '''
+    # Input parameters:
+    count = 10
+    dim = (1, 128, 128)  
+    res = 10 # in nm
+    rnd.seed(42)
+    w_max = 10
+    # Create lists for magnetic objects:
+    mag_shape_list = np.zeros((count,) + dim)
+    beta_list      = np.zeros(count) 
+    magnitude_list = np.zeros(count)
+    for i in range(count):
+        width  = (1, rnd.randint(1, w_max), rnd.randint(1, w_max))
+        center = (rnd.randrange(int(width[0]/2), dim[0]-int(width[0]/2)),
+                  rnd.randrange(int(width[1]/2), dim[1]-int(width[1]/2)),
+                  rnd.randrange(int(width[2]/2), dim[2]-int(width[2]/2)))
+        mag_shape_list[i,...] = mc.Shapes.slab(dim, center, width)
+        beta_list[i] = 2*pi*rnd.random()
+        magnitude_list[i] = 1#rnd.random()
+    # Create magnetic distribution
+    magnitude = mc.create_mag_dist_comb(mag_shape_list, beta_list, magnitude_list) 
+    mag_data = MagData(res, magnitude)
+    mag_data.quiver_plot()
+    mag_data.save_to_llg('../output/mag_dist_random_slabs.txt')
+    projection = pj.simple_axis_projection(mag_data)
+    phase_map  = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))    
+    hi.display(hi.holo_image(phase_map, 10))
+    
+    
+if __name__ == "__main__":
+    try:
+        create_random_slabs()
+    except:
+        type, value, tb = sys.exc_info()
+        traceback.print_exc()
+        pdb.post_mortem(tb)
\ No newline at end of file