Hopefully made hyperspy import (now at beginning of pyramid package) work!

Added PyCharm files!
Commit before Reformatting with PyCharms!

.idea/.name

+Pyramid
\ No newline at end of file

.idea/Pyramid.iml

+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/pyramid" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/scripts" isTestSource="false" />
+    </content>
+    <orderEntry type="jdk" jdkName="Python 2.7.11 (C:\Anaconda2\python.exe)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="module" module-name="HyperSpy" />
+    <orderEntry type="module" module-name="Jutil" />
+    <orderEntry type="module" module-name="Publications" />
+    <orderEntry type="module" module-name="Script-Vault" />
+  </component>
+  <component name="TestRunnerService">
+    <option name="projectConfiguration" value="Nosetests" />
+    <option name="PROJECT_TEST_RUNNER" value="Nosetests" />
+  </component>
+</module>
\ No newline at end of file

.idea/encodings.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Encoding">
+    <file url="PROJECT" charset="UTF-8" />
+  </component>
+</project>
\ No newline at end of file

.idea/misc.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectLevelVcsManager" settingsEditedManually="false">
+    <OptionsSetting value="true" id="Add" />
+    <OptionsSetting value="true" id="Remove" />
+    <OptionsSetting value="true" id="Checkout" />
+    <OptionsSetting value="true" id="Update" />
+    <OptionsSetting value="true" id="Status" />
+    <OptionsSetting value="true" id="Edit" />
+    <ConfirmationsSetting value="0" id="Add" />
+    <ConfirmationsSetting value="0" id="Remove" />
+  </component>
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 2.7.11 (C:\Anaconda2\python.exe)" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file

.idea/modules.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/../HyperSpy/.idea/HyperSpy.iml" filepath="$PROJECT_DIR$/../HyperSpy/.idea/HyperSpy.iml" />
+      <module fileurl="file://$PROJECT_DIR$/../Jutil/.idea/Jutil.iml" filepath="$PROJECT_DIR$/../Jutil/.idea/Jutil.iml" />
+      <module fileurl="file://$PROJECT_DIR$/../Publications/.idea/Publications.iml" filepath="$PROJECT_DIR$/../Publications/.idea/Publications.iml" />
+      <module fileurl="file://$PROJECT_DIR$/.idea/Pyramid.iml" filepath="$PROJECT_DIR$/.idea/Pyramid.iml" />
+      <module fileurl="file://$PROJECT_DIR$/../Script-Vault/.idea/Script-Vault.iml" filepath="$PROJECT_DIR$/../Script-Vault/.idea/Script-Vault.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file

desktop.ini

 [.ShellClassInfo]
-IconResource=C:\Users\Jan\Home\PhD Thesis\Spyder\Pyramid\docs\icon.ico,0
+IconResource=C:\Users\Jan\Home\PhD Thesis\Projects\Pyramid\docs\icon.ico,0
 [ViewState]
 Mode=
 Vid=

pyramid/__init__.py

@@ -47,30 +47,17 @@ numcore
     Provides fast numerical functions for core routines.
 
 """
+import logging
+
+_log = logging.getLogger(__name__)
+try:  # Try importing HyperSpy (here because otherwise API Errors might occur):
+    import hyperspy.api
+except ImportError:
+    _log.error('Could not load hyperspy package!')
 
-from . import analytic
-from . import magcreator
-from . import reconstruction
-from . import fft
-from .costfunction import *  # analysis:ignore
-from .dataset import *  # analysis:ignore
-from .diagnostics import *  # analysis:ignore
-from .forwardmodel import *  # analysis:ignore
-from .kernel import *  # analysis:ignore
-from .magdata import *  # analysis:ignore
-from .phasemap import *  # analysis:ignore
-from .phasemapper import *  # analysis:ignore
-from .projector import *  # analysis:ignore
-from .regularisator import *  # analysis:ignore
-from .ramp import *  # analysis:ignore
-from .quaternion import *  # analysis:ignore
-from .colormap import *  # analysis:ignore
-from .config import *  # analysis:ignore
 from .version import version as __version__
 from .version import hg_revision as __hg_revision__
 
-import logging
-_log = logging.getLogger(__name__)
 _log.info("Starting Pyramid V{} HG{}".format(__version__, __hg_revision__))
 del logging
 

pyramid/colormap.py

@@ -5,15 +5,13 @@
 """This module provides a custom :class:`~.DirectionalColormap` colormap class which has a few
 additional functions and can encode three-dimensional directions."""
 
+import logging
+from numbers import Number
 
-import numpy as np
 import matplotlib as mpl
 import matplotlib.pyplot as plt
+import numpy as np
 from PIL import Image
-from numbers import Number
-
-import logging
-
 
 __all__ = ['DirectionalColormap', 'TransparentColormap']
 
@@ -245,7 +243,9 @@ class TransparentColormap(mpl.colors.LinearSegmentedColormap):
 
     _log = logging.getLogger(__name__+'.TransparentColormap')
 
-    def __init__(self, r=1., g=0., b=0., alpha_range=[0., 1.]):
+    def __init__(self, r=1., g=0., b=0., alpha_range=None):
+        if alpha_range is None:
+            alpha_range = [0., 1.]
         self._log.debug('Calling __create_directional_colormap')
         red = [(0., 0., r), (1., r, 1.)]
         green = [(0., 0., g), (1., g, 1.)]

pyramid/magdata.py

@@ -18,12 +18,18 @@ from scipy.ndimage.interpolation import zoom
 from pyramid import fft
 from pyramid.colormap import DirectionalColormap
 
+_log = logging.getLogger(__name__)
+try:  # Try importing HyperSpy:
+    import hyperspy.api as hs
+except ImportError:
+    hs = None
+    _log.error('Could not load hyperspy package!')
+
 __all__ = ['MagData']
 
 
 class MagData(object):
-
-    '''Class for storing magnetization data.
+    """Class for storing magnetization data.
 
     Represents 3-dimensional magnetic distributions with 3 components which are stored as a
     2-dimensional numpy array in `magnitude`, but which can also be accessed as a vector via
@@ -47,7 +53,7 @@ class MagData(object):
     mag_vec: :class:`~numpy.ndarray` (N=1)
         Vector containing the magnetic distribution.
 
-    '''
+    """
 
     _log = logging.getLogger(__name__+'.MagData')
 
@@ -194,7 +200,7 @@ class MagData(object):
         '''
         self._log.debug('Calling scale_down')
         assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
-        self.a = self.a * 2**n
+        self.a *= 2 ** n
         for t in range(n):
             # Pad if necessary:
             pz, py, px = self.dim[0] % 2, self.dim[1] % 2, self.dim[2] % 2
@@ -229,7 +235,7 @@ class MagData(object):
         assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
         assert 5 > order >= 0 and isinstance(order, (int, long)), \
             'order must be a positive integer between 0 and 5!'
-        self.a = self.a / 2**n
+        self.a /= 2 ** n
         self.magnitude = np.array((zoom(self.magnitude[0], zoom=2**n, order=order),
                                    zoom(self.magnitude[1], zoom=2**n, order=order),
                                    zoom(self.magnitude[2], zoom=2**n, order=order)))
@@ -484,10 +490,8 @@ class MagData(object):
         '''
         self._log.debug('Calling to_signal')
         # Try importing HyperSpy:
-        try:
-            import hyperspy.api as hs
-        except ImportError:
-            self._log.error('Could not load hyperspy package!')
+        if hs is None:
+            self._log.error('This method recquires the hyperspy package!')
             return
         # Create signal:
         signal = hs.signals.Signal(np.rollaxis(self.magnitude, 0, 4))
@@ -575,18 +579,16 @@ class MagData(object):
 
         '''
         cls._log.debug('Calling load_from_hdf5')
+        if hs is None:
+            self._log.error('This method recquires the hyperspy package!')
+            return
         # Use relative path if filename isn't already absolute:
         if not os.path.isabs(filename):
             from pyramid import DIR_FILES
             directory = os.path.join(DIR_FILES, 'magdata')
             filename = os.path.join(directory, filename)
         # Load data from file:
-        try:
-            import hyperspy.api as hs
-            return MagData.from_signal(hs.load(filename))
-        except ImportError:
-            cls._log.error('Could not load hyperspy package!')
-            return
+        return MagData.from_signal(hs.load(filename))
 
     def save_to_llg(self, filename='magdata.txt'):
         '''Save magnetization data in a file with LLG-format.

pyramid/phasemap.py

@@ -4,21 +4,26 @@
 #
 """This module provides the :class:`~.PhaseMap` class for storing phase map data."""
 
-
+import logging
 import os
-import numpy as np
-from scipy.ndimage.interpolation import zoom
 from numbers import Number
-from PIL import Image
+
 import matplotlib as mpl
 import matplotlib.pyplot as plt
-from mpl_toolkits.mplot3d import Axes3D
+import numpy as np
+from PIL import Image
 from matplotlib.ticker import MaxNLocator, FuncFormatter
+from mpl_toolkits.mplot3d import Axes3D
+from scipy.ndimage.interpolation import zoom
 
 from pyramid.colormap import DirectionalColormap, TransparentColormap
 
-import logging
-
+_log = logging.getLogger(__name__)
+try:  # Try importing HyperSpy:
+    import hyperspy.api as hs
+except ImportError:
+    hs = None
+    _log.error('Could not load hyperspy package!')
 
 __all__ = ['PhaseMap']
 
@@ -287,7 +292,7 @@ class PhaseMap(object):
         '''
         self._log.debug('Calling scale_down')
         assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
-        self.a = self.a * 2**n
+        self.a *= 2 ** n
         for t in range(n):
             # Pad if necessary:
             pv, pu = self.dim_uv[0] % 2, self.dim_uv[1] % 2
@@ -326,7 +331,7 @@ class PhaseMap(object):
         assert n > 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
         assert 5 > order >= 0 and isinstance(order, (int, long)), \
             'order must be a positive integer between 0 and 5!'
-        self.a = self.a / 2**n
+        self.a /= 2 ** n
         self.phase = zoom(self.phase, zoom=2**n, order=order)
         self.mask = zoom(self.mask, zoom=2**n, order=0)
         self.confidence = zoom(self.confidence, zoom=2**n, order=order)
@@ -418,11 +423,8 @@ class PhaseMap(object):
 
         '''
         self._log.debug('Calling to_signal')
-        # Try importing HyperSpy:
-        try:
-            import hyperspy.api as hs
-        except ImportError:
-            self._log.error('Could not load hyperspy package!')
+        if hs is None:
+            self._log.error('This method recquires the hyperspy package!')
             return
         # Create signal:
         signal = hs.signals.Image(self.phase)
@@ -476,7 +478,7 @@ class PhaseMap(object):
         return cls(a, phase, mask, confidence, unit)
 
     def save_to_hdf5(self, filename='phasemap.hdf5'):
-        '''Save magnetization data in a file with HyperSpys HDF5-format.
+        """Save magnetization data in a file with HyperSpys HDF5-format.
 
         Parameters
         ----------
@@ -488,7 +490,7 @@ class PhaseMap(object):
         -------
         None
 
-        '''
+        """
         self._log.debug('Calling save_to_hdf5')
         # Construct path if filename isn't already absolute:
         if not os.path.isabs(filename):
@@ -516,18 +518,16 @@ class PhaseMap(object):
 
         '''
         cls._log.debug('Calling load_from_hdf5')
+        if hs is None:
+            cls._log.error('This method recquires the hyperspy package!')
+            return
         # Use relative path if filename isn't already absolute:
         if not os.path.isabs(filename):
             from pyramid import DIR_FILES
             directory = os.path.join(DIR_FILES, 'phasemap')
             filename = os.path.join(directory, filename)
         # Load data from file:
-        try:
-            import hyperspy.api as hs
-            return PhaseMap.from_signal(hs.load(filename))
-        except ImportError:
-            cls._log.error('Could not load hyperspy package!')
-            return
+        return PhaseMap.from_signal(hs.load(filename))
 
     def save_to_txt(self, filename='phasemap.txt', skip_header=False):
         '''Save :class:`~.PhaseMap` data in a file with txt-format.

pyramid/tests/test_compliance.py

-# -*- coding: utf-8 -*-
-"""Testcase for the compliance with PEP8."""
-
-
-import os
-import sys
-import datetime
-import unittest
-
-import re
-import pep8
-
-
-class TestCaseCompliance(unittest.TestCase):
-    """TestCase for checking the pep8 compliance of the pyramid package."""
-
-    # Pyramid directory:
-    path = os.path.abspath(os.path.join(os.path.split(os.path.realpath(__file__))[0], '..', '..'))
-
-    def get_files_to_check(self, rootdir):
-        filepaths = []
-        for root, dirs, files in os.walk(rootdir):
-            for filename in files:
-                if ((filename.endswith('.py') or filename.endswith('.pyx'))
-                        and root != os.path.join(self.path, 'scripts', 'gui')):
-                            filepaths.append(os.path.join(root, filename))
-        return filepaths
-
-    def test_pep8(self):
-        '''Test for pep8 compliance.'''
-        files = self.get_files_to_check(os.path.join(self.path, 'pyramid')) \
-            + self.get_files_to_check(os.path.join(self.path, 'scripts')) \
-            + self.get_files_to_check(os.path.join(self.path, 'pyramid', 'tests'))
-        ignores = ('E125', 'E226', 'E228', 'W503')
-        pep8.MAX_LINE_LENGTH = 99
-        pep8style = pep8.StyleGuide(quiet=False)
-        pep8style.options.ignore = ignores
-        stdout_buffer = sys.stdout
-        with open(os.path.join(self.path, 'pyramid', 'tests', '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:', ', '.join(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 PEP8 violations detected!'
-            else:
-                print '---->   {} PEP8 violations detected!'.format(result.total_errors)
-            print '\nTODOS:'
-            todos_found = False
-            todo_count = 0
-            regex = ur'# TODO: (.*)'
-            for py_file in files:
-                with open(py_file) as f:
-                    for line in f:
-                        todo = re.findall(regex, line)
-                        if todo and not todo[0] == "(.*)'":
-                            todos_found = True
-                            todo_count += 1
-                            print '{}: {}'.format(f.name, todo[0])
-            if todos_found:
-                print '---->   {} TODOs found!'.format(todo_count)
-            else:
-                print 'No TODOS found!'
-        sys.stdout = stdout_buffer
-        error_message = 'Found {} PEP8 violations!'.format(result.total_errors)
-        if todo_count > 0:
-            error_message += ' Found {} TODOs!'.format(todo_count)
-        self.assertEqual(result.total_errors, 0, error_message)
-
-
-if __name__ == '__main__':
-    suite = unittest.TestLoader().loadTestsFromTestCase(TestCaseCompliance)
-    unittest.TextTestRunner(verbosity=2).run(suite)