Starting 0.2.0 rc.1 (Supersedes #29)

diffsims/generators/diffraction_generator.py

@@ -53,9 +53,9 @@ class DiffractionGenerator(object):
     max_excitation_error : float
         The maximum extent of the relrods in reciprocal angstroms. Typically
         equal to 1/{specimen thickness}.
-    debye_waller_factors : dict of str : float
+    debye_waller_factors : dict of str or float
         Maps element names to their temperature-dependent Debye-Waller factors.
-
+    scattering_params : 'lobato' or 'xtables'
     """
     # TODO: Refactor the excitation error to a structure property.
 
@@ -67,17 +67,8 @@ def __init__(self,
         self.wavelength = get_electron_wavelength(accelerating_voltage)
         self.max_excitation_error = max_excitation_error
         self.debye_waller_factors = debye_waller_factors or {}
+        self.scattering_params_string = scattering_params
 
-        scattering_params_dict = {
-            'lobato': 'lobato',
-            'xtables': 'xtables'
-        }
-        if scattering_params in scattering_params_dict:
-            self.scattering_params = scattering_params_dict[scattering_params]
-        else:
-            raise NotImplementedError("The scattering parameters `{}` is not implemented. "
-                                      "See documentation for available "
-                                      "implementations.".format(scattering_params))
 
     def calculate_ed_data(self,
                           structure,
@@ -109,7 +100,7 @@ def calculate_ed_data(self,
         max_excitation_error = self.max_excitation_error
         debye_waller_factors = self.debye_waller_factors
         latt = structure.lattice
-        scattering_params = self.scattering_params
+        scattering_params = self.scattering_params_string
 
         # Obtain crystallographic reciprocal lattice points within `max_r` and
         # g-vector magnitudes for intensity calculations.
@@ -179,7 +170,7 @@ def calculate_profile_data(self, structure,
         """
         max_r = reciprocal_radius
         wavelength = self.wavelength
-        scattering_params = self.scattering_params
+        scattering_params = self.scattering_params_string
 
         latt = structure.lattice
         is_hex = is_lattice_hexagonal(latt)

diffsims/libraries/diffraction_library.py

@@ -16,38 +16,8 @@
 # You should have received a copy of the GNU General Public License
 # along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
 
-import pickle
 import numpy as np
 
-
-def load_DiffractionLibrary(filename, safety=False):
-    """Loads a previously saved diffraction library.
-
-    Parameters
-    ----------
-    filename : str
-        The location of the file to be loaded
-    safety : bool (defaults to False)
-        Unpickling is risky, this variable requires you to acknowledge this.
-
-    Returns
-    -------
-    DiffractionLibrary
-        Previously saved Library
-
-    See Also
-    --------
-    DiffractionLibrary.pickle_library()
-
-    """
-    if safety:
-        with open(filename, 'rb') as handle:
-            return pickle.load(handle)
-    else:
-        raise RuntimeError('Unpickling is risky, turn safety to True if \
-        trust the author of this content')
-
-
 def _get_library_entry_from_angles(library, phase, angles):
     """Finds an element that is orientation within 1e-5 of that specified.
 
@@ -152,19 +122,3 @@ def get_library_entry(self, phase=None, angle=None):
             'pixel_coords': phase_entry['pixel_coords'][orientation_index],
             'pattern_norm': np.linalg.norm(phase_entry['intensities'][orientation_index])
         }
-
-    def pickle_library(self, filename):
-        """Saves a diffraction library in the pickle format.
-
-        Parameters
-        ----------
-        filename : str
-            The location in which to save the file
-
-        See Also
-        --------
-        load_DiffractionLibrary()
-
-        """
-        with open(filename, 'wb') as handle:
-            pickle.dump(self, handle, protocol=pickle.HIGHEST_PROTOCOL)

diffsims/libraries/vector_library.py

@@ -16,37 +16,8 @@
 # You should have received a copy of the GNU General Public License
 # along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
 
-import pickle
 import numpy as np
 
-
-def load_VectorLibrary(filename, safety=False):
-    """Loads a previously saved vectorlibrary.
-
-    Parameters
-    ----------
-    filename : str
-        The location of the file to be loaded
-    safety : bool (defaults to False)
-        Unpickling is risky, this variable requires you to acknowledge this.
-
-    Returns
-    -------
-    VectorLibrary
-        Previously saved Library
-
-    See Also
-    --------
-    VectorLibrary.pickle_library()
-    """
-    if safety:
-        with open(filename, 'rb') as handle:
-            return pickle.load(handle)
-    else:
-        raise RuntimeError('Unpickling is risky, turn safety to True if \
-        trust the author of this content')
-
-
 class DiffractionVectorLibrary(dict):
     """Maps crystal structure (phase) to diffraction vectors.
 
@@ -74,19 +45,3 @@ def __init__(self, *args, **kwargs):
         self.identifiers = None
         self.structures = None
         self.reciprocal_radius = None
-
-    def pickle_library(self, filename):
-        """Saves a vector library in the pickle format.
-
-        Parameters
-        ----------
-        filename : str
-            The location in which to save the file
-
-        See Also
-        --------
-            load_VectorLibrary()
-
-        """
-        with open(filename, 'wb') as handle:
-            pickle.dump(self, handle, protocol=pickle.HIGHEST_PROTOCOL)

diffsims/tests/test_library/test_diffraction_library.py

@@ -25,7 +25,6 @@
 
 from diffsims.sims.diffraction_simulation import DiffractionSimulation
 
-from diffsims.libraries.diffraction_library import load_DiffractionLibrary
 from diffsims.libraries.structure_library import StructureLibrary
 
 
@@ -57,22 +56,6 @@ def test_get_library_small_offset(get_library):
                                          angle=(1e-8, 0, 0))['intensities']
     assert np.allclose(alpha, beta)
 
-
-def test_library_io(get_library):
-    get_library.pickle_library('file_01.pickle')
-    loaded_library = load_DiffractionLibrary('file_01.pickle', safety=True)
-    os.remove('file_01.pickle')
-    # We can't check that the entire libraries are the same as the memory
-    # location of the 'Sim' changes
-    for i in range(len(get_library['Phase']['orientations'])):
-        np.testing.assert_allclose(get_library['Phase']['orientations'][i],
-                                   loaded_library['Phase']['orientations'][i])
-        np.testing.assert_allclose(get_library['Phase']['intensities'][i],
-                                   loaded_library['Phase']['intensities'][i])
-        np.testing.assert_allclose(get_library['Phase']['pixel_coords'][i],
-                                   loaded_library['Phase']['pixel_coords'][i])
-
-
 @pytest.mark.xfail(raises=ValueError)
 def test_angle_but_no_phase(get_library):
     # we have given an angle but no phase
@@ -86,9 +69,3 @@ def test_unknown_library_entry(get_library):
     assert isinstance(get_library.get_library_entry(phase='Phase',
                                                     angle=(1e-3, 0, 0))['Sim'],
                       DiffractionSimulation)
-
-
-@pytest.mark.xfail(raises=RuntimeError)
-def test_unsafe_loading(get_library):
-    get_library.pickle_library('file_01.pickle')
-    loaded_library = load_DiffractionLibrary('file_01.pickle')

diffsims/tests/test_library/test_vector_library.py

@@ -23,7 +23,6 @@
 
 from diffsims.generators.library_generator import VectorLibraryGenerator
 
-from diffsims.libraries.vector_library import load_VectorLibrary
 from diffsims.libraries.structure_library import StructureLibrary
 
 
@@ -32,19 +31,3 @@ def get_library(default_structure):
     structure_library = StructureLibrary(['Phase'], [default_structure], [[(0, 0, 0), (0, 0.2, 0)]])
     vlg = VectorLibraryGenerator(structure_library)
     return vlg.get_vector_library(0.5)
-
-
-def test_library_io(get_library):
-    get_library.pickle_library('file_01.pickle')
-    loaded_library = load_VectorLibrary('file_01.pickle', safety=True)
-    os.remove('file_01.pickle')
-    # we can't check that the entire libraries are the same as the memory
-    # location of the 'Sim' changes
-    np.testing.assert_allclose(get_library['Phase']['measurements'], loaded_library['Phase']['measurements'])
-    np.testing.assert_allclose(get_library['Phase']['indices'], loaded_library['Phase']['indices'])
-
-
-@pytest.mark.xfail(raises=RuntimeError)
-def test_unsafe_loading(get_library):
-    get_library.pickle_library('file_01.pickle')
-    loaded_library = load_VectorLibrary('file_01.pickle')

diffsims/version.py

@@ -2,7 +2,7 @@
 __copyright__ = "Copyright 2017-2019, Diffraction Simulations in Python"
 __credits__ = ["Duncan Johnstone", "Phillip Crout", "Ben Martineau", "Simon Hogas"]
 __license__ = "GPL"
-__version__ = "0.1.4"
+__version__ = "0.2.0-rc.1dev"
 __maintainer__ = "Duncan Johnstone"
 __email__ = "dnj23@cam.ac.uk"
 __status__ = "Development"