Starting 0.2.0-rc.1

.coveragerc

@@ -3,7 +3,5 @@ source = diffsims
 include = */diffsims/*
 omit =
      */diffsims/__init__.py
-     */diffsims/utils/atomic_scattering_params.py
-     */diffsims/utils/scattering_params.py
      */diffsims/version.py
      */diffsims/utils/__init__.py

PULL_REQUEST_TEMPLATE.md

@@ -2,18 +2,12 @@
 name: Pull request 
 about: A pull request that fixes a bug or adds a feature
 
-- [ ] ready for review and merge?
 ---
 
 **Release Notes**
-> major or minor (all but urgent bugfixes go in the former)
 > new feature / improvement / bugfix / developer change
 Summary: 1 line per end-user relevant change
 
-**What does this PR do? Please describe and/or link to an open issue.**
-A clear and concise description of what the code in this PR does. Does it fix a bug or add a new feature?
-If it is related to an open issue, reference it here.
-
 **Describe alternatives you've considered**
 A clear and concise description of any alternative solutions or features you've considered.
 

diffsims/generators/diffraction_generator.py

@@ -26,7 +26,9 @@
 from diffsims.sims.diffraction_simulation import DiffractionSimulation
 from diffsims.sims.diffraction_simulation import ProfileSimulation
 
-from diffsims.utils.atomic_scattering_params import ATOMIC_SCATTERING_PARAMS
+from diffsims.utils import get_method_from_string
+from diffsims.utils.xtables_scattering_params import ATOMIC_SCATTERING_PARAMS
+from diffsims.utils.lobato_scattering_params import ATOMIC_SCATTERING_PARAMS_LOBATO
 from diffsims.utils.sim_utils import get_electron_wavelength,\
     get_kinematical_intensities, get_unique_families, get_points_in_sphere, \
     get_vectorized_list_for_atomic_scattering_factors, is_lattice_hexagonal
@@ -59,6 +61,7 @@ class DiffractionGenerator(object):
     """
     # TODO: Refactor the excitation error to a structure property.
 
+
     def __init__(self,
                  accelerating_voltage,
                  max_excitation_error,
@@ -67,17 +70,12 @@ 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 {}
+
+        scattering_params_dict = {'xtables':ATOMIC_SCATTERING_PARAMS,
+                                  'lobato':ATOMIC_SCATTERING_PARAMS_LOBATO}
+        self.scattering_params = get_method_from_string(scattering_params,
+                                                        scattering_params_dict)
 
-        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,
@@ -96,7 +94,7 @@ def calculate_ed_data(self,
             reciprocal angstroms.
         with_direct_beam : bool
             If True, the direct beam is included in the simulated diffraction
-            pattern. If False, it is not.
+            pattern.
 
         Returns
         -------

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/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
 
 
@@ -58,21 +57,6 @@ def test_get_library_small_offset(get_library):
     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 +70,3 @@ 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/utils/__init__.py

@@ -15,3 +15,16 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
+
+
+def get_method_from_string(string,method_dict):
+    """
+
+    """
+
+    if string in method_dict.keys():
+        return method_dict[string]
+    else:
+        raise NotImplementedError("The option `{}` is not implemented. "
+                                    "See documentation for available "
+                                    "implementations.".format(method_dict.keys()))

diffsims/utils/sim_utils.py

@@ -27,12 +27,16 @@
 from transforms3d.euler import mat2euler
 from transforms3d.euler import euler2mat
 
-from .atomic_scattering_params import ATOMIC_SCATTERING_PARAMS
+from . import get_method_from_string
+from .xtables_scattering_params import ATOMIC_SCATTERING_PARAMS
 from .lobato_scattering_params import ATOMIC_SCATTERING_PARAMS_LOBATO
 
 #from diffsims.sims.diffraction_simulation import DiffractionSimulation
 from diffsims.utils.vector_utils import get_angle_cartesian
 
+scattering_params_dict = {'xtables':ATOMIC_SCATTERING_PARAMS,
+                          'lobato':ATOMIC_SCATTERING_PARAMS_LOBATO}
+
 
 def get_electron_wavelength(accelerating_voltage):
     """Calculates the (relativistic) electron wavelength in Angstroms for a
@@ -113,31 +117,6 @@ def is_perm(hkl1, hkl2):
 
     return pretty_unique
 
-
-def get_scattering_params_dict(scattering_params):
-    """Get scattering parameter dictionary from name.
-
-    Parameters
-    ----------
-    scattering_params : string
-        Name of scattering factors. One of 'lobato', 'xtables'.
-
-    Returns
-    -------
-    scattering_params_dict : dict
-        Dictionary of scattering parameters mapping from element name.
-    """
-    if scattering_params == 'lobato':
-        scattering_params_dict = ATOMIC_SCATTERING_PARAMS_LOBATO
-    elif scattering_params == 'xtables':
-        scattering_params_dict = ATOMIC_SCATTERING_PARAMS
-    else:
-        raise NotImplementedError("The scattering parameters `{}` are not implemented. "
-                                  "See documentation for available "
-                                  "implementations.".format(scattering_params))
-    return scattering_params_dict
-
-
 def get_vectorized_list_for_atomic_scattering_factors(structure,
                                                       debye_waller_factors,
                                                       scattering_params):
@@ -168,7 +147,7 @@ def get_vectorized_list_for_atomic_scattering_factors(structure,
         Debye-Waller factors for each atom in the structure.
     """
 
-    scattering_params_dict = get_scattering_params_dict(scattering_params)
+    scattering_params_dict = get_method_from_string(scattering_params,scattering_params_dict)
 
     n_structures = len(structure)
     coeffs = np.empty((n_structures, 5, 2))
@@ -306,7 +285,7 @@ def simulate_kinematic_scattering(atomic_coordinates,
         ElectronDiffraction simulation.
     """
     # Get atomic scattering parameters for specified element.
-    coeffs = np.array(get_scattering_params_dict(scattering_params)[element])
+    coeffs = np.array(get_method_from_string(scattering_params,scattering_params_dict)[element])
 
     # Calculate electron wavelength for given keV.
     wavelength = get_electron_wavelength(accelerating_voltage)

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.1"
 __maintainer__ = "Duncan Johnstone"
 __email__ = "dnj23@cam.ac.uk"
 __status__ = "Development"