REF: Refactor into submodules

Have combined relevant modules into folders:

* crystal : Lattice, Sample, Material, Symmetry, structure_factors, etc
* fileio : load_data, load_instrument, etc
* instrument : instrument, tools, goniometer, monochromator, analyzer, etc
* scattering : pattern (new, renamed from scattering), polarization, etc.
* data : analysis, data

Plot modules are contained within the appropriate subfolder for relevant modules to prevent circular imports

Added UTF encoding strings to all files to avoid import errors in python 2

Added loaders folder to fileio which will contain filetype-specific loaders for loading data, instruments, etc.

neutronpy/__init__.py

@@ -3,24 +3,24 @@
 '''
 from __future__ import absolute_import
 from . import constants
+from . import fileio
 from . import functions
+from . import instrument
 from . import models
 from . import spurion
-from . import io
-from . import polarization
-from . import symmetry
-from .kmpfit import Fitter
-from .energy import Energy
+from . import scattering
+from .crystal import Lattice
+from .crystal import Material
+from .crystal import Sample
+from .crystal import symmetry
 from .data import Data
-from . import instrument
+from .energy import Energy
+from .kmpfit import Fitter
 from .instrument import Instrument
-from .sample import Sample
-from .material import Material
-from .lattice import Lattice
 
 try:
     from . import gui
 except ImportError:
     print('Warning: PyQt5 not found, cannot run Resolution GUI')
 
-__version__ = '1.0.0b1'
+__version__ = '1.0.0b2'

neutronpy/constants.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 r'''Useful constants for neutron scattering calculations, including:
 
 * ``magnetic_form_factors()`` : Magnetic Ion j-values

neutronpy/crystal/__init__.py

@@ -0,0 +1,6 @@
+from .atom import Atom, MagneticAtom
+from .lattice import Lattice
+from .material import Material
+from .sample import Sample
+from .symmetry import SpaceGroup
+from . import symmetry

neutronpy/atom.py → neutronpy/crystal/atom.py

@@ -1,5 +1,6 @@
+# -*- coding: utf-8 -*-
 import numpy as np
-import neutronpy.constants as const
+from ..constants import periodic_table, scattering_lengths
 
 
 class Atom(object):
@@ -40,14 +41,14 @@ def __init__(self, ion, pos, occupancy=1., Mcell=None, massNorm=False, Uiso=0, U
         self.Uaniso = np.matrix(Uaniso)
 
         if massNorm is True:
-            self.mass = const.periodic_table()[ion]['mass']
-            self.b = (const.scattering_lengths()[ion]['Coh b'] * self.occupancy * self.Mcell / np.sqrt(self.mass))
+            self.mass = periodic_table()[ion]['mass']
+            self.b = (scattering_lengths()[ion]['Coh b'] * self.occupancy * self.Mcell / np.sqrt(self.mass))
         else:
-            self.b = const.scattering_lengths()[ion]['Coh b'] / 10.
+            self.b = scattering_lengths()[ion]['Coh b'] / 10.
 
-        self.coh_xs = const.scattering_lengths()[ion]['Coh xs']
-        self.inc_xs = const.scattering_lengths()[ion]['Inc xs']
-        self.abs_xs = const.scattering_lengths()[ion]['Abs xs']
+        self.coh_xs = scattering_lengths()[ion]['Coh xs']
+        self.inc_xs = scattering_lengths()[ion]['Inc xs']
+        self.abs_xs = scattering_lengths()[ion]['Abs xs']
 
 
 class MagneticAtom(object):

neutronpy/lattice.py → neutronpy/crystal/lattice.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 r'''Handles lattice geometries to find rotations and transformations
 
 '''

neutronpy/material.py → neutronpy/crystal/material.py

@@ -4,12 +4,12 @@
 '''
 import numpy as np
 import neutronpy.constants as const
+from .atom import Atom, MagneticAtom
 from .plot import PlotMaterial
+from .sample import Sample
 from .structure_factors import NuclearStructureFactor, MagneticStructureFactor
-from .scattering import HKLGenerator
 from .symmetry import SpaceGroup
-from .sample import Sample
-from .atom import Atom, MagneticAtom
+#from ..scattering.pattern import HKLGenerator
 
 
 class MagneticUnitCell(Sample):
@@ -45,7 +45,7 @@ def __init__(self, unit_cell):
         super(MagneticUnitCell, self).__init__(a, b, c, alpha, beta, gamma)
 
 
-class Material(Sample, NuclearStructureFactor, MagneticStructureFactor, HKLGenerator, PlotMaterial):
+class Material(Sample, NuclearStructureFactor, MagneticStructureFactor, PlotMaterial):
     r'''Class for the Material being supplied for the structure factor calculation
 
     Parameters

neutronpy/crystal/plot.py

@@ -0,0 +1,42 @@
+import numpy as np
+
+
+class PlotMaterial(object):
+    r'''Class containing plotting methods for Material object
+
+    Methods
+    -------
+    plot_unit_cell
+
+    '''
+    def plot_unit_cell(self):
+        r'''Plots the unit cell and atoms of the material.
+
+        '''
+
+        import matplotlib.pyplot as plt
+        from mpl_toolkits.mplot3d import Axes3D  # @UnresolvedImport
+        from itertools import product, combinations
+
+        fig = plt.figure()
+        ax = fig.gca(projection='3d')
+
+        # draw unit cell
+        for s, e in combinations(np.array(list(product([0, self.abc[0]], [0, self.abc[1]], [0, self.abc[2]]))), 2):
+            if np.sum(np.abs(s - e)) in self.abc:
+                ax.plot3D(*zip(s, e), color="b")
+
+        # plot atoms
+        x, y, z, m = [], [], [], []
+        for item in self.atoms:
+            x.append(item.pos[0] * self.abc[0])
+            y.append(item.pos[1] * self.abc[1])
+            z.append(item.pos[2] * self.abc[2])
+            m.append(item.mass)
+
+        ax.scatter(x, y, z, s=m)
+
+        plt.axis('scaled')
+        plt.axis('off')
+
+        plt.show()

neutronpy/structure_factors.py → neutronpy/crystal/structure_factors.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 r'''Structure Factors
 
 NuclearStructureFactor
@@ -6,7 +7,7 @@
 
 '''
 import numpy as np
-from .constants import magnetic_ion_j
+from ..constants import magnetic_ion_j
 
 
 class NuclearStructureFactor(object):

neutronpy/symmetry.py → neutronpy/crystal/symmetry.py

@@ -3,7 +3,7 @@
 
 '''
 import numpy as np
-from neutronpy.constants import symmetry
+from ..constants import symmetry
 
 space_groups = symmetry()['space_groups']
 

neutronpy/data/__init__.py

@@ -0,0 +1,2 @@
+from .data import Data
+from .rawdata import RawData