Merge pull request #11 from dnjohnstone/orix0.1.0

Orix0.1.0

docs/source/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 #
-# texpy documentation build configuration file, created by
+# orix documentation build configuration file, created by
 # sphinx-quickstart on Tue Mar 20 12:05:50 2018.
 #
 # This file is execfile()d with the current directory set to its

docs/source/index.rst

@@ -1,4 +1,4 @@
-.. texpy documentation master file, created by
+.. orix documentation master file, created by
    sphinx-quickstart on Tue Mar 20 12:05:50 2018.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.

docs/source/installation.rst

@@ -61,7 +61,7 @@ Installation from source
 1. Visit `the source code on GitHub <https://github.com/pyxem/orix>`_ and
    download the zip file or simply click
    `here <https://github.com/pyxem/orix/archive/master.zip>`_ to download
-   texpy as a zip file.
+   orix as a zip file.
 2. Unzip the downloaded file to a convenient local directory.
 3. Open a terminal and navigate to the top level "orix" directory.
 4. Ensure you are using Python version 3.5 or higher:
@@ -73,13 +73,10 @@ Installation from source
    If not, consider upgrading your python version, or start a virtual
    environment with Python 3.5 or higher.
 
-5. Install texpy:
+5. Install orix:
 
    .. code:: shell
 
       > pip install .
 
-   This will install texpy alongside numpy and matplotlib.
-
-
-
+   This will install orix alongside numpy and matplotlib.

docs/source/plotting.rst

@@ -6,13 +6,13 @@ a work in progress, but several tools are already available. The process builds
 upon the way data is plotted in `matplotlib <https://matplotlib.org/>`_.
 
 Any plotting session will begin by importing both the matplotlib plotting API
-and the texpy plotting API.
+and the orix plotting API.
 
 .. ipython::
 
     In [1]: import matplotlib.pyplot as plt
 
-    In [2]: import texpy.plot
+    In [2]: import orix.plot
 
     In [3]: %matplotlib qt5  # Setting the backend.
 
@@ -35,9 +35,3 @@ simplest is:
 .. ipython::
 
     In [4]: ax = plt.figure().add_subplot(111)
-
-
-
-
-
-

docs/source/quickstart.rst

@@ -59,7 +59,7 @@ The following code demonstrates a number of ways objects can be initialized.
    <ipython-input-10-422ccfdd4ab4> in <module>()
    ----> 1 w = Vector3d(np.random.random((4, 4)))
 
-   ~\Documents\phd\dev\texpy\texpy\base\__init__.py in __init__(self, data)
+   ~\Documents\phd\dev\orix\orix\base\__init__.py in __init__(self, data)
         41         self.data = data
         42         if data.shape[-1] != self.dim:
    ---> 43             raise DimensionError(self)
@@ -244,4 +244,3 @@ Most orix objects are mathematical.
 
 For a complete description of each object's mathematical properties, refer
 to the full :doc:`api`.
-

orix/__init__.py

@@ -16,4 +16,4 @@
 __version__ = "0.1.0"
 __author__ = "Ben Martineau"
 __author_email__ = "[email protected]"
-__description__ = "Spatially-resolved quaternion, rotation, orientation handling in Python, developed for texture analysis."
+__description__ = "Orientation, rotation, quaternion, and crystal symmetry handling in Python."

orix/base/__init__.py

@@ -1,3 +1,21 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 import numpy as np
 
 

orix/grid/s1grid.py

@@ -1,3 +1,21 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 import numpy as np
 
 
@@ -14,4 +32,4 @@ def minimum(self):
 
     @property
     def maximum(self):
-        return np.max(self.points)
+        return np.max(self.points)

orix/grid/s2grid.py

@@ -1,3 +1,21 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 import numpy as np
 from orix.vector import Vector3d
 from orix.grid.s1grid import S1Grid

orix/io/__init__.py

@@ -1,3 +1,21 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 """Load and save utilities.
 
 .. warning::

orix/objects.py

@@ -1,2 +1,20 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 from orix.quaternion.orientation import Orientation, Misorientation
-from orix.vector.neo_euler import *
+from orix.vector.neo_euler import *

orix/plot/__init__.py

@@ -1 +1,19 @@
-from .rotation_plot import RodriguesPlot
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
+from .rotation_plot import RodriguesPlot

orix/plot/rotation_plot.py

@@ -1,3 +1,21 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 from matplotlib import projections
 from mpl_toolkits.mplot3d import Axes3D
 from orix.vector.neo_euler import Rodrigues, AxAngle

orix/quaternion/__init__.py

@@ -1,3 +1,21 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 """Four-dimensional objects.
 
 In a simplified sense, quaternions are an extension of the concept of complex

orix/quaternion/orientation.py

@@ -1,3 +1,21 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 """Rotations respecting symmetry.
 
 An orientation is simply a rotation with respect to some reference frame. In

orix/quaternion/orientation_region.py

@@ -1,3 +1,21 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 """An orientation region is some subset of the complete space of orientations.
 
 The complete orientation space represents every possible orientation of an

orix/quaternion/rotation.py

@@ -1,3 +1,21 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 """Point transformations of objects.
 
 Rotations are transformations of three-dimensional space leaving the

orix/quaternion/symmetry.py

@@ -1,3 +1,21 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 """Collections of transformations representing a symmetry group.
 
 An object's symmetry can be characterized by the transformations relating

orix/scalar/__init__.py

@@ -1,3 +1,21 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018-2019 The pyXem developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix.  If not, see <http://www.gnu.org/licenses/>.
+
 """Dimensionless quantities.
 
 As well as themselves representing physical quantities, Scalars
@@ -201,4 +219,4 @@ def reshape(self, *args):
 
     def flatten(self):
         """Scalar : A new object with the same data in a single column."""
-        return self.__class__(self.data.T.flatten())
+        return self.__class__(self.data.T.flatten())