diff --git a/docs/source/conf.py b/docs/source/conf.py index 67e8fee6..3b02109d 100644 --- a/docs/source/conf.py +++ b/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 diff --git a/docs/source/index.rst b/docs/source/index.rst index c8ef0814..98ce728d 100644 --- a/docs/source/index.rst +++ b/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. diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 11ba05ce..edd85a26 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -61,7 +61,7 @@ Installation from source 1. Visit `the source code on GitHub `_ and download the zip file or simply click `here `_ 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. diff --git a/docs/source/plotting.rst b/docs/source/plotting.rst index 40b9bbf8..f3928947 100644 --- a/docs/source/plotting.rst +++ b/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 `_. 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) - - - - - - diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst index 97f569ae..10423a3b 100644 --- a/docs/source/quickstart.rst +++ b/docs/source/quickstart.rst @@ -59,7 +59,7 @@ The following code demonstrates a number of ways objects can be initialized. in () ----> 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`. - diff --git a/orix/__init__.py b/orix/__init__.py index 150cf461..c7ddc671 100644 --- a/orix/__init__.py +++ b/orix/__init__.py @@ -16,4 +16,4 @@ __version__ = "0.1.0" __author__ = "Ben Martineau" __author_email__ = "pyxem.team@gmail.com" -__description__ = "Spatially-resolved quaternion, rotation, orientation handling in Python, developed for texture analysis." +__description__ = "Orientation, rotation, quaternion, and crystal symmetry handling in Python." diff --git a/orix/base/__init__.py b/orix/base/__init__.py index 2434082d..cbdff029 100644 --- a/orix/base/__init__.py +++ b/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 . + import numpy as np diff --git a/orix/grid/s1grid.py b/orix/grid/s1grid.py index f8f57cce..4a93f405 100644 --- a/orix/grid/s1grid.py +++ b/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 . + import numpy as np @@ -14,4 +32,4 @@ def minimum(self): @property def maximum(self): - return np.max(self.points) \ No newline at end of file + return np.max(self.points) diff --git a/orix/grid/s2grid.py b/orix/grid/s2grid.py index a8e12d37..3dfca76d 100644 --- a/orix/grid/s2grid.py +++ b/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 . + import numpy as np from orix.vector import Vector3d from orix.grid.s1grid import S1Grid diff --git a/orix/io/__init__.py b/orix/io/__init__.py index 533291cf..14b78864 100644 --- a/orix/io/__init__.py +++ b/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 . + """Load and save utilities. .. warning:: diff --git a/orix/objects.py b/orix/objects.py index 55fc81dd..ce04b69a 100644 --- a/orix/objects.py +++ b/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 . + from orix.quaternion.orientation import Orientation, Misorientation -from orix.vector.neo_euler import * \ No newline at end of file +from orix.vector.neo_euler import * diff --git a/orix/plot/__init__.py b/orix/plot/__init__.py index 9cd8bdf2..3d3ee813 100644 --- a/orix/plot/__init__.py +++ b/orix/plot/__init__.py @@ -1 +1,19 @@ -from .rotation_plot import RodriguesPlot \ No newline at end of file +# -*- 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 . + +from .rotation_plot import RodriguesPlot diff --git a/orix/plot/rotation_plot.py b/orix/plot/rotation_plot.py index c1ee1474..cdec36f1 100644 --- a/orix/plot/rotation_plot.py +++ b/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 . + from matplotlib import projections from mpl_toolkits.mplot3d import Axes3D from orix.vector.neo_euler import Rodrigues, AxAngle diff --git a/orix/quaternion/__init__.py b/orix/quaternion/__init__.py index 8eaa2feb..97942783 100644 --- a/orix/quaternion/__init__.py +++ b/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 . + """Four-dimensional objects. In a simplified sense, quaternions are an extension of the concept of complex diff --git a/orix/quaternion/orientation.py b/orix/quaternion/orientation.py index d280d39f..ee7901f6 100644 --- a/orix/quaternion/orientation.py +++ b/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 . + """Rotations respecting symmetry. An orientation is simply a rotation with respect to some reference frame. In diff --git a/orix/quaternion/orientation_region.py b/orix/quaternion/orientation_region.py index e07e3ecc..53210fbf 100644 --- a/orix/quaternion/orientation_region.py +++ b/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 . + """An orientation region is some subset of the complete space of orientations. The complete orientation space represents every possible orientation of an diff --git a/orix/quaternion/rotation.py b/orix/quaternion/rotation.py index b2d83cac..50b8d0ba 100644 --- a/orix/quaternion/rotation.py +++ b/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 . + """Point transformations of objects. Rotations are transformations of three-dimensional space leaving the diff --git a/orix/quaternion/symmetry.py b/orix/quaternion/symmetry.py index 82d3d5fc..5a3aebd8 100644 --- a/orix/quaternion/symmetry.py +++ b/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 . + """Collections of transformations representing a symmetry group. An object's symmetry can be characterized by the transformations relating diff --git a/orix/scalar/__init__.py b/orix/scalar/__init__.py index 1f9f60cc..3de6df87 100644 --- a/orix/scalar/__init__.py +++ b/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 . + """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()) \ No newline at end of file + return self.__class__(self.data.T.flatten()) diff --git a/orix/symmetry.py b/orix/symmetry.py index a06b56c5..1fb537d9 100644 --- a/orix/symmetry.py +++ b/orix/symmetry.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 . + from orix.quaternion.symmetry import * from orix.quaternion.orientation_region import OrientationRegion diff --git a/orix/vector/__init__.py b/orix/vector/__init__.py index c8986194..4b69d186 100644 --- a/orix/vector/__init__.py +++ b/orix/vector/__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 . + """Three-dimensional quantities. Vectors can represent positions in three-dimensional space and are also diff --git a/orix/vector/neo_euler.py b/orix/vector/neo_euler.py index 2e22bdbf..be61e3e9 100644 --- a/orix/vector/neo_euler.py +++ b/orix/vector/neo_euler.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 . + """Neo-Eulerian vectors parametrize rotations as vectors. The rotation is specified by an axis of rotation and an angle. Different diff --git a/orix/vector/spherical_region.py b/orix/vector/spherical_region.py index 7dc338bf..ac946f85 100644 --- a/orix/vector/spherical_region.py +++ b/orix/vector/spherical_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 . + """Vectors describing a segment of a sphere. Each entry represents a plane normal in 3-d. Vectors can lie in, on, or outside @@ -55,4 +73,4 @@ def __ge__(self, x): ndarray """ - return np.all(self.dot_outer(x) > -1e-9, axis=0) \ No newline at end of file + return np.all(self.dot_outer(x) > -1e-9, axis=0)