Image quality, chunk and pattern modules, some FFT routines

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

.travis.yml

@@ -60,7 +60,7 @@ install:
   # Install dependencies with conda or pip
   - source ./ci/travis_install_with_$ENV.sh
 
-  # Install KikuchiPy
+  # Install kikuchipy
   - pip install -e .
 
 script:

README.rst

@@ -28,7 +28,7 @@
     :target: https://doi.org/10.5281/zenodo.3597646
     :alt: DOI
 
-*KikuchiPy is an open-source Python library for processing and analysis of
+*kikuchipy is an open-source Python library for processing and analysis of
 electron backscatter diffraction (EBSD) patterns.*
 
 The library builds upon the tools for multi-dimensional data analysis provided
@@ -40,7 +40,7 @@ inherits all relevant methods from HyperSpy's Signal2D and `Signal
 Note that the project is in an alpha stage, and there will likely be breaking
 changes with each release.
 
-KikuchiPy is released under the GPL v3 license.
+kikuchipy is released under the GPL v3 license.
 
 User guide
 ----------
@@ -57,12 +57,12 @@ Everyone is welcome to contribute. Please read our `contributor guide
 Code of Conduct
 ---------------
 
-KikuchiPy has a `Code of Conduct
+kikuchipy has a `Code of Conduct
 <https://kikuchipy.readthedocs.io/en/latest/code_of_conduct.html>`_
-that should be honoured by everyone who participates in the KikuchiPy community.
+that should be honoured by everyone who participates in the kikuchipy community.
 
 Cite
 ----
 
-If analysis using KikuchiPy forms a part of published work, please consider
+If analysis using kikuchipy forms a part of published work, please consider
 recognizing the code development by citing the DOI above.

doc/_static/color_style.py

@@ -0,0 +1,14 @@
+import matplotlib.pyplot as plt
+import matplotlib.colors as mcolors
+import numpy as np
+
+# Getting the nice colors
+extent = (0, 255)
+n = 20
+idx = np.linspace(extent[0], extent[1], n, dtype=int)
+
+# winter, cividis, viridis, inferno, magma, plasma, etc
+rgb_idx = plt.get_cmap("viridis")(idx)[:, :3]
+
+# Print to sys.out
+print([mcolors.to_hex(i) for i in rgb_idx])

doc/_static/image/concatenate_images.sh

@@ -12,8 +12,10 @@ convert ${PATPROC}/pattern_raw.jpg ${PATPROC}/pattern_static.jpg +append ${PATPR
 convert ${PATPROC}/pattern_static.jpg ${PATPROC}/pattern_dynamic.jpg +append ${PATPROC}/dynamic_correction.jpg
 convert ${PATPROC}/pattern_dynamic.jpg ${PATPROC}/pattern_adapthist.jpg +append ${PATPROC}/adapthist.jpg
 convert ${PATPROC}/pattern_scan_static.png ${PATPROC}/pattern_scan_averaged.png +append ${PATPROC}/average_neighbour_pattern.jpg
+convert ${PATPROC}/contrast_stretching_before.png ${PATPROC}/contrast_stretching_after.png +append ${PATPROC}/contrast_stretching.jpg
+convert ${PATPROC}/rescale_intensities_before.png ${PATPROC}/rescale_intensities_after.png +append ${PATPROC}/rescale_intensities.jpg
 
-# Change pattern size
+# Change image size
 convert ${PATPROC}/pattern_dynamic.jpg ${CHANGES}/pattern_cropped.jpg +append ${CHANGES}/change_pattern_size.jpg
 
 # Virtual image

doc/_static/style.css

@@ -0,0 +1,224 @@
+/* Colors
+white: #ffffff
+
+black: #24292e
+
+dark grey: #24292e
+gray: #404448
+light gray: #f6f8fa
+very light gray: #fafbfc
+very very light gray: #fcfffc
+
+blue: #0366d6
+light blue: #3598d6
+lighter blue: #68b1e0
+
+green GitHub: #2cbe4e
+green viridis: 3bbb75
+yellow: #fde725
+
+*/
+
+/* Change code blocks font and bump up font size slightly (normally 12px)*/
+.rst-content pre.literal-block, .rst-content div[class^="highlight"] pre, .rst-content .linenodiv pre {
+	font-family: 'Inconsolata', monospace !important;
+	font-size: 14px !important;
+	white-space: pre-wrap;
+}
+
+/* All page */
+body {
+    font-family: "Fira Sans", sans-serif;
+}
+
+/* Text */
+p {
+    color: #24292e;
+}
+
+/* Links */
+.wy-nav-content-wrap p a {
+    color: #0366d6;
+}
+.wy-nav-content-wrap footer a {
+    color: #0366d6;
+}
+.wy-breadcrumbs li a {
+    color: #0366d6;
+}
+
+/* Links hover */
+.wy-nav-content-wrap p a:hover {
+    color: #0366d6;
+    text-decoration: underline;
+}
+.wy-nav-content-wrap footer a:hover {
+    color: #0366d6;
+    text-decoration: underline;
+}
+.wy-breadcrumbs li a:hover {
+    color: #0366d6;
+    text-decoration: underline;
+}
+
+/* Content background */
+.wy-nav-content-wrap {
+    background-color: #ffffff;
+}
+
+/* Content background */
+.wy-nav-content {
+    max-width: 940px;
+    background-color: #ffffff;
+}
+
+/* Sidebar */
+.wy-nav-side {
+    background-color: #ffffff;
+    color: #404688;
+/*    border-right: 1px solid #e1e4e5; */
+}
+
+/* Sidebar search link (title) */
+.wy-side-nav-search a {
+    color: #0366d6;
+}
+/* Sidebar search link (version) */
+.wy-side-nav-search div.version {
+    color: #24292e;
+}
+.wy-side-nav-search a:hover {
+    background-color: #ffffff;
+}
+
+/* Sidebar search */
+.wy-side-nav-search {
+    background-color: #ffffff;
+}
+
+/* Sidebar toc header */
+.wy-menu p.caption {
+    color: #24292e; /* 24292e 2cbe4e 3bbb75 */
+    text-transform: none;
+}
+.wy-menu li a:active {
+    color: #3598d6;
+}
+.wy-menu li.current a {
+    background-color: #ffffff;
+    color: #0366d6;
+    border-right: none;
+}
+.wy-menu li.current a:hover {
+    background-color: #ffffff;
+    color: #0366d6;
+    border-right: none;
+}
+/* Toctree level 1 */
+.wy-menu li.toctree-l1.current > a {
+    background-color: #0366d6;
+    color: #ffffff;
+    border-top: none;
+    border-bottom: none;
+}
+.wy-menu li.toctree-l1.current > a:hover {
+    background-color: #fde725;
+    color: #0366d6;
+}
+/* Toctree level 2 */
+.wy-menu li.toctree-l2 a {
+    background-color: #3598d6;
+    color: #ffffff;
+}
+.wy-menu li.toctree-l2 a:hover {
+    background-color: #fde725;
+    color: #0366d6;
+}
+.wy-menu li.toctree-l2.current a {
+    background-color: #3598d6;
+    color: #ffffff; /* f5f5f5 */
+}
+.wy-menu li.toctree-l2.current a:hover {
+    background-color: #fde725;
+    color: #0366d6;
+}
+/* Toctree level 3 */
+.wy-menu li.toctree-l2.current li.toctree-l3 a {
+    background-color: #68b1e0;
+    color: #ffffff;
+    font-size: 14px;
+}
+.wy-menu li.toctree-l2.current li.toctree-l3 a:hover {
+    background-color: #fde725;
+    color: #0366d6;
+}
+
+/* Sidebar expand span buttons */
+.wy-menu li a span.toctree-expand {
+    color: #0366d6;
+}
+.wy-menu li a:hover span.toctree-expand {
+    color: #0366d6;
+}
+.wy-menu li.current a span.toctree-expand {
+    color: #ffffff;
+}
+.wy-menu li.current a:hover span.toctree-expand {
+    color: #0366d6;
+}
+
+/* Sidebar toc links */
+.wy-menu a {
+    color: #0366d6;
+}
+
+/* Sidebar toc links hover */
+.wy-side-nav-search a:hover {
+    background-color: #fde725;
+}
+
+/* Sidebar toc links hover background */
+.wy-menu a:hover {
+    background-color: #fde725;
+}
+
+/* Nav top */
+.wy-nav-top {
+    background-color: #0366d6;
+}
+.wy-nav-top a {
+    color: #ffffff;
+}
+.wy-nav-top a:visited {
+    color: #ffffff;
+}
+
+/* Permalinks */
+a:visited {
+    color: #0366d6;
+}
+
+/* Formatting for code blocks */
+.highlight {
+	background-color: #f6f8fa;
+}
+
+/* Formatting for inline code */
+.literal {
+	background-color: #f6f8fa;
+}
+
+
+/* Override table width restrictions (taken from Dask) */
+@media screen and (min-width: 767px) {
+
+   .wy-table-responsive table td {
+      /* !important prevents the common CSS stylesheets from overriding
+         this as on RTD they are loaded after this stylesheet */
+      white-space: normal !important;
+   }
+
+   .wy-table-responsive {
+      overflow: visible !important;
+   }
+}

doc/_templates/layout.html

@@ -0,0 +1,5 @@
+{% extends "!layout.html" %}
+{% block extrahead %}
+  <link href="{{ pathto('_static/style.css', True) }}" rel="stylesheet"
+        type="text/css">
+{% endblock extrahead %}