Merge pull request #42 from SarthakJariwala/v0.4.x

Update example gallery and readme
SarthakJariwala · Sep 6, 2020 · 01154c0 · 01154c0
2 parents 49b8fed + ae827ae
commit 01154c0
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diff --git a/.gitignore b/.gitignore
@@ -44,6 +44,7 @@ sdist/*
 docs/api/*
 docs/_rst/*
 docs/_build/*
+docs/auto_examples/*
 cover/*
 MANIFEST
 

diff --git a/README.md b/README.md
@@ -4,51 +4,46 @@
 [![Codecov](https://codecov.io/gh/SarthakJariwala/seaborn-image/branch/master/graph/badge.svg)](https://codecov.io/gh/SarthakJariwala/seaborn-image)
 [![PyPI](https://img.shields.io/pypi/v/seaborn-image.svg)](https://pypi.org/project/seaborn-image/)
 [![Documentation Status](https://readthedocs.org/projects/seaborn-image/badge/?version=latest)](https://seaborn-image.readthedocs.io/en/latest/?badge=latest)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
 
 <div class="row">
 
-  <a>
-  <img src="./examples/image_0.png" height="180" width="200">
+  <a href="https://seaborn-image.readthedocs.io/auto_examples/plot_image_hist.html">
+  <img src="./images/sphx_glr_plot_image_hist_001.png" height="120" width="170">
   </a>
 
-  <a>
-  <img src="./examples/image_1.png" height="180" width="200">
+  <a href="https://seaborn-image.readthedocs.io/auto_examples/plot_filter.html">
+  <img src="./images/sphx_glr_plot_filter_001.png" height="120" width="130">
   </a>
 
-  <a>
-  <img src="./examples/image_3.png" height="165" width="400">
+  <a href="https://seaborn-image.readthedocs.io/auto_examples/plot_fft.html">
+  <img src="./images/sphx_glr_plot_fft_001.png" height="120" width="120">
   </a>
 
-</div>
-
-<div class="row">
-
-  <a>
-  <img src="./examples/image_5.png" height="250" width="375">
+  <a href="https://seaborn-image.readthedocs.io/auto_examples/plot_filtergrid.html">
+  <img src="./images/sphx_glr_plot_filtergrid_001.png" height="120" width="120">
   </a>
 
-</div>
-
-<div class="row">
-
-  <a>
-  <img src="./examples/image_4.png" height="600" width="600">
+  <a href="https://seaborn-image.readthedocs.io/auto_examples/plot_image_robust.html">
+  <img src="./images/sphx_glr_plot_image_robust_001.png" height="120" width="260">
   </a>
 
 </div>
 
+
 Seaborn-like image data visualization using matplotlib, scikit-image and scipy.
 
 ## Description
 
-Seaborn-image is a seaborn like python **image** visualization and processing library
+Seaborn-image is a seaborn-like python **image** visualization and processing library
 based on matplotlib, scipy and scikit-image.
 
-The aim of seaborn-image is to provide a high-level API to **process and plot attractive images quickly and effectively**.
+The aim of `seaborn-image` is to provide a high-level API to **process and plot attractive images quickly and effectively**.
 
 ## Documentation
 
-Check out the docs [here](https://seaborn-image.readthedocs.io/)
+Check out the docs [here](https://seaborn-image.readthedocs.io/).
 
 
 ## Installation
@@ -58,57 +53,5 @@ pip install seaborn-image
 ```
 
 ## Usage
-### Simple usage
-
-```python
-
-import seaborn_image as isns
-
-"""Plot image"""
-isns.imgplot(data)
-
-"""Plot image with scalebar"""
-isns.imgplot(data, dx=0.01, units="um")
-
-"""Add colorbar label"""
-isns.imgplot(data, dx=0.01, units="um", cbar_label="Height (nm)")
-```
-<a>
-<img src="./examples/image_0.png" height="275" width="300">
-</a>
-
-### Plot image with a histogram
-
-```python
-import seaborn_image as isns
-
-isns.imghist(data, dx=150, units="nm", cbar_label="Height (nm)", cmap="ice")
-```
-
-<a>
-<img src="./examples/image_5.png" height="300" width="450">
-</a>
-
-### Set context like seaborn
-
-```python
-
-import seaborn_image as isns
-
-isns.set_context("notebook") # Other options include paper, talk, presentation, poster
-```
-
-### Apply image filters (from scipy and skimage) and plot
-
-```python
-
-import seaborn_image as isns
-
-isns.filterplot(data, filter="gaussian", sigma=5, cbar_label="Height (nm)")
-```
-
-<a>
-<img src="./examples/image_3.png" height="260" width="600">
-</a>
 
-Check out the more information [here](https://seaborn-image.readthedocs.io/)
+Check out the [quickstart guide](https://seaborn-image.readthedocs.io/en/latest/quickstart.html) and [examples](https://seaborn-image.readthedocs.io/auto_examples/index.html).
diff --git a/docs/Makefile b/docs/Makefile
@@ -51,7 +51,8 @@ help:
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
 clean:
-	rm -rf $(BUILDDIR)/* $(AUTODOCDIR)
+	rm -rf $(BUILDDIR)/*
+	rm -rf auto_examples/
 
 $(AUTODOCDIR): $(MODULEDIR)
 	mkdir -p $@

diff --git a/docs/conf.py b/docs/conf.py
@@ -8,17 +8,29 @@
 extensions = [
     "sphinx.ext.autodoc",
     "sphinx.ext.napoleon",
-    "sphinxcontrib.images",
+    "sphinx_gallery.gen_gallery",
     "matplotlib.sphinxext.plot_directive",
 ]
 html_static_path = ["_static"]
 
-
+# for matplotlib plot-directive
 plot_include_source = True
 plot_formats = [("png", 90)]
 plot_html_show_formats = False
 plot_html_show_source_link = False
 
+# sphinx-gallery
+sphinx_gallery_conf = {
+    "examples_dirs": "../examples",  # path to your example scripts
+    "gallery_dirs": "auto_examples",  # path to where to save gallery generated output
+    "image_scrapers": ("matplotlib"),  # collect images created
+    "capture_repr": (),
+    "download_all_examples": False,
+    "line_numbers": False,
+    "show_memory": False,
+    "thumbnail_size": (500, 500),
+}
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -76,7 +88,7 @@
     "navbar_links": [
         ("Quickstart", "quickstart"),
         ("How-to?", "how_to"),
-        ("Gallery", "gallery"),
+        ("Gallery", "auto_examples/index"),
         ("Releases", "https://github.com/SarthakJariwala/seaborn-image/releases", True),
         ("Reference", "reference"),
     ],

diff --git a/docs/gallery.rst b/docs/gallery.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -2,19 +2,27 @@
 seaborn-image: image data visualization
 =======================================
 
-.. list-table::
+|img1| |img2| |img3| |img4|
 
-    * - .. image:: ../examples/image_1.png
-            :width: 150px
-            :height: 140px
+.. |img1| image:: /auto_examples/images/thumb/sphx_glr_plot_image_hist_thumb.png
+    :width: 190px
+    :height: 180px
 
-        .. image:: ../examples/image_5.png
-            :width: 200px
-            :height: 140px
+.. |img2| image:: /auto_examples/images/thumb/sphx_glr_plot_filter_thumb.png
+    :width: 140px
+    :height: 140px
 
-        .. image:: ../examples/image_4.png
-            :width:  140px
-            :height: 140px
+.. |img3| image:: /auto_examples/images/thumb/sphx_glr_plot_fft_thumb.png
+    :width: 120px
+    :height: 120px
+
+.. |img4| image:: /auto_examples/images/thumb/sphx_glr_plot_filtergrid_thumb.png
+    :width: 140px
+    :height: 140px
+
+.. .. |img5| image:: /auto_examples/images/thumb/sphx_glr_plot_image_robust_thumb.png
+..     :width: 200px
+..     :height: 200px
 
 
 Description
@@ -27,7 +35,7 @@ The aim of seaborn-image is to provide a high-level API to **process and plot at
 **and effectively**.
 
 To get started with ``seaborn_image``, check out the :doc:`quickstart page <quickstart>`.
-To view example images, check out the :doc:`gallery page <gallery>`.
+To view example images, check out the :doc:`gallery page <auto_examples/index>`.
 For specific how-to questions, refer to the :doc:`how-to page <how_to>`.
 
 Check out the source code on `github <https://github.com/SarthakJariwala/seaborn-image>`_.
@@ -84,7 +92,7 @@ Contents
 
    Quickstart <quickstart>
    How-to? <how_to>
-   Gallery <gallery>
+   Gallery <auto_examples/index>
    License <license>
    Authors <authors>
    Changelog <https://github.com/SarthakJariwala/seaborn-image/releases>

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,3 +1,3 @@
-sphinx==2.3.1
+sphinx==3.2.1
+sphinx-gallery==0.8.0
 sphinx_bootstrap_theme==0.7.1
-sphinxcontrib-images==0.9.2
diff --git a/examples/README.rst b/examples/README.rst
@@ -0,0 +1,4 @@
+Example gallery
+===============
+
+Seaborn-image example gallery
diff --git a/examples/image_0.png b/examples/image_0.png
diff --git a/examples/image_1.png b/examples/image_1.png
diff --git a/examples/image_2.png b/examples/image_2.png
diff --git a/examples/image_3.png b/examples/image_3.png
diff --git a/examples/image_4.png b/examples/image_4.png
diff --git a/examples/image_5.png b/examples/image_5.png
diff --git a/examples/image_plot.py b/examples/image_plot.py
diff --git a/examples/plot_fft.py b/examples/plot_fft.py
@@ -0,0 +1,10 @@
+"""
+Fast Fourier Transform
+======================
+"""
+
+import seaborn_image as isns
+
+img = isns.load_image("polymer")
+
+_ = isns.fftplot(img, cmap="viridis", cbar=False, despine=False)
diff --git a/examples/plot_filter.py b/examples/plot_filter.py
@@ -0,0 +1,10 @@
+"""
+Image Filter
+============
+"""
+
+import seaborn_image as isns
+
+img = isns.load_image("polymer")
+
+_ = isns.filterplot(img, "median", size=5, cmap="ice", despine=False)
diff --git a/examples/plot_filtergrid.py b/examples/plot_filtergrid.py
@@ -0,0 +1,19 @@
+"""
+FilterGrid
+==========
+"""
+
+import seaborn_image as isns
+
+img = isns.load_image("polymer")
+
+g = isns.FilterGrid(
+    img,
+    "gaussian",
+    row="sigma",
+    col="mode",
+    sigma=[2, 3, 4],
+    mode=["reflect", "nearest", "mirror"],
+    despine=False,
+    cmap="magma",
+)
diff --git a/examples/plot_image.py b/examples/plot_image.py
@@ -0,0 +1,12 @@
+"""
+Image plot
+==========
+
+"""
+
+import seaborn_image as isns
+
+img = isns.load_image("polymer")
+img_scale = {"dx": 15, "units": "nm"}
+
+_ = isns.imgplot(img, dx=15, units="nm", despine=False)
diff --git a/examples/plot_image_hist.py b/examples/plot_image_hist.py
@@ -0,0 +1,10 @@
+"""
+Image distribution
+==================
+
+"""
+import seaborn_image as isns
+
+img = isns.load_image("polymer")
+
+_ = isns.imghist(img, cmap="YlGnBu_r", dx=15, units="nm", despine=False)
diff --git a/examples/plot_image_robust.py b/examples/plot_image_robust.py
@@ -0,0 +1,17 @@
+"""
+Outlier correction
+==================
+"""
+
+import matplotlib.pyplot as plt
+
+import seaborn_image as isns
+
+img = isns.load_image("polymer outliers")
+
+f, axes = plt.subplots(1, 2)
+
+_ = isns.imgplot(img, ax=axes[0], cmap="inferno", despine=False)
+_ = isns.imgplot(
+    img, ax=axes[1], robust=True, perc=(2, 99.99), cmap="inferno", despine=False
+)
diff --git a/images/sphx_glr_plot_fft_001.png b/images/sphx_glr_plot_fft_001.png
diff --git a/images/sphx_glr_plot_filter_001.png b/images/sphx_glr_plot_filter_001.png
diff --git a/images/sphx_glr_plot_filtergrid_001.png b/images/sphx_glr_plot_filtergrid_001.png
diff --git a/images/sphx_glr_plot_image_001.png b/images/sphx_glr_plot_image_001.png
diff --git a/images/sphx_glr_plot_image_hist_001.png b/images/sphx_glr_plot_image_hist_001.png
diff --git a/images/sphx_glr_plot_image_robust_001.png b/images/sphx_glr_plot_image_robust_001.png
diff --git a/noxfile.py b/noxfile.py
@@ -4,7 +4,7 @@
 
 import nox
 
-locations = "src", "tests", "noxfile.py", "docs/conf.py"
+locations = "src", "tests", "noxfile.py", "docs/conf.py", "examples"
 nox.options.sessions = "safety", "tests", "xdoctest"