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0.7.0

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mluerig committed Jul 9, 2019
1 parent 1c0f59e commit b209f2ab052214434a1d11706740ccfa120ad00f
@@ -1,6 +1,8 @@
Unreleased
==========

- ADD MORE TESTING (e.g. object finder)

- internal: decluttering of base module / outhousing of classes and methods
- no cropping for scale possible
- project management globally acessible through base functions
@@ -11,6 +13,14 @@ Unreleased
Known bugs
==========
- high GUI / windows sometimes crash. Stop Kernel and use "cv2.destroyAllWindows()"
- "filename not found" for "multiple" mode in object finder

0.7.0
------
- full landmark functionality added (refer to "landmark_maker" readme in the docs)
- additionally: measure length of "curvy" specimens from within the landmarking function
- generic image registration (aka feature recognition) added, will be properly introduced and documented in the next version


0.6.1
------
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 1bdec34a64024258870cf92fc24d5e53
config: 59824b2973ccfed6c8cc0c250bef5c7b
tags: 645f666f9bcd5a90fca523b33c5a78b7
@@ -34,6 +34,13 @@ polygon_maker
:members:
:undoc-members:

landmark_maker
------------------------------------------------------

.. autoclass:: phenopype.landmarks.landmark_maker
:members:
:undoc-members:



object_finder
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '0.6.1',
VERSION: '0.7.0',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
@@ -5,7 +5,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Index &#8212; phenopype 0.6.1 documentation</title>
<title>Index &#8212; phenopype 0.7.0 documentation</title>
<link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -37,7 +37,7 @@
</button>
<a class="navbar-brand" href="index.html">
phenopype</a>
<span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.7.0</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">
@@ -105,6 +105,7 @@ <h1 id="index">Index</h1>
<div class="genindex-jumpbox">
<a href="#D"><strong>D</strong></a>
| <a href="#F"><strong>F</strong></a>
| <a href="#L"><strong>L</strong></a>
| <a href="#O"><strong>O</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#S"><strong>S</strong></a>
@@ -118,7 +119,11 @@ <h2 id="D">D</h2>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="index.html#phenopype.base.polygon_maker.draw">draw() (phenopype.base.polygon_maker method)</a>

<ul>
<li><a href="index.html#phenopype.landmarks.landmark_maker.draw">(phenopype.landmarks.landmark_maker method)</a>
</li>
</ul></li>
</ul></td>
</tr></table>

@@ -130,6 +135,14 @@ <h2 id="F">F</h2>
</ul></td>
</tr></table>

<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="index.html#phenopype.landmarks.landmark_maker">landmark_maker (class in phenopype.landmarks)</a>
</li>
</ul></td>
</tr></table>

<h2 id="O">O</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
@@ -4,7 +4,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>phenopype - API reference &#8212; phenopype 0.6.1 documentation</title>
<title>phenopype - API reference &#8212; phenopype 0.7.0 documentation</title>
<link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -36,7 +36,7 @@
</button>
<a class="navbar-brand" href="#">
phenopype</a>
<span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.7.0</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">
@@ -69,6 +69,7 @@
<li><a class="reference internal" href="#project-maker">project_maker</a></li>
<li><a class="reference internal" href="#scale-maker">scale_maker</a></li>
<li><a class="reference internal" href="#polygon-maker">polygon_maker</a></li>
<li><a class="reference internal" href="#landmark-maker">landmark_maker</a></li>
<li><a class="reference internal" href="#object-finder">object_finder</a></li>
<li><a class="reference internal" href="#save-csv">save_csv</a></li>
<li><a class="reference internal" href="#save-img">save_img</a></li>
@@ -133,11 +134,11 @@ <h2>project_maker<a class="headerlink" href="#project-maker" title="Permalink to
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>image_dir</strong> (<em>str</em>) – path to directory with images</li>
<li><strong>project_name</strong> (<em>str</em><em> (</em><em>optional</em><em>)</em>) – name of your project</li>
<li><strong>mode</strong> (<em>str</em><em> (</em><em>optional</em><em>, </em><em>default: &quot;dir&quot;</em><em>)</em>) – tree mode loops through all subdirectories of the tree, dir only takes valid files from upper directory</li>
<li><strong>filetypes</strong> (<em>list</em><em> (</em><em>optional</em><em>)</em>) – single or multiple string patterns to target files with certain endings</li>
<li><strong>include</strong> (<em>list</em><em> (</em><em>optional</em><em>)</em>) – single or multiple string patterns to target certain files to include - can be used together with exclude</li>
<li><strong>exclude</strong> (<em>list</em><em> (</em><em>optional</em><em>)</em>) – single or multiple string patterns to target certain files to include - can be used together with include</li>
<li><strong>project_name</strong> (<em>str</em><em> (</em><em>&quot;My project</em><em>, </em><em>-current date-&quot;</em><em>)</em>) – name of your project</li>
<li><strong>mode</strong> (<em>str</em><em> (</em><em>&quot;dir&quot;</em><em>)</em>) – “dir” searches current directory for valid files; “tree” walks through all subdirectories</li>
<li><strong>filetypes</strong> (<em>list</em>) – single or multiple string patterns to target files with certain endings</li>
<li><strong>include</strong> (<em>list</em>) – single or multiple string patterns to target certain files to include - can be used together with exclude</li>
<li><strong>exclude</strong> (<em>list</em>) – single or multiple string patterns to target certain files to include - can be used together with include</li>
</ul>
</td>
</tr>
@@ -178,7 +179,7 @@ <h2>scale_maker<a class="headerlink" href="#scale-maker" title="Permalink to thi
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>image</strong> (<em>str</em><em> or </em><em>array</em>) – absolute or relative path to OR numpy array of image containing the scale</li>
<li><strong>show</strong> (<em>bool</em><em> (</em><em>optional</em><em>, </em><em>default: False</em><em>)</em>) – show result of scale detection procedure on current image</li>
<li><strong>resize</strong> (<em>(</em><em>optional</em><em>, </em><em>default: 1</em><em>)</em>) – resize image to speed up detection process (WARNING: too low values may result in poor detection results or even crashes)</li>
<li><strong>resize</strong> (<em>num</em><em> (</em><em>optional</em><em>, </em><em>default: 1</em><em>)</em>) – resize image to speed up detection process (WARNING: too low values may result in poor detection results or even crashes)</li>
</ul>
</td>
</tr>
@@ -213,7 +214,7 @@ <h2>polygon_maker<a class="headerlink" href="#polygon-maker" title="Permalink to
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>include</strong> (<em>bool</em><em> (</em><em>default: True</em><em>)</em>) – determine whether resulting mask is to include or exclude objects within</li>
<li><strong>label</strong> (<em>(</em><em>default: &quot;area1&quot;</em><em>)</em>) – passes a label to the mask</li>
<li><strong>label</strong> (<em>str</em><em> (</em><em>default: &quot;area1&quot;</em><em>)</em>) – passes a label to the mask</li>
<li><strong>mode</strong> (<em>str</em><em> (</em><em>default: &quot;rectangle&quot;</em><em>)</em>) – zoom into the scale with “rectangle” or “polygon”.</li>
</ul>
</td>
@@ -224,6 +225,38 @@ <h2>polygon_maker<a class="headerlink" href="#polygon-maker" title="Permalink to

</dd></dl>

</div>
<div class="section" id="landmark-maker">
<h2>landmark_maker<a class="headerlink" href="#landmark-maker" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="phenopype.landmarks.landmark_maker">
<em class="property">class </em><code class="descclassname">phenopype.landmarks.</code><code class="descname">landmark_maker</code><span class="sig-paren">(</span><em>image</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#phenopype.landmarks.landmark_maker" title="Permalink to this definition">¶</a></dt>
<dd><p>Intialize landmarks_maker, loads image.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>image</strong> (<em>str</em><em> or </em><em>array</em>) – absolute or relative path to OR numpy array of image</li>
<li><strong>scale</strong> (<em>num</em><em> (</em><em>1</em><em>)</em>) – pixel to mm-ratio</li>
<li><strong>ID</strong> (<em>str</em><em> (</em><em>NA</em><em>)</em>) – specimen ID; “query” is special flag for user entry</li>
<li><strong>point_size</strong> (<em>num</em><em> (</em><em>1/300 of image diameter</em><em>)</em>) – size of the landmarks on the image in pixels</li>
<li><strong>point_col</strong> (<em>value</em><em> (</em><em>red</em><em>)</em>) – colour of landmark (red, green, blue, black, white)</li>
<li><strong>label_size</strong> (<em>num</em><em> (</em><em>1/1500 of image diamter</em><em>)</em>) – size of the numeric landmark label in pixels</li>
<li><strong>label_col</strong> (<em>value</em><em> (</em><em>black</em><em>)</em>) – colour of label (red, green, blue, black, white)</li>
<li><strong>draw_line</strong> (<em>bool</em><em> (</em><em>False</em><em>)</em>) – flag to draw arc and measure it’s length</li>
</ul>
</td>
</tr>
</tbody>
</table>
<dl class="method">
<dt id="phenopype.landmarks.landmark_maker.draw">
<code class="descname">draw</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#phenopype.landmarks.landmark_maker.draw" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>

</dd></dl>

</div>
<div class="section" id="object-finder">
<h2>object_finder<a class="headerlink" href="#object-finder" title="Permalink to this headline">¶</a></h2>
@@ -262,14 +295,15 @@ <h2>object_finder<a class="headerlink" href="#object-finder" title="Permalink to
<dt>determines the type of operations to be performed on the detected objects:</dt>
<dd><ul class="first last">
<li>”diameter” of the bounding circle of our object</li>
<li>”area” | inside the contour of our object</li>
<li>”area” within the contour of our object</li>
<li>”grayscale” mean and standard deviation of grayscale pixel values inside the object contours</li>
<li>”bgr” mean and standard deviation of blue, green and red pixel values inside the object contours</li>
<li>”skeletonize” attempts to transform object into a skeleton form using the technique of Zhang-Suen. WARNING: can be slow for large objects</li>
</ul>
</dd>
</dl>
</li>
<li><strong>scale</strong> (<em>num</em><em> (</em><em>1</em><em>)</em>) – pixel to mm-ratio</li>
<li><strong>mode</strong> (<em>str</em><em> (</em><em>default: &quot;multiple&quot;</em><em>)</em>) – detect all, or only [“single”] largest object or multiple</li>
<li><strong>mask</strong> (<em>list</em>) – phenoype mask-objects (lists of boolean mask, label, and include-argument) to include or exclude an area from the procedure</li>
<li><strong>show</strong> (<em>bool</em><em> (</em><em>default: True</em><em>)</em>) – display the detection results</li>
@@ -328,7 +362,8 @@ <h2>save_img<a class="headerlink" href="#save-img" title="Permalink to this head
<li><strong>image</strong> (<em>array</em>) – image to save</li>
<li><strong>name</strong> (<em>str</em>) – name for saved image</li>
<li><strong>save_dir</strong> (<em>str</em>) – location to save image</li>
<li><strong>append</strong> (<em>str</em><em> (</em><em>optional</em><em>)</em>) – append image name with string to prevent overwriting</li>
<li><strong>append</strong> (<em>str</em><em> (</em><em>&quot;&quot;</em><em>)</em>) – append image name with string to prevent overwriting</li>
<li><strong>extension</strong> (<em>str</em><em> (</em><em>&quot;&quot;</em><em>)</em>) – file extension to save image with</li>
<li><strong>overwrite</strong> (<em>bool</em><em> (</em><em>optional</em><em>, </em><em>default: False</em><em>)</em>) – overwrite images if name exists</li>
</ul>
</td>
@@ -1,6 +1,6 @@
# Sphinx inventory version 2
# Project: phenopype
# Version: 0.6.1
# Version: 0.7.0
# The remainder of this file is compressed using zlib.
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@@ -4,7 +4,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Search &#8212; phenopype 0.6.1 documentation</title>
<title>Search &#8212; phenopype 0.7.0 documentation</title>
<link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -44,7 +44,7 @@
</button>
<a class="navbar-brand" href="index.html">
phenopype</a>
<span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.7.0</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">

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