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0.7.2

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mluerig committed Jul 24, 2019
1 parent 9025caa commit af8742743758aca6293b01e6ddce76bc8d8686d2
@@ -4,16 +4,24 @@ Unreleased
- ADD MORE TESTING (e.g. object finder)

- internal: decluttering of base module / outhousing of classes and methods
- declutter landmark module (self.)
- no cropping for scale possible
- project management globally acessible through base functions
- a quick-thresholding method in marked area for single images
- object_finder returns histogram of length, area and grayscale of all objects
- scale_maker is initialized empty to return scale object, that can either draw or detect scales and return mask objects (tuple of 3)

-
Known bugs
==========
- high GUI / windows sometimes crash. Stop Kernel and use "cv2.destroyAllWindows()"


0.7.2
------
- landmark_maker has now (limited) mousewheel zooming functionality, future releases will provide full gapless zooming
- changed instructions for phenopype installation: make virtual env in conda for better package control (e.g. avoid different opencv versions)
-

0.7.1
------
bugfix:
@@ -22,7 +30,7 @@ bugfix:
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
- additionally: measure length of curvy specimens from within the landmarking function ("arc")
- generic image registration (aka feature recognition) added, will be properly introduced and documented in the next version


@@ -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: 59824b2973ccfed6c8cc0c250bef5c7b
config: 6b9b07afbf84d8f840bef19667bfce81
tags: 645f666f9bcd5a90fca523b33c5a78b7
@@ -1,7 +1,7 @@
phenopype - API reference
======================================================

So far I have only managed to put together an API reference list for the basic functions. What is still missing are the tracking and landmarking methods. Will follow soon.
So far I have only managed to put together an API reference list for the basic functions. What is still missing are the tracking methods, and all utility function. Will follow soon.

* :ref:`genindex`
* :ref:`modindex`
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '0.7.0',
VERSION: '0.7.2',
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 0.7.0 documentation</title>
<title>Index &#8212; phenopype 0.7.2 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>0.7.0</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.7.2</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">
@@ -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 0.7.0 documentation</title>
<title>phenopype - API reference &#8212; phenopype 0.7.2 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>0.7.0</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.7.2</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">
@@ -116,7 +116,7 @@

<div class="section" id="phenopype-api-reference">
<h1>phenopype - API reference<a class="headerlink" href="#phenopype-api-reference" title="Permalink to this headline">¶</a></h1>
<p>So far I have only managed to put together an API reference list for the basic functions. What is still missing are the tracking and landmarking methods. Will follow soon.</p>
<p>So far I have only managed to put together an API reference list for the basic functions. What is still missing are the tracking methods, and all utility function. Will follow soon.</p>
<ul class="simple">
<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
<li><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></li>
@@ -160,7 +160,6 @@ <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 template</li>
<li><strong>value</strong> (<em>int</em><em> (</em><em>default: 10</em><em>)</em>) – distance to measure between two points</li>
<li><strong>unit</strong> (<em>str</em><em> (</em><em>default: &quot;mm&quot;</em><em>)</em>) – unit that the scale should be in</li>
<li><strong>mode</strong> (<em>str</em><em> (</em><em>default: &quot;rectangle&quot;</em><em>)</em>) – grab the scale with a polygon or a box</li>
<li><strong>zoom</strong> (<em>bool</em><em> (</em><em>default: False</em><em>)</em>) – zoom into the scale after drawin it for higher accuracy</li>
</ul>
@@ -236,7 +235,7 @@ <h2>landmark_maker<a class="headerlink" href="#landmark-maker" title="Permalink
<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">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first 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>
@@ -248,6 +247,14 @@ <h2>landmark_maker<a class="headerlink" href="#landmark-maker" title="Permalink
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><ul class="simple">
<li><em>.df = pandas data frame with landmarks (and arc-length, if selected)</em></li>
<li><em>.drawn = image array with drawn landmarks (and lines)</em></li>
<li><em>.ID = provided specimen ID</em></li>
</ul>
</p>
</td>
</tr>
</tbody>
</table>
<dl class="method">
@@ -1,6 +1,6 @@
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# Project: phenopype
# Version: 0.7.0
# Version: 0.7.2
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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 0.7.0 documentation</title>
<title>Search &#8212; phenopype 0.7.2 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>0.7.0</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.7.2</b></span>
</div>

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

Some generated files are not rendered by default. Learn more.

@@ -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 0.7.0 documentation</title>
<title>Index &#8212; phenopype 0.7.2 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>0.7.0</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.7.2</b></span>
</div>

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

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