Merge pull request #552 from camicroscope/develop

For 3.9.8

HISTORY.md

@@ -24,9 +24,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * **Version 1**
     * [1.0.x](#camicroscope-10)
 
-### caMicroscope [Unreleased](https://github.com/camicroscope/camicroscope/compare/v3.9.4...camicroscope:develop)
+### caMicroscope [Unreleased](https://github.com/camicroscope/camicroscope/compare/v3.9.8...camicroscope:develop)
 ###### TBD
 
+
+### caMicroscope [3.9.8](https://github.com/camicroscope/camicroscope/compare/v3.9.6...camicroscope:v3.9.8)
+###### 2021-10-21
+* Add Segmentation -> Annotation Functionality [#542](https://github.com/camicroscope/caMicroscope/pull/542)
+* Margin and Table UI Fixes [#549](https://github.com/camicroscope/caMicroscope/pull/549) [#551](https://github.com/camicroscope/caMicroscope/pull/551)
+* Add Pathdb Quad Lookup
+* Add Docs link to landing
+* retry slides one time if they have an error
+
 ### caMicroscope [3.9.6](https://github.com/camicroscope/camicroscope/compare/v3.9.4...camicroscope:v3.9.6)
 ###### 2021-08-05
 * Some integration with the "Smartpen" concept [#526](https://github.com/camicroscope/caMicroscope/pull/526), [#532](https://github.com/camicroscope/caMicroscope/pull/532)

README.md

@@ -31,8 +31,8 @@ The toolbar is in the top-left of the main content window. Use the toolbar butto
 | ![](https://fonts.gstatic.com/s/i/materialicons/apps/v4/24px.svg)      | Annotations | Opens the Annotation panel, where you can select which annotation set to view, name that annotation set, add optional notes about the annotation set, save the annotation set, and reset the panel to its original state. |
 | ![](https://fonts.gstatic.com/s/i/materialicons/view_list/v4/24px.svg)      | Layer Manager      | Opens the Layers Manager panel, where you can select which layers to view. |
 | ![](https://fonts.gstatic.com/s/i/materialicons/home/v4/24px.svg)      | Home      | Return to the data table so that you can open another slide.|
-| ![](https://fonts.gstatic.com/s/i/materialicons/create/v4/24px.svg)      | Draw      |  Draw thin lines, thick lines, or polygons on the image. To maintain the integrity of measurements, avoid drawing shapes that overlap or intersect one another. |
-| ![](https://fonts.gstatic.com/s/i/materialicons/colorize/v4/24px.svg)      | Preset Labels      |  Use a preset annotation type immediately to quickly annotate a silde consistently. |
+| ![](https://fonts.gstatic.com/s/i/materialicons/create/v4/24px.svg)      | Draw      |  Draw thin lines, thick lines, or polygons on the image. Annotations can also be computer aided using the Smart-pen tool. Draw them, stretch them, remove them. To maintain the integrity of measurements, avoid drawing shapes that overlap or intersect one another. |
+| ![](https://fonts.gstatic.com/s/i/materialicons/colorize/v4/24px.svg)      | Preset Labels      |  Use a preset annotation type immediately to quickly annotate a slide consistently. |
 | ![](https://fonts.gstatic.com/s/i/materialicons/search/v4/24px.svg)       | Magnifier      |The Magnifier works like a magnifying glass and allows you to see the slide at normal magnification (1.0), low magnification (0.5), or high magnification (2.0). Click a magnification level and place the bounding box on the area of the slide you want to magnify. |
 | ![](https://fonts.gstatic.com/s/i/materialicons/space_bar/v4/24px.svg)      | Measurement      | Drag this tool on the slide to learn the measurement in micrometers. |
 | ![](https://fonts.gstatic.com/s/i/materialicons/share/v4/24px.svg)      | Share View      |Opens a window with a URL to the current presentation state of the slide including the magnification level, layers that are currently open, and your position on the image.|

apps/Info.html

@@ -63,17 +63,15 @@
 							<li class="nav-item link" style="font-family: sans-serif;">
 							   <a class="nav-link" href="landing/landing.html"> <i class="fas fa-home"></i> Home</a>
 							</li>
-							<li class="nav-item active link" style="font-family: sans-serif;">
+							<li class="nav-item link" style="font-family: sans-serif;">
 								<a class="nav-link" href="table.html"> <i class="fas fa-list-ul"></i>  Slides</a>
 							</li>
-							<li class="nav-item link">
+							<li class="nav-item active link">
 								<a class="nav-link" href="Info.html"> <i class="fas fa-info-circle"></i> Info</a>
 							</li>
 							<li class="nav-item link">
 								<a class="nav-link" href="./dev-workbench/workbench.html"> <i class="fas fa-pencil-ruler"></i> Workbench</a>
 							</li>
-						</ul>
-						<ul class="navbar-nav ms-auto">
 							<li class="nav-item link" style="font-family: sans-serif;">
 								<a class="nav-link" href="./signup/signup.html"> <i class="fas fa-user-plus"></i> Signup</a>
 							</li>

apps/landing/landing.html

@@ -36,7 +36,7 @@
 
 <nav class="navbar navbar-expand-lg navbar-dark fixed-top bg-dark" style="position: sticky; margin-top: -4em;">
     <div class="container-fluid">
-        <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
+        <button class="navbar-toggler m-1" type="button" data-bs-toggle="collapse" data-bs-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
             <span class="navbar-toggler-icon"></span>
             </button>
             <div class="collapse navbar-collapse" id="navbarSupportedContent" >
@@ -53,8 +53,6 @@
                     <li class="nav-item link">
                         <a class="nav-link" href="../dev-workbench/workbench.html"> <i class="fas fa-pencil-ruler"></i> Workbench</a>
                     </li>
-                </ul>
-                <ul class="navbar-nav ms-auto">
                     <li class="nav-item link" style="font-family: sans-serif;">
                         <a class="nav-link" href="../signup/signup.html"> <i class="fas fa-user-plus"></i> Signup</a>
                     </li>
@@ -97,11 +95,11 @@ <h3>caMicroscope</h3>
                 </div>
             </section>
             <section class="post">
-                <a target="_blank" href="https://github.com/camicroscope/" class="image"><img src="./code.jpg" alt=""/></a>
+                <a target="_blank" href="https://camicroscope.github.io/docs/" class="image"><img src="./code.jpg" alt=""/></a>
                 <div class="content">
-                    <h3>Source Code</h3>
-                    <p>Get and use the code, or file issues on our github repositories.</p>
-                    <a target="_blank" href="https://github.com/camicroscope/" class="button">More</a>
+                    <h3>Documentation</h3>
+                    <p>Read documentation for using and developing caMicroscope.</p>
+                    <a target="_blank" href="https://camicroscope.github.io/docs/" class="button">More</a>
                 </div>
             </section>
         </div>

apps/segment/segment.css

@@ -197,7 +197,7 @@ ul.disabled {
 #choice_panel .modalbox-content{
     width: 25%;
 
-   
+
 }
 #details_panel .modalbox-content{
     width: 25%;
@@ -313,19 +313,19 @@ ul.disabled {
 }
 .btn-del{
       background-color: red;
-      border: none; 
-      color: white; 
-      padding: 12px 16px; 
-      font-size: 14px; 
-      cursor: pointer; 
+      border: none;
+      color: white;
+      padding: 12px 16px;
+      font-size: 14px;
+      cursor: pointer;
 }
 body{
     color: black;
 }
 
 
 .btn-sel {
-  
+
   border: 10px ;
   border-color: black;
   padding: 10px;
@@ -431,21 +431,21 @@ body{
 }
 
 #ext1{
-   
+
   text-align: center;
   font-size: 16px;
 
 
 }
 #ext2{
-   
+
   text-align: center;
   font-size: 16px;
 
 }
 .extract{
   padding : 3% 6% 3% 6%;
-  
+
   color: white;
   background-color:#46a049 !important;
   border-radius: 7%;
@@ -454,7 +454,7 @@ body{
 }
 
 .extract:hover {
-    
+
     transform: scale(1.2);
     cursor: pointer;
 
@@ -505,4 +505,4 @@ body{
 @keyframes fadeout {
   from {bottom: 30px; opacity: 1;}
   to {bottom: 0; opacity: 0;}
-}
+}

apps/segment/segment.html

@@ -135,6 +135,7 @@
   <script type='text/javascript' src='../../core/Store.js'></script>
   <script type='text/javascript' src='../../core/CaMic.js'></script>
 
+  <script type='text/javascript' src='../../core/extension/segment-annotation.js'></script>
   <script type='text/javascript' src='../../core/extension/openseadragon-canvas-draw-overlay.js'></script>
   <script type='text/javascript' src='../../core/extension/openseadragon-overlays-manage.js'></script>
   <script type='text/javascript' src='../../core/extension/openseadragon-measurement-tool/openseadragon-measurement-tool.js'></script>