fix(brushTool)

README.md

@@ -6,32 +6,38 @@
 
 ## Dicom Image Toolkit for CornestoneJS
 
-### Current version: 0.9.4
+### Current version: 0.9.5
 
 This library provides common dicom functionalities to be used in web-applications. Multiplanar reformat on axial, sagittal and coronal viewports is included as well as custom loader/exporter for nrrd files and orthogonal reslice.
 
 - `index` main file
-- `image_parsing` parse dicom files and return a cornestone data structure ready to be used for rendering
+- `dataDictionary` json file for dicom tags
+- `image_colormaps` provides color maps functionalities
+- `image_contours` using to populate cornerstone tool for segmentation contours on 2D images
 - `image_io` import a dicom image in .nrrd format and build contiguous array for exporting data as volume
 - `image_layers` provide support for multi-layer cornerstone fusion renderer
 - `image_loading` initialize loader and custom loaders
-- `image_contours` using to populate cornerstone tool for segmentation contours on 2D images
-- `image_tools` using to handle standard and custom cornerstone tools
+- `image_parsing` parse dicom files and return a cornestone data structure ready to be used for rendering
 - `image_rendering` provides rendering functionalities
 - `image_store` provides data storage functionalities, vuex support is integrated
+- `image_tools` using to handle standard and custom cornerstone tools
 - `image_utils` utility functions on pixels and metadata tags
-- `image_colormaps` provides color maps functionalities
-- `dataDictionary` json file for dicom tags
 - `loaders/commonLoader` common functionalities for custom loaders
 - `loaders/dicomLoader` custom loader for DICOM files with support for multiplanar reformat (axial, sagittal and coronal planes)
+- `loaders/fileLoader` custom loader for png/jpg files
 - `loaders/nrrdLoader`custom loader for nrrd files with support for multiplanar reformat (axial, sagittal and coronal planes)
 - `loaders/resliceLoader` custom loader for resliced data
-- `tools/customTool` is a the main file used to initialize custom cornerstone tools
+- `parsers/nrrd` custom parser for nrrd data
 - `tools/contourTool` is a custom cornerstone tool for 2D visualization of segmented images
 - `tools/diameterTool` is a custom cornerstone tool for 2D visualization of diameter widgets
 - `tools/editMaskTool` is a custom cornerstone tool for 2D visualization of segmentation masks with brush functionalities
 - `tools/seedTool` is a custom cornerstone tool for 2D interactive seeding with custom colors and labels
-- `tools/default` default tools map and configuration
+- `tools/thresholdsBrushTool` is a custom cornerstone tool for handling thresholds in a brush tool
+- `tools/tools.default` default tools map and configuration
+- `tools/tools.io` import and export functionalities for tools
+- `tools/tools.main` tools main functionalities
+- `tools/tools.state` tools state management
+
 
 Full documentation is available at http://www.dvisionlab.com/Larvitar/.
 
@@ -46,10 +52,14 @@ Full documentation is available at http://www.dvisionlab.com/Larvitar/.
 # Dependencies
 
 - `cornerstone`
+- `cornerstone-tools`
 - `dicomParser`
 - `wadoImageLoader`
+- `webImageLoader`
+- `fileImageLoader`
 - `lodash`
-- `nrrd-js`
+- `pako`
+- `papaparse`
 
 # Installation
 

docs/index.html

@@ -70,31 +70,36 @@ <h3> </h3>
 </p> 
 <h1 id="larvitar">Larvitar</h1>
 <h2 id="dicom-image-toolkit-for-cornestonejs">Dicom Image Toolkit for CornestoneJS</h2>
-<h3 id="current-version%3A-0.9.4">Current version: 0.9.4</h3>
+<h3 id="current-version%3A-0.9.5">Current version: 0.9.5</h3>
 <p>This library provides common dicom functionalities to be used in web-applications. Multiplanar reformat on axial, sagittal and coronal viewports is included as well as custom loader/exporter for nrrd files and orthogonal reslice.</p>
 <ul>
 <li><code>index</code> main file</li>
-<li><code>image_parsing</code> parse dicom files and return a cornestone data structure ready to be used for rendering</li>
+<li><code>dataDictionary</code> json file for dicom tags</li>
+<li><code>image_colormaps</code> provides color maps functionalities</li>
+<li><code>image_contours</code> using to populate cornerstone tool for segmentation contours on 2D images</li>
 <li><code>image_io</code> import a dicom image in .nrrd format and build contiguous array for exporting data as volume</li>
 <li><code>image_layers</code> provide support for multi-layer cornerstone fusion renderer</li>
 <li><code>image_loading</code> initialize loader and custom loaders</li>
-<li><code>image_contours</code> using to populate cornerstone tool for segmentation contours on 2D images</li>
-<li><code>image_tools</code> using to handle standard and custom cornerstone tools</li>
+<li><code>image_parsing</code> parse dicom files and return a cornestone data structure ready to be used for rendering</li>
 <li><code>image_rendering</code> provides rendering functionalities</li>
 <li><code>image_store</code> provides data storage functionalities, vuex support is integrated</li>
+<li><code>image_tools</code> using to handle standard and custom cornerstone tools</li>
 <li><code>image_utils</code> utility functions on pixels and metadata tags</li>
-<li><code>image_colormaps</code> provides color maps functionalities</li>
-<li><code>dataDictionary</code> json file for dicom tags</li>
 <li><code>loaders/commonLoader</code> common functionalities for custom loaders</li>
 <li><code>loaders/dicomLoader</code> custom loader for DICOM files with support for multiplanar reformat (axial, sagittal and coronal planes)</li>
+<li><code>loaders/fileLoader</code> custom loader for png/jpg files</li>
 <li><code>loaders/nrrdLoader</code>custom loader for nrrd files with support for multiplanar reformat (axial, sagittal and coronal planes)</li>
 <li><code>loaders/resliceLoader</code> custom loader for resliced data</li>
-<li><code>tools/customTool</code> is a the main file used to initialize custom cornerstone tools</li>
+<li><code>parsers/nrrd</code> custom parser for nrrd data</li>
 <li><code>tools/contourTool</code> is a custom cornerstone tool for 2D visualization of segmented images</li>
 <li><code>tools/diameterTool</code> is a custom cornerstone tool for 2D visualization of diameter widgets</li>
 <li><code>tools/editMaskTool</code> is a custom cornerstone tool for 2D visualization of segmentation masks with brush functionalities</li>
 <li><code>tools/seedTool</code> is a custom cornerstone tool for 2D interactive seeding with custom colors and labels</li>
-<li><code>tools/default</code> default tools map and configuration</li>
+<li><code>tools/thresholdsBrushTool</code> is a custom cornerstone tool for handling thresholds in a brush tool</li>
+<li><code>tools/tools.default</code> default tools map and configuration</li>
+<li><code>tools/tools.io</code> import and export functionalities for tools</li>
+<li><code>tools/tools.main</code> tools main functionalities</li>
+<li><code>tools/tools.state</code> tools state management</li>
 </ul>
 <p>Full documentation is available at http://www.dvisionlab.com/Larvitar/.</p>
 <h1 id="contributors">Contributors</h1>
@@ -107,10 +112,14 @@ <h1 id="contributors">Contributors</h1>
 <h1 id="dependencies">Dependencies</h1>
 <ul>
 <li><code>cornerstone</code></li>
+<li><code>cornerstone-tools</code></li>
 <li><code>dicomParser</code></li>
 <li><code>wadoImageLoader</code></li>
+<li><code>webImageLoader</code></li>
+<li><code>fileImageLoader</code></li>
 <li><code>lodash</code></li>
-<li><code>nrrd-js</code></li>
+<li><code>pako</code></li>
+<li><code>papaparse</code></li>
 </ul>
 <h1 id="installation">Installation</h1>
 <p><code>yarn add larvitar</code></p>

docs/tools_thresholdsBrushTool.js.html

@@ -147,7 +147,7 @@ <h1 class="page-title">tools/thresholdsBrushTool.js</h1>
   const { rows, columns } = image;
   const x0 = Math.floor(xCoord);
   const y0 = Math.floor(yCoord);
-  const circleArray = [];
+  let circleArray = [];
 
   // if no thresholds, set all pixels range
   if (!thresholds) {

imaging/tools/thresholdsBrushTool.js

@@ -95,7 +95,7 @@ function getCircleWithThreshold(
   const { rows, columns } = image;
   const x0 = Math.floor(xCoord);
   const y0 = Math.floor(yCoord);
-  const circleArray = [];
+  let circleArray = [];
 
   // if no thresholds, set all pixels range
   if (!thresholds) {

package.json

@@ -4,7 +4,7 @@
     "dicom",
     "imaging"
   ],
-  "version": "0.9.4",
+  "version": "0.9.5",
   "description": "javascript library for loading, rendering and interact with DICOM images",
   "main": "index.js",
   "repository": {