Bugfixes in interface

bin/substrates.py

@@ -983,7 +983,6 @@ class SubstrateTab(object):
                     
                 else:
                     if self.color_physiboss and self.color_physiboss_node is not None and self.color_physiboss_node[0] != '<':
-                        
                         if int(child.attrib['id'][4:]) in states_dict.keys():
                             if self.color_physiboss_node in states_dict[int(child.attrib['id'][4:])]:
                                 rgb = [0, 0.5, 0]

data/PhysiCell_settings.xml

@@ -113,7 +113,7 @@
 		</full_data>
 		
 		<SVG>
-			<interval units="min">15</interval>
+			<interval units="min">5</interval>
 			<enable>true</enable>
 		</SVG>
 		

data/initial.xml

@@ -11,9 +11,9 @@
 		</software>
 		<citation />
 		<current_time units="min">0.000000</current_time>
-		<current_runtime units="sec">0.133552</current_runtime>
-		<created>2020-10-23T16:20:55Z</created>
-		<last_modified>2020-10-23T16:20:55Z</last_modified>
+		<current_runtime units="sec">0.137806</current_runtime>
+		<created>2020-10-26T10:21:52Z</created>
+		<last_modified>2020-10-26T10:21:52Z</last_modified>
 	</metadata>
 	<microenvironment>
 		<domain name="microenvironment">

pc4covid19.ipynb

@@ -18,20 +18,7 @@
      }
     }
    },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<style>.container { width:100% !important; }</style>"
-      ],
-      "text/plain": [
-       "<IPython.core.display.HTML object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "from IPython.core.display import display, HTML\n",
     "display(HTML(\"<style>.container { width:100% !important; }</style>\"))\n",
@@ -56,164 +43,7 @@
      }
     }
    },
-   "outputs": [
-    {
-     "data": {
-      "application/javascript": [
-       "\n",
-       "requirejs.undef('filepicker');\n",
-       "\n",
-       "define('filepicker', [\"@jupyter-widgets/base\"], function(widgets) {\n",
-       "\n",
-       "    var FilePickerView = widgets.DOMWidgetView.extend({\n",
-       "        render: function(){\n",
-       "            this.file = document.createElement('input');\n",
-       "            this.file.setAttribute('class', 'fileinput');\n",
-       "            this.file.setAttribute('id', this.cid);\n",
-       "            this.file.multiple = this.model.get('multiple');\n",
-       "            this.file.required = true;\n",
-       "            this.file.setAttribute('type', 'file');\n",
-       "            this.file.setAttribute('style', 'display:none');\n",
-       "\n",
-       "            this.label = document.createElement('label');\n",
-       "            this.label.setAttribute('for', this.cid);\n",
-       "            this.label.setAttribute('style', 'border: 1px solid; border-radius: 5px; display: inline-block; padding: 6px 12px');\n",
-       "\n",
-       "            this.icon = document.createElement('i');\n",
-       "            this.icon.setAttribute(\"class\", \"fa fa-upload\");\n",
-       "\n",
-       "            if (this.file.multiple) {\n",
-       "                this.labelstr = \"  Upload Files\";\n",
-       "            } else {\n",
-       "                this.labelstr = \"  Upload File\";\n",
-       "            }\n",
-       "            this.label.innerHTML = this.labelstr;\n",
-       "            this.label.prepend(this.icon);\n",
-       "            this.el.appendChild(this.label);\n",
-       "            this.el.appendChild(this.file);\n",
-       "            this.listenTo(this.model, 'change:send', this._send_changed, this);\n",
-       "            this.listenTo(this.model, 'change:reset', this._reset, this);\n",
-       "            this.update();\n",
-       "        },\n",
-       "\n",
-       "        events: {\n",
-       "            // List of events and their handlers.\n",
-       "            'change': 'handle_file_change'\n",
-       "        },\n",
-       "\n",
-       "        _reset: function() {\n",
-       "            this.label.innerHTML = this.labelstr;\n",
-       "            this.label.prepend(this.icon);\n",
-       "            this.file.removeAttribute(\"disabled\");\n",
-       "        },\n",
-       "\n",
-       "        _send_changed: function() {\n",
-       "            var that = this;\n",
-       "            var send = this.model.get('send');\n",
-       "            var fnum = send[0];\n",
-       "            var offset = send[1];\n",
-       "            var chunk_size=64*1024;\n",
-       "            var reader;\n",
-       "\n",
-       "            if (fnum == -1) {\n",
-       "                // ignore\n",
-       "                return\n",
-       "            }\n",
-       "\n",
-       "            if (offset == 0) {\n",
-       "                this.model.set('sent', -1);\n",
-       "                this.touch();\n",
-       "            }\n",
-       "\n",
-       "            // console.log('send: ' + fnum + ' ' + offset);\n",
-       "            function tob64( buffer ) {\n",
-       "                var binary = '';\n",
-       "                var bytes = new Uint8Array( buffer );\n",
-       "                var len = bytes.byteLength;\n",
-       "                for (var i = 0; i < len; i++) {\n",
-       "                    binary += String.fromCharCode( bytes[ i ] );\n",
-       "                }\n",
-       "                return window.btoa( binary );\n",
-       "            }\n",
-       "\n",
-       "            var reader_done = function (event) {\n",
-       "                // chunk is finished.  Send to python\n",
-       "                if (event.target.error == null) {\n",
-       "                    var b64 = tob64(event.target.result);\n",
-       "                    that.model.set('data', b64);\n",
-       "                    that.model.set('sent', offset);\n",
-       "                    that.touch();\n",
-       "                } else {\n",
-       "                    console.log(\"Read error: \" + event.target.error);\n",
-       "                    that.model.set('data', '');\n",
-       "                    that.model.set('sent', -2);\n",
-       "                    that.touch();\n",
-       "                }\n",
-       "                that.touch();\n",
-       "            }\n",
-       "        \n",
-       "            var chunk_reader = function (_offset, _f) {\n",
-       "                // console.log('CR' + ' ' + _f + ' ' + _offset);\n",
-       "                reader = new FileReader();\n",
-       "                var chunk = _f.slice(_offset, chunk_size + _offset);            \n",
-       "                reader.readAsArrayBuffer(chunk);\n",
-       "                reader.onload = reader_done;\n",
-       "            }\n",
-       "    \n",
-       "            // OK. request next chunk\n",
-       "            chunk_reader(offset, this.files[fnum]);\n",
-       "        },\n",
-       "        \n",
-       "        \n",
-       "        handle_file_change: function(evt) {\n",
-       "\n",
-       "            var _files = evt.target.files;\n",
-       "            var filenames = [];\n",
-       "            var file_readers = [];\n",
-       "            this.files = [];\n",
-       "\n",
-       "            for (var i = 0; i < _files.length; i++) {\n",
-       "                var file = _files[i];\n",
-       "                console.log(\"Filename: \" + file.name);\n",
-       "                console.log(\"Type: \" + file.type);\n",
-       "                console.log(\"Size: \" + file.size + \" bytes\");\n",
-       "                this.files.push(file);\n",
-       "                filenames.push([file.name, file.size]);\n",
-       "            };\n",
-       "            \n",
-       "            // Set the filenames of the files.\n",
-       "            this.model.set('filenames', filenames);\n",
-       "            this.touch();\n",
-       "\n",
-       "            // update the label\n",
-       "            if (filenames.length == 0) {\n",
-       "                this.label.innerHTML = this.labelstr;\n",
-       "                this.file.removeAttribute(\"disabled\");\n",
-       "            } else if (filenames.length == 1) {\n",
-       "                this.label.innerHTML = \"  \" + filenames[0][0];\n",
-       "                this.file.setAttribute('disabled', 'true');\n",
-       "            } else {\n",
-       "                this.label.innerHTML = \"  \" + filenames.length + \" files selected\";\n",
-       "                this.file.setAttribute('disabled', 'true');           \n",
-       "            };\n",
-       "            this.label.prepend(this.icon);\n",
-       "        },\n",
-       "    });\n",
-       "\n",
-       "    // Register the FilePickerView with the widget manager.\n",
-       "    return {\n",
-       "        FilePickerView: FilePickerView\n",
-       "    };\n",
-       "});\n"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "import sys, os\n",
     "sys.path.insert(0, os.path.abspath('bin'))\n",
@@ -222,7 +52,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {
     "extensions": {
      "jupyter_dashboards": {
@@ -243,29 +73,14 @@
     },
     "scrolled": false
    },
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "935b02b1ef1a4d1397a0da518893897d",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "VBox(children=(HBox(children=(Dropdown(description='Load Config', options={'DEFAULT': '/home/vincent/Work/code…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "pc4covid19.gui"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {
     "extensions": {
      "jupyter_dashboards": {
@@ -321,10 +136,10 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.6.5"
   },
   "tool": true
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
\ No newline at end of file