Merge pull request #412 from pixlise/development

Release 4.45.0

Author: pnemere

CHANGELOG.md

@@ -1,4 +1,14 @@
-## 4.44.0 (Latest)
+## 4.45.0 (Latest)
+
+### Features
+- Expression Picker now remembers your last opened section
+- ROI Picker now remembers your last selected sections
+- MIST ROIs can now include a per-PMC confidence value column that affects ROI opacity on context image
+- **Custom ROI Colors** Adds support for custom ROI colors via a color picker. Preset colors should still be preferred where possible.
+- Expression language (in Lua only) now has 2 new functions: `readCache` and `writeCache` to allow reuse of calculated data between other expressions. Also added new constants: `instrument`, `scanId`, `quantId`, `maxSpectrumChannel` and `elevAngle`. Running expressions is also about 10% faster due to not recomputing the results of `spectrum()` calls when the same channels are requested.
+- Removed Back to V3 button
+
+## 4.44.0 (2024-09-27)
 
 ### Bug Fixes
 - Fixes spectrum export exporting detector A values for detector B
@@ -12,7 +22,6 @@
 - Fixes bug with sharing workspaces that include expression groups
 - Allows longer RGB Mix names to be saved
 
-
 ## 4.42.0 (2024-09-18)
 
 ### Bug Fixes

client/angular.json

@@ -248,7 +248,8 @@
                 "./node_modules"
               ]
             },
-            "scripts": []
+            "scripts": [],
+            "karmaConfig": "karma.conf.js"
           }
         },
         "lint": {

client/karma.conf.js

@@ -0,0 +1,66 @@
+// Karma configuration file, see link for more information
+// https://karma-runner.github.io/1.0/config/configuration-file.html
+
+module.exports = function (config) {
+  config.set({
+    basePath: '',
+    frameworks: ['jasmine', '@angular-devkit/build-angular'],
+    plugins: [
+      require('karma-jasmine'),
+      require('karma-chrome-launcher'),
+      require('karma-jasmine-html-reporter'),
+      require('karma-coverage'),
+      require('@angular-devkit/build-angular/plugins/karma')
+    ],
+    client: {
+      jasmine: {
+        // you can add configuration options for Jasmine here
+        // the possible options are listed at https://jasmine.github.io/api/edge/Configuration.html
+        // for example, you can disable the random execution with `random: false`
+        // or set a specific seed with `seed: 4321`
+        timeoutInterval: 29999
+      },
+      clearContext: false // leave Jasmine Spec Runner output visible in browser
+    },
+    jasmineHtmlReporter: {
+      suppressAll: true // removes the duplicated traces
+    },
+    coverageReporter: {
+      dir: require('path').join(__dirname, './coverage/pixlise'),
+      subdir: '.',
+      reporters: [
+        { type: 'html' },
+        { type: 'text-summary' }
+      ]
+    },
+    reporters: ['progress', 'kjhtml'],
+    browsers: ['Chrome'],
+    restartOnFileChange: true,
+    files: [
+      {
+        pattern: "src/app/expression-language/test-data/**/*.bin",
+        watched: false,
+        served: true,
+        included: false,
+      },
+      {
+        pattern: "src/app/expression-language/test-data/**/*.lua",
+        watched: false,
+        served: true,
+        included: false,
+      },
+      {
+        pattern: "src/app/expression-language/test-data/**/*.json",
+        watched: false,
+        served: true,
+        included: false,
+      },
+      {
+        pattern: "src/app/expression-language/test-data/input-data/*.csv",
+        watched: false,
+        served: true,
+        included: false,
+      },
+    ],
+  });
+};

client/package-lock.json

@@ -42,6 +42,7 @@
     "marked": "^4.3.0",
     "mathjs": "^11.8.2",
     "monaco-editor": "^0.44.0",
+    "ngx-color-picker": "^17.0.0",
     "ngx-dropzone": "^3.1.0",
     "ngx-markdown": "^16.0.0",
     "papaparse": "^5.4.1",
@@ -93,4 +94,4 @@
     "http": false,
     "https": false
   }
-}
+}

client/package.json

@@ -28,20 +28,13 @@
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE.
 -->
-<ng-template #v3ConfirmDialog>
-  <feedback-dialog></feedback-dialog>
-</ng-template>
 
 <ng-template #changeLogDialog>
   <div class="change-log-container">
     <h1>
       Change Log (Updated {{ uiVersionLastCommitDate * 1000 | date: "mediumDate" }})
       <action-button (onClick)="closeChangeLogDialog()" action="close" color="rgb(var(--clr-gray-30))"></action-button>
     </h1>
-    <div class="v3-container">
-      <span class="title">NOTE: PIXLISE v3 will be retired at the end of September 2024!</span>
-      <push-button class="back-to-v3" [customDialog]="v3ConfirmDialog" buttonStyle="v3Button">Back to v3</push-button>
-    </div>
     <div class="change-log">
       <markdown lineHighlight [lineOffset]="5" src="/assets/CHANGELOG.md"> </markdown>
     </div>
@@ -154,7 +147,6 @@ <h1>
         <!-- <span>Updated {{ uiVersionLastCommitDate * 1000 | date: "mediumDate" }}</span> -->
         <span>{{ uiVersion }}</span>
       </push-button>
-      <!-- <push-button class="back-to-v3" [customDialog]="v3ConfirmDialog" buttonStyle="v3Button">Back to v3</push-button> -->
       <icon-button
         title="Notifications"
         (click)="onNotificationsMenu()"

client/src/app/components/toolbar/toolbar.component.html

@@ -138,10 +138,6 @@
           }
         }
       }
-
-      .back-to-v3 {
-        white-space: pre;
-      }
     }
   }
 }
@@ -247,25 +243,6 @@ user-icon {
     }
   }
 
-  .v3-container {
-    display: flex;
-    align-items: center;
-
-    padding-left: 16px;
-
-    border-top: 1px solid rgb(68, 76, 80);
-    padding-top: 8px;
-
-    margin-right: -16px;
-    padding-right: 16px;
-
-    color: rgb(var(--clr-gray-30));
-
-    .back-to-v3 {
-      margin-left: auto;
-    }
-  }
-
   .change-log {
     height: 400px;
     width: 600px;

client/src/app/components/toolbar/toolbar.component.scss

@@ -708,25 +708,6 @@ export class ToolbarComponent implements OnInit, OnDestroy {
     return "https://discuss." + EnvConfigurationInitService.appConfig.appDomain;
   }
 
-  private closeIssueDialog(): void {
-    if (this.submitIssueDialog && this.submitIssueDialog instanceof PushButtonComponent) {
-      (this.submitIssueDialog as PushButtonComponent).closeDialog();
-    }
-  }
-
-  onSubmitIssue(leftPage: boolean): void {
-    let strippedIssue = this.userIssue.trim();
-    if (strippedIssue.length > 0) {
-      this._snackService.openSuccess("Thanks for the feedback!");
-      this.userIssue = "";
-      SentryHelper.logMsg(false, "User Feedback (Back to V3): \n" + strippedIssue);
-    } else if (leftPage) {
-      SentryHelper.logMsg(false, "User Feedback (Back to V3): No feedback given");
-    }
-
-    this.closeIssueDialog();
-  }
-
   closeChangeLogDialog(): void {
     if (this.changeLogBtn && this.changeLogBtn instanceof PushButtonComponent) {
       (this.changeLogBtn as PushButtonComponent).closeDialog();

client/src/app/components/toolbar/toolbar.component.ts

@@ -31,6 +31,10 @@ import { PMCDataValues } from "src/app/expression-language/data-values";
 
 // Query data sources (interfaces)
 export interface QuantifiedDataQuerierSource {
+  getQuantId(): string;
+  getScanId(): string;
+  getInstrument(): string;
+  getElevAngle(): number;
   getQuantifiedDataForDetector(detectorId: string, dataLabel: string): Promise<PMCDataValues>;
   getElementList(): Promise<string[]>;
   getPMCList(): Promise<number[]>;
@@ -44,6 +48,7 @@ export interface PseudoIntensityDataQuerierSource {
 }
 
 export interface SpectrumDataQuerierSource {
+  getMaxSpectrumChannel(): number;
   getSpectrumRangeMapData(channelStart: number, channelEnd: number, detectorExpr: string): Promise<PMCDataValues>;
   // If sumOrMax==true, returns sum of differences between A and B otherwise max difference seen between A and B
   getSpectrumDifferences(channelStart: number, channelEnd: number, sumOrMax: boolean): Promise<PMCDataValues>;

client/src/app/expression-language/data-sources.ts

@@ -123,6 +123,14 @@ export class PMCDataValues {
     return result;
   }
 
+  static makeWithValuesMinMax(values: PMCDataValue[], range: MinMax, isBinary: boolean) {
+    const result = new PMCDataValues();
+    result._valueRange = range;
+    result.values = values;
+    result.isBinary = isBinary;
+    return result;
+  }
+
   static filterToCommonPMCsOnly(values: (PMCDataValues | null | undefined)[]): (PMCDataValues | null)[] {
     const result: (PMCDataValues | null)[] = [];
     if (values.length === 0) {
@@ -159,6 +167,17 @@ export class PMCDataValues {
     });
   }
 
+  addValue(v: PMCDataValue) {
+    if (!v.isUndefined) {
+      this._valueRange.expand(v.value);
+    }
+    this.values.push(v);
+
+    if (v.value != 0 && v.value != 1) {
+      this.isBinary = false;
+    }
+  }
+
   private setValues(values: PMCDataValue[]) {
     if (values && values.length) {
       this.values = values;
@@ -249,16 +268,16 @@ export class PMCDataValues {
   // For example, Math.sin taking in map value as arg
   // Executes this for each value in map
   public mathFunc(theMathFunc: (num: number) => number): PMCDataValues {
-    //let result = new PMCDataValues();
-    const result: PMCDataValue[] = [];
+    const result = new PMCDataValues();
+    result.isBinary = true; // pre-set for detection in addValue
 
     for (let c = 0; c < this.values.length; c++) {
       let towrite = theMathFunc(this.values[c].value);
       if (this.values[c].isUndefined) {
         towrite = 0;
       }
 
-      result./*values.*/ push(new PMCDataValue(this.values[c].pmc, towrite, this.values[c].isUndefined));
+      result.addValue(new PMCDataValue(this.values[c].pmc, towrite, this.values[c].isUndefined));
     }
 
     /* This was failing for some trig functions... seemed like min vs max were backwards?!
@@ -270,7 +289,7 @@ export class PMCDataValues {
 
         return result;
 */
-    return PMCDataValues.makeWithValues(result);
+    return result;
   }
 
   public operationWithScalar(operation: QuantOp, scalar: number, scalarIsLeft: boolean): PMCDataValues {