Add computing time pseudo experiment

Former-commit-id: 5deb5c15

AngularApp/prototype/src/app/api.service.ts

@@ -111,6 +111,14 @@ export class ApiService {
     return await response.json();
   }
 
+  /**
+   * Calculate the LSH parameters
+   */
+  async getParameters(): Promise<number[]> {
+    const response = await fetch('http://127.0.0.1:5000/get-lsh-parameters');
+    return await response.json();
+  }
+
   /**
    * Do another iteration of LSH, with weights, and return important information
    */

AngularApp/prototype/src/app/overview-window/overview-window.component.html

@@ -2,7 +2,7 @@
   <as-split direction="horizontal">
     <as-split-area [size]="10">
       <div class="channel_header">
-        Channels
+        Tracks
       </div>
       <div class="content">
         <button (click)="setSelection()">Set</button>
@@ -34,8 +34,8 @@
           Set as query
         </button>
       </div>
-      <div class="overview">
-        <zingchart-angular #chart [id]="id" (wheel)="scroll($event)" [height]="height"></zingchart-angular>
+      <div class="overview" id="overview">
+<!--        <zingchart-angular #chart [id]="id" (wheel)="scroll($event)" [height]="height"></zingchart-angular>-->
       </div>
     </as-split-area>
   </as-split>

AngularApp/prototype/src/app/overview-window/overview-window.component.ts

@@ -9,7 +9,7 @@ import * as d3 from 'd3';
   styleUrls: ['./overview-window.component.css']
 })
 export class OverviewWindowComponent implements OnInit {
-  @ViewChild('chart') chart;
+  @ViewChild('overview') chart;
   private initialHeight;
   public config;
   public graphset = [];
@@ -193,6 +193,15 @@ export class OverviewWindowComponent implements OnInit {
           zooming: true,
           markers: []
         },
+        plot: {
+          exact: false,
+          smartSampling: true,
+          sampleStep: 1, // scroll step 1 is not sampling. Setting this this value to 2 will sample every other data point
+          scrollStepMultiplier: 5,
+          hintTs: true, // tells the library you have timestamps as keys and activates a small optimization technique
+          maxNodes: 150, // max nodes to have event listeners for eg) tooltips wont show but crosshair will
+          maxTrackers: 150,
+        },
         'scale-y': {
           zooming: false,
           'auto-fit': true
@@ -215,7 +224,7 @@ export class OverviewWindowComponent implements OnInit {
         }]
       });
     });
-    zingchart.bind('zingchart-ng-1', 'zoom', (e) => {
+    zingchart.bind('overview', 'zoom', (e) => {
       console.log("zoom");
       if (e.stopupdate) {
         return;
@@ -223,9 +232,11 @@ export class OverviewWindowComponent implements OnInit {
         this._minx = e.xmin;
         this._maxx = e.xmax;
       }
-      if (e.graphid !== `zingchart-ng-1-graph-preview`) {
-        this.chart.zoomto({
-          graphid: `zingchart-ng-1-graph-preview`,
+      if (e.graphid !== `overview-graph-preview`) {
+        zingchart.exec(
+          'overview',
+          'zoomto', {
+          graphid: `overview-graph-preview`,
           xmin: e.xmin,
           xmax: e.xmax,
           stopupdate: true
@@ -235,7 +246,9 @@ export class OverviewWindowComponent implements OnInit {
         if (i === e.graphid) {
           continue;
         }
-        this.chart.zoomto({
+        zingchart.exec(
+          'overview',
+          'zoomto', {
             graphid: i,
             xmin: e.xmin,
             xmax: e.xmax,
@@ -247,12 +260,17 @@ export class OverviewWindowComponent implements OnInit {
       layout: `${this.graphset.length}x1`,
       graphset: this.graphset
     };
-    this.chart.setdata({
-      data: this.config
-    });
+    // this.chart.setdata({
+    //   data: this.config
+    // });
     console.log("showing plot");
     this._minx = 0;
     this._maxx = this.state.rawData[0].values.length / 10;
+    zingchart.render({
+      id: 'overview',
+      data: this.config,
+      output: 'canvas'
+    });
     // await this.debugClicked();
   }
 
@@ -281,6 +299,15 @@ export class OverviewWindowComponent implements OnInit {
           zooming: true,
           markers: []
         },
+        plot: {
+          exact: false,
+          smartSampling: true,
+          sampleStep: 1, // scroll step 1 is not sampling. Setting this this value to 2 will sample every other data point
+          scrollStepMultiplier: 5,
+          hintTs: true, // tells the library you have timestamps as keys and activates a small optimization technique
+          maxNodes: 150, // max nodes to have event listeners for eg) tooltips wont show but crosshair will
+          maxTrackers: 150,
+        },
         'scale-y': {
           zooming: false,
           'auto-fit': true
@@ -307,11 +334,16 @@ export class OverviewWindowComponent implements OnInit {
       layout: `${this.graphset.length}x1`,
       graphset: this.graphset
     };
-    this.chart.setdata({
-      data: this.config
-    });
-    // this.chart.addgraph(this.graphset[4]);
     console.log("showing plot");
+    // this.chart.setdata({
+    //   data: this.config
+    // });
+    zingchart.exec(
+      'overview',
+      'setdata',
+      { data: this.config }
+    );
+    // this.chart.addgraph(this.graphset[4]);
     this.minx = 0;
     this.maxx = 120;
   }
@@ -362,10 +394,11 @@ export class OverviewWindowComponent implements OnInit {
         channel.series[2].values = this.candidateLabels;
       }
     }
-    this.chart.setdata({
-      data: this.config
-    });
-
+    zingchart.exec(
+      'overview',
+      'setdata',
+      { data: this.config }
+    );
   }
 
   ping() {
@@ -423,9 +456,11 @@ export class OverviewWindowComponent implements OnInit {
         channel.series[2].values = this.candidateLabels;
       }
     }
-    this.chart.setdata({
-      data: this.config
-    });
+    zingchart.exec(
+      'overview',
+      'setdata',
+      { data: this.config }
+    );
   }
 
   // async clicked(clickData) {
@@ -470,8 +505,10 @@ export class OverviewWindowComponent implements OnInit {
       this._minx = Math.min(this._minx + q, this.state.rawData[0].values.length - 1);
       this._maxx = Math.min(this._maxx + q, this.state.rawData[0].values.length - 1);
     }
-    this.chart.zoomto({
-      graphid: `zingchart-ng-1-graph-preview`,
+    zingchart.exec(
+      'overview',
+      'zoomto', {
+        graphid: `overview-graph-preview`,
         xmin: this._minx,
         xmax: this._maxx,
       });
@@ -513,14 +550,18 @@ export class OverviewWindowComponent implements OnInit {
 
   set maxx(max: number) {
     this._maxx = max / 10;
-    this.chart.zoomto({
-      graphid: `zingchart-ng-1-graph-preview`,
+    zingchart.exec(
+      'overview',
+      'zoomto', {
+        graphid: `overview-graph-preview`,
         xmin: this._minx,
         xmax: this._maxx,
         stopupdate: true
       });
     for (let i = 1; i < this.graphset.length; i ++) {
-      this.chart.zoomto({
+      zingchart.exec(
+        'overview',
+        'zoomto', {
           graphid: i,
           xmin: this._minx,
           xmax: this._maxx,
@@ -535,14 +576,18 @@ export class OverviewWindowComponent implements OnInit {
 
   set minx(min: number) {
     this._minx = min / 10;
-    this.chart.zoomto({
-      graphid: `zingchart-ng-1-graph-preview`,
+    zingchart.exec(
+      'overview',
+      'zoomto', {
+        graphid: `overview-graph-preview`,
         xmin: this._minx,
         xmax: this._maxx,
         stopupdate: true
       });
     for (let i = 1; i < this.graphset.length; i ++) {
-      this.chart.zoomto({
+      zingchart.exec(
+        'overview',
+        'zoomto', {
           graphid: i,
           xmin: this._minx,
           xmax: this._maxx,

AngularApp/prototype/src/app/state.service.ts

@@ -92,17 +92,21 @@ export class StateService {
     this.onNewWindows.emit();
   }
 
+
+
   /**
    * This function performs the first iteration of LSH
    */
   async lshInitial(): Promise<void> {
     this._weights = Array(this._queryWindow.length).fill(1);
     const t0 = new Date().getTime();
+    this.loadingText = 'Calculating optimal LSH parameters';
+    this._lshParameters = await this.api.getParameters();
     this.loadingText = 'Creating LSH model';
-    this.lshData = await this.api.lshInitial(this._queryWindow);
-    this.loadingText = '';
+    const lshData = await this.api.lshUpdate(this._queryWindow, this._weights, this._lshParameters);
     this.computedTime = new Date().getTime() - t0;
-    this._lshParameters = this.lshData.parameters;
+    this.loadingText = '';
+    this.lshData = lshData;
   }
 
   /**
@@ -113,9 +117,10 @@ export class StateService {
     this._weights = await this.api.getWeights(this._queryWindow, labels, this._weights, hashFunctions);
     const t0 = new Date().getTime();
     this.loadingText = 'Creating LSH model';
-    this.lshData = await this.api.lshUpdate(this._queryWindow, this._weights, this._lshParameters);
-    this.loadingText = '';
+    const lshData = await this.api.lshUpdate(this._queryWindow, this._weights, this._lshParameters);
     this.computedTime = new Date().getTime() - t0;
+    this.loadingText = '';
+    this.lshData = lshData;
   }
 
   /**

Flaskserver/.idea/workspace.xml

@@ -20,16 +20,12 @@
   </component>
   <component name="ChangeListManager">
     <list default="true" id="556080ba-825c-4b55-a92a-867a4df4fb32" name="Default Changelist" comment="">
-      <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/app.module.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/app.module.ts" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/main/main.component.html" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/main/main.component.html" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/main/main.component.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/main/main.component.ts" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/overview-window/overview-window.component.css" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/overview-window/overview-window.component.css" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/overview-window/overview-window.component.html" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/overview-window/overview-window.component.html" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/overview-window/overview-window.component.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/overview-window/overview-window.component.ts" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/state.service.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/state.service.ts" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/main.py" beforeDir="false" afterPath="$PROJECT_DIR$/main.py" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/pseudo.py" beforeDir="false" afterPath="$PROJECT_DIR$/pseudo.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/../experiments/Results &amp; Graphs.ipynb" beforeDir="false" afterPath="$PROJECT_DIR$/../experiments/Results &amp; Graphs.ipynb" afterDir="false" />
     </list>
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />

Flaskserver/main.py

@@ -97,6 +97,17 @@ def initialize():
     print('LSH done: ' + str(time()-t0))
     return response
 
+@app.route('/get-lsh-parameters', methods=['GET'])
+def get_lsh_parameters():
+    t0 = time()
+    data = np.load(data_path)
+    data = np.swapaxes(data, 1, 2)
+    parameters = pseudo.get_lsh_parameters(data)
+
+    response = orjson.dumps(parameters)
+    print('Parameter calculation done: ' + str(time()-t0))
+    return response
+
 
 """
 Does LSH and returns a bunch of useful information

Flaskserver/pseudo.py

@@ -7,6 +7,13 @@ from libs.DBA_multivariate import performDBA
 from tslearn.metrics import dtw
 from collections import defaultdict
 
+"""
+data: 3d array [m][t][d]
+"""
+def get_lsh_parameters(data):
+    parameters = preprocess(data)
+    return [float(parameters[1]), float(parameters[1]), float(parameters[1])]
+
 """
 data: 3d array [m][t][d]
 query: 2d array [t][d]

experiments/Test computing time of large time series.ipynb

+%% Cell type:code id: tags:
+
+``` python
+import pandas as pd
+import numpy as np
+from time import time
+
+datafile = 'data/21.csv'
+
+N = 100
+T = 100
+M = 100000
+
+data = np.random.uniform(size=(M, T, N))
+
+#and convert it to numpy array:
+data = np.array(data, dtype = "float32")
+```
+
+%% Cell type:markdown id: tags:
+
+We sample a number of subwindows which will be used as query for the search algorithms
+
+%% Cell type:code id: tags:
+
+``` python
+import random
+from time import time
+
+targets = random.sample(list(range(len(data))), 10)
+print(targets)
+```
+
+%%%% Output: stream
+
+    [23484, 81670, 8609, 31051, 42832, 14303, 85653, 67886, 17319, 93188]
+
+%% Cell type:markdown id: tags:
+
+## PSEUDo
+
+%% Cell type:markdown id: tags:
+
+For the LSH algorithm some preprocessing is done to find the right LSH parameters.
+
+%% Cell type:code id: tags:
+
+``` python
+import sys
+
+sys.path.insert(0, '../Flaskserver')
+import importlib
+from pseudo import preprocess
+import _lsh
+
+topk_dtw = []
+
+print('Preprocessing:')
+t0 = time()
+r,a,sd = preprocess(data, data.shape[2])
+print('Preprocessing done. Took {:.2f} seconds ({:.1f} minutes).'.format(time() - t0, (time() - t0) / 60))
+pseudo_preprocess_time = time() - t0
+```
+
+%%%% Output: stream
+
+    Preprocessing:
+    r = 100
+    smaller
+    r = 50.0
+    smaller
+    r = 25.0
+    bigger
+    r = 37.5
+    bigger
+    r = 43.75
+    smaller
+    r = 40.625
+    bigger
+    r = 42.1875
+    smaller
+    r = 41.40625
+    smaller
+    r = 41.015625
+    Mean: 41.028657241907524
+    Stdev: 0.16600796717920388
+    Ratio mean: 0.9930308931432998
+    Ratio stdev: 0.004133342888573115
+    Theta: 40.60035668658518
+    r: 3.7478993980502606
+    Preprocessing time: 11.971427917480469
+    Preprocessing done. Took 11.97 seconds (0.2 minutes).
+
+%% Cell type:markdown id: tags:
+
+Now we run the LSH algorithm for all targets and calculate the most similar subwindows
+
+%% Cell type:code id: tags:
+
+``` python
+from collections import defaultdict
+t0 = time()
+total_lsh_times = []
+all_lsh_candidates = []
+for i, target in enumerate(targets):
+    t1 = time()
+    query = data[target]
+    print('doing lsh')
+    lsh_candidates, lsh_distances, _ = _lsh.lsh(data, query, r, a, sd, 0)
+#     topk_dtw.append(candidates)
+    dict = defaultdict(int)
+    for l in range(len(lsh_candidates)):
+        for k in range(len(lsh_candidates[0])):
+            for a in range(len(lsh_candidates[0][0])):
+                dict[lsh_candidates[l][k][a]] += lsh_distances[l][k][a]
+    sorted_dict = {k: v for k, v in sorted(dict.items(), key=lambda item: item[1])}
+    candidates = list(sorted_dict.keys())
+    total_lsh_times.append(time()-t1)
+    print('Target #{} done! Took {:.2f} seconds ({:.1f} minutes).'.format(i, time() - t1, (time() - t1) / 60))
+    all_lsh_candidates.append(candidates)
+
+# print(candidates[0:10])
+print('Done! Took {:.2f} seconds ({:.1f} minutes).'.format(time() - t0, (time() - t0) / 60))
+```
+
+%%%% Output: stream
+
+    doing lsh
+    Target #0 done! Took 14.48 seconds (0.2 minutes).
+    doing lsh
+    Target #1 done! Took 14.31 seconds (0.2 minutes).
+    doing lsh
+    Target #2 done! Took 14.30 seconds (0.2 minutes).
+    doing lsh
+    Target #3 done! Took 14.17 seconds (0.2 minutes).
+    doing lsh
+    Target #4 done! Took 14.30 seconds (0.2 minutes).
+    doing lsh
+    Target #5 done! Took 14.31 seconds (0.2 minutes).
+    doing lsh
+    Target #6 done! Took 14.18 seconds (0.2 minutes).
+    doing lsh
+    Target #7 done! Took 13.75 seconds (0.2 minutes).
+    doing lsh
+    Target #8 done! Took 13.80 seconds (0.2 minutes).
+    doing lsh
+    Target #9 done! Took 14.17 seconds (0.2 minutes).
+    Done! Took 141.76 seconds (2.4 minutes).
+
+%% Cell type:code id: tags:
+
+``` python
+from collections import defaultdict
+t0 = time()
+total_lsh_times_ed = []
+all_lsh_candidates_ed = []
+for i, target in enumerate(targets):
+    t1 = time()
+    query = data[target]
+    print('doing lsh')
+    lsh_candidates, lsh_distances, _ = _lsh.lsh(data, query, r, a, sd, 1)
+#     topk_dtw.append(candidates)
+    dict = defaultdict(int)
+    for l in range(len(lsh_candidates)):
+        for k in range(len(lsh_candidates[0])):
+            for a in range(len(lsh_candidates[0][0])):
+                dict[lsh_candidates[l][k][a]] += lsh_distances[l][k][a]
+    sorted_dict = {k: v for k, v in sorted(dict.items(), key=lambda item: item[1])}
+    candidates = list(sorted_dict.keys())
+    total_lsh_times_ed.append(time()-t1)
+    print('Target #{} done! Took {:.2f} seconds ({:.1f} minutes).'.format(i, time() - t1, (time() - t1) / 60))
+    all_lsh_candidates_ed.append(candidates)
+
+# print(candidates[0:10])
+print('Done! Took {:.2f} seconds ({:.1f} minutes).'.format(time() - t0, (time() - t0) / 60))
+```
+
+%%%% Output: stream
+
+    doing lsh
+    Target #0 done! Took 9.85 seconds (0.2 minutes).
+    doing lsh
+    Target #1 done! Took 9.73 seconds (0.2 minutes).
+    doing lsh
+    Target #2 done! Took 9.58 seconds (0.2 minutes).
+    doing lsh
+    Target #3 done! Took 9.60 seconds (0.2 minutes).
+    doing lsh
+    Target #4 done! Took 9.84 seconds (0.2 minutes).
+    doing lsh
+    Target #5 done! Took 9.74 seconds (0.2 minutes).
+    doing lsh
+
+%% Cell type:code id: tags:
+
+``` python
+```
+
+%% Cell type:code id: tags:
+
+``` python
+```