From 36a81897abe3172c215a1e15e66a972bc94acecf Mon Sep 17 00:00:00 2001
From: Dylan Kruyff <d.l.w.kruyff@students.uu.nl>
Date: Sat, 28 Nov 2020 18:51:33 +0100
Subject: [PATCH] Refactor code
Former-commit-id: a63b132756f09dfeb25d2cce191947dca121d2f6
---
AngularApp/prototype/src/app/api.service.ts | 71 ++-
.../progress-view/progress-view.component.ts | 108 +---
AngularApp/prototype/src/app/state.service.ts | 112 ++--
.../table-overview.component.ts | 6 +-
Flaskserver/.idea/workspace.xml | 19 +-
Flaskserver/__pycache__/DBA.cpython-38.pyc | Bin 4285 -> 0 bytes
Flaskserver/__pycache__/DBA.cpython-39.pyc | Bin 4269 -> 0 bytes
Flaskserver/__pycache__/bigwig.cpython-38.pyc | Bin 7806 -> 0 bytes
Flaskserver/__pycache__/main.cpython-38.pyc | Bin 14695 -> 3405 bytes
.../__pycache__/preprocessing.cpython-38.pyc | Bin 0 -> 4100 bytes
Flaskserver/__pycache__/pseudo.cpython-38.pyc | Bin 0 -> 7381 bytes
Flaskserver/__pycache__/utils.cpython-38.pyc | Bin 1180 -> 0 bytes
Flaskserver/{ => data}/.gitattributes | 0
Flaskserver/{ => data}/21.csv | 0
.../{ => data}/NW_Ground_Stations_2016.csv | 0
Flaskserver/{ => data}/chip_w-3000_r-25.h5 | 0
Flaskserver/{ => data}/data.pkl | 0
Flaskserver/{ => data}/parameters.npy | 0
Flaskserver/{ => data}/processed-data | Bin
Flaskserver/{ => data}/processed-data.npy | 0
Flaskserver/{ => data}/query | 0
Flaskserver/{ => data}/test.bigWig | 0
Flaskserver/{ => libs}/DBA.py | 0
Flaskserver/{ => libs}/DBA_multivariate.py | 0
.../DBA_multivariate.cpython-38.pyc | Bin 6075 -> 6080 bytes
.../__pycache__/bigwig.cpython-38.pyc} | Bin 7782 -> 7811 bytes
Flaskserver/{ => libs}/bigwig.py | 0
Flaskserver/{ => libs}/setup.py | 0
Flaskserver/{ => libs}/utils.py | 0
Flaskserver/main.py | 590 +++++-------------
Flaskserver/preprocessing.py | 118 ++++
Flaskserver/pseudo.py | 243 ++++++++
Flaskserver/topk.npy | 3 -
33 files changed, 653 insertions(+), 617 deletions(-)
delete mode 100644 Flaskserver/__pycache__/DBA.cpython-38.pyc
delete mode 100644 Flaskserver/__pycache__/DBA.cpython-39.pyc
delete mode 100644 Flaskserver/__pycache__/bigwig.cpython-38.pyc
create mode 100644 Flaskserver/__pycache__/preprocessing.cpython-38.pyc
create mode 100644 Flaskserver/__pycache__/pseudo.cpython-38.pyc
delete mode 100644 Flaskserver/__pycache__/utils.cpython-38.pyc
rename Flaskserver/{ => data}/.gitattributes (100%)
rename Flaskserver/{ => data}/21.csv (100%)
rename Flaskserver/{ => data}/NW_Ground_Stations_2016.csv (100%)
rename Flaskserver/{ => data}/chip_w-3000_r-25.h5 (100%)
rename Flaskserver/{ => data}/data.pkl (100%)
rename Flaskserver/{ => data}/parameters.npy (100%)
rename Flaskserver/{ => data}/processed-data (100%)
rename Flaskserver/{ => data}/processed-data.npy (100%)
rename Flaskserver/{ => data}/query (100%)
rename Flaskserver/{ => data}/test.bigWig (100%)
rename Flaskserver/{ => libs}/DBA.py (100%)
rename Flaskserver/{ => libs}/DBA_multivariate.py (100%)
rename Flaskserver/{ => libs}/__pycache__/DBA_multivariate.cpython-38.pyc (97%)
rename Flaskserver/{__pycache__/bigwig.cpython-39.pyc => libs/__pycache__/bigwig.cpython-38.pyc} (71%)
rename Flaskserver/{ => libs}/bigwig.py (100%)
rename Flaskserver/{ => libs}/setup.py (100%)
rename Flaskserver/{ => libs}/utils.py (100%)
create mode 100644 Flaskserver/preprocessing.py
create mode 100644 Flaskserver/pseudo.py
delete mode 100644 Flaskserver/topk.npy
diff --git a/AngularApp/prototype/src/app/api.service.ts b/AngularApp/prototype/src/app/api.service.ts
index 80573ff4..9b23e33d 100644
--- a/AngularApp/prototype/src/app/api.service.ts
+++ b/AngularApp/prototype/src/app/api.service.ts
@@ -7,11 +7,12 @@ export interface RawData {
export interface LshData {
candidates: number[][][];
- tables: {[bucket: string]: number[]}[];
+ distances: number[][][];
average_candidates: number[];
average_distances: number[];
+ tables: {[bucket: string]: number[]}[];
+ average_table: {[bucket: string]: number[]};
samples: number[];
- distances: number[][][];
hash_functions: number[][];
parameters?: number[];
}
@@ -25,23 +26,37 @@ export interface TableInfoData {
distances: number[][];
}
+export interface Parameters {
+ windowsize: number;
+ hashsize: number;
+ tablesize: number;
+ stepsize: number;
+}
+
@Injectable({
providedIn: 'root'
})
+/**
+ * This service acts as the interface between the client and server side.
+ */
export class ApiService {
constructor() { }
- // Read input data
+ /**
+ * Read input data. The format is a list of channels, where each channel is an object of type RawData
+ */
async readFile(): Promise<RawData[]> {
- const response = await fetch('http://127.0.0.1:5000/read-mts-data');
+ const response = await fetch('http://127.0.0.1:5000/read-data');
return await response.json();
}
- // Split data into windows and normalize
- async createWindows(parameters): Promise<any> {
+ /**
+ * Split the data into windows (server side)
+ */
+ async createWindows(parameters: Parameters): Promise<any> {
const postData = {parameters};
- const response = await fetch('http://127.0.0.1:5000/create-mts-windows', {
+ await fetch('http://127.0.0.1:5000/create-windows', {
method: 'POST',
headers: {
'Accept': 'application/json',
@@ -51,32 +66,39 @@ export class ApiService {
});
}
- // Calculate parameters for LSH + find candidates using LSH
- async lshInitial(query): Promise<LshData> {
- const response = await fetch('http://127.0.0.1:5000/initialize', {
+ /**
+ * Get weights which will be applied to the LSH hash functions
+ */
+ async getWeights(query: number[][], labels: {[index: number]: boolean}, weights: number[], hash_functions: number[][]): Promise<number[]> {
+ const response = await fetch('http://127.0.0.1:5000/weights', {
method: 'POST',
headers: {
'Accept': 'application/json',
'Content-Type': 'application/json'
},
- body: new Blob( [ JSON.stringify({query}) ], { type: 'text/plain' } )
+ body: new Blob( [ JSON.stringify({query, labels, weights, hash_functions}) ], { type: 'text/plain' } )
});
return await response.json();
}
- async getWeights(query: number[][], labels: {[index: number]: boolean}, weights: number[], hash_functions: number[][]): Promise<number[]> {
- const response = await fetch('http://127.0.0.1:5000/weights', {
+ /**
+ * Do the first iteration of LSH and return important information
+ */
+ async lshInitial(query: number[][]): Promise<LshData> {
+ const response = await fetch('http://127.0.0.1:5000/initialize', {
method: 'POST',
headers: {
'Accept': 'application/json',
'Content-Type': 'application/json'
},
- body: new Blob( [ JSON.stringify({query, labels, weights, hash_functions}) ], { type: 'text/plain' } )
+ body: new Blob( [ JSON.stringify({query}) ], { type: 'text/plain' } )
});
return await response.json();
}
- // Find candidates using LSH with weights
+ /**
+ * Do another iteration of LSH, with weights, and return important information
+ */
async lshUpdate(query, weights, parameters): Promise<LshData> {
const response = await fetch('http://127.0.0.1:5000/update', {
method: 'POST',
@@ -89,20 +111,24 @@ export class ApiService {
return await response.json();
}
- // Get query window based on windows labeled correct
- async getQueryWindow(window): Promise<number[][]> {
+ /**
+ * Get query window based on windows labeled correct
+ */
+ async getQueryWindow(indices: number | {[index: number]: boolean}): Promise<number[][]> {
const response = await fetch('http://127.0.0.1:5000/query', {
method: 'POST',
headers: {
'Accept': 'application/json',
'Content-Type': 'application/json'
},
- body: JSON.stringify({window})
+ body: JSON.stringify({indices})
});
return await response.json();
}
- // Get data of a window by indices
+ /**
+ * Get data of a window by indices
+ */
async getWindowByIndices(indices: number[]): Promise<number[][][]> {
const response = await fetch('http://127.0.0.1:5000/window', {
method: 'POST',
@@ -115,14 +141,17 @@ export class ApiService {
return await response.json();
}
- async getTableInfo(windows): Promise<TableInfoData> {
+ /**
+ * Get additional information for a given table
+ */
+ async getTableInfo(table: number[][]): Promise<TableInfoData> {
const response = await fetch('http://127.0.0.1:5000/table-info', {
method: 'POST',
headers: {
'Accept': 'application/json',
'Content-Type': 'application/json'
},
- body: JSON.stringify({windows})
+ body: JSON.stringify({table})
});
return await response.json();
}
diff --git a/AngularApp/prototype/src/app/progress-view/progress-view.component.ts b/AngularApp/prototype/src/app/progress-view/progress-view.component.ts
index 69e5c657..c379c9e5 100644
--- a/AngularApp/prototype/src/app/progress-view/progress-view.component.ts
+++ b/AngularApp/prototype/src/app/progress-view/progress-view.component.ts
@@ -1,6 +1,7 @@
import {Component, OnInit, ViewChild} from '@angular/core';
import {StateService} from '../state.service';
import * as d3 from 'd3';
+import {TableInfoData} from '../api.service';
@Component({
selector: 'app-progress-view',
@@ -21,12 +22,14 @@ export class ProgressViewComponent implements OnInit {
constructor(private state: StateService) { }
ngOnInit(): void {
- this.state.onNewTableInfo.subscribe(() => { this.showgraph(); });
- this.state.onNewTableInfo.subscribe(() => { this.showHistogram(); });
+ this.state.onNewLshData.subscribe(() => {
+ this.showgraph();
+ this.showHistogram();
+ });
}
showHistogram() {
- const table = this.state._averageTable;
+ const table = this.state.lshData.average_table;
this.hist = {
data: [{
x: Object.keys(table),
@@ -162,7 +165,7 @@ export class ProgressViewComponent implements OnInit {
d3.selectAll('circle').transition().style('stroke', undefined);
d3.select('#node-' + v.value).transition().style('stroke', 'black').style('stroke-width', 20);
const data = this.hist;
- data.data[0].marker.line.width = Object.keys(this.state._averageTable).map((key) => {
+ data.data[0].marker.line.width = Object.keys(this.state.lshData.average_table).map((key) => {
return Number(key) === v.value ? 4 : 0;
});
this.hist = data;
@@ -177,102 +180,15 @@ export class ProgressViewComponent implements OnInit {
}
public get table() {
- return this.state._averageTable;
+ return this.state.lshData.average_table;
}
async showgraph() {
- const nodes = [];
- const links = [];
- const keys = Object.keys(this.table);
- this.hoverPlot(this.state.tableInfo.prototypes);
- const distances = this.state.tableInfo.distances;
-
- // for (const key in this.table) {
- // const size = this.table[key].length;
- // nodes.push({id: key, group: Number(key), size: size});
- // }
- // for (const key in this.table) {
- // for (const key2 in this.table) {
- // if (key === key2) {
- // continue;
- // }
- // links.push({source: key, target: key2, value: 0.001 * (100 - 5 * distances[keys.indexOf(key)][keys.indexOf(key2)])});
- // }
- // }
- // const graph = {nodes, links};
- //
- // const svg = d3.select('#visual');
- // const width = +svg.attr('width');
- // const height = +svg.attr('height');
- //
- // svg.selectAll('*').remove();
- //
- // const simulation = d3.forceSimulation()
- // .force('link', d3.forceLink().id((d: any) => d.id))
- // .force('charge', d3.forceManyBody().strength(100)) // Gravity force
- // .force('collide', d3.forceCollide().radius(25).iterations(3)) // Repulsion force
- // .force('center', d3.forceCenter(width / 2, height / 2)); // Position force
- //
- // const link = svg.append('g')
- // .selectAll('line')
- // .data(graph.links)
- // .enter().append('line')
- // .attr('stroke', 'grey')
- // .attr('stroke-width', (d: any) => d.value);
- //
- // const node = svg.append('g')
- // .selectAll('circle')
- // .data(graph.nodes)
- // .enter().append('circle')
- // .attr('r', (d: any) => 5 * Math.log(d.size) / Math.log(10))
- // .attr('fill', (d: any) => this.getColor(d.group / graph.nodes.length))
- // .attr('id', (d: any) => 'node-' + d.group)
- // .on('mouseover', (d: any) => {this.sliderValue = d.group; })
- // .call(d3.drag()
- // .on('start', dragstarted)
- // .on('drag', dragged)
- // .on('end', dragended));
- //
- // simulation
- // .nodes(graph.nodes as any)
- // .on('tick', ticked);
- //
- // simulation.force<any>('link')
- // .links(graph.links);
- //
- // function ticked() {
- // link
- // .attr('x1', (d: any) => d.source.x)
- // .attr('y1', (d: any) => d.source.y)
- // .attr('x2', (d: any) => d.target.x)
- // .attr('y2', (d: any) => d.target.y);
- //
- // node
- // .attr('cx', (d: any) => d.x)
- // .attr('cy', (d: any) => d.y);
- // }
- //
- // function dragstarted(d) {
- // if (!d3.event.active) {
- // simulation.alphaTarget(0.1).restart();
- // }
- // d.fx = d.x;
- // d.fy = d.y;
- // }
- //
- // function dragged(d) {
- // d.fx = d3.event.x;
- // d.fy = d3.event.y;
- // }
- //
- // function dragended(d) {
- // if (!d3.event.active) {
- // simulation.alphaTarget(0);
- // }
- // d.fx = null;
- // d.fy = null;
- // }
+ const tableInfo: TableInfoData = await this.state.getTableInfo(Object.values(this.state.lshData.average_table));
+ this.hoverPlot(tableInfo.prototypes);
+ const distances = tableInfo.distances;
}
+
getColor(value) {
const hue=((1-value)*120).toString(10);
return ["hsl(",hue,",100%,50%)"].join("");
diff --git a/AngularApp/prototype/src/app/state.service.ts b/AngularApp/prototype/src/app/state.service.ts
index c711c42c..4745c9eb 100644
--- a/AngularApp/prototype/src/app/state.service.ts
+++ b/AngularApp/prototype/src/app/state.service.ts
@@ -1,38 +1,42 @@
import {EventEmitter, Injectable} from '@angular/core';
-import {ApiService, LshData, RawData, TableInfoData} from './api.service';
+import {ApiService, LshData, Parameters, RawData, TableInfoData} from './api.service';
@Injectable({
providedIn: 'root'
})
+/**
+ * This service acts as the state of the entire application. Components can subscribe to EventEmitters within this state to update their
+ * contents.
+ */
export class StateService {
- public loadingProgress: number = 0;
-
+ /**
+ * These are all LSH specific variables. The variables can be accessed using the getters and setters
+ */
private _rawData: RawData[];
private _lshData: LshData;
- private _tableInfo: TableInfoData;
private _queryWindow: number[][];
- private _table: {[bucket: string]: number[]}[];
- public _averageTable: {[bucket: string]: number[]};
private _weights: number[];
-
- private _currentTab: number;
private _labels = {};
- private _sliderValue;
private _lshParameters: number[];
-
- private states = [];
-
public windowSize = 120;
public nrOfTables = 5;
public hashSize = 5;
public stepSize = 200;
+
+ /**
+ * These are all GUI variables
+ */
+ public loadingProgress = 0;
public querySelectionMode = true;
+ private _currentTab: number;
+ private _sliderValue;
+ /**
+ * These are all EventEmitters. Subscribe to these if you want to be informed about an update in state.
+ */
public onNewData: EventEmitter<void> = new EventEmitter<void>();
public onNewWindows: EventEmitter<void> = new EventEmitter<void>();
public onNewQuery: EventEmitter<void> = new EventEmitter<void>();
- public onNewTable: EventEmitter<void> = new EventEmitter<void>();
- public onNewTableInfo: EventEmitter<void> = new EventEmitter<void>();
public onNewLshData: EventEmitter<void> = new EventEmitter<void>();
public onNewLabels: EventEmitter<void> = new EventEmitter<void>();
@@ -43,6 +47,9 @@ export class StateService {
this.initialize();
}
+ /**
+ * This function initializes the application. It retrieves the raw data and creates windows.
+ */
async initialize(): Promise<void> {
this.loadingProgress = 0;
await this.getRawData();
@@ -51,72 +58,73 @@ export class StateService {
this.loadingProgress = 100;
}
+ /**
+ * This function resets the application. It re-creates the windows
+ */
async reset(): Promise<void> {
this.loadingProgress = 50;
await this.createWindows();
this.loadingProgress = 100;
}
+ /**
+ * This function retrieves the raw data
+ */
async getRawData(): Promise<void> {
this.rawData = await this.api.readFile();
}
+ /**
+ * This function creates the windows on the server side
+ */
async createWindows(): Promise<void> {
await this.api.createWindows(this.parameters);
this.onNewWindows.emit();
}
+ /**
+ * This function performs the first iteration of LSH
+ */
async lshInitial(): Promise<void> {
+ this._weights = Array(this._queryWindow.length).fill(1);
this.lshData = await this.api.lshInitial(this._queryWindow);
- console.log('data loaded');
this._lshParameters = this.lshData.parameters;
- this._weights = [1, 1, 1];
- this.createTable();
}
+ /**
+ * This function performs every other iteration of LSH
+ */
async update(labels, hashFunctions): Promise<void> {
this._weights = await this.api.getWeights(this._queryWindow, labels, this._weights, hashFunctions);
- console.log(this._weights);
this.lshData = await this.api.lshUpdate(this._queryWindow, this._weights, this._lshParameters);
- this.createTable();
}
+ /**
+ * This function retrieves additional information given a table
+ */
async getTableInfo(table: number[][]): Promise<TableInfoData> {
- // console.log(this.tableInfo);
return await this.api.getTableInfo(table);
}
+ /**
+ * This function retrieves the query
+ */
async getQueryWindow(windowIndex: number | {[index: number]: boolean}): Promise<number[][]> {
this.queryWindow = await this.api.getQueryWindow(windowIndex);
console.log(this.queryWindow);
return this._queryWindow;
}
+ /**
+ * This function retrieves the window given the window index
+ */
async getWindow(indices: number[]): Promise<number[][][]> {
return await this.api.getWindowByIndices(indices);
}
- async createTable() {
- console.log('setting table param');
- this.table = this.lshData.tables;
- console.log('table param set');
- const averageTable = {};
- const length = this.lshData.average_distances.length;
- const median = this.lshData.average_distances[Math.ceil(length / 2)];
- const stepsize = median / 10;
- const indices: number[] = this.lshData.average_distances.map((x) => x > median * 2 ? 19 : Math.floor(x / stepsize));
- this.lshData.average_candidates.forEach((candidate: number, index: number) => {
- if (averageTable[indices[index]] === undefined)
- {
- averageTable[indices[index]] = [];
- }
- averageTable[indices[index]].push(candidate);
- });
- this._averageTable = averageTable;
- console.log('table created');
- this.tableInfo = await this.getTableInfo(Object.values(this._averageTable));
- }
-
+ /**
+ * These are all setters and getters
+ */
public set rawData(v: RawData[]) {
this._rawData = v;
console.log(this._rawData);
@@ -137,26 +145,6 @@ export class StateService {
return this._lshData;
}
- public set tableInfo(v: TableInfoData) {
- this._tableInfo = v;
- this.onNewTableInfo.emit();
- }
-
- public get tableInfo(): TableInfoData {
- return this._tableInfo;
- }
-
- public set table(v: {[bucket: string]: number[]}[]) {
- console.log(v);
- this._table = v;
- console.log('emitting onNewTable');
- this.onNewTable.emit();
- }
-
- public get table(): {[bucket: string]: number[]}[] {
- return this._table;
- }
-
public set labels(v) {
this._labels = v;
this.onNewLabels.emit();
@@ -197,7 +185,7 @@ export class StateService {
return this._lshParameters;
}
- public get parameters(): {[parameter: string]: number} {
+ public get parameters(): Parameters {
return {
windowsize: this.windowSize,
hashsize: this.hashSize,
diff --git a/AngularApp/prototype/src/app/table-overview/table-overview.component.ts b/AngularApp/prototype/src/app/table-overview/table-overview.component.ts
index e7894e53..0aef1ba5 100644
--- a/AngularApp/prototype/src/app/table-overview/table-overview.component.ts
+++ b/AngularApp/prototype/src/app/table-overview/table-overview.component.ts
@@ -15,7 +15,7 @@ export class TableOverviewComponent implements OnInit {
constructor(private state: StateService) { }
ngOnInit(): void {
- this.state.onNewTable.subscribe(() => {
+ this.state.onNewLshData.subscribe(() => {
this.createHistograms();
this.createPrototypes();
});
@@ -132,7 +132,7 @@ export class TableOverviewComponent implements OnInit {
console.log('creating table histograms');
this.subplots = [];
this.averages = [];
- const tables = this.state.table;
+ const tables = this.state.lshData.tables;
console.log('start of table histograms');
tables.forEach((table, index) => {
console.log(index);
@@ -181,7 +181,7 @@ export class TableOverviewComponent implements OnInit {
// }
public get tables() {
- return this.state.table;
+ return this.state.lshData.tables;
}
public get visible() {
diff --git a/Flaskserver/.idea/workspace.xml b/Flaskserver/.idea/workspace.xml
index 88459681..25b40fe7 100644
--- a/Flaskserver/.idea/workspace.xml
+++ b/Flaskserver/.idea/workspace.xml
@@ -20,18 +20,23 @@
</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/api.service.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/api.service.ts" afterDir="false" />
- <change beforePath="$PROJECT_DIR$/../AngularApp/prototype/src/app/labeling-window/labeling-window.component.ts" beforeDir="false" afterPath="$PROJECT_DIR$/../AngularApp/prototype/src/app/labeling-window/labeling-window.component.ts" 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" />
</list>
<option name="SHOW_DIALOG" value="false" />
<option name="HIGHLIGHT_CONFLICTS" value="true" />
<option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
<option name="LAST_RESOLUTION" value="IGNORE" />
</component>
+ <component name="FileTemplateManagerImpl">
+ <option name="RECENT_TEMPLATES">
+ <list>
+ <option value="Python Script" />
+ </list>
+ </option>
+ </component>
<component name="Git.Settings">
<option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$/.." />
</component>
@@ -50,6 +55,10 @@
<property name="nodejs_npm_path_reset_for_default_project" value="true" />
</component>
<component name="RecentsManager">
+ <key name="MoveFile.RECENT_KEYS">
+ <recent name="$PROJECT_DIR$/data" />
+ <recent name="$PROJECT_DIR$/libs" />
+ </key>
<key name="CopyFile.RECENT_KEYS">
<recent name="$PROJECT_DIR$" />
</key>
@@ -144,6 +153,10 @@
<screen x="72" y="27" width="1848" height="1053" />
</state>
<state x="779" y="311" width="424" height="491" key="FileChooserDialogImpl/72.27.1848.1053@72.27.1848.1053" timestamp="1606260652750" />
+ <state x="687" y="162" width="618" height="783" key="find.popup" timestamp="1606586473850">
+ <screen x="72" y="27" width="1848" height="1053" />
+ </state>
+ <state x="687" y="162" width="618" height="783" key="find.popup/72.27.1848.1053@72.27.1848.1053" timestamp="1606586473850" />
<state x="659" y="259" width="672" height="678" key="search.everywhere.popup" timestamp="1604929652702">
<screen x="72" y="27" width="1848" height="1053" />
</state>
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similarity index 100%
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similarity index 100%
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rename to Flaskserver/data/21.csv
diff --git a/Flaskserver/NW_Ground_Stations_2016.csv b/Flaskserver/data/NW_Ground_Stations_2016.csv
similarity index 100%
rename from Flaskserver/NW_Ground_Stations_2016.csv
rename to Flaskserver/data/NW_Ground_Stations_2016.csv
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similarity index 100%
rename from Flaskserver/chip_w-3000_r-25.h5
rename to Flaskserver/data/chip_w-3000_r-25.h5
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similarity index 100%
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rename to Flaskserver/data/data.pkl
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similarity index 100%
rename from Flaskserver/parameters.npy
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similarity index 100%
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rename to Flaskserver/data/processed-data
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similarity index 100%
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similarity index 100%
rename from Flaskserver/query
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diff --git a/Flaskserver/test.bigWig b/Flaskserver/data/test.bigWig
similarity index 100%
rename from Flaskserver/test.bigWig
rename to Flaskserver/data/test.bigWig
diff --git a/Flaskserver/DBA.py b/Flaskserver/libs/DBA.py
similarity index 100%
rename from Flaskserver/DBA.py
rename to Flaskserver/libs/DBA.py
diff --git a/Flaskserver/DBA_multivariate.py b/Flaskserver/libs/DBA_multivariate.py
similarity index 100%
rename from Flaskserver/DBA_multivariate.py
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similarity index 97%
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diff --git a/Flaskserver/bigwig.py b/Flaskserver/libs/bigwig.py
similarity index 100%
rename from Flaskserver/bigwig.py
rename to Flaskserver/libs/bigwig.py
diff --git a/Flaskserver/setup.py b/Flaskserver/libs/setup.py
similarity index 100%
rename from Flaskserver/setup.py
rename to Flaskserver/libs/setup.py
diff --git a/Flaskserver/utils.py b/Flaskserver/libs/utils.py
similarity index 100%
rename from Flaskserver/utils.py
rename to Flaskserver/libs/utils.py
diff --git a/Flaskserver/main.py b/Flaskserver/main.py
index 713ce99f..fbfcdbad 100644
--- a/Flaskserver/main.py
+++ b/Flaskserver/main.py
@@ -2,24 +2,12 @@ from flask import Flask, request
import numpy as np
from flask_cors import CORS
from time import time
-import pandas as pd
import orjson
-import bigwig
-import bbi
-import _ucrdtw
-import _lsh
-import math
-import dask.dataframe as dd
import os.path
-from random import sample
-from DBA_multivariate import performDBA
-from tslearn.metrics import dtw
-from sklearn import preprocessing
-from collections import defaultdict
-from dtaidistance import dtw_ndim
-from scipy.spatial.distance import euclidean
+import pseudo
+import preprocessing
-from fastdtw import fastdtw
+data_path = 'data/processed-data.npy'
reload = False
@@ -30,478 +18,222 @@ CORS(app)
def index():
return "hi"
+
+"""
+Returns raw data
+
+Output: [{
+ index: 1d array [x]
+ values: 1d array [x]
+}]
+"""
@app.route('/read-data', methods=['GET'])
def read_data():
t0 = time()
- size = bbi.chromsizes('test.bigWig')['chr1']
- bins = 100000
- data = bigwig.get('test.bigWig', 'chr1', 0, size, bins)
- print(data.shape)
- response = [
- {
- "index": list(range(0, size, int(size/(bins)))),
- "values": data.tolist()
- },
- {
- "index": list(range(0, size, int(size / (bins)))),
- "values": data.tolist()
- },
- {
- "index": list(range(0, size, int(size / (bins)))),
- "values": data.tolist()
- }
- ]
+ response = preprocessing.read_mts_data()
response = orjson.dumps(response)
print('Data read: ' + str(time()-t0))
return response
-@app.route('/read-mts-data', methods=['GET'])
-def read_mts_data():
- filename = 'data.pkl'
- if (not os.path.isfile(filename)):
- print("start")
- df = dd.read_csv("NW_Ground_Stations_2016.csv", usecols=['number_sta', 'date', 't', 'hu', 'td'])
- print("read file")
- df = df.loc[df['number_sta'].isin([14066001, 14137001, 14216001, 14372001, 22092001, 22113006, 22135001])].fillna(0)
- print("split rows")
- df = df.compute()
- df.to_pickle(filename)
- print("to_pandas")
- df = pd.read_pickle(filename)
- df.dropna(subset=['t'], inplace=True)
- response = [
- {
- "index": df.loc[df['number_sta'] == 14066001].loc[:, 'date'].values.astype(str).tolist(),
- "values": df.loc[df['number_sta'] == 14066001].loc[:, 't'].values.tolist()
- },
- {
- "index": df.loc[df['number_sta'] == 14066001].loc[:, 'date'].values.astype(str).tolist(),
- "values": df.loc[df['number_sta'] == 14066001].loc[:, 'hu'].values.tolist()
- },
- {
- "index": df.loc[df['number_sta'] == 14066001].loc[:, 'date'].values.astype(str).tolist(),
- "values": df.loc[df['number_sta'] == 14066001].loc[:, 'td'].values.tolist()
- }
- ]
- print("response ready")
- response = orjson.dumps(response)
- return response
-@app.route('/create-mts-windows', methods=['POST'])
-def create_mts_windows():
- t0 = time()
- if (not os.path.isfile('processed-data.npy')):
- filename = 'data.pkl'
- df = pd.read_pickle(filename)
- channels = list()
- channels.append(df.loc[df['number_sta'] == 14066001].loc[:, 't'].fillna(0).values.tolist())
- channels.append(df.loc[df['number_sta'] == 14066001].loc[:, 'hu'].fillna(0).values.tolist())
- channels.append(df.loc[df['number_sta'] == 14066001].loc[:, 'td'].fillna(0).values.tolist())
- print("Data read: " + str(time()-t0))
- # raw_data = request.json
- window_size = 120 #int(raw_data['parameters']["windowsize"])
- print("Processing: " + str(time()-t0))
- data = [([values[i:i+window_size] for values in channels]) for i in range(0, len(channels[0]) - window_size, 1)]
- print("Raw windows: " + str(time()-t0))
- windows = []
- for i in range(len(data)):
- if i % 5000 == 0:
- print(i)
- windows.append(preprocessing.minmax_scale(data[i], (-1, 1), axis=1))
- print("Preprocessed: " + str(time()-t0))
- np.save('processed-data', windows)
- # data = np.load('processed-data.npy')
- # data = np.reshape(data, (len(data), len(data[0][0]), len(data[0])))
- # r, a, sd = preprocess(data, 11.5)
- # np.save('parameters', np.array([r, a, sd]))
- print("Sending response: " + str(time()-t0))
- return '1'
+"""
+Creates windows
+Input: {
+ parameters: {
+ windowssize: int
+ }
+}
+Output: '1'
+"""
@app.route('/create-windows', methods=['POST'])
def create_windows():
t0 = time()
- if (not os.path.isfile('processed-data.npy')):
- # raw_data = request.json
- # window_size = int(raw_data['parameters']["windowsize"])
- window_size = 120
- data = bigwig.chunk(
- 'test.bigWig',
- 12000,
- int(12000 / window_size),
- int(12000 / 6),
- ['chr1'],
- verbose=True,
- )
- data = np.reshape(data, (len(data), 1, len(data[0])))
- data2 = np.copy(data)
- np.random.shuffle(data2)
- data3 = np.copy(data)
- np.random.shuffle(data3)
-
- data = np.concatenate((data, data2), axis=1)
- data = np.concatenate((data, data3), axis=1)
- # data = np.repeat(data, repeats=3, axis=1)
- np.save('processed-data', data)
- print('Windows created: ' + str(time()-t0))
- return '1'
-
-@app.route('/create-test-windows', methods=['POST'])
-def create_test_windows():
- t0 = time()
- if (not os.path.isfile('processed-data.npy')):
- datafile = '21.csv'
-
- data = pd.read_csv(datafile, header=None)
-
- # and convert it to numpy array:
- npdata = np.array(data)
- print('data loaded')
- window_data = [npdata[i:i + 120, 0:5] for i in range(0, npdata.shape[0] - 120, int(120 / 8))]
- del npdata
- print('data created')
- np_window_data = np.repeat(window_data, repeats=3, axis=0)
- print(np_window_data.shape)
- del window_data
- data = np.reshape(np_window_data, (len(np_window_data), 5, len(np_window_data[0])))
- print(data.shape)
- np.save('processed-data', data)
+ if (not os.path.isfile(data_path)):
+ raw_data = request.json
+ window_size = int(raw_data['parameters']["windowsize"])
+ preprocessing.create_eeg_windows(window_size, 5)
print('Windows created: ' + str(time()-t0))
return '1'
+"""
+Does first iteration of LSH and returns a bunch of useful information
+
+Input: {
+ query: 2d array [d][t]
+}
+
+Output: {
+ hash_functions: 3d array [k][l][d]
+ candidates: 3d array [k][l][i]
+ distances: 3d array [k][l][i]
+ average_candidates: 1d array [i]
+ average_distances: 1d array [i]
+ tables: [{
+ bucket: 1d array
+ }]
+ average_table: {
+ bucket: 1d array
+ }
+ samples: 1d array
+ parameters: 1d array
+}
+"""
@app.route('/initialize', methods=['POST'])
def initialize():
t0 = time()
raw_data = orjson.loads(request.data)
- data = np.load('processed-data.npy')
+ data = np.load(data_path)
data = np.swapaxes(data, 1, 2)
- # data = np.reshape(data, (len(data), len(data[0][0]), len(data[0])))
query = raw_data["query"]
query = np.swapaxes(query, 0, 1)
- # query = np.reshape(query, (len(query[0]), len(query)))
- parameters = preprocess(data)
# parameters = np.load('parameters.npy')
- r = parameters[0]
- a = parameters[1]
- sd = parameters[2]
-
- candidates, distances, hf = _lsh.lsh(data, query, r, a, sd)
- print(distances)
-
- dict = defaultdict(int)
- for l in range(len(candidates)):
- for k in range(len(candidates[0])):
- for i in range(len(candidates[0][0])):
- dict[candidates[l][k][i]] += distances[l][k][i]
- sorted_dict = {k: v for k, v in sorted(dict.items(), key=lambda item: item[1])}
- average_candidates = list(sorted_dict.keys())
- average_distances = list(sorted_dict.values())
-
- tables = []
- samples_set = set()
- candidates = candidates.tolist()
- for l in range(len(candidates)):
- for k in range(len(candidates[0])):
- samples_set.update(candidates[l][k][0:5])
- dict = defaultdict(list)
- length = len(distances[l][k])
- median = distances[l][k][math.ceil(length/2)]
- stepsize = median / 10
- indices = list(map(lambda x: 19 if x > median * 2 else math.floor(x / stepsize), distances[l][k]))
- for i in range(len(candidates[0][0])):
- dict[str(indices[i])].append(candidates[l][k][i])
- tables.append(dict)
-
- samples = np.array(list(filter(lambda x: x in samples_set, average_candidates))).tolist()
-
-
- response = {
- "hash_functions": hf.reshape((len(candidates) * len(candidates[0]), len(query[0]))).tolist(),
- "candidates": candidates,
- "tables": tables,
- "distances": distances.tolist(),
- "samples": list(samples),
- "average_candidates": np.array(average_candidates).tolist(),
- "average_distances": np.array(average_distances).tolist(),
- "parameters": [float(r), float(a), float(sd)]
- }
- response = orjson.dumps(response)
- print('LSH done: ' + str(time()-t0))
- return response
-@app.route('/weights', methods=['POST'])
-def weights():
- alpha = 0.2
- raw_data = orjson.loads(request.data)
- labels = raw_data["labels"]
- hash_functions = raw_data["hash_functions"]
- query = raw_data["query"]
- old_weights = raw_data["weights"]
- data = np.load('processed-data.npy')
- all_good_windows = data[[[int(index) for index, value in labels.items() if value is True]]]
-
- good_distances = np.zeros(len(query))
- for window in all_good_windows:
- for i in range(len(all_good_windows[0])):
- good_distances[i] += _ucrdtw.ucrdtw(query[i], window[i], 0.05, False)[1]
- if len(all_good_windows) != 0:
- good_distances = np.square(good_distances)
- good_distances /= np.sum(good_distances)
- good_distances = np.ones(len(query)) - good_distances
- good_distances /= np.sum(good_distances)
- good_distances *= len(all_good_windows[0])
- good_distances = np.sqrt(good_distances)
-
- if len(hash_functions) != 0:
- summed_hash_functions = np.sum(hash_functions, axis=0)
- summed_hash_functions = np.square(summed_hash_functions)
- normalized_hash_functions = summed_hash_functions / np.sum(summed_hash_functions)
- normalized_hash_functions *= len(hash_functions[0])
-
- if len(hash_functions) + len(all_good_windows) == 0:
- print("no update")
- new_weights = old_weights
- elif len(hash_functions) == 0:
- print("only windows")
- new_weights = alpha * np.array(old_weights) + (1 - alpha) * good_distances
- elif len(all_good_windows) == 0:
- print("only tables")
- new_weights = alpha * np.array(old_weights) + (1 - alpha) * normalized_hash_functions
- else:
- print("tables & windows")
- new_weights = alpha * np.array(old_weights) + 0.5 * (1-alpha) * good_distances + 0.5 * (1-alpha) * normalized_hash_functions
-
- print(new_weights)
-
- response = orjson.dumps(new_weights.tolist())
+ lsh_data = pseudo.lsh(data, query)
+
+ response = orjson.dumps(lsh_data)
+ print('LSH done: ' + str(time()-t0))
return response
+"""
+Does LSH and returns a bunch of useful information
+
+Input: {
+ query: 2d array [d][t]
+}
+
+Output: {
+ hash_functions: 3d array [k][l][d]
+ candidates: 3d array [k][l][i]
+ distances: 3d array [k][l][i]
+ average_candidates: 1d array [i]
+ average_distances: 1d array [i]
+ tables: [{
+ bucket: 1d array
+ }]
+ average_table: {
+ bucket: 1d array
+ }
+ samples: 1d array
+}
+"""
@app.route('/update', methods=['POST'])
def update():
t0 = time()
raw_data = orjson.loads(request.data)
- data = np.load('processed-data.npy')
+ data = np.load(data_path)
data = np.swapaxes(data, 1, 2)
- # data = np.reshape(data, (len(data), len(data[0][0]), len(data[0])))
query = raw_data["query"]
query = np.swapaxes(query, 0, 1)
- # query = np.reshape(query, (len(query[0]), len(query)))
weights = raw_data["weights"]
parameters = raw_data["parameters"]
- candidates, distances, hf = _lsh.lsh(data, query, parameters[0], parameters[1], parameters[2], weights)
- dict = defaultdict(int)
- for l in range(len(candidates)):
- for k in range(len(candidates[0])):
- for i in range(len(candidates[0][0])):
- dict[candidates[l][k][i]] += distances[l][k][i]
- sorted_dict = {k: v for k, v in sorted(dict.items(), key=lambda item: item[1])}
- average_candidates = list(sorted_dict.keys())
- average_distances = list(sorted_dict.values())
-
- tables = []
- samples_set = set()
- candidates = candidates.tolist()
- for l in range(len(candidates)):
- for k in range(len(candidates[0])):
- samples_set.update(candidates[l][k][0:5])
- dict = defaultdict(list)
- length = len(distances[l][k])
- median = distances[l][k][math.ceil(length/2)]
- stepsize = median / 10
- indices = list(map(lambda x: 19 if x > median * 2 else math.floor(x / stepsize), distances[l][k]))
- for i in range(len(candidates[0][0])):
- dict[str(indices[i])].append(candidates[l][k][i])
- tables.append(dict)
-
- samples = np.array(list(filter(lambda x: x in samples_set, average_candidates))).tolist()
-
- response = {
- "hash_functions": hf.reshape((len(candidates) * len(candidates[0]), len(query[0]))).tolist(),
- "candidates": candidates,
- "tables": tables,
- "samples": list(samples),
- "average_candidates": np.array(average_candidates).tolist(),
- "average_distances": np.array(average_distances).tolist(),
- "distances": distances.tolist(),
- }
- response = orjson.dumps(response)
+ lsh_data = pseudo.lsh(data, query, parameters=parameters, weights=weights)
+
+ response = orjson.dumps(lsh_data)
print('LSH done: ' + str(time()-t0))
return response
+
+"""
+Calculates new weights for LSH algorithm
+
+Input: {
+ labels: 1d array [?]
+ hash_functions: 2d array [?][d]
+ query: 2d array [d][t]
+ weights: 1d array [d]
+}
+
+Output: 1d array [d]
+"""
+@app.route('/weights', methods=['POST'])
+def weights():
+ raw_data = orjson.loads(request.data)
+ labels = raw_data["labels"]
+ hash_functions = raw_data["hash_functions"]
+ query = raw_data["query"]
+ old_weights = raw_data["weights"]
+ data = np.load(data_path)
+
+ new_weights = pseudo.weights(data, query, old_weights, labels, hash_functions)
+
+ response = orjson.dumps(new_weights)
+ return response
+
+
+"""
+Calculates query based on given indices
+
+Input: {
+ indices: 1d array [?]
+}
+
+Output: 2d array [d][t]
+"""
@app.route('/query', methods=['POST'])
def query():
t0 = time()
raw_data = orjson.loads(request.data)
- windowIndices = raw_data['window']
- if isinstance(windowIndices, int):
- output = np.load('processed-data.npy')[windowIndices]
- response = orjson.dumps(output.tolist())
- print("Query done: " + str(time() - t0))
- return response
- else:
- indices = [int(index) for index, value in windowIndices.items() if value is True]
- data = np.load('processed-data.npy')[indices]
- output = performDBA(data)
- response = orjson.dumps(output.tolist())
- print("Query done: " + str(time()-t0))
- return response
+ window_indices = raw_data['indices']
+ data = np.load(data_path)
+
+ response = pseudo.query(data, window_indices)
+
+ response = orjson.dumps(response)
+ print("Query done: " + str(time() - t0))
+ return response
+
+
+"""
+Returns values of windows on given indices
+Input: {
+ indices: 1d array [x]
+}
+
+Output: 3d array [x][d][t]
+"""
@app.route('/window', methods=['POST'])
def window():
t0 = time()
raw_data = orjson.loads(request.data)
indices = raw_data['indices']
- output = np.load('processed-data.npy')[indices]
+
+ output = np.load(data_path)[indices]
+
response = orjson.dumps(output.tolist())
- print("Query done: " + str(time() - t0))
+ print("Window(s) done: " + str(time() - t0))
return response
+
+"""
+Returns additional information on given table
+
+Input: {
+ table: 2d array [x][?]
+}
+
+Output: {
+ prototypes: {
+ average: 1d array [t]
+ max: 1d array [t]
+ min: 1d array [t]
+ }
+ distances: 2d array [x][x]
+}
+"""
@app.route('/table-info', methods=['POST'])
def table_info():
t0 = time()
raw_data = orjson.loads(request.data)
- all_windows = raw_data['windows']
- data = np.load('processed-data.npy')
- prototypes = []
- for windows in all_windows:
- actual_windows = data[windows]
- average_values = np.average(actual_windows, 0)
- std_values = np.std(actual_windows, 0)
- max_values = average_values + std_values
- min_values = average_values - std_values
- prototypes.append({
- 'average': average_values.tolist(),
- 'max': max_values.tolist(),
- 'min': min_values.tolist()
- })
- # distances = [[dtw(np.array(v["average"]), np.array(w["average"]), global_constraint='sakoe_chiba', sakoe_chiba_radius=int(0.05 * 120)) for j, w in enumerate(prototypes)] for i, v in enumerate(prototypes)]
- response = orjson.dumps({'prototypes': prototypes, 'distances': []})
- print("Averages calculated: " + str(time() - t0))
- return response
-
-def preprocess(data, r=10.0):
- # return 0.10882589134534404, 3.1202154563478928, 0.9705780396843037
- # data = np.load('processed-data.npy')
- # data = np.reshape(data, (59999, 20, 120))
- # data = np.repeat(data, repeats=1, axis=1)
- subset = []
- t0 = time()
-
- i = 0
- while i < len(data):
- if i % 999 == 0:
- print(r)
- print(str(i) + ':' + str(len(subset)))
-
- state = 1
- for s in subset:
- if np.linalg.norm(data[i] - data[s]) < r:
- state = 0
- break
- if state == 1:
- subset.append(i)
-
- i = i + 1
- if i == 10000 and len(subset) < 10:
- r = r / 2
- subset = []
- i = 0
- if len(subset) > 200:
- r = r + r / 2
- subset = []
- i = 0
-
- # subset = sample(list(range(len(data))), 200)
- print("r = " + str(r))
- dtw_distances = []
- eq_distances = []
- for i, index_1 in enumerate(subset):
- print(i)
- for j, index_2 in enumerate(subset):
- if index_1 == index_2:
- continue
- e = np.linalg.norm(data[index_1] - data[index_2])
- if (math.isnan(e) or e == 0):
- eq_distances.append(0.0001)
- dtw_distances.append(0.0001)
- continue
- eq_distances.append(e)
- d = 0
- # d, _ = fastdtw(data[index_1], data[index_2], dist=euclidean)
- d = dtw(data[index_1], data[index_2], global_constraint='sakoe_chiba', sakoe_chiba_radius=int(0.05*120))
- # d = _ucrdtw.ucrdtw(data[index_1], data[index_2], 0.05, False)[1]
- # d = dtw.dtw(data[index_1], data[index_2], dist_method="Euclidean", window_type="sakoechiba", window_args={"window_size": 120}).distance
- dtw_distances.append(d)
-
- ratios = np.array(dtw_distances)/np.array(eq_distances)
- mean_dtw = np.mean(dtw_distances)
- sd_dtw = np.std(dtw_distances)
- mean_eq = np.mean(eq_distances)
- sd_eq = np.std(eq_distances)
- a = np.mean(ratios)
- sd = np.std(ratios)
- theta = mean_dtw + -2.58 * sd_dtw
- # theta = mean_eq + -2.58 * sd_eq
- r = theta / ((a-sd)*math.sqrt(120))
- if r < 0:
- r = mean_dtw / 100
- # r = theta / (math.sqrt(120))
- print('Mean: ' + str(mean_dtw))
- print('Stdev: ' + str(sd_dtw))
- print('Ratio mean: ' + str(a))
- print('Ratio stdev: ' + str(sd))
- print('Theta: ' + str(theta))
- print('r: ' + str(r))
- print('Preprocessing time: ' + str(time() - t0))
- return r, a, sd
-
-def debug_test_lsh():
- data = np.load('processed-data.npy')
- # data = np.repeat(data, repeats=7, axis=1)
- print(data.shape)
- data = np.reshape(data, (len(data), len(data[0][0]), len(data[0])))
-
- r, a, sd = preprocess(data, 11.25)
- create_windows()
- query_n = 1234
- t0 = time()
- query = data[query_n]
- data = data.astype('double')
- dict = defaultdict(int)
- candidates, distances, hf = _lsh.lsh(data, query, r, a, sd)
- print("Calculated approximate in: " + str(time()-t0))
- for l in range(len(candidates)):
- for k in range(len(candidates[0])):
- for i in range(len(candidates[0][0])):
- dict[candidates[l][k][i]] += distances[l][k][i]
- sorted_dict = {k: v for k, v in sorted(dict.items(), key=lambda item: item[1])}
- candidates = list(sorted_dict.keys())
-
- print(candidates[0:20])
+ table = raw_data['table']
+ data = np.load(data_path)
- t0 = time()
- # distances = [dtw_ndim.distance_fast(window, query) for window in data]
- distances = [dtw(window, query, global_constraint='sakoe_chiba', sakoe_chiba_radius=int(0.05*120)) for window in data]
- topk_dtw = sorted(range(len(distances)), key=lambda k: distances[k])
- print("Calculated exact dtw in: " + str(time()-t0))
- print(topk_dtw[0:20])
+ response = pseudo.table_info(data, table)
- t0 = time()
- l2distances = [np.linalg.norm(window - query) for window in data]
- print("Calculated exact l2 in: " + str(time()-t0))
-
- # # distances_ed = [distance.euclidean(query, window) for window in data]
- # # topk_ed = sorted(range(len(distances_ed)), key=lambda k: distances_ed[k])
- #
- accuracy = 0
- for index in topk_dtw[0:20]:
- if index in candidates:
- accuracy += 1
- print(accuracy)
-
-# read_mts_data()
-# create_mts_windows()
-# debug_test_lsh()
\ No newline at end of file
+ print("Averages calculated: " + str(time() - t0))
+ return response
\ No newline at end of file
diff --git a/Flaskserver/preprocessing.py b/Flaskserver/preprocessing.py
new file mode 100644
index 00000000..fe389268
--- /dev/null
+++ b/Flaskserver/preprocessing.py
@@ -0,0 +1,118 @@
+import numpy as np
+import pandas as pd
+from libs import bigwig
+import bbi
+import dask.dataframe as dd
+import os.path
+from sklearn import preprocessing
+
+def read_data():
+ size = bbi.chromsizes('test.bigWig')['chr1']
+ bins = 100000
+ data = bigwig.get('data/test.bigWig', 'chr1', 0, size, bins)
+ print(data.shape)
+ response = [
+ {
+ "index": list(range(0, size, int(size/(bins)))),
+ "values": data.tolist()
+ },
+ {
+ "index": list(range(0, size, int(size / (bins)))),
+ "values": data.tolist()
+ },
+ {
+ "index": list(range(0, size, int(size / (bins)))),
+ "values": data.tolist()
+ }
+ ]
+ return response
+
+def read_mts_data():
+ filename = 'data/data.pkl'
+ if (not os.path.isfile(filename)):
+ print("start")
+ df = dd.read_csv("NW_Ground_Stations_2016.csv", usecols=['number_sta', 'date', 't', 'hu', 'td'])
+ print("read file")
+ df = df.loc[df['number_sta'].isin([14066001, 14137001, 14216001, 14372001, 22092001, 22113006, 22135001])].fillna(0)
+ print("split rows")
+ df = df.compute()
+ df.to_pickle(filename)
+ print("to_pandas")
+ df = pd.read_pickle(filename)
+ df.dropna(subset=['t'], inplace=True)
+ response = [
+ {
+ "index": df.loc[df['number_sta'] == 14066001].loc[:, 'date'].values.astype(str).tolist(),
+ "values": df.loc[df['number_sta'] == 14066001].loc[:, 't'].values.tolist()
+ },
+ {
+ "index": df.loc[df['number_sta'] == 14066001].loc[:, 'date'].values.astype(str).tolist(),
+ "values": df.loc[df['number_sta'] == 14066001].loc[:, 'hu'].values.tolist()
+ },
+ {
+ "index": df.loc[df['number_sta'] == 14066001].loc[:, 'date'].values.astype(str).tolist(),
+ "values": df.loc[df['number_sta'] == 14066001].loc[:, 'td'].values.tolist()
+ }
+ ]
+ return response
+
+def create_peax_windows_12kb(window_size):
+ data = bigwig.chunk(
+ 'test.bigWig',
+ 12000,
+ int(12000 / window_size),
+ int(12000 / 6),
+ ['chr1'],
+ verbose=True,
+ )
+ data = np.reshape(data, (len(data), 1, len(data[0])))
+ np.save(data_path, data)
+ return '1'
+
+def create_peax_windows_12kb_mts(window_size):
+ data = bigwig.chunk(
+ 'test.bigWig',
+ 12000,
+ int(12000 / window_size),
+ int(12000 / 6),
+ ['chr1'],
+ verbose=True,
+ )
+ data = np.reshape(data, (len(data), 1, len(data[0])))
+ data2 = np.copy(data)
+ np.random.shuffle(data2)
+ data3 = np.copy(data)
+ np.random.shuffle(data3)
+
+ data = np.concatenate((data, data2), axis=1)
+ data = np.concatenate((data, data3), axis=1)
+ np.save(data_path, data)
+ return '1'
+
+def create_eeg_windows(window_size, nr_of_channels):
+ datafile = '21.csv'
+ data = pd.read_csv(datafile, header=None)
+ npdata = np.array(data)
+ window_data = [npdata[i:i + window_size, 0:nr_of_channels] for i in range(0, npdata.shape[0] - window_size, int(window_size / 8))]
+ del npdata
+ np_window_data = np.repeat(window_data, repeats=3, axis=0)
+ del window_data
+ data = np.reshape(np_window_data, (len(np_window_data), nr_of_channels, len(np_window_data[0])))
+ np.save(data_path, data)
+ return '1'
+
+def create_weather_windows(window_size):
+ filename = 'data/data.pkl'
+ df = pd.read_pickle(filename)
+ channels = list()
+ channels.append(df.loc[df['number_sta'] == 14066001].loc[:, 't'].fillna(0).values.tolist())
+ channels.append(df.loc[df['number_sta'] == 14066001].loc[:, 'hu'].fillna(0).values.tolist())
+ channels.append(df.loc[df['number_sta'] == 14066001].loc[:, 'td'].fillna(0).values.tolist())
+ data = [([values[i:i+window_size] for values in channels]) for i in range(0, len(channels[0]) - window_size, 1)]
+ windows = []
+ for i in range(len(data)):
+ if i % 5000 == 0:
+ print(i)
+ windows.append(preprocessing.minmax_scale(data[i], (-1, 1), axis=1))
+ np.save('processed-data', windows)
+ return '1'
\ No newline at end of file
diff --git a/Flaskserver/pseudo.py b/Flaskserver/pseudo.py
new file mode 100644
index 00000000..9adf51db
--- /dev/null
+++ b/Flaskserver/pseudo.py
@@ -0,0 +1,243 @@
+import numpy as np
+from time import time
+import _ucrdtw
+import _lsh
+import math
+from libs.DBA_multivariate import performDBA
+from tslearn.metrics import dtw
+from collections import defaultdict
+
+def lsh(data, query, parameters = None, weights = None):
+ if parameters is None:
+ parameters = preprocess(data)
+ r = parameters[0]
+ a = parameters[1]
+ sd = parameters[2]
+
+ if weights is None:
+ candidates, distances, hf = _lsh.lsh(data, query, r, a, sd)
+ else:
+ candidates, distances, hf = _lsh.lsh(data, query, r, a, sd, weights)
+
+ dict = defaultdict(int)
+ for l in range(len(candidates)):
+ for k in range(len(candidates[0])):
+ for i in range(len(candidates[0][0])):
+ dict[candidates[l][k][i]] += distances[l][k][i]
+ sorted_dict = {k: v for k, v in sorted(dict.items(), key=lambda item: item[1])}
+ average_candidates = np.array(list(sorted_dict.keys())).tolist()
+ average_distances = np.array(list(sorted_dict.values())).tolist()
+
+ tables = []
+ samples_set = set()
+ candidates = candidates.tolist()
+ for l in range(len(candidates)):
+ for k in range(len(candidates[0])):
+ samples_set.update(candidates[l][k][0:5])
+ dict = defaultdict(list)
+ length = len(distances[l][k])
+ median = distances[l][k][math.ceil(length/2)]
+ stepsize = median / 10
+ indices = list(map(lambda x: 19 if x > median * 2 else math.floor(x / stepsize), distances[l][k]))
+ for i in range(len(candidates[0][0])):
+ dict[str(indices[i])].append(candidates[l][k][i])
+ tables.append(dict)
+
+ length = len(average_distances)
+ median = average_distances[math.ceil(length/2)]
+ stepsize = median / 10
+ indices = list(map(lambda x: 19 if x > median * 2 else math.floor(x / stepsize), average_distances))
+ average_table = defaultdict(list)
+ for i in range(len(average_candidates)):
+ average_table[str(indices[i])].append(average_candidates[i])
+
+ samples = np.array(list(filter(lambda x: x in samples_set, average_candidates))).tolist()
+
+
+ response = {
+ "hash_functions": hf.reshape((len(candidates) * len(candidates[0]), len(query[0]))).tolist(),
+ "candidates": candidates,
+ "distances": distances.tolist(),
+ "average_candidates": average_candidates,
+ "average_distances": average_distances,
+ "tables": tables,
+ "average_table": average_table,
+ "samples": list(samples),
+ "parameters": [float(r), float(a), float(sd)]
+ }
+ return response
+
+def preprocess(data, r=10.0):
+ subset = []
+ t0 = time()
+
+ i = 0
+ while i < len(data):
+ if i % 999 == 0:
+ print(r)
+ print(str(i) + ':' + str(len(subset)))
+
+ state = 1
+ for s in subset:
+ if np.linalg.norm(data[i] - data[s]) < r:
+ state = 0
+ break
+ if state == 1:
+ subset.append(i)
+
+ i = i + 1
+ if i == 10000 and len(subset) < 10:
+ r = r / 2
+ subset = []
+ i = 0
+ if len(subset) > 200:
+ r = r + r / 2
+ subset = []
+ i = 0
+
+ # subset = sample(list(range(len(data))), 200)
+ print("r = " + str(r))
+ dtw_distances = []
+ eq_distances = []
+ for i, index_1 in enumerate(subset):
+ print(i)
+ for j, index_2 in enumerate(subset):
+ if index_1 == index_2:
+ continue
+ e = np.linalg.norm(data[index_1] - data[index_2])
+ if (math.isnan(e) or e == 0):
+ eq_distances.append(0.0001)
+ dtw_distances.append(0.0001)
+ continue
+ eq_distances.append(e)
+ d = dtw(data[index_1], data[index_2], global_constraint='sakoe_chiba', sakoe_chiba_radius=int(0.05*120))
+ dtw_distances.append(d)
+
+ ratios = np.array(dtw_distances)/np.array(eq_distances)
+ mean_dtw = np.mean(dtw_distances)
+ sd_dtw = np.std(dtw_distances)
+ mean_eq = np.mean(eq_distances)
+ sd_eq = np.std(eq_distances)
+ a = np.mean(ratios)
+ sd = np.std(ratios)
+ theta = mean_dtw + -2.58 * sd_dtw
+ # theta = mean_eq + -2.58 * sd_eq
+ r = theta / ((a-sd)*math.sqrt(120))
+ if r < 0:
+ r = mean_dtw / 100
+ # r = theta / (math.sqrt(120))
+ print('Mean: ' + str(mean_dtw))
+ print('Stdev: ' + str(sd_dtw))
+ print('Ratio mean: ' + str(a))
+ print('Ratio stdev: ' + str(sd))
+ print('Theta: ' + str(theta))
+ print('r: ' + str(r))
+ print('Preprocessing time: ' + str(time() - t0))
+ return r, a, sd
+
+def weights(data, query, old_weights, labels, hash_functions):
+ alpha = 0.2
+ all_good_windows = data[[[int(index) for index, value in labels.items() if value is True]]]
+
+ good_distances = np.zeros(len(query))
+ for window in all_good_windows:
+ for i in range(len(all_good_windows[0])):
+ good_distances[i] += _ucrdtw.ucrdtw(query[i], window[i], 0.05, False)[1]
+ if len(all_good_windows) != 0:
+ good_distances = np.square(good_distances)
+ if np.sum(good_distances) != 0:
+ good_distances /= np.sum(good_distances)
+ good_distances = np.ones(len(query)) - good_distances
+ good_distances /= np.sum(good_distances)
+ good_distances *= len(all_good_windows[0])
+ good_distances = np.sqrt(good_distances)
+
+ if len(hash_functions) != 0:
+ summed_hash_functions = np.sum(hash_functions, axis=0)
+ summed_hash_functions = np.square(summed_hash_functions)
+ normalized_hash_functions = summed_hash_functions / np.sum(summed_hash_functions)
+ normalized_hash_functions *= len(hash_functions[0])
+
+ if len(hash_functions) + len(all_good_windows) == 0:
+ print("no update")
+ new_weights = old_weights
+ elif len(hash_functions) == 0:
+ print("only windows")
+ new_weights = alpha * np.array(old_weights) + (1 - alpha) * good_distances
+ elif len(all_good_windows) == 0:
+ print("only tables")
+ new_weights = alpha * np.array(old_weights) + (1 - alpha) * normalized_hash_functions
+ else:
+ print("tables & windows")
+ new_weights = alpha * np.array(old_weights) + 0.5 * (1-alpha) * good_distances + 0.5 * (1-alpha) * normalized_hash_functions
+
+ print(new_weights)
+ return new_weights.tolist()
+
+def table_info(data, table):
+ prototypes = []
+ for cluster in table:
+ windows = data[cluster]
+ average_values = np.average(windows, 0)
+ std_values = np.std(windows, 0)
+ max_values = average_values + std_values
+ min_values = average_values - std_values
+ prototypes.append({
+ 'average': average_values.tolist(),
+ 'max': max_values.tolist(),
+ 'min': min_values.tolist()
+ })
+ # distances = [[dtw(np.array(v["average"]), np.array(w["average"]), global_constraint='sakoe_chiba', sakoe_chiba_radius=int(0.05 * 120)) for j, w in enumerate(prototypes)] for i, v in enumerate(prototypes)]
+ return {'prototypes': prototypes, 'distances': []}
+
+def query(data, window_indices):
+ if isinstance(window_indices, int):
+ output = data[window_indices]
+ else:
+ indices = [int(index) for index, value in window_indices.items() if value is True]
+ indices_windows = data[indices]
+ output = performDBA(indices_windows)
+ return output.tolist()
+
+def debug_test_lsh():
+ data = np.load('processed-data.npy')
+ # data = np.repeat(data, repeats=7, axis=1)
+ print(data.shape)
+ data = np.reshape(data, (len(data), len(data[0][0]), len(data[0])))
+
+ r, a, sd = preprocess(data, 11.25)
+ query_n = 1234
+ t0 = time()
+ query = data[query_n]
+ data = data.astype('double')
+ dict = defaultdict(int)
+ candidates, distances, hf = _lsh.lsh(data, query, r, a, sd)
+ print("Calculated approximate in: " + str(time()-t0))
+ for l in range(len(candidates)):
+ for k in range(len(candidates[0])):
+ for i in range(len(candidates[0][0])):
+ dict[candidates[l][k][i]] += distances[l][k][i]
+ sorted_dict = {k: v for k, v in sorted(dict.items(), key=lambda item: item[1])}
+ candidates = list(sorted_dict.keys())
+
+ print(candidates[0:20])
+
+ t0 = time()
+ # distances = [dtw_ndim.distance_fast(window, query) for window in data]
+ distances = [dtw(window, query, global_constraint='sakoe_chiba', sakoe_chiba_radius=int(0.05*120)) for window in data]
+ topk_dtw = sorted(range(len(distances)), key=lambda k: distances[k])
+ print("Calculated exact dtw in: " + str(time()-t0))
+ print(topk_dtw[0:20])
+
+ t0 = time()
+ l2distances = [np.linalg.norm(window - query) for window in data]
+ print("Calculated exact l2 in: " + str(time()-t0))
+
+ # # distances_ed = [distance.euclidean(query, window) for window in data]
+ # # topk_ed = sorted(range(len(distances_ed)), key=lambda k: distances_ed[k])
+ #
+ accuracy = 0
+ for index in topk_dtw[0:20]:
+ if index in candidates:
+ accuracy += 1
+ print(accuracy)
diff --git a/Flaskserver/topk.npy b/Flaskserver/topk.npy
deleted file mode 100644
index cd3b20f8..00000000
--- a/Flaskserver/topk.npy
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:76c9d862591f8291da412257fb4eff58ec5f567d7c7b14a46de3d5269958c863
-size 997096
--
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