From 9c85fdb8ea62089908ae5405ebb36b470503947b Mon Sep 17 00:00:00 2001 From: khavinshankar Date: Mon, 15 Apr 2024 20:32:41 +0530 Subject: [PATCH] added ocr logic as a util in middleware --- package-lock.json | 1412 +++++++++++++++++++++++++++--- package.json | 2 + src/cron/automatedDailyRounds.ts | 159 +--- src/types/asset.ts | 82 ++ src/types/care.ts | 6 + src/types/ocr.ts | 21 + src/utils/autoDataExtractor.ts | 206 ----- src/utils/configs.ts | 7 +- src/utils/ocr.ts | 73 ++ 9 files changed, 1493 insertions(+), 475 deletions(-) create mode 100644 src/types/care.ts delete mode 100644 src/utils/autoDataExtractor.ts create mode 100644 src/utils/ocr.ts diff --git a/package-lock.json b/package-lock.json index 58443d9..81e9881 100644 --- a/package-lock.json +++ b/package-lock.json @@ -33,7 +33,9 @@ "morgan": "^1.10.0", "node-cron": "^3.0.3", "onvif": "^0.6.5", + "openai": "^4.33.1", "pidusage": "^3.0.0", + "sharp": "^0.33.3", "swagger-jsdoc": "^6.1.0", "swagger-ui-express": "^4.3.0", "uuid": 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"integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==" + }, "yaml": { "version": "2.0.0-1", "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.0.0-1.tgz", diff --git a/package.json b/package.json index de980ca..2555ccf 100644 --- a/package.json +++ b/package.json @@ -24,7 +24,9 @@ "morgan": "^1.10.0", "node-cron": "^3.0.3", "onvif": "^0.6.5", + "openai": "^4.33.1", "pidusage": "^3.0.0", + "sharp": "^0.33.3", "swagger-jsdoc": "^6.1.0", "swagger-ui-express": "^4.3.0", "uuid": "^9.0.1" diff --git a/src/cron/automatedDailyRounds.ts b/src/cron/automatedDailyRounds.ts index 1c2cd05..d43801f 100644 --- a/src/cron/automatedDailyRounds.ts +++ b/src/cron/automatedDailyRounds.ts @@ -1,112 +1,28 @@ import axios, { AxiosResponse } from "axios"; -import FormData from "form-data"; import fs from "fs"; import path from "path"; import { staticObservations } from "@/controller/ObservationController"; import prisma from "@/lib/prisma"; +import { AssetBed } from "@/types/asset"; +import { CameraParams } from "@/types/camera"; +import { CarePaginatedResponse } from "@/types/care"; import { DailyRoundObservation, Observation, ObservationType, } from "@/types/observation"; +import { OCRV2Response } from "@/types/ocr"; import { CameraUtils } from "@/utils/CameraUtils"; import { isValid } from "@/utils/ObservationUtils"; import { generateHeaders } from "@/utils/assetUtils"; -import { careApi, ocrApi, saveDailyRound } from "@/utils/configs"; +import { careApi, openaiApiKey, saveDailyRound } from "@/utils/configs"; import { getPatientId } from "@/utils/dailyRoundUtils"; import { downloadImage } from "@/utils/downloadImageWithDigestRouter"; +import { parseVitalsFromImage } from "@/utils/ocr"; const UPDATE_INTERVAL = 60 * 60 * 1000; -type CarePaginatedResponse = { - count: number; - next: string | null; - previous: string | null; - results: T[]; -}; - -type AssetBed = { - id: string; - bed_object: { - id: string; - name: string; - bed_type: "ICU" | "WARD"; - location_object: { - id: string; - facility: { - id: string; - name: string; - }; - location_type: "OTHER" | "WARD" | "ICU"; - created_date: string; - modified_date: string; - name: string; - description: string; - middleware_address: string | null; - }; - is_occupied: boolean; - created_date: string; - modified_date: string; - description: string; - meta: any; - }; - asset_object: { - id: string; - status: "ACTIVE" | "INACTIVE"; - asset_type: "INTERNAL" | "EXTERNAL"; - location_object: { - id: string; - facility: { - id: string; - name: string; - }; - location_type: "OTHER" | "WARD" | "ICU"; - created_date: string; - modified_date: string; - name: string; - description: string; - middleware_address: string | null; - }; - last_service: string | null; - resolved_middleware: { - hostname: string; - source: string; - }; - created_date: string; - modified_date: string; - name: string; - description: string; - asset_class: "ONVIF" | "HL7MONITOR" | "VENTILATOR"; - is_working: boolean; - not_working_reason: string; - serial_number: string; - warranty_details: string; - meta: { - asset_type: "CAMERA" | "MONITOR" | "VENTILATOR"; - local_ip_address: string; - camera_access_key: string; - }; - vendor_name: string; - support_name: string; - support_phone: string; - support_email: string; - qr_code_id: string | null; - manufacturer: string | null; - warranty_amc_end_of_validity: string | null; - }; - created_date: string; - modified_date: string; - meta: { - error: string; - bed_id: string; - utcTime: string; - position: { x: number; y: number; zoom: number }; - moveStatus: { zoom: "IDLE" | "MOVING"; panTilt: "IDLE" | "MOVING" }; - preset_name: string; - }; -}; - export async function getMonitorPreset(bedId: string, assetId: string) { const response = await axios.get< unknown, @@ -144,13 +60,6 @@ export async function getMonitorPreset(bedId: string, assetId: string) { }; } -type CameraParams = { - hostname: string; - username: string; - password: string; - port: number; -}; - export async function saveImageLocally( snapshotUrl: string, camParams: CameraParams, @@ -167,60 +76,15 @@ export async function saveImageLocally( return imagePath; } -type OCRV2Response = { - status: number; - message: "success" | "error"; - data: { - time_stamp: string | null; - ecg: { - Heart_Rate_bpm: number | null; - }; - nibp: { - systolic_mmhg: number | null; - diastolic_mmhg: number | null; - mean_arterial_pressure_mmhg: number | null; - }; - spO2: { - oxygen_saturation_percentage: number | null; - }; - respiration_rate: { - breaths_per_minute: number | null; - }; - temperature: { - fahrenheit: number | null; - }; - }; -}; - export async function getVitalsFromImage(imageUrl: string) { - const bodyFormData = new FormData(); - bodyFormData.append("image", fs.createReadStream(imageUrl)); + const image = fs.readFileSync(imageUrl); + const data = (await parseVitalsFromImage(image)) as OCRV2Response | null; - if (!ocrApi) { - console.error("OCR_URL is not defined"); - return null; - } - - const response = await axios.post>( - ocrApi, - bodyFormData, - { - headers: { - ...bodyFormData.getHeaders(), - }, - }, - ); - - if (response.status !== 200) { - console.error( - `OCR analysis failed for the image ${imageUrl}`, - response.statusText, - JSON.stringify(response.data), - ); + if (!data) { + console.error("Failed to parse vitals from image"); return null; } - const data = response.data.data; const date = data.time_stamp ? new Date(data.time_stamp) : new Date(); const isoDate = date.toString() !== "Invalid Date" @@ -404,7 +268,7 @@ export async function automatedDailyRounds() { console.log(`Vitals from observations: ${JSON.stringify(vitals)}`); - if (!vitals && ocrApi) { + if (!vitals && openaiApiKey) { if (!asset_beds || asset_beds.length === 0) { console.error( `No asset beds found for the asset ${monitor.externalId}`, @@ -418,6 +282,7 @@ export async function automatedDailyRounds() { asset_beds[0].asset_object.meta.camera_access_key.split(":"); const position = asset_beds[0].meta.position; const camera = { + useSecure: false, hostname: asset_beds[0].asset_object.meta.local_ip_address, username, password, diff --git a/src/types/asset.ts b/src/types/asset.ts index 947f0ee..51f68d3 100644 --- a/src/types/asset.ts +++ b/src/types/asset.ts @@ -1,5 +1,6 @@ import type { AssetType } from "@prisma/client"; + export interface AssetConfig { id: string; name: string; @@ -11,3 +12,84 @@ export interface AssetConfig { password?: string; port?: number; } + +export type AssetBed = { + id: string; + bed_object: { + id: string; + name: string; + bed_type: "ICU" | "WARD"; + location_object: { + id: string; + facility: { + id: string; + name: string; + }; + location_type: "OTHER" | "WARD" | "ICU"; + created_date: string; + modified_date: string; + name: string; + description: string; + middleware_address: string | null; + }; + is_occupied: boolean; + created_date: string; + modified_date: string; + description: string; + meta: any; + }; + asset_object: { + id: string; + status: "ACTIVE" | "INACTIVE"; + asset_type: "INTERNAL" | "EXTERNAL"; + location_object: { + id: string; + facility: { + id: string; + name: string; + }; + location_type: "OTHER" | "WARD" | "ICU"; + created_date: string; + modified_date: string; + name: string; + description: string; + middleware_address: string | null; + }; + last_service: string | null; + resolved_middleware: { + hostname: string; + source: string; + }; + created_date: string; + modified_date: string; + name: string; + description: string; + asset_class: "ONVIF" | "HL7MONITOR" | "VENTILATOR"; + is_working: boolean; + not_working_reason: string; + serial_number: string; + warranty_details: string; + meta: { + asset_type: "CAMERA" | "MONITOR" | "VENTILATOR"; + local_ip_address: string; + camera_access_key: string; + }; + vendor_name: string; + support_name: string; + support_phone: string; + support_email: string; + qr_code_id: string | null; + manufacturer: string | null; + warranty_amc_end_of_validity: string | null; + }; + created_date: string; + modified_date: string; + meta: { + error: string; + bed_id: string; + utcTime: string; + position: { x: number; y: number; zoom: number }; + moveStatus: { zoom: "IDLE" | "MOVING"; panTilt: "IDLE" | "MOVING" }; + preset_name: string; + }; +}; \ No newline at end of file diff --git a/src/types/care.ts b/src/types/care.ts new file mode 100644 index 0000000..4dd0fb9 --- /dev/null +++ b/src/types/care.ts @@ -0,0 +1,6 @@ +export type CarePaginatedResponse = { + count: number; + next: string | null; + previous: string | null; + results: T[]; +}; diff --git a/src/types/ocr.ts b/src/types/ocr.ts index 917b47e..d41774f 100644 --- a/src/types/ocr.ts +++ b/src/types/ocr.ts @@ -18,3 +18,24 @@ export interface OCRObservationV1Sanitized { diastolic: number | null; } | null; } + +export type OCRV2Response = { + time_stamp: string | null; + ecg: { + Heart_Rate_bpm: number | null; + }; + nibp: { + systolic_mmhg: number | null; + diastolic_mmhg: number | null; + mean_arterial_pressure_mmhg: number | null; + }; + spO2: { + oxygen_saturation_percentage: number | null; + }; + respiration_rate: { + breaths_per_minute: number | null; + }; + temperature: { + fahrenheit: number | null; + }; +}; diff --git a/src/utils/autoDataExtractor.ts b/src/utils/autoDataExtractor.ts deleted file mode 100644 index 9c5b833..0000000 --- a/src/utils/autoDataExtractor.ts +++ /dev/null @@ -1,206 +0,0 @@ -import axios from "axios"; -import FormData from "form-data"; -import fs from "fs"; -import path from "path"; - -import type { CameraAsset, CameraParams, CameraPreset } from "@/types/camera"; -import type { - OCRObservationV1Raw, - OCRObservationV1Sanitized, -} from "@/types/ocr"; -import { CameraUtils } from "@/utils/CameraUtils"; -import { ocrApi, saveOCRImages, waitBeforeOCRCapture } from "@/utils/configs"; -import { downloadImage } from "@/utils/downloadImageWithDigestRouter"; - -const celsiusToFahrenheit = (celsius: string) => { - const celsiusNumber = parseFloat(celsius); - const fahrenheit = (celsiusNumber * 9) / 5 + 32; - return fahrenheit; -}; - -const validator = ( - value: number | string | null | undefined, - parser: (value: any) => number, - minvalue?: number, - maxValue?: number, -) => { - if (value === null || value === undefined || isNaN(Number(value))) { - return null; - } - - value = parser(value); - - if (minvalue !== undefined && value < minvalue) { - return null; - } - - if (maxValue !== undefined && value > maxValue) { - return null; - } - - return value; -}; - -const getSanitizedData = (data: OCRObservationV1Raw) => { - console.log("Data from OCR: ", data); - - const sanitizedData: OCRObservationV1Sanitized = {}; - sanitizedData["spo2"] = validator(data?.["SpO2"], parseInt); - - sanitizedData["ventilator_spo2"] = validator( - sanitizedData.spo2, - parseInt, - 0, - 100, - ); - - sanitizedData["resp"] = validator( - data?.["Respiratory Rate"], - parseInt, - 10, - 70, - ); - - sanitizedData["pulse"] = validator(data?.["Pulse Rate"], parseInt, 0, 100); - - sanitizedData["temperature"] = validator( - data?.["Temperature"], - celsiusToFahrenheit, - 95, - 106, - ); - - const bp = validator(data?.["Blood Pressure"], parseFloat); - sanitizedData["bp"] = bp ? { systolic: bp, mean: bp, diastolic: bp } : null; - - return sanitizedData; -}; - -const fileToBase64 = (filePath: string) => { - try { - if (!fs.existsSync(filePath)) { - return null; - } - - const buffer = fs.readFileSync(filePath); - return buffer.toString("base64"); - } catch (err) { - console.log("Error in fileToBase64: ", err); - return null; - } -}; - -const extractData = async ( - camParams: CameraParams, - monitorPreset = { x: 0, y: 0, zoom: 0 }, -): Promise<[OCRObservationV1Sanitized, string | null]> => { - try { - console.log("Moving to coordinates: ", monitorPreset); - await CameraUtils.absoluteMove({ camParams, ...monitorPreset }); - - CameraUtils.lockCamera(camParams.hostname); - - // TODO: replace timeout with a better solution - await new Promise((resolve) => - setTimeout(resolve, waitBeforeOCRCapture * 1000), - ); - - const snapshotUrl = await CameraUtils.getSnapshotUri({ camParams }); - - CameraUtils.unlockCamera(camParams.hostname); - - const fileName = "image-" + new Date().getTime() + ".jpeg"; - const imagePath = path.resolve("images", fileName); - await downloadImage( - snapshotUrl.uri, - imagePath, - camParams.username, - camParams.password, - ); - // const testImg = path.resolve("images", "test.png") - - // POST request with image to ocr - const bodyFormData = new FormData(); - bodyFormData.append("image", fs.createReadStream(imagePath)); - - if (!ocrApi) { - throw new Error("OCR_URL is not defined"); - } - - const response = await axios.post(ocrApi, bodyFormData, { - headers: { - ...bodyFormData.getHeaders(), - }, - }); - - if (!saveOCRImages) { - fs.unlink(imagePath, (err) => { - if (err) { - // TODO: Critical logger setup - console.error(err); - } - }); - } - - return [getSanitizedData(response.data.data), fileToBase64(imagePath)]; - } catch (err) { - console.log("Error in extractData: ", err); - CameraUtils.unlockCamera(camParams.hostname); - return [ - { - spo2: null, - ventilator_spo2: null, - resp: null, - pulse: null, - temperature: null, - bp: null, - }, - null, - ]; - } -}; - -const _getCamParams = (params: { - hostname: string; - username: string; - password: string; - port: string | number; -}) => { - const { hostname, username, password, port } = params; - - const camParams = { - useSecure: Number(port) === 443, - hostname, - username, - password, - port: Number(port), - }; - - return camParams; -}; - -export const updateObservationAuto = async ( - cameraParams: CameraAsset, - monitorPreset: CameraPreset, -): Promise<[OCRObservationV1Sanitized, string | null]> => { - try { - const cameraParamsSanitized = _getCamParams(cameraParams); - - const payload = await extractData(cameraParamsSanitized, monitorPreset); - - return payload; - } catch (err) { - console.log(err); - return [ - { - spo2: null, - ventilator_spo2: null, - resp: null, - pulse: null, - temperature: null, - bp: null, - }, - null, - ]; - } -}; diff --git a/src/utils/configs.ts b/src/utils/configs.ts index d7cc402..0a5e14f 100644 --- a/src/utils/configs.ts +++ b/src/utils/configs.ts @@ -1,5 +1,6 @@ import * as dotenv from "dotenv"; + dotenv.config(); export const nodeEnv = process.env.NODE_ENV ?? "development"; @@ -32,8 +33,4 @@ export const s3BucketName = process.env.S3_BUCKET_NAME; export const s3AccessKeyId = process.env.S3_ACCESS_KEY_ID; export const s3SecretAccessKey = process.env.S3_SECRET_ACCESS_KEY; -export const ocrApi = process.env.OCR_URL; -export const saveOCRImages = process.env.SAVE_OCR_IMAGES === "true"; -export const waitBeforeOCRCapture = parseInt( - process.env.WAIT_BEFORE_OCR_CAPTURE ?? "0", -); +export const openaiApiKey = process.env.OPENAI_API_KEY ?? ""; \ No newline at end of file diff --git a/src/utils/ocr.ts b/src/utils/ocr.ts new file mode 100644 index 0000000..eae7445 --- /dev/null +++ b/src/utils/ocr.ts @@ -0,0 +1,73 @@ +import { openaiApiKey } from "./configs"; +import OpenAI from "openai"; +import sharp from "sharp"; + +const openai = new OpenAI({ + apiKey: openaiApiKey, +}); + +export async function compressImage(image: Buffer) { + return await sharp(image).resize(1000).jpeg({ quality: 80 }).toBuffer(); +} + +export function encodeImage(image: Buffer) { + return Buffer.from(image).toString("base64"); +} + +export function parseOpenAiResponse(response: string) { + try { + const data = JSON.parse(response); + return data; + } catch (e) { + console.error("Failed to parse OpenAI response", e); + return null; + } +} + +export async function parseVitalsFromImage(image: Buffer) { + const compressedImage = await compressImage(image); + const b64Image = encodeImage(compressedImage); + const imageUrl = `data:image/jpeg;base64,${b64Image}`; + + const completions = await openai.chat.completions.create({ + model: "gpt-4-vision-preview", + max_tokens: 4096, + temperature: 0.4, + messages: [ + { + role: "system", + content: ` + You are an expert 5Para Monitor reader of patients. You are given 5Para Monitor image, analyze it and predict patient's reading, you will output the readings in minified JSON format only. + + Tips to analyze the ocr data: monitor can be zoomed in or zoomed out, most of the times readings that we want are at extreme right of the monitor screen, use expertise in reading 5ParaMonitor to make educated guesses about the correct reading of a field. + + NOTE: Many fields from below example can be missing, you need to output null for those fields. + + Example output in minified JSON format: + {"time_stamp":"yyyy-mm-ddThh:mm:ss","ecg":{"Heart_Rate_bpm":},"nibp":{"systolic_mmhg":,"diastolic_mmhg":,"mean_arterial_pressure_mmhg":},"spO2":{"oxygen_saturation_percentage":},"respiration_rate":{"breaths_per_minute":},"temperature":{"fahrenheit":}} + `.trim(), + }, + { + role: "user", + + content: [ + { + type: "image_url", + image_url: { + url: imageUrl, + }, + }, + ], + }, + ], + }); + + const response = completions.choices.shift()?.message.content; + + if (!response) { + console.error("Failed to get response from OpenAI"); + return null; + } + + return parseOpenAiResponse(response); +}