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305 lines
13 KiB
305 lines
13 KiB
package com.iflytop.a800.task;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.JsonNode;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.iflytop.a800.TaskBase;
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import com.iflytop.a800.device.Device;
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import com.iflytop.a800.model.MdbIdChip;
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import com.iflytop.a800.model.MdbProject;
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import com.iflytop.a800.model.MdbTest;
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import com.iflytop.a800.resource.*;
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import com.iflytop.a800.utils.ScanResultAnalysisAlgo;
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import com.iflytop.uf.UfCmdSnippetExecutor;
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import com.iflytop.uf.util.UfCommon;
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import com.iflytop.uf.util.UfJsonHelper;
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import java.util.*;
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public class TubeTestTask extends TaskBase {
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// 测试试管
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public TestTube tube;
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// 测试项目
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public MdbProject project;
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public TestTubeRack tubeRack;
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public String status;
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// 测试记录
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private MdbTest test;
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// 缓冲液试管
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private BufferTube bufferTube;
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// 大容量缓冲液试管
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private LargeBufferTube largeBufferTube;
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// 测试卡
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private TestCard testCard;
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// id chip
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private MdbIdChip idChip;
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// 任务准备
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public void prepare() {
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var device = Device.getInstance();
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this.bufferTube = device.bufferTube.alloc();
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if ("yes".equals(this.project.isLargeBufferRequired)) {
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this.largeBufferTube = device.largeBufferTube.getTube();
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}
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this.testCard = device.testCard.alloc();
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this.idChip = new MdbIdChip();
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this.idChip.peakCount = 3;
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this.idChip.itemCount = 1;
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this.idChip.scanPeakCount = 3;
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this.idChip.items = UfJsonHelper.objectToJson(List.of(Map.of(
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"item", "hsCRP",
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"isPiecewiseFunction", false,
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"nonPiecewiseFunction", Map.of(
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"xValueSource", 1,
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"serum", Map.of("a", 1.0, "b", 2.0, "c", 3.0, "d", 4.0),
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"wb", Map.of("a", 1.0, "b", 2.0, "c", 3.0, "d", 4.0)
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)
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)));
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// 测试记录
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this.test = new MdbTest();
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this.test.save();
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}
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@Override
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public void run() {
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this.prepare();
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ObjectMapper jsonMapper = new ObjectMapper();
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JsonNode stepsJsonTree = null;
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try {
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stepsJsonTree = jsonMapper.readTree(this.project.steps);
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} catch (JsonProcessingException e) {
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throw new RuntimeException(e);
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}
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for ( JsonNode stepNode : stepsJsonTree ) {
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var stepEnable = stepNode.get("enable").asBoolean();
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if ( !stepEnable ) {
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continue;
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}
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var stepAction = stepNode.get("action").asText();
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switch ( stepAction ) {
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// case "shaking" : this.shake(stepNode); break;
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case "puncture" : this.executeStepPuncture(stepNode); break;
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case "aspirate" : this.executeStepAspirate(stepNode); break;
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case "mixing" : this.executeStepMixing(stepNode); break;
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case "drop-tip" : this.executeStepDropTip(stepNode); break;
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case "incubate" : this.executeStepIncubate(stepNode); break;
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case "analysis" : this.executeStepAnalysis(stepNode); break;
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}
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}
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}
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// 摇匀
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private void shake( JsonNode stepNode ) {
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UfCmdSnippetExecutor.execute("SampleTestShake");
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}
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// 取盖
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private void uncap() {
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UfCmdSnippetExecutor.execute("SampleTestUnCap");
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}
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// 穿孔
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private void executeStepPuncture( JsonNode stepNode ) {
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Device device = Device.getInstance();
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var pipette = device.pipette;
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pipette.tipPickUp();
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pipette.puncture(this.bufferTube);
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}
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// 吸液
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private void executeStepAspirate( JsonNode stepNode ) {
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Device device = Device.getInstance();
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var pipette = device.pipette;
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pipette.tipPickUp();
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String source = stepNode.get("source").asText();
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Integer volume = stepNode.get("volume").asInt();
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if ( "LargeBufferTube".equals(source) ) {
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pipette.aspirateFromLargeBufferTube(this.largeBufferTube, volume);
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} else if ( "Sample".equals(source) && "EmergencyTube".equals(this.tube.type) ) {
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pipette.aspirateFromEmergencyTube(this.tube.index, volume);
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} else if ( "Sample".equals(source) && "SampleEpp0_5Tube".equals(this.tube.type) ) {
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pipette.aspirateFromSampleEpp0_5(this.tube.index, volume);
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} else if ( "Sample".equals(source) && "SampleEpp1_5Tube".equals(this.tube.type) ) {
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pipette.aspirateFromSampleEpp1_5(this.tube.index, volume);
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} else if ( "Sample".equals(source) && "SampleWholeBlood5mlTube".equals(this.tube.type) ) {
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pipette.aspirateFromWholeBlood5ml(this.tube.index, volume);
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} else if ( "Sample".equals(source) && "SampleWholeBlood3mlTube".equals(this.tube.type) ) {
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pipette.aspirateFromWholeBlood3ml(this.tube.index, volume);
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} else {
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throw new RuntimeException(String.format("无效的取样源 : %s/%s",source,this.tube.type));
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}
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pipette.dispense(this.bufferTube);
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}
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// 混匀
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private void executeStepMixing( JsonNode stepNode ) {
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Device device = Device.getInstance();
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var pipette = device.pipette;
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var mixCount = stepNode.get("count").asInt();
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var mixVolume = stepNode.get("volume").asInt();
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pipette.mix(this.bufferTube, mixCount, mixVolume);
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}
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// 丢弃吸头
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private void executeStepDropTip( JsonNode stepNode ) {
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Device device = Device.getInstance();
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var pipette = device.pipette;
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pipette.tipDrop();
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}
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// 孵育
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private void executeStepIncubate( JsonNode stepNode ) {
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Device device = Device.getInstance();
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device.incubator.pushNewCard(this.testCard.boxIndex);
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var pipette = device.pipette;
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pipette.tipPickUp();
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Integer volume = stepNode.get("volume").asInt();
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pipette.aspirateFromBufferTubeAndDispenseToTestCard(this.bufferTube, volume);
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pipette.tipDrop();
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Integer duration = stepNode.get("duration").asInt();
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UfCommon.delay(duration);
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}
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// 扫描
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private void executeStepAnalysis( JsonNode stepNode ) {
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// 扫描
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Device device = Device.getInstance();
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// device.incubator.exitToScanner();
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var scanner = device.scanner;
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scanner.scanTypeF();
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var scanResult = scanner.readResult();
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scanner.dropCard();
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// 计算
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var algo = new ScanResultAnalysisAlgo();
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var algoResult = algo.calculate(scanResult, this.idChip.peakCount);
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// 处理
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String sampleType = "WB"; // @TODO : 这里要从样本中取 ~~~~
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List<Map<String, Object>> results = new ArrayList<>();
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var projects = UfJsonHelper.jsonToNode(idChip.items);
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for ( var i=0; i< idChip.itemCount; i++ ) {
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double valueX = 0;
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JsonNode funcInfo = null;
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var project = projects.get(i);
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var itemName = project.get("item").asText();
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var isPiecewiseFunction = project.get("isPiecewiseFunction").asBoolean();
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if ( !isPiecewiseFunction ) { // 非分段函数
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var func = project.get("nonPiecewiseFunction");
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var xValueSource = func.get("xValueSource").asInt();
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valueX = this.calculateRatio(algoResult, xValueSource, itemName);
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funcInfo = func.get("serum");
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if ("WB".equals(sampleType)) {
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funcInfo = func.get("wb");
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}
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} else { // 分段函数
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var func = project.get("piecewiseFunction");
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var piecewiseValueSrc = func.get("piecewiseValueSrc").asInt();
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var piecewiseValueSrcValue = this.calculateRatio(algoResult, piecewiseValueSrc, itemName);
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var piecewiseValue = func.get("piecewiseValue").asDouble();
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if ( piecewiseValueSrcValue > piecewiseValue ) { // 高浓度
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var highXValueSource = func.get("highXValueSource").asInt();
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valueX = this.calculateRatio(algoResult, highXValueSource, itemName);
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funcInfo = func.get("serumHigh");
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if ("WB".equals(sampleType)) {
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funcInfo = func.get("wbHigh");
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}
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} else { // 低浓度
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var lowXValueSource = func.get("lowXValueSource").asInt();
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valueX = this.calculateRatio(algoResult, lowXValueSource, itemName);
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funcInfo = func.get("serumLow");
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if ("WB".equals(sampleType)) {
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funcInfo = func.get("wbLow");
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}
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}
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}
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double valueD = funcInfo.get("d").asDouble();
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double valueB = funcInfo.get("b").asDouble();
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double valueC = funcInfo.get("c").asDouble();
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double valueA = funcInfo.get("a").asDouble();
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double value = valueA * Math.pow(valueX,3) + valueB * Math.pow(valueX,2) + valueC * valueX + valueD;
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// @TODO : 单位也要从配置中读取
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results.add(Map.of("name",itemName,"value",value,"unit","xx/xx"));
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}
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this.test.result = UfJsonHelper.objectToJson(results);
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this.test.save();
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}
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/**
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* @link https://iflytop1.feishu.cn/docx/UnRtdSG4qouMTaxzRb2cjiTTnZe
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* @link https://iflytop1.feishu.cn/docx/A0CHdQL6OoTTCSx8MB7cQKEjnSc
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* @param result - algo result
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* @param xSource - x source
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* @return double - value of ratio
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*/
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private double calculateRatio(ScanResultAnalysisAlgo.AlgoResult result, int xSource, String itenName) {
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// 计算 ratio
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Map<String, Float> ratios = new HashMap<>();
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if ( 5 == idChip.scanPeakCount ) {
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var peaks = result.peakInfos;
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ratios.put("ratio", peaks[3].area / peaks[4].area); // T/C
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ratios.put("antiRatio", peaks[3].area / peaks[4].area); // H/C
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ratios.put("antiTestRatio", peaks[3].area / peaks[2].area); // T/H
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ratios.put("rfRatio", peaks[1].area / peaks[4].area); // R/C
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ratios.put("rtRatio", peaks[3].area / peaks[1].area); // T/R
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ratios.put("t4Ratio", peaks[0].area / peaks[4].area); // T4/C
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ratios.put("t4t3Ratio", peaks[1].area / peaks[0].area); // R/T4
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} else if ( 4 == idChip.scanPeakCount && Objects.equals(idChip.scanType, 1) ) { // F 光学
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var peaks = result.peakInfos; // H T C
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ratios.put("ratio", peaks[1].area / peaks[2].area); // T/C
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ratios.put("antiRatio", peaks[0].area / peaks[2].area); // H/C
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ratios.put("antiTestRatio", peaks[1].area / peaks[0].area); // T/H
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ratios.put("rfRatio", peaks[0].area / peaks[2].area); // R/C @TODO : 待定， 三联卡F光学没有R
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ratios.put("rtRatio", peaks[1].area / peaks[0].area); // T/R @TODO : 待定， 三联卡F光学没有R
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} else if ( 4 == idChip.scanPeakCount && Objects.equals(idChip.scanType, 2) ) { // T 光学
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var peaks = result.peakInfos; // R H T C
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ratios.put("ratio", peaks[2].area / peaks[3].area); // T/C
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ratios.put("antiRatio", peaks[1].area / peaks[3].area); // H/C
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ratios.put("antiTestRatio", peaks[2].area / peaks[1].area); // T/H
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ratios.put("rfRatio", peaks[0].area / peaks[3].area); // R/C
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ratios.put("rtRatio", peaks[2].area / peaks[0].area); // T/R
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} else if ( 3 == idChip.scanPeakCount ) {
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var peaks = result.peakInfos; // H T C
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ratios.put("ratio", peaks[1].area / peaks[2].area); // T/C
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ratios.put("antiRatio", peaks[0].area / peaks[2].area); // H/C
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ratios.put("antiTestRatio", peaks[1].area / peaks[0].area); // T/H
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} else if ("PCT".equals(itenName)) {
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var peaks = result.peakInfos; // C T
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ratios.put("ratio", peaks[1].area / peaks[0].area); // T/C
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} else if ( 2 == idChip.scanPeakCount ) {
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var peaks = result.peakInfos; // T C
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ratios.put("ratio", peaks[0].area / peaks[1].area); // T/C
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} else {
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throw new RuntimeException("unknown scan peak count" + idChip.scanPeakCount);
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}
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// calculate ratio by x source
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if ( 1 == xSource ) {
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return ratios.get("ratio");
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} else if ( 2 == xSource ) {
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return ratios.get("antiTestRatio");
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} else if ( 3 == xSource ) {
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return ratios.get("antiRatio");
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} else if ( 4 == xSource ) {
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return ratios.get("ratio") + ratios.get("antiTestRatio");
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} else if ( 5 == xSource ) {
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// @TODO : 这里 R-ratio 不知道是啥
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throw new RuntimeException("不知道 R-Ratio 是啥");
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} else if ( 6 == xSource ) {
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return ratios.get("t4Ratio");
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} else {
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throw new RuntimeException("unknown x source" + xSource);
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}
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}
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}
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