a8000/src/main/java/com/iflytop/a800/task/TubeTestTask.java

package com.iflytop.a800.task;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.iflytop.a800.TaskBase;
import com.iflytop.a800.device.Device;
import com.iflytop.a800.model.MdbIdChip;
import com.iflytop.a800.model.MdbProject;
import com.iflytop.a800.model.MdbTest;
import com.iflytop.a800.resource.*;
import com.iflytop.a800.utils.ScanResultAnalysisAlgo;
import com.iflytop.uf.UfCmdSnippetExecutor;
import com.iflytop.uf.util.UfCommon;
import com.iflytop.uf.util.UfJsonHelper;
import java.util.*;
public class TubeTestTask extends TaskBase {
    // 测试试管
    public TestTube tube;
    // 测试项目
    public MdbProject project;

    public TestTubeRack tubeRack;
    public String status;

    // 测试记录
    private MdbTest test;
    // 缓冲液试管
    private BufferTube bufferTube;
    // 大容量缓冲液试管
    private LargeBufferTube largeBufferTube;
    // 测试卡
    private TestCard testCard;
    // id chip
    private MdbIdChip idChip;

    // 任务准备
    public void prepare() {
        var device = Device.getInstance();
        this.bufferTube = device.bufferTube.alloc();
        if ("yes".equals(this.project.isLargeBufferRequired)) {
            this.largeBufferTube = device.largeBufferTube.getTube();
        }
        this.testCard = device.testCard.alloc();
        this.idChip = new MdbIdChip();
        this.idChip.peakCount = 3;
        this.idChip.itemCount = 1;
        this.idChip.scanPeakCount = 3;
        this.idChip.items = UfJsonHelper.objectToJson(List.of(Map.of(
            "item", "hsCRP",
            "isPiecewiseFunction", false,
            "nonPiecewiseFunction", Map.of(
                "xValueSource", 1,
                "serum", Map.of("a", 1.0, "b", 2.0, "c", 3.0, "d", 4.0),
                "wb", Map.of("a", 1.0, "b", 2.0, "c", 3.0, "d", 4.0)
            )
        )));

        // 测试记录
        this.test = new MdbTest();
        this.test.save();
    }

    @Override
    public void run() {
        this.prepare();

        ObjectMapper jsonMapper = new ObjectMapper();
        JsonNode stepsJsonTree = null;
        try {
            stepsJsonTree = jsonMapper.readTree(this.project.steps);
        } catch (JsonProcessingException e) {
            throw new RuntimeException(e);
        }

        for ( JsonNode stepNode : stepsJsonTree ) {
            var stepEnable = stepNode.get("enable").asBoolean();
            if ( !stepEnable ) {
                continue;
            }

            var stepAction = stepNode.get("action").asText();
            switch ( stepAction ) {
//            case "shaking"  : this.shake(stepNode); break;
            case "puncture" : this.executeStepPuncture(stepNode); break;
            case "aspirate" : this.executeStepAspirate(stepNode); break;
            case "mixing"   : this.executeStepMixing(stepNode); break;
            case "drop-tip" : this.executeStepDropTip(stepNode); break;
            case "incubate" : this.executeStepIncubate(stepNode); break;
            case "analysis" : this.executeStepAnalysis(stepNode); break;
            }
        }
    }

    // 摇匀
    private void shake( JsonNode stepNode ) {
        UfCmdSnippetExecutor.execute("SampleTestShake");
    }

    // 取盖
    private void uncap() {
        UfCmdSnippetExecutor.execute("SampleTestUnCap");
    }

    // 穿孔
    private void executeStepPuncture( JsonNode stepNode ) {
        Device device = Device.getInstance();
        var pipette = device.pipette;
        pipette.tipPickUp();
        pipette.puncture(this.bufferTube);
    }

    // 吸液
    private void executeStepAspirate( JsonNode stepNode ) {
        Device device = Device.getInstance();
        var pipette = device.pipette;
        pipette.tipPickUp();
        String source = stepNode.get("source").asText();
        Integer volume = stepNode.get("volume").asInt();
        if ( "LargeBufferTube".equals(source) ) {
            pipette.aspirateFromLargeBufferTube(this.largeBufferTube, volume);
        } else if ( "Sample".equals(source) && "EmergencyTube".equals(this.tube.type) ) {
            pipette.aspirateFromEmergencyTube(this.tube.index, volume);
        } else if ( "Sample".equals(source) && "SampleEpp0_5Tube".equals(this.tube.type) ) {
            pipette.aspirateFromSampleEpp0_5(this.tube.index, volume);
        } else if ( "Sample".equals(source) && "SampleEpp1_5Tube".equals(this.tube.type) ) {
            pipette.aspirateFromSampleEpp1_5(this.tube.index, volume);
        } else if ( "Sample".equals(source) && "SampleWholeBlood5mlTube".equals(this.tube.type) ) {
            pipette.aspirateFromWholeBlood5ml(this.tube.index, volume);
        } else if ( "Sample".equals(source) && "SampleWholeBlood3mlTube".equals(this.tube.type) ) {
            pipette.aspirateFromWholeBlood3ml(this.tube.index, volume);
        } else {
            throw new RuntimeException(String.format("无效的取样源 : %s/%s",source,this.tube.type));
        }
        pipette.dispense(this.bufferTube);
    }

    // 混匀
    private void executeStepMixing( JsonNode stepNode ) {
        Device device = Device.getInstance();
        var pipette = device.pipette;
        var mixCount = stepNode.get("count").asInt();
        var mixVolume = stepNode.get("volume").asInt();
        pipette.mix(this.bufferTube, mixCount, mixVolume);
    }

    // 丢弃吸头
    private void executeStepDropTip( JsonNode stepNode ) {
        Device device = Device.getInstance();
        var pipette = device.pipette;
        pipette.tipDrop();
    }

    // 孵育
    private void executeStepIncubate( JsonNode stepNode ) {
        Device device = Device.getInstance();
        device.incubator.pushNewCard(this.testCard.boxIndex);

        var pipette = device.pipette;
        pipette.tipPickUp();

        Integer volume = stepNode.get("volume").asInt();
        pipette.aspirateFromBufferTubeAndDispenseToTestCard(this.bufferTube, volume);

        pipette.tipDrop();

        Integer duration = stepNode.get("duration").asInt();
        UfCommon.delay(duration);
    }

    // 扫描
    private void executeStepAnalysis( JsonNode stepNode ) {
        // 扫描
        Device device = Device.getInstance();
//        device.incubator.exitToScanner();
        var scanner = device.scanner;
        scanner.scanTypeF();
        var scanResult = scanner.readResult();
        scanner.dropCard();

        // 计算
        var algo = new ScanResultAnalysisAlgo();
        var algoResult = algo.calculate(scanResult, this.idChip.peakCount);

        // 处理
        String sampleType = "WB"; // @TODO : 这里要从样本中取 ~~~~
        List<Map<String, Object>> results = new ArrayList<>();
        var projects = UfJsonHelper.jsonToNode(idChip.items);
        for ( var i=0; i< idChip.itemCount; i++ ) {
            double valueX = 0;
            JsonNode funcInfo = null;

            var project = projects.get(i);
            var itemName = project.get("item").asText();
            var isPiecewiseFunction = project.get("isPiecewiseFunction").asBoolean();
            if ( !isPiecewiseFunction ) { // 非分段函数
                var func = project.get("nonPiecewiseFunction");
                var xValueSource = func.get("xValueSource").asInt();
                valueX = this.calculateRatio(algoResult, xValueSource, itemName);
                funcInfo = func.get("serum");
                if ("WB".equals(sampleType)) {
                    funcInfo = func.get("wb");
                }
            } else { // 分段函数
                var func = project.get("piecewiseFunction");
                var piecewiseValueSrc = func.get("piecewiseValueSrc").asInt();
                var piecewiseValueSrcValue = this.calculateRatio(algoResult, piecewiseValueSrc, itemName);
                var piecewiseValue = func.get("piecewiseValue").asDouble();
                if ( piecewiseValueSrcValue > piecewiseValue ) { // 高浓度
                    var highXValueSource = func.get("highXValueSource").asInt();
                    valueX = this.calculateRatio(algoResult, highXValueSource, itemName);
                    funcInfo = func.get("serumHigh");
                    if ("WB".equals(sampleType)) {
                        funcInfo = func.get("wbHigh");
                    }
                } else { // 低浓度
                    var lowXValueSource = func.get("lowXValueSource").asInt();
                    valueX = this.calculateRatio(algoResult, lowXValueSource, itemName);
                    funcInfo = func.get("serumLow");
                    if ("WB".equals(sampleType)) {
                        funcInfo = func.get("wbLow");
                    }
                }
            }

            double valueD = funcInfo.get("d").asDouble();
            double valueB = funcInfo.get("b").asDouble();
            double valueC = funcInfo.get("c").asDouble();
            double valueA = funcInfo.get("a").asDouble();
            double value =  valueA * Math.pow(valueX,3) + valueB * Math.pow(valueX,2) + valueC * valueX + valueD;

            // @TODO : 单位也要从配置中读取
            results.add(Map.of("name",itemName,"value",value,"unit","xx/xx"));
        }

        this.test.result = UfJsonHelper.objectToJson(results);
        this.test.save();
    }

    /**
     * @link https://iflytop1.feishu.cn/docx/UnRtdSG4qouMTaxzRb2cjiTTnZe
     * @link https://iflytop1.feishu.cn/docx/A0CHdQL6OoTTCSx8MB7cQKEjnSc
     * @param result - algo result
     * @param xSource - x source
     * @return double - value of ratio
     */
    private double calculateRatio(ScanResultAnalysisAlgo.AlgoResult result, int xSource, String itenName) {
        // 计算 ratio
        Map<String, Float> ratios = new HashMap<>();
        if ( 5 == idChip.scanPeakCount ) {
            var peaks = result.peakInfos;
            ratios.put("ratio", peaks[3].area / peaks[4].area); // T/C
            ratios.put("antiRatio", peaks[3].area / peaks[4].area); // H/C
            ratios.put("antiTestRatio", peaks[3].area / peaks[2].area); // T/H
            ratios.put("rfRatio", peaks[1].area / peaks[4].area); // R/C
            ratios.put("rtRatio", peaks[3].area / peaks[1].area); // T/R
            ratios.put("t4Ratio", peaks[0].area / peaks[4].area); // T4/C
            ratios.put("t4t3Ratio", peaks[1].area / peaks[0].area); // R/T4
        } else if ( 4 == idChip.scanPeakCount && Objects.equals(idChip.scanType, 1) ) { // F 光学
            var peaks = result.peakInfos; // H T C
            ratios.put("ratio", peaks[1].area / peaks[2].area); // T/C
            ratios.put("antiRatio", peaks[0].area / peaks[2].area); // H/C
            ratios.put("antiTestRatio", peaks[1].area / peaks[0].area); // T/H
            ratios.put("rfRatio", peaks[0].area / peaks[2].area); // R/C @TODO : 待定， 三联卡F光学没有R
            ratios.put("rtRatio", peaks[1].area / peaks[0].area); // T/R @TODO : 待定， 三联卡F光学没有R
        } else if ( 4 == idChip.scanPeakCount && Objects.equals(idChip.scanType, 2) ) { // T 光学
            var peaks = result.peakInfos; // R H T C
            ratios.put("ratio", peaks[2].area / peaks[3].area); // T/C
            ratios.put("antiRatio", peaks[1].area / peaks[3].area); // H/C
            ratios.put("antiTestRatio", peaks[2].area / peaks[1].area); // T/H
            ratios.put("rfRatio", peaks[0].area / peaks[3].area); // R/C
            ratios.put("rtRatio", peaks[2].area / peaks[0].area); // T/R
        } else if ( 3 == idChip.scanPeakCount ) {
            var peaks = result.peakInfos; // H T C
            ratios.put("ratio", peaks[1].area / peaks[2].area); // T/C
            ratios.put("antiRatio", peaks[0].area / peaks[2].area); // H/C
            ratios.put("antiTestRatio", peaks[1].area / peaks[0].area); // T/H
        } else if ("PCT".equals(itenName)) {
            var peaks = result.peakInfos; // C T
            ratios.put("ratio", peaks[1].area / peaks[0].area); // T/C
        } else if ( 2 == idChip.scanPeakCount ) {
            var peaks = result.peakInfos; // T C
            ratios.put("ratio", peaks[0].area / peaks[1].area); // T/C
        } else {
            throw new RuntimeException("unknown scan peak count" + idChip.scanPeakCount);
        }

        // calculate ratio by x source
        if ( 1 == xSource ) {
            return ratios.get("ratio");
        } else if ( 2 == xSource ) {
            return ratios.get("antiTestRatio");
        } else if ( 3 == xSource ) {
            return ratios.get("antiRatio");
        } else if ( 4 == xSource ) {
            return ratios.get("ratio") + ratios.get("antiTestRatio");
        } else if ( 5 == xSource ) {
            // @TODO : 这里 R-ratio 不知道是啥
            throw new RuntimeException("不知道 R-Ratio 是啥");
        } else if ( 6 == xSource ) {
            return ratios.get("t4Ratio");
        } else {
            throw new RuntimeException("unknown x source" + xSource);
        }
    }
}