brukerconverter - npm Package Compare versions

Comparing version 0.2.0 to 1.0.0

bower.json

 {
   "name": "brukerconverter",
-  "version": "0.1.1",
+  "version": "1.0.0",
   "main": "build/brukerconverter.js",
@@ -10,9 +10,2 @@ "homepage": "https://github.com/cheminfo-js/brukerconverter",
   "description": "Parse and convert Bruker raw data",
-<<<<<<< HEAD
-  "main": [
-    "dist/brukerconverter.js",
-    "dist/brukerconverter.min.js"
-  ]
-=======
->>>>>>> origin/master
   "moduleType": [
@@ -19,0 +12,0 @@ "amd",

package.json

 {
   "name": "brukerconverter",
-  "version": "0.2.0",
+  "version": "1.0.0",
   "description": "Parse and convert Bruker raw data",
@@ -32,5 +32,5 @@ "main": "./src/brukerconverter.js",
     "iobuffer": "^2.0.0",
-    "jcampconverter": "^2.1.0",
+    "jcampconverter": "^2.3.0",
     "jszip": "^2.5.0"
   }
 }

src/brukerconverter.js

@@ -13,2 +13,4 @@ "use strict";
 function readZIP(zipFile, options) {
+    options = options || {};
+
     var zip = new JSZip();
@@ -22,12 +24,16 @@ zip.load(zipFile, options);
         'acqu2s': TEXT,
-        'pdata/1/procs': TEXT,
-        'pdata/1/proc2s': TEXT,
-        'pdata/1/1r': BINARY,
-        'pdata/1/1i': BINARY,
-        'pdata/1/2rr': BINARY
+        'procs': TEXT,
+        'proc2s': TEXT,
+        '1r': BINARY,
+        '1i': BINARY,
+        '2rr': BINARY
     };
+    var folders = zip.filter(function (relativePath, file) {
+        if(relativePath.indexOf("ser")>=0||relativePath.indexOf("fid")>=0
+            ||relativePath.indexOf("1r")>=0||relativePath.indexOf("2rr")>=0){
+            return true;
+        }
 
-    var folders = zip.filter(function (relativePath, file) {
-        if(/^\d+$/.test(relativePath.substr(0, relativePath.length - 1)))
-            return true
+        return false;
+
     });
@@ -39,7 +45,8 @@
         var len = folders[i].name.length;
-        var currFolder = zip.folder(folders[i].name.substr(0, len - 1));
+        var name = folders[i].name;
+        name = name.substr(0,name.lastIndexOf("/")+1);
+        var currFolder = zip.folder(name);
         var currFiles = currFolder.filter(function (relativePath, file) {
             return files[relativePath] ? true : false;
         });
-
         var brukerFiles = {};
@@ -50,3 +57,3 @@
             var name = currFiles[j].name.substr(idx + 1);
-            if(files[name] === BINARY || files['pdata/1/' + name] === BINARY) {
+            if(files[name] === BINARY) {
                 brukerFiles[name] = new IOBuffer(currFiles[j].asArrayBuffer());
@@ -57,4 +64,4 @@ } else {
         }
-
-        spectra[i] = convert(brukerFiles);
+        //console.log(folders[i].name);
+        spectra[i] = {"filename":folders[i].name,value:convert(brukerFiles,options)};
     }
@@ -65,15 +72,53 @@
 
-function convert(brukerFiles) {
+function convert(brukerFiles, options) {
+    options = options || {};
+    var start = new Date();
+    var result;
     if(brukerFiles['ser'] || brukerFiles['2rr']) {
-        return convert2D(brukerFiles);
+        result =  convert2D(brukerFiles, options);
     } else if(brukerFiles['1r'] || brukerFiles['1i'] || brukerFiles['fid']) {
-        return convert1D(brukerFiles);
+        result =   convert1D(brukerFiles, options);
     } else {
         throw new RangeError('The current files are invalid');
     }
+
+    if (result.twoD && !options.noContours) {
+        //console.log("Countours");
+        add2D(result);
+        if (result.profiling) result.profiling.push({
+            action: 'Finished countour plot calculation',
+            time: new Date() - start
+        });
+        if (!options.keepSpectra) {
+            delete result.spectra;
+        }
+    }
+
+    var spectra = result.spectra;
+    if (options.xy) { // the spectraData should not be a oneD array but an object with x and y
+        if (spectra.length > 0) {
+            for (var i=0; i<spectra.length; i++) {
+                var spectrum=spectra[i];
+                if (spectrum.data.length>0) {
+                    for (var j=0; j<spectrum.data.length; j++) {
+                        var data=spectrum.data[j];
+                        var newData={x: new Array(data.length/2), y:new Array(data.length/2)};
+                        for (var k=0; k<data.length; k=k+2) {
+                            newData.x[k/2]=data[k];
+                            newData.y[k/2]=data[k+1];
+                        }
+                        spectrum.data[j]=newData;
+                    }
+
+                }
+            }
+        }
+    }
+
+    return result;
 }
 
-function convert1D(files) {
+function convert1D(files, options) {
     if(files['1r'] || files['1i']) {
-        var result = parseData(files["procs"]);
+        var result = parseData(files["procs"], options);
 
@@ -87,4 +132,4 @@ if(files['1r']) {
     } else if(files['fid']) {
-        result = parseData(files['procs']);
-        var temp = parseData(files['acqus']);
+        result = parseData(files['procs'], options);
+        var temp = parseData(files['acqus'], options);
 
@@ -98,3 +143,2 @@ var keys = Object.keys(temp.info);
         }
-
         setFIDSpectrumData(files['fid'], result)
@@ -105,34 +149,54 @@ }
 
-function convert2D(files) {
+function convert2D(files, options) {
+    var SF,SW_p,offset;
     if(files['2rr']) {
-        var result = parseData(files['procs']);
-        var temp = parseData(files['proc2s']);
+        var result = parseData(files['procs'], options);
+        var temp = parseData(files['proc2s'], options);
+        result.info.nbSubSpectra = temp.info['$SI'] = parseInt(temp.info['$SI']);
+        SF = temp.info['$SF'] = parseFloat(temp.info['$SF']);
+        SW_p = temp.info['$SWP'] = parseFloat(temp.info['$SWP']);
+        offset = temp.info['$OFFSET'] = parseFloat(temp.info['$OFFSET']);
+
     } else if(files['ser']) {
-        result = parseData(files['acqus']);
-        temp = parseData(files['acqu2s']);
+        result = parseData(files['acqus'], options);
+        temp = parseData(files['acqu2s'], options);
+        result.info.nbSubSpectra = temp.info['$SI'] = parseInt(temp.info['$TD']);
+        result.info['$SI'] = parseInt(result.info['$TD']);
+        SW_p = temp.info['$SWH'] = parseFloat(temp.info['$SWH']);
+        result.info["$SWP"]=result.info["$SWH"];
+        result.info["$SF"]=parseFloat(temp.info['$SFO1']);
+        result.info['$OFFSET']=0;
+        SF = temp.info['$SFO2'] = parseFloat(temp.info['$SFO2']);
+        offset=0;
+        result.info['$AXNUC']=result.info['$NUC1'];
+        temp.info['$AXNUC']=temp.info['$NUC1'];
     }
 
-    result.info.nbSubSpectra = temp.info['$SI'] = parseInt(temp.info['$SI']);
-    var SW_p = temp.info['$SWP'] = parseFloat(temp.info['$SWP']);
-    var SF = temp.info['$SF'] = parseFloat(temp.info['$SF']);
-    var offset = temp.info['$OFFSET'] = parseFloat(temp.info['$OFFSET']);
-
     result.info.firstY = offset;
     result.info.lastY = offset - SW_p / SF;
     result.info['$BF2'] = SF;
-    result.info['$SF01'] = SF;
+    result.info['$SFO1'] = SF;
 
+    var nbSubSpectra = result.info.nbSubSpectra;
+    var pageValue = result.info.firstY;
+    var deltaY = (result.info.lastY-result.info.firstY)/(nbSubSpectra-1);
+
     if(files['2rr']) {
         setXYSpectrumData(files['2rr'], result, '2rr', true);
-        result.spectra[0].setYUnits = 'PPM';
     } else if(files['ser']) {
         setXYSpectrumData(files['ser'], result, 'ser', true);
-        result.spectra[0].setYUnits = 'HZ';
     }
 
-    var dataType = files['ser'] ? 'TYPE_2DNMR_FID' : 'TYPE_2DNMR_SPECTRUM';
-    for(var i = 0; i < result.spectra.length; ++i) {
-        result.spectra[i].DataType = dataType;
+    for(var i = 0; i < nbSubSpectra; i++) {
+        pageValue+=deltaY;
+        result.spectra[i].pageValue=pageValue;
+        if(files['2rr']) {
+            result.spectra[i].setYUnits = 'PPM';
+        } else if(files['ser']) {
+            result.spectra[i].setYUnits = 'HZ';
+        }
     }
 
+    var dataType = files['ser'] ? 'TYPE_2DNMR_FID' : 'TYPE_2DNMR_SPECTRUM';
+
     result.info['2D_Y_NUCLEUS'] = temp.info['$AXNUC'];
@@ -145,2 +209,4 @@ result.info['2D_X_NUCLEUS'] = result.info['$AXNUC'];
 
+    result.twoD = true;
+
     return result;
@@ -154,3 +220,4 @@ }
     var SF = parseFloat(spectra.info["$SF"]);
-    var BF = parseFloat(spectra.info["$BF1"]);
+    var BF = SF;
+    //var BF = parseFloat(spectra.info["$BF1"]);
     var offset = spectra.shiftOffsetVal;//parseFloat(spectra.info["$OFFSET"]);
@@ -160,3 +227,3 @@
     spectra.info["$BF1"] = BF;
-    spectra.info["$SF01"] = SF;
+    spectra.info["$SFO1"] = SF;
     spectra.info.brukerReference = BF;
@@ -170,5 +237,2 @@
 
-    //console.log(file);
-    //console.log("");
-
     if(endian)
@@ -179,7 +243,7 @@ file.setLittleEndian();
 
-    //spectra.spectra = new Array(nbSubSpectra);
-    for(var i = 0; i < nbSubSpectra; ++i) {
+    for(var i = 0; i < nbSubSpectra; i++) {
         var toSave = {
             dataType : "NMR Spectrum",
             dataTable : "(X++(R..R))",
+            nbPoints : td,
             firstX : offset,
@@ -189,3 +253,7 @@ lastX : offset - SW_p / SF,
             yUnit : "Arbitrary",
-            data:[{x:new Array(td),y:new Array(td)}]
+            data:[new Array(td*2)],//[{x:new Array(td),y:new Array(td)}],
+            isXYdata:true,
+            observeFrequency:SF,
+            title:spectra.info['TITLE'],
+            deltaX:-(SW_p / SF)/(td-1)
 
@@ -195,15 +263,23 @@ };
         var x = offset;
+        var deltaX = toSave.deltaX;
         if(real) {
-            for(var k = 0; k < td - 1; ++k) {
-                toSave.data[0].x[k] = x;
-                toSave.data[0].y[k] = file.readInt32();
-                x += SF;
+            for(var k = 0; k < td; ++k) {
+                toSave.data[0][2*k] = x;
+                toSave.data[0][2*k+1] = file.readInt32();
+                if(toSave.data[0][2*k+1]===null||isNaN(toSave.data[0][2*k+1])){
+                    toSave.data[0][2*k+1] = 0;
+                }
+                x += deltaX;
             }
         } else {
-            for(k = td - 1; k > 0; --k) {
-                toSave.data[0].x[k] = x;
-                toSave.data[0].y[k] = file.readInt32();
-                x += SF;
+            for(k = td - 1; k >= 0; --k) {
+                toSave.data[0][2*k] = x;
+                toSave.data[0][2*k+1] = file.readInt32();
+                if(toSave.data[0][2*k+1]===null||isNaN(toSave.data[0][2*k+1])) {
+                    toSave.data[0][2*k+1] = 0;
+                }
+                x += deltaX;
             }
         }
+
         spectra.spectra.push(toSave);
@@ -213,5 +289,7 @@ }
 
-function parseData(file) {
+function parseData(file, options) {
+    var keepRecordsRegExp=/.*/;
+    if (options.keepRecordsRegExp) keepRecordsRegExp=options.keepRecordsRegExp;
     return Converter.convert(file, {
-        keepRecordsRegExp:/.*/
+        keepRecordsRegExp:keepRecordsRegExp
     });
@@ -222,19 +300,18 @@ }
     var td = spectra.info['$TD'] = parseInt(spectra.info['$TD']);
-    var SW_p = spectra.info['$SWP'] = parseFloat(spectra.info['$SWP']);
-    if(SW_p !== 0) {
-        spectra.info['$SWH'] = SW_p;
-    }
+
     var SW_h = spectra.info['$SWH'] = parseFloat(spectra.info['$SWH']);
+    var SW = spectra.info['$SW'] = parseFloat(spectra.info['$SW']);
 
-    var SF = spectra.info['$SF01'] = parseFloat(spectra.info['$SF01']);
-    var BF = spectra.info['$BF1'] = parseFloat(spectra.info['$BF1']);
+    var SF = spectra.info['$SFO1'] = parseFloat(spectra.info['$SFO1']);
+    var BF =  parseFloat(spectra.info['$BF1']);
+    spectra.info['$BF1'] = BF;
 
-    spectra.info['$SF'] = parseFloat(spectra.info['$SF']);
-    if(spectra.info['$SF'] !== 0) {
-        BF = spectra.info['$SF'];
-    }
+    //var DW = 1 / (2 * SW_h);
+    //var AQ = td * DW;
+    var AQ = SW;
+    var DW = AQ/(td-1);
 
-    var DW = 1 / (2 * SW_h);
-    var AQ = td * DW;
+    //console.log(DW+" "+SW+" "+td);
 
+
     var endian = parseInt(spectra.info["$BYTORDP"]);
@@ -258,3 +335,7 @@ endian = endian ? 0 : 1;
             yUnit : "Arbitrary",
-            data:[{x:new Array(td),y:new Array(td)}]
+            data:[new Array(2*td)],//[{x:new Array(td),y:new Array(td)}],
+            isXYdata:true,
+            observeFrequency:SF,
+            title:spectra.info['TITLE'],
+            deltaX:DW
         };
@@ -266,17 +347,191 @@ spectra.spectra.push(toSave);
 
+    var y;
     for(i = 0; file.available(8); ++i, x += DW) {
-        spectra.spectra[0].data[0].y[i] = file.readInt32();
-        spectra.spectra[0].data[0].x[i] = x;
-        spectra.spectra[1].data[0].y[i] = file.readInt32();
-        spectra.spectra[1].data[0].x[i] = x;
+        y = file.readInt32();
+        if(y===null || isNaN(y)){
+            y=0;
+        }
+        spectra.spectra[0].data[0][2*i+1] = y;
+        spectra.spectra[0].data[0][2*i] = x;
+        y = file.readInt32();
+        if(y===null || isNaN(y)){
+            y=0;
+        }
+        if(y===null || isNaN(y)){
+            y=0;
+        }
+        spectra.spectra[1].data[0][2*i+1] = y;
+        spectra.spectra[1].data[0][2*i] = x;
+
     }
 
     for(; i < td; ++i, x += DW) {
-        spectra.spectra[0].data[0].y[i] = 0;
-        spectra.spectra[0].data[0].x[i] = x;
-        spectra.spectra[1].data[0].y[i] = 0;
-        spectra.spectra[1].data[0].x[i] = x;
+        spectra.spectra[0].data[0][2*i+1] = 0;
+        spectra.spectra[0].data[0][2*i] = x;
+        spectra.spectra[1].data[0][2*i+1] = 0;
+        spectra.spectra[1].data[0][2*i] = x;
     }
 }
 
+/**
+ * Those functions should disappear if add2D becomes accessible in jcampconvert
+ * @param spectra
+ * @returns {{z: Array, minX: *, maxX: *, minY: *, maxY: *, minZ: *, maxZ: *, noise: number}}
+ */
+
+function convertTo3DZ(spectra) {
+    var noise = 0;
+    var minZ = spectra[0].data[0][0];
+    var maxZ = minZ;
+    var ySize = spectra.length;
+    var xSize = spectra[0].data[0].length / 2;
+    var z = new Array(ySize);
+    for (var i = 0; i < ySize; i++) {
+        z[i] = new Array(xSize);
+        for (var j = 0; j < xSize; j++) {
+            z[i][j] = spectra[i].data[0][j * 2 + 1];
+            if (z[i][j] < minZ) minZ = spectra[i].data[0][j * 2 + 1];
+            if (z[i][j] > maxZ) maxZ = spectra[i].data[0][j * 2 + 1];
+            if (i !== 0 && j !== 0) {
+                noise += Math.abs(z[i][j] - z[i][j - 1]) + Math.abs(z[i][j] - z[i - 1][j]);
+            }
+        }
+    }
+    return {
+        z: z,
+        minX: spectra[0].data[0][0],
+        maxX: spectra[0].data[0][spectra[0].data[0].length - 2],
+        minY: spectra[0].pageValue,
+        maxY: spectra[ySize - 1].pageValue,
+        minZ: minZ,
+        maxZ: maxZ,
+        noise: noise / ((ySize - 1) * (xSize - 1) * 2)
+    };
+
+}
+
+function add2D(result) {
+    var zData = convertTo3DZ(result.spectra);
+    result.contourLines = generateContourLines(zData);
+    delete zData.z;
+    result.minMax = zData;
+}
+
+
+function generateContourLines(zData, options) {
+    //console.time('generateContourLines');
+    var noise = zData.noise;
+    var z = zData.z;
+    var contourLevels = [];
+    var nbLevels = 7;
+    var povarHeight = new Float32Array(4);
+    var isOver = [];
+    var nbSubSpectra = z.length;
+    var nbPovars = z[0].length;
+    var pAx, pAy, pBx, pBy;
+
+    var x0 = zData.minX;
+    var xN = zData.maxX;
+    var dx = (xN - x0) / (nbPovars - 1);
+    var y0 = zData.minY;
+    var yN = zData.maxY;
+    var dy = (yN - y0) / (nbSubSpectra - 1);
+    var minZ = zData.minZ;
+    var maxZ = zData.maxZ;
+
+    //System.out.prvarln('y0 '+y0+' yN '+yN);
+    // -------------------------
+    // Povars attribution
+    //
+    // 0----1
+    // |  / |
+    // | /  |
+    // 2----3
+    //
+    // ---------------------d------
+
+    var lineZValue;
+    for (var level = 0; level < nbLevels * 2; level++) { // multiply by 2 for positif and negatif
+        var contourLevel = {};
+        contourLevels.push(contourLevel);
+        var side = level % 2;
+        if (side === 0) {
+            lineZValue = (maxZ - 5 * noise) * Math.exp(level / 2 - nbLevels) + 5 * noise;
+        } else {
+            lineZValue = -(maxZ - 5 * noise) * Math.exp(level / 2 - nbLevels) - 5 * noise;
+        }
+        var lines = [];
+        contourLevel.zValue = lineZValue;
+        contourLevel.lines = lines;
+
+        if (lineZValue <= minZ || lineZValue >= maxZ) continue;
+
+        for (var iSubSpectra = 0; iSubSpectra < nbSubSpectra - 1; iSubSpectra++) {
+            for (var povar = 0; povar < nbPovars - 1; povar++) {
+                povarHeight[0] = z[iSubSpectra][povar];
+                povarHeight[1] = z[iSubSpectra][povar + 1];
+                povarHeight[2] = z[(iSubSpectra + 1)][povar];
+                povarHeight[3] = z[(iSubSpectra + 1)][(povar + 1)];
+
+                for (var i = 0; i < 4; i++) {
+                    isOver[i] = (povarHeight[i] > lineZValue);
+                }
+
+                // Example povar0 is over the plane and povar1 and
+                // povar2 are below, we find the varersections and add
+                // the segment
+                if (isOver[0] !== isOver[1] && isOver[0] !== isOver[2]) {
+                    pAx = povar + (lineZValue - povarHeight[0]) / (povarHeight[1] - povarHeight[0]);
+                    pAy = iSubSpectra;
+                    pBx = povar;
+                    pBy = iSubSpectra + (lineZValue - povarHeight[0]) / (povarHeight[2] - povarHeight[0]);
+                    lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                }
+                if (isOver[3] !== isOver[1] && isOver[3] !== isOver[2]) {
+                    pAx = povar + 1;
+                    pAy = iSubSpectra + 1 - (lineZValue - povarHeight[3]) / (povarHeight[1] - povarHeight[3]);
+                    pBx = povar + 1 - (lineZValue - povarHeight[3]) / (povarHeight[2] - povarHeight[3]);
+                    pBy = iSubSpectra + 1;
+                    lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                }
+                // test around the diagonal
+                if (isOver[1] !== isOver[2]) {
+                    pAx = povar + 1 - (lineZValue - povarHeight[1]) / (povarHeight[2] - povarHeight[1]);
+                    pAy = iSubSpectra + (lineZValue - povarHeight[1]) / (povarHeight[2] - povarHeight[1]);
+                    if (isOver[1] !== isOver[0]) {
+                        pBx = povar + 1 - (lineZValue - povarHeight[1]) / (povarHeight[0] - povarHeight[1]);
+                        pBy = iSubSpectra;
+                        lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                    }
+                    if (isOver[2] !== isOver[0]) {
+                        pBx = povar;
+                        pBy = iSubSpectra + 1 - (lineZValue - povarHeight[2]) / (povarHeight[0] - povarHeight[2]);
+                        lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                    }
+                    if (isOver[1] !== isOver[3]) {
+                        pBx = povar + 1;
+                        pBy = iSubSpectra + (lineZValue - povarHeight[1]) / (povarHeight[3] - povarHeight[1]);
+                        lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                    }
+                    if (isOver[2] !== isOver[3]) {
+                        pBx = povar + (lineZValue - povarHeight[2]) / (povarHeight[3] - povarHeight[2]);
+                        pBy = iSubSpectra + 1;
+                        lines.push(pAx * dx + x0, pAy * dy + y0, pBx * dx + x0, pBy * dy + y0);
+                    }
+                }
+            }
+        }
+    }
+    // console.timeEnd('generateContourLines');
+    return {
+        minX: zData.minX,
+        maxX: zData.maxX,
+        minY: zData.minY,
+        maxY: zData.maxY,
+        segments: contourLevels
+    };
+    //return contourLevels;
+}
+
+
 module.exports =  {
@@ -283,0 +538,0 @@ convertZip: readZIP,

New alerts

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

New author

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A new npm collaborator published a version of the package for the first time. New collaborators are usually benign additions to a project, but do indicate a change to the security surface area of a package.

Found 1 instance in 1 package

Fixed alerts

No v1

Quality

Package is not semver >=1. This means it is not stable and does not support ^ ranges.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

21271

increased by80.35%

Lines of code

475

increased by90%

Number of low quality alerts

1

decreased by-50%

Worsened metrics

Number of medium supply chain risk alerts

2

increased byInfinity%

Dependency changes

• Updatedjcampconverter@^2.3.0