brukerconverter - npm Package Compare versions

Comparing version 1.0.0 to 1.0.1

bower.json

 {
   "name": "brukerconverter",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "main": "build/brukerconverter.js",
@@ -5,0 +5,0 @@ "homepage": "https://github.com/cheminfo-js/brukerconverter",

package.json

 {
   "name": "brukerconverter",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "description": "Parse and convert Bruker raw data",
@@ -25,4 +25,4 @@ "main": "./src/brukerconverter.js",
   "devDependencies": {
-    "mocha-better-spec-reporter": "^3.0.1",
-    "mocha": "^2.4.5",
+    "mocha-better-spec-reporter": "3.0.1",
+    "mocha": "2.4.5",
     "should": "^8.2.2",
@@ -29,0 +29,0 @@ "cheminfo-tools": "1.3.4"

src/brukerconverter.js

@@ -50,3 +50,5 @@ "use strict";
         var brukerFiles = {};
-
+        if(name.indexOf("pdata")>=0){
+            brukerFiles['acqus'] = zip.file(name.replace(/pdata\/[0-9]\//,"acqus")).asText();
+        }
         for(var j = 0; j < currFiles.length; ++j) {
@@ -117,5 +119,14 @@ var idx = currFiles[j].name.lastIndexOf('/');
 function convert1D(files, options) {
+    var result = parseData(files["procs"], options);
+    var temp = parseData(files['acqus'], options);
+
+    var keys = Object.keys(temp.info);
+    for (var i = 0; i < keys.length; i++) {
+        var currKey = keys[i];
+        if(result.info[currKey] === undefined) {
+            result.info[currKey] = temp.info[currKey];
+        }
+    }
+
     if(files['1r'] || files['1i']) {
-        var result = parseData(files["procs"], options);
-
         if(files['1r']) {
@@ -128,3 +139,12 @@ setXYSpectrumData(files['1r'], result, '1r', true);
     } else if(files['fid']) {
-        result = parseData(files['procs'], options);
+        setFIDSpectrumData(files['fid'], result)
+    }
+    
+    return result;
+}
+
+function convert2D(files, options) {
+    var SF,SW_p,SW,offset;
+    if(files['2rr']) {
+        var result = parseData(files['procs'], options);
         var temp = parseData(files['acqus'], options);
@@ -139,12 +159,4 @@
         }
-        setFIDSpectrumData(files['fid'], result)
-    }
-    return result;
-}
-
-function convert2D(files, options) {
-    var SF,SW_p,offset;
-    if(files['2rr']) {
-        var result = parseData(files['procs'], options);
-        var temp = parseData(files['proc2s'], options);
+        
+        temp = parseData(files['proc2s'], options);
         result.info.nbSubSpectra = temp.info['$SI'] = parseInt(temp.info['$SI']);
@@ -160,7 +172,11 @@ SF = temp.info['$SF'] = parseFloat(temp.info['$SF']);
         result.info['$SI'] = parseInt(result.info['$TD']);
-        SW_p = temp.info['$SWH'] = parseFloat(temp.info['$SWH']);
+        //SW_p = temp.info['$SWH'] = parseFloat(temp.info['$SWH']);
+
+        SW_p = temp.info["$SW"];
+
         result.info["$SWP"]=result.info["$SWH"];
         result.info["$SF"]=parseFloat(temp.info['$SFO1']);
         result.info['$OFFSET']=0;
-        SF = temp.info['$SFO2'] = parseFloat(temp.info['$SFO2']);
+        SF = temp.info['$SFO1'] = parseFloat(temp.info['$SFO1']);
+        SF = 1;
         offset=0;
@@ -183,3 +199,3 @@ result.info['$AXNUC']=result.info['$NUC1'];
     } else if(files['ser']) {
-        setXYSpectrumData(files['ser'], result, 'ser', true);
+        setFIDSpectrumData(files['ser'], result, 'ser', true);
     }
@@ -190,7 +206,2 @@
         result.spectra[i].pageValue=pageValue;
-        if(files['2rr']) {
-            result.spectra[i].setYUnits = 'PPM';
-        } else if(files['ser']) {
-            result.spectra[i].setYUnits = 'HZ';
-        }
     }
@@ -304,4 +315,2 @@
     //console.log(DW+" "+SW+" "+td);
-
-
     var endian = parseInt(spectra.info["$BYTORDP"]);
@@ -315,3 +324,6 @@ endian = endian ? 0 : 1;
 
-    for(var i = 0; i < 2; ++i) {
+    var nbSubSpectra = spectra.info.nbSubSpectra ? spectra.info.nbSubSpectra : 1;
+    spectra.spectra = new Array(nbSubSpectra);
+    
+    for(var j = 0; j < nbSubSpectra/2; j++) {
         var toSave = {
@@ -324,3 +336,3 @@ dataType : "NMR FID",
             nucleus : spectra.info["$NUC1"] ? spectra.info["$NUC1"] : undefined,
-            xUnit : "Hz",
+            xUnit : "Sec",
             yUnit : "Arbitrary",
@@ -333,33 +345,46 @@ data:[new Array(2*td)],//[{x:new Array(td),y:new Array(td)}],
         };
-        spectra.spectra.push(toSave);
-    }
+        spectra.spectra[j*2] = toSave;
 
-    var x = 0;
+        toSave = {
+            dataType : "NMR FID",
+            dataTable : "(X++(I..I))",
+            nbPoints : td,
+            firstX : 0,
+            lastX : AQ,
+            nucleus : spectra.info["$NUC1"] ? spectra.info["$NUC1"] : undefined,
+            xUnit : "Sec",
+            yUnit : "Arbitrary",
+            data:[new Array(2*td)],//[{x:new Array(td),y:new Array(td)}],
+            isXYdata:true,
+            observeFrequency:SF,
+            title:spectra.info['TITLE'],
+            deltaX:DW
+        };
+        spectra.spectra[j*2+1] = toSave;
+        
+        var x = 0;
+        var y;
+        for(var i = 0; file.available(8)&&i<td; i++, x = i*DW) {
+            y = file.readInt32();
+            if(y===null || isNaN(y)){
+                y=0;
+            }
+            spectra.spectra[j*2].data[0][2*i+1] = y;
+            spectra.spectra[j*2].data[0][2*i] = x;
+            y = file.readInt32();
+            if(y===null || isNaN(y)){
+                y=0;
+            }
+            spectra.spectra[j*2+1].data[0][2*i+1] = y;
+            spectra.spectra[j*2+1].data[0][2*i] = x;
 
-    var y;
-    for(i = 0; file.available(8); ++i, x += DW) {
-        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;
+
+        for(; i < td; i++, x = i*DW) {
+            spectra.spectra[j*2].data[0][2*i+1] = 0;
+            spectra.spectra[j*2].data[0][2*i] = x;
+            spectra.spectra[j*2+1].data[0][2*i+1] = 0;
+            spectra.spectra[j*2+1].data[0][2*i] = x;
         }
-        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][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;
-    }
 }
@@ -366,0 +391,0 @@

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Found 1 instance in 1 package

Fixed alerts

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Major refactor

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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.

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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.

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Improved metrics

Total package byte prevSize

22313

increased by4.9%

Lines of code

497

increased by4.63%

Number of medium supply chain risk alerts

0

decreased by-100%

No dependency changes