Merge pull request #76 from Jollyfant/dev

Dev

changelog/index.html

@@ -76,6 +76,36 @@ <h5> Paleomagnetism.org 2 - Changelog </h5>
           <p> The following page records changes that were made and fixes that were applied to the application. 
         </div>
 
+        <div id="accordion">
+
+          <div class="card">
+            <div class="card-header" id="headingFive">
+              <button class="btn btn-link" data-toggle="collapse" data-target="#collapseFive" aria-expanded="true" aria-controls="collapseFive">
+                Paleomagnetism.org 2.2.0 - Parsing is Difficult! <small class="text-muted">&nbsp; 2020-11-20</small>
+              </button>
+            </div>
+            <div id="collapseFive" class="collapse show" aria-labelledby="headingFive" data-parent="#accordion">
+              <div class="card-body">
+              <b> Change Summary </b>
+				<p> Some bugs were fixed reading various input formats.
+              <ul>
+                <p> <b> Features </b>
+                <li> Added input format for the Geophysical Survey of Finland (GTK).
+                <li> Added Cenieh regular importing.
+              </ul>
+
+              <ul>
+                <p> <b> Fixes </b>
+                <li> Fixed graph scaling for very small intensities.
+                <li> Fixed bug reading BGN2G input format (PGL Beijing, University of Barcelona) where some lines were dropped.
+              </ul>
+
+              </div>
+            </div>
+          </div>
+
+          <p>
+
         <div id="accordion">
 
           <div class="card">

interpretation/index.html

@@ -108,8 +108,10 @@ <h5> Paleomagnetism.org 2 - Interpretation </h5>
                         <option value="BLACKMNT">Black Mountain Lab (.xPCA)</option>
                         <option value="UNKNOWN">Black Mountain Lab (.dms)</option>
                         <option value="CALTECH">Caltech Institute of Technology</option>
-                        <option value="CENIEH">Cenieh</option>
+                        <option value="CENIEH">Cenieh Core</option>
+                        <option value="CENIEHREG">Cenieh Regular</option>
                         <option value="BCN2G">PGL Beijing</option>
+                        <option value="GTK">Geological Survey of Finland</option>
                         <!-- Uses BCN2G -->
                         <option value="NGU">Geological Survey of Norway</option>
                         <option value="BCN2G">University of Barcelona</option>

interpretation/js/importing.js

@@ -1,3 +1,67 @@
+function importGTK(file) {
+
+  function capitalize(string) {
+    return string.charAt(0).toUpperCase() + string.slice(1)
+  }
+
+  var lines = file.data.split(/\r?\n/);
+
+  let name = lines[1].split(":")[1].trim();
+  let lithology = capitalize(lines[2].split(":")[1].trim().toLowerCase());
+
+  let metadata = lines[7].split(/\s+/);
+  let latitude = Number(metadata[1]);
+  let longitude = Number(metadata[2]);
+  let coreAzimuth = Number(metadata[3]);
+  let coreDip = 90 - Number(metadata[4]);
+  let beddingStrike = Number(metadata[5]);
+  let beddingDip = Number(metadata[6]);
+  let volume = Number(metadata[7]);
+  let mass = Number(metadata[8]);
+
+  let demagnetizationType = lines[8].slice(0, 2) === "AF" ? "alternating" : "thermal";
+
+  let steps = new Array();
+
+  // Parse data lines
+  for(var i = 9; i < lines.length - 1; i++) {
+    let line = lines[i];
+    let step = line.slice(0, 4);
+    let dec = Number(line.slice(7, 12));
+    let inc = Number(line.slice(13, 19));
+    // Intensity in mA/m (Satu, pers. comm. 2020)
+    let intensity = 1E3 * Number(line.slice(24, 30));
+    let coordinates = new Direction(dec, inc, intensity).toCartesian();
+    steps.push(new Measurement(step, coordinates, null))
+  }
+
+  // Add the data to the application
+  specimens.push({
+    "demagnetizationType": demagnetizationType,
+    "coordinates": "specimen",
+    "format": "GTK",
+    "version": __VERSION__,
+    "created": new Date().toISOString(),
+    "steps": steps,
+    "level": null,
+    "longitude": longitude,
+    "latitude": latitude,
+    "age": null,
+    "ageMin": null,
+    "ageMax": null,
+    "lithology": lithology,
+    "sample": name,
+    "name": name,
+    "volume": volume,
+    "beddingStrike": beddingStrike,
+    "beddingDip": beddingDip,
+    "coreAzimuth": coreAzimuth,
+    "coreDip": coreDip, 
+    "interpretations": new Array()
+  });
+
+}
+
 function importMontpellier(file) {
 
   var object = new Object();
@@ -312,7 +376,11 @@ function importMagic(file) {
             //throw(new Exception("Specimen " + object.specimen + " is defined multiple times."));
           }
 
-          var methods = object["method_codes"].split(":");
+          try {
+            var methods = object["method_codes"].split(":");
+          } catch(e) {
+            var methods = [];
+          }
 
           // Create a new specimen
           magicSpecimens[object.specimen] = {
@@ -324,7 +392,7 @@ function importMagic(file) {
             "minStep": Number(object["meas_step_min"]),
             "maxStep": Number(object["meas_step_max"]),
             "anchored": methods.includes("DE-BFL-A"),
-            "type": ((methods.includes("DE-BFP") || methods.includes("DE-BFP-G")) ? "TAU3" : "TAU1"),
+            //"type": ((methods.includes("DE-BFP") || methods.includes("DE-BFP-G")) ? "TAU3" : "TAU1"),
             "unit": object["meas_step_unit"],
             //
             "created": new Date().toISOString(),
@@ -1286,12 +1354,113 @@ function importCenieh(file) {
   });
 
   // Add all specimens in the hashmap to the application
-  ceniehSpecimens.forEach(function(specimen) {
-    specimens.push(specimen);
+  Object.keys(ceniehSpecimens).forEach(function(specimen) {
+    specimens.push(ceniehSpecimens[specimen]);
+  });
+
+}
+
+function importCeniehRegular(file) {
+
+  var lines = file.data.split(LINE_REGEXP).filter(Boolean);
+
+  var parsedData = new Array();
+  var rotatedVectors = new Array();
+  var rotatedTectonicVectors = new Array();
+  let demagnetizationType = lines[0].split("\t")[1].includes("AF") ? "alternating" : "thermal";
+
+  for(var i = 1; i < lines.length; i++) {
+
+    var parameters = lines[i].split(/[\t\s]+/);
+    var sampleName = parameters[0];
+    var step = parameters[1];
+    var intensity = Number(parameters[2]);
+    var dec = Number(parameters[3]);
+    var inc = Number(parameters[4]);
+    rotatedVectors.push({"dec": Number(parameters[5]), "inc": Number(parameters[6])});
+    rotatedTectonicVectors.push({"dec": Number(parameters[22]), "inc": Number(parameters[23])});
+
+    // Given intensity is in emu/cc (1E3 A/m)
+    var cartesianCoordinates = new Direction(dec, inc, intensity / 1E-9).toCartesian();
+
+    parsedData.push(new Measurement(step, cartesianCoordinates, null));
+
+  }
+
+  var beddingString = prompt("Sample " + sampleName + " - please enter: core azimuth,core dip,bedding strike,bedding dip (e.g. 121,24,0,0)");
+
+  var coreAzimuth = Number(beddingString.split(",")[0]);
+  var coreDip = Number(beddingString.split(",")[1]);
+  var beddingStrike = Number(beddingString.split(",")[2]);
+  var beddingDip = Number(beddingString.split(",")[3]);
+
+  if(beddingString.split(",").length !== 4) {
+    throw("Not enough parameters!");
+  }
+
+  // The input format has the rotated vectors
+  // We check if the user input core azi & dip match what is expected
+  var b = parsedData.map(function(x) {
+    return new Coordinates(x.x, x.y, x.z);
+  }).map(function(direction) {
+    return direction.rotateTo(coreAzimuth, coreDip).toVector(Direction);
+  });
+
+  // Check and raise if discrepancy: defer with settimeout to prevent being overwritten
+  for(var i = 0; i < rotatedVectors.length; i++) {
+    if(Math.round(b[i].dec) !== Math.round(rotatedVectors[i].dec) || Math.round(b[i].inc) !== Math.round(rotatedVectors[i].inc)) {
+      setTimeout(function() {
+        let error = "Found: <b>" + Math.round(b[i].dec) + ", " + Math.round(b[i].inc) + "</b> while expecting: <b>" + Math.round(rotatedVectors[i].dec) + ", " + Math.round(rotatedVectors[i].inc) + "</b>!";
+        notify("warning", "Core parameters inconsistent for Cenieh Regular import. Continue on own risk! <br> Details: " + error);
+      });
+      break;
+    }
+  }
+
+  // Make sure to check tectonic as well
+  var c = parsedData.map(function(x) {
+    return new Coordinates(x.x, x.y, x.z);
+  }).map(function(direction) {
+    return direction.rotateTo(coreAzimuth, coreDip).correctBedding(beddingStrike, beddingDip).toVector(Direction);
+  });
+
+  // Check and raise if discrepancy: defer with settimeout to prevent being overwritten
+  for(var i = 0; i < rotatedTectonicVectors.length; i++) {
+    if(Math.round(c[i].dec) !== Math.round(rotatedTectonicVectors[i].dec) || Math.round(c[i].inc) !== Math.round(rotatedTectonicVectors[i].inc)) {
+      setTimeout(function() {
+        let error = "Found: <b>" + Math.round(c[i].dec) + ", " + Math.round(c[i].inc) + "</b> while expecting: <b>" + Math.round(rotatedTectonicVectors[i].dec) + ", " + Math.round(rotatedTectonicVectors[i].inc) + "</b>!";
+        notify("warning", "Bedding parameters inconsistent for Cenieh Regular import. Continue on own risk! <br> Details: " + error);
+      });
+      break;
+    }
+  }
+
+  specimens.push({
+    "demagnetizationType": demagnetizationType,
+    "coordinates": "specimen",
+    "format": "CENIEHREG",
+    "version": __VERSION__,
+    "created": new Date().toISOString(),
+    "steps": parsedData,
+    "name": sampleName,
+    "volume": 10.0, // 10cc @ Mark Sier,
+    "longitude": null,
+    "latitude": null,
+    "age": null,
+    "ageMin": null,
+    "ageMax": null,
+    "lithology": null,
+    "sample": sampleName,
+    "beddingStrike": Number(beddingStrike),
+    "beddingDip": Number(beddingDip),
+    "coreAzimuth": Number(coreAzimuth),
+    "coreDip": Number(coreDip),
+    "interpretations": new Array()
   });
 
 }
 
+
 function importMunich(file) {
 
   /*
@@ -1416,9 +1585,9 @@ function importBCN2G(file) {
 
     // Each parameter is delimited by at least one NULL byte
     var parameters = line.split(/\u0000+/);
- 
+
     // Something wrong with a broken line? See #72
-    if(parameters.length !== 30) {
+    if(parameters.length < 25) {
       return null;
     }
 

interpretation/js/index.js

@@ -86,6 +86,8 @@ function addDegmagnetizationFiles(format, files) {
       return files.forEach(importApplicationSaveOld);
     case "HELSINKI":
       return files.forEach(importHelsinki);
+    case "GTK":
+      return files.forEach(importGTK);
     case "CALTECH":
       return files.forEach(importCaltech);
     case "BCN2G":
@@ -102,6 +104,8 @@ function addDegmagnetizationFiles(format, files) {
       return files.forEach(importBCN2G);
     case "CENIEH":
       return files.forEach(importCenieh);
+    case "CENIEHREG":
+      return files.forEach(importCeniehRegular);
     case "MAGIC":
       return files.forEach(importMagic);
     case "JR5":

js/utils.js

@@ -1,5 +1,5 @@
 let __DEBUG__ = false;
-let __VERSION__ = "2.1.0";
+let __VERSION__ = "2.2.0";
 const __DOI__ = "10.5281/zenodo.4001578"
 const RADIANS = Math.PI / 180;
 const PROJECTION_TYPE = "AREA";

team/index.html

@@ -73,7 +73,7 @@
 
         <div class="alert alert-light" role="alert">
           <h5> Paleomagnetism.org 2 - Team & Contact </h5>
-          <p> The following group of people were involved in the development of Paleomagnetism.org. Other contributors can be found under the reference page. Your suggestions, questions, and comments are welcome and the team can be contacted through <a href="mailto:paleomagnetism.org@gmail.com">email</a>.
+          <p> The following group of people were involved in the development of Paleomagnetism.org. Other contributors can be found under the reference page. Your suggestions, questions, and comments are welcome and the team can be contacted through <a href="mailto:paleomagnetism.org@gmail.com">email</a> (paleomagnetism.org@gmail.com).
         </div>