add bacteria report

create_report.html

@@ -226,6 +226,7 @@
             write_sample_description(sample);
             get_result_main(sample_chooser.value);
             get_result_nema(sample_chooser.value);
+            get_result_bact(sample_chooser.value);
           }
       }
 
@@ -251,6 +252,7 @@
       write_sample_description(sample);
       get_result_main(this.value);
       get_result_nema(this.value);
+      get_result_bact(this.value);
 
     };
 
@@ -390,7 +392,7 @@
               Math.pow((item.width*Number(microscope_setup.FoV_Width)),2.0)*Math.PI/4.0;
             break
           case "Actinobacteria":
-            total.Actinobacteria += item.length*Number(microscope_setup.FoV_Width);
+            total.Actinobacteria += item.length*Number(microscope_setup.FoV_Width)*Math.PI/4.0;
             break
           case "Flagelate":
             total.Flagelate +=1;
@@ -571,5 +573,189 @@
       newRow.insertCell(2).innerHTML = count * multiplication_factor_nema_scan;
     }
 
+// bacteria
+function get_result_bact(sampleID){
+  const transaction = db.transaction('bacterial_scan');
+  const objStore = transaction.objectStore('bacterial_scan')
+  const index = objStore.index("sampleID");
+  const get_request = index.get(sampleID);
+  get_request.onsuccess = () => {
+    bact_scan_result = get_request.result;
+
+    get_prep_protocol_bact(get_request.result);
+    get_microscope_setup_bact(get_request.result);
+  }
+
+  get_request.onerror = (err)=> {
+      console.error(`Error to get all setups: ${err}`)
+  }
+}
+function get_prep_protocol_bact(result_obj){
+  const request = db.transaction('prep_protocol')
+                        .objectStore('prep_protocol')
+                        .get(Number(result_obj.prepID));
+
+  request.onsuccess = () => {
+    prep_protocol_bact = request.result;
+    if (microscope_setup_bact && prep_protocol_bact && bact_scan_result){
+      write_bact_scan_description(bact_scan_result, prep_protocol_bact, microscope_setup_bact);
+      render_bact_scan_table(bact_scan_result);
+
+    }
+
+  }
+
+  request.onerror = (err)=> {
+      console.error(`Error to get all setups: ${err}`)
+  }
+}
+
+function get_microscope_setup_bact(result_obj){
+  const request = db.transaction('microscope_setup')
+                        .objectStore('microscope_setup')
+                        .get(Number(result_obj.setupID));
+
+  request.onsuccess = () => {
+    microscope_setup_bact = request.result;
+    if (microscope_setup_bact && prep_protocol_bact && bact_scan_result){
+      write_bact_scan_description(bact_scan_result, prep_protocol_bact, microscope_setup_bact);
+      render_bact_scan_table(bact_scan_result.result);
+    }
+
+  }
+
+  request.onerror = (err)=> {
+      console.error(`Error to get all setups: ${err}`)
+  }
+}
+function write_bact_scan_description(result, protocol, setup){
+  console.log('hi from writer')
+  // observed height in um -> sample size [uL] * 10^9 / coverslip Area [mm²] * 10^6
+  //                       -> yields  1000 * samplesize[uL] / coverslipArea[mm²]
+        let observed_height_bact = 1000 * Number(protocol.Sample_Size)  /
+            (Number(setup.Slip_Height) * Number(setup.Slip_Width));
+  // observed Volume in uL -> height [um] * FoV [um²] = um³ -- 1 um³ = 1* 10^-9 uL
+        let observed_volume_bact = observed_height_bact *
+            Number(setup.FoV_Width)*Number(setup.FoV_Height)*Math.pow(10, -9);
+
+        multiplication_factor_bact_scan = result.dilution / observed_volume_bact;
+
+        document.querySelector("#bact_scan_datetime").textContent = result.datetime;
+        document.querySelector("#prep_protocol_name_bact").textContent = protocol.name;
+        document.querySelector("#cam_setup_name_bact").textContent = setup.name;
+        document.querySelector("#coverslip_height_bact").textContent = setup.Slip_Height;
+        document.querySelector("#coverslip_width_bact").textContent = setup.Slip_Width;
+        document.querySelector("#sample_volume_bact").textContent = prep_protocol.Sample_Size;
+        document.querySelector("#observed_height_bact").textContent = observed_height_bact.toFixed(2);
+        document.querySelector("#FoV_height_bact").textContent = microscope_setup.FoV_Height;
+        document.querySelector("#FoV_width_bact").textContent = microscope_setup.FoV_Width;
+
+        document.querySelector("#observed_volume_bact").textContent = observed_volume_bact.toExponential(2);
+        document.querySelector("#dilution_factor_bact").textContent = result.dilution;
+
+        document.querySelector("#factor_bact").textContent = multiplication_factor_bact_scan;
+
+
+
+}
+var bact_table = document.querySelector("#bact_scan_table");
+
+function render_bact_scan_table(result){
+  let counts = [];
+  if (result[0][0].length == 0){
+    for (let i=0; i<result.length; i++){
+      let res = result[i][1].slice(0, -1).map(Number);;
+      counts.push(res);
+    }
+  } else {
+    for (let i=0; i<result.length; i++){
+      counts.push(update_bact_count(result[i][0]));
+    }
+  }
+  console.log(counts);
+  means = [];
+  sds = [];
+  for (let i=0; i<counts[0].length; i++){
+    let sum = 0;
+    for (let j=0; j<counts.length; j++){
+      sum += counts[j][i];
+    }
+    means.push(sum/counts.length);
+  }
+  for (let i=0; i<counts[0].length; i++){
+    let sd = 0;
+    for (let j=0; j<counts.length; j++){
+      sd += Math.pow(means[i] - counts[j][i],2);
+    }
+    sd = Math.sqrt(sd/counts.length);
+    sds.push(sd);
+  }
+  console.log(means);
+  console.log(sds);
+
+  keys = [
+    'Bacilli','','Cocci','','Pathogenic',''
+  ]
+  for (let i=0; i<means.length; i+=2){
+    render_bact_scan_table_row(keys[i], [means[i],means[i+1]], [sds[i],sds[i+1]]);
+  }
+  document.querySelector("#bacterial_biomass").textContent = (means[1] + means[3] +
+    means[5]).toFixed(2) + " +- " + (sds[1] + sds[3] + sds[5]).toFixed(2);
+  document.querySelector("#fungal_biomass").textContent = Number(result_table.children[1].
+    children[0].children[1].innerHTML) + " +/- " + (Number(result_table.children[1].
+      children[0].children[2].innerHTML)*Number(result_table.children[1].
+        children[0].children[1].innerHTML)).toFixed(2);
+
+  document.querySelector("#f_to_b_biomass").textContent =
+  Number(result_table.children[1].children[0].children[1].innerHTML).toFixed(2) /
+  (means[1] + means[3] + means[5]).toFixed(2);
+
+}
+
+function render_bact_scan_table_row(key, mean, sd){
+  console.log(mean)
+  let newRow = bact_table.children[1].insertRow();
+  newRow.insertCell(0).innerHTML = key;
+  newRow.insertCell(1).innerHTML = mean[0] + " +/- " + sd[0];
+  newRow.insertCell(2).innerHTML = mean[1].toFixed(2) + " +/- " + sd[1].toFixed(2);
+  newRow.insertCell(3).innerHTML = (mean[0] * multiplication_factor_bact_scan).toFixed(2)
+            + " +/- " + (100*(sd[0]/mean[0])).toFixed(2);
+  newRow.insertCell(4).innerHTML = (mean[1] * multiplication_factor_bact_scan*Math.pow(10,-6)).toExponential(2)
+            + " +/- " + (100*(sd[1]/mean[1])).toFixed(2);
+
+
+
+}
+
+function update_bact_count(bacteria){
+  let bc = 0;
+  let cc = 0;
+  let pc = 0;
+  let abc = 0;
+  let acc = 0;
+  let apc = 0;
+  bacteria.forEach(function (item, index) {
+    switch(item[1]){
+      case "Bacteria":
+        bc += 1
+        abc += item[2];
+        break;
+      case "Cocci":
+        cc += 1
+        acc += item[2];
+        break;
+      case "Vibrio":
+      case "Spirilla":
+      case "Spirochetes":
+        pc += 1
+        apc += item[2];
+        break;
+    }
+
+  });
+return [bc, abc, cc, acc, pc, apc];
+
+}
+
   </script>
 </html>