---
title: LJP Theory and Correction
description: What causes Liquid Junction Potential (LJP) and how to correct for it in patch-clamp experiments
date: 2021-01-13
tags: science
---

# Liquid Junction Potential (LJP) Theory and Correction

This page contains notes about the analytical methods [LJPcalc](https://swharden.com/LJPcalc/) uses to calculate LJP from ion tables
 as well as notes for experimenters about what causes LJP and how to compensate for it in electrophysiology experiments.

> 💡 **Use [LJPcalc](https://swharden.com/LJPcalc/) to calculate Liquid Junction Potential (LJP) in your browser**

## Table of Contents

![](TOC)

## LJP Calculation Notes

### LJPcalc Calculation Method

LJPcalc calculates the liquid junction potential according to the stationary Nernst-Planck equation which is typically regarded as superior to the simpler Henderson equation used by most commercial LJP calculators. Both equations produce nearly identical LJPs, but the Henderson equation becomes inaccurate as ion concentrations increase, and also when calculating LJP for solutions containing polyvalent ions.

### LJPcalc Ion Mobility Library

LJPcalc uses an extensive [ion mobility library](../iontable)

The ion mobility table is stored in Markdown format. Not only does Markdown make it easy to display the table nicely in a browser, 
but it also makes the table easy to edit in any text editor. Users desiring to use their own ion mobilities or add new ions to the table
can do so by editing the `IonTable.md` file adjacent to `LJPcalc.exe` as needed.

### Influence of Ion Sequence on Calculated LJP

> 💡 LJPcalc automatically sorts the ion table into an ideal sequence prior to solving for LJP. Attention only needs to be paid to the ion sequence if automatic sorting is disabled.

When calculating LJP for a set of ions it is important to consider the sequence in which they are listed. Additional information can be found in [Marino et al., 2014](https://arxiv.org/abs/1403.3640) which describes the exact computational methods employed by LJPcalc.

* **The last ion's c0 may be overridden** to achieve electroneutrality on the c0 side. This will not occur if the sum of charge on the c0 side is zero.

* **cL for most ions will be slightly adjusted** to achieve electroneutrality on the cL side. The second-to-last ion's cL (which cannot equal its c0) will remain fixed, while the last cL will be adjusted to achieve electroneutrality. During the solving process all cL values (but the second-from-last) will be slightly adjusted. The adjustments are likely negligible experimentally, but this is why cL values in the output table slightly differ from those given for inputs.

### Effect of Temperature on LJP

**The LJP is temperature dependent.** There are two sources of temperature-dependent variation: the Einstein relation and the conductivity table. The former can be easily defined at calculation time, while the latter requires modifying conductances in the ion mobility table. These modifications typically have a small effect on the LJP, so standard temperature (25C) can be assumed for most applications.

**The [Einstein relation](https://en.wikipedia.org/wiki/Einstein_relation_(kinetic_theory))** defines diffusion as **`D = µ * k * T`** where:

* **`D`** is the diffusion coefficient
* **`µ`** (mu) is [ionic mobility](https://en.wikipedia.org/wiki/Electrical_mobility)
* **`k`** is the [Boltzmann constant](https://en.wikipedia.org/wiki/Boltzmann_constant) (1.380649e-23 J / K)
* **`T`** is temperature (K)

**The ion conductivity table is temperature-specific.** Ion conductivity was measured experimentally and varies with temperature. The ion conductivity table here assumes standard temperature (25C), but ion conductivity values can be found for many ions at nonstandard temperatures. LJPcalc users desiring to perform LJP calculations at nonstandard temperatures are encouraged to build their own temperature-specific ion tables.

### Calculating Ionic Mobility from Charge and Conductivity

Ionic mobility is **`µ = Λ / (N * e² * |z|)`** where:

* **`µ`** (mu) is [ionic mobility](https://en.wikipedia.org/wiki/Electrical_mobility) (m² / V / sec)
* **`Λ`** (Lambda) is [molar conductivity](https://en.wikipedia.org/wiki/Molar_conductivity) (S * cm²/ mol)
* **`N`** is the [Avogadro constant](https://en.wikipedia.org/wiki/Avogadro_constant) (6.02214076e23 particles / mol)
* **`e`** is the [elementary charge](https://en.wikipedia.org/wiki/Elementary_charge) (1.602176634e-19 Coulombs)
* **`z`** is the absolute value of the [elementary charge](https://en.wikipedia.org/wiki/Elementary_charge) of the ion

## How to Correct for LJP in Electrophysiology Experiments

Patch-clamp electrophysiologists impale cells with glass microelectrodes to measure or clamp their voltage.
Amplifier offset voltage is adjusted to achieve a reading of zero volts when the pipette is in open-tip configuration with the bath,
but this voltage includes offset for a _liquid junction potential_ (LJP) caused by the free exchange of ions with different mobilities between the pipette and bath solutions.
Whole-cell patch-clamp experiments typically fill the pipette with large anions like gluconate, aspartate, or methanesulfonate, and their low mobility 
(relative to ions like K, Na, and Cl) causes them to accumulate in the pipette and produce a LJP (where the bath is more positive than then pipette).
After establishment of whole-cell configuration, ions no longer freely move between pipette and bath solutions (they are separated by the cell membrane), so
there is effectively no LJP but the offset voltage is still offsetting as if LJP were present. By knowing the LJP, the scientist can
adjust offset voltage to compensate for it, resulting in more accurate measured and clamped voltages.

<p align="center">V<sub>meter</sub> = V<sub>cell</sub> + LJP</p>

**To correct for LJP,** the electrophysiologist must calculate LJP mathematically (using software like LJPcalc) or estimate it experimentally (see the section on this topic below). Once the LJP is known it can be compensated for experimentally to improve accuracy of recorded and clamped voltages.

<p align="center">V<sub>cell</sub> = V<sub>meter</sub> - LJP</p>

> ⚠️ This method assumes that the amplifier voltage was zeroed at the start of the experiment when the pipette was in open-tip configuration 
with the bath, and that concentration of chloride (if using Ag/AgCl electrodes) in the internal and bath solutions are stable throughout experiments.

<div align="center">

![](ljp.png)

</div>

### Example Patch-Clamp LJP Calculation & Correction

This ion set came from in [Figl et al., 2003](https://medicalsciences.med.unsw.edu.au/sites/default/files/soms/page/ElectroPhysSW/AxoBits39New.pdf) Page 8. They have been loaded into LJPcalc such that the pipette solution is c0 and the bath solution is cL. Note that the order of ions has been adjusted to place the most abundant two ions at the bottom. This is ideal for LJPcalc's analytical method.


 Name       | Charge | pipette (mM) | bath (mM)      
------------|--------|--------------|---------
 K          | +1     | 145          | 2.8
 Na         | +1     | 13           | 145
 Mg         | +2     | 1            | 2
 Ca         | +2     | 0            | 1
 HEPES      | -1     | 5            | 5
 Gluconate  | -1     | 145          | 0           
 Cl         | -1     | 10           | 148.8


Loading this table into LJPcalc produces the following output:

```
Values for cL were adjusted to achieve electro-neutrality:

 Name               | Charge | Conductivity (E-4) | C0 (mM)      | CL (mM)      
--------------------|--------|--------------------|--------------|--------------
 K                  | +1     | 73.5               | 145          | 2.8098265   
 Na                 | +1     | 50.11              | 13           | 144.9794365 
 Mg                 | +2     | 53.06              | 1            | 1.9998212   
 Ca                 | +2     | 59.5               | 0            | 0.9999109   
 HEPES              | -1     | 22.05              | 5            | 4.9990023   
 Gluconate          | -1     | 24.255             | 145          | 0           
 Cl                 | -1     | 76.31              | 10           | 148.789725

Equations were solved in 88.91 ms
LJP at 20 C (293.15 K) = 16.052319631180264 mV
```

> 💡 _[Figl et al., 2003](https://medicalsciences.med.unsw.edu.au/sites/default/files/soms/page/ElectroPhysSW/AxoBits39New.pdf) Page 8 calculated a LJP of 15.6 mV for this ion set (720 µV lesser magnitude than our calculated LJP). As discussed above, differences in ion mobility table values and use of the Nernst-Planck vs. Henderson equation can cause commercial software to report values slightly different than LJPcalc. Experimentally these small differences are negligible, but values produced by LJPcalc are assumed to be more accurate. See [Marino et al., 2014](https://arxiv.org/abs/1403.3640) for discussion._

If we have patch-clamp data that indicates a neuron rests at -48.13 mV, what is its true resting potential? Now that we know the LJP, we can subtract it from our measurement:

<p align="center">V<sub>cell</sub> = V<sub>measured</sub> - LJP</p>

<p align="center">V<sub>cell</sub> = -48.13 - 16.05 mV</p>

<p align="center">V<sub>cell</sub> = -64.18 mV</p>

We now know our cell rests at -64.18 mV.

### Zeroed Voltage = LJP + Two Electrode Half-Cell Potentials

The patch-clamp amplifier is typically zeroed at the start of every experiment when the patch pipette is in open-tip configuration 
with the bath solution. An offset voltage (V<sub>offset</sub>) is applied such that the V<sub>measured</sub> is zero. 
This process incorporates 3 potentials into the offset voltage:

* **liquid junction potential (LJP)** between the **pipette** solution and the **bath** solution (mostly from small mobile ions)
* **half-cell potential (HCP)** between the **reference electrode** and the **bath** solution (mostly from Cl)
* **half-cell potential (HCP)** between the **recording electrode** and the **pipette** solution (mostly from Cl)

When the amplifier is zeroed before to experiments, all 3 voltages are incorporated into the offset voltage. 
Since the LJP is the only one that changes after forming whole-cell configuration with a patched cell (it is eliminated),
it is the only one that needs to be known and compensated for to achieve a true zero offset (the rest remain constant).

However, if the [Cl] of the internal or bath solutions change during the course of an experiment 
(most likely to occur when an Ag/AgCl pellet is immersed in a flowing bath solution), 
the half-cell potentials become significant and affect V<sub>measured</sub> as they change. 
This is why agar bridge references are preferred over Ag/AgCl pellets.
See [Figl et al., 2003](https://medicalsciences.med.unsw.edu.au/sites/default/files/soms/page/ElectroPhysSW/AxoBits39New.pdf) 
for more information about LJPs as they relate to electrophysiological experiments.

### Measuring LJP Experimentally

It is possible to measure LJP experimentally, but this technique is often discouraged because issues with KCl reference electrodes make it difficult 
to accurately measure ([Barry and Diamond, 1970](https://link.springer.com/article/10.1007/BF01868010)). However, experimental measurement 
may be the only option to calculate LJP for solutions containing ions with unknown mobilities.

**To measure LJP Experimentally:**<br>
&bull; **Step 1:** Zero the amplifier with intracellular solution in the bath and in your pipette<br>
&bull; **Step 2:** Replace the bath with extracellular solution<br>
&bull; **Step 3:** The measured voltage is the negative LJP (invert its sign to get LJP)

> **✔️ Confirm no drift is present** by replacing the bath with intracellular solution after step 3 to verify the reading is 0. 
If it is not 0, some type of drift is occurring and the measured LJP is not accurate.

> **❓ Why invert the sign of the LJP?** The LJP measured in step 2 is the LJP of the _pipette_ relative to 
the _bath_, but in electrophysiology experiments convention is to refer to LJP as that of the _bath_ relative to the _pipette_. 
LJPs for experiments using typical ACSF bath and physiological K-gluconate pipette solutions are usually near +15 mV.

> **⚠️ Do not measure LJP using a Ag/AgCl reference electrode!** because mobility will be low when the bath is filled with intracellular solution (physiological intracellular solutions have low [Cl]). 
Use a 3M KCl reference electrode instead, allowing high [K] mobility in intracellular solution and high [Cl] mobility in extracellular solution.

## References

* **[Marino et al. (2014)](https://arxiv.org/abs/1403.3640)** - describes a computational method to calculate LJP according to the stationary Nernst-Planck equation. The JAVA software described in this manuscript is open-source and now on GitHub ([JLJP](https://github.com/swharden/jljp)). Figure 1 directly compares LJP calculated by the Nernst-Planck vs. Henderson equation.

* **[Perram and Stiles (2006)](https://pubs.rsc.org/en/content/articlelanding/2006/cp/b601668e)** - A review of several methods used to calculate liquid junction potential. This manuscript provides excellent context for the history of LJP calculations and describes the advantages and limitations of each.

* **[Shinagawa (1980)](https://www.ncbi.nlm.nih.gov/pubmed/7401663)** _"Invalidity of the Henderson diffusion equation shown by the exact solution of the Nernst-Planck equations"_ - a manuscript which argues that the Henderson equation is inferior to solved Nernst-Planck-Poisson equations due to how it accounts for ion flux in the charged diffusion zone.

* **[Lin (2011)](http://www.sci.osaka-cu.ac.jp/~ohnita/2010/TCLin.pdf)** _"The Poisson The Poisson-Nernst-Planck (PNP) system for ion transport (PNP) system for ion transport"_ - a PowerPoint presentation which reviews mathematical methods to calculate LJP with notes related to its application in measuring voltage across cell membranes.

* **[Nernst-Planck equation](https://en.wikipedia.org/wiki/Nernst%E2%80%93Planck_equation)** (Wikipedia)

* **[Goldman Equation](https://en.wikipedia.org/wiki/Goldman_equation)** (Wikipedia)

* **[EGTA charge and pH](https://www.sciencedirect.com/science/article/pii/S0165027099000369?via%3Dihub#FIG1)** - Empirical determination of EGTA charge state distribution as a function of pH.

* **[LJPCalcWin](https://medicalsciences.med.unsw.edu.au/sites/default/files/soms/page/ElectroPhysSW/JPCalcWin-Demo%20Manual.pdf)** - A Program for Calculating Liquid Junction Potentials

* **[LJP Corrections](http://beenhakkerlab.org/lab-links/ephys/Guides/Theory/Liquid-Junction-Potential-Corrections-Axon.pdf)** (Axon Instruments Application Note) describes how to calculate LJP using ClampEx and LJPCalcWin and also summarizes how to measure LJP experimentally

* **[LJP Corrections](https://medicalsciences.med.unsw.edu.au/sites/default/files/soms/page/ElectroPhysSW/AxoBits39New.pdf)** (Figl et al., AxoBits 39) summarizes LJP and discusses measurement and calculation with ClampEx

---
title: Google Charts in Blazor
date: 2021-01-12 19:15:00
tags: blazor, csharp
---

# Google Charts in Blazor

**Google Charts is a free interactive JavaScript charting framework.** The [Google Chart Gallery](https://developers.google.com/chart/interactive/docs/gallery) showcases many of the available chart types and options. This project shows how to create data from C# functions in Blazor, then use JavaScript interop to pass arrays into JavaScript for display with Google Charts.

<div class="text-center">

[![](blazor-google-charts.jpg)](app)

</div>

* [Google Charts with Blazor Demo](app) 👈 Try it live!

* Source code: [blazor-google-charts.zip](blazor-google-charts.zip)

## index.razor

This page contains a `div` where the chart will be displayed, controls for customizing settings, and a few functions in the code-behind to call a JavaScript function that updates the chart.

```html
@page "/"
@inject IJSRuntime JsRuntime

<!-- this is where the Google Chart is displayed -->
<div id="chart_div" style="height: 400px;"></div>

<!-- buttons call C# functions -->
<button @onclick="PlotSin">Sin</button>
<button @onclick="PlotRandom">Random</button>
<button @onclick="PlotWalk">Walk</button>
<button @onclick="PlotRandomXY">RandomXY</button>

<!-- a slider bound to a C# field -->
<input type="range" @bind="PointCount" @bind:event="oninput">
```

```cs
@code{
    private int PointCount = 123;
    Random Rand = new Random();

    private void PlotData(double[] xs, double[] ys)
    {
        // This function calls a JavaScript function to update the chart.
		// Notice how multiple parameters are passed in.
        JsRuntime.InvokeVoidAsync("createNewChart", new { xs, ys });
    }

    private void PlotSin()
    {
        double[] xs = Enumerable.Range(0, PointCount).Select(x => (double)x).ToArray();
        double[] ys = xs.Select(x => Math.Sin(x / 10)).ToArray();
        PlotData(xs, ys);
    }

    private void PlotRandom()
    {
        double[] xs = Enumerable.Range(0, PointCount).Select(x => (double)x).ToArray();
        double[] ys = xs.Select(x => (Rand.NextDouble() - .5) * 1000).ToArray();
        PlotData(xs, ys);
    }

    private void PlotWalk()
    {
        double[] xs = Enumerable.Range(0, PointCount).Select(x => (double)x).ToArray();
        double[] ys = new double[PointCount];
        for (int i = 1; i < ys.Length; i++)
            ys[i] = ys[i - 1] + Rand.NextDouble() - .5;
        PlotData(xs, ys);
    }

    private void PlotRandomXY()
    {
        double[] xs = Enumerable.Range(0, PointCount).Select(x => Rand.NextDouble()).ToArray();
        double[] ys = Enumerable.Range(0, PointCount).Select(x => Rand.NextDouble()).ToArray();
        PlotData(xs, ys);
    }
}
```

## index.html

These JavaScript blocks were added just before the closing `</body>` tag

```js
<script type='text/javascript' src='https://www.gstatic.com/charts/loader.js'></script>

<script>
    google.charts.load('current', { packages: ['corechart', 'line'] });

    // draw an empty chart when the page first loads
    google.charts.setOnLoadCallback(initChart);
    function initChart() {
        var xs = [];
        var ys = [];
        window.createNewChart({xs, ys});
    }

    // draw a new chart given X/Y values
    window.createNewChart = (params) => {
        var xs = params.xs;
        var ys = params.ys;

        var data = new google.visualization.DataTable();
        data.addColumn('number', 'X');
        data.addColumn('number', 'Y');

        for (var i = 0; i < ys.length; i++) {
            data.addRow([xs[i], ys[i]]);
        }

        var options = {
            hAxis: { title: 'Horizontal Axis Label' },
            vAxis: { title: 'Vertical Axis Label' },
            title: 'This is a Google Chart in Blazor',
            legend: { position: 'none' },
        };

        var chart = new google.visualization.LineChart(document.getElementById('chart_div'));

        chart.draw(data, options);
    };

</script>
```

## Automatic Resizing

Plots look bad when the window is resized because Google Charts adopts a fixed size on each render. To give the appearance of fluid charts (that resize to fit their container as its size changes), add some JavaScript to re-render on every resize.

```js
window.onresize = function () { initChart(); };
```

We can't call our existing `createNewChart()` method because that expects data (from C#/Blazor) passed-in as a parameter. To support this type of resizing, the call from C# must be modified to _store_ data arrays at the window level so they can be later accessed when the chart is plotted again. This would take some re-structuring of this project, but it's possible.

## Conclusions

* Google Charts is a straightforward way to display data in mouse-interactive graphs on the web. 

* JS interop allows Blazor to pass data to a JavaScript function that can plot it on a Google Chart.

* Extra steps are required to automatically resize a Google Chart when its container size changes.

* For interactive graphs in desktop applications, check out [ScottPlot](https://swharden.com/scottplot) (an open-source plotting library for .NET that makes it easy to interactively display large datasets).

## Resources

* Live demo: [Google Charts with Blazor Demo](app)

* Source code: [blazor-google-charts.zip](blazor-google-charts.zip)

* Source code on GitHub: [/examples/2021-01-10-blazor-google-charts](https://github.com/swharden/Csharp-Data-Visualization/tree/master/examples/2021-01-10-blazor-google-charts)

* [C# Data Visualization](https://github.com/swharden/Csharp-Data-Visualization) on GitHub

---
title: Mystify your Browser with Blazor
date: 2021-01-09 22:16:00
tags: blazor, csharp
---

# Mystify your Browser with Blazor

**The project simulates the classic _Mystify your Mind_ screensaver from Windows 3 using client-side Blazor.** The graphics model logic is entirely C# and the web interface has user-facing options (razor components) to customize its behavior in real time. To render a frame JavaScript calls a C# function that returns JSON containing an array of line details (colors and coordinates) so a JavaScript render function can draw them on a HTML canvas. While [.NET APIs for drawing on canvases](https://swharden.com/blog/2021-01-07-blazor-canvas-animated-graphics/) exist, I find this method to be a bit more versatile because it does not require any external libraries, and it only makes a single JS interop call on each render so it is appreciably faster.

<div class="text-center">

[![](blazor-mystify.gif)](app)

</div>

### Live Demo

* [Mystify your Browser with Blazor](app/) 👈 ***Launch the demo***

## The C# Graphics Model

The point of this article is to discuss strategies for rendering graphics using client-side Blazor and WebAssembly, so I won't detail how the polygons are tracked here. Source code for these classes can be viewed on GitHub ([MystifyBlazor/Models](https://github.com/swharden/Csharp-Data-Visualization/tree/master/examples/2021-01-09-blazor-mystify/MystifyBlazor/Models)) or downloaded with this project ([blazor-mystify.zip](blazor-mystify.zip)).

* [`Models/Color.cs`](https://github.com/swharden/Csharp-Data-Visualization/blob/master/examples/2021-01-09-blazor-mystify/MystifyBlazor/Models/Color.cs) - Represents a color and has methods to help with hue-shifting

* [`Models/Corner.cs`](https://github.com/swharden/Csharp-Data-Visualization/blob/master/examples/2021-01-09-blazor-mystify/MystifyBlazor/Models/Corner.cs) - Represents a corner of a polygon (position, direction, and velocity) and has logic to move forward in time and bounce off walls

* [`Models/Polygon.cs`](https://github.com/swharden/Csharp-Data-Visualization/blob/master/examples/2021-01-09-blazor-mystify/MystifyBlazor/Models/Polygon.cs) - A polygon is just a color and a list of corners that are connected by a single line.

* [`Models/Shape.cs`](https://github.com/swharden/Csharp-Data-Visualization/blob/master/examples/2021-01-09-blazor-mystify/MystifyBlazor/Models/Shape.cs) - A Shape is a moving polygon, and this class contains a list of polygons (a historical record of a single polygon's configuration as it changed over time).

* [`Models/Field.cs`](https://github.com/swharden/Csharp-Data-Visualization/blob/master/examples/2021-01-09-blazor-mystify/MystifyBlazor/Models/Field.cs) - Represents the rectangular render area and holds multiple shapes. 
  * This is the only class Blazor directly interacts with3
  * Configuration options (like rainbow mode) are public fields that can be bound to inputs on Razor pages
  * This class can return rendering instructions as JSON. This is just an array of lines, each with a color and an array of X/Y points.

## index.razor

### Canvas and Holder

This is the HTML that holds the HTML canvas. By using CSS to make the canvas background black I don't have to concern myself with manually drawing a black background on every new frame.

Note that I'm using [Bootstrap 5](https://getbootstrap.com/) (not the Bootstrap 4 that currently comes with new Blazor projects), so the classes may be slightly different.

```html
@page "/"

<div class="bg-white shadow mt-3" id="myCanvasHolder">
    <canvas id="myCanvas" style="background-color: black;"></canvas>
</div>
```

### Code-Behind

The only goals here are to start the JavaScript render loop and provide a method JavaScript can call to get line data in JSON format. Notice the method called by JavaScript accepts `width` and `height` arguments so the data model can properly adjust to canvases that change size as the browser window changes dimensions.

```cs
@inject IJSRuntime JsRuntime

@code
{
    Models.Field MystifyField = new Models.Field();

    protected override void OnInitialized()
    {
        JsRuntime.InvokeAsync<object>("initRenderJS", DotNetObjectReference.Create(this));
    }

    [JSInvokable]
    public string UpdateModel(double width, double height)
    {
        MystifyField.Advance(width, height);
        return MystifyField.GetJSON();
    }
}
```

### Data Binding

User-facing configuration is achieved by binding public fields of the graphics model directly to input elements.

```html
<input type="range" 
    @bind="MystifyField.Speed" 
    @bind:event="oninput">

<input type="range" min="1"max="20"
    @bind="MystifyField.ShapeCount" 
    @bind:event="oninput">
    
<input type="range" min="3" max="20"
    @bind="MystifyField.CornerCount" 
    @bind:event="oninput" >
    
<input type="range" min="1" max="50"
    @bind="MystifyField.HistoryCount"
    @bind:event="oninput">

<button @onclick="MystifyField.RandomizeColors">
    Random Colors
</button>

<input type="checkbox" @bind="MystifyField.Rainbow">
```

## index.html

This file contains JavaScript to start the renderer (an infinite loop) and request line data as JSON from a C# function in each render.

Notice that the aspect ratio of the canvas is maintained by setting its with to be a fraction of its height. The canvas width and height are passed as arguments to the C# function which updates the model.

```html
<script>

    function renderJS() {

        // resize the canvas to fit its parent (resizing clears the canvas too)
        var holder = document.getElementById('myCanvasHolder');
        var canvas = document.getElementById('myCanvas');
        canvas.width = holder.clientWidth;
        canvas.height = canvas.width * .6;

        // tell C# about the latest dimensions, advance the model, and parse the new data
        var dataString = window.theInstance.invokeMethod('UpdateModel', canvas.width, canvas.height);
        var polys = JSON.parse(dataString);

        // render each polygon
        var lineCount = 0;
        var ctx = document.getElementById('myCanvas').getContext('2d');
        ctx.lineWidth = 2;
        for (var i = 0; i < polys.length; i++) {
            var poly = polys[i];
            var color = poly.shift();

            ctx.beginPath();
            for (var j = 0; j < poly.length; j++) {
                x = parseFloat(poly[j][0]);
                y = parseFloat(poly[j][1]);
                if (j == 0) {
                    ctx.moveTo(x, y);
                } else {
                    ctx.lineTo(x, y);
                }
            }
            ctx.strokeStyle = color;
            ctx.closePath();
            ctx.stroke();
            lineCount += 1;
        }

        window.requestAnimationFrame(renderJS);
    }

    window.initRenderJS = (instance) => {
        window.theInstance = instance;
        window.requestAnimationFrame(renderJS);
    };

</script>
```

## JSON

The JSON that C# passes to the JavaScript renderer is just an array of lines, each with a color and an array of X/Y points. This is an example JSON packet to render a single frame:

```
["#00FFB4",[665.26,767.31], [1098.58,250.94], [1159.48,206.49], [717.52,194.45]],
["#00FFB4",[660.94,757.61], [1089.18,257.06], [1166.11,203.76], [720.90,201.92]],
["#00FFB4",[656.62,747.92], [1079.78,263.18], [1172.73,201.03], [724.29,209.40]],
["#00FFB4",[652.30,738.22], [1070.38,269.31], [1179.36,198.30], [727.67,216.88]],
["#00FFB4",[647.98,728.53], [1060.98,275.43], [1185.99,195.57], [731.05,224.36]],
["#0049FF",[1219.26,656.86], [5.34,599.35], [454.87,716.81], [276.93,416.92]],
["#0049FF",[1224.78,648.28], [0.00,602.83], [455.97,708.21], [286.48,408.14]],
["#0049FF",[1230.30,639.69], [6.55,606.32], [457.08,699.61], [296.03,399.35]],
["#0049FF",[1235.81,631.11], [13.10,609.80], [458.19,691.02], [305.58,390.57]],
["#0049FF",[1241.33,622.53], [19.65,613.28], [459.29,682.42], [315.13,381.79]]
```

## Alternatively you can Render from C# 

There are wrappers to let you draw on a HTML canvas from .NET, allowing you to write your render function in C# instead of JavaScript. It is a bit of added complexity (requires a package) and is a bit slower (additional JavaScript interop calls), so I did not choose to use it for this project. 

See my earlier article [_Draw Animated Graphics in the Browser with Blazor WebAssembly_](https://swharden.com/blog/2021-01-07-blazor-canvas-animated-graphics) for an example of how to draw on a canvas from C# using the [`Blazor.Extensions.Canvas`](https://github.com/BlazorExtensions/Canvas) package.

## Performance Notes

Vanilla JavaScript will probably always be faster at rendering graphics in the browser than Blazor. If your application requires fast graphics, you'll have to write all your graphics model logic and render system in JavaScript. The great advantage of Blazor is that existing C# code that has already been developed (and extensively tested) can be used in the browser. At the time of writing, Speed is not Blazor's strong suit.

* This system starts to choke when the model represents more than a few lines. The bottleneck seems to be encoding all the data as JSON on the C# side.

* I tried using StringBuilder everywhere and also using `int` instead of `float`, but it did not produce large improvements.

* I also tired using the [`Blazor.Extensions.Canvas`](https://github.com/BlazorExtensions/Canvas) package so I could make all the rendering calls from C# (eliminating the conversion to JSON step). Because this required so many individual interop calls (even with batching), it was about twice as slow as the JS renderer implemented in the code above.

## Resources

* Download this project: [blazor-mystify.zip](blazor-mystify.zip)

* Launch the demo: [Mystify your Browser with Blazor](app/)

* Browse source on GitHub: [C# Data Visualization: MystifyBlazor](https://github.com/swharden/Csharp-Data-Visualization/tree/master/examples/2021-01-09-blazor-mystify/)

---
title: Boids in your Browser with Blazor
date: 2021-01-08 22:58:00
tags: blazor, csharp
---

# Boids in your Browser with Blazor

**This project implements the [Boids flocking algorithm](https://en.wikipedia.org/wiki/Boids) in C# and uses Blazor WebAssembly to render it in the browser.** Drone birds (bird-oids, or boids) follow a simple set of rules to determine their angle and velocity. When many boids are placed in a field together, interesting group behaviors emerge. Details about the boid flocking algorithm are discussed in depth elsewhere. This article summarizes how to configure a Blazor application to _model_ graphics with C# and _render_ them with JavaScript.

<div class="text-center">

[![](blazor-boids.gif)](app)

</div>

### Live Demo

* Boids with default settings: [app/](app/)

* Boids with custom settings: [app/?boids=100&predators=5](app/?boids=100&predators=5)

* Pro tip: resize your window really small and watch what happens!

## The C# Boids Model

The code that manages the field of boids is entirely written in C#. It tracks the positions of boids and advances their positions and directions over time, but it does not manage rendering. Briefly, 

* A `BoidField` has a width, height, and array of Boids
* Each `Boid` has a position, direction, and velocity
* Each `Boid` can advance itself by considering the positions of all the other boids:
  * Rule 1: boids steer toward the center of mass of nearby boids
  * Rule 2: boids adjust direction to match nearby boids
  * Rule 3: boids adjust speed to match a match a target
  * Rule 4: boids steer away from very close boids
  * Rule 5: boids steer away from boids marked as predators
  * Rule 6: boids are repelled by the edge of the window

## Model with C#, Render with JavaScript

At the time of writing, the most performant way to render high frame rates in the browser is to write your model and business logic entirely in JavaScript. The purpose of this project is _not_ to make the most performant model possible, but rather to explore what can be done with client-side Blazor and WebAssembly. There is a strong advantage to being able to keep keeping your graphics model and business logic in C#, especially if it is already written and extensively tested.

In my _[Draw Animated Graphics in the Browser with Blazor WebAssembly](https://swharden.com/blog/2021-01-07-blazor-canvas-animated-graphics/)_ article we used `Blazor.Extensions.Canvas` to draw on a HTML Canvas from C# code. Although this worked, it was limited by the fact that interop calls can be slow. Even though they can be batched, they still represent a significant bottleneck when thousands of calls need to be made on every frame.

In this project I used C# to model the field of boids, converted the field to JSON (with each boid having a X/Y position and a rotation), and had JavaScript parse the boid array and render each boid using a rendering function inside JavaScript.

## Source Code

The full source code can be downloaded here ([blazor-boids.zip](blazor-boids.zip)) or navigated on GitHub [C# Data Visualization: Blazor Boids](https://github.com/swharden/Csharp-Data-Visualization/tree/master/examples/2021-01-08-blazor-boids/BlazorBoids). The C# code for `Boid` and `BoidField` can be found there. What I'll focus on here is the key Blazor code required to manage the model and render it using JavaScript.

### index.razor

There are a lot of different things going on here. Most of them can be figured out with a little visual inspection. Here are the highlights:

* A canvas is created inside a div, each with a unique ID so they can be referenced from JavaScript.

* A `IJSRuntime` is injected so JS functions can be called from C#. Specifically, the `initRenderJS` is called when the component is first rendered.

* A `NavigationManager` is injected to let us easily work with query strings (Note that `QueryHelpers` requires the `Microsoft.AspNetCore.WebUtilities` NuGet package).

* A `boidField` graphics model is created as a private field and initialized `OnAfterRender` using query strings to customize the initializer parameters.

* The `UpdateModel()` method is decorated with `JSInvokable` so it can be called from JavaScript. It accepts a width and height (which may change if the browser size changes) and can resize the `boidField` as needed. It advances the model then converts the positions and directions of all boids to JSON and returns it as a string.

```cs
@page "/"
@using System.Text;
@inject IJSRuntime JsRuntime
@inject NavigationManager NavManager
@using Microsoft.AspNetCore.WebUtilities

<div id="boidsHolder" style="position: fixed; width: 100%; height: 100%">
    <canvas id="boidsCanvas"></canvas>
</div>

@code{
    private Random rand = new Random();
    private Models.Field boidField;

    protected override async Task OnAfterRenderAsync(bool firstRender)
    {
        // call the initialization JavaScript function
        await JsRuntime.InvokeAsync<object>("initRenderJS", DotNetObjectReference.Create(this));
        await base.OnInitializedAsync();

        // use a query string to customize the number of boids
        int boidCount = 75;
        var uri = NavManager.ToAbsoluteUri(NavManager.Uri);
        if (QueryHelpers.ParseQuery(uri.Query).TryGetValue("boids", out var boidCountString))
            if (int.TryParse(boidCountString, out int parsedBoidCount))
                boidCount = parsedBoidCount;

        // use a query string to customize the number of predators
        int predatorCount = 3;
        if (QueryHelpers.ParseQuery(uri.Query).TryGetValue("predators", out var predatorCountString))
            if (int.TryParse(predatorCountString, out int parsedPredatorCount))
                predatorCount = parsedPredatorCount;

        // create the model using the custom settings
        boidField = new Models.Field(800, 600, boidCount, predatorCount);
    }

    [JSInvokable]
    public string UpdateModel(double width, double height)
    {
        if (boidField is null)
            return "";

        boidField.Resize(width, height);
        boidField.Advance(bounceOffWalls: true, wrapAroundEdges: false);

        StringBuilder sb = new StringBuilder("[");
        foreach (var boid in boidField.Boids)
        {
            double x = boid.X;
            double y = boid.Y;
            double r = boid.GetAngle() / 360;
            sb.Append($"[{x:0.0},{y:0.0},{r:0.000}],");
        }

        sb.Append(boidField.PredatorCount.ToString());
        sb.Append("]");
        return sb.ToString();
    }
}
```

### index.html

Two JavaScript functions are added to the HTML:

* `renderJS()` - this function calls C# to update the model and request the latest data, then calls itself to create an infinite render loop. Each time it executes it:
  * resizes the canvas to fit the div it's inside of
  * calls the C# `UpdateModel()` method (passing in the latest canvas size)
  * parses the JSON the C# method returns to obtain an array of boid details
  * clears the canvas by filling it with a blue color
  * renders each boid (by translating and rotating the canvas, not the boid)
  * requests itself be rendered again so rendering continues infinitely
* `initRenderJS` - this function is called from Blazor so the running instance can be referenced in the future. It also starts the infinite render loop.

```html
<script>

    function renderJS() {

        // resize the canvas to fit its parent (resizing clears the canvas too)
        var holder = document.getElementById('boidsHolder');
        var canvas = document.getElementById('boidsCanvas');
        canvas.width = holder.clientWidth;
        canvas.height = holder.clientHeight;

        // tell C# about the latest dimensions, advance the model, and parse the new data
        var boidsString = window.theInstance.invokeMethod('UpdateModel', canvas.width, canvas.height);
        var boids = JSON.parse(boidsString);
        var predatorCount = boids.pop();

        // render each boid
		var ctx = document.getElementById('boidsCanvas').getContext('2d');
        for (var i = 0; i < boids.length; i++) {
            var predator = i < predatorCount;
            var boid = boids[i];
            var x = boid[0];
            var y = boid[1];
            var rotation = boid[2];
            ctx.save();
            ctx.translate(x, y);
            ctx.rotate(rotation * 2 * Math.PI);
            ctx.beginPath();
            ctx.moveTo(0, 0);
            ctx.lineTo(4, -2);
            ctx.lineTo(0, 10);
            ctx.lineTo(-4, -2);
            ctx.lineTo(0, 0);
            ctx.closePath();
            ctx.fillStyle = predator ? '#FFFF00' : '#FFFFFF';
            ctx.fill();
            ctx.restore();
        }

        // call this same function to render the next frame
        window.requestAnimationFrame(renderJS);
    }

    window.initRenderJS = (instance) => {
        window.theInstance = instance;
        window.requestAnimationFrame(renderJS);
    };

</script>
```

## Resources

### Blazor Boids

* Launch _Blazor Boids_ with default settings: [app/](app/)

* Launch _Blazor Boids_ with custom settings: [app/?boids=100&predators=5](app/?boids=100&predators=5)

### Blazor Source Code

* Download source: [blazor-boids.zip](blazor-boids.zip)

* View source on GitHub: [C# Data Visualization: Blazor Boids](https://github.com/swharden/Csharp-Data-Visualization/tree/master/examples/2021-01-08-blazor-boids/BlazorBoids)

* [Draw Animated Graphics in the Browser with Blazor WebAssembly](https://swharden.com/blog/2021-01-07-blazor-canvas-animated-graphics/) uses a render loop written in C# (instead of JavaScript) using `Blazor.Extensions.Canvas`. It's a bit slower as a result, but for simple models it has the advantage of not having to write a JavaScript rendering method.

### Boids in C# (Windows Application)

* [Boids in C#](https://swharden.com/CsharpDataVis/boids/boids.md.html) - a Windows application that runs much faster than this Blazor app. It has controls to customize flocking parameters. This was the source of the C# model I used for this Blazor app.

<div class="text-center">

[![](boids-csharp-opengl.png)](https://swharden.com/CsharpDataVis/boids/boids.md.html)

</div>

### JavaScript Boids Simulators

**Obviously a native JavaScript Boids simulator will be much faster.** Implementing this Blazor app in JavaScript would have meant translating the model from C# to JavaScript. For performance-critical rendering-intensive applications, this is the way to go at the time of writing.

* [Boids algorithm demonstration](https://eater.net/boids) by Ben Eater (featured in SmarterEveryDay's [YouTube Video](https://youtu.be/4LWmRuB-uNU?t=187) about flocking birds)
* [Boids: Flocking made simple](http://www.harmendeweerd.nl/boids/) by Harmen de Weerd
* [Flocking](https://processing.org/examples/flocking.html) by Daniel Shiffman
* [Flocking Simulation](http://www.emergentmind.com/boids) by Matt Mazur
* [Simulate How Birds Flock in Processing](https://medium.com/swlh/boids-a-simple-way-to-simulate-how-birds-flock-in-processing-69057930c229) by Takuma Kakehi

### Literature
* [Boids: Background and Update](https://www.red3d.com/cwr/boids/) by Craig Reynolds (the inventor of boids)
* [Boids on Wikipedia](https://en.wikipedia.org/wiki/Boids)
* [3 Simple Rules of Flocking Behaviors: Alignment, Cohesion, and Separation](https://gamedevelopment.tutsplus.com/tutorials/3-simple-rules-of-flocking-behaviors-alignment-cohesion-and-separation--gamedev-3444)
* [Boids Code Golf](https://codegolf.stackexchange.com/questions/154277/implement-the-boids-algorithm)

---
title: Draw Animated Graphics in the Browser with Blazor WebAssembly
date: 2021-01-07 21:46:00
tags: blazor, csharp
---

# Draw Animated Graphics in the Browser with Blazor WebAssembly

**Client-side Blazor allows C# graphics models to be rendered in the browser.** This means .NET developers can create web apps with business logic written (and tested) in C# instead of being forced to write their business logic in a totally different language (JavaScript) just to get it to run in the browser. In this project we'll create an interactive graphics model (a field of balls that bounce off the edge of the screen) entirely in C#, and draw the model on the screen using an API that allows us to interact with a HTML5 Canvas.

<div class="text-center">

[![](blazor-canvas-demo.gif)](app)

</div>

* [**View the live demo**](app)
* [**Download the source code**](blazor-canvas.zip)

## Strategy

**At the time of this writing Blazor WebAssembly can't directly paint on the screen, so JavaScript is required somewhere to make this happen.** The [`Blazor.Extensions.Canvas`](https://github.com/BlazorExtensions/Canvas) package has a Canvas component and provides a C# API for all of its JavaScript methods, allowing you to draw on the canvas entirely from C#. 

**Rendering gets a little slower every time a JavaScript function is called from Blazor.** If a large number of shapes are required (a lot of JavaScript calls), performance may be limited compared to a similar application written entirely in JavaScript. For high performance rendering of many objects, a rendering loop written entirely in JavaScript may be required.

**This method is good for simple models with a limited number of shapes.** It allows the business logic (and tests) to remain entirely in C#. The same graphics model code could be displayed in the browser (using HTML canvas) or on the desktop in WPF and WinForms apps (using System.Drawing or SkiaSharp).

## Step 1: Create a Pure C# Graphics Model

**I'm using _graphics model_ to describe the state of the field of balls and logic required to move each ball around.** Ideally this logic would be isolated in a separate library. At the time of writing a .NET Standard C# library seems like a good idea, so the same graphics model could be used in .NET Framework and .NET Core environments.

### Models/Ball.cs

```cs
public class Ball
{
    public double X { get; private set; }
    public double Y { get; private set; }
    public double XVel { get; private set; }
    public double YVel { get; private set; }
    public double Radius { get; private set; }
    public string Color { get; private set; }

    public Ball(double x, double y, double xVel, double yVel, double radius, string color)
    {
        (X, Y, XVel, YVel, R, Color) = (x, y, xVel, yVel, radius, color);
    }

    public void StepForward(double width, double height)
    {
        X += XVel;
        Y += YVel;
        if (X < 0 || X > width)
            XVel *= -1;
        if (Y < 0 || Y > height)
            YVel *= -1;

        if (X < 0)
            X += 0 - X;
        else if (X > width)
            X -= X - width;

        if (Y < 0)
            Y += 0 - Y;
        if (Y > height)
            Y -= Y - height;
    }
}
```

### Models/Field.cs

```cs
public class Field
{
    public readonly List<Ball> Balls = new List<Ball>();
    public double Width { get; private set; }
    public double Height { get; private set; }

    public void Resize(double width, double height) =>
        (Width, Height) = (width, height);

    public void StepForward()
    {
        foreach (Ball ball in Balls)
            ball.StepForward(Width, Height);
    }

    private double RandomVelocity(Random rand, double min, double max)
    {
        double v = min + (max - min) * rand.NextDouble();
        if (rand.NextDouble() > .5)
            v *= -1;
        return v;
    }


    private string RandomColor(Random rand) => 
	    string.Format("#{0:X6}", rand.Next(0xFFFFFF));
	
    public void AddRandomBalls(int count = 10)
    {
        double minSpeed = .5;
        double maxSpeed = 5;
        double radius = 10;
        Random rand = new Random();

        for (int i = 0; i < count; i++)
        {
            Balls.Add(
                new Ball(
                    x: Width * rand.NextDouble(),
                    y: Height * rand.NextDouble(),
                    xVel: RandomVelocity(rand, minSpeed, maxSpeed),
                    yVel: RandomVelocity(rand, minSpeed, maxSpeed),
                    radius: radius,
                    color: RandomColor(rand);
                )
            );
        }
    }
}
```

## Step 2: Get the Blazor.Extensions.Canvas Package

Use NuGet to install [Blazor.Extensions.Canvas](https://github.com/BlazorExtensions/Canvas)

```cs
Install-Package Blazor.Extensions.Canvas
```

## Step 3: Add a script to index.html

**This JavaScript sets-up the render loop** which automatically calls `RenderInBlazor` C# method on every frame. It also calls the `ResizeInBlazor` C# function whenever the canvas is resized so the graphics model's dimensions can be updated. You can place it just before the closing `</body>` tag.

**This code will automatically resize the canvas and graphics model to fit the window,** but for a fixed-size canvas you can omit the `addEventListener` and `resizeCanvasToFitWindow` calls.

```html
<script src='_content/Blazor.Extensions.Canvas/blazor.extensions.canvas.js'></script>
<script>
    function renderJS(timeStamp) {
        theInstance.invokeMethodAsync('RenderInBlazor', timeStamp);
        window.requestAnimationFrame(renderJS);
    }

    function resizeCanvasToFitWindow() {
        var holder = document.getElementById('canvasHolder');
        var canvas = holder.querySelector('canvas');
        if (canvas) {
            canvas.width = window.innerWidth;
            canvas.height = window.innerHeight;
            theInstance.invokeMethodAsync('ResizeInBlazor', canvas.width, canvas.height);
        }
    }

    window.initRenderJS = (instance) => {
        window.theInstance = instance;
        window.addEventListener("resize", resizeCanvasToFitWindow);
        resizeCanvasToFitWindow();
        window.requestAnimationFrame(renderJS);
    };
</script>
```

## Step 4: Create a page for the Canvas and Render code

This step ties everything together:
 * **The graphics model**: a private class stored at this level
 * **The canvas component**: a protected field
 * **The canvas**: a Razor component referencing the canvas component
 * **The init code**: which tells JavaScipt to start the render loop
 * **The render method**: C# function called from the JavaScript render loop when a frame is to be drawn
 * **The resize method**: C# function called from JavaScript to update the model when the canvas size changes
* **JavaScript runtime injection**: This allows Blazor/JavaScript interoperability (JS interop)

For simplicity it's demonstrated here using a code-behind, but a clearer strategy would be to move the render logic into its own class/file.

```cs
@page "/"

@using Blazor.Extensions
@using Blazor.Extensions.Canvas
@using Blazor.Extensions.Canvas.Canvas2D
@inject IJSRuntime JsRuntime;

<div id="canvasHolder" style="position: fixed; width: 100%; height: 100%">
    <BECanvas Width="600" Height="400" @ref="CanvasRef"></BECanvas>
</div>

@code{
    private Models.Field BallField = new Models.Field();
    private Canvas2DContext ctx;
    protected BECanvasComponent CanvasRef;
    private DateTime LastRender;

    protected override async Task OnAfterRenderAsync(bool firstRender)
    {
        this.ctx = await CanvasRef.CreateCanvas2DAsync();
        await JsRuntime.InvokeAsync<object>("initRenderJS", DotNetObjectReference.Create(this));
        await base.OnInitializedAsync();
    }

    [JSInvokable]
    public void ResizeInBlazor(double width, double height) => BallField.Resize(width, height);

    [JSInvokable]
    public async ValueTask RenderInBlazor(float timeStamp)
    {
        if (BallField.Balls.Count == 0)
            BallField.AddRandomBalls(50);
        BallField.StepForward();

        double fps = 1.0 / (DateTime.Now - LastRender).TotalSeconds;
        LastRender = DateTime.Now;

        await this.ctx.BeginBatchAsync();
        await this.ctx.ClearRectAsync(0, 0, BallField.Width, BallField.Height);
        await this.ctx.SetFillStyleAsync("#003366");
        await this.ctx.FillRectAsync(0, 0, BallField.Width, BallField.Height);
        await this.ctx.SetFontAsync("26px Segoe UI");
        await this.ctx.SetFillStyleAsync("#FFFFFF");
        await this.ctx.FillTextAsync("Blazor WebAssembly + HTML Canvas", 10, 30);
        await this.ctx.SetFontAsync("16px consolas");
        await this.ctx.FillTextAsync($"FPS: {fps:0.000}", 10, 50);
        await this.ctx.SetStrokeStyleAsync("#FFFFFF");
        foreach (var ball in BallField.Balls)
        {
            await this.ctx.BeginPathAsync();
            await this.ctx.ArcAsync(ball.X, ball.Y, ball.Radius, 0, 2 * Math.PI, false);
            await this.ctx.SetFillStyleAsync(ball.Color);
            await this.ctx.FillAsync();
            await this.ctx.StrokeAsync();
        }
        await this.ctx.EndBatchAsync();
    }
}
```

**Notice how the JavaScript calls are wrapped in `BeginBatchAsync` and `EndBatchAsync`.** This allows the calls between these two statements to be bundled into a single call. Since Blazor/JavaScript interop calls are the primary bottleneck in this system, limiting the number of individual JavaScript calls has a large influence on final performance.

## Notes and References

> **💡 I observed a strong performance increase when upgrading from .NET Core 3.1 to .NET 5.** If you can, [Migrate your Blazor project to .NET 5](https://docs.microsoft.com/en-us/aspnet/core/migration/31-to-50#update-blazor-webassembly-projects) or newer

* **A hybrid JavaScript/C# architecture is be possible** involving exchange of graphics model _data_, whereby JavaScript is used to render a model but C# is used to advanced the model. This could be achieved with a single interop call passing model data as JSON. This is explored in the later blog posts [Mystify your Browser with Blazor](https://swharden.com/blog/2021-01-09-blazor-mystify/) and [Boids in your Browser with Blazor](https://swharden.com/blog/2021-01-08-blazor-boids/).

* **Live demo of this project**: [Ball field demo](app)

* **Source code for this project**: [blazor-canvas.zip](app)

* **C# Data Visualization:** https://github.com/swharden/Csharp-Data-Visualization