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Node.js Version Build Status

Web socket API for moving data to and from hdf5 files.

Installing

pnpm config set hdf5_home_linux <your native hdf path>
pnpm install

App usage

load script

  <script type="text/javascript" src="HDF5Interface.js"></script>

In the case of writing and immediately reading use the callback of makeDataset:

    var data=new Float64Array([1.0, 2.0, 3.0, 5.0]);
    var hdf5Interface=new HDF5Interface(9900);
    hdf5Interface.createGroup("pmcservices/x-ray/refinement");
    hdf5Interface.makeDataset("pmcservices/x-ray/refinement/Matrix", data, function(){
    hdf5Interface.readDataset("pmcservices/x-ray/refinement/Matrix", function(data, metaData){
        console.log(data);
        var dataStr="[";
        for(var i=0;i<data.length;i++){
            dataStr+=data[i].toFixed(1);
            if(i<data.length-1)dataStr+=", ";
        }
        dataStr+="]";
        document.getElementById("results").appendChild(document.createTextNode(dataStr));
    });
    });

metaData will have rank, rows and if rank is 2, columns.

It is now possible to write a whole image to the h5, read a whole image or read just a region of an image. Will have to explore the cross over point for applying compression on the websocket transfer.

The following works with the 2d context of a canvas to display a 400x400 rectangle from a large image:

                var imageInfo=hdf5Interface.getImageInfo("NASA/plates/734344main_g306_wide_large.jpg");
                console.log(imageInfo);
                hdf5Interface.requestImageRegion("NASA/plates/734344main_g306_wide_large.jpg", {start: [(imageInfo.width-1)/2, (imageInfo.height-1)/2, 0], stride: [1, 1, 1], count: [400, 400, 4]}, function(data, metaData){
                    console.log(metaData);
                    document.getElementById("results").appendChild(document.createTextNode(JSON.stringify(metaData)));
                    var viewportCanvas = document.getElementById('viewportCanvas');
                    var viewPortContext = viewportCanvas.getContext("2d");
                    var imageData=viewPortContext.createImageData(metaData.width, metaData.height);
                    var pos=0;
                    // Got new data
                   var dv = new DataView(data);
                    for(var i=0;i<data.byteLength;i+=metaData.planes)
                    {
                            // set red, green, blue, and alpha:
                            imageData.data[pos++] =dv.getUint8(i);
                            imageData.data[pos++] = dv.getUint8(i+1);
                            imageData.data[pos++] = dv.getUint8(i+2);
                            (metaData.planes>3) ? imageData.data[pos++] =dv.getUint8(i+3) : imageData.data[pos++] = 255; // opaque alpha
                    }
                     // Display new data in browser!
                    viewPortContext.putImageData(imageData, 100, 100);
            
                });

It is now possible to bring up a mosaic of tiles from an image picking a central tile to start with. https://github.com/HDF-NI/hdf5.ws/blob/master/test/examples/panningimages.html#L67

{start: [offsetX, offsetY, 0], stride: [1, 1, 1], count: [tileSize, tileSize, 4], boundary: 10}

The boundary is how many tiles out to the edge of the final region from the initial center tile.

Testing - Current Status

The tests are performed by cypress.

pnpm test

For the 'test panning images' test I copy the http://www.nasa.gov/images/content/734344main_g306_wide_large.jpg picture to hdf5.ws/test/examples folder.

But the more pressing issue is the handling of large images. Working on the algorithms to bring regions up in the most efficient manner. Currently can bring up regions in a tiled fashion without any compression.