feat: can compress image data before sending it to over the websocket

README.md

@@ -5,6 +5,17 @@ Used for https://github.com/glue-viz/glue-jupyter
 
 (currently requires latest developer version of bqplot)
 
+## Usage
+
+### ImageGL
+
+See https://py.cafe/maartenbreddels/bqplot-image-gl-demo for a demo of the ImageGL widget.
+
+Preview image:
+![preview image](https://py.cafe/preview/maartenbreddels/bqplot-image-gl-demo)
+
+
+
 # Installation
 
 To install use pip:

bqplot_image_gl/imagegl.py

@@ -1,3 +1,4 @@
+import os
 import ipywidgets as widgets
 import bqplot
 from traittypes import Array
@@ -6,10 +7,15 @@
 from bqplot.marks import shape
 from bqplot.traits import array_to_json, array_from_json
 from bqplot_image_gl._version import __version__
+from .serialize import image_data_serialization
 
 __all__ = ['ImageGL', 'Contour']
 
 
+# can be 'png', 'webp' or 'none'
+DEFAULT_IMAGE_DATA_COMPRESSION = os.environ.get("BQPLOT_IMAGE_GL_IMAGE_DATA_COMPRESSION", "none")
+
+
 @widgets.register
 class ImageGL(bqplot.Mark):
     """An example widget."""
@@ -24,7 +30,8 @@ class ImageGL(bqplot.Mark):
                         scaled=True,
                         rtype='Color',
                         atype='bqplot.ColorAxis',
-                        **array_serialization)
+                        **image_data_serialization)
+    compression = Unicode(DEFAULT_IMAGE_DATA_COMPRESSION, allow_none=True).tag(sync=True)
     interpolation = Unicode('nearest', allow_none=True).tag(sync=True)
     opacity = Float(1.0).tag(sync=True)
     x = Array(default_value=(0, 1)).tag(sync=True, scaled=True,

bqplot_image_gl/serialize.py

@@ -0,0 +1,98 @@
+from PIL import Image
+import numpy as np
+import io
+
+from bqplot.traits import array_serialization
+
+
+def array_to_image_or_array(array, widget):
+    if widget.compression in ["png", "webp"]:
+        return array_to_image(array, widget.compression)
+    else:
+        return array_serialization["to_json"](array, widget)
+
+
+def not_implemented(image):
+    # the widget never sends the image data back to the kernel
+    raise NotImplementedError("deserializing is not implemented yet")
+
+
+def array_to_image(array, image_format):
+    # convert the array to a png image with intensity values only
+    array = np.array(array, copy=False)
+    min, max = None, None
+    use_colormap = False
+    if array.ndim == 2:
+        use_colormap = True
+        min = np.nanmin(array)
+        max = np.nanmax(array)
+
+        array = (array - min) / (max - min)
+        # only convert to uint8 if the array is float
+        if array.dtype.kind == "f":
+            array_bytes = (array * 255).astype(np.uint8)
+        else:
+            array_bytes = array
+        intensity_image = Image.fromarray(array_bytes, mode="L")
+
+        # create a mask image with 0 for NaN values and 255 for valid values
+        isnan = ~np.isnan(array)
+        mask = (isnan * 255).astype(np.uint8)
+        mask_image = Image.fromarray(mask, mode="L")
+
+        # merge the intensity and mask image into a single image
+        image = Image.merge("LA", (intensity_image, mask_image))
+    else:
+        # if floats, convert to uint8
+        if array.dtype.kind == "f":
+            array_bytes = (array * 255).astype(np.uint8)
+        elif array.dtype == np.uint8:
+            array_bytes = array
+        else:
+            raise ValueError(
+                "Only float arrays or uint8 arrays are supported, your array has dtype"
+                "{array.dtype}"
+            )
+        if array.shape[2] == 3:
+            image = Image.fromarray(array_bytes, mode="RGB")
+        elif array.shape[2] == 4:
+            image = Image.fromarray(array_bytes, mode="RGBA")
+        else:
+            raise ValueError(
+                "Only 2D arrays or 3D arrays with 3 or 4 channels are supported, "
+                f"your array has shape {array.shape}"
+            )
+
+    # and serialize it to a PNG
+    png_data = io.BytesIO()
+    image.save(png_data, format=image_format, lossless=True)
+    png_bytes = png_data.getvalue()
+    original_byte_length = array.nbytes
+    uint8_byte_length = array_bytes.nbytes
+    compressed_byte_length = len(png_bytes)
+    return {
+        "type": "image",
+        "format": image_format,
+        "use_colormap": use_colormap,
+        "min": min,
+        "max": max,
+        "data": png_bytes,
+        # this metadata is only useful/needed for debugging
+        "shape": array.shape,
+        "info": {
+            "original_byte_length": original_byte_length,
+            "uint8_byte_length": uint8_byte_length,
+            "compressed_byte_length": compressed_byte_length,
+            "compression_ratio": original_byte_length / compressed_byte_length,
+            "MB": {
+                "original": original_byte_length / 1024 / 1024,
+                "uint8": uint8_byte_length / 1024 / 1024,
+                "compressed": compressed_byte_length / 1024 / 1024,
+            },
+        },
+    }
+
+
+image_data_serialization = dict(
+    to_json=array_to_image_or_array, from_json=not_implemented
+)

js/lib/contour.js

@@ -34,19 +34,40 @@ class ContourModel extends bqplot.MarkModel {
         this.update_data();
     }
 
-    update_data() {
+    async update_data() {
         const image_widget = this.get('image');
         const level = this.get('level')
         // we support a single level or multiple
         this.thresholds = Array.isArray(level) ? level : [level];
         if(image_widget) {
                 const image = image_widget.get('image')
-                this.width = image.shape[1];
-                this.height = image.shape[0];
+                let data = null;
+                if(image.image) {
+                    const imageNode = image.image;
+                    this.width = imageNode.width;
+                    this.height = imageNode.height;
+                    // conver the image to a typed array using canvas
+                    const canvas = document.createElement('canvas');
+                    canvas.width = this.width
+                    canvas.height = this.height
+                    const ctx = canvas.getContext('2d');
+                    ctx.drawImage(imageNode, 0, 0);
+                    const imageData = ctx.getImageData(0, 0, imageNode.width, imageNode.height);
+                    const {min, max}  = image;
+                    // use the r channel as the data, and scale to the range
+                    data = new Float32Array(imageData.data.length / 4);
+                    for(var i = 0; i < data.length; i++) {
+                        data[i] = (imageData.data[i*4] / 255) * (max - min) + min;
+                    }
+                } else {
+                    this.width = image.shape[1];
+                    this.height = image.shape[0];
+                    data = image.data;
+                }
                 this.contours = this.thresholds.map((threshold) => d3contour
                                                     .contours()
                                                     .size([this.width, this.height])
-                                                    .contour(image.data, [threshold])
+                                                    .contour(data, [threshold])
                                                     )
         } else {
             this.width = 1;   // precomputed contour_lines will have to be in normalized

js/lib/imagegl.js

@@ -38,9 +38,24 @@ class ImageGLModel extends bqplot.MarkModel {
         super.initialize(attributes, options);
         this.on_some_change(['x', 'y'], this.update_data, this);
         this.on_some_change(["preserve_domain"], this.update_domains, this);
+        this.listenTo(this, "change:image", () => {
+            const previous = this.previous("image");
+            if(previous.image && previous.image.src) {
+                URL.revokeObjectURL(previous.image.src);
+            }
+        }, this);
+
         this.update_data();
     }
 
+    close(comm_closed) {
+        const image = this.get("image");
+        if(image.image && image.image.src) {
+            URL.revokeObjectURL(previous.image.src);
+        }
+        return super.close(comm_closed);
+    }
+
     update_data() {
         this.mark_data = {
             x: this.get("x"), y: this.get("y")
@@ -79,9 +94,24 @@ ImageGLModel.serializers = Object.assign({}, bqplot.MarkModel.serializers,
                                          { x: serialize.array_or_json,
                                            y: serialize.array_or_json,
                                            image: {
-                                                deserialize: (obj, manager) => {
-                                                    let state = {buffer: obj.value, dtype: obj.dtype, shape: obj.shape};
-                                                    return jupyter_dataserializers.JSONToArray(state);
+                                                deserialize: async (obj, manager) => {
+                                                    if(obj.type == "image") {
+                                                        // the data is encoded in an image with LA format
+                                                        // luminance for the intensity, alpha for the mask
+                                                        let image = new Image();
+                                                        const blob = new Blob([obj.data], {type: `image/${obj.format}`});
+                                                        const url = URL.createObjectURL(blob);
+                                                        image.src = url;
+                                                        await new Promise((resolve, reject) => {
+                                                            image.onload = resolve;
+                                                            image.onerror = reject;
+                                                        } );
+                                                        return {image, min: obj.min, max: obj.max, use_colormap: obj.use_colormap};
+                                                    } else {
+                                                        // otherwise just a 'normal' ndarray
+                                                        let state = {buffer: obj.value, dtype: obj.dtype, shape: obj.shape};
+                                                        return jupyter_dataserializers.JSONToArray(state);
+                                                    }
                                                 },
                                                 serialize: (ar) => {
                                                     const {buffer, dtype, shape} = jupyter_dataserializers.arrayToJSON(ar);
@@ -114,6 +144,10 @@ class ImageGLView extends bqplot.Mark {
                         // basically the corners of the image
                         image_domain_x  : { type: "2f", value: [0.0, 1.0] },
                         image_domain_y  : { type: "2f", value: [0.0, 1.0] },
+                        // in the case we use an image for the values, the image is normalized, and we need to scale
+                        // it back to a particular image range
+                        // This needs to be set to [0, 1] for array data (which is not normalized)
+                        range_image  : { type: "2f", value: [0.0, 1.0] },
                         // extra opacity value
                         opacity: {type: 'f', value: 1.0}
                     },
@@ -280,39 +314,56 @@ class ImageGLView extends bqplot.Mark {
     update_image(skip_render) {
         var image = this.model.get("image");
         var type = null;
-        var data = image.data;
-        if(data instanceof Uint8Array) {
-            type =  THREE.UnsignedByteType;
-        } else if(data instanceof Float64Array) {
-            console.warn('ImageGLView.data is a Float64Array which WebGL does not support, will convert to a Float32Array (consider sending float32 data for better performance).');
-            data = Float32Array.from(data);
-            type =  THREE.FloatType;
-        } else if(data instanceof Float32Array) {
-            type =  THREE.FloatType;
-        } else {
-            console.error('only types uint8 and float32 are supported');
-            return;
-        }
-        if(this.scales.image.model.get('scheme') && image.shape.length == 2) {
-            if(this.texture)
+        if(image.image) {
+            // the data is encoded in an image with LA format
+            if(this.texture) {
                 this.texture.dispose();
-            this.texture = new THREE.DataTexture(data, image.shape[1], image.shape[0], THREE.LuminanceFormat, type);
+            }
+            this.texture = new THREE.Texture(image.image);
             this.texture.needsUpdate = true;
+            this.texture.flipY = false;
             this.image_material.uniforms.image.value = this.texture;
-            this.image_material.defines.USE_COLORMAP = true;
+            this.image_material.defines.USE_COLORMAP = image.use_colormap;
             this.image_material.needsUpdate = true;
-        } else if(image.shape.length == 3) {
-            this.image_material.defines.USE_COLORMAP = false;
-            if(this.texture)
-                this.texture.dispose();
-            if(image.shape[2] == 3)
-                this.texture = new THREE.DataTexture(data, image.shape[1], image.shape[0], THREE.RGBFormat, type);
-            if(image.shape[2] == 4)
-                this.texture = new THREE.DataTexture(data, image.shape[1], image.shape[0], THREE.RGBAFormat, type);
-            this.texture.needsUpdate = true;
-            this.image_material.uniforms.image.value = this.texture;
+            this.image_material.uniforms.range_image.value = [image.min, image.max];
         } else {
-            console.error('image data not understood');
+            // we are not dealing with an image, but with an array
+            // which is not normalized, so we can reset the range_image
+            this.image_material.uniforms.range_image.value = [0, 1];
+            var data = image.data;
+            if(data instanceof Uint8Array) {
+                type =  THREE.UnsignedByteType;
+            } else if(data instanceof Float64Array) {
+                console.warn('ImageGLView.data is a Float64Array which WebGL does not support, will convert to a Float32Array (consider sending float32 data for better performance).');
+                data = Float32Array.from(data);
+                type =  THREE.FloatType;
+            } else if(data instanceof Float32Array) {
+                type =  THREE.FloatType;
+            } else {
+                console.error('only types uint8 and float32 are supported');
+                return;
+            }
+            if(this.scales.image.model.get('scheme') && image.shape.length == 2) {
+                if(this.texture)
+                    this.texture.dispose();
+                this.texture = new THREE.DataTexture(data, image.shape[1], image.shape[0], THREE.LuminanceFormat, type);
+                this.texture.needsUpdate = true;
+                this.image_material.uniforms.image.value = this.texture;
+                this.image_material.defines.USE_COLORMAP = true;
+                this.image_material.needsUpdate = true;
+            } else if(image.shape.length == 3) {
+                this.image_material.defines.USE_COLORMAP = false;
+                if(this.texture)
+                    this.texture.dispose();
+                if(image.shape[2] == 3)
+                    this.texture = new THREE.DataTexture(data, image.shape[1], image.shape[0], THREE.RGBFormat, type);
+                if(image.shape[2] == 4)
+                    this.texture = new THREE.DataTexture(data, image.shape[1], image.shape[0], THREE.RGBAFormat, type);
+                this.texture.needsUpdate = true;
+                this.image_material.uniforms.image.value = this.texture;
+            } else {
+                console.error('image data not understood');
+            }
         }
         this.texture.magFilter = interpolations[this.model.get('interpolation')];
         this.texture.minFilter = interpolations[this.model.get('interpolation')];

js/shaders/image-fragment.glsl

@@ -16,6 +16,9 @@ uniform vec2 domain_y;
 uniform vec2 image_domain_x;
 uniform vec2 image_domain_y;
 
+uniform vec2 range_image;
+
+
 bool isnan(float val)
 {
   return (val < 0.0 || 0.0 < val || val == 0.0) ? false : true;
@@ -32,7 +35,10 @@ void main(void) {
     float y_normalized   = scale_transform_linear(y_domain_value, vec2(0., 1.), image_domain_y);
     vec2 tex_uv = vec2(x_normalized, y_normalized);
 #ifdef USE_COLORMAP
-    float raw_value = texture2D(image, tex_uv).r;
+    // r (or g or b) is used for the value, alpha for the mask (is 0 if a nan is found)
+    vec2 pixel_value = texture2D(image, tex_uv).ra;
+    float raw_value = pixel_value[0] * (range_image[1] - range_image[0]) + range_image[0];
+    float opacity_image = pixel_value[1];
     float value = (raw_value - color_min) / (color_max - color_min);
     vec4 color;
     if(isnan(value)) // nan's are interpreted as missing values, and 'not shown'
@@ -41,8 +47,9 @@ void main(void) {
         color = texture2D(colormap, vec2(value, 0.5));
 #else
     vec4 color = texture2D(image, tex_uv);
+    float opacity_image = 1.0;
 #endif
     // since we're working with pre multiplied colors (regarding blending)
     // we also need to multiply rgb by opacity
-    gl_FragColor = color * opacity;
+    gl_FragColor = color * opacity * opacity_image;
 }

setup.py

@@ -51,7 +51,8 @@
     include_package_data=True,
     install_requires=[
         'ipywidgets>=7.0.0',
-        'bqplot>=0.12'
+        'bqplot>=0.12',
+        'pillow',
     ],
     packages=find_packages(),
     zip_safe=False,