How to save spatial reference to GeoTIFF created by node-gdal? - javascript

I am trying to create a GeoTIFF using node-gdal and set the spatial reference to it. The spatial reference is from an existing file and write the code like this
// read an existing file and get its spatial reference
let dataset = gdal.open(filePath);
this.bandData = dataset.bands.get(1);
this.rasterSize = dataset.rasterSize;
this.geoTransform = dataset.geoTransform;
this.spatialReference = dataset.spatialReference;
// save the same spatial reference to a new file
let driver = gdal.drivers.get('GTiff');
let dataset = driver.create(filePath, this.rasterSize.x, this.rasterSize.y, 1, gdal.GDT_Byte);
let bandData = dataset.bands.get(1);
bandData.pixels.write(0, 0, this.rasterSize.x, this.rasterSize.y, data);
dataset.spatialReference = this.spatialReference;
dataset.geoTransform = this.geoTransform;
dataset.flush();
However, when I load the saved file with QGIS, it suggests the GeoTIFF doesn't have any projection information.
The full code can be found HERE.

This is obviously a typo :-(
this.spatialReference = dataset.spatialReference;
should be
this.src = dataset.src;

Related

Script to export all Android-relevant resolutions for each layer in an artboard

Context
For Android development I am trying to create a script for Illustrator that exports my vector-work from each layer to the .png-format, whereby each export has to be provided in all density (ppi)-formats Android needs. I know that I can export images like:
png24_settings = function ( ) {
var options = new ExportOptionsPNG24();
options.antiAliasing = true;
options... = ...
...
return options;
}
var file_destination = "Some string with the destination path and name"
var doc = app.activeDocument; //Retrieve active document
doc.exportFile(file_destination, ExportType.PNG24, png24_settings() ); // Exports visible canvas
Each layer can be exported by looping over the layers and setting all other layers invisible.
However, I cannot create a loop with the given function that helps me with my density problem.
Question
The exportFile()-func does not take any resolution parameter and, thus, cannot be used to create the different density-files needed for Android (hdpi, xhdpi, ...).
Which option do I have to export each single layer in all the necessary ppi-formats?
With some consultation of the docs I was able to solve my problem.
There exists a function called imageCapture() which contains a resolution-parameter for the desired ppi (link to docs). Note that this function will export all visible layers on an artboard. Thus, the iteration for the export needs to take care of visibility.
With this information, I can iterate over each layer in my artboard and do the export.
The script would look like the one provided below. I know its a little exhaustive, but I hope it helps to get a clear understanding.
Provide setup information
// Provide density-information necessary for android
android_densities = [
120 // ldpi
, 160 // mdpi
, 240 // hdpi
, 320 // xhdpi
, 480 // xxhdpi
, 640 // xxxhdpi
]
// Provide settings for image export which takes the respective density as argument
setOptions = function(density) {
var options = new ImageCaptureOptions();
options.artBoardClipping = true;
options.resolution = density // Your desired ppi
options... // Provide other options you'd also like to implement.
return options;
}
// Initialize current document as document to work with
var doc = app.activeDocument; //Gets the active document
// Retrieve current directory of illustrator-document as default path to save to
// If you want to save anywhere else, just provide it here
var filePath = (app.activeDocument.fullName.parent.fsName).toString().replace(/\\/g, '/');
// Select current artboard according to current document
// This is the artboard you want to export your layers from
var activeAB = doc.artboards[doc.artboards.getActiveArtboardIndex()];
Note: Android-densities are provided here in the docs.
Iterative export
// Export, for example, all visible layers.
// Thus, all layers are first iterated, checked for visibility and set invisible.
// Because of the last step all elements have to be cached in an array (= export_layers)
export_layers= []; // Store layers to export
for(var i=0; i<doc.layers.length; i++){
var layer = doc.layers[i];
if(layer.visible){
export_layers.push(i);
doc.layers[i].visible=false;
};
}
// Do exports
for(var exportElement=0; exportElement<export_layers.length; exportElement++) {
// Get layer to export
var layer = doc.layers[export_layers[exportElement]];
// Set this layer visible (it is the only layer visible now, because imageCapture will export all visible layers)
doc.layers[export_layers[exportElement]].visible=true;
// Iterate over all densities
for(var densityElement=0; densityElement<android_densities.length; densityElement++) {
// Provide path and name for output image
var destination_of_file = new File(filePath + "/" + layer.name + "_" + String(android_densities[densityElement]) + ".png");
// Save file with resolution
doc.imageCapture(destination_of_file, activeAB.artboardRect, setOptions(android_densities[densityElement]));
}
// Set visibility to false again for next layer to be exported correctly
doc.layers[export_layers[exportElement]].visible=false;
}
// Finally, reset the visibility-status prior to the export
for(var resetElement=0; i<export_layers.length; resetElement++) {
doc.layers[export_layers[resetElement]].visible=true;
}
After that you should have all layers in all densities in your specified folder. Of course this can be much more elegant by providing a folder for each resolution and so on - I just tried to keep it to the point for the answer :)

Running Frozen Tensorflow model on NodeJS

I'm new to tensorflowjs (and js in general), however I need to run a trained model on it.
Currently I converted the model to json format, but struggle to feed data to it:
const tf = require('#tensorflow/tfjs')
const tfn = require('#tensorflow/tfjs-node-gpu')
async function start() {
const handler = tfn.io.fileSystem("./model/model.json");
const model = await tf.loadGraphModel(handler);
let latents = tf.randomNormal([1,512], 'float32');
let labels = tf.zeros([1, 0]);
model.predict([latents, labels]);
}
start();
But I receive an error saying The Conv2D op currently supports NHWC tensor format on the CPU. The op was given the format: NCHW
So as I understood, it is a tfjs issue, so I tried to create a float32 array and pass it to model like this:
var f32array = new Float32Array(512);
model.predict([f32array, labels]);
But then I see an error saying the dtype of dict['Gs/latents_in'] provided in model.execute(dict) must be float32, but was undefined
With python, I'm running inference by using this code:
graph = load_graph("dash/frozen_model.pb")
x = graph.get_tensor_by_name('prefix/Gs/latents_in:0')
x2 = graph.get_tensor_by_name('prefix/Gs/labels_in:0')
y = graph.get_tensor_by_name('prefix/Gs/images_out:0')
with tf.Session(graph=graph, config = config) as sess:
while True:
start_time = time.time()
latents = np.random.randn(1, 512).astype(np.float32)
labels = np.zeros([latents.shape[0], 0], np.float32)
y_out = sess.run(y, feed_dict = { x: latents, x2: labels})
Would appreciate any help
Passing the data as Float32Array will not work since model.predict expects either a tensor or an array of tensors.
As indicated by the error:
The Conv2D op currently supports NHWC tensor format on the CPU. The op was given the format: NCHW
the conv2D as of the version 1.6 in js only supports the format NHWC. The only thing you can do is to change the model in python in order to use only the NHWC format.

How to train a model in nodejs (tensorflow.js)?

I want to make a image classifier, but I don't know python.
Tensorflow.js works with javascript, which I am familiar with. Can models be trained with it and what would be the steps to do so?
Frankly I have no clue where to start.
The only thing I figured out is how to load "mobilenet", which apparently is a set of pre-trained models, and classify images with it:
const tf = require('#tensorflow/tfjs'),
mobilenet = require('#tensorflow-models/mobilenet'),
tfnode = require('#tensorflow/tfjs-node'),
fs = require('fs-extra');
const imageBuffer = await fs.readFile(......),
tfimage = tfnode.node.decodeImage(imageBuffer),
mobilenetModel = await mobilenet.load();
const results = await mobilenetModel.classify(tfimage);
which works, but it's no use to me because I want to train my own model using my images with labels that I create.
=======================
Say I have a bunch of images and labels. How do I use them to train a model?
const myData = JSON.parse(await fs.readFile('files.json'));
for(const data of myData){
const image = await fs.readFile(data.imagePath),
labels = data.labels;
// how to train, where to pass image and labels ?
}
First of all, the images needs to be converted to tensors. The first approach would be to create a tensor containing all the features (respectively a tensor containing all the labels). This should the way to go only if the dataset contains few images.
const imageBuffer = await fs.readFile(feature_file);
tensorFeature = tfnode.node.decodeImage(imageBuffer) // create a tensor for the image
// create an array of all the features
// by iterating over all the images
tensorFeatures = tf.stack([tensorFeature, tensorFeature2, tensorFeature3])
The labels would be an array indicating the type of each image
labelArray = [0, 1, 2] // maybe 0 for dog, 1 for cat and 2 for birds
One needs now to create a hot encoding of the labels
tensorLabels = tf.oneHot(tf.tensor1d(labelArray, 'int32'), 3);
Once there is the tensors, one would need to create the model for training. Here is a simple model.
const model = tf.sequential();
model.add(tf.layers.conv2d({
inputShape: [height, width, numberOfChannels], // numberOfChannels = 3 for colorful images and one otherwise
filters: 32,
kernelSize: 3,
activation: 'relu',
}));
model.add(tf.layers.flatten());
model.add(tf.layers.dense({units: 3, activation: 'softmax'}));
Then the model can be trained
model.fit(tensorFeatures, tensorLabels)
If the dataset contains a lot of images, one would need to create a tfDataset instead. This answer discusses why.
const genFeatureTensor = image => {
const imageBuffer = await fs.readFile(feature_file);
return tfnode.node.decodeImage(imageBuffer)
}
const labelArray = indice => Array.from({length: numberOfClasses}, (_, k) => k === indice ? 1 : 0)
function* dataGenerator() {
const numElements = numberOfImages;
let index = 0;
while (index < numFeatures) {
const feature = genFeatureTensor(imagePath);
const label = tf.tensor1d(labelArray(classImageIndex))
index++;
yield {xs: feature, ys: label};
}
}
const ds = tf.data.generator(dataGenerator).batch(1) // specify an appropriate batchsize;
And use model.fitDataset(ds) to train the model
The above is for training in nodejs. To do such a processing in the browser, genFeatureTensor can be written as follow:
function loadImage(url){
return new Promise((resolve, reject) => {
const im = new Image()
im.crossOrigin = 'anonymous'
im.src = 'url'
im.onload = () => {
resolve(im)
}
})
}
genFeatureTensor = image => {
const img = await loadImage(image);
return tf.browser.fromPixels(image);
}
One word of caution is that doing heavy processing might block the main thread in the browser. This is where web workers come into play.
Consider the exemple https://codelabs.developers.google.com/codelabs/tfjs-training-classfication/#0
What they do is:
take a BIG png image (a vertical concatenation of images)
take some labels
build the dataset (data.js)
then train
The building of the dataset is as follows:
images
The big image is divided into n vertical chunks.
(n being chunkSize)
Consider a chunkSize of size 2.
Given the pixel matrix of image 1:
1 2 3
4 5 6
Given the pixel matrix of image 2 is
7 8 9
1 2 3
The resulting array would be
1 2 3 4 5 6 7 8 9 1 2 3 (the 1D concatenation somehow)
So basically at the end of the processing, you have a big buffer representing
[...Buffer(image1), ...Buffer(image2), ...Buffer(image3)]
labels
That kind of formatting is done a lot for classification problems. Instead of classifying with a number, they take a boolean array.
To predict 7 out of 10 classes we would consider
[0,0,0,0,0,0,0,1,0,0] // 1 in 7e position, array 0-indexed
What you can do to get started
Take your image (and its associated label)
Load your image to the canvas
Extract its associated buffer
Concatenate all your image's buffer as a big buffer. That's it for xs.
Take all your associated labels, map them as a boolean array, and concatenate them.
Below, I subclass MNistData::load (the rest can be let as is (except in script.js where you need to instantiate your own class instead)
I still generate 28x28 images, write a digit on it, and get a perfect accuracy since I don't include noise or voluntarily wrong labelings.
import {MnistData} from './data.js'
const IMAGE_SIZE = 784;// actually 28*28...
const NUM_CLASSES = 10;
const NUM_DATASET_ELEMENTS = 5000;
const NUM_TRAIN_ELEMENTS = 4000;
const NUM_TEST_ELEMENTS = NUM_DATASET_ELEMENTS - NUM_TRAIN_ELEMENTS;
function makeImage (label, ctx) {
ctx.fillStyle = 'black'
ctx.fillRect(0, 0, 28, 28) // hardcoded, brrr
ctx.fillStyle = 'white'
ctx.fillText(label, 10, 20) // print a digit on the canvas
}
export class MyMnistData extends MnistData{
async load() {
const canvas = document.createElement('canvas')
canvas.width = 28
canvas.height = 28
let ctx = canvas.getContext('2d')
ctx.font = ctx.font.replace(/\d+px/, '18px')
let labels = new Uint8Array(NUM_DATASET_ELEMENTS*NUM_CLASSES)
// in data.js, they use a batch of images (aka chunksize)
// let's even remove it for simplification purpose
const datasetBytesBuffer = new ArrayBuffer(NUM_DATASET_ELEMENTS * IMAGE_SIZE * 4);
for (let i = 0; i < NUM_DATASET_ELEMENTS; i++) {
const datasetBytesView = new Float32Array(
datasetBytesBuffer, i * IMAGE_SIZE * 4,
IMAGE_SIZE);
// BEGIN our handmade label + its associated image
// notice that you could loadImage( images[i], datasetBytesView )
// so you do them by bulk and synchronize after your promises after "forloop"
const label = Math.floor(Math.random()*10)
labels[i*NUM_CLASSES + label] = 1
makeImage(label, ctx)
const imageData = ctx.getImageData(0, 0, canvas.width, canvas.height);
// END you should be able to load an image to canvas :)
for (let j = 0; j < imageData.data.length / 4; j++) {
// NOTE: you are storing a FLOAT of 4 bytes, in [0;1] even though you don't need it
// We could make it with a uint8Array (assuming gray scale like we are) without scaling to 1/255
// they probably did it so you can copy paste like me for color image afterwards...
datasetBytesView[j] = imageData.data[j * 4] / 255;
}
}
this.datasetImages = new Float32Array(datasetBytesBuffer);
this.datasetLabels = labels
//below is copy pasted
this.trainIndices = tf.util.createShuffledIndices(NUM_TRAIN_ELEMENTS);
this.testIndices = tf.util.createShuffledIndices(NUM_TEST_ELEMENTS);
this.trainImages = this.datasetImages.slice(0, IMAGE_SIZE * NUM_TRAIN_ELEMENTS);
this.testImages = this.datasetImages.slice(IMAGE_SIZE * NUM_TRAIN_ELEMENTS);
this.trainLabels =
this.datasetLabels.slice(0, NUM_CLASSES * NUM_TRAIN_ELEMENTS);// notice, each element is an array of size NUM_CLASSES
this.testLabels =
this.datasetLabels.slice(NUM_CLASSES * NUM_TRAIN_ELEMENTS);
}
}
I found a tutorial [1] how to use existing model to train new classes. Main code parts here:
index.html head:
<script src="https://unpkg.com/#tensorflow-models/knn-classifier"></script>
index.html body:
<button id="class-a">Add A</button>
<button id="class-b">Add B</button>
<button id="class-c">Add C</button>
index.js:
const classifier = knnClassifier.create();
....
// Reads an image from the webcam and associates it with a specific class
// index.
const addExample = async classId => {
// Capture an image from the web camera.
const img = await webcam.capture();
// Get the intermediate activation of MobileNet 'conv_preds' and pass that
// to the KNN classifier.
const activation = net.infer(img, 'conv_preds');
// Pass the intermediate activation to the classifier.
classifier.addExample(activation, classId);
// Dispose the tensor to release the memory.
img.dispose();
};
// When clicking a button, add an example for that class.
document.getElementById('class-a').addEventListener('click', () => addExample(0));
document.getElementById('class-b').addEventListener('click', () => addExample(1));
document.getElementById('class-c').addEventListener('click', () => addExample(2));
....
Main idea is to use existing network to make its prediction and then substitute the found label with your own one.
Complete code is in the tutorial. Another promising, more advanced one in [2]. It needs strict pre processing, so I leave it only here, I mean it is so much more advanced one.
Sources:
[1] https://codelabs.developers.google.com/codelabs/tensorflowjs-teachablemachine-codelab/index.html#6
[2] https://towardsdatascience.com/training-custom-image-classification-model-on-the-browser-with-tensorflow-js-and-angular-f1796ed24934
TL;DR
MNIST is the image recognition Hello World. After learning it by heart, these questions in your mind are easy to solve.
Question setting:
Your main question written is
// how to train, where to pass image and labels ?
inside your code block. For those I found perfect answer from examples of Tensorflow.js examples section: MNIST example. My below links have pure javascript and node.js versions of it and Wikipedia explanation. I will go them through on the level necessary to answer the main question in your mind and I will add also perspectives how your own images and labels have anything to do with MNIST image set and the examples using it.
First things first:
Code snippets.
where to pass images (Node.js sample)
async function loadImages(filename) {
const buffer = await fetchOnceAndSaveToDiskWithBuffer(filename);
const headerBytes = IMAGE_HEADER_BYTES;
const recordBytes = IMAGE_HEIGHT * IMAGE_WIDTH;
const headerValues = loadHeaderValues(buffer, headerBytes);
assert.equal(headerValues[0], IMAGE_HEADER_MAGIC_NUM);
assert.equal(headerValues[2], IMAGE_HEIGHT);
assert.equal(headerValues[3], IMAGE_WIDTH);
const images = [];
let index = headerBytes;
while (index < buffer.byteLength) {
const array = new Float32Array(recordBytes);
for (let i = 0; i < recordBytes; i++) {
// Normalize the pixel values into the 0-1 interval, from
// the original 0-255 interval.
array[i] = buffer.readUInt8(index++) / 255;
}
images.push(array);
}
assert.equal(images.length, headerValues[1]);
return images;
}
Notes:
MNIST dataset is a huge image, where in one file there are several images like tiles in puzzle, each and every with same size, side by side, like boxes in x and y coordination table. Each box has one sample and corresponding x and y in the labels array has the label. From this example, it is not a big deal to turn it to several files format, so that actually only one pic at a time is given to the while loop to handle.
Labels:
async function loadLabels(filename) {
const buffer = await fetchOnceAndSaveToDiskWithBuffer(filename);
const headerBytes = LABEL_HEADER_BYTES;
const recordBytes = LABEL_RECORD_BYTE;
const headerValues = loadHeaderValues(buffer, headerBytes);
assert.equal(headerValues[0], LABEL_HEADER_MAGIC_NUM);
const labels = [];
let index = headerBytes;
while (index < buffer.byteLength) {
const array = new Int32Array(recordBytes);
for (let i = 0; i < recordBytes; i++) {
array[i] = buffer.readUInt8(index++);
}
labels.push(array);
}
assert.equal(labels.length, headerValues[1]);
return labels;
}
Notes:
Here, labels are also byte data in a file. In Javascript world, and with the approach you have in your starting point, labels could also be a json array.
train the model:
await data.loadData();
const {images: trainImages, labels: trainLabels} = data.getTrainData();
model.summary();
let epochBeginTime;
let millisPerStep;
const validationSplit = 0.15;
const numTrainExamplesPerEpoch =
trainImages.shape[0] * (1 - validationSplit);
const numTrainBatchesPerEpoch =
Math.ceil(numTrainExamplesPerEpoch / batchSize);
await model.fit(trainImages, trainLabels, {
epochs,
batchSize,
validationSplit
});
Notes:
Here model.fit is the actual line of code that does the thing: trains the model.
Results of the whole thing:
const {images: testImages, labels: testLabels} = data.getTestData();
const evalOutput = model.evaluate(testImages, testLabels);
console.log(
`\nEvaluation result:\n` +
` Loss = ${evalOutput[0].dataSync()[0].toFixed(3)}; `+
`Accuracy = ${evalOutput[1].dataSync()[0].toFixed(3)}`);
Note:
In Data Science, also this time here, the most faschinating part is to know how well the model survives the test of new data and no labels, can it label them or not? For that is the evaluation part that now prints us some numbers.
Loss and accuracy: [4]
The lower the loss, the better a model (unless the model has over-fitted to the training data). The loss is calculated on training and validation and its interperation is how well the model is doing for these two sets. Unlike accuracy, loss is not a percentage. It is a summation of the errors made for each example in training or validation sets.
..
The accuracy of a model is usually determined after the model parameters are learned and fixed and no learning is taking place. Then the test samples are fed to the model and the number of mistakes (zero-one loss) the model makes are recorded, after comparison to the true targets.
More information:
In the github pages, in README.md file, there is a link to tutorial, where all in the github example is explained in greater detail.
[1] https://github.com/tensorflow/tfjs-examples/tree/master/mnist
[2] https://github.com/tensorflow/tfjs-examples/tree/master/mnist-node
[3] https://en.wikipedia.org/wiki/MNIST_database
[4] How to interpret "loss" and "accuracy" for a machine learning model

JavaScript callback to get selected glyph index in Bokeh

I've created a visual graph using Bokeh that shows a network I created using Networkx. I now want to use TapTool to show information pertinent to any node on the graph that I click on. The graph is just nodes and edges. I know I should be able to use var inds = cb_obj.selected['1d'].indices; in the JavaScript callback function to get the indices of the nodes (glyphs) that were clicked on, but that's not working somehow and I get the error message, Uncaught TypeError: Cannot read property '1d' of undefined. A nudge in the right direction would be greatly appreciated.
Below is my code. Please note that I've defined my plot as a Plot() and not as a figure(). I don't think that's the reason for the issue, but just wanted to mention it. Also, I'm using window.alert(inds); just to see what values I get. That's not my ultimate purpose, but I expect that bit to work anyway.
def draw_graph_____(self, my_network):
self.graph_height, self.graph_width, self.graph_nodes, self.graph_edges, self.node_coords, self.node_levels = self.compute_graph_layout(my_network)
graph = nx.DiGraph()
graph.add_nodes_from(self.graph_nodes)
graph.add_edges_from(self.graph_edges)
plot = Plot(plot_width = self.graph_width, plot_height = self.graph_height, x_range = Range1d(0.0, 1.0), y_range = Range1d(0.0, 1.0))
plot.title.text = "Graph Demonstration"
graph_renderer = from_networkx(graph, self.graph_layout, scale = 1, center = (-100, 100))
graph_renderer.node_renderer.data_source.data["node_names"] = self.graph_nodes
graph_renderer.node_renderer.data_source.data["index"] = self.graph_nodes
graph_renderer.node_renderer.glyph = Circle(size = 40, fill_color = Spectral4[0])
graph_renderer.node_renderer.selection_glyph = Circle(size = 40, fill_color = Spectral4[2])
graph_renderer.node_renderer.hover_glyph = Circle(size = 40, fill_color = Spectral4[1])
graph_renderer.edge_renderer.glyph = MultiLine(line_color = "#CCCCCC", line_alpha = 0.8, line_width = 5)
graph_renderer.edge_renderer.selection_glyph = MultiLine(line_color = Spectral4[2], line_width = 5)
graph_renderer.edge_renderer.hover_glyph = MultiLine(line_color = Spectral4[1], line_width = 5)
graph_renderer.selection_policy = NodesAndLinkedEdges()
graph_renderer.inspection_policy = NodesAndLinkedEdges()
x_coord = [coord[0] for coord in self.node_coords]
y_coord = [coord[1] for coord in self.node_coords]
y_offset = []
for level in self.node_levels:
for item in self.node_levels[level]:
if self.node_levels[level].index(item) % 2 == 0:
y_offset.append(20)
else:
y_offset.append(-40)
graph_renderer.node_renderer.data_source.data["x_coord"] = x_coord
graph_renderer.node_renderer.data_source.data["y_coord"] = y_coord
graph_renderer.node_renderer.data_source.data["y_offset"] = y_offset
labels_source = graph_renderer.node_renderer.data_source
labels = LabelSet(x = "x_coord", y = "y_coord", text = 'node_names', text_font_size = "12pt", level = 'glyph',
x_offset = -50, y_offset = "y_offset", source = labels_source, render_mode = 'canvas')
plot.add_layout(labels)
callback = CustomJS(args = dict(source = graph_renderer.node_renderer.data_source), code =
"""
console.log(cb_obj)
var inds = cb_obj.selected['1d'].indices;
window.alert(inds);
""")
plot.add_tools(HoverTool(tooltips = [("Node", "#node_names"), ("Recomm", "Will put a sample recommendation message here later")]))
plot.add_tools(TapTool(callback = callback))
plot.renderers.append(graph_renderer)
output_file("interactive_graphs.html")
show(plot)
My imports are as follows, by the way:
import collections
import networkx as nx
import numpy as np
from bokeh.io import output_file, show
from bokeh.models import Circle, ColumnDataSource, CustomJS, Div, HoverTool, LabelSet, MultiLine, OpenURL, Plot, Range1d, TapTool
from bokeh.models.graphs import from_networkx, NodesAndLinkedEdges
from bokeh.palettes import Spectral4
I'm sorry for not posting entire code, but that would require quite a few changes to make dummy data and show other files and functions (which I should have), but I thought just this one function may suffice for the identification of the issue. If not, I'm happy to share more code. Thanks!
The problem is that the callback is not attached to a data source. The value of cb_obj is whatever object triggers the callback. But only ColumnDataSource objects have a selected property, so only callbacks on data sources will have cb_obj.selected. If you are wanting to have a callback fire whenever a selection changes, i.e. whenever a node is clicked on, then you'd want to have the callback on the data source. [1]
However, if you want to have a callback when a node is merely hovered over (but not clicked on) that is an inspection, not a selection. You will want to follow this example:
https://docs.bokeh.org/en/latest/docs/user_guide/interaction/callbacks.html#customjs-for-hover
Although it is not often used (and thus not documented terribly well) the callback for hover tools gets passed additional information in a cb_data parameter. This cb_data parameter is used as a catch-all mechanism for tools to be able to pass extra things, specific to the tool, on to the callback. In the case of hover tools, cb_data is an object that has .index and .geometry attributes. So cb_data.index['1d'].indices has the indices of the points that are currently hovered over. The .geometry attribute as information about the kind of hit test that was performed (i.e. was a single point? or a vertical or horizontal span? And what was the location of the point or span?)
[1] Alternatively, tap tools also pass a specialized cb_data as described above. It is an object with a .source property that the the data source that made a selection. So cb_data.source.selected should work. In practice I never use this though, since a callback on the data source works equally well.

How to clamp GeoJSON data format to terrain in Cesium Sandcastle?

I have terrain view in Cesium Sandcastle and I have loaded roads data in GeoJSON format, they are lines. I want to clamp them on terrain, like this example (in drop-down menu choose "Sample line positions and draw with depth test disabled") -> http://cesiumjs.org/Cesium/Apps/Sandcastle/index.html?src=Ground%20Clamping.html&label=Tutorials
In the example, the line you see is defined within code, but I have data (roads) on my PC which is loaded in app. When loaded, roads are flat (under the terrain) and somehow I have to clamp them on terrain but don't know how.
I have tried using the existing code from the example but haven't succeed.
This is my code for now:
//Add terrain
var viewer = new Cesium.Viewer('cesiumContainer');
var cesiumTerrainProviderMeshes = new Cesium.CesiumTerrainProvider({
url : 'https://assets.agi.com/stk-terrain/v1/tilesets/world/tiles',
requestWaterMask : true,
requestVertexNormals : true
});
viewer.terrainProvider = cesiumTerrainProviderMeshes;
viewer.scene.globe.depthTestAgainstTerrain = true;
//Load data (roads)
var dataSource = Cesium.GeoJsonDataSource.load('../../SampleData/ceste_rab_okvir.geojson');
viewer.dataSources.add(dataSource);
viewer.zoomTo(dataSource);
I know there is Cesium.GeoJsonDataSource.clampToGround, but as I'm not a developer, I don't understand how to write it in my code.
Does anyone knows how to do it? Or maybe there is another way to clamp roads to terrain?
Thanks in advance.
I've figured it out. It should be written like this:
//Add terrain
var viewer = new Cesium.Viewer('cesiumContainer');
var cesiumTerrainProviderMeshes = new Cesium.CesiumTerrainProvider({
url : 'https://assets.agi.com/stk-terrain/v1/tilesets/world/tiles',
requestWaterMask : true,
requestVertexNormals : true
});
viewer.terrainProvider = cesiumTerrainProviderMeshes;
viewer.scene.globe.depthTestAgainstTerrain = true;
//Load data (roads)
Cesium.GeoJsonDataSource.clampToGround = true;
var dataSource = Cesium.GeoJsonDataSource.load('../../SampleData/ceste_rab_okvir.geojson');
viewer.dataSources.add(dataSource);
viewer.zoomTo(dataSource);

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