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Transfers of stacks and using ndarrays

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This commit is contained in:
Richard 2021-05-11 21:43:33 +01:00
parent 782ff05477
commit b0f26f1b1e
3 changed files with 168 additions and 9 deletions
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30
openflexure_microscope/api/static/src/components/tabContentComponents/galleryComponents/scanCard.vue
View file

@ -40,6 +40,29 @@
</div>
<div class="uk-card-footer uk-padding-small">
<button
v-if="openScanInImjoyMenuItemsPresent"
class="uk-icon"
type="button"
>
<img
style="width:25px;"
src="https://imjoy.io/static/img/imjoy-icon.svg"
/>
</button>
<div uk-dropdown="pos: top-center">
<ul class="uk-nav uk-dropdown-nav">
<li v-for="item in openScanInImjoyMenuItems" :key="item.name">
<a
href="#"
class="uk-text-emphasis"
@click="item.callback(name, allURLs)"
><i class="material-icons">launch</i>{{ item.title }}</a
>
</li>
</ul>
</div>
&nbsp;
<span
v-for="tag in tags"
:key="tag"
@ -53,6 +76,7 @@
<script>
import axios from "axios";
import { mapState } from "vuex";
// Export main app
export default {
@ -100,7 +124,11 @@ export default {
urls.push(capture.links.self.href);
}
return urls;
}
},
openScanInImjoyMenuItemsPresent: function() {
return this.openScanInImjoyMenuItems.length > 0;
},
...mapState(["openScanInImjoyMenuItems"])
},
methods: {

141
openflexure_microscope/api/static/src/components/tabContentComponents/imjoyContent.vue
View file

@ -113,6 +113,64 @@ async function pollAction(response) {
return r;
}
/**
* Create a new Image element and wait for it to load.
*
* This returns a Promise, so you can "await" the image
* element rather than needing to add a callback.
*/
function loadImageFromUrl(src) {
// Create an Image, and return it once it has loaded
// see https://stackoverflow.com/a/66180709
// no need to declare async, as it returns a Promise
return new Promise((resolve, reject) => {
const img = new Image();
// We must set crossOrigin="anonymous" in order
// to avoid security errors when we get the pixel
// data
img.crossOrigin = "anonymous";
img.onload = () => resolve(img);
img.onerror = reject;
img.src = src;
});
}
/**
* Retrieve an image from a URL, and return the RGB data
* in a format that can be cast to an ndarray
*
* This follows a slightly convoluted recipe, where we
* "draw" the image, and then extract the pixels from the
* 2D canvas.
*/
async function imageUrlToNdarray(url) {
// see https://stackoverflow.com/questions/934012/get-image-data-url-in-javascript
const img = await loadImageFromUrl(url);
const canvas = document.createElement("canvas");
canvas.width = img.width;
canvas.height = img.height;
const ctx = canvas.getContext("2d");
ctx.drawImage(img, 0, 0, img.width, img.height);
const imageData = ctx.getImageData(0, 0, img.width, img.height);
const rgbaData = imageData.data; // This gets the RGBA values as an ArrayBuffer
// convert RGBA to RGB
const rgbData = new Uint8Array(new ArrayBuffer(img.height * img.width * 3));
for (let i = 0; i < img.height; i++) {
for (let j = 0; j < img.width; j++) {
const pos = i * img.width + j;
rgbData[pos * 3] = rgbaData[pos * 4];
rgbData[pos * 3 + 1] = rgbaData[pos * 4 + 1];
rgbData[pos * 3 + 2] = rgbaData[pos * 4 + 2];
}
}
return {
_rtype: "ndarray",
_rdtype: "uint8",
_rshape: [img.height, img.width, 3],
_rvalue: rgbData.buffer
};
}
export default {
name: "ImJoyContent",
@ -151,7 +209,7 @@ export default {
// however, some browser features won't work (e.g. webrtc)
// unless we explicitly set `base_frame` in the plugin to
// https://lib.imjoy.io/default_base_frame.html
default_base_frame: 'http://lib.imjoy.io/default_base_frame.html',
default_base_frame: "http://lib.imjoy.io/default_base_frame.html",
imjoy_api: {
async showDialog(plugin, config, exta_config) {
return await imjoy.pm.createWindow(plugin, config, exta_config);
@ -318,7 +376,7 @@ export default {
});
},
async getPosition() {
const {z} = await getPositionAsObject();
const { z } = await getPositionAsObject();
return z;
},
async setXYPosition(x, y) {
@ -329,11 +387,11 @@ export default {
});
},
async getXYPosition() {
const {x, y} = await getPositionAsObject();
const { x, y } = await getPositionAsObject();
return [x, y];
},
async getXYZPosition() {
const {x, y, z} = await getPositionAsObject();
const { x, y, z } = await getPositionAsObject();
return [x, y, z];
},
async setXYZPosition(x, y, z) {
@ -405,6 +463,15 @@ export default {
try {
const self = this;
/*async function obtainImageJ() {
self.$root.$emit("globalSwitchTab", "ImJoy");
if(!self.viewers.imagej) {
await self.startImageJ();
}
self.selectWindow("ImageJ.JS");
return self.viewers.imagej;
}*/
this.$store.commit("addOpenInImjoyMenuItem", {
title: "Kaibu",
async callback(name, imageUrl) {
@ -435,6 +502,68 @@ export default {
});
}
});
this.$store.commit("addOpenInImjoyMenuItem", {
title: "ImageJ.JS [ndarray]",
async callback(name, imageUrl) {
self.$root.$emit("globalSwitchTab", "ImJoy");
if (!self.viewers.imagej) {
await self.startImageJ();
}
self.selectWindow("ImageJ.JS");
const viewer = self.viewers.imagej;
const ndarray = await imageUrlToNdarray(imageUrl);
await viewer.viewImage(ndarray, {
name: name.replace(".jpeg", "")
});
}
});
this.$store.commit("addOpenScanInImjoyMenuItem", {
title: "ImageJ.JS",
async callback(name, allURLs) {
self.$root.$emit("globalSwitchTab", "ImJoy");
if (!self.viewers.imagej) {
await self.startImageJ();
}
self.selectWindow("ImageJ.JS");
const viewer = self.viewers.imagej;
// allURLs is a list of URLs for *capture objects*, so
// first we need to retrieve them, then extract image URLs
// and finally turn image URLs into "numpy arrays" (RGB data).
const imagesAsNdarrays = await Promise.all(
allURLs.map(async url => {
const r = await axios.get(url);
return imageUrlToNdarray(r.data.links.download.href);
})
);
// Construct an array to hold all the images, based on the first image
// TODO: assert that _rdtype is uint8, _rshape is the same, _rtype is ndarray
const shape = imagesAsNdarrays[0]._rshape;
const totalSize = imagesAsNdarrays.reduce(
(total, image) => total + image._rvalue.byteLength,
0
);
const stackData = new Uint8Array(new ArrayBuffer(totalSize));
const transferredBytes = imagesAsNdarrays.reduce((total, image) => {
console.log(`inserting image at ${total} bytes`);
// TODO: is it bad to populate stackData as a "side effect"?
stackData.set(image._rvalue, total);
//assert image._rshape == shape;
return total + image._rvalue.byteLength;
}, 0);
const stackNdarray = {
_rtype: "ndarray",
_rdtype: "uint8",
_rshape: [imagesAsNdarrays.length, shape[0], shape[1], shape[2]],
_rdata: stackData
};
console.log(
`Stack is ${transferredBytes} and will have shape: ${stackNdarray._rshape}`
);
await viewer.viewImage(stackNdarray, {
name: "ScanImages"
});
}
});
} catch (e) {
alert(`Failed to setup viewers, error: ${e}`);
} finally {
@ -498,9 +627,7 @@ export default {
return axios.get(this.getPositionUri).then(r => r.data);
},
async setStagePosition(payload) {
return axios
.post(this.moveActionUri, payload)
.then(pollAction)
return axios.post(this.moveActionUri, payload).then(pollAction);
}
}
};

6
openflexure_microscope/api/static/src/store.js
View file

@ -15,7 +15,8 @@ export default new Vuex.Store({
IHIEnabled: false,
appTheme: "system",
activeStreams: {},
openInImjoyMenuItems: []
openInImjoyMenuItems: [],
openScanInImjoyMenuItems: []
},
mutations: {
@ -60,6 +61,9 @@ export default new Vuex.Store({
},
addOpenInImjoyMenuItem(state, newItem) {
state.openInImjoyMenuItems.push(newItem);
}, // TODO: add a mutation to remove items when plugins are unloaded
addOpenScanInImjoyMenuItem(state, newItem) {
state.openScanInImjoyMenuItems.push(newItem);
} // TODO: add a mutation to remove items when plugins are unloaded
},