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Support imagej.js stack, upgrade core;

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This commit is contained in:
Wei Ouyang 2021-05-14 11:11:06 +02:00
parent 7585e24744
commit 508d9d9acf
3 changed files with 286 additions and 216 deletions
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66
openflexure_microscope/api/static/src/components/tabContentComponents/imjoyContent.vue
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@ -352,7 +352,7 @@ export default {
});
}
};
this.imjoy.pm.registerService({ name: "openflexure" }, service);
this.imjoy.pm.registerService({ name: "#openflexure" }, service);
},
closeWindow(w) {
if (w) {
@ -473,6 +473,48 @@ export default {
});
this.$store.commit("imjoy/addOpenScanItem", {
title: "ImageJ.JS",
async callback(name, allURLs) {
const viewer = await self.openImageJ();
// 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 await 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(new Uint8Array(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.buffer
};
console.log(
`Stack is ${transferredBytes} and will have shape: ${stackNdarray._rshape}`
);
await viewer.viewImage(stackNdarray, {
name: "ScanImages"
});
}
});
this.$store.commit("imjoy/addOpenScanItem", {
title: "ImageJ.JS [JPEGs]",
async callback(name, allURLs) {
const viewer = await self.openImageJ();
// allURLs is a list of URLs for *capture objects*, so
@ -509,30 +551,10 @@ export default {
`Stack is ${transferredBytes} and will have shape: ${stackNdarray._rshape}`
);
await viewer.viewImage(stackNdarray, {
name: "ScanImages"
name: "ScanImages" //TODO: fix the name
});
}
});
this.$store.commit("imjoy/addOpenScanItem", {
title: "ImageJ.JS [JPEGs]",
async callback(name, allURLs) {
const viewer = await self.openImageJ();
// 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).
await Promise.all(
allURLs.map(async url => {
const r = await axios.get(url);
const ndarray = await imageUrlToNdarray(
r.data.links.download.href
);
return viewer.viewImage(ndarray, {
name: r.data.name.replace(".jpeg", "")
});
})
);
}
});
} catch (e) {
alert(`Failed to setup viewers, error: ${e}`);
} finally {