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Merge branch 'fix-imagejs-stack' into 'imjoy-support'

Browse source 
Support imagej.js stack, upgrade imjoy-core

See merge request rwb27/openflexure-microscope-server!4
This commit is contained in:
Richard Bowman 2021-05-18 09:53:30 +00:00
commit 1aae062774
3 changed files with 249 additions and 220 deletions
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openflexure_microscope/api/static/package-lock.json generated
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"ws": {
"version": "7.4.5",
"resolved": "https://registry.npmjs.org/ws/-/ws-7.4.5.tgz",
"integrity": "sha512-xzyu3hFvomRfXKH8vOFMU3OguG6oOvhXMo3xsGy3xWExqaM2dxBbVxuD99O7m3ZUFMvvscsZDqxfgMaRr/Nr1g=="
}
}
},
"socket.io-parser": {
"version": "4.0.4",
"resolved": "https://registry.npmjs.org/socket.io-parser/-/socket.io-parser-4.0.4.tgz",
"integrity": "sha512-t+b0SS+IxG7Rxzda2EVvyBZbvFPBCjJoyHuE0P//7OAsN23GItzDRdWa6ALxZI/8R5ygK7jAR6t028/z+7295g==",
"requires": {
"@types/component-emitter": "^1.2.10",
"component-emitter": "~1.3.0",
"debug": "~4.3.1"
},
"dependencies": {
"debug": {
"version": "4.3.1",
"resolved": "https://registry.npmjs.org/debug/-/debug-4.3.1.tgz",
"integrity": "sha512-doEwdvm4PCeK4K3RQN2ZC2BYUBaxwLARCqZmMjtF8a51J2Rb0xpVloFRnCODwqjpwnAoao4pelN8l3RJdv3gRQ==",
"requires": {
"ms": "2.1.2"
}
},
"ms": {
"version": "2.1.2",
"resolved": "https://registry.npmjs.org/ms/-/ms-2.1.2.tgz",
"integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w=="
}
}
},
@ -14004,104 +14150,6 @@
}
}
},
"vue-loader-v16": {
"version": "npm:vue-loader@16.1.2",
"resolved": "https://registry.npmjs.org/vue-loader/-/vue-loader-16.1.2.tgz",
"integrity": "sha512-8QTxh+Fd+HB6fiL52iEVLKqE9N1JSlMXLR92Ijm6g8PZrwIxckgpqjPDWRP5TWxdiPaHR+alUWsnu1ShQOwt+Q==",
"dev": true,
"optional": true,
"requires": {
"chalk": "^4.1.0",
"hash-sum": "^2.0.0",
"loader-utils": "^2.0.0"
},
"dependencies": {
"ansi-styles": {
"version": "4.3.0",
"resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
"integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==",
"dev": true,
"optional": true,
"requires": {
"color-convert": "^2.0.1"
}
},
"chalk": {
"version": "4.1.0",
"resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.0.tgz",
"integrity": "sha512-qwx12AxXe2Q5xQ43Ac//I6v5aXTipYrSESdOgzrN+9XjgEpyjpKuvSGaN4qE93f7TQTlerQQ8S+EQ0EyDoVL1A==",
"dev": true,
"optional": true,
"requires": {
"ansi-styles": "^4.1.0",
"supports-color": "^7.1.0"
}
},
"color-convert": {
"version": "2.0.1",
"resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
"integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==",
"dev": true,
"optional": true,
"requires": {
"color-name": "~1.1.4"
}
},
"color-name": {
"version": "1.1.4",
"resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz",
"integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
"dev": true,
"optional": true
},
"emojis-list": {
"version": "3.0.0",
"resolved": "https://registry.npmjs.org/emojis-list/-/emojis-list-3.0.0.tgz",
"integrity": "sha512-/kyM18EfinwXZbno9FyUGeFh87KC8HRQBQGildHZbEuRyWFOmv1U10o9BBp8XVZDVNNuQKyIGIu5ZYAAXJ0V2Q==",
"dev": true,
"optional": true
},
"has-flag": {
"version": "4.0.0",
"resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz",
"integrity": "sha512-EykJT/Q1KjTWctppgIAgfSO0tKVuZUjhgMr17kqTumMl6Afv3EISleU7qZUzoXDFTAHTDC4NOoG/ZxU3EvlMPQ==",
"dev": true,
"optional": true
},
"json5": {
"version": "2.1.3",
"resolved": "https://registry.npmjs.org/json5/-/json5-2.1.3.tgz",
"integrity": "sha512-KXPvOm8K9IJKFM0bmdn8QXh7udDh1g/giieX0NLCaMnb4hEiVFqnop2ImTXCc5e0/oHz3LTqmHGtExn5hfMkOA==",
"dev": true,
"optional": true,
"requires": {
"minimist": "^1.2.5"
}
},
"loader-utils": {
"version": "2.0.0",
"resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.0.tgz",
"integrity": "sha512-rP4F0h2RaWSvPEkD7BLDFQnvSf+nK+wr3ESUjNTyAGobqrijmW92zc+SO6d4p4B1wh7+B/Jg1mkQe5NYUEHtHQ==",
"dev": true,
"optional": true,
"requires": {
"big.js": "^5.2.2",
"emojis-list": "^3.0.0",
"json5": "^2.1.2"
}
},
"supports-color": {
"version": "7.2.0",
"resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz",
"integrity": "sha512-qpCAvRl9stuOHveKsn7HncJRvv501qIacKzQlO/+Lwxc9+0q2wLyv4Dfvt80/DPn2pqOBsJdDiogXGR9+OvwRw==",
"dev": true,
"optional": true,
"requires": {
"has-flag": "^4.0.0"
}
}
}
},
"vue-observe-visibility": {
"version": "0.4.6",
"resolved": "https://registry.npmjs.org/vue-observe-visibility/-/vue-observe-visibility-0.4.6.tgz",
@ -14840,9 +14888,9 @@
}
},
"xmlhttprequest-ssl": {
"version": "1.5.5",
"resolved": "https://registry.npmjs.org/xmlhttprequest-ssl/-/xmlhttprequest-ssl-1.5.5.tgz",
"integrity": "sha1-wodrBhaKrcQOV9l+gRkayPQ5iz4="
"version": "1.6.2",
"resolved": "https://registry.npmjs.org/xmlhttprequest-ssl/-/xmlhttprequest-ssl-1.6.2.tgz",
"integrity": "sha512-tYOaldF/0BLfKuoA39QMwD4j2m8lq4DIncqj1yuNELX4vz9+z/ieG/vwmctjJce+boFHXstqhWnHSxc4W8f4qg=="
},
"xtend": {
"version": "4.0.2",

2
openflexure_microscope/api/static/package.json
View file

@ -11,7 +11,7 @@
"lint:fix": "vue-cli-service lint --fix"
},
"dependencies": {
"imjoy-core": "^0.13.73",
"imjoy-core": "^0.13.74",
"material-design-icons": "^3.0.1",
"mousetrap": "^1.6.5",
"vue-observe-visibility": "^0.4.6"

33
openflexure_microscope/api/static/src/components/tabContentComponents/imjoyContent.vue
View file

@ -352,7 +352,7 @@ export default {
});
}
};
this.imjoy.pm.registerService({ name: "openflexure" }, service);
this.imjoy.pm.registerService({ name: "#openflexure" }, service);
},
closeWindow(w) {
if (w) {
@ -472,7 +472,7 @@ export default {
}
});
this.$store.commit("imjoy/addOpenScanItem", {
title: "ImageJ.JS",
title: "ImageJ.JS [stack]",
async callback(name, allURLs) {
const viewer = await self.openImageJ();
// allURLs is a list of URLs for *capture objects*, so
@ -481,7 +481,7 @@ export default {
const imagesAsNdarrays = await Promise.all(
allURLs.map(async url => {
const r = await axios.get(url);
return imageUrlToNdarray(r.data.links.download.href);
return await imageUrlToNdarray(r.data.links.download.href);
})
);
// Construct an array to hold all the images, based on the first image
@ -495,7 +495,7 @@ export default {
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);
stackData.set(new Uint8Array(image._rvalue), total);
//assert image._rshape == shape;
return total + image._rvalue.byteLength;
}, 0);
@ -503,36 +503,16 @@ export default {
_rtype: "ndarray",
_rdtype: "uint8",
_rshape: [imagesAsNdarrays.length, shape[0], shape[1], shape[2]],
_rdata: stackData
_rvalue: stackData.buffer
};
console.log(
`Stack is ${transferredBytes} and will have shape: ${stackNdarray._rshape}`
);
await viewer.viewImage(stackNdarray, {
name: "ScanImages"
name
});
}
});
this.$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: ${e}`);
} finally {
@ -540,6 +520,7 @@ export default {
}
},
async addWindow(w) {
// Here we can add check w.standalone if we want to allow the plugin to decide whether to open in a new tab.
this.$store.commit("imjoy/addTab", w);
await this.$nextTick();
//this.$forceUpdate();