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"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", diff --git a/openflexure_microscope/api/static/package.json b/openflexure_microscope/api/static/package.json index eea4b212..d1c31011 100644 --- a/openflexure_microscope/api/static/package.json +++ b/openflexure_microscope/api/static/package.json @@ -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" diff --git a/openflexure_microscope/api/static/src/components/tabContentComponents/imjoyContent.vue b/openflexure_microscope/api/static/src/components/tabContentComponents/imjoyContent.vue index bba47a64..4dbbe395 100644 --- a/openflexure_microscope/api/static/src/components/tabContentComponents/imjoyContent.vue +++ b/openflexure_microscope/api/static/src/components/tabContentComponents/imjoyContent.vue @@ -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 {