Merge branch 'smart-stack-controls' into 'master'
Added controls for smart stack See merge request openflexure/openflexure-microscope-server!134
This commit is contained in:
Kaspar Emanuel
commit
6d25dcfa9e
2 changed files with 116 additions and 34 deletions
18
openflexure_microscope/api/static/package-lock.json
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18
openflexure_microscope/api/static/package-lock.json
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@ -2971,12 +2971,6 @@
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"unique-filename": "^1.1.1"
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}
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},
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"caniuse-lite": {
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"version": "1.0.30001165",
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"resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001165.tgz",
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"integrity": "sha512-8cEsSMwXfx7lWSUMA2s08z9dIgsnR5NAqjXP23stdsU3AUWkCr/rr4s4OFtHXn5XXr6+7kam3QFVoYyXNPdJPA==",
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"dev": true
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},
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"color-convert": {
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"version": "2.0.1",
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"resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
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@ -3902,12 +3896,6 @@
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"node-releases": "^1.1.67"
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}
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},
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"caniuse-lite": {
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"version": "1.0.30001165",
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"resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001165.tgz",
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"integrity": "sha512-8cEsSMwXfx7lWSUMA2s08z9dIgsnR5NAqjXP23stdsU3AUWkCr/rr4s4OFtHXn5XXr6+7kam3QFVoYyXNPdJPA==",
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"dev": true
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},
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"electron-to-chromium": {
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"version": "1.3.615",
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"resolved": "https://registry.npmjs.org/electron-to-chromium/-/electron-to-chromium-1.3.615.tgz",
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@ -4724,9 +4712,9 @@
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}
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},
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"caniuse-lite": {
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"version": "1.0.30001020",
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"resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001020.tgz",
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"integrity": "sha512-yWIvwA68wRHKanAVS1GjN8vajAv7MBFshullKCeq/eKpK7pJBVDgFFEqvgWTkcP2+wIDeQGYFRXECjKZnLkUjA==",
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"version": "1.0.30001249",
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"resolved": "https://registry.npmjs.org/caniuse-lite/-/caniuse-lite-1.0.30001249.tgz",
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"integrity": "sha512-vcX4U8lwVXPdqzPWi6cAJ3FnQaqXbBqy/GZseKNQzRj37J7qZdGcBtxq/QLFNLLlfsoXLUdHw8Iwenri86Tagw==",
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"dev": true
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},
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"case-sensitive-paths-webpack-plugin": {
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@ -244,10 +244,70 @@
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</div>
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</div>
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</li>
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<!--Show stack and scan if scan plugin is enabled-->
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<li v-if="scanUri" :class="{ 'uk-open': smartStack && scanCapture }">
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<a class="uk-accordion-title" href="#">Smart Stack</a>
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<div
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class="uk-accordion-content"
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:class="{ 'uk-disabled': !scanCapture }"
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>
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<div class="uk-margin">
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<label
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><input
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v-model="smartStack"
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class="uk-checkbox"
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type="checkbox"
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/>
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Enable smart stacking</label
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>
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</div>
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<p>
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Smart stacking is an experimental closed-loop Z stack, that checks
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the Z stack is centred on the focus. It requires Z stacking to be
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enabled above (we recommend 9 images in Z) and you must select
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"fast" autofocus.
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</p>
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<div :class="{ 'uk-disabled': !smartStack }">
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<div class="uk-margin-small uk-margin-remove-bottom">
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<label class="uk-form-label" for="form-stacked-text"
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>Autofocus range (steps)</label
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>
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<input
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v-model="smartStackAutofocusDz"
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class="uk-input uk-form-small"
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type="number"
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min="1000"
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/>
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</div>
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<div class="uk-margin-small uk-margin-remove-bottom">
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<label class="uk-form-label" for="form-stacked-text"
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>Alignment range (steps)</label
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>
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<input
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v-model="smartStackAlignDist"
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class="uk-input uk-form-small"
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type="number"
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min="100"
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/>
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</div>
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</div>
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</div>
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</li>
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</ul>
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<div v-if="scanCapture" class="uk-margin uk-margin-remove-top">
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<taskSubmitter
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v-if="smartStack"
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:submit-url="smartScanUri"
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:submit-data="smartScanPayload"
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:submit-label="'Start Smart Scan'"
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:button-primary="true"
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@response="onScanResponse"
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@error="modalError"
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>
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</taskSubmitter>
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<taskSubmitter
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v-if="!smartStack"
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:submit-url="scanUri"
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:submit-data="scanPayload"
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:submit-label="'Start Scan'"
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@ -305,7 +365,14 @@ function defaultCaptureSettings() {
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annotations: {
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Client: "openflexure-microscope-jsclient:builtin"
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},
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scanUri: null
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smartStack: false,
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smartStackThreshold: 0.9,
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smartStackPeakWidth: 200,
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smartStackAlignDist: 900,
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smartStackBacklash: 100,
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smartStackFitStyle: "chevy",
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smartStackMAndMIndex: 10,
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smartStackAutofocusDz: 3000
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};
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}
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@ -322,7 +389,9 @@ export default {
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data: function() {
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return {
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...defaultCaptureSettings(),
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scanCapture: false // Don't remember the "scan" tickbox in local storage.
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scanCapture: false, // Don't remember the "scan" tickbox in local storage.
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scanUri: null,
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smartScanUri: null
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};
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},
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@ -372,18 +441,6 @@ export default {
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},
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scanPayload: function() {
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var payload = this.basePayload;
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// Scan params
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payload.grid = [this.scanSteps.x, this.scanSteps.y, this.scanSteps.z];
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payload.stride_size = [
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this.scanStepSize.x,
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this.scanStepSize.y,
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this.scanStepSize.z
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];
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payload.style = this.scanStyle.toLowerCase();
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payload.namemode = this.namingStyle.toLowerCase();
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// Convert AF selector to dz
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var afDeltas = {
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Off: 0,
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@ -392,11 +449,32 @@ export default {
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Fine: 10,
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Fast: 2000
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};
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payload.autofocus_dz = afDeltas[this.scanDeltaZ];
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payload.fast_autofocus = this.scanDeltaZ == "Fast";
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return payload;
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return {
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...this.basePayload,
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// Scan params
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grid: [this.scanSteps.x, this.scanSteps.y, this.scanSteps.z],
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stride_size: [
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this.scanStepSize.x,
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this.scanStepSize.y,
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this.scanStepSize.z
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],
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style: this.scanStyle.toLowerCase(),
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namemode: this.namingStyle.toLowerCase(),
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autofocus_dz: afDeltas[this.scanDeltaZ],
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fast_autofocus: this.scanDeltaZ == "Fast"
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};
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},
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smartScanPayload: function() {
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return {
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...this.scanPayload,
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threshold: this.smartStackThreshold,
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width: this.smartStackPeakWidth,
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align_dist: this.smartStackAlignDist,
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backlash: this.smartStackBacklash,
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fit_style: this.smartStackFitStyle,
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m_and_m_index: this.smartStackMAndMIndex,
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autofocus_dz: this.smartStackAutofocusDz
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};
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}
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},
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@ -446,6 +524,22 @@ export default {
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.catch(error => {
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this.modalError(error); // Let mixin handle error
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});
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axios
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.get(this.pluginsUri) // Get a list of plugins
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.then(response => {
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var plugins = response.data;
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var foundExtension = plugins.find(
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e => e.title === "org.openflexure.smart-stack"
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);
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if (foundExtension) {
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// Get plugin action link
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this.smartScanUri = foundExtension.links.tile.href;
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}
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})
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.catch(error => {
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this.modalError(error); // Let mixin handle error
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});
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},
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onScanResponse: function() {
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