chore(reorganization) Moving longitudinal feature to Lesiontracker package (#208)

2018-06-18 18:03:34 +02:00
1 parent 1643e9f7d6
commit 9f73ae0153
@@ -8,3 +8,5 @@ import './trialOptionsModal/recistDescription.html';

 import './trialOptionsModal/trialOptionsModal.html';
 import './trialOptionsModal/trialOptionsModal.js';
+
+import './longitudinal';
@@ -0,0 +1,110 @@
+import { Meteor } from 'meteor/meteor';
+import { OHIF } from 'meteor/ohif:core';
+
+/**
+ * Loads multiple unassociated studies in the Viewer
+ */
+const getAssociationAssessment = () => {
+    // default result value
+    const assessment = {
+        selected: 0,
+        associated: 0
+    };
+
+    // check if timepointApi is available
+    const timepointApi = OHIF.studylist.timepointApi;
+    if (timepointApi) {
+        // Get a Cursor pointing to the selected Studies from the StudyList
+        const selectedStudies = OHIF.studylist.getSelectedStudies();
+        if (selectedStudies.length > 0) {
+            assessment.selected = selectedStudies.length;
+            // Loop through the selected Studies and return true if at least one study has no association.
+            for (let i = selectedStudies.length - 1; i >= 0; --i) {
+                let study = selectedStudies[i],
+                    timepoints = timepointApi.study(study.studyInstanceUid);
+                if (timepoints && timepoints.length > 0) {
+                    assessment.associated++;
+                }
+            }
+        }
+    }
+
+    return assessment;
+};
+
+/**
+ * Removes all present study / timepoint associations from the Clinical Trial
+ */
+const removeTimepointAssociations = event => {
+    const dialogSettings = {
+        title: 'Remove Association',
+        message: 'Measurements related to this Study and Timepoint will be erased. Do you really want to delete this association?',
+        confirmClass: 'btn-danger',
+        position: {
+            x: event.clientX,
+            y: event.clientY
+        }
+    };
+
+    OHIF.ui.showDialog('dialogConfirm', dialogSettings).then(() => {
+        // Get a Cursor pointing to the selected Studies from the StudyList
+        const selectedStudies = OHIF.studylist.getSelectedStudies();
+
+        // Find the Timepoint that was previously referenced
+        const timepointApi = OHIF.studylist.timepointApi;
+        if (!timepointApi) {
+            OHIF.log.error('Remove Study/Timepoint Association: No Timepoint API found.');
+            return;
+        }
+
+        // Loop through the Cursor of Selected Studies
+        selectedStudies.forEach(study => {
+            const studyInstanceUid = study.studyInstanceUid;
+            const timepoints = timepointApi.study(studyInstanceUid);
+            const timepointIds = timepoints.map(t => t.timepointId);
+            timepointApi.disassociateStudy(timepointIds, studyInstanceUid);
+        });
+    });
+};
+
+Meteor.startup(() => {
+    if (!OHIF.studylist) return;
+
+    OHIF.studylist.dropdown.setItems([{
+        action: OHIF.studylist.viewStudies,
+        text: 'View',
+        separatorAfter: true
+    }, {
+        action: () => OHIF.ui.showDialog('dialogStudyAssociation'),
+        text: 'Associate',
+        disabled: () => {
+            const assessment = getAssociationAssessment();
+            return assessment.selected < 1;
+        }
+    }, {
+        action: removeTimepointAssociations,
+        text: 'Remove Association',
+        separatorAfter: true,
+        disabled: () => {
+            const assessment = getAssociationAssessment();
+            return assessment.selected < 1 || assessment.selected !== assessment.associated;
+        }
+    }, {
+        action: OHIF.studylist.viewSeriesDetails,
+        text: 'View Series Details'
+    }, {
+        text: 'Anonymize',
+        disabled: true
+    }, {
+        text: 'Send',
+        disabled: true,
+        separatorAfter: true
+    }, {
+        action: OHIF.studylist.exportSelectedStudies,
+        text: 'Export',
+        title: 'Export Selected Studies'
+    }, {
+        text: 'Delete',
+        disabled: true
+    }]);
+});
@@ -0,0 +1,11 @@
+// Longitudinal Components imports
+import './longitudinalStudyListStudy/longitudinalStudyListStudy.html';
+import './longitudinalStudyListStudy/longitudinalStudyListStudy.styl';
+import './longitudinalStudyListStudy/longitudinalStudyListStudy.js';
+
+import './longitudinalViewportOverlay/imageViewportIcons.html';
+import './longitudinalViewportOverlay/longitudinalViewportOverlay.html';
+import './longitudinalViewportOverlay/longitudinalViewportOverlay.js';
+import './longitudinalViewportOverlay/longitudinalViewportOverlay.styl';
+
+import './dropdown.js';
@@ -0,0 +1,28 @@
+<template name="longitudinalStudyListStudy">
+    <tr class="studylistStudy noselect {{#if this.selected}}active{{/if}}">
+        <td>
+            {{#if reviewerTip}}
+                <i class="fa fa-exclamation-circle reviewerTip" data-toggle="tooltip" data-placement="bottom" title="{{reviewerTip}}"></i>
+            {{/if}}
+            {{formatPN patientName}}
+        </td>
+        <td>
+            {{patientId}}
+        </td>
+        <td>
+            {{accessionNumber}}
+        </td>
+        <td>
+            {{formatDA studyDate}} {{ #if timepointName }}({{timepointName}}){{ /if }}
+        </td>
+        <td>
+            {{modalities}}
+        </td>
+        <td>
+            {{studyDescription}}
+        </td>
+        <td>
+            {{numberOfStudyRelatedInstances}}
+        </td>
+    </tr>
+</template>
@@ -0,0 +1,80 @@
+import { Meteor } from 'meteor/meteor';
+import { Template } from 'meteor/templating';
+import { OHIF } from 'meteor/ohif:core';
+
+// Use Aldeed's meteor-template-extension package to replace the
+// default StudyListStudy template.
+// See https://github.com/aldeed/meteor-template-extension
+const defaultTemplate = 'studylistStudy';
+
+if (OHIF.studylist) {
+    Template.longitudinalStudyListStudy.replaces(defaultTemplate);
+
+    // Add the TimepointName helper to the default template. The
+    // HTML of this template is replaced with that of longitudinalStudyListStudy
+    Template[defaultTemplate].helpers({
+        timepointName() {
+            const instance = Template.instance();
+            const timepointApi = OHIF.studylist.timepointApi;
+            if (!timepointApi) {
+                return;
+            }
+
+            const timepoint = timepointApi.study(instance.data.studyInstanceUid)[0];
+            if (!timepoint) {
+                return;
+            }
+
+            return timepointApi.name(timepoint);
+        },
+
+        reviewerTip() {
+            const instance = Template.instance();
+            const timepointApi = OHIF.studylist.timepointApi;
+            if (!timepointApi || !window.Reviewers) {
+                return;
+            }
+
+            const timepoint = timepointApi.study(instance.data.studyInstanceUid);
+            if (!timepoint) {
+                return;
+            }
+
+            const timepointReviewers = window.Reviewers.findOne({ timepointId: timepoint.timepointId });
+            if (!timepointReviewers) {
+                return;
+            }
+
+            return getReviewerTipText(timepointReviewers.reviewers);
+        }
+    });
+
+    function getReviewerTipText(reviewers) {
+        if (!reviewers || !reviewers.length) {
+            return;
+        }
+
+        const newReviewers = reviewers.filter(function(reviewer) {
+            return reviewer.userId !== Meteor.userId();
+        });
+
+        if (!newReviewers.length) {
+            return;
+        }
+
+        let tipText = 'The study is being reviewed by ';
+        newReviewers.forEach(function(reviewer, index) {
+            if (reviewer.userId === Meteor.userId()) {
+                return;
+            }
+
+            if (index > 0) {
+                tipText += ',';
+            }
+
+            tipText += reviewer.userName;
+        });
+
+        return tipText;
+    }
+}
@@ -0,0 +1,5 @@
+.studylistStudy
+  cursor: pointer
+
+  .reviewerTip
+    color: darkred
@@ -0,0 +1 @@
+<template name="imageViewportIcons"></template>
@@ -0,0 +1,84 @@
+<template name="longitudinalViewportOverlay">
+    <div class="imageViewerViewportOverlay noselect {{#if gt numImages 1}}controlsVisible{{/if}}">
+        {{#unless tagDisplaySpecified}}
+            <div class="topleft dicomTag">
+                <div>{{patientId}}</div>
+                <div>{{patientName}}</div>
+                <div>{{getGenderAndAge}}</div>
+                <div class="icons-section">
+                    {{#if linked}}
+                        <svg class="icon-link">
+                            <use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href={{absoluteUrl "packages/ohif_viewerbase/assets/icons.svg#icon-viewport-link"}}></use>
+                        </svg>
+                    {{/if}}
+                    {{>imageViewportIcons this}}
+                </div>
+            </div>
+            <div class="topright dicomTag">
+                <div>{{seriesDescription}}</div>
+                <div>{{studyInfo 'AccessionNumber'}}</div>
+                <div>{{formatDA (studyInfo 'AcquisitionDate')}} {{formatTM (studyInfo 'AcquisitionTime')}}</div>
+                <div>{{#if seriesNumber}}S: {{seriesNumber}}{{#if gt numImages 1}},{{/if}} {{/if}}{{#if gt numImages 1}}I: {{imageIndex}}/{{numImages}}{{/if}}</div>
+                <div class='timepointName'>{{timepointName}}</div>
+            </div>
+            <div class="bottomright dicomTag">
+                <div class="stationName">{{studyInfo 'StationName'}}</div>
+                <div class="manufacturerModel">{{studyInfo 'ManufacturersModelName'}}</div>
+                <div class="institutionName">{{studyInfo 'InstitutionName'}}</div>
+            </div>
+            <div class="bottomleft dicomTag">
+                <div>
+                    <span>{{#if location}}Loc: {{formatNumberPrecision location 2}} mm{{/if}}</span>
+                    <span>{{#if thickness}}Thick: {{formatNumberPrecision thickness 2}} mm{{/if}}</span>
+                    <span>{{#if spacingBetweenSlices}}Spacing: {{formatNumberPrecision spacingBetweenSlices 2}} mm{{/if}}</span>
+                </div>
+                <div>{{#if zoom}}Zoom: {{formatNumberPrecision zoom 2}}x{{/if}}</div>
+                <div>{{wwwc}}</div>
+            </div>
+        {{/unless}}
+
+        {{#if tagDisplayRightOnly}}
+            <div class="topright dicomTag">
+                <div>{{formatPN patientName}}</div>
+                <div>{{patientId}}</div>
+                <div class='timepointName'>{{timepointName}}</div>
+                <div>{{studyDescription}}</div>
+                <div>{{formatDA studyDate}} {{formatTM studyTime}}</div>
+            </div>
+            <div class="bottomright dicomTag">
+                <div>{{#if seriesNumber}}Ser: {{seriesNumber}}{{/if}}</div>
+                <div>{{#if gt numImages 1}}Img: {{instanceNumber}} ({{imageIndex}}/{{numImages}}){{/if}}</div>
+                <div>{{#if frameRate}}{{formatNumberPrecision frameRate 2}} FPS{{/if}}</div>
+                <div>{{imageDimensions}}</div>
+                <div>{{seriesDescription}}</div>
+                <div>{{#if zoom}}Zoom: {{formatNumberPrecision zoom 0}}%{{/if}}</div>
+                <div class="compressionIndicator">{{compression}}</div>
+                <div>{{wwwc}}</div>
+            </div>
+        {{/if}}
+
+        {{#if tagDisplayLeftOnly}}
+            <div class="topleft dicomTag">
+                <div>{{formatPN patientName}}</div>
+                <div>{{patientId}}</div>
+                <div class='timepointName'>{{timepointName}}</div>
+                <div>{{studyDescription}}</div>
+                <div>{{formatDA studyDate}} {{formatTM studyTime}}</div>
+            </div>
+            <div class="bottomleft dicomTag">
+                <div>{{#if seriesNumber}}Ser: {{seriesNumber}}{{/if}}</div>
+                <div>{{#if gt numImages 1}}Img: {{instanceNumber}} ({{imageIndex}}/{{numImages}}){{/if}}</div>
+                <div>{{#if frameRate}}{{formatNumberPrecision frameRate 2}} FPS{{/if}}</div>
+                <div>{{imageDimensions}}</div>
+                <div>{{seriesDescription}}</div>
+                <div>{{#if zoom}}Zoom: {{formatNumberPrecision zoom 0}}%{{/if}}</div>
+                <div class="compressionIndicator">{{compression}}</div>
+                <div>{{wwwc}}</div>
+            </div>
+        {{/if}}
+
+        {{#if gt numImages 1}}
+            {{>imageControls imageIndex=imageIndex numImages=numImages}}
+        {{/if}}
+    </div>
+</template>
@@ -0,0 +1,179 @@
+import { Template } from 'meteor/templating';
+import { Session } from 'meteor/session';
+import { Tracker } from 'meteor/tracker';
+import { ReactiveVar } from 'meteor/reactive-var';
+import { _ } from 'meteor/underscore';
+import { moment } from 'meteor/momentjs:moment';
+import { OHIF } from 'meteor/ohif:core';
+import { cornerstone } from 'meteor/ohif:cornerstone';
+
+// Use Aldeed's meteor-template-extension package to replace the
+// default viewportOverlay template.
+// See https://github.com/aldeed/meteor-template-extension
+const defaultTemplate = 'viewportOverlay';
+Template.longitudinalViewportOverlay.replaces(defaultTemplate);
+
+Template[defaultTemplate].onCreated(() => {
+    const instance = Template.instance();
+    instance.instanceMetadata = new ReactiveVar();
+
+    const { DICOMTagDescriptions } = OHIF.viewerbase;
+    instance.getValueByTagKeyword = tagKeyword => {
+        const instanceMetadata = instance.instanceMetadata.get();
+        const tagObject = DICOMTagDescriptions.find(tagKeyword);
+        if (!instanceMetadata || !tagObject) return;
+        return instanceMetadata.getRawValue(tagObject.tag);
+    };
+});
+
+Template[defaultTemplate].onRendered(() => {
+    const instance = Template.instance();
+    const { studyInstanceUid, seriesInstanceUid } = instance.data;
+
+    Tracker.autorun(computation => {
+        Session.get('CornerstoneNewImage' + instance.data.viewportIndex);
+        if (computation.firstRun) return;
+        computation.stop();
+        const imageIndex = instance.getImageIndex();
+        OHIF.studies.loadStudy(studyInstanceUid).then(studyMetadata => {
+            const seriesMetadata = studyMetadata.getSeriesByUID(seriesInstanceUid);
+            const instanceMetadata = seriesMetadata.getInstanceByIndex(imageIndex);
+            if (!instanceMetadata) return;
+            instance.instanceMetadata.set(instanceMetadata);
+        });
+    });
+});
+
+// Add the TimepointName helper to the default template. The
+// HTML of this template is replaced with that of longitudinalViewportOverlay
+Template[defaultTemplate].helpers({
+    studyInfo(tagKeyword) {
+        const instance = Template.instance();
+        instance.instanceMetadata.dep.depend();
+        return instance.getValueByTagKeyword(tagKeyword);
+    },
+
+    getGenderAndAge() {
+        const instance = Template.instance();
+        const values = [];
+        values.push(instance.getValueByTagKeyword('PatientSex'));
+
+        const patientAge = instance.getValueByTagKeyword('PatientAge');
+        const patientBirthDate = instance.getValueByTagKeyword('PatientBirthDate');
+        if (patientAge) {
+            values.push(patientAge);
+        } else if (patientBirthDate) {
+            const date = moment(patientBirthDate, 'YYYYMMDD');
+            const yearDiff = moment().diff(date, 'years');
+            if (yearDiff) {
+                values.push((yearDiff + 'Y').padStart(4, '0'));
+            } else {
+                const monthDiff = moment().diff(date, 'months');
+                if (monthDiff) {
+                    values.push((monthDiff + 'M').padStart(4, '0'));
+                } else {
+                    const dayDiff = moment().diff(date, 'days') || 0;
+                    values.push((dayDiff + 'D').padStart(4, '0'));
+                }
+            }
+        }
+
+        return values.filter(value => !!value).join(', ');
+    },
+
+    thickness() {
+        const instance = Template.instance();
+        Session.get('CornerstoneNewImage' + instance.data.viewportIndex);
+
+        return instance.getValueByTagKeyword('SliceThickness');
+    },
+
+    location() {
+        const instance = Template.instance();
+        Session.get('CornerstoneNewImage' + instance.data.viewportIndex);
+
+        const sliceLocation = instance.getValueByTagKeyword('SliceLocation');
+        const tablePosition = instance.getValueByTagKeyword('TablePosition');
+        const imagePositionPatient = instance.getValueByTagKeyword('ImagePositionPatient');
+        return sliceLocation || tablePosition || imagePositionPatient;
+    },
+
+    spacingBetweenSlices() {
+        const instance = Template.instance();
+        Session.get('CornerstoneNewImage' + instance.data.viewportIndex);
+
+        // TODO: Otherwise, displays a value derived from successive values
+        // of Image Position (Patient) (0020,0032) perpendicular to
+        // the Image Orientation (Patient) (0020,0037)
+
+        return instance.getValueByTagKeyword('SpacingBetweenSlices');
+    },
+
+    zoom() {
+        const instance = Template.instance();
+        const { viewportIndex } = instance.data;
+        const { getElementIfNotEmpty } = OHIF.viewerbase;
+        Session.get('CornerstoneImageRendered' + viewportIndex);
+
+        const element = getElementIfNotEmpty(viewportIndex);
+        if (!element) return;
+
+        const viewport = cornerstone.getViewport(element);
+        if (!viewport) return;
+
+        return viewport.scale;
+    },
+
+    wwwc() {
+        const instance = Template.instance();
+        const { viewportIndex } = instance.data;
+        const { getElementIfNotEmpty, wlPresets } = OHIF.viewerbase;
+        Session.get('CornerstoneImageRendered' + viewportIndex);
+        wlPresets.changeObserver.depend();
+
+        const element = getElementIfNotEmpty(viewportIndex);
+        if (!element) return;
+
+        const viewport = cornerstone.getViewport(element);
+        if (!viewport) return;
+
+        const ww = viewport.voi.windowWidth.toFixed(0);
+        const wc = viewport.voi.windowCenter.toFixed(0);
+        const result = [`W: ${ww}, L: ${wc}`];
+
+        // Check if there's a preset with this W/L
+        const preset = _.findWhere(OHIF.viewer.wlPresets, {
+            ww: parseInt(ww),
+            wc: parseInt(wc)
+        });
+
+        // Append the preset name to the result if found
+        if (preset) {
+            result .push(`(${preset.id})`);
+        }
+
+        return result.join(' ');
+    },
+
+    timepointName() {
+        const instance = Template.instance();
+        const studyInstanceUid = instance.data.studyInstanceUid;
+
+        const timepointApi = OHIF.viewer.timepointApi;
+        if (!timepointApi) return;
+
+        const timepoints = timepointApi.study(studyInstanceUid);
+        if (!timepoints || !timepoints.length) {
+            return;
+        }
+
+        const timepoint = timepoints[0];
+
+        return timepointApi.name(timepoint);
+    },
+
+    linked() {
+        const linkedViewports = Session.get('StackImagePositionOffsetSynchronizerLinkedViewports') || [];
+        return (linkedViewports.indexOf(this.viewportIndex) !== -1);
+    }
+});
@@ -0,0 +1,4 @@
+@require '{ohif:design}/app'
+
+.imageViewerViewportOverlay .icons-section .icon-link
+  transform(translateY(3px))
				`@@ -0,0 +1 @@`
				`<template name="imageViewportIcons"></template>`