Skip to content

Commit

Permalink
Make sure vector layer is properly redimensionned (neuroanatomy#368)
Browse files Browse the repository at this point in the history
  • Loading branch information
@denishov
denishov committed Oct 4, 2023
1 parent 11bf5dd commit 5eb59e1
Show file tree
Hide file tree
Showing 2 changed files with 86 additions and 84 deletions.
169 changes: 85 additions & 84 deletions view/brainbox/src/components/ProjectPage.vue
View file
Original file line number Diff line number Diff line change
Expand Up @@ -90,12 +90,15 @@ const crdtProvider = new HocuspocusProvider({
const { annotationsAccessLevel, BrainBox, AtlasMakerWidget } = window;
const { baseURL } = Vue.inject('config');
const props = defineProps({
defineProps({
project: {
type: Object,
required: true
},
projectName: String
projectName: {
type: String,
default: ''
}
});
const {
Expand All @@ -106,10 +109,7 @@ const {
displayScript,
currentLabel,
ontology,
currentView,
currentSlice,
currentFile,
totalSlices,
fullscreen,
alpha,
brightness,
Expand Down Expand Up @@ -164,17 +164,80 @@ const extractVolumeKeys = () => {
return keys;
};
const fetchFiles = async () => {
const fetchedFiles = await doFetchFiles([], 0);
store.files.push(...populateTextAnnotations(fetchedFiles));
const getDefaultAtlas = (annotation) => {
const date = new Date();
return {
name: annotation.name,
project: projectInfo.shortname,
created: date.toJSON(),
modified: date.toJSON(),
modifiedBy: AtlasMakerWidget.User.username,
filename: Math.random().toString(36)
.slice(2) + '.nii.gz', // automatically generated filename
labels: annotation.values,
owner: AtlasMakerWidget.User.username,
type: 'volume',
access: annotationsAccessLevel
};
};
const reduced = Vue.computed(() => !displayChat.value && !displayScript.value);
// make sure that all mri files have volume annotations as set in the project info
const populateVolumeAnnotations = (file) => {
const volumeAnnotationsUnproxified = projectInfo.annotations.list.filter(
(anno) => anno.type === 'volume'
);
let annotationIndex = -1;
volumeAnnotationsUnproxified.forEach((annotation) => {
annotationIndex = file.mri.atlas.findIndex(
(atlas) =>
atlas.name === annotation.name &&
atlas.project === projectInfo.shortname
);
const valueChange = (content, index, selector) => {
set(store.files[index], selector, content);
if (annotationIndex >= 0) {
return;
}
// If no layer was found, create it
const atlas = getDefaultAtlas(annotation);
file.mri.atlas.push(atlas);
});
};
// make sure that all mri files have text annotations as set in the project info
const populateTextAnnotations = (files) => files.map((file) => {
if (!file.mri) {
file.mri = {};
}
if (!file.mri.annotations) {
file.mri.annotations = {};
}
if (!file.mri.annotations[projectInfo.shortname]) {
file.mri.annotations[projectInfo.shortname] = {};
}
const textAnnotations = projectInfo.annotations.list.filter(
(annotation) => annotation.type === 'text'
);
for (let i = 0; i < textAnnotations.length; i++) {
const annName = textAnnotations[i].name;
if (!file.mri.annotations[projectInfo.shortname][annName]) {
const date = new Date();
file.mri.annotations[projectInfo.shortname][annName] = {
created: date.toJSON(),
modified: date.toJSON(),
modifiedBy: AtlasMakerWidget.User.username,
type: 'text'
};
}
}
return file;
});
const doFetchFiles = async (files, cursor) => {
const params = {
start: cursor,
Expand All @@ -197,6 +260,16 @@ const doFetchFiles = async (files, cursor) => {
return files;
};
const fetchFiles = async () => {
const fetchedFiles = await doFetchFiles([], 0);
store.files.push(...populateTextAnnotations(fetchedFiles));
};
const reduced = Vue.computed(() => !displayChat.value && !displayScript.value);
const valueChange = (content, index, selector) => {
set(store.files[index], selector, content);
};
const setupKeyDownListeners = () => {
document.addEventListener('keydown', (event) => {
const selectedTr = document.querySelector('tr.selected');
Expand All @@ -223,24 +296,6 @@ const setupKeyDownListeners = () => {
});
};
const getDefaultAtlas = (annotation) => {
const date = new Date();
return {
name: annotation.name,
project: projectInfo.shortname,
created: date.toJSON(),
modified: date.toJSON(),
modifiedBy: AtlasMakerWidget.User.username,
filename: Math.random().toString(36)
.slice(2) + '.nii.gz', // automatically generated filename
labels: annotation.values,
owner: AtlasMakerWidget.User.username,
type: 'volume',
access: annotationsAccessLevel
};
};
const getMRIParams = (file) => {
// make sure we don't send proxified refs to AtlasMaker as it's bad for perfs
const plainFile = JSON.parse(JSON.stringify(file));
Expand Down Expand Up @@ -300,61 +355,6 @@ const selectVolumeAnnotation = async (selectedAtlas) => {
currentLabel.value = 0;
};
// make sure that all mri files have volume annotations as set in the project info
const populateVolumeAnnotations = (file) => {
const volumeAnnotations = projectInfo.annotations.list.filter(
(anno) => anno.type === 'volume'
);
let annotationIndex = -1;
volumeAnnotations.forEach((annotation) => {
annotationIndex = file.mri.atlas.findIndex(
(atlas) =>
atlas.name === annotation.name &&
atlas.project === projectInfo.shortname
);
if (annotationIndex >= 0) {
return;
}
// If no layer was found, create it
const atlas = getDefaultAtlas(annotation);
file.mri.atlas.push(atlas);
});
};
// make sure that all mri files have text annotations as set in the project info
const populateTextAnnotations = (files) => files.map((file) => {
if (!file.mri) {
file.mri = {};
}
if (!file.mri.annotations) {
file.mri.annotations = {};
}
if (!file.mri.annotations[projectInfo.shortname]) {
file.mri.annotations[projectInfo.shortname] = {};
}
const textAnnotations = projectInfo.annotations.list.filter(
(annotation) => annotation.type === 'text'
);
for (let i = 0; i < textAnnotations.length; i++) {
const annName = textAnnotations[i].name;
if (!file.mri.annotations[projectInfo.shortname][annName]) {
const date = new Date();
file.mri.annotations[projectInfo.shortname][annName] = {
created: date.toJSON(),
modified: date.toJSON(),
modifiedBy: AtlasMakerWidget.User.username,
type: 'text'
};
}
}
return file;
});
const delay = (ms) => new Promise((resolve) => setTimeout(resolve, ms));
const handleLayoutChange = async () => {
Expand All @@ -364,6 +364,7 @@ const handleLayoutChange = async () => {
const handleResize = () => {
AtlasMakerWidget.resizeWindow();
AtlasMakerWidget.drawImages();
};
const handleOntologyLabelClick = (index) => {
Expand Down
1 change: 1 addition & 0 deletions view/brainbox/src/components/Tools.vue
View file
Original file line number Diff line number Diff line change
Expand Up @@ -378,6 +378,7 @@ const toggleFullscreen = () => {
fullscreen.value = !fullscreen.value;
setTimeout(() => {
AtlasMakerWidget.resizeWindow();
AtlasMakerWidget.drawImages();
}, 250);
};
Expand Down

0 comments on commit 5eb59e1

Please sign in to comment.