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Commit ed0ac0be authored by Schiffer, Christian's avatar Schiffer, Christian
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Implemented changes for import of predictions

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atlas_server/src/app.py
+ 8
− 2
View file @ ed0ac0be
......@@ -523,7 +523,9 @@ class AnnotationImportExport(Resource):
class PredictionAnnotationExport(Resource):
@annotation_namespace.doc("Retrieve annotations based on predictions of a specific task")
def get(self, project_id, task_id):
import os
import requests
from atlaslib.files import get_section_number_from_string
from .config import ATLAS_CONTROLLER_URL
# Determine
......@@ -535,11 +537,15 @@ class PredictionAnnotationExport(Resource):
return
result = result.json()
annotations = {}
for item in result:
section = get_section_number_from_string(os.path.basename(item["path"]))
annotations[section] = item["annotations"]
return {
"project_id": project_id,
"task_id": task_id,
"path": result["path"],
"annotations": result["annotations"],
"annotations": annotations,
}
......
microdraw/src/atlas_ui.js
+ 77
− 65
View file @ ed0ac0be
......@@ -3,7 +3,7 @@ if (debug) {
}
var atlasRegions = [];
var atlasServerApiUrl = "http://medpc076.ime.kfa-juelich.de:5000/api"
var atlasServerApiUrl = "http://medpc076.ime.kfa-juelich.de:5000/api"
//var atlasServerApiUrl = "http://localhost:5000/api"
// var serverHost = "medpc076.ime.kfa-juelich.de"
// var serverPort = 80
......@@ -42,21 +42,24 @@ function Task() {
}
function AnnotationImport() {
this.src_host = "imedv02.ime.kfa-juelich.de";
// This is fixed for now. Always import into running instance.
this.dst_host = "atlasui_microdraw-mariadb_1";
this.src_user = null;
this.dst_user = null;
this.src_path = null;
this.dst_path = null;
this.annotation_items = [];
this.loading_state = false;
this.src_host = "imedv02.ime.kfa-juelich.de";
// This is fixed for now. Always import into running instance.
this.dst_host = "atlasui_microdraw-mariadb_1";
this.src_user = null;
this.dst_user = null;
this.src_path = null;
this.dst_path = null;
this.annotation_items = [];
this.loading_state = false;
this.project_import = null;
this.src_project = 0;
this.src_task = 0;
}
function AnnotationImportItem(section, annotations) {
this.section = section;
this.annotations = annotations;
this.loading_state = false;
this.section = section;
this.annotations = annotations;
this.loading_state = false;
}
function compareRegions(region0, region1) {
......@@ -581,33 +584,42 @@ var app = new Vue({
window.location.href = target_link;
},
initializeAnnotationImport: function() {
if (typeof(myOrigin.user) == "object") {
this.annotation_import.src_user = null;
this.annotation_import.dst_user = null;
} else {
this.annotation_import.src_user = myOrigin.user;
this.annotation_import.dst_user = myOrigin.user;
}
this.annotation_import.src_path = myOrigin.source;
this.annotation_import.dst_path = myOrigin.source;
if (typeof(myOrigin.user) == "object") {
this.annotation_import.src_user = null;
this.annotation_import.dst_user = null;
} else {
this.annotation_import.src_user = myOrigin.user;
this.annotation_import.dst_user = myOrigin.user;
}
this.annotation_import.src_path = myOrigin.source;
this.annotation_import.dst_path = myOrigin.source;
},
getAnnotations: function() {
console.log("get annotations");
console.log("get annotations");
let user = this.annotation_import.src_user;
let user = this.annotation_import.src_user;
if (user === null) {
alert("Please enter a source user before retrieving annotations.");
return;
}
this.annotation_import.annotation_items = [];
let host = encodeURIComponent(btoa(this.annotation_import.src_host));
let path = encodeURIComponent(btoa(this.annotation_import.src_path));
this.annotation_import.annotation_items = [];
let endpoint = null;
if (this.annotation_import.project_import) {
// Import predictions from a specific project
let project = this.annotation_import.src_project;
let task = this.annotation_import.src_task;
endpoint = `${atlasServerApiUrl}/predictions/${project}/tasks/${task}`;
} else {
// Import predictions from a specific user
if (user === null) {
alert("Please enter a source user before retrieving annotations.");
return;
}
let host = encodeURIComponent(btoa(this.annotation_import.src_host));
let path = encodeURIComponent(btoa(this.annotation_import.src_path));
endpoint = `${atlasServerApiUrl}/annotations/${host}/${user}/${path}`;
}
let endpoint = `${atlasServerApiUrl}/annotations/${host}/${user}/${path}`;
let _this = this;
this.annotation_import.loading_state = true;
this.annotation_import.loading_state = true;
$.ajax({
url: endpoint,
type: "GET",
......@@ -619,40 +631,40 @@ var app = new Vue({
_this.annotation_items = [];
console.log(annotations);
for (let key in annotations) {
let value = annotations[key];
_this.annotation_import.annotation_items.push(new AnnotationImportItem(key, value));
let value = annotations[key];
_this.annotation_import.annotation_items.push(new AnnotationImportItem(key, value));
}
},
error: function (jqXHR, textStatus, errorThrown) {
post_message(`Error getting annotations status: ${textStatus} ${errorThrown}`);
},
complete: function(data) {
_this.annotation_import.loading_state = false;
_this.annotation_import.loading_state = false;
}
});
},
importAll: function(overwrite) {
if (!this.checkUser()) {
return;
}
for (let annotation in this.annotation_import.annotation_items) {
this.importAnnotation(this.annotation_import.annotation_items[annotation], overwrite);
}
if (!this.checkUser()) {
return;
}
for (let annotation in this.annotation_import.annotation_items) {
this.importAnnotation(this.annotation_import.annotation_items[annotation], overwrite);
}
},
importAnnotation: function(annotation, overwrite) {
if (!this.checkUser()) {
return;
}
console.log(annotation);
if (!this.checkUser()) {
return;
}
console.log(annotation);
let user = this.annotation_import.dst_user;
console.log(`Importing annotation to user ${this.annotation_import.dst_user} at ${this.annotation_import.dst_host}`);
let host = encodeURIComponent(btoa(this.annotation_import.dst_host));
let path = encodeURIComponent(btoa(this.annotation_import.dst_path));
let user = this.annotation_import.dst_user;
console.log(`Importing annotation to user ${this.annotation_import.dst_user} at ${this.annotation_import.dst_host}`);
let host = encodeURIComponent(btoa(this.annotation_import.dst_host));
let path = encodeURIComponent(btoa(this.annotation_import.dst_path));
let endpoint = `${atlasServerApiUrl}/annotations/${host}/${user}/${path}`;
if (overwrite) {
endpoint = `${endpoint}?overwrite=True`;
endpoint = `${endpoint}?overwrite=True`;
}
console.log(endpoint);
let _this = this;
......@@ -660,7 +672,7 @@ var app = new Vue({
data[annotation.section] = annotation.annotations;
// Disable buttons while importing
annotation.loading_state = true;
annotation.loading_state = true;
$.ajax({
url: endpoint,
type: "POST",
......@@ -670,30 +682,30 @@ var app = new Vue({
crossDomain: true,
success: function (data) {
// Remove annotation from list
_this.removeImportAnnotation(annotation);
_this.removeImportAnnotation(annotation);
},
error: function (jqXHR, textStatus, errorThrown) {
post_message(`Error importing annotation: ${textStatus} ${errorThrown}`);
},
complete: function(data) {
annotation.loading_state = false;
annotation.loading_state = false;
}
});
},
checkUser: function() {
let user_ok = this.annotation_import.dst_user !== null && this.annotation_import.dst_user !== ""
if (!user_ok) {
alert("Please enter a target user before importing annotations.");
return false;
}
return true;
let user_ok = this.annotation_import.dst_user !== null && this.annotation_import.dst_user !== ""
if (!user_ok) {
alert("Please enter a target user before importing annotations.");
return false;
}
return true;
},
removeImportAnnotation: function(annotation) {
for (let idx in this.annotation_import.annotation_items) {
if (this.annotation_import.annotation_items[idx] === annotation) {
this.annotation_import.annotation_items.splice(idx, 1);
}
}
for (let idx in this.annotation_import.annotation_items) {
if (this.annotation_import.annotation_items[idx] === annotation) {
this.annotation_import.annotation_items.splice(idx, 1);
}
}
}
},
created: function () {
......
microdraw/src/microdraw.html
+ 22
− 9
View file @ ed0ac0be
......@@ -527,31 +527,44 @@
<div class="modal-body">
<div class="form">
<div class="form-row">
<label class="col-form-label">Source host</label>
<label class="col-form-label col-2">Source host</label>
<div class="col-4">
<input v-model="annotation_import.src_host" class="form-control" type="text"
data-toggle="tooltip" data-placement="top" title="Host of the machine to retrieve annotations from. If you do not know what this is, leave the default value untouched.">
</div>
<div class="col-4">
<input type="checkbox" v-model="annotation_import.project_import" id="atlas_ui_import_form_project_import"
data-toggle="tooltip" data-placement="top" title="Switch between import from user and import from predictions of specific task.">
<label for="atlas_ui_import_form_project_import">Import predictions</label>
</div>
</div>
<div class="form-row">
<label class="col-form-label">Source user</label>
<label class="col-form-label col-2" v-if="annotation_import.project_import">Project ID</label>
<label class="col-form-label col-2" v-else>Source user</label>
<div class="col-4">
<input v-model="annotation_import.src_user" type="text" class="form-control"
<input type="number" min="0" v-model="annotation_import.src_project" type="text" class="form-control" v-if="annotation_import.project_import"
data-toggle="tooltip" data-placement="top" title="ID of project to import predictions from.">
<input v-model="annotation_import.src_user" type="text" class="form-control" v-else
data-toggle="tooltip" data-placement="top" title="Microdraw user on source host to retrieve annotations from.">
</div>
<label class="col-form-label">Destination user</label>
<label class="col-form-label col-2">Destination user</label>
<div class="col-4">
<input v-model="annotation_import.dst_user" type="text" class="form-control"
data-toggle="tooltip" data-placement="top" title="Microdraw user to import annotations to.">
</div>
</div>
<div class="form-row">
<label class="col-form-label">Source path</label>
<label class="col-form-label col-2" v-if="annotation_import.project_import">Task ID</label>
<label class="col-form-label col-2" v-else>Source path</label>
<div class="col-4">
<input v-model="annotation_import.src_path" type="text" class="form-control"
<input type="number" min="0" v-model="annotation_import.src_task" type="text" class="form-control" v-if="annotation_import.project_import"
data-toggle="tooltip" data-placement="top" title="ID of task to import predictions from.">
<input v-model="annotation_import.src_path" type="text" class="form-control" v-else
data-toggle="tooltip" data-placement="top" title="Microdraw path to import annotations from.">
</div>
<label class="col-form-label">Destination path</label>
<label class="col-form-label col-2">Destination path</label>
<div class="col-4">
<input v-model="annotation_import.dst_path" type="text" class="form-control"
data-toggle="tooltip" data-placement="top" title="Microdraw path to import annotations to.">
......@@ -581,10 +594,10 @@
<input v-model="ann_item.section" class="form-control" type="text" readonly />
</div>
<label class="col-2 col-form-label text-right">Annotations</label>
<div class="col-1">
<div class="col-2">
<input v-model="ann_item.annotations.Regions.length" class="form-control" type="text" readonly />
</div>
<div class="col-3">
<div class="col-2">
</div>
<div class="col-3">
<div class="btn-group" role="group">
......
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