From ed0ac0be69050bbc691c3ed375fcc041ff861d70 Mon Sep 17 00:00:00 2001
From: Christian Schiffer <c.schiffer@fz-juelich.de>
Date: Fri, 9 Apr 2021 08:01:22 +0200
Subject: [PATCH] Implemented changes for import of predictions
---
atlas_server/src/app.py | 10 ++-
microdraw/src/atlas_ui.js | 142 +++++++++++++++++++----------------
microdraw/src/microdraw.html | 31 +++++---
3 files changed, 107 insertions(+), 76 deletions(-)
diff --git a/atlas_server/src/app.py b/atlas_server/src/app.py
index e8bd0ec..771e16b 100644
--- a/atlas_server/src/app.py
+++ b/atlas_server/src/app.py
@@ -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,
}
diff --git a/microdraw/src/atlas_ui.js b/microdraw/src/atlas_ui.js
index 657ff7b..03b5477 100644
--- a/microdraw/src/atlas_ui.js
+++ b/microdraw/src/atlas_ui.js
@@ -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 () {
diff --git a/microdraw/src/microdraw.html b/microdraw/src/microdraw.html
index 0effafe..99cc822 100755
--- a/microdraw/src/microdraw.html
+++ b/microdraw/src/microdraw.html
@@ -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">
--
GitLab