From e27e9901ba5d76d940775c70ce8beadf4d1c8d06 Mon Sep 17 00:00:00 2001
From: Christian Schiffer <c.schiffer@fz-juelich.de>
Date: Thu, 22 Aug 2024 13:48:07 +0200
Subject: [PATCH] Fixed saving logic
---
atlas_server/src/app.py | 302 +++--
atlas_server/src/db.py | 178 +--
atlas_server/src/models.py | 84 +-
microdraw/src/atlas_ui.js | 21 +-
microdraw/src/microdraw.html | 2489 +++++++++++++++++++++++-----------
5 files changed, 2057 insertions(+), 1017 deletions(-)
diff --git a/atlas_server/src/app.py b/atlas_server/src/app.py
index 1b7da3f..352499d 100644
--- a/atlas_server/src/app.py
+++ b/atlas_server/src/app.py
@@ -4,69 +4,132 @@ from flask import Flask, request
from flask_restx import Api, Resource, fields, abort
from . import models
-from .db import Database, ProjectNotFoundError, TaskNotFoundError, JobNotFoundError, ForbiddenOperationError
-from .scheduler import submit_training_job, submit_prediction_job, get_job_status, cancel_job, JobStatusNotFoundError, JobNotFoundError, JobSubmissionError
+from .db import (
+ Database,
+ ProjectNotFoundError,
+ TaskNotFoundError,
+ JobNotFoundError,
+ ForbiddenOperationError,
+)
+from .scheduler import (
+ submit_training_job,
+ submit_prediction_job,
+ get_job_status,
+ cancel_job,
+ JobStatusNotFoundError,
+ JobNotFoundError,
+ JobSubmissionError,
+)
app = Flask(__name__)
# Setup flask with CORS, since we do requests to atlas controller
-api = Api(app,
- prefix="/api",
- version="1.0",
- title="ATLaS UI API",
- description="API serving as backend for the ATLaS UI")
+api = Api(
+ app,
+ prefix="/api",
+ version="1.0",
+ title="ATLaS UI API",
+ description="API serving as backend for the ATLaS UI",
+)
# -----------------------------------
# Namespace definitions
# -----------------------------------
-project_namespace = api.namespace("projects", description="Operations to deal with projects")
-annotation_namespace = api.namespace("annotations", description="Operations to deal with annotations")
-predictions_namespace = api.namespace("predictions", description="Operations to deal with predictions")
+project_namespace = api.namespace(
+ "projects", description="Operations to deal with projects"
+)
+annotation_namespace = api.namespace(
+ "annotations", description="Operations to deal with annotations"
+)
+predictions_namespace = api.namespace(
+ "predictions", description="Operations to deal with predictions"
+)
# -----------------------------------
# Model definitions
# -----------------------------------
-annotation_model = api.model("AnnotationModel",
- {
- "section": fields.Integer(description="Section number the annotation corresponds to."),
- "name": fields.String(description="Name of the annotation."),
- "original_name": fields.String(description="Original name of the annotation before automatic renaming. May be None."),
- "path": fields.String(description="Path of the annotation.")
- })
-
-task_model = api.model("TaskModel",
- {
- "task_id": fields.Integer(description="ID of the task."),
- "name": fields.String(description="The name of the task."),
- "annotations": fields.List(fields.Nested(annotation_model), description="Annotations to add to the task."),
- "no_aux_labels": fields.Boolean(description="Whether to use auxiliary labels.", required=False),
- "model": fields.String(description="Model to use.", required=False),
- })
-
-project_model = api.model("ProjectModel",
- {
- "project_id": fields.Integer(description="ID of the project."),
- "name": fields.String(description="The name of the project."),
- "brain": fields.Integer(description="Number of the brain the projects refers to."),
- "owner": fields.String(description="Owner of the project."),
- "tasks": fields.List(fields.Nested(task_model), description="List of tasks of the project.")
- })
-
-job_configuration_model = api.model("JobConfigurationModel",
- {
- "account": fields.String(description="Account to submit job with, e.g. jinm14.", required=True),
- "time": fields.String(description="Time limit for job in format HH:MM:SS.", required=True),
- "job_type": fields.String(description="Type of the job which is being submitted.", required=True),
- "gres": fields.String(description="Generic resources to request for job, e.g. \"gpus:4\""),
- "mail_type": fields.String(description="Mail type to use for e-mail notifications."),
- "mail_user": fields.String(description="E-mail address to send notifications to."),
- "num_nodes": fields.Integer(description="Number of nodes to allocate for the job."),
- "partition": fields.String(description="Partition to allocate job on, e.g. \"batch\" or \"gpus\""),
- "reservation": fields.String(description="Reservation to use for running the job."),
- "model": fields.String(description="Model configuration to train."),
- "kwargs": fields.String(description="Keyword arguments for configuration encoded as JSON"),
- })
+annotation_model = api.model(
+ "AnnotationModel",
+ {
+ "section": fields.Integer(
+ description="Section number the annotation corresponds to."
+ ),
+ "name": fields.String(description="Name of the annotation."),
+ "original_name": fields.String(
+ description="Original name of the annotation before automatic renaming. May be None."
+ ),
+ "path": fields.String(description="Path of the annotation."),
+ },
+)
+
+task_model = api.model(
+ "TaskModel",
+ {
+ "task_id": fields.Integer(description="ID of the task."),
+ "name": fields.String(description="The name of the task."),
+ "annotations": fields.List(
+ fields.Nested(annotation_model),
+ description="Annotations to add to the task.",
+ ),
+ "no_aux_labels": fields.Boolean(
+ description="Whether to use auxiliary labels.", required=False
+ ),
+ "model": fields.String(description="Model to use.", required=False),
+ },
+)
+
+project_model = api.model(
+ "ProjectModel",
+ {
+ "project_id": fields.Integer(description="ID of the project."),
+ "name": fields.String(description="The name of the project."),
+ "brain": fields.Integer(
+ description="Number of the brain the projects refers to."
+ ),
+ "owner": fields.String(description="Owner of the project."),
+ "tasks": fields.List(
+ fields.Nested(task_model), description="List of tasks of the project."
+ ),
+ },
+)
+
+job_configuration_model = api.model(
+ "JobConfigurationModel",
+ {
+ "account": fields.String(
+ description="Account to submit job with, e.g. jinm14.", required=True
+ ),
+ "time": fields.String(
+ description="Time limit for job in format HH:MM:SS.", required=True
+ ),
+ "job_type": fields.String(
+ description="Type of the job which is being submitted.", required=True
+ ),
+ "gres": fields.String(
+ description='Generic resources to request for job, e.g. "gpus:4"'
+ ),
+ "mail_type": fields.String(
+ description="Mail type to use for e-mail notifications."
+ ),
+ "mail_user": fields.String(
+ description="E-mail address to send notifications to."
+ ),
+ "num_nodes": fields.Integer(
+ description="Number of nodes to allocate for the job."
+ ),
+ "partition": fields.String(
+ description='Partition to allocate job on, e.g. "batch" or "gpus"'
+ ),
+ "reservation": fields.String(
+ description="Reservation to use for running the job."
+ ),
+ "model": fields.String(description="Model configuration to train."),
+ "kwargs": fields.String(
+ description="Keyword arguments for configuration encoded as JSON"
+ ),
+ },
+)
_project_schema = models.ProjectSchema()
_task_schema = models.TaskSchema()
@@ -78,6 +141,7 @@ _job_configuration_schema = models.JobConfigurationSchema()
# Actual API definitions
# -----------------------------------
+
@project_namespace.route("/")
class ProjectList(Resource):
@project_namespace.doc("Get all projects")
@@ -194,10 +258,11 @@ class Task(Resource):
def get(self, project_id, task_id):
try:
with Database() as db:
- task = db.get_task_by_id(project_id=project_id,
- task_id=task_id)
+ task = db.get_task_by_id(project_id=project_id, task_id=task_id)
except TaskNotFoundError:
- abort(404, f"No task found for project id {project_id} and task id {task_id}")
+ abort(
+ 404, f"No task found for project id {project_id} and task id {task_id}"
+ )
return
return _task_schema.dump(task)
@@ -226,11 +291,15 @@ class Task(Resource):
try:
with Database() as db:
- db.update_task_values(project_id=project_id, task_id=task_id, key_value_dict=data)
+ db.update_task_values(
+ project_id=project_id, task_id=task_id, key_value_dict=data
+ )
# Get the modified data to return it
task = db.get_task_by_id(project_id=project_id, task_id=task_id)
except TaskNotFoundError:
- abort(404, f"No task found for project id {project_id} and task id {task_id}")
+ abort(
+ 404, f"No task found for project id {project_id} and task id {task_id}"
+ )
return
except ForbiddenOperationError as ex:
abort(403, ex.message)
@@ -269,38 +338,51 @@ class TaskJobList(Resource):
annotations = task.annotations
# noinspection PyUnresolvedReferences
job_type = job_configuration.job_type
- if job_type.lower() in ("training", "train", "training_prediction", "train_predict", "train+predict"):
+ if job_type.lower() in (
+ "training",
+ "train",
+ "training_prediction",
+ "train_predict",
+ "train+predict",
+ ):
with_prediction = "predict" in job_type.lower()
- job_id = submit_training_job(brain=brain,
- annotations=annotations,
- job_configuration=job_configuration,
- project_id=project_id,
- task_id=task_id,
- with_prediction=with_prediction,
- **kwargs)
+ job_id = submit_training_job(
+ brain=brain,
+ annotations=annotations,
+ job_configuration=job_configuration,
+ project_id=project_id,
+ task_id=task_id,
+ with_prediction=with_prediction,
+ **kwargs,
+ )
elif job_type in ("prediction", "predict"):
- job_id = submit_prediction_job(brain=brain,
- job_configuration=job_configuration,
- project_id=project_id,
- task_id=task_id)
+ job_id = submit_prediction_job(
+ brain=brain,
+ job_configuration=job_configuration,
+ project_id=project_id,
+ task_id=task_id,
+ )
else:
abort(400, f"Invalid job type: {job_type}")
return
# Save job id into the task
- job = models.Job(job_id=job_id,
- job_configuration=job_configuration)
+ job = models.Job(job_id=job_id, job_configuration=job_configuration)
job = _job_schema.dump(job)
- db.update_task_values(project_id=project_id,
- task_id=task_id,
- key_value_dict={"jobs": job},
- operation="add")
+ db.update_task_values(
+ project_id=project_id,
+ task_id=task_id,
+ key_value_dict={"jobs": job},
+ operation="add",
+ )
except ProjectNotFoundError:
abort(404, f"No project found for id {project_id}")
return
except TaskNotFoundError:
- abort(404, f"No task found for project id {project_id} and task id {task_id}")
+ abort(
+ 404, f"No task found for project id {project_id} and task id {task_id}"
+ )
return
except JobSubmissionError as ex:
abort(500, f"Error submitting job: {ex.message}")
@@ -312,15 +394,20 @@ class TaskJobList(Resource):
@project_namespace.route("/<int:project_id>/tasks/<int:task_id>/jobs/<int:job_id>")
class TaskJob(Resource):
- @project_namespace.doc("Get information about a specific job associated with a task")
+ @project_namespace.doc(
+ "Get information about a specific job associated with a task"
+ )
def get(self, project_id, task_id, job_id):
try:
with Database() as db:
- job = db.get_job_by_id(project_id=project_id,
- task_id=task_id,
- job_id=job_id)
+ job = db.get_job_by_id(
+ project_id=project_id, task_id=task_id, job_id=job_id
+ )
except JobNotFoundError:
- abort(404, f"No job found for project {project_id} - task {task_id} - project {project_id}")
+ abort(
+ 404,
+ f"No job found for project {project_id} - task {task_id} - project {project_id}",
+ )
return
# Dump job to dict and add the job status from the batch system
@@ -329,8 +416,10 @@ class TaskJob(Resource):
result["status"] = get_job_status(job_id=job_id)
except JobStatusNotFoundError:
# If the job status could not be found, it could mean the job has finished to long ago
- result["status"] = f"Could not determine job status for job with id {job_id}. " \
- f"This could mean that the job does not exist or finished too long ago."
+ result["status"] = (
+ f"Could not determine job status for job with id {job_id}. "
+ f"This could mean that the job does not exist or finished too long ago."
+ )
return result
@@ -344,16 +433,20 @@ class TaskJob(Resource):
jobs = [job for job in task.jobs if job.job_id != job_id]
jobs = _job_schema.dump(jobs, many=True)
# Update task with changed jobs list
- db.update_task_values(project_id=project_id,
- task_id=task_id,
- key_value_dict={"jobs": jobs},
- operation="set")
+ db.update_task_values(
+ project_id=project_id,
+ task_id=task_id,
+ key_value_dict={"jobs": jobs},
+ operation="set",
+ )
except JobNotFoundError:
abort(404, f"Could not cancel job {job_id}: Job not found.")
return {"message": "success"}
-@project_namespace.route("/<int:project_id>/tasks/<int:task_id>/tile_server_config/<base_file_b64>")
+@project_namespace.route(
+ "/<int:project_id>/tasks/<int:task_id>/tile_server_config/<base_file_b64>"
+)
class TaskTileServerConfig(Resource):
@project_namespace.doc("Create a tile server configuration for the task")
@@ -362,7 +455,11 @@ class TaskTileServerConfig(Resource):
import requests
import base64
from atlaslib.files import get_section_number_from_string
- from .config import TILE_SERVER_OUTPUT_DIR, ATLAS_CONTROLLER_URL, TILE_SERVER_HOST
+ from .config import (
+ TILE_SERVER_OUTPUT_DIR,
+ ATLAS_CONTROLLER_URL,
+ TILE_SERVER_HOST,
+ )
# Download the base file
base_file = base64.b64decode(base_file_b64).decode("utf-8")
@@ -418,7 +515,11 @@ class TaskTileServerConfig(Resource):
h, w = prediction["shape"]
section = f"{get_section_number_from_string(path):04d}"
section_overlays = overlays.get(section, {})
- url = "function(level, x, y){return '" + f"{TILE_SERVER_HOST}/get_tile?level=' + level + '&y=' + y + '&x=' + x + '&ts=256&img={path}&dataset=/{cmap_args}'" + ";}"
+ url = (
+ "function(level, x, y){return '"
+ + f"{TILE_SERVER_HOST}/get_tile?level=' + level + '&y=' + y + '&x=' + x + '&ts=256&img={path}&dataset=/{cmap_args}'"
+ + ";}"
+ )
section_overlays[overlay_name] = {
"getTileUrl": url,
"height": h,
@@ -462,8 +563,7 @@ class AnnotationImportExport(Resource):
return
try:
- annotations = db.export_annotations(json_path=path,
- user_name=user)
+ annotations = db.export_annotations(json_path=path, user_name=user)
except Exception as ex:
abort(500, f"Error while retrieving annotations: {ex}")
return
@@ -514,11 +614,15 @@ class AnnotationImportExport(Resource):
overwrite = request.args.get("overwrite", False)
for section, structures in annotations.items():
structures = parse_microdraw_json(structures)
- annotations_for_section = Annotations(structures=structures, section=int(section))
- db.import_annotations(json_path=path,
- user_name=user,
- annotations=annotations_for_section,
- overwrite=overwrite)
+ annotations_for_section = Annotations(
+ structures=structures, section=int(section)
+ )
+ db.import_annotations(
+ json_path=path,
+ user_name=user,
+ annotations=annotations_for_section,
+ overwrite=overwrite,
+ )
except Exception as ex:
abort(500, f"Error importing annotations into database: {ex}")
return
@@ -533,7 +637,9 @@ class AnnotationImportExport(Resource):
@predictions_namespace.route("/<int:project_id>/tasks/<int:task_id>")
class PredictionAnnotationExport(Resource):
- @annotation_namespace.doc("Retrieve annotations based on predictions of a specific task")
+ @annotation_namespace.doc(
+ "Retrieve annotations based on predictions of a specific task"
+ )
def get(self, project_id, task_id):
import os
import requests
@@ -543,7 +649,9 @@ class PredictionAnnotationExport(Resource):
# Determine
work_dir = f"atlas_ui_project{project_id}_task{task_id}"
# Query predictions
- result = requests.get(url=f"{ATLAS_CONTROLLER_URL}/predictions/{work_dir}?annotations=true")
+ result = requests.get(
+ url=f"{ATLAS_CONTROLLER_URL}/predictions/{work_dir}?annotations=true"
+ )
if result.status_code >= 400:
abort(404, f"Failed to find predictions")
return
diff --git a/atlas_server/src/db.py b/atlas_server/src/db.py
index 54c65a1..7fc1757 100644
--- a/atlas_server/src/db.py
+++ b/atlas_server/src/db.py
@@ -4,7 +4,13 @@ Access to Mondo database
"""
from pymongo import MongoClient, DESCENDING
from . import models
-from .config import DATABASE_HOST, DATABASE_PORT, DATABASE_NAME, DATABASE_USERNAME, DATABASE_PASSWORD
+from .config import (
+ DATABASE_HOST,
+ DATABASE_PORT,
+ DATABASE_NAME,
+ DATABASE_USERNAME,
+ DATABASE_PASSWORD,
+)
from marshmallow.schema import EXCLUDE
_project_schema = models.ProjectSchema(unknown=EXCLUDE)
@@ -14,6 +20,7 @@ _job_schema = models.JobSchema(unknown=EXCLUDE)
def _get_timestamp():
from time import time
+
return int(time())
@@ -63,10 +70,12 @@ class Database(object):
def open(self):
if self.client:
raise RuntimeError("Cannot open connection: Connection already open.")
- self.client = MongoClient(DATABASE_HOST,
- username=DATABASE_USERNAME,
- password=DATABASE_PASSWORD,
- port=DATABASE_PORT)
+ self.client = MongoClient(
+ DATABASE_HOST,
+ username=DATABASE_USERNAME,
+ password=DATABASE_PASSWORD,
+ port=DATABASE_PORT,
+ )
return self
def close(self):
@@ -89,10 +98,6 @@ class Database(object):
def projects(self):
return self.database.projects
- @property
- def project_ids(self):
- return self.database.project_ids
-
def _update_project_fields(self, project_id, key_value_dict, operation="set"):
"""
Update a single field
@@ -113,10 +118,9 @@ class Database(object):
raise ForbiddenOperationError(message)
mongo_operation = operations[operation]
- update_res = self.projects.update_one({"project_id": project_id},
- {
- mongo_operation: key_value_dict
- })
+ update_res = self.projects.update_one(
+ {"project_id": project_id}, {mongo_operation: key_value_dict}
+ )
# Raise error if no projects were affected
# This means the project id does not exist
if operation == "delete":
@@ -136,18 +140,21 @@ class Database(object):
"""
# Update modified data of project
modified_date = _get_timestamp()
- self.projects.update_one({"project_id": project_id},
- {
- "$set":
- {
- "modified": str(modified_date),
- },
- })
+ self.projects.update_one(
+ {"project_id": project_id},
+ {
+ "$set": {
+ "modified": str(modified_date),
+ },
+ },
+ )
return modified_date
def insert_project(self, project):
- # Find current maximum project id
- max_existing = self.project_ids.find_one(sort=[("project_id", DESCENDING)])
+ # Find current maximum project id. Important: Here, we search for __all__ projects, including deleted ones.
+ max_existing = self.projects.find_one(
+ {}, sort={"project_id": -1}, projection={"_id": False, "project_id": True}
+ )
if max_existing:
new_id = max_existing["project_id"] + 1
else:
@@ -165,15 +172,13 @@ class Database(object):
document = _project_to_mongodb_item(project=project)
# Insert into database
self.projects.insert_one(document)
- # Insert project id
- self.project_ids.insert_one({"project_id": new_id, "next_task_id": 1, })
return document
def update_project_values(self, project_id, key_value_dict):
- self._update_project_fields(project_id=project_id,
- key_value_dict=key_value_dict,
- operation="set")
+ self._update_project_fields(
+ project_id=project_id, key_value_dict=key_value_dict, operation="set"
+ )
def get_project_by_id(self, project_id):
"""
@@ -181,24 +186,35 @@ class Database(object):
Args:
project_id (int): Id of the project.
+ include_deleted_tasks (bool): Include deleted tasks.
Returns:
atlas_server.models.Project
"""
- project = self.projects.find_one({"project_id": project_id})
+ project = self.projects.find_one(
+ {
+ "project_id": project_id,
+ }
+ )
if not project:
raise ProjectNotFoundError(project_id=project_id)
return _project_schema.load(project, unknown=EXCLUDE)
def get_projects_for_user(self, username):
- projects = list(self.projects.find({"owner": username}))
+ projects = list(
+ self.projects.find(
+ {
+ "owner": username,
+ }
+ )
+ )
# noinspection PyTypeChecker
return _project_schema.load(projects, many=True, unknown=EXCLUDE)
def delete_project(self, project_id):
- deleted_res = self.projects.delete_one({"project_id": project_id})
- if deleted_res.deleted_count == 0:
- raise ProjectNotFoundError(project_id=project_id)
+ self._update_project_fields(
+ project_id=project_id, key_value_dict={"deleted": True}, operation="set"
+ )
def _update_task_fields(self, project_id, task_id, key_value_dict, operation="set"):
"""
@@ -221,7 +237,13 @@ class Database(object):
mongo_operation = operations[operation]
# Modify the update dict to match the update syntax. We prefix "tasks.$." before each key
update_dict = {f"tasks.$.{key}": value for key, value in key_value_dict.items()}
- update_res = self.projects.update_one({"project_id": project_id, "tasks.task_id": task_id, }, {mongo_operation: update_dict})
+ update_res = self.projects.update_one(
+ {
+ "project_id": project_id,
+ "tasks.task_id": task_id,
+ },
+ {mongo_operation: update_dict},
+ )
# Raise error if no projects were affected
# This means the project id does not exist
affected_count = update_res.modified_count
@@ -232,12 +254,14 @@ class Database(object):
self._update_task_modified_date(project_id=project_id, task_id=task_id)
def _delete_task(self, project_id, task_id):
- selection_dict = {"project_id": project_id, "tasks.task_id": task_id}
- delete_dict = {"$pull": {"tasks": {"task_id": task_id}}}
- update_res = self.projects.update_one(selection_dict, delete_dict)
- affected_count = update_res.modified_count
- if affected_count == 0:
- raise TaskNotFoundError(project_id=project_id, task_id=task_id)
+ self._update_task_fields(
+ project_id=project_id,
+ task_id=task_id,
+ # "Delete" task by setting them to deleted
+ key_value_dict={
+ "deleted": True,
+ },
+ )
def _update_task_modified_date(self, project_id, task_id):
"""
@@ -245,13 +269,17 @@ class Database(object):
"""
# Update modified data of project
modified_date = _get_timestamp()
- self.projects.update_one({"project_id": project_id, "tasks.task_id": task_id, },
- {
- "$set":
- {
- "task.$.modified": str(modified_date),
- },
- })
+ self.projects.update_one(
+ {
+ "project_id": project_id,
+ "tasks.task_id": task_id,
+ },
+ {
+ "$set": {
+ "task.$.modified": str(modified_date),
+ },
+ },
+ )
return modified_date
# noinspection PyUnresolvedReferences
@@ -260,17 +288,11 @@ class Database(object):
project = self.get_project_by_id(project_id=project_id)
if project is None:
raise ProjectNotFoundError(project_id)
- project_ids = self.project_ids.find_one({"project_id": project_id})
- if not project_ids:
- # Fallback for projects which have no entry in project_ids
- if not project.tasks:
- new_task_id = 1
- else:
- new_task_id = max(task.task_id for task in project.tasks) + 1
- project_ids.insert_one({"project_id": project_id, "next_task_id": new_task_id})
+ task_ids = [task.task_id for task in project.tasks]
+ if task_ids:
+ new_task_id = max(task_ids) + 1
else:
- new_task_id = project_ids["next_task_id"]
-
+ new_task_id = 1
task.task_id = new_task_id
# Add created and modified info to task
task.created = _get_timestamp()
@@ -278,55 +300,51 @@ class Database(object):
# Serialize task
document = _task_schema.dump(task)
# Insert task into the projects task list
- self._update_project_fields(project_id=project_id,
- key_value_dict={
- "tasks": document
- },
- operation="add")
- # Update next task id
- self.project_ids.update_one({"project_id": project_id}, {"$set": {"next_task_id": new_task_id + 1}})
+ self._update_project_fields(
+ project_id=project_id, key_value_dict={"tasks": document}, operation="add"
+ )
+
return document
def get_task_by_id(self, project_id, task_id):
res = self.projects.find_one(
{
"project_id": project_id,
- "tasks.task_id": task_id
+ "tasks.task_id": task_id,
},
# Projection, only get the specific task
{
"tasks.$": 1,
- }
+ },
)
if not res:
raise TaskNotFoundError(project_id=project_id, task_id=task_id)
return _task_schema.load(res["tasks"][0])
def update_task_values(self, project_id, task_id, key_value_dict, operation="set"):
- self._update_task_fields(project_id=project_id,
- task_id=task_id,
- key_value_dict=key_value_dict,
- operation=operation)
+ self._update_task_fields(
+ project_id=project_id,
+ task_id=task_id,
+ key_value_dict=key_value_dict,
+ operation=operation,
+ )
def delete_task(self, project_id, task_id):
- # delete_res = self.projects.
- self._delete_task(project_id=project_id,
- task_id=task_id)
+ self._delete_task(project_id=project_id, task_id=task_id)
def get_job_by_id(self, project_id, task_id, job_id):
# We cannot do double nested updates with mongoDB, so we get the task
# and search for the task in the result set
try:
- task = self.get_task_by_id(project_id=project_id,
- task_id=task_id)
+ task = self.get_task_by_id(project_id=project_id, task_id=task_id)
except TaskNotFoundError:
- raise JobNotFoundError(project_id=project_id,
- task_id=task_id,
- job_id=job_id)
+ raise JobNotFoundError(
+ project_id=project_id, task_id=task_id, job_id=job_id
+ )
# Search for the job
# noinspection PyUnresolvedReferences
job = [job for job in task.jobs if job.job_id == job_id]
if not job:
- raise JobNotFoundError(project_id=project_id,
- task_id=task_id,
- job_id=job_id)
+ raise JobNotFoundError(
+ project_id=project_id, task_id=task_id, job_id=job_id
+ )
diff --git a/atlas_server/src/models.py b/atlas_server/src/models.py
index 265fa20..aaff649 100644
--- a/atlas_server/src/models.py
+++ b/atlas_server/src/models.py
@@ -18,7 +18,6 @@ class JobConfigurationSchema(Schema):
model = fields.String(allow_none=True)
kwargs = fields.String(allow_none=True)
-
# noinspection PyUnusedLocal
@post_load
def create_job_configuration(self, data, **kwargs):
@@ -57,6 +56,7 @@ class TaskSchema(Schema):
jobs = fields.List(fields.Nested(JobSchema))
no_aux_labels = fields.Boolean(allow_none=True)
model = fields.String(allow_none=True)
+ deleted = fields.Boolean(allow_none=True)
# noinspection PyUnusedLocal
@post_load
@@ -72,6 +72,7 @@ class ProjectSchema(Schema):
tasks = fields.List(fields.Nested(TaskSchema))
created = fields.Integer()
modified = fields.Integer()
+ deleted = fields.Boolean(allow_none=True)
# noinspection PyUnusedLocalname
@post_load
@@ -80,15 +81,18 @@ class ProjectSchema(Schema):
class Project(object):
- def __init__(self,
- project_id=None,
- name=None,
- brain=None,
- owner=None,
- tasks=None,
- jobs=None,
- created=None,
- modified=None):
+ def __init__(
+ self,
+ project_id=None,
+ name=None,
+ brain=None,
+ owner=None,
+ tasks=None,
+ jobs=None,
+ created=None,
+ modified=None,
+ deleted=None,
+ ):
self.project_id = project_id
self.name = name
self.brain = brain
@@ -107,21 +111,25 @@ class Project(object):
self.created = created
self.modified = modified
+ self.deleted = deleted
def __repr__(self):
return f"Project(project_id={self.project_id}, name={self.name}, owner={self.owner})"
class Task(object):
- def __init__(self,
- task_id=None,
- name=None,
- created=None,
- modified=None,
- annotations=None,
- jobs=None,
- no_aux_labels=None,
- model=None):
+ def __init__(
+ self,
+ task_id=None,
+ name=None,
+ created=None,
+ modified=None,
+ annotations=None,
+ jobs=None,
+ no_aux_labels=None,
+ model=None,
+ deleted=None,
+ ):
self.task_id = task_id
self.name = name
self.annotations = annotations
@@ -143,17 +151,14 @@ class Task(object):
self.created = created
self.modified = modified
+ self.deleted = deleted
def __repr__(self):
return f"Task(task_id={self.task_id}, name={self.name})"
class Annotation(object):
- def __init__(self,
- section=None,
- original_name=None,
- name=None,
- path=None):
+ def __init__(self, section=None, original_name=None, name=None, path=None):
self.section = section
self.name = name
self.path = path
@@ -163,10 +168,7 @@ class Annotation(object):
class Job(object):
- def __init__(self,
- job_id=None,
- status=None,
- job_configuration=None):
+ def __init__(self, job_id=None, status=None, job_configuration=None):
self.job_id = job_id
self.status = status
self.job_configuration = job_configuration
@@ -176,18 +178,20 @@ class Job(object):
class JobConfiguration(object):
- def __init__(self,
- account=None,
- time=None,
- job_type=None,
- gres=None,
- mail_type=None,
- mail_user=None,
- num_nodes=None,
- partition=None,
- reservation=None,
- model=None,
- kwargs=None):
+ def __init__(
+ self,
+ account=None,
+ time=None,
+ job_type=None,
+ gres=None,
+ mail_type=None,
+ mail_user=None,
+ num_nodes=None,
+ partition=None,
+ reservation=None,
+ model=None,
+ kwargs=None,
+ ):
self.account = account
self.time = time
self.job_type = job_type
diff --git a/microdraw/src/atlas_ui.js b/microdraw/src/atlas_ui.js
index 81fb361..18d6414 100644
--- a/microdraw/src/atlas_ui.js
+++ b/microdraw/src/atlas_ui.js
@@ -170,6 +170,12 @@ var app = new Vue({
}
return annotations;
},
+ existing_projects: function () {
+ // Only existing projects
+ return this.projects.filter((item) => {
+ return !item.deleted;
+ });
+ },
sorted_tasks: function () {
if (this.selected_project === null) {
// No tasks
@@ -180,7 +186,9 @@ var app = new Vue({
a.name.localeCompare(b.name),
);
}
- return this.selected_project.tasks;
+ return this.selected_project.tasks.filter((item) => {
+ return !item.deleted;
+ });
},
},
methods: {
@@ -204,7 +212,7 @@ var app = new Vue({
success: function (data) {
_this.projects = data;
if (_this.projects.length > 0) {
- _this.selected_project = _this.projects[0];
+ _this.selected_project = _this.existing_projects[0];
}
post_message(`Got ${_this.projects.length} projects from server.`);
},
@@ -260,6 +268,11 @@ var app = new Vue({
// To edit a project, we set it as selected project
this.selected_project = project;
},
+ getProjectTasks: function (project) {
+ return project.tasks.filter((item) => {
+ return !item.deleted;
+ });
+ },
saveProject: function (project) {
if (project.created === undefined) {
// This is a new project, so we add it to the project list
@@ -323,8 +336,8 @@ var app = new Vue({
});
}
},
- deleteProject: function (project_index) {
- let project = this.projects[project_index];
+ deleteProject: function (project) {
+ let project_index = this.projects.findIndex((item) => item === project);
// Confirm delete
let confirm_delete = confirm(
diff --git a/microdraw/src/microdraw.html b/microdraw/src/microdraw.html
index 88b6cff..1bbcf02 100755
--- a/microdraw/src/microdraw.html
+++ b/microdraw/src/microdraw.html
@@ -1,336 +1,724 @@
<html>
+ <head>
+ <title>MicroDraw</title>
+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width,user-scalable=no" />
+ <link
+ rel="stylesheet"
+ href="https://stackpath.bootstrapcdn.com/bootstrap/4.2.1/css/bootstrap.min.css"
+ integrity="sha384-GJzZqFGwb1QTTN6wy59ffF1BuGJpLSa9DkKMp0DgiMDm4iYMj70gZWKYbI706tWS"
+ crossorigin="anonymous"
+ />
+ <link rel="stylesheet" href="css/microdraw.css" type="text/css" />
+ <link rel="stylesheet" href="css/atlas_ui.css" type="text/css" />
+ <link rel="shortcut icon" type="image/x-icon" href="favicon.ico" />
+ </head>
- <head>
- <title>MicroDraw</title>
- <meta charset="utf-8">
- <meta name="viewport" content="width=device-width,user-scalable=no" />
- <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.2.1/css/bootstrap.min.css" integrity="sha384-GJzZqFGwb1QTTN6wy59ffF1BuGJpLSa9DkKMp0DgiMDm4iYMj70gZWKYbI706tWS" crossorigin="anonymous">
- <link rel="stylesheet" href="css/microdraw.css" type="text/css" />
- <link rel="stylesheet" href="css/atlas_ui.css" type="text/css" />
- <link rel="shortcut icon" type="image/x-icon" href="favicon.ico" />
- </head>
-
- <body>
- <!-- Load javascript -->
- <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"></script>
- <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.6/umd/popper.min.js" integrity="sha384-wHAiFfRlMFy6i5SRaxvfOCifBUQy1xHdJ/yoi7FRNXMRBu5WHdZYu1hA6ZOblgut" crossorigin="anonymous"></script>
- <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.2.1/js/bootstrap.min.js" integrity="sha384-B0UglyR+jN6CkvvICOB2joaf5I4l3gm9GU6Hc1og6Ls7i6U/mkkaduKaBhlAXv9k" crossorigin="anonymous"></script>
- <div id="atlas_app">
- <div id="menuButton">
- <img class="button" id="openMenu" title="Menu" src="img/openMenu.svg" />
- </div>
-
- <!-- Toolbar -->
- <div id="menuBar" class="table">
-
- <div class="md-row">
- <div id="login"></div>
- <img class="button" id="closeMenu" title="Close Menu" src="img/closeMenu.svg" />
- </div>
-
- <div class="md-row">
- <div id="myNavigator"></div>
- </div>
-
- <div class="md-row">
- <div class="cell" style="text-align:center">
- <div class="buttonGroup">
- <img class="button" id="zoom" title="Navigator" src="img/navigate.svg" />
- <img class="button" id="home" title="Home" src="img/home.svg" />
- <img class="button" id="zoom-in" title="Zoom in" src="img/plus.svg" />
- <img class="button" id="zoom-out" title="Zoom out" src="img/minus.svg" />
- <img class="button" id="rotate-right" title="Rotate right" src="img/plus.svg" />
- <img class="button" id="rotate-left" title="Rotate left" src="img/minus.svg" />
-
- <div>
- <img class="button" id="prev" title="Previous slice" src="img/prev.svg" />
- <input id="slice-name" list="slice-names" style="width:80px" />
- <img class="button" id="next" title="Next slice" src="img/next.svg" />
- </div>
- <input type="range" id="slider" class="sliderClass" />
- </div>
- <div class="buttonGroup">
- <img class="button" id="select" title="Select" src="img/select.svg" />
- <img class="button" id="draw" title="Draw" src="img/draw.svg" />
- <img class="button" id="draw-polygon" title="Draw polygon" src="img/draw-polygon.svg" />
- <img class="button" id="simplify" title="Simplify" src="img/simplify.svg" />
- <img class="button" id="addpoint" title="Add point" src="img/addPoint.svg" />
- <img class="button" id="delpoint" title="Delete point" src="img/deletePoint.svg" />
- <img class="button" id="addregion" title="Union of regions" src="img/union.svg" />
- <img class="button" id="delregion" title="Subtraction of regions" src="img/subtract.svg" />
- <img class="button" id="splitregion" title="Split region" src="img/split.svg" />
- <img class="button" id="rotate" title="Rotate region" src="img/rotate.svg" />
- <img class="button" id="flip" title="Flip region" src="img/flip.svg" />
- <img class="button" id="snappoint" title="Snap two points on top of each other"
- src="img/rotate.svg" />
- <img class="button" id="handle" title="Toggle handles" src="img/handle.svg" />
- <img class="button" id="text" title="Add text" src="img/text.svg" />
- <img class="button" id="point" title="Add point" src="img/addCross.svg" />
- </div>
- <div class="buttonGroup">
- <img class="button" id="save" title="Save annotations" src="img/save.svg" />
- <img class="button" id="copy" title="Copy path" src="img/copy.svg" />
- <img class="button" id="paste" title="Paste path" src="img/paste.svg" />
- <img class="button" id="delete" title="Delete region" src="img/delete.svg" />
- <img class="button" id="load" title="Load annotations from db" src="img/load.svg" />
- </div>
-
- <div class="buttonGroup">
- <select id="overlays">
- <option value="none">No Overlay</option>
- </select>
- <input type="range" class="sliderClass" id="alpha-overlay"
- title="Change the transparency of the overlay" />
- </div>
- <div id="mouseCoordinates" class="small-text">
- x: 0, y: 0
- </div>
- <div id="rgbValues" class="small-text">
- RGB: (000,000,000)
- </div>
- </div>
-
- </div>
-
- <div class="md-row">
- <div class="btn-group" role="group" aria-label="basic example">
- <button v-on:click="initializeAtlas" type="button" class="btn btn-primary" data-toggle="modal"
- data-target="#atlas_ui_projects_modal">
- ATLaS UI
- </button>
- <button type="button" class="btn btn-secondary" data-toggle="modal"
- v-on:click="initializeAnnotationImport" data-target="#atlas_ui_imports_modal">
- Import
- </button>
- </div>
- </div>
-
- <div class="md-row">
- <div class="cell">
- <br />Regions <img class="eye" id="eye_all" title="Toggle all regions" src="img/eyeOpened.svg">
- <div id="regionList"></div>
- </div>
- </div>
- </div>
-
- <div id="colorSelector">
- stroke color
- <select id="selectStrokeColor" onChange="onSelectStrokeColor();">
- <option value="0">black</option>
- <option value="1">white</option>
- <option value="2">red</option>
- <option value="3">green</option>
- <option value="4">blue</option>
- <option value="5">yellow</option>
- </select>
- <br>
- <br>
- stroke width
- <input type="button" id="strokeWidthDec" value="-" onClick="onStrokeWidthDec();"><input type="button"
- id="strokeWidthInc" value="+" onClick="onStrokeWidthInc();">
- <br>
- <br>
- fill color
- <input type="color" id="fillColorPicker" value="#ff0000" onChange="onFillColorPicker(this.value);">
- <br>
- <br>
- α<input type="range" min="0" max="100" id="alphaSlider" onInput="onAlphaSlider(this.value);"><input
- id="alphaFill" onInput="onAlphaInput(this.value);">
- <br>
- <br>
- <input type="button" id="okStrokeColor" value="ok" onClick="setRegionColor();">
- </div>
- <!-- Region Picker -->
- <div id="regionPicker">
- </div>
- <!-- OpenSeadragon viewer -->
- <div id="openseadragon1" style="width:100%">
- </div>
- <!-- alert/info box after saving -->
- <div id="saveDialog"></div>
- <!-- naat logo -->
- <a id="logo" href="http://neuroanatomy.github.io">
- <img src="img/naat.svg" style="width:2.5em" />
- </a>
- <!-- ATLaS UI dialogue -->
- <div class="modal fade" id="atlas_ui_projects_modal" tabindex="-1" role="dialog"
- aria-labelledby="exampleModalLabel" aria-hidden="true">
- <div class="modal-dialog modal-lg" role="document">
- <div class="modal-content">
- <!-- Header of dialogue -->
- <div class="modal-header">
- <h5 class="modal-title" id="exampleModalLabel">ATLaS UI</h5>
- <button type="button" class="close" data-dismiss="modal" aria-label="Close">
- <span aria-hidden="true">×</span>
- </button>
- </div>
-
- <!-- Body of dialogue -->
- <div class="modal-body">
- <!-- List of projects -->
- <div class="form-group">
- <label for="atlas_project_list">Projects</label>
- <ol id="atlas_project_list"
- class="list-group atlas_project_list border border-dark rounded bg-light">
- <li v-for="(project, index) in projects" class="list-group-item list-group-item-action">
- <div class="form-row">
- <!-- <label class="col-1 col-form-label">Name</label> -->
- <div class="col-1">
- <input v-model="project.project_id" class="form-control" type="text" readonly />
- </div>
- <div class="col-4">
- <input v-model="project.name" class="form-control" type="text" readonly />
- </div>
- <label class="col-1 col-form-label">Brain</label>
- <div class="col-1">
- <input v-model="project.brain" type="text" class="form-control" readonly>
- </div>
- <label class="col-1 col-form-label">Tasks</label>
- <div class="col-1">
- <input v-model="project.tasks.length" type="text" class="form-control"
- readonly>
- </div>
- <div class="col-3">
- <div class="btn-group float-right" role="group">
- <button type="button" class="btn btn-primary" data-toggle="modal"
- data-target="#atlas_ui_tasks_modal" v-on:click="editProject(project)">Edit</button>
- <div class="btn-group" role="group">
- <button type="button" class="btn btn-danger"
- v-on:click="deleteProject(index)">Delete</button>
- </div>
- </div>
- </div>
- </div>
- </li>
- </ol>
- </div>
-
- <!-- Button group -->
- <div class="btn-group" role="group">
- <button v-on:click="newProject" type="button" class="btn btn-primary" data-toggle="modal"
- data-target="#atlas_ui_tasks_modal">New project...</button>
- </div>
- <!-- Log messages -->
- <!-- <div class="overflow-auto" id="messages"></div> -->
- </div>
- <div class="modal-footer">
- <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
- </div>
- </div>
- </div>
- </div>
- <div class="modal fade" id="atlas_ui_tasks_modal" tabindex="-1" role="dialog"
- aria-labelledby="exampleModalLabel" aria-hidden="true" v-if="selected_project !== null">
- <div class="modal-dialog modal-xl" role="document">
- <div class="modal-content">
- <!-- Header of dialogue -->
- <div class="modal-header">
- <h5 class="modal-title" id="exampleModalLabel">
- {{selected_project.project_id}} - {{selected_project.name}}
- </h5>
- <button type="button" class="close" data-dismiss="modal" aria-label="Close" v-on:click="closeProject()">
- <span aria-hidden="true">×</span>
- </button>
- </div>
-
- <!-- Body of dialogue -->
- <div class="modal-body">
- <div class="form-group">
- <!-- Project information -->
- <div class="form-group">
- <label for="atlas_ui_project_form_name">Name</label>
- <input v-model="selected_project.name" type="text" class="form-control"
- id="atlas_ui_project_form_name">
- </div>
- <div class="form-group">
- <label for="atlas_ui_project_form_brain">Brain</label>
- <input v-model="selected_project.brain" type="text" class="form-control"
- id="atlas_ui_project_form_brain">
- </div>
-
-
- <!-- List of tasks -->
- <label for="atlas_task_list">Tasks</label>
- <ol id="atlas_task_list"
- class="list-group atlas_task_list border border-dark rounded bg-light"
- v-if="selected_project !== null">
- <li v-for="(task, index) in sorted_tasks"
- class="list-group-item list-group-item-action">
- <div class="form-row">
- <input v-model="task.task_id" class="col-1 form-control" type="text" readonly />
- <div class="col-2">
- <input v-model="task.name" class="form-control" type="text" readonly />
- </div>
- <label class="col-2 col-form-label text-right">Annotations</label>
- <div class="col-1">
- <input v-model="task.annotations.length" class="form-control" type="text"
- readonly />
- </div>
- <label class="col-1 col-form-label text-right">Jobs</label>
- <div class="col-1">
- <input v-model="task.jobs.length" class="form-control" type="text"
- readonly />
- </div>
- <div class="col-4">
- <div class="btn-group float-right" role="group">
- <button type="button" class="btn btn-primary" data-toggle="modal"
- data-target="#atlas_ui_annotations_modal"
- v-on:click="editTask(task)">Edit</button>
- <button type="button" class="btn btn-info" data-toggle="modal"
- data-target="#atlas_ui_jobs_modal" v-on:click="showJobsForTask(selected_project, task)">Jobs</button>
- <button type="button" class="btn btn-default" v-on:click="getResultLink(selected_project, task)">
- <img src="static/results.svg" width="20" height="20"/>
- </button>
- <button type="button" class="btn btn-danger" v-on:click="deleteTask(selected_project, task)">Delete</button>
-
- </div>
- </div>
- </div>
- </li>
- </ol>
- </div>
-
-
- <!-- Button group -->
- <div class="btn-group" role="group">
- <button v-on:click="newTask" type="button" class="btn btn-primary" data-toggle="modal"
- data-target="#atlas_ui_annotations_modal">New task...</button>
- <button type="button" class="btn btn-success" data-toggle="modal" data-target="#atlas_ui_task_wizard_modal"
- v-on:click="initializeTaskWizard">Task wizard</button>
- </div>
- <div class="btn-group" role="group">
- <button type="button" class="btn btn-info" v-on:click="submitAllJobsForProject(selected_project, submitTrainingJob)">Train all</button>
- <button type="button" class="btn btn-info" v-on:click="submitAllJobsForProject(selected_project, submitPredictionJob)">Predict all</button>
- <button type="button" class="btn btn-info" v-on:click="submitAllJobsForProject(selected_project, submitTrainingPredictionJob)">Train+Predict all</button>
- <button type="button" class="btn btn-danger" v-on:click="cancelAllJobsForProject(selected_project)">Cancel all</button>
- </div>
-
- <div class="form-group" id="atlas_ui_task_options">
- <input type="checkbox" v-model="sort_tasks_by_name" id="atlas_ui_task_sort_by_name"/>
- <label for="atlas_ui_task_sort_by_name">Sort by name</label><p>
- </div>
- </div>
- <div class="modal-footer">
- <button type="button" class="btn btn-primary" data-dismiss="modal"
- v-on:click="saveProject(selected_project)">Save</button>
- <button type="button" class="btn btn-secondary" data-dismiss="modal" v-on:click="closeProject()">Close</button>
- </div>
- </div>
- </div>
- </div>
-
- <div class="modal fade" id="atlas_ui_annotations_modal" tabindex="-1" role="dialog"
- aria-labelledby="exampleModalLabel" aria-hidden="true" v-if="selected_task !== null">
- <div class="modal-dialog modal-lg" role="document">
- <div class="modal-content">
- <!-- Header of dialogue -->
- <div class="modal-header">
- <h5 class="modal-title" id="exampleModalLabel">
- {{selected_task.task_id}} - {{selected_project.name}} - {{selected_task.name}}</h5>
- <button type="button" class="close" data-dismiss="modal" aria-label="Close" v-on:click="closeTask()">
- <span aria-hidden="true">×</span>
- </button>
- </div>
+ <body>
+ <!-- Load javascript -->
+ <script
+ src="https://code.jquery.com/jquery-3.3.1.slim.min.js"
+ integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo"
+ crossorigin="anonymous"
+ ></script>
+ <script
+ src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.6/umd/popper.min.js"
+ integrity="sha384-wHAiFfRlMFy6i5SRaxvfOCifBUQy1xHdJ/yoi7FRNXMRBu5WHdZYu1hA6ZOblgut"
+ crossorigin="anonymous"
+ ></script>
+ <script
+ src="https://stackpath.bootstrapcdn.com/bootstrap/4.2.1/js/bootstrap.min.js"
+ integrity="sha384-B0UglyR+jN6CkvvICOB2joaf5I4l3gm9GU6Hc1og6Ls7i6U/mkkaduKaBhlAXv9k"
+ crossorigin="anonymous"
+ ></script>
+ <div id="atlas_app">
+ <div id="menuButton">
+ <img class="button" id="openMenu" title="Menu" src="img/openMenu.svg" />
+ </div>
+
+ <!-- Toolbar -->
+ <div id="menuBar" class="table">
+ <div class="md-row">
+ <div id="login"></div>
+ <img
+ class="button"
+ id="closeMenu"
+ title="Close Menu"
+ src="img/closeMenu.svg"
+ />
+ </div>
+
+ <div class="md-row">
+ <div id="myNavigator"></div>
+ </div>
+
+ <div class="md-row">
+ <div class="cell" style="text-align: center">
+ <div class="buttonGroup">
+ <img
+ class="button"
+ id="zoom"
+ title="Navigator"
+ src="img/navigate.svg"
+ />
+ <img class="button" id="home" title="Home" src="img/home.svg" />
+ <img
+ class="button"
+ id="zoom-in"
+ title="Zoom in"
+ src="img/plus.svg"
+ />
+ <img
+ class="button"
+ id="zoom-out"
+ title="Zoom out"
+ src="img/minus.svg"
+ />
+ <img
+ class="button"
+ id="rotate-right"
+ title="Rotate right"
+ src="img/plus.svg"
+ />
+ <img
+ class="button"
+ id="rotate-left"
+ title="Rotate left"
+ src="img/minus.svg"
+ />
+
+ <div>
+ <img
+ class="button"
+ id="prev"
+ title="Previous slice"
+ src="img/prev.svg"
+ />
+ <input id="slice-name" list="slice-names" style="width: 80px" />
+ <img
+ class="button"
+ id="next"
+ title="Next slice"
+ src="img/next.svg"
+ />
+ </div>
+ <input type="range" id="slider" class="sliderClass" />
+ </div>
+ <div class="buttonGroup">
+ <img
+ class="button"
+ id="select"
+ title="Select"
+ src="img/select.svg"
+ />
+ <img class="button" id="draw" title="Draw" src="img/draw.svg" />
+ <img
+ class="button"
+ id="draw-polygon"
+ title="Draw polygon"
+ src="img/draw-polygon.svg"
+ />
+ <img
+ class="button"
+ id="simplify"
+ title="Simplify"
+ src="img/simplify.svg"
+ />
+ <img
+ class="button"
+ id="addpoint"
+ title="Add point"
+ src="img/addPoint.svg"
+ />
+ <img
+ class="button"
+ id="delpoint"
+ title="Delete point"
+ src="img/deletePoint.svg"
+ />
+ <img
+ class="button"
+ id="addregion"
+ title="Union of regions"
+ src="img/union.svg"
+ />
+ <img
+ class="button"
+ id="delregion"
+ title="Subtraction of regions"
+ src="img/subtract.svg"
+ />
+ <img
+ class="button"
+ id="splitregion"
+ title="Split region"
+ src="img/split.svg"
+ />
+ <img
+ class="button"
+ id="rotate"
+ title="Rotate region"
+ src="img/rotate.svg"
+ />
+ <img
+ class="button"
+ id="flip"
+ title="Flip region"
+ src="img/flip.svg"
+ />
+ <img
+ class="button"
+ id="snappoint"
+ title="Snap two points on top of each other"
+ src="img/rotate.svg"
+ />
+ <img
+ class="button"
+ id="handle"
+ title="Toggle handles"
+ src="img/handle.svg"
+ />
+ <img
+ class="button"
+ id="text"
+ title="Add text"
+ src="img/text.svg"
+ />
+ <img
+ class="button"
+ id="point"
+ title="Add point"
+ src="img/addCross.svg"
+ />
+ </div>
+ <div class="buttonGroup">
+ <img
+ class="button"
+ id="save"
+ title="Save annotations"
+ src="img/save.svg"
+ />
+ <img
+ class="button"
+ id="copy"
+ title="Copy path"
+ src="img/copy.svg"
+ />
+ <img
+ class="button"
+ id="paste"
+ title="Paste path"
+ src="img/paste.svg"
+ />
+ <img
+ class="button"
+ id="delete"
+ title="Delete region"
+ src="img/delete.svg"
+ />
+ <img
+ class="button"
+ id="load"
+ title="Load annotations from db"
+ src="img/load.svg"
+ />
+ </div>
+
+ <div class="buttonGroup">
+ <select id="overlays">
+ <option value="none">No Overlay</option>
+ </select>
+ <input
+ type="range"
+ class="sliderClass"
+ id="alpha-overlay"
+ title="Change the transparency of the overlay"
+ />
+ </div>
+ <div id="mouseCoordinates" class="small-text">x: 0, y: 0</div>
+ <div id="rgbValues" class="small-text">RGB: (000,000,000)</div>
+ </div>
+ </div>
+
+ <div class="md-row">
+ <div class="btn-group" role="group" aria-label="basic example">
+ <button
+ v-on:click="initializeAtlas"
+ type="button"
+ class="btn btn-primary"
+ data-toggle="modal"
+ data-target="#atlas_ui_projects_modal"
+ >
+ ATLaS UI
+ </button>
+ <button
+ type="button"
+ class="btn btn-secondary"
+ data-toggle="modal"
+ v-on:click="initializeAnnotationImport"
+ data-target="#atlas_ui_imports_modal"
+ >
+ Import
+ </button>
+ </div>
+ </div>
+
+ <div class="md-row">
+ <div class="cell">
+ <br />Regions
+ <img
+ class="eye"
+ id="eye_all"
+ title="Toggle all regions"
+ src="img/eyeOpened.svg"
+ />
+ <div id="regionList"></div>
+ </div>
+ </div>
+ </div>
+
+ <div id="colorSelector">
+ stroke color
+ <select id="selectStrokeColor" onChange="onSelectStrokeColor();">
+ <option value="0">black</option>
+ <option value="1">white</option>
+ <option value="2">red</option>
+ <option value="3">green</option>
+ <option value="4">blue</option>
+ <option value="5">yellow</option>
+ </select>
+ <br />
+ <br />
+ stroke width
+ <input
+ type="button"
+ id="strokeWidthDec"
+ value="-"
+ onClick="onStrokeWidthDec();"
+ /><input
+ type="button"
+ id="strokeWidthInc"
+ value="+"
+ onClick="onStrokeWidthInc();"
+ />
+ <br />
+ <br />
+ fill color
+ <input
+ type="color"
+ id="fillColorPicker"
+ value="#ff0000"
+ onChange="onFillColorPicker(this.value);"
+ />
+ <br />
+ <br />
+ α<input
+ type="range"
+ min="0"
+ max="100"
+ id="alphaSlider"
+ onInput="onAlphaSlider(this.value);"
+ /><input id="alphaFill" onInput="onAlphaInput(this.value);" />
+ <br />
+ <br />
+ <input
+ type="button"
+ id="okStrokeColor"
+ value="ok"
+ onClick="setRegionColor();"
+ />
+ </div>
+ <!-- Region Picker -->
+ <div id="regionPicker"></div>
+ <!-- OpenSeadragon viewer -->
+ <div id="openseadragon1" style="width: 100%"></div>
+ <!-- alert/info box after saving -->
+ <div id="saveDialog"></div>
+ <!-- naat logo -->
+ <a id="logo" href="http://neuroanatomy.github.io">
+ <img src="img/naat.svg" style="width: 2.5em" />
+ </a>
+ <!-- ATLaS UI dialogue -->
+ <div
+ class="modal fade"
+ id="atlas_ui_projects_modal"
+ tabindex="-1"
+ role="dialog"
+ aria-labelledby="exampleModalLabel"
+ aria-hidden="true"
+ >
+ <div class="modal-dialog modal-lg" role="document">
+ <div class="modal-content">
+ <!-- Header of dialogue -->
+ <div class="modal-header">
+ <h5 class="modal-title" id="exampleModalLabel">ATLaS UI</h5>
+ <button
+ type="button"
+ class="close"
+ data-dismiss="modal"
+ aria-label="Close"
+ >
+ <span aria-hidden="true">×</span>
+ </button>
+ </div>
+
+ <!-- Body of dialogue -->
+ <div class="modal-body">
+ <!-- List of projects -->
+ <div class="form-group">
+ <label for="atlas_project_list">Projects</label>
+ <ol
+ id="atlas_project_list"
+ class="list-group atlas_project_list border border-dark rounded bg-light"
+ >
+ <li
+ v-for="(project, index) in existing_projects"
+ class="list-group-item list-group-item-action"
+ >
+ <div class="form-row">
+ <!-- <label class="col-1 col-form-label">Name</label> -->
+ <div class="col-1">
+ <input
+ v-model="project.project_id"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <div class="col-4">
+ <input
+ v-model="project.name"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <label class="col-1 col-form-label">Brain</label>
+ <div class="col-1">
+ <input
+ v-model="project.brain"
+ type="text"
+ class="form-control"
+ readonly
+ />
+ </div>
+ <label class="col-1 col-form-label">Tasks</label>
+ <div class="col-1">
+ <input
+ v-model="getProjectTasks(project).length"
+ type="text"
+ class="form-control"
+ readonly
+ />
+ </div>
+ <div class="col-3">
+ <div class="btn-group float-right" role="group">
+ <button
+ type="button"
+ class="btn btn-primary"
+ data-toggle="modal"
+ data-target="#atlas_ui_tasks_modal"
+ v-on:click="editProject(project)"
+ >
+ Edit
+ </button>
+ <div class="btn-group" role="group">
+ <button
+ type="button"
+ class="btn btn-danger"
+ v-on:click="deleteProject(project)"
+ >
+ Delete
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+ </li>
+ </ol>
+ </div>
+
+ <!-- Button group -->
+ <div class="btn-group" role="group">
+ <button
+ v-on:click="newProject"
+ type="button"
+ class="btn btn-primary"
+ data-toggle="modal"
+ data-target="#atlas_ui_tasks_modal"
+ >
+ New project...
+ </button>
+ </div>
+ <!-- Log messages -->
+ <!-- <div class="overflow-auto" id="messages"></div> -->
+ </div>
+ <div class="modal-footer">
+ <button
+ type="button"
+ class="btn btn-secondary"
+ data-dismiss="modal"
+ >
+ Close
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+ <div
+ class="modal fade"
+ id="atlas_ui_tasks_modal"
+ tabindex="-1"
+ role="dialog"
+ aria-labelledby="exampleModalLabel"
+ aria-hidden="true"
+ v-if="selected_project !== null"
+ >
+ <div class="modal-dialog modal-xl" role="document">
+ <div class="modal-content">
+ <!-- Header of dialogue -->
+ <div class="modal-header">
+ <h5 class="modal-title" id="exampleModalLabel">
+ {{selected_project.project_id}} - {{selected_project.name}}
+ </h5>
+ <button
+ type="button"
+ class="close"
+ data-dismiss="modal"
+ aria-label="Close"
+ v-on:click="closeProject()"
+ >
+ <span aria-hidden="true">×</span>
+ </button>
+ </div>
+
+ <!-- Body of dialogue -->
+ <div class="modal-body">
+ <div class="form-group">
+ <!-- Project information -->
+ <div class="form-group">
+ <label for="atlas_ui_project_form_name">Name</label>
+ <input
+ v-model="selected_project.name"
+ type="text"
+ class="form-control"
+ id="atlas_ui_project_form_name"
+ />
+ </div>
+ <div class="form-group">
+ <label for="atlas_ui_project_form_brain">Brain</label>
+ <input
+ v-model="selected_project.brain"
+ type="text"
+ class="form-control"
+ id="atlas_ui_project_form_brain"
+ />
+ </div>
+
+ <!-- List of tasks -->
+ <label for="atlas_task_list">Tasks</label>
+ <ol
+ id="atlas_task_list"
+ class="list-group atlas_task_list border border-dark rounded bg-light"
+ v-if="selected_project !== null"
+ >
+ <li
+ v-for="(task, index) in sorted_tasks"
+ class="list-group-item list-group-item-action"
+ >
+ <div class="form-row" v-if="!task.deleted">
+ <input
+ v-model="task.task_id"
+ class="col-1 form-control"
+ type="text"
+ readonly
+ />
+ <div class="col-2">
+ <input
+ v-model="task.name"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <label class="col-2 col-form-label text-right"
+ >Annotations</label
+ >
+ <div class="col-1">
+ <input
+ v-model="task.annotations.length"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <label class="col-1 col-form-label text-right"
+ >Jobs</label
+ >
+ <div class="col-1">
+ <input
+ v-model="task.jobs.length"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <div class="col-4">
+ <div class="btn-group float-right" role="group">
+ <button
+ type="button"
+ class="btn btn-primary"
+ data-toggle="modal"
+ data-target="#atlas_ui_annotations_modal"
+ v-on:click="editTask(task)"
+ >
+ Edit
+ </button>
+ <button
+ type="button"
+ class="btn btn-info"
+ data-toggle="modal"
+ data-target="#atlas_ui_jobs_modal"
+ v-on:click="showJobsForTask(selected_project, task)"
+ >
+ Jobs
+ </button>
+ <button
+ type="button"
+ class="btn btn-default"
+ v-on:click="getResultLink(selected_project, task)"
+ >
+ <img
+ src="static/results.svg"
+ width="20"
+ height="20"
+ />
+ </button>
+ <button
+ type="button"
+ class="btn btn-danger"
+ v-on:click="deleteTask(selected_project, task)"
+ >
+ Delete
+ </button>
+ </div>
+ </div>
+ </div>
+ </li>
+ </ol>
+ </div>
+
+ <!-- Button group -->
+ <div class="btn-group" role="group">
+ <button
+ v-on:click="newTask"
+ type="button"
+ class="btn btn-primary"
+ data-toggle="modal"
+ data-target="#atlas_ui_annotations_modal"
+ >
+ New task...
+ </button>
+ <button
+ type="button"
+ class="btn btn-success"
+ data-toggle="modal"
+ data-target="#atlas_ui_task_wizard_modal"
+ v-on:click="initializeTaskWizard"
+ >
+ Task wizard
+ </button>
+ </div>
+ <div class="btn-group" role="group">
+ <button
+ type="button"
+ class="btn btn-info"
+ v-on:click="submitAllJobsForProject(selected_project, submitTrainingJob)"
+ >
+ Train all
+ </button>
+ <button
+ type="button"
+ class="btn btn-info"
+ v-on:click="submitAllJobsForProject(selected_project, submitPredictionJob)"
+ >
+ Predict all
+ </button>
+ <button
+ type="button"
+ class="btn btn-info"
+ v-on:click="submitAllJobsForProject(selected_project, submitTrainingPredictionJob)"
+ >
+ Train+Predict all
+ </button>
+ <button
+ type="button"
+ class="btn btn-danger"
+ v-on:click="cancelAllJobsForProject(selected_project)"
+ >
+ Cancel all
+ </button>
+ </div>
+
+ <div class="form-group" id="atlas_ui_task_options">
+ <input
+ type="checkbox"
+ v-model="sort_tasks_by_name"
+ id="atlas_ui_task_sort_by_name"
+ />
+ <label for="atlas_ui_task_sort_by_name">Sort by name</label>
+ <p></p>
+ </div>
+ </div>
+ <div class="modal-footer">
+ <button
+ type="button"
+ class="btn btn-primary"
+ data-dismiss="modal"
+ v-on:click="saveProject(selected_project)"
+ >
+ Save
+ </button>
+ <button
+ type="button"
+ class="btn btn-secondary"
+ data-dismiss="modal"
+ v-on:click="closeProject()"
+ >
+ Close
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <div
+ class="modal fade"
+ id="atlas_ui_annotations_modal"
+ tabindex="-1"
+ role="dialog"
+ aria-labelledby="exampleModalLabel"
+ aria-hidden="true"
+ v-if="selected_task !== null"
+ >
+ <div class="modal-dialog modal-lg" role="document">
+ <div class="modal-content">
+ <!-- Header of dialogue -->
+ <div class="modal-header">
+ <h5 class="modal-title" id="exampleModalLabel">
+ {{selected_task.task_id}} - {{selected_project.name}} -
+ {{selected_task.name}}
+ </h5>
+ <button
+ type="button"
+ class="close"
+ data-dismiss="modal"
+ aria-label="Close"
+ v-on:click="closeTask()"
+ >
+ <span aria-hidden="true">×</span>
+ </button>
+ </div>
<!-- Body of dialogue -->
<div class="modal-body">
@@ -338,161 +726,317 @@
<!-- Project information -->
<div class="form-group">
<label for="atlas_ui_task_form_name">Name</label>
- <input v-model="selected_task.name" type="text" class="form-control"
- id="atlas_ui_task_form_name">
- <label for="atlas_ui_task_form_filter">Annotation filter</label>
- <input v-model="annotation_filter" type="text" class="form-control"
- id="atlas_ui_task_form_filter">
+ <input
+ v-model="selected_task.name"
+ type="text"
+ class="form-control"
+ id="atlas_ui_task_form_name"
+ />
+ <label for="atlas_ui_task_form_filter"
+ >Annotation filter</label
+ >
+ <input
+ v-model="annotation_filter"
+ type="text"
+ class="form-control"
+ id="atlas_ui_task_form_filter"
+ />
<label for="atlas_ui_task_form_model">Model</label>
- <select class="form-control" id="atlas_ui_task_form_model" v-model="selected_task.model">
- <option v-for="model in model_options">
- {{ model }}
- </option>
+ <select
+ class="form-control"
+ id="atlas_ui_task_form_model"
+ v-model="selected_task.model"
+ >
+ <option v-for="model in model_options">{{ model }}</option>
</select>
- <input type="checkbox" v-model="enable_auto_rename" id="atlas_ui_task_form_auto_rename"/>
- <label for="atlas_ui_task_form_auto_rename">Enable auto-rename</label>
-
- <input type="checkbox" v-model="selected_task.no_aux_labels" id="atlas_ui_task_form_aux_labels"/>
- <label for="atlas_ui_task_form_aux_labels">No auxiliary labels</label>
- </div>
-
- <!-- List of annotations -->
- <label for="atlas_annotation_list">Annotations</label>
- <ol id="atlas_annotation_list_selected"
- class="list-group atlas_annotation_list border border-dark rounded bg-light"
- v-if="selected_task !== null">
- <li v-for="(annotation, index) in selected_task.annotations"
- class="list-group-item list-group-item-action">
- <div class="form-row">
- <label class="col-1 col-form-label text-right">Name</label>
- <div class="col-3">
- <input v-model="annotation.name" class="form-control" type="text"
- readonly />
- </div>
- <label class="col-1 col-form-label text-right">Section</label>
- <div class="col-2">
- <input v-model="annotation.section" class="form-control" type="text"
- readonly />
- </div>
- <div class="col-5">
- <div class="btn-group float-right" role="group">
- <button type="button" class="btn btn-danger"
- v-on:click="removeAnnotationFromTask(index)">Remove</button>
- </div>
- </div>
- </div>
- </li>
- </ol>
-
- <label for="atlas_annotation_list">Available annotations</label>
- <ol id="atlas_annotation_list_available"
- class="list-group atlas_annotation_list border border-dark rounded bg-light"
- v-if="selected_task !== null">
- <li v-for="(annotation, index) in available_annotations" v-if="filterAnnotation(annotation_filter, annotation.name)" class="list-group-item list-group-item-action">
- <div class="form-row">
- <label class="col-1 col-form-label">Name</label>
- <div class="col-3">
- <input v-model="annotation.name" class="form-control" type="text" />
- </div>
- <label class="col-1 col-form-label">Section</label>
- <div class="col-2">
- <input v-model="annotation.section" class="form-control" type="text"
- readonly />
- </div>
- <div class="col-5">
- <div class="btn-group float-right" role="group">
- <button type="button" class="btn btn-primary"
- v-on:click="addAnnotationToTask(index)">Add</button>
- </div>
- </div>
- </div>
- </li>
- </ol>
- </div>
- </div>
- <div class="modal-footer">
- <button type="button" class="btn btn-primary" data-dismiss="modal"
- v-on:click="saveTask(selected_project, selected_task)">Save</button>
- <button type="button" class="btn btn-secondary" data-dismiss="modal" v-on:click="closeTask()">Close</button>
- </div>
- </div>
- </div>
- </div>
-
- <div class="modal fade" id="atlas_ui_task_wizard_modal" tabindex="-1" aria-labelledby="exampleModalLabel" aria-hidden="true" role="dialog">
- <div class="modal-dialog modal-xl" role="document">
- <div class="modal-content">
- <!-- Header of dialogue -->
- <div class="modal-header">
- <h5 class="modal-title" id="exampleModalLabel">Task wizard</h5>
- <!-- <div class="text-center" v-if="task_wizard.loading"> -->
- <!-- <div class="spinner-border spinner-border-sm m-1" role="status"> -->
- <!-- <span class="sr-only">Loading...</span> -->
- <!-- </div> -->
- <!-- </div> -->
- <button type="button" class="close" data-dismiss="modal" aria-label="Close">
- <span aria-hidden="true">×</span>
- </button>
- </div>
-
- <!-- Body of dialogue -->
- <div class="modal-body">
- <div class="container col-12">
- <div class="row">
-
- <!-- Sections -->
- <div class="col-3 form">
- <div class="form-group">
- <label for="atlas_task_wizard_section_list">Sections</label>
- <ol id="atlas_task_wizard_section_list"
- class="list-group atlas_task_wizard_section_list border border-dark rounded bg-light">
- <li v-for="(section_item, index) in task_wizard.section_data" class="list-group-item list-group-item-action">
- <div class="form-row">
- <button type="button" class="btn col-12" v-bind:class="{'btn-primary': section_item.selected, 'btn-danger': ! section_item.selected }" v-on:click="taskWizardSectionToggle(section_item)">
- {{ section_item.section }} ({{ section_item.annotations.length }} annotations)
- </button>
- </div>
- </li>
- </ol>
- </div>
- <div class="btn-group" role="group" id="atlas_ui_task_wizard_section_controls">
- <button type="button" class="btn btn-primary" v-on:click="taskWizardSectionSelect(true)" :disabled="task_wizard.section_data.length == 0">Enable all</button>
- <button type="button" class="btn btn-danger" v-on:click="taskWizardSectionSelect(false)" :disabled="task_wizard.section_data.length == 0">Disable all</button>
- </div>
- <div class="btn-group" role="group" id="atlas_ui_task_wizard_section_controls2">
- <button type="button" class="btn btn-success" v-on:click="taskWizardAutoPair" data-toggle="modal" data-target="#atlas_ui_task_wizard_import_modal">Import</button>
- </div>
- </div>
-
- <!-- Annotations -->
- <div class="col-4 form">
- <div class="form-group">
- <label for="atlas_task_wizard_annotation_list">Annotations</label>
- <ol id="atlas_task_wizard_annotation_list" class="atlas_task_wizard_annotation_list list-group border border-dark rounded bg-light">
- <li v-for="(annotation_item, index) in task_wizard_annotations" class="list-group-item list-group-item-action">
- <div class="form-row">
- <label class="col-2">
- {{ annotation_item.section_item.section }}
- </label>
- <div class="col-8">
- <input v-model="annotation_item.annotation.name" class="form-control" type="text"/>
- </div>
- <div class="col-2">
- <div class="btn-group float-right" role="group">
- <button type="button" class="btn btn-primary" v-on:click="taskWizardAddAnnotation(task_wizard.selected_task, annotation_item)">+</button>
- </div>
- </div>
- </div>
- </li>
- </ol>
- </div>
- <div class="form-group">
- <label for="atlas_ui_task_wizard_filter">Annotation filter (supports RegExp)</label>
- <input v-model="annotation_filter" type="text" class="form-control" id="atlas_ui_task_wizard_filter">
- </div>
- </div>
+ <input
+ type="checkbox"
+ v-model="enable_auto_rename"
+ id="atlas_ui_task_form_auto_rename"
+ />
+ <label for="atlas_ui_task_form_auto_rename"
+ >Enable auto-rename</label
+ >
+
+ <input
+ type="checkbox"
+ v-model="selected_task.no_aux_labels"
+ id="atlas_ui_task_form_aux_labels"
+ />
+ <label for="atlas_ui_task_form_aux_labels"
+ >No auxiliary labels</label
+ >
+ </div>
+
+ <!-- List of annotations -->
+ <label for="atlas_annotation_list">Annotations</label>
+ <ol
+ id="atlas_annotation_list_selected"
+ class="list-group atlas_annotation_list border border-dark rounded bg-light"
+ v-if="selected_task !== null"
+ >
+ <li
+ v-for="(annotation, index) in selected_task.annotations"
+ class="list-group-item list-group-item-action"
+ >
+ <div class="form-row">
+ <label class="col-1 col-form-label text-right"
+ >Name</label
+ >
+ <div class="col-3">
+ <input
+ v-model="annotation.name"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <label class="col-1 col-form-label text-right"
+ >Section</label
+ >
+ <div class="col-2">
+ <input
+ v-model="annotation.section"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <div class="col-5">
+ <div class="btn-group float-right" role="group">
+ <button
+ type="button"
+ class="btn btn-danger"
+ v-on:click="removeAnnotationFromTask(index)"
+ >
+ Remove
+ </button>
+ </div>
+ </div>
+ </div>
+ </li>
+ </ol>
+
+ <label for="atlas_annotation_list">Available annotations</label>
+ <ol
+ id="atlas_annotation_list_available"
+ class="list-group atlas_annotation_list border border-dark rounded bg-light"
+ v-if="selected_task !== null"
+ >
+ <li
+ v-for="(annotation, index) in available_annotations"
+ v-if="filterAnnotation(annotation_filter, annotation.name)"
+ class="list-group-item list-group-item-action"
+ >
+ <div class="form-row">
+ <label class="col-1 col-form-label">Name</label>
+ <div class="col-3">
+ <input
+ v-model="annotation.name"
+ class="form-control"
+ type="text"
+ />
+ </div>
+ <label class="col-1 col-form-label">Section</label>
+ <div class="col-2">
+ <input
+ v-model="annotation.section"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <div class="col-5">
+ <div class="btn-group float-right" role="group">
+ <button
+ type="button"
+ class="btn btn-primary"
+ v-on:click="addAnnotationToTask(index)"
+ >
+ Add
+ </button>
+ </div>
+ </div>
+ </div>
+ </li>
+ </ol>
+ </div>
+ </div>
+ <div class="modal-footer">
+ <button
+ type="button"
+ class="btn btn-primary"
+ data-dismiss="modal"
+ v-on:click="saveTask(selected_project, selected_task)"
+ >
+ Save
+ </button>
+ <button
+ type="button"
+ class="btn btn-secondary"
+ data-dismiss="modal"
+ v-on:click="closeTask()"
+ >
+ Close
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <div
+ class="modal fade"
+ id="atlas_ui_task_wizard_modal"
+ tabindex="-1"
+ aria-labelledby="exampleModalLabel"
+ aria-hidden="true"
+ role="dialog"
+ >
+ <div class="modal-dialog modal-xl" role="document">
+ <div class="modal-content">
+ <!-- Header of dialogue -->
+ <div class="modal-header">
+ <h5 class="modal-title" id="exampleModalLabel">Task wizard</h5>
+ <!-- <div class="text-center" v-if="task_wizard.loading"> -->
+ <!-- <div class="spinner-border spinner-border-sm m-1" role="status"> -->
+ <!-- <span class="sr-only">Loading...</span> -->
+ <!-- </div> -->
+ <!-- </div> -->
+ <button
+ type="button"
+ class="close"
+ data-dismiss="modal"
+ aria-label="Close"
+ >
+ <span aria-hidden="true">×</span>
+ </button>
+ </div>
+
+ <!-- Body of dialogue -->
+ <div class="modal-body">
+ <div class="container col-12">
+ <div class="row">
+ <!-- Sections -->
+ <div class="col-3 form">
+ <div class="form-group">
+ <label for="atlas_task_wizard_section_list"
+ >Sections</label
+ >
+ <ol
+ id="atlas_task_wizard_section_list"
+ class="list-group atlas_task_wizard_section_list border border-dark rounded bg-light"
+ >
+ <li
+ v-for="(section_item, index) in task_wizard.section_data"
+ class="list-group-item list-group-item-action"
+ >
+ <div class="form-row">
+ <button
+ type="button"
+ class="btn col-12"
+ v-bind:class="{'btn-primary': section_item.selected, 'btn-danger': ! section_item.selected }"
+ v-on:click="taskWizardSectionToggle(section_item)"
+ >
+ {{ section_item.section }} ({{
+ section_item.annotations.length }} annotations)
+ </button>
+ </div>
+ </li>
+ </ol>
+ </div>
+ <div
+ class="btn-group"
+ role="group"
+ id="atlas_ui_task_wizard_section_controls"
+ >
+ <button
+ type="button"
+ class="btn btn-primary"
+ v-on:click="taskWizardSectionSelect(true)"
+ :disabled="task_wizard.section_data.length == 0"
+ >
+ Enable all
+ </button>
+ <button
+ type="button"
+ class="btn btn-danger"
+ v-on:click="taskWizardSectionSelect(false)"
+ :disabled="task_wizard.section_data.length == 0"
+ >
+ Disable all
+ </button>
+ </div>
+ <div
+ class="btn-group"
+ role="group"
+ id="atlas_ui_task_wizard_section_controls2"
+ >
+ <button
+ type="button"
+ class="btn btn-success"
+ v-on:click="taskWizardAutoPair"
+ data-toggle="modal"
+ data-target="#atlas_ui_task_wizard_import_modal"
+ >
+ Import
+ </button>
+ </div>
+ </div>
+
+ <!-- Annotations -->
+ <div class="col-4 form">
+ <div class="form-group">
+ <label for="atlas_task_wizard_annotation_list"
+ >Annotations</label
+ >
+ <ol
+ id="atlas_task_wizard_annotation_list"
+ class="atlas_task_wizard_annotation_list list-group border border-dark rounded bg-light"
+ >
+ <li
+ v-for="(annotation_item, index) in task_wizard_annotations"
+ class="list-group-item list-group-item-action"
+ >
+ <div class="form-row">
+ <label class="col-2">
+ {{ annotation_item.section_item.section }}
+ </label>
+ <div class="col-8">
+ <input
+ v-model="annotation_item.annotation.name"
+ class="form-control"
+ type="text"
+ />
+ </div>
+ <div class="col-2">
+ <div class="btn-group float-right" role="group">
+ <button
+ type="button"
+ class="btn btn-primary"
+ v-on:click="taskWizardAddAnnotation(task_wizard.selected_task, annotation_item)"
+ >
+ +
+ </button>
+ </div>
+ </div>
+ </div>
+ </li>
+ </ol>
+ </div>
+ <div class="form-group">
+ <label for="atlas_ui_task_wizard_filter"
+ >Annotation filter (supports RegExp)</label
+ >
+ <input
+ v-model="annotation_filter"
+ type="text"
+ class="form-control"
+ id="atlas_ui_task_wizard_filter"
+ />
+ </div>
+ </div>
<!-- Tasks -->
<div class="col-5">
@@ -500,334 +1044,687 @@
<div class="form">
<div class="form-group">
<label for="atlas_ui_task_wizard_task_name">Name</label>
- <input v-model="task_wizard.selected_task.name" type="text" class="form-control" id="atlas_ui_task_wizard_task_name">
+ <input
+ v-model="task_wizard.selected_task.name"
+ type="text"
+ class="form-control"
+ id="atlas_ui_task_wizard_task_name"
+ />
</div>
<div class="form-group">
<div>
- <input type="checkbox" v-model="enable_auto_rename" id="atlas_ui_task_wizard_auto_rename"/>
- <label for="atlasui_ui_task_wizard_auto_rename">Enable auto-rename</label>
- <input type="checkbox" v-model="task_wizard.selected_task.no_aux_labels" id="atlas_ui_task_form_aux_labels"/>
- <label for="atlas_ui_task_form_aux_labels">No auxiliary labels</label>
+ <input
+ type="checkbox"
+ v-model="enable_auto_rename"
+ id="atlas_ui_task_wizard_auto_rename"
+ />
+ <label for="atlasui_ui_task_wizard_auto_rename"
+ >Enable auto-rename</label
+ >
+ <input
+ type="checkbox"
+ v-model="task_wizard.selected_task.no_aux_labels"
+ id="atlas_ui_task_form_aux_labels"
+ />
+ <label for="atlas_ui_task_form_aux_labels"
+ >No auxiliary labels</label
+ >
</div>
<div>
- <input type="checkbox" v-model="task_wizard.section_naming" id="atlas_ui_task_form_section_naming"/>
- <label for="atlas_ui_task_form_section_naming">Name by sections</label>
+ <input
+ type="checkbox"
+ v-model="task_wizard.section_naming"
+ id="atlas_ui_task_form_section_naming"
+ />
+ <label for="atlas_ui_task_form_section_naming"
+ >Name by sections</label
+ >
</div>
<div class="form-group row">
- <label class="col-sm-2 col-form-label" for="atlas_ui_task_wizard_model">Model</label>
- <select class="form-control col-sm-10" id="atlas_ui_task_wizard_model" v-model="task_wizard.model">
+ <label
+ class="col-sm-2 col-form-label"
+ for="atlas_ui_task_wizard_model"
+ >Model</label
+ >
+ <select
+ class="form-control col-sm-10"
+ id="atlas_ui_task_wizard_model"
+ v-model="task_wizard.model"
+ >
<option v-for="model in model_options">
- {{ model }}
+ {{ model }}
</option>
</select>
</div>
</div>
- <div class="form-group">
- <!-- List of annotations -->
- <label for="atlas_annotation_list_selected">Annotations</label>
- <ol id="atlas_annotation_list_selected" class="list-group atlas_task_wizard_small_list border border-dark rounded bg-light">
- <li v-for="(annotation, index) in task_wizard.selected_task.annotations" class="list-group-item list-group-item-action">
- <div class="form-row">
- <label class="col-2">
- {{ annotation.section }}
- </label>
- <div class="col-8">
- <input v-model="annotation.name" class="form-control" type="text"/>
- </div>
- <div class="col-2">
- <div class="btn-group float-right" role="group">
- <button type="button" class="btn btn-danger" v-on:click="taskWizardRemoveAnnotation(task_wizard.selected_task, index)">-</button>
- </div>
- </div>
- </div>
- </li>
- </ol>
- </div>
-
- <div class="form-group">
- <div class="btn-group" role="group">
- <button type="button" class="btn btn-primary" v-on:click="taskWizardAddTask(task_wizard.selected_task)" :disabled="task_wizard.selected_task.annotations.length == 0">Save task</button>
- <button type="button" class="btn btn-success" v-on:click="taskWizardAddAll(task_wizard.selected_task)" :disabled="task_wizard_annotations.length == 0">Add annotations</button>
- <button type="button" class="btn btn-danger" v-on:click="taskWizardRemoveAll(task_wizard.selected_task)" :disabled="task_wizard.selected_task.annotations.length == 0">Remove annotations</button>
- </div>
- </div>
-
- <div class="form-group">
- <!-- List of annotations -->
- <label for="atlas_ui_task_wizard_task_list">Tasks</label>
- <ol id="atlas_ui_task_wizard_task_list" class="list-group atlas_task_wizard_small_list border border-dark rounded bg-light">
- <li v-for="(task, index) in task_wizard.tasks" class="list-group-item list-group-item-action">
- <div class="form-row">
- <div class="col-9">
- <input v-model="task.name" class="form-control" type="text" readonly/>
- </div>
- <div class="col-3">
- <div class="btn-group float-right" role="group">
- <button type="button" class="btn btn-primary" v-on:click="taskWizardEditTask(index)">Edit</button>
- <button type="button" class="btn btn-danger" v-on:click="taskWizardRemoveTask(index)">-</button>
- </div>
- </div>
- </div>
- </li>
- </ol>
- </div>
- </div>
- </div>
-
- </div>
- </div>
-
- <!-- Loading overlay -->
- <div class="loader_overlay" v-bind:class="[task_wizard.loading ? 'show' : '']"></div>
- <div class="spanner" v-bind:class="[task_wizard.loading ? 'show' : '']">
- <div class="loader"></div>
- <p>Loading annotations...</p>
- </div>
-
- </div>
-
- <div class="modal-footer">
- <button type="button" class="btn btn-primary" data-dismiss="modal" v-on:click="taskWizardSave()">Save</button>
- <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
- </div>
- </div>
- </div>
- </div>
-
- <div class="modal fade" id="atlas_ui_task_wizard_import_modal" tabindex="-1" aria-labelledby="exampleModalLabel" aria-hidden="true" role="dialog">
- <div class="modal-dialog modal-xl" role="document">
- <div class="modal-content">
- <!-- Header of dialogue -->
- <div class="modal-header">
- <h5 class="modal-title" id="exampleModalLabel">Import</h5>
- <button type="button" class="close" data-dismiss="modal" aria-label="Close">
- <span aria-hidden="true">×</span>
- </button>
- </div>
-
- <!-- Body of dialogue -->
- <div class="modal-body">
- <div class="container col-12">
- <div class="row">
- <textarea class="form-control" id="atlas_ui_task_wizard_import_text" v-model="task_wizard.import_text" placeholder="Enter sections to import. One task per line."></textarea>
- </div>
- </div>
- </div>
- <div class="modal-footer">
- <button type="button" class="btn btn-primary" v-on:click="taskWizardImport()">Import</button>
- <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
- </div>
- </div>
- </div>
- </div>
-
- <div class="modal fade" id="atlas_ui_jobs_modal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel"
- aria-hidden="true" v-if="selected_task !== null">
- <div class="modal-dialog modal-lg" role="document">
- <div class="modal-content">
- <!-- Header of dialogue -->
- <div class="modal-header">
- <h5 class="modal-title" id="exampleModalLabel">
- {{selected_project.name}} - {{selected_task.name}}</h5>
- <button type="button" class="close" data-dismiss="modal" aria-label="Close" v-on:click="closeTask()">
- <span aria-hidden="true">×</span>
- </button>
- </div>
-
- <!-- Body of dialogue -->
- <div class="modal-body">
- <div class="form-group">
- <label for="atlas_job_list">Jobs</label>
- <ol id="atlas_job_list"
- class="list-group atlas_job_list border border-dark rounded bg-light"
- v-if="selected_task !== null">
- <li v-for="(job, index) in selected_task.jobs"
- class="list-group-item list-group-item-action">
- <div class="form-row">
- <label class="col-1 col-form-label text-right">ID</label>
- <div class="col-2">
- <input v-model="job.job_id" class="form-control" type="text" readonly />
- </div>
- <!-- <label class="col-1 col-form-label text-right">Type</label> -->
- <div class="col-2">
- <input v-model="job.job_configuration.job_type" class="form-control"
- type="text" readonly />
- </div>
- <label class="col-1 col-form-label text-right">Status</label>
- <div class="col-3">
- <input v-model="job.status" class="form-control"
- type="text" readonly />
- </div>
- <div class="col-3">
- <div class="btn-group float-right" role="group">
- <button type="button" class="btn btn-info" v-on:click="getJobStatus(selected_project, selected_task, job)">Status</button>
- <button type="button" class="btn btn-danger"
- v-on:click="cancelJob(selected_project, selected_task, index)">Cancel</button>
- </div>
- </div>
- </div>
- </li>
- </ol>
- </div>
- <!-- Button group -->
- <div class="btn-group" role="group">
- <button type="button" class="btn btn-primary" v-on:click="submitTrainingJob(selected_project, selected_task)">Start training</button>
- <button type="button" class="btn btn-primary" v-on:click="submitPredictionJob(selected_project, selected_task)">Start prediction</button>
- <button type="button" class="btn btn-primary" v-on:click="submitTrainingPredictionJob(selected_project, selected_task)">Start training & prediction</button>
- <button type="button" class="btn btn-secondary" v-on:click="getJobStatusForAll(selected_project, selected_task)">Update all</button>
- <!-- <button type="button" class="btn btn-danger"
+ <div class="form-group">
+ <!-- List of annotations -->
+ <label for="atlas_annotation_list_selected"
+ >Annotations</label
+ >
+ <ol
+ id="atlas_annotation_list_selected"
+ class="list-group atlas_task_wizard_small_list border border-dark rounded bg-light"
+ >
+ <li
+ v-for="(annotation, index) in task_wizard.selected_task.annotations"
+ class="list-group-item list-group-item-action"
+ >
+ <div class="form-row">
+ <label class="col-2">
+ {{ annotation.section }}
+ </label>
+ <div class="col-8">
+ <input
+ v-model="annotation.name"
+ class="form-control"
+ type="text"
+ />
+ </div>
+ <div class="col-2">
+ <div class="btn-group float-right" role="group">
+ <button
+ type="button"
+ class="btn btn-danger"
+ v-on:click="taskWizardRemoveAnnotation(task_wizard.selected_task, index)"
+ >
+ -
+ </button>
+ </div>
+ </div>
+ </div>
+ </li>
+ </ol>
+ </div>
+
+ <div class="form-group">
+ <div class="btn-group" role="group">
+ <button
+ type="button"
+ class="btn btn-primary"
+ v-on:click="taskWizardAddTask(task_wizard.selected_task)"
+ :disabled="task_wizard.selected_task.annotations.length == 0"
+ >
+ Save task
+ </button>
+ <button
+ type="button"
+ class="btn btn-success"
+ v-on:click="taskWizardAddAll(task_wizard.selected_task)"
+ :disabled="task_wizard_annotations.length == 0"
+ >
+ Add annotations
+ </button>
+ <button
+ type="button"
+ class="btn btn-danger"
+ v-on:click="taskWizardRemoveAll(task_wizard.selected_task)"
+ :disabled="task_wizard.selected_task.annotations.length == 0"
+ >
+ Remove annotations
+ </button>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <!-- List of annotations -->
+ <label for="atlas_ui_task_wizard_task_list"
+ >Tasks</label
+ >
+ <ol
+ id="atlas_ui_task_wizard_task_list"
+ class="list-group atlas_task_wizard_small_list border border-dark rounded bg-light"
+ >
+ <li
+ v-for="(task, index) in task_wizard.tasks"
+ class="list-group-item list-group-item-action"
+ >
+ <div class="form-row">
+ <div class="col-9">
+ <input
+ v-model="task.name"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <div class="col-3">
+ <div class="btn-group float-right" role="group">
+ <button
+ type="button"
+ class="btn btn-primary"
+ v-on:click="taskWizardEditTask(index)"
+ >
+ Edit
+ </button>
+ <button
+ type="button"
+ class="btn btn-danger"
+ v-on:click="taskWizardRemoveTask(index)"
+ >
+ -
+ </button>
+ </div>
+ </div>
+ </div>
+ </li>
+ </ol>
+ </div>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <!-- Loading overlay -->
+ <div
+ class="loader_overlay"
+ v-bind:class="[task_wizard.loading ? 'show' : '']"
+ ></div>
+ <div
+ class="spanner"
+ v-bind:class="[task_wizard.loading ? 'show' : '']"
+ >
+ <div class="loader"></div>
+ <p>Loading annotations...</p>
+ </div>
+ </div>
+
+ <div class="modal-footer">
+ <button
+ type="button"
+ class="btn btn-primary"
+ data-dismiss="modal"
+ v-on:click="taskWizardSave()"
+ >
+ Save
+ </button>
+ <button
+ type="button"
+ class="btn btn-secondary"
+ data-dismiss="modal"
+ >
+ Close
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <div
+ class="modal fade"
+ id="atlas_ui_task_wizard_import_modal"
+ tabindex="-1"
+ aria-labelledby="exampleModalLabel"
+ aria-hidden="true"
+ role="dialog"
+ >
+ <div class="modal-dialog modal-xl" role="document">
+ <div class="modal-content">
+ <!-- Header of dialogue -->
+ <div class="modal-header">
+ <h5 class="modal-title" id="exampleModalLabel">Import</h5>
+ <button
+ type="button"
+ class="close"
+ data-dismiss="modal"
+ aria-label="Close"
+ >
+ <span aria-hidden="true">×</span>
+ </button>
+ </div>
+
+ <!-- Body of dialogue -->
+ <div class="modal-body">
+ <div class="container col-12">
+ <div class="row">
+ <textarea
+ class="form-control"
+ id="atlas_ui_task_wizard_import_text"
+ v-model="task_wizard.import_text"
+ placeholder="Enter sections to import. One task per line."
+ ></textarea>
+ </div>
+ </div>
+ </div>
+ <div class="modal-footer">
+ <button
+ type="button"
+ class="btn btn-primary"
+ v-on:click="taskWizardImport()"
+ >
+ Import
+ </button>
+ <button
+ type="button"
+ class="btn btn-secondary"
+ data-dismiss="modal"
+ >
+ Close
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <div
+ class="modal fade"
+ id="atlas_ui_jobs_modal"
+ tabindex="-1"
+ role="dialog"
+ aria-labelledby="exampleModalLabel"
+ aria-hidden="true"
+ v-if="selected_task !== null"
+ >
+ <div class="modal-dialog modal-lg" role="document">
+ <div class="modal-content">
+ <!-- Header of dialogue -->
+ <div class="modal-header">
+ <h5 class="modal-title" id="exampleModalLabel">
+ {{selected_project.name}} - {{selected_task.name}}
+ </h5>
+ <button
+ type="button"
+ class="close"
+ data-dismiss="modal"
+ aria-label="Close"
+ v-on:click="closeTask()"
+ >
+ <span aria-hidden="true">×</span>
+ </button>
+ </div>
+
+ <!-- Body of dialogue -->
+ <div class="modal-body">
+ <div class="form-group">
+ <label for="atlas_job_list">Jobs</label>
+ <ol
+ id="atlas_job_list"
+ class="list-group atlas_job_list border border-dark rounded bg-light"
+ v-if="selected_task !== null"
+ >
+ <li
+ v-for="(job, index) in selected_task.jobs"
+ class="list-group-item list-group-item-action"
+ >
+ <div class="form-row">
+ <label class="col-1 col-form-label text-right">ID</label>
+ <div class="col-2">
+ <input
+ v-model="job.job_id"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <!-- <label class="col-1 col-form-label text-right">Type</label> -->
+ <div class="col-2">
+ <input
+ v-model="job.job_configuration.job_type"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <label class="col-1 col-form-label text-right"
+ >Status</label
+ >
+ <div class="col-3">
+ <input
+ v-model="job.status"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <div class="col-3">
+ <div class="btn-group float-right" role="group">
+ <button
+ type="button"
+ class="btn btn-info"
+ v-on:click="getJobStatus(selected_project, selected_task, job)"
+ >
+ Status
+ </button>
+ <button
+ type="button"
+ class="btn btn-danger"
+ v-on:click="cancelJob(selected_project, selected_task, index)"
+ >
+ Cancel
+ </button>
+ </div>
+ </div>
+ </div>
+ </li>
+ </ol>
+ </div>
+ <!-- Button group -->
+ <div class="btn-group" role="group">
+ <button
+ type="button"
+ class="btn btn-primary"
+ v-on:click="submitTrainingJob(selected_project, selected_task)"
+ >
+ Start training
+ </button>
+ <button
+ type="button"
+ class="btn btn-primary"
+ v-on:click="submitPredictionJob(selected_project, selected_task)"
+ >
+ Start prediction
+ </button>
+ <button
+ type="button"
+ class="btn btn-primary"
+ v-on:click="submitTrainingPredictionJob(selected_project, selected_task)"
+ >
+ Start training & prediction
+ </button>
+ <button
+ type="button"
+ class="btn btn-secondary"
+ v-on:click="getJobStatusForAll(selected_project, selected_task)"
+ >
+ Update all
+ </button>
+ <!-- <button type="button" class="btn btn-danger"
v-on:click="cancelAllJobs(selected_project, selected_task)">Cancel all</button> -->
- </div>
- </div>
- <div class="modal-footer">
- <!-- <button type="button" class="btn btn-primary" data-dismiss="modal"
+ </div>
+ </div>
+ <div class="modal-footer">
+ <!-- <button type="button" class="btn btn-primary" data-dismiss="modal"
v-on:click="saveTask(selected_project, selected_task)">Save</button> -->
- <button type="button" class="btn btn-secondary" data-dismiss="modal" v-on:click="closeTask()">Close</button>
- </div>
- </div>
- </div>
- </div>
-
- <div class="modal fade" id="atlas_ui_imports_modal" tabindex="-1" role="dialog"
- aria-labelledby="exampleModalLabel" aria-hidden="true">
- <div class="modal-dialog modal-lg" role="document">
- <div class="modal-content">
- <!-- Header of dialogue -->
- <div class="modal-header">
- <h5 class="modal-title" id="exampleModalLabel">Import annotations</h5>
- <button type="button" class="close" data-dismiss="modal" aria-label="Close">
- <span aria-hidden="true">×</span>
- </button>
- </div>
-
- <!-- Body of dialogue -->
- <div class="modal-body">
- <div class="form">
- <div class="form-row">
- <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 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 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 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 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 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 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.">
- </div>
- <div class="col-1">
- </div>
- </div>
- <br>
- <div class="form-row">
- <div class="btn-group float-right" role="group">
- <button type="button" class="btn btn-primary" v-on:click="getAnnotations" :disabled="annotation_import.loading_state"
- data-toggle="tooltip" data-placement="top" title="Retrieve annotations from source host. Enter source host, user and path first.">
- Retrieve source annotations
- </button>
- </div>
- </div>
- <br>
-
- <!-- List of annotations -->
- <ol id="atlas_import_list"
- class="list-group atlas_task_list border border-dark rounded bg-light">
- <li v-for="ann_item in annotation_import.annotation_items"
- class="list-group-item list-group-item-action">
- <div class="form-row">
- <label class="col-1 col-form-label text-right">Section</label>
- <div class="col-2">
- <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-2">
- <input v-model="ann_item.annotations.Regions.length" class="form-control" type="text" readonly />
- </div>
- <div class="col-2">
- </div>
- <div class="col-3">
- <div class="btn-group" role="group">
- <button type="button" class="btn btn-primary" v-on:click="importAnnotation(ann_item, false)" :disabled="ann_item.loading_state"
- data-toggle="tooltip" data-placement="top" title="Add annotations without overwriting existing annotations.">Add</button>
- <button type="button" class="btn btn-danger" v-on:click="importAnnotation(ann_item, true)" :disabled="ann_item.loading_state"
- data-toggle="tooltip" data-placement="top" title="Overwrite existing annotations for this section.">Overwrite</button>
- </div>
- </div>
- </div>
- </li>
- </ol>
- </div>
- <br>
-
- <!-- Button group -->
- <div class="btn-group" role="group">
- <button v-on:click="importAll(false)" type="button" class="btn btn-primary"
- data-toggle="tooltip" data-placement="top" title="Add all annotations without overwriting existing annotations.">
- Add all
- </button>
- <button v-on:click="importAll(true)" type="button" class="btn btn-danger"
- data-toggle="tooltip" data-placement="top" title="Overwrite all existing annotations.">
- Overwrite all
- </button>
- </div>
- </div>
- <div class="modal-footer">
- <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
- </div>
- </div>
- </div>
- </div>
-
- <!-- Discard changes dialogue -->
- </div>
- <!-- development version, includes helpful console warnings -->
- <script src="https://cdn.jsdelivr.net/npm/vue/dist/vue.js"></script>
- <!-- <script src="https://unpkg.com/vue-contextmenu"></script> -->
- <script src="lib/paper-full-0.9.25.min.js"></script>
- <script src="lib/openseadragon/openseadragon.js"></script>
- <script src="lib/openseadragon-viewerinputhook.min.js"></script>
- <script src="lib/OpenSeadragonScalebar/openseadragon-scalebar.js"></script>
- <script src="lib/openseadragonrgb/dist/openseadragonrgb.js"></script>
- <script src="lib/jquery-1.11.0.min.js"></script>
- <script src="lib/mylogin/login.js"></script>
- <script src="neurolex-ontology.js"></script>
- <script src="base.js"></script>
- <script src="cross.js"></script>
- <script src="configuration.js"></script>
- <script src="microdraw.js"></script>
- <script src="atlas_ui.js"></script>
- </body>
+ <button
+ type="button"
+ class="btn btn-secondary"
+ data-dismiss="modal"
+ v-on:click="closeTask()"
+ >
+ Close
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <div
+ class="modal fade"
+ id="atlas_ui_imports_modal"
+ tabindex="-1"
+ role="dialog"
+ aria-labelledby="exampleModalLabel"
+ aria-hidden="true"
+ >
+ <div class="modal-dialog modal-lg" role="document">
+ <div class="modal-content">
+ <!-- Header of dialogue -->
+ <div class="modal-header">
+ <h5 class="modal-title" id="exampleModalLabel">
+ Import annotations
+ </h5>
+ <button
+ type="button"
+ class="close"
+ data-dismiss="modal"
+ aria-label="Close"
+ >
+ <span aria-hidden="true">×</span>
+ </button>
+ </div>
+
+ <!-- Body of dialogue -->
+ <div class="modal-body">
+ <div class="form">
+ <div class="form-row">
+ <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 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
+ 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 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 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
+ 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 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."
+ />
+ </div>
+ <div class="col-1"></div>
+ </div>
+ <br />
+ <div class="form-row">
+ <div class="btn-group float-right" role="group">
+ <button
+ type="button"
+ class="btn btn-primary"
+ v-on:click="getAnnotations"
+ :disabled="annotation_import.loading_state"
+ data-toggle="tooltip"
+ data-placement="top"
+ title="Retrieve annotations from source host. Enter source host, user and path first."
+ >
+ Retrieve source annotations
+ </button>
+ </div>
+ </div>
+ <br />
+
+ <!-- List of annotations -->
+ <ol
+ id="atlas_import_list"
+ class="list-group atlas_task_list border border-dark rounded bg-light"
+ >
+ <li
+ v-for="ann_item in annotation_import.annotation_items"
+ class="list-group-item list-group-item-action"
+ >
+ <div class="form-row">
+ <label class="col-1 col-form-label text-right"
+ >Section</label
+ >
+ <div class="col-2">
+ <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-2">
+ <input
+ v-model="ann_item.annotations.Regions.length"
+ class="form-control"
+ type="text"
+ readonly
+ />
+ </div>
+ <div class="col-2"></div>
+ <div class="col-3">
+ <div class="btn-group" role="group">
+ <button
+ type="button"
+ class="btn btn-primary"
+ v-on:click="importAnnotation(ann_item, false)"
+ :disabled="ann_item.loading_state"
+ data-toggle="tooltip"
+ data-placement="top"
+ title="Add annotations without overwriting existing annotations."
+ >
+ Add
+ </button>
+ <button
+ type="button"
+ class="btn btn-danger"
+ v-on:click="importAnnotation(ann_item, true)"
+ :disabled="ann_item.loading_state"
+ data-toggle="tooltip"
+ data-placement="top"
+ title="Overwrite existing annotations for this section."
+ >
+ Overwrite
+ </button>
+ </div>
+ </div>
+ </div>
+ </li>
+ </ol>
+ </div>
+ <br />
+
+ <!-- Button group -->
+ <div class="btn-group" role="group">
+ <button
+ v-on:click="importAll(false)"
+ type="button"
+ class="btn btn-primary"
+ data-toggle="tooltip"
+ data-placement="top"
+ title="Add all annotations without overwriting existing annotations."
+ >
+ Add all
+ </button>
+ <button
+ v-on:click="importAll(true)"
+ type="button"
+ class="btn btn-danger"
+ data-toggle="tooltip"
+ data-placement="top"
+ title="Overwrite all existing annotations."
+ >
+ Overwrite all
+ </button>
+ </div>
+ </div>
+ <div class="modal-footer">
+ <button
+ type="button"
+ class="btn btn-secondary"
+ data-dismiss="modal"
+ >
+ Close
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+ <!-- Discard changes dialogue -->
+ </div>
+ <!-- development version, includes helpful console warnings -->
+ <script src="https://cdn.jsdelivr.net/npm/vue/dist/vue.js"></script>
+ <!-- <script src="https://unpkg.com/vue-contextmenu"></script> -->
+ <script src="lib/paper-full-0.9.25.min.js"></script>
+ <script src="lib/openseadragon/openseadragon.js"></script>
+ <script src="lib/openseadragon-viewerinputhook.min.js"></script>
+ <script src="lib/OpenSeadragonScalebar/openseadragon-scalebar.js"></script>
+ <script src="lib/openseadragonrgb/dist/openseadragonrgb.js"></script>
+ <script src="lib/jquery-1.11.0.min.js"></script>
+ <script src="lib/mylogin/login.js"></script>
+ <script src="neurolex-ontology.js"></script>
+ <script src="base.js"></script>
+ <script src="cross.js"></script>
+ <script src="configuration.js"></script>
+ <script src="microdraw.js"></script>
+ <script src="atlas_ui.js"></script>
+ </body>
</html>
--
GitLab