Add Volume Tasks (#3712)

* [WIP] volume tasks * fix volume task creation + requesting. TODO: download * allow to choose volume tasks via UI for simple task creation * enforce page reload when switching from/to/between volume tasks; show tracing type in dashboard * add tracing type to task type * multi-task download: fetch volume data * add enums to evolutions * scalafmt * add volume data to multi-task zip downloads * scalafmt * add tasktype tracing type to test db * validate tracing type when reading task type from db * adapt front-end to volume task types * update some flow types * update snapshots * update changelog + migrations * add error handling for the as-yet unsupported volume task features * disable nml upload if volume task is selected * remove superfluous return type * update evolution numbers * persist volume task bounding box in nml * read volume task bounding box from nml after re-upload * scalafmt * don't clip rendering of color layer in volume tasks * undo change to saving skeleton bounding box to nml * don't clip segmentation outside task bounding box * fix typo * Update CHANGELOG.md * apply PR feedback * remove typ attribute from task * update snapshots
scalableminds · Feb 6, 2019 · f279737 · f279737
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,13 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.md).
 ## Unreleased
 [Commits](https://github.com/scalableminds/webknossos/compare/19.02.0...HEAD)
 
+### Added
+
+- Added the possibility to create volume annotation tasks. When creating a task type, select whether to create `volume` or `skeleton` tasks. Note that compound viewing for volume tasks is not supported yet. Same for creating volume tasks from uploaded nml/data files. [#3712](https://github.com/scalableminds/webknossos/pull/3712)
+
+### Changed
+
+
 ### Fixed
 
 - The modals for a new task description and recommended task settings are no longer shown in read-only tracings. [#3724](https://github.com/scalableminds/webknossos/pull/3724)

diff --git a/MIGRATIONS.md b/MIGRATIONS.md
@@ -8,7 +8,7 @@ User-facing changes are documented in the [changelog](CHANGELOG.md).
 -
 
 ### Postgres Evolutions:
--
+- [038-add-tasktype-tracingtype.sql](conf/evolutions/038-add-tasktype-tracingtype.sql)
 
 
 ## [19.02.0](https://github.com/scalableminds/webknossos/releases/tag/19.02.0) - 2019-02-04

diff --git a/app/assets/javascripts/admin/api_flow_types.js b/app/assets/javascripts/admin/api_flow_types.js
@@ -221,6 +221,7 @@ export type APITaskType = {
   +teamName: string,
   +settings: APISettings,
   +recommendedConfiguration: ?string,
+  +tracingType: "skeleton" | "volume",
 };
 
 export type TaskStatus = { +open: number, +active: number, +finished: number };

diff --git a/app/assets/javascripts/admin/task/task_create_form_view.js b/app/assets/javascripts/admin/task/task_create_form_view.js
@@ -1,5 +1,18 @@
 // @flow
-import { Form, Select, Button, Card, Radio, Upload, Modal, Icon, InputNumber, Spin } from "antd";
+import {
+  Row,
+  Col,
+  Form,
+  Select,
+  Button,
+  Card,
+  Radio,
+  Upload,
+  Modal,
+  Icon,
+  InputNumber,
+  Spin,
+} from "antd";
 import { type RouterHistory, withRouter } from "react-router-dom";
 import React from "react";
 import _ from "lodash";
@@ -160,7 +173,6 @@ class TaskCreateFormView extends React.PureComponent<Props, State> {
               formValues.nmlFiles = formValues.nmlFiles.map(
                 wrapperFile => wrapperFile.originFileObj,
               );
-
               response = await createTaskFromNML(formValues);
             } else {
               response = await createTasks([formValues]);
@@ -183,6 +195,20 @@ class TaskCreateFormView extends React.PureComponent<Props, State> {
     return e && e.fileList;
   };
 
+  isVolumeTaskType = (taskTypeId?: string): boolean => {
+    const selectedTaskTypeId = taskTypeId || this.props.form.getFieldValue("taskTypeId");
+    const selectedTaskType = this.state.taskTypes.find(
+      taskType => taskType.id === selectedTaskTypeId,
+    );
+    return selectedTaskType != null ? selectedTaskType.tracingType === "volume" : false;
+  };
+
+  onChangeTaskType = (taskTypeId: string) => {
+    if (this.isVolumeTaskType(taskTypeId)) {
+      this.setState({ isNMLSpecification: false });
+    }
+  };
+
   render() {
     const { getFieldDecorator } = this.props.form;
     const isEditingMode = this.props.taskId != null;
@@ -207,6 +233,7 @@ class TaskCreateFormView extends React.PureComponent<Props, State> {
                     style={fullWidth}
                     autoFocus
                     disabled={isEditingMode}
+                    onChange={this.onChangeTaskType}
                   >
                     {this.state.taskTypes.map((taskType: APITaskType) => (
                       <Option key={taskType.id} value={taskType.id}>
@@ -217,24 +244,29 @@ class TaskCreateFormView extends React.PureComponent<Props, State> {
                 )}
               </FormItem>
 
-              <FormItem label="Experience Domain" hasFeedback>
-                {getFieldDecorator("neededExperience.domain", {
-                  rules: [{ required: true }],
-                })(
-                  <SelectExperienceDomain
-                    disabled={isEditingMode}
-                    placeholder="Select an Experience Domain"
-                    notFoundContent={messages["task.domain_does_not_exist"]}
-                    width={100}
-                  />,
-                )}
-              </FormItem>
-
-              <FormItem label="Experience Value" hasFeedback>
-                {getFieldDecorator("neededExperience.value", {
-                  rules: [{ required: true }, { type: "number" }],
-                })(<InputNumber style={fullWidth} disabled={isEditingMode} />)}
-              </FormItem>
+              <Row gutter={8}>
+                <Col span={12}>
+                  <FormItem label="Experience Domain" hasFeedback>
+                    {getFieldDecorator("neededExperience.domain", {
+                      rules: [{ required: true }],
+                    })(
+                      <SelectExperienceDomain
+                        disabled={isEditingMode}
+                        placeholder="Select an Experience Domain"
+                        notFoundContent={messages["task.domain_does_not_exist"]}
+                        width={100}
+                      />,
+                    )}
+                  </FormItem>
+                </Col>
+                <Col span={12}>
+                  <FormItem label="Experience Value" hasFeedback>
+                    {getFieldDecorator("neededExperience.value", {
+                      rules: [{ required: true }, { type: "number" }],
+                    })(<InputNumber style={fullWidth} disabled={isEditingMode} />)}
+                  </FormItem>
+                </Col>
+              </Row>
 
               <FormItem label={instancesLabel} hasFeedback>
                 {getFieldDecorator("openInstances", {
@@ -296,6 +328,7 @@ class TaskCreateFormView extends React.PureComponent<Props, State> {
                   onChange={(evt: SyntheticInputEvent<*>) =>
                     this.setState({ isNMLSpecification: evt.target.value === "nml" })
                   }
+                  disabled={this.isVolumeTaskType()}
                 >
                   <Radio value="manual" disabled={isEditingMode}>
                     Manually Specify Starting Postion

diff --git a/app/assets/javascripts/admin/tasktype/task_type_create_view.js b/app/assets/javascripts/admin/tasktype/task_type_create_view.js
@@ -1,5 +1,5 @@
 // @flow
-import { Form, Checkbox, Input, Select, Card, Button } from "antd";
+import { Button, Card, Checkbox, Form, Input, Radio, Select } from "antd";
 import { type RouterHistory, withRouter } from "react-router-dom";
 import React from "react";
 import _ from "lodash";
@@ -16,6 +16,8 @@ import RecommendedConfigurationView, {
   DEFAULT_RECOMMENDED_CONFIGURATION,
 } from "admin/tasktype/recommended_configuration_view";
 
+const RadioGroup = Radio.Group;
+
 const FormItem = Form.Item;
 const { Option } = Select;
 const { TextArea } = Input;
@@ -94,10 +96,11 @@ class TaskTypeCreateView extends React.PureComponent<Props, State> {
 
   render() {
     const { getFieldDecorator } = this.props.form;
-    const titlePrefix = this.props.taskTypeId ? "Update " : "Create";
+    const isEditingMode = this.props.taskTypeId != null;
+    const titlePrefix = isEditingMode ? "Update " : "Create";
 
     return (
-      <div className="container">
+      <div className="container" style={{ maxWidth: 1600, margin: "0 auto" }}>
         <Card title={<h3>{titlePrefix} Task Type</h3>}>
           <Form onSubmit={this.handleSubmit} layout="vertical">
             <FormItem label="Summary" hasFeedback>
@@ -152,6 +155,21 @@ class TaskTypeCreateView extends React.PureComponent<Props, State> {
               })(<TextArea rows={10} />)}
             </FormItem>
 
+            <FormItem label="Tracing Type">
+              {getFieldDecorator("tracingType", {
+                initialValue: "skeleton",
+              })(
+                <RadioGroup>
+                  <Radio value="skeleton" disabled={isEditingMode}>
+                    Skeleton
+                  </Radio>
+                  <Radio value="volume" disabled={isEditingMode}>
+                    Volume
+                  </Radio>
+                </RadioGroup>,
+              )}
+            </FormItem>
+
             <FormItem label="Allowed Modes" hasFeedback>
               {getFieldDecorator("settings.allowedModes", {
                 rules: [{ required: true }],
@@ -170,18 +188,6 @@ class TaskTypeCreateView extends React.PureComponent<Props, State> {
               )}
             </FormItem>
 
-            <FormItem label="Settings">
-              {getFieldDecorator("settings.somaClickingAllowed", {
-                valuePropName: "checked",
-              })(<Checkbox>Allow Single-node-tree mode (&quot;Soma clicking&quot;)</Checkbox>)}
-            </FormItem>
-
-            <FormItem>
-              {getFieldDecorator("settings.branchPointsAllowed", {
-                valuePropName: "checked",
-              })(<Checkbox>Allow Branchpoints</Checkbox>)}
-            </FormItem>
-
             <FormItem label="Preferred Mode" hasFeedback>
               {getFieldDecorator("settings.preferredMode")(
                 <Select allowClear optionFilterProp="children" style={{ width: "100%" }}>
@@ -193,6 +199,25 @@ class TaskTypeCreateView extends React.PureComponent<Props, State> {
               )}
             </FormItem>
 
+            <div
+              style={{
+                display:
+                  this.props.form.getFieldValue("tracingType") === "skeleton" ? "block" : "none",
+              }}
+            >
+              <FormItem label="Settings">
+                {getFieldDecorator("settings.somaClickingAllowed", {
+                  valuePropName: "checked",
+                })(<Checkbox>Allow Single-node-tree mode (&quot;Soma clicking&quot;)</Checkbox>)}
+              </FormItem>
+
+              <FormItem>
+                {getFieldDecorator("settings.branchPointsAllowed", {
+                  valuePropName: "checked",
+                })(<Checkbox>Allow Branchpoints</Checkbox>)}
+              </FormItem>
+            </div>
+
             <FormItem>
               <RecommendedConfigurationView
                 form={this.props.form}

diff --git a/app/assets/javascripts/admin/tasktype/task_type_list_view.js b/app/assets/javascripts/admin/tasktype/task_type_list_view.js
@@ -182,12 +182,24 @@ class TaskTypeListView extends React.PureComponent<Props, State> {
                 dataIndex="settings"
                 key="allowedModes"
                 width={100}
-                render={settings =>
-                  settings.allowedModes.map(mode => (
-                    <Tag key={mode} color={mode === settings.preferredMode ? "blue" : null}>
-                      {mode}
-                    </Tag>
-                  ))
+                render={(settings, taskType) =>
+                  [
+                    taskType.tracingType === "skeleton" ? (
+                      <Tag color="green" key="tracingType">
+                        skeleton
+                      </Tag>
+                    ) : (
+                      <Tag color="orange" key="tracingType">
+                        volume
+                      </Tag>
+                    ),
+                  ].concat(
+                    settings.allowedModes.map(mode => (
+                      <Tag key={mode} color={mode === settings.preferredMode ? "blue" : null}>
+                        {mode}
+                      </Tag>
+                    )),
+                  )
                 }
               />
               <Column

diff --git a/app/assets/javascripts/dashboard/dashboard_task_list_view.js b/app/assets/javascripts/dashboard/dashboard_task_list_view.js
@@ -386,6 +386,8 @@ class DashboardTaskListView extends React.PureComponent<PropsWithRouter, State>
         <span style={{ marginRight: 8 }}>
           {task.type.summary} (<FormattedDate timestamp={task.created} />)
         </span>
+        {task.annotation.tracing.skeleton == null ? null : <Tag color="green">skeleton</Tag>}
+        {task.annotation.tracing.volume == null ? null : <Tag color="orange">volume</Tag>}
         {task.type.settings.allowedModes.map(mode => (
           <Tag key={mode}>{mode}</Tag>
         ))}

diff --git a/app/assets/javascripts/oxalis/api/api_latest.js b/app/assets/javascripts/oxalis/api/api_latest.js
@@ -371,23 +371,28 @@ class TracingApi {
     const state = Store.getState();
     const { annotationType, annotationId } = state.tracing;
     const { task } = state;
+    if (task == null) {
+      // Satisfy flow
+      throw new Error("Cannot find task to finish.");
+    }
 
     await Model.save();
     await finishAnnotation(annotationId, annotationType);
     try {
       const annotation = await requestTask();
 
       const isDifferentDataset = state.dataset.name !== annotation.dataSetName;
-      const isDifferentTaskType = annotation.task.type.id !== Utils.__guard__(task, x => x.type.id);
+      const isDifferentTaskType = annotation.task.type.id !== task.type.id;
+      const involvesVolumeTask = state.tracing.volume != null || annotation.tracing.volume != null;
 
-      const currentScript = task != null && task.script != null ? task.script.gist : null;
+      const currentScript = task.script != null ? task.script.gist : null;
       const nextScript = annotation.task.script != null ? annotation.task.script.gist : null;
       const isDifferentScript = currentScript !== nextScript;
 
       const newTaskUrl = `/annotations/${annotation.typ}/${annotation.id}`;
 
       // In some cases the page needs to be reloaded, in others the tracing can be hot-swapped
-      if (isDifferentDataset || isDifferentTaskType || isDifferentScript) {
+      if (isDifferentDataset || isDifferentTaskType || isDifferentScript || involvesVolumeTask) {
         location.href = newTaskUrl;
       } else {
         await this.restart(annotation.typ, annotation.id, ControlModeEnum.TRACE);

diff --git a/app/assets/javascripts/oxalis/model/accessors/dataset_accessor.js b/app/assets/javascripts/oxalis/model/accessors/dataset_accessor.js
@@ -94,7 +94,7 @@ export function getByteCount(dataset: APIDataset, layerName: string): number {
   return getByteCountFromLayer(getLayerByName(dataset, layerName));
 }
 
-type Boundary = { lowerBoundary: Vector3, upperBoundary: Vector3 };
+export type Boundary = { lowerBoundary: Vector3, upperBoundary: Vector3 };
 
 export function getLayerBoundaries(dataset: APIDataset, layerName: string): Boundary {
   const { topLeft, width, height, depth } = getLayerByName(dataset, layerName).boundingBox;

diff --git a/app/assets/javascripts/oxalis/model/bucket_data_handling/data_cube.js b/app/assets/javascripts/oxalis/model/bucket_data_handling/data_cube.js
@@ -120,13 +120,25 @@ class DataCube {
       this.cubes[i] = new CubeEntry(zoomedCubeBoundary);
     }
 
-    this.boundingBox = new BoundingBox(getSomeTracing(Store.getState().tracing).boundingBox, this);
+    const shouldBeRestrictedByTracingBoundingBox = () => {
+      const { task } = Store.getState();
+      const isVolumeTask = task != null && task.type.tracingType === "volume";
+      return !isVolumeTask;
+    };
+    this.boundingBox = new BoundingBox(
+      shouldBeRestrictedByTracingBoundingBox()
+        ? getSomeTracing(Store.getState().tracing).boundingBox
+        : null,
+      this,
+    );
 
     listenToStoreProperty(
       state => getSomeTracing(state.tracing).boundingBox,
       boundingBox => {
-        this.boundingBox = new BoundingBox(boundingBox, this);
-        this.forgetOutOfBoundaryBuckets();
+        if (shouldBeRestrictedByTracingBoundingBox()) {
+          this.boundingBox = new BoundingBox(boundingBox, this);
+          this.forgetOutOfBoundaryBuckets();
+        }
       },
     );
   }

diff --git a/app/assets/javascripts/oxalis/model/reducers/reducer_helpers.js b/app/assets/javascripts/oxalis/model/reducers/reducer_helpers.js
@@ -4,7 +4,9 @@ import Maybe from "data.maybe";
 
 import type { APIAnnotation, ServerBoundingBox } from "admin/api_flow_types";
 import type { Annotation, BoundingBoxObject } from "oxalis/store";
+import type { Boundary } from "oxalis/model/accessors/dataset_accessor";
 import type { BoundingBoxType } from "oxalis/constants";
+import { V3 } from "libs/mjs";
 import * as Utils from "libs/utils";
 
 export function convertServerBoundingBoxToFrontend(
@@ -32,6 +34,17 @@ export function convertFrontendBoundingBoxToServer(
     .getOrElse(null);
 }
 
+export function convertBoundariesToBoundingBox(boundary: Boundary): BoundingBoxObject {
+  const [width, height, depth] = V3.sub(boundary.upperBoundary, boundary.lowerBoundary);
+  return {
+    width,
+    height,
+    depth,
+    topLeft: boundary.lowerBoundary,
+  };
+}
+
+// Currently unused.
 export function convertPointToVecInBoundingBox(boundingBox: ServerBoundingBox): BoundingBoxObject {
   return {
     width: boundingBox.width,
-Original file line number
+Diff line change
@@ Expand Up @@
     -
     ### Postgres Evolutions:
-    -
+    - [038-add-tasktype-tracingtype.sql](conf/evolutions/038-add-tasktype-tracingtype.sql)
     ## [19.02.0](https://github.com/scalableminds/webknossos/releases/tag/19.02.0) - 2019-02-04
@@ Expand Down @@