From 10fb4e4798d4de5b6e7ff8178d30469b6571e706 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Wed, 14 Aug 2024 14:32:42 +0200
Subject: [PATCH 01/19] use tps instead of affine in compose

---
 .../composition_wizard/04_configure_new_dataset.tsx       | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index 98e7c471cad..6586f93a746 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -55,9 +55,13 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
     const transformationArr =
       sourcePoints.length > 0 && targetPoints.length > 0
         ? [
+            // {
+            //   type: "affine" as const,
+            //   matrix: flatToNestedMatrix(estimateAffineMatrix4x4(sourcePoints, targetPoints)),
+            // },
             {
-              type: "affine" as const,
-              matrix: flatToNestedMatrix(estimateAffineMatrix4x4(sourcePoints, targetPoints)),
+              type: "thin_plate_spline" as const,
+              correspondences: { source: sourcePoints, target: targetPoints },
             },
           ]
         : [];

From d571e52970ac4dcb74b57b9a93f4aa6140da3f12 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Wed, 14 Aug 2024 14:33:04 +0200
Subject: [PATCH 02/19] temporarily disable some CI checks

---
 .circleci/not-on-master.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.circleci/not-on-master.sh b/.circleci/not-on-master.sh
index 581393ebead..e3078cdb9ce 100755
--- a/.circleci/not-on-master.sh
+++ b/.circleci/not-on-master.sh
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 set -Eeuo pipefail
 
-if [ "${CIRCLE_BRANCH}" == "master" ]; then
+# if [ "${CIRCLE_BRANCH}" == "master" ]; then
   echo "Skipping this step on master..."
-else
-  exec "$@"
-fi
+# else
+#   exec "$@"
+# fi

From 0f7eebb9ff73a056ef0dc8e90d22f5920b8a9647 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Wed, 14 Aug 2024 17:14:15 +0200
Subject: [PATCH 03/19] always sort trees when composing datasets with
 landmarks

---
 .../admin/dataset/composition_wizard/02_upload_files.tsx     | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx b/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
index 6bd0ac87973..aee0b57194c 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
@@ -173,7 +173,10 @@ async function parseNmlFiles(fileList: FileList): Promise<Partial<WizardContext>
     throw new SoftError("The two NML files should have the same tree count.");
   }
 
-  for (const [tree1, tree2] of _.zip(Utils.values(trees1), Utils.values(trees2))) {
+  for (const [tree1, tree2] of _.zip(
+    Utils.values(trees1).sort((a, b) => a.treeId - b.treeId),
+    Utils.values(trees2).sort((a, b) => a.treeId - b.treeId),
+  )) {
     if (tree1 == null || tree2 == null) {
       // Satisfy TS. This should not happen, as we checked before that both tree collections
       // have the same size.

From 509b7db13645cb7171e428ba8332953946c97d2c Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Wed, 14 Aug 2024 17:14:46 +0200
Subject: [PATCH 04/19] add UI checkbox for affine vs tps

---
 .../04_configure_new_dataset.tsx              | 67 ++++++++++++-------
 frontend/javascripts/types/api_flow_types.ts  |  3 +
 2 files changed, 46 insertions(+), 24 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index 6586f93a746..1899507cf6b 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -5,7 +5,7 @@ import {
   DatasetNameFormItem,
   layerNameRules,
 } from "admin/dataset/dataset_components";
-import { Button, Col, Form, FormInstance, Input, List, Row, Tooltip } from "antd";
+import { Button, Checkbox, Col, Form, FormInstance, Input, List, Row, Tooltip } from "antd";
 import { FormItemWithInfo } from "dashboard/dataset/helper_components";
 import FolderSelection from "dashboard/folders/folder_selection";
 import { estimateAffineMatrix4x4 } from "libs/estimate_affine";
@@ -13,12 +13,18 @@ import Toast from "libs/toast";
 import * as Utils from "libs/utils";
 import _ from "lodash";
 import messages from "messages";
-import { Vector3 } from "oxalis/constants";
 import { flatToNestedMatrix } from "oxalis/model/accessors/dataset_accessor";
 import { OxalisState } from "oxalis/store";
 import React, { useState } from "react";
 import { useSelector } from "react-redux";
-import { APIDataLayer, APIDataset, APIDatasetId, APITeam, LayerLink } from "types/api_flow_types";
+import {
+  APIDataLayer,
+  APIDataset,
+  APIDatasetId,
+  APITeam,
+  areDatasetsIdentical,
+  LayerLink,
+} from "types/api_flow_types";
 import { syncValidator } from "types/validation";
 import { WizardComponentProps } from "./common";
 import { useEffectOnlyOnce } from "libs/react_hooks";
@@ -50,24 +56,9 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
     form.setFieldsValue({ layers: newLayers });
   };
 
-  const handleTransformImport = async (sourcePoints: Vector3[], targetPoints: Vector3[]) => {
-    const datasets = linkedDatasets;
-    const transformationArr =
-      sourcePoints.length > 0 && targetPoints.length > 0
-        ? [
-            // {
-            //   type: "affine" as const,
-            //   matrix: flatToNestedMatrix(estimateAffineMatrix4x4(sourcePoints, targetPoints)),
-            // },
-            {
-              type: "thin_plate_spline" as const,
-              correspondences: { source: sourcePoints, target: targetPoints },
-            },
-          ]
-        : [];
-
+  const handleTransformImport = async () => {
     const newLinks: LayerLink[] = (
-      _.flatMap(datasets, (dataset) =>
+      _.flatMap(linkedDatasets, (dataset) =>
         dataset.dataSource.dataLayers.map((layer) => [dataset, layer]),
       ) as [APIDataset, APIDataLayer][]
     ).map(
@@ -78,21 +69,46 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
         },
         sourceName: dataLayer.name,
         newName: dataLayer.name,
-        transformations: dataset === datasets[0] ? transformationArr : [],
+        transformations: [],
       }),
     );
     form.setFieldsValue({ layers: newLinks });
   };
 
   useEffectOnlyOnce(() => {
-    handleTransformImport(wizardContext.sourcePoints, wizardContext.targetPoints);
+    handleTransformImport();
   });
 
   const handleSubmit = async () => {
     if (activeUser == null) {
       throw new Error("Cannot create dataset without being logged in.");
     }
-    const layers = form.getFieldValue(["layers"]);
+    const layersWithoutTransforms = form.getFieldValue(["layers"]);
+    const useThinPlateSplines = form.getFieldValue("useThinPlateSplines");
+
+    function withTransforms(layers: LayerLink[]) {
+      const { sourcePoints, targetPoints } = wizardContext;
+      const transformationArr =
+        sourcePoints.length > 0 && targetPoints.length > 0
+          ? [
+              useThinPlateSplines
+                ? {
+                    type: "thin_plate_spline" as const,
+                    correspondences: { source: sourcePoints, target: targetPoints },
+                  }
+                : {
+                    type: "affine" as const,
+                    matrix: flatToNestedMatrix(estimateAffineMatrix4x4(sourcePoints, targetPoints)),
+                  },
+            ]
+          : [];
+      return layers.map((layer) => ({
+        ...layer,
+        transformations: areDatasetsIdentical(layer.datasetId, linkedDatasets[0])
+          ? transformationArr
+          : [],
+      }));
+    }
 
     const uploadableDatastores = props.datastores.filter((datastore) => datastore.allowsUpload);
     const datastoreToUse = uploadableDatastores[0];
@@ -109,7 +125,7 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
         targetFolderId: form.getFieldValue(["targetFolderId"]),
         organizationName: activeUser.organization,
         voxelSize: linkedDatasets.slice(-1)[0].dataSource.scale,
-        layers,
+        layers: withTransforms(layersWithoutTransforms),
       });
     } finally {
       setIsLoading(false);
@@ -184,6 +200,9 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
             );
           }}
         </Form.Item>
+        <FormItem name={["useThinPlateSplines"]} valuePropName="checked">
+          <Checkbox>Use Thin-Plate-Splines (Experimental)</Checkbox>
+        </FormItem>
 
         <FormItem
           style={{
diff --git a/frontend/javascripts/types/api_flow_types.ts b/frontend/javascripts/types/api_flow_types.ts
index fd34df077f4..b8c3f5261ae 100644
--- a/frontend/javascripts/types/api_flow_types.ts
+++ b/frontend/javascripts/types/api_flow_types.ts
@@ -167,6 +167,9 @@ export type MutableAPIDatasetId = {
   owningOrganization: string;
   name: string;
 };
+export function areDatasetsIdentical(a: APIDatasetId, b: APIDatasetId) {
+  return a.owningOrganization === b.owningOrganization && a.name === b.name;
+}
 export type APIDatasetId = Readonly<MutableAPIDatasetId>;
 export type APIDatasetDetails = {
   readonly species?: string;

From b624b5823dfc4987da42691a7ebe5420aa829385 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Wed, 14 Aug 2024 17:21:31 +0200
Subject: [PATCH 05/19] fix that p tag cannot contain ul

---
 frontend/javascripts/admin/dataset/dataset_upload_view.tsx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/dataset_upload_view.tsx b/frontend/javascripts/admin/dataset/dataset_upload_view.tsx
index 2b842421d81..765b542184a 100644
--- a/frontend/javascripts/admin/dataset/dataset_upload_view.tsx
+++ b/frontend/javascripts/admin/dataset/dataset_upload_view.tsx
@@ -1008,7 +1008,7 @@ function FileUploadArea({
             color: "var(--ant-color-primary)",
           }}
         />
-        <p
+        <div
           style={{
             maxWidth: 800,
             textAlign: "center",
@@ -1139,7 +1139,7 @@ function FileUploadArea({
               </div>
             </>
           ) : null}
-        </p>
+        </div>
       </div>
 
       {files.length > 0 ? (

From ddf1d2642389f06ad916f536d184ec29c9fab959 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Fri, 16 Aug 2024 09:19:57 +0200
Subject: [PATCH 06/19] also sort nodes by id

---
 .../admin/dataset/composition_wizard/02_upload_files.tsx      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx b/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
index aee0b57194c..a49513e6cbf 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
@@ -182,8 +182,8 @@ async function parseNmlFiles(fileList: FileList): Promise<Partial<WizardContext>
       // have the same size.
       throw new SoftError("A tree was unexpectedly parsed as null. Please try again");
     }
-    const nodes1 = Array.from(tree1.nodes.values());
-    const nodes2 = Array.from(tree2.nodes.values());
+    const nodes1 = Array.from(tree1.nodes.values()).sort((a, b) => a.id - b.id);
+    const nodes2 = Array.from(tree2.nodes.values()).sort((a, b) => a.id - b.id);
     for (const [node1, node2] of _.zip(nodes1, nodes2)) {
       if ((node1 == null) !== (node2 == null)) {
         throw new SoftError(

From 5aae4d95abcf67089fb2070df9a69903c80f7469 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Fri, 16 Aug 2024 14:08:16 +0200
Subject: [PATCH 07/19] fix inverted TPS transform creation when loading
 dataset; add more comments

---
 .../admin/dataset/composition_wizard/02_upload_files.tsx      | 4 ++--
 .../dataset/composition_wizard/04_configure_new_dataset.tsx   | 1 +
 frontend/javascripts/libs/estimate_affine.ts                  | 3 ++-
 .../javascripts/oxalis/model/accessors/dataset_accessor.ts    | 2 +-
 .../oxalis/model/helpers/transformation_helpers.ts            | 2 ++
 5 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx b/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
index a49513e6cbf..e3d30151f49 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
@@ -204,8 +204,8 @@ async function parseNmlFiles(fileList: FileList): Promise<Partial<WizardContext>
 
   return {
     datasets: datasets || [],
-    sourcePoints,
-    targetPoints,
+    sourcePoints, // The first dataset (will be transformed to match the second later)
+    targetPoints, // The second dataset (won't be transformed by default)
     currentWizardStep: "SelectDatasets",
   };
 }
diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index 1899507cf6b..49886101871 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -104,6 +104,7 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
           : [];
       return layers.map((layer) => ({
         ...layer,
+        // The first dataset will be transformed to match the second.
         transformations: areDatasetsIdentical(layer.datasetId, linkedDatasets[0])
           ? transformationArr
           : [],
diff --git a/frontend/javascripts/libs/estimate_affine.ts b/frontend/javascripts/libs/estimate_affine.ts
index 715a87d1385..12bdd608aca 100644
--- a/frontend/javascripts/libs/estimate_affine.ts
+++ b/frontend/javascripts/libs/estimate_affine.ts
@@ -3,8 +3,8 @@ import { Matrix4x4 } from "mjs";
 import { Matrix, solve } from "ml-matrix";
 import { Vector3 } from "oxalis/constants";
 
-// Estimates an affine matrix that transforms from source points to target points.
 export default function estimateAffine(sourcePoints: Vector3[], targetPoints: Vector3[]) {
+  /* Estimates an affine matrix that transforms from source points to target points. */
   // Number of correspondences
   const N = sourcePoints.length;
 
@@ -52,5 +52,6 @@ export function estimateAffineMatrix4x4(
   sourcePoints: Vector3[],
   targetPoints: Vector3[],
 ): Matrix4x4 {
+  /* Estimates an affine matrix that transforms from source points to target points. */
   return estimateAffine(sourcePoints, targetPoints).to1DArray() as any as Matrix4x4;
 }
diff --git a/frontend/javascripts/oxalis/model/accessors/dataset_accessor.ts b/frontend/javascripts/oxalis/model/accessors/dataset_accessor.ts
index 46f0df76b90..a65ea04a6e4 100644
--- a/frontend/javascripts/oxalis/model/accessors/dataset_accessor.ts
+++ b/frontend/javascripts/oxalis/model/accessors/dataset_accessor.ts
@@ -722,7 +722,7 @@ function _getOriginalTransformsForLayerOrNull(
   } else if (type === "thin_plate_spline") {
     const { source, target } = transformation.correspondences;
 
-    return createThinPlateSplineTransform(target, source, dataset.dataSource.scale.factor);
+    return createThinPlateSplineTransform(source, target, dataset.dataSource.scale.factor);
   }
 
   console.error(
diff --git a/frontend/javascripts/oxalis/model/helpers/transformation_helpers.ts b/frontend/javascripts/oxalis/model/helpers/transformation_helpers.ts
index 4f0ac826a27..08b63097c89 100644
--- a/frontend/javascripts/oxalis/model/helpers/transformation_helpers.ts
+++ b/frontend/javascripts/oxalis/model/helpers/transformation_helpers.ts
@@ -34,6 +34,7 @@ export function createAffineTransformFromMatrix(
 }
 
 export function createAffineTransform(source: Vector3[], target: Vector3[]): Transform {
+  /* Creates an affine transform that transforms from source points to target points. */
   const affineMatrix = estimateAffineMatrix4x4(source, target);
 
   return {
@@ -48,6 +49,7 @@ export function createThinPlateSplineTransform(
   target: Vector3[],
   scale: Vector3,
 ): Transform {
+  /* Creates a TPS that transforms from source points to target points. */
   const affineMatrix = estimateAffineMatrix4x4(source, target);
   const affineMatrixInv = estimateAffineMatrix4x4(target, source);
 

From cef63e841c2dcfae35f6b770de2f7c09942d589f Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Fri, 16 Aug 2024 14:40:50 +0200
Subject: [PATCH 08/19] render dataset description as markdown in dashboard;
 update dataset description after composing

---
 .../04_configure_new_dataset.tsx              | 50 ++++++++++++++++---
 .../dashboard/folders/details_sidebar.tsx     |  3 +-
 frontend/javascripts/libs/estimate_affine.ts  | 19 ++++---
 3 files changed, 57 insertions(+), 15 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index 49886101871..80074a22fce 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -1,5 +1,5 @@
 import { DeleteOutlined } from "@ant-design/icons";
-import { createDatasetComposition } from "admin/admin_rest_api";
+import { createDatasetComposition, updateDatasetPartial } from "admin/admin_rest_api";
 import {
   AllowedTeamsFormItem,
   DatasetNameFormItem,
@@ -83,8 +83,11 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
     if (activeUser == null) {
       throw new Error("Cannot create dataset without being logged in.");
     }
-    const layersWithoutTransforms = form.getFieldValue(["layers"]);
-    const useThinPlateSplines = form.getFieldValue("useThinPlateSplines");
+    const layersWithoutTransforms = form.getFieldValue(["layers"]) as LayerLink[];
+    // todop: does this throw when the ui was not rendered?
+    const useThinPlateSplines = form.getFieldValue("useThinPlateSplines") as boolean;
+
+    const affineMeanError = { meanError: 0 };
 
     function withTransforms(layers: LayerLink[]) {
       const { sourcePoints, targetPoints } = wizardContext;
@@ -98,7 +101,9 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
                   }
                 : {
                     type: "affine" as const,
-                    matrix: flatToNestedMatrix(estimateAffineMatrix4x4(sourcePoints, targetPoints)),
+                    matrix: flatToNestedMatrix(
+                      estimateAffineMatrix4x4(sourcePoints, targetPoints, affineMeanError),
+                    ),
                   },
             ]
           : [];
@@ -128,6 +133,35 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
         voxelSize: linkedDatasets.slice(-1)[0].dataSource.scale,
         layers: withTransforms(layersWithoutTransforms),
       });
+
+      const uniqueDatasets = _.uniqBy(
+        layersWithoutTransforms.map((layer) => layer.datasetId),
+        (id) => id.owningOrganization + "-" + id.name,
+      );
+      const datasetMarkdownLinks = uniqueDatasets
+        .map((el) => `- [${el.name}](/datasets/${el.owningOrganization}/${el.name})`)
+        .join("\n");
+
+      await updateDatasetPartial(
+        { owningOrganization: activeUser.organization, name: newDatasetName },
+        {
+          description: [
+            "This dataset was composed from:",
+            datasetMarkdownLinks,
+            "",
+            "The layers were combined " +
+              (wizardContext.sourcePoints.length === 0
+                ? "without any transforms"
+                : `with ${
+                    useThinPlateSplines
+                      ? `Thin-Plate-Splines (${wizardContext.sourcePoints.length} correspondences)`
+                      : `an affine transformation (mean error: ${affineMeanError})`
+                  }`) +
+              ".",
+          ].join("\n"),
+        },
+        // todop test
+      );
     } finally {
       setIsLoading(false);
     }
@@ -201,9 +235,11 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
             );
           }}
         </Form.Item>
-        <FormItem name={["useThinPlateSplines"]} valuePropName="checked">
-          <Checkbox>Use Thin-Plate-Splines (Experimental)</Checkbox>
-        </FormItem>
+        {wizardContext.sourcePoints.length > 0 && (
+          <FormItem name={["useThinPlateSplines"]} valuePropName="checked">
+            <Checkbox>Use Thin-Plate-Splines (Experimental)</Checkbox>
+          </FormItem>
+        )}
 
         <FormItem
           style={{
diff --git a/frontend/javascripts/dashboard/folders/details_sidebar.tsx b/frontend/javascripts/dashboard/folders/details_sidebar.tsx
index 0f816a92e22..4abfeee27e8 100644
--- a/frontend/javascripts/dashboard/folders/details_sidebar.tsx
+++ b/frontend/javascripts/dashboard/folders/details_sidebar.tsx
@@ -23,6 +23,7 @@ import { useSelector } from "react-redux";
 import { OxalisState } from "oxalis/store";
 import { getOrganization } from "admin/admin_rest_api";
 import { useQuery } from "@tanstack/react-query";
+import Markdown from "libs/markdown_adapter";
 
 export function DetailsSidebar({
   selectedDatasets,
@@ -148,7 +149,7 @@ function DatasetDetails({ selectedDataset }: { selectedDataset: APIDatasetCompac
 
         <div style={{ marginBottom: 4 }}>
           <div className="sidebar-label">Description</div>
-          <div>{fullDataset?.description}</div>
+          <Markdown>{fullDataset?.description}</Markdown>
         </div>
 
         <div style={{ marginBottom: 4 }}>
diff --git a/frontend/javascripts/libs/estimate_affine.ts b/frontend/javascripts/libs/estimate_affine.ts
index 12bdd608aca..dc077ee675a 100644
--- a/frontend/javascripts/libs/estimate_affine.ts
+++ b/frontend/javascripts/libs/estimate_affine.ts
@@ -3,7 +3,11 @@ import { Matrix4x4 } from "mjs";
 import { Matrix, solve } from "ml-matrix";
 import { Vector3 } from "oxalis/constants";
 
-export default function estimateAffine(sourcePoints: Vector3[], targetPoints: Vector3[]) {
+export default function estimateAffine(
+  sourcePoints: Vector3[],
+  targetPoints: Vector3[],
+  optInfoOut?: { meanError: number },
+) {
   /* Estimates an affine matrix that transforms from source points to target points. */
   // Number of correspondences
   const N = sourcePoints.length;
@@ -31,11 +35,11 @@ export default function estimateAffine(sourcePoints: Vector3[], targetPoints: Ve
   const x = xMatrix.to1DArray();
   const error = Matrix.sub(b, new Matrix(A).mmul(xMatrix)).to1DArray();
   if (!process.env.IS_TESTING) {
-    console.log(
-      "Affine estimation error: ",
-      error,
-      `(mean=${_.mean(error.map((el) => Math.abs(el)))})`,
-    );
+    const meanError = _.mean(error.map((el) => Math.abs(el)));
+    console.log("Affine estimation error: ", error, `(mean=${meanError})`);
+    if (optInfoOut) {
+      optInfoOut.meanError = meanError;
+    }
   }
 
   const affineMatrix = new Matrix([
@@ -51,7 +55,8 @@ export default function estimateAffine(sourcePoints: Vector3[], targetPoints: Ve
 export function estimateAffineMatrix4x4(
   sourcePoints: Vector3[],
   targetPoints: Vector3[],
+  optInfoOut?: { meanError: number },
 ): Matrix4x4 {
   /* Estimates an affine matrix that transforms from source points to target points. */
-  return estimateAffine(sourcePoints, targetPoints).to1DArray() as any as Matrix4x4;
+  return estimateAffine(sourcePoints, targetPoints, optInfoOut).to1DArray() as any as Matrix4x4;
 }

From 5a690e10ebbb50c013a1d35526c90bdbae4dd909 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Fri, 16 Aug 2024 16:13:20 +0200
Subject: [PATCH 09/19] fix mean error formatting in description

---
 .../dataset/composition_wizard/04_configure_new_dataset.tsx  | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index 80074a22fce..e73d9c3e0ad 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -28,6 +28,7 @@ import {
 import { syncValidator } from "types/validation";
 import { WizardComponentProps } from "./common";
 import { useEffectOnlyOnce } from "libs/react_hooks";
+import { formatNumber } from "libs/format_utils";
 
 const FormItem = Form.Item;
 
@@ -155,7 +156,9 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
                 : `with ${
                     useThinPlateSplines
                       ? `Thin-Plate-Splines (${wizardContext.sourcePoints.length} correspondences)`
-                      : `an affine transformation (mean error: ${affineMeanError})`
+                      : `an affine transformation (mean error: ${formatNumber(
+                          affineMeanError.meanError,
+                        )} vx)`
                   }`) +
               ".",
           ].join("\n"),

From 8fcc8eeee480f0d10512138e837b116870bb8017 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Mon, 19 Aug 2024 13:39:13 +0200
Subject: [PATCH 10/19] disable TPS checkbox for now

---
 .../dataset/composition_wizard/03_select_datasets.tsx      | 6 +++++-
 .../composition_wizard/04_configure_new_dataset.tsx        | 7 +++----
 .../javascripts/dashboard/explorative_annotations_view.tsx | 2 +-
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/03_select_datasets.tsx b/frontend/javascripts/admin/dataset/composition_wizard/03_select_datasets.tsx
index 5dc73e6294d..8ad912cb6d7 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/03_select_datasets.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/03_select_datasets.tsx
@@ -48,7 +48,11 @@ export default function SelectDatasets({ wizardContext, setWizardContext }: Wiza
 
   return (
     <div>
-      <p>Select the datasets that you want to combine or doublecheck the pre-selected datasets.</p>
+      <p>
+        Select the datasets that you want to combine or doublecheck the pre-selected datasets. Note
+        that the order of the datasets is important and needs to be equal to the order of the files
+        from the upload.
+      </p>
       <DatasetSelectionComponent
         datasetValues={datasetValues}
         setDatasetValues={setDatasetValues}
diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index e73d9c3e0ad..314c1ff95a4 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -31,6 +31,7 @@ import { useEffectOnlyOnce } from "libs/react_hooks";
 import { formatNumber } from "libs/format_utils";
 
 const FormItem = Form.Item;
+const ALLOW_TPS_IN_COMPOSITION = false;
 
 export function ConfigureNewDataset(props: WizardComponentProps) {
   const formRef = React.useRef<FormInstance<any>>(null);
@@ -85,8 +86,7 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
       throw new Error("Cannot create dataset without being logged in.");
     }
     const layersWithoutTransforms = form.getFieldValue(["layers"]) as LayerLink[];
-    // todop: does this throw when the ui was not rendered?
-    const useThinPlateSplines = form.getFieldValue("useThinPlateSplines") as boolean;
+    const useThinPlateSplines = (form.getFieldValue("useThinPlateSplines") ?? false) as boolean;
 
     const affineMeanError = { meanError: 0 };
 
@@ -163,7 +163,6 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
               ".",
           ].join("\n"),
         },
-        // todop test
       );
     } finally {
       setIsLoading(false);
@@ -238,7 +237,7 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
             );
           }}
         </Form.Item>
-        {wizardContext.sourcePoints.length > 0 && (
+        {ALLOW_TPS_IN_COMPOSITION && wizardContext.sourcePoints.length > 0 && (
           <FormItem name={["useThinPlateSplines"]} valuePropName="checked">
             <Checkbox>Use Thin-Plate-Splines (Experimental)</Checkbox>
           </FormItem>
diff --git a/frontend/javascripts/dashboard/explorative_annotations_view.tsx b/frontend/javascripts/dashboard/explorative_annotations_view.tsx
index 357a2e98ad2..0e18a0a4b51 100644
--- a/frontend/javascripts/dashboard/explorative_annotations_view.tsx
+++ b/frontend/javascripts/dashboard/explorative_annotations_view.tsx
@@ -682,7 +682,7 @@ class ExplorativeAnnotationsView extends React.PureComponent<Props, State> {
           return (
             <>
               <div>
-                <UserOutlined />
+                <UserOutlined className="icon-margin-right" />
                 {ownerName}
               </div>
               <div className="flex-container">

From c6227b1520bd79d69316e4343aea22ed435349e4 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Mon, 19 Aug 2024 13:39:38 +0200
Subject: [PATCH 11/19] restore ci

---
 .circleci/not-on-master.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.circleci/not-on-master.sh b/.circleci/not-on-master.sh
index e3078cdb9ce..581393ebead 100755
--- a/.circleci/not-on-master.sh
+++ b/.circleci/not-on-master.sh
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 set -Eeuo pipefail
 
-# if [ "${CIRCLE_BRANCH}" == "master" ]; then
+if [ "${CIRCLE_BRANCH}" == "master" ]; then
   echo "Skipping this step on master..."
-# else
-#   exec "$@"
-# fi
+else
+  exec "$@"
+fi

From 7ccf57cb633f6c9f228f0d84975dbadecb6f2fca Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Mon, 19 Aug 2024 13:47:05 +0200
Subject: [PATCH 12/19] update changelog

---
 CHANGELOG.unreleased.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
index cbe39f2b42f..1158f910a5c 100644
--- a/CHANGELOG.unreleased.md
+++ b/CHANGELOG.unreleased.md
@@ -49,6 +49,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed that activating the skeleton tab would always change the active position to the active node. [#7958](https://github.com/scalableminds/webknossos/pull/7958)
 - Fixed that skeleton groups couldn't be collapsed or expanded in locked annotations. [#7988](https://github.com/scalableminds/webknossos/pull/7988)
 - Fixed uploading datasets in neuroglancer precomputed and n5 data format. [#8008](https://github.com/scalableminds/webknossos/pull/8008)
+- Various fixes for composing datasets with landmarks. Note that the interpretation of correspondence points was inverted for thin plate splines. [#7992](https://github.com/scalableminds/webknossos/pull/7992)
 
 ### Removed
 

From e74a0690d2ccefe932f986b9ca9af429b769ec45 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Tue, 20 Aug 2024 09:23:49 +0200
Subject: [PATCH 13/19] make optInfoOut writing independent from IS_TESTING

---
 frontend/javascripts/libs/estimate_affine.ts | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/frontend/javascripts/libs/estimate_affine.ts b/frontend/javascripts/libs/estimate_affine.ts
index dc077ee675a..7413361dbc9 100644
--- a/frontend/javascripts/libs/estimate_affine.ts
+++ b/frontend/javascripts/libs/estimate_affine.ts
@@ -34,12 +34,12 @@ export default function estimateAffine(
   const xMatrix = solve(A, b);
   const x = xMatrix.to1DArray();
   const error = Matrix.sub(b, new Matrix(A).mmul(xMatrix)).to1DArray();
+  const meanError = _.mean(error.map((el) => Math.abs(el)));
+  if (optInfoOut) {
+    optInfoOut.meanError = meanError;
+  }
   if (!process.env.IS_TESTING) {
-    const meanError = _.mean(error.map((el) => Math.abs(el)));
     console.log("Affine estimation error: ", error, `(mean=${meanError})`);
-    if (optInfoOut) {
-      optInfoOut.meanError = meanError;
-    }
   }
 
   const affineMatrix = new Matrix([

From 734d4264fd1f6b6f69ba440aa40b646185ca2744 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Tue, 20 Aug 2024 14:10:43 +0200
Subject: [PATCH 14/19] ask user for landmark augmentation when affine
 estimation fails; assert >= landmarks; test tps creation eagerly etc

---
 .../composition_wizard/02_upload_files.tsx    |  4 +
 .../04_configure_new_dataset.tsx              | 91 ++++++++++++++-----
 .../model/helpers/transformation_helpers.ts   |  8 ++
 .../oxalis/model/sagas/saga_helpers.ts        |  2 +-
 4 files changed, 81 insertions(+), 24 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx b/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
index e3d30151f49..352442e0661 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx
@@ -197,6 +197,10 @@ async function parseNmlFiles(fileList: FileList): Promise<Partial<WizardContext>
     }
   }
 
+  if (sourcePoints.length < 3) {
+    throw new SoftError("Each file should contain at least 3 nodes.");
+  }
+
   const datasets = await tryToFetchDatasetsByName(
     [datasetName1, datasetName2],
     "Could not derive datasets from NML. Please specify these manually.",
diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index 314c1ff95a4..5bc025f35d3 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -5,7 +5,7 @@ import {
   DatasetNameFormItem,
   layerNameRules,
 } from "admin/dataset/dataset_components";
-import { Button, Checkbox, Col, Form, FormInstance, Input, List, Row, Tooltip } from "antd";
+import { Button, Checkbox, Col, Form, FormInstance, Input, List, Modal, Row, Tooltip } from "antd";
 import { FormItemWithInfo } from "dashboard/dataset/helper_components";
 import FolderSelection from "dashboard/folders/folder_selection";
 import { estimateAffineMatrix4x4 } from "libs/estimate_affine";
@@ -25,14 +25,27 @@ import {
   areDatasetsIdentical,
   LayerLink,
 } from "types/api_flow_types";
+import ErrorHandling from "libs/error_handling";
 import { syncValidator } from "types/validation";
 import { WizardComponentProps } from "./common";
 import { useEffectOnlyOnce } from "libs/react_hooks";
 import { formatNumber } from "libs/format_utils";
+import { checkLandmarksForThinPlateSpline } from "oxalis/model/helpers/transformation_helpers";
+import { Vector3 } from "oxalis/constants";
 
 const FormItem = Form.Item;
 const ALLOW_TPS_IN_COMPOSITION = false;
 
+async function guardedWithErrorToast(fn: () => Promise<any>) {
+  try {
+    await fn();
+  } catch (error) {
+    Toast.error("An error unexpected occurred. Please check the console for details");
+    console.error(error);
+    ErrorHandling.notify(error as Error);
+  }
+}
+
 export function ConfigureNewDataset(props: WizardComponentProps) {
   const formRef = React.useRef<FormInstance<any>>(null);
 
@@ -90,24 +103,27 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
 
     const affineMeanError = { meanError: 0 };
 
-    function withTransforms(layers: LayerLink[]) {
-      const { sourcePoints, targetPoints } = wizardContext;
-      const transformationArr =
-        sourcePoints.length > 0 && targetPoints.length > 0
-          ? [
-              useThinPlateSplines
-                ? {
-                    type: "thin_plate_spline" as const,
-                    correspondences: { source: sourcePoints, target: targetPoints },
-                  }
-                : {
-                    type: "affine" as const,
-                    matrix: flatToNestedMatrix(
-                      estimateAffineMatrix4x4(sourcePoints, targetPoints, affineMeanError),
-                    ),
-                  },
-            ]
-          : [];
+    function withTransforms(layers: LayerLink[], sourcePoints: Vector3[], targetPoints: Vector3[]) {
+      if (sourcePoints.length + targetPoints.length === 0) {
+        return layers;
+      }
+
+      const transformationArr = [
+        useThinPlateSplines
+          ? {
+              type: "thin_plate_spline" as const,
+              correspondences: { source: sourcePoints, target: targetPoints },
+            }
+          : {
+              type: "affine" as const,
+              matrix: flatToNestedMatrix(
+                estimateAffineMatrix4x4(sourcePoints, targetPoints, affineMeanError),
+              ),
+            },
+      ];
+      if (useThinPlateSplines) {
+        checkLandmarksForThinPlateSpline(sourcePoints, targetPoints);
+      }
       return layers.map((layer) => ({
         ...layer,
         // The first dataset will be transformed to match the second.
@@ -124,6 +140,35 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
       return;
     }
 
+    let layersWithTransforms;
+    const { sourcePoints, targetPoints } = wizardContext;
+    try {
+      layersWithTransforms = withTransforms(layersWithoutTransforms, sourcePoints, targetPoints);
+    } catch (exception) {
+      const tryAugmentation = await new Promise((resolve) => {
+        Modal.confirm({
+          title: "Augment landmarks?",
+          content:
+            "The provided landmarks can't be used for affine estimation, possibly " +
+            "due to their planar nature. Should a constant translation in the Z " +
+            "direction be assumed, and the landmarks adjusted accordingly?",
+          onOk: () => resolve(true),
+          onCancel: () => resolve(false),
+        });
+      });
+      const augmentLandmarks = (points: Vector3[]) =>
+        points.concat(points.map((p) => [p[0], p[1], p[2] + 1]));
+      if (tryAugmentation) {
+        layersWithTransforms = withTransforms(
+          layersWithoutTransforms,
+          augmentLandmarks(sourcePoints),
+          augmentLandmarks(targetPoints),
+        );
+      } else {
+        throw exception;
+      }
+    }
+
     const newDatasetName = form.getFieldValue(["name"]);
     setIsLoading(true);
     try {
@@ -132,7 +177,7 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
         targetFolderId: form.getFieldValue(["targetFolderId"]),
         organizationName: activeUser.organization,
         voxelSize: linkedDatasets.slice(-1)[0].dataSource.scale,
-        layers: withTransforms(layersWithoutTransforms),
+        layers: layersWithTransforms,
       });
 
       const uniqueDatasets = _.uniqBy(
@@ -151,11 +196,11 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
             datasetMarkdownLinks,
             "",
             "The layers were combined " +
-              (wizardContext.sourcePoints.length === 0
+              (sourcePoints.length === 0
                 ? "without any transforms"
                 : `with ${
                     useThinPlateSplines
-                      ? `Thin-Plate-Splines (${wizardContext.sourcePoints.length} correspondences)`
+                      ? `Thin-Plate-Splines (${sourcePoints.length} correspondences)`
                       : `an affine transformation (mean error: ${formatNumber(
                           affineMeanError.meanError,
                         )} vx)`
@@ -175,7 +220,7 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
     // Using Forms here only to validate fields and for easy layout
     <div style={{ padding: 5 }}>
       <p>Please configure the dataset that is about to be created.</p>
-      <Form form={form} layout="vertical" onFinish={handleSubmit}>
+      <Form form={form} layout="vertical" onFinish={() => guardedWithErrorToast(handleSubmit)}>
         <Row gutter={8}>
           <Col span={12}>
             <DatasetNameFormItem activeUser={activeUser} />
diff --git a/frontend/javascripts/oxalis/model/helpers/transformation_helpers.ts b/frontend/javascripts/oxalis/model/helpers/transformation_helpers.ts
index 08b63097c89..8b9b081f83e 100644
--- a/frontend/javascripts/oxalis/model/helpers/transformation_helpers.ts
+++ b/frontend/javascripts/oxalis/model/helpers/transformation_helpers.ts
@@ -44,6 +44,14 @@ export function createAffineTransform(source: Vector3[], target: Vector3[]): Tra
   };
 }
 
+export function checkLandmarksForThinPlateSpline(source: Vector3[], target: Vector3[]) {
+  // Strictly speaking, the TPS transform is not needed here, because it will
+  // be created when the actual dataset is opened. However, if the landmarks
+  // cannot be loaded into a TPS (e.g., because the landmarks are planar and
+  // affine estimation will crash), we want to detect this here automatically.
+  createThinPlateSplineTransform(source, target, [1, 1, 1]);
+}
+
 export function createThinPlateSplineTransform(
   source: Vector3[],
   target: Vector3[],
diff --git a/frontend/javascripts/oxalis/model/sagas/saga_helpers.ts b/frontend/javascripts/oxalis/model/sagas/saga_helpers.ts
index bc5572b4d74..7586b3ecc93 100644
--- a/frontend/javascripts/oxalis/model/sagas/saga_helpers.ts
+++ b/frontend/javascripts/oxalis/model/sagas/saga_helpers.ts
@@ -78,7 +78,7 @@ export function askUserForLockingActiveMapping(
         cancelText: "Abort Annotation Action",
         width: 600,
         onOk: lockMapping,
-        onCancel: async () => {
+        onCancel: () => {
           reject({ isMappingLockedIfNeeded: false, reason: "User aborted." });
         },
       });

From 173e0935ee298cb1685fbcd36232bb57c035a17f Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Wed, 21 Aug 2024 08:56:43 +0200
Subject: [PATCH 15/19] move allowThinPlateSplines into wk dev flags

---
 .../composition_wizard/04_configure_new_dataset.tsx | 13 +++++++------
 frontend/javascripts/oxalis/api/wk_dev.ts           |  3 +++
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index 5bc025f35d3..0a97c87b237 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -32,9 +32,9 @@ import { useEffectOnlyOnce } from "libs/react_hooks";
 import { formatNumber } from "libs/format_utils";
 import { checkLandmarksForThinPlateSpline } from "oxalis/model/helpers/transformation_helpers";
 import { Vector3 } from "oxalis/constants";
+import { WkDevFlags } from "oxalis/api/wk_dev";
 
 const FormItem = Form.Item;
-const ALLOW_TPS_IN_COMPOSITION = false;
 
 async function guardedWithErrorToast(fn: () => Promise<any>) {
   try {
@@ -282,11 +282,12 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
             );
           }}
         </Form.Item>
-        {ALLOW_TPS_IN_COMPOSITION && wizardContext.sourcePoints.length > 0 && (
-          <FormItem name={["useThinPlateSplines"]} valuePropName="checked">
-            <Checkbox>Use Thin-Plate-Splines (Experimental)</Checkbox>
-          </FormItem>
-        )}
+        {WkDevFlags.datasetComposition.allowThinPlateSplines &&
+          wizardContext.sourcePoints.length > 0 && (
+            <FormItem name={["useThinPlateSplines"]} valuePropName="checked">
+              <Checkbox>Use Thin-Plate-Splines (Experimental)</Checkbox>
+            </FormItem>
+          )}
 
         <FormItem
           style={{
diff --git a/frontend/javascripts/oxalis/api/wk_dev.ts b/frontend/javascripts/oxalis/api/wk_dev.ts
index 25f6d63521b..f4548080fe5 100644
--- a/frontend/javascripts/oxalis/api/wk_dev.ts
+++ b/frontend/javascripts/oxalis/api/wk_dev.ts
@@ -24,6 +24,9 @@ export const WkDevFlags = {
   meshing: {
     marchingCubeSizeInTargetMag: [64, 64, 64] as Vector3,
   },
+  datasetComposition: {
+    allowThinPlateSplines: false,
+  },
 };
 
 export default class WkDev {

From c2a9a700466359b77ac7fa563c63dd241a22372f Mon Sep 17 00:00:00 2001
From: Philipp Otto <philippotto@users.noreply.github.com>
Date: Wed, 21 Aug 2024 17:04:03 +0200
Subject: [PATCH 16/19] Update
 frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx

Co-authored-by: MichaelBuessemeyer <39529669+MichaelBuessemeyer@users.noreply.github.com>
---
 .../dataset/composition_wizard/04_configure_new_dataset.tsx     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index 0a97c87b237..b609bfba78b 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -40,7 +40,7 @@ async function guardedWithErrorToast(fn: () => Promise<any>) {
   try {
     await fn();
   } catch (error) {
-    Toast.error("An error unexpected occurred. Please check the console for details");
+    Toast.error("An unexpected error occurred. Please check the console for details");
     console.error(error);
     ErrorHandling.notify(error as Error);
   }

From ff5415b20deff2ba5803b4f01b5eb044dab5ee08 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Wed, 21 Aug 2024 17:05:33 +0200
Subject: [PATCH 17/19] move guardedWithErrorToast fn

---
 .../04_configure_new_dataset.tsx                | 17 +++++------------
 frontend/javascripts/libs/utils.ts              | 12 ++++++++++++
 2 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index 0a97c87b237..760387ecb3a 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -25,7 +25,6 @@ import {
   areDatasetsIdentical,
   LayerLink,
 } from "types/api_flow_types";
-import ErrorHandling from "libs/error_handling";
 import { syncValidator } from "types/validation";
 import { WizardComponentProps } from "./common";
 import { useEffectOnlyOnce } from "libs/react_hooks";
@@ -36,16 +35,6 @@ import { WkDevFlags } from "oxalis/api/wk_dev";
 
 const FormItem = Form.Item;
 
-async function guardedWithErrorToast(fn: () => Promise<any>) {
-  try {
-    await fn();
-  } catch (error) {
-    Toast.error("An error unexpected occurred. Please check the console for details");
-    console.error(error);
-    ErrorHandling.notify(error as Error);
-  }
-}
-
 export function ConfigureNewDataset(props: WizardComponentProps) {
   const formRef = React.useRef<FormInstance<any>>(null);
 
@@ -220,7 +209,11 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
     // Using Forms here only to validate fields and for easy layout
     <div style={{ padding: 5 }}>
       <p>Please configure the dataset that is about to be created.</p>
-      <Form form={form} layout="vertical" onFinish={() => guardedWithErrorToast(handleSubmit)}>
+      <Form
+        form={form}
+        layout="vertical"
+        onFinish={() => Utils.guardedWithErrorToast(handleSubmit)}
+      >
         <Row gutter={8}>
           <Col span={12}>
             <DatasetNameFormItem activeUser={activeUser} />
diff --git a/frontend/javascripts/libs/utils.ts b/frontend/javascripts/libs/utils.ts
index dd146d2277e..bee78ba2633 100644
--- a/frontend/javascripts/libs/utils.ts
+++ b/frontend/javascripts/libs/utils.ts
@@ -16,6 +16,8 @@ import type {
 import window, { document, location } from "libs/window";
 import { ArbitraryObject, Comparator } from "types/globals";
 import dayjs from "dayjs";
+import Toast from "./toast";
+import ErrorHandling from "libs/error_handling";
 
 type UrlParams = Record<string, string>;
 // Fix JS modulo bug
@@ -1300,3 +1302,13 @@ export function generateRandomId(length: number) {
   }
   return result;
 }
+
+export async function guardedWithErrorToast(fn: () => Promise<any>) {
+  try {
+    await fn();
+  } catch (error) {
+    Toast.error("An error unexpected occurred. Please check the console for details");
+    console.error(error);
+    ErrorHandling.notify(error as Error);
+  }
+}

From 6bee6c5ffd84a5d3ff1b7dee252048bab4038550 Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Wed, 21 Aug 2024 19:30:07 +0200
Subject: [PATCH 18/19] format

---
 .../04_configure_new_dataset.tsx              | 35 ++++++++++---------
 1 file changed, 18 insertions(+), 17 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index c9a32333e7c..760387ecb3a 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -100,15 +100,15 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
       const transformationArr = [
         useThinPlateSplines
           ? {
-            type: "thin_plate_spline" as const,
-            correspondences: { source: sourcePoints, target: targetPoints },
-          }
+              type: "thin_plate_spline" as const,
+              correspondences: { source: sourcePoints, target: targetPoints },
+            }
           : {
-            type: "affine" as const,
-            matrix: flatToNestedMatrix(
-              estimateAffineMatrix4x4(sourcePoints, targetPoints, affineMeanError),
-            ),
-          },
+              type: "affine" as const,
+              matrix: flatToNestedMatrix(
+                estimateAffineMatrix4x4(sourcePoints, targetPoints, affineMeanError),
+              ),
+            },
       ];
       if (useThinPlateSplines) {
         checkLandmarksForThinPlateSpline(sourcePoints, targetPoints);
@@ -185,15 +185,16 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
             datasetMarkdownLinks,
             "",
             "The layers were combined " +
-            (sourcePoints.length === 0
-              ? "without any transforms"
-              : `with ${useThinPlateSplines
-                ? `Thin-Plate-Splines (${sourcePoints.length} correspondences)`
-                : `an affine transformation (mean error: ${formatNumber(
-                  affineMeanError.meanError,
-                )} vx)`
-              }`) +
-            ".",
+              (sourcePoints.length === 0
+                ? "without any transforms"
+                : `with ${
+                    useThinPlateSplines
+                      ? `Thin-Plate-Splines (${sourcePoints.length} correspondences)`
+                      : `an affine transformation (mean error: ${formatNumber(
+                          affineMeanError.meanError,
+                        )} vx)`
+                  }`) +
+              ".",
           ].join("\n"),
         },
       );

From 4bab1a9fba755e62d25e12be69b8feac18bde9dc Mon Sep 17 00:00:00 2001
From: Philipp Otto <philipp.4096@gmail.com>
Date: Thu, 22 Aug 2024 09:26:02 +0200
Subject: [PATCH 19/19] fix cyclic dependency

---
 .../composition_wizard/04_configure_new_dataset.tsx |  8 ++------
 frontend/javascripts/libs/toast.tsx                 | 13 +++++++++++++
 frontend/javascripts/libs/utils.ts                  | 12 ------------
 3 files changed, 15 insertions(+), 18 deletions(-)

diff --git a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
index 760387ecb3a..3f6689a6a74 100644
--- a/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
+++ b/frontend/javascripts/admin/dataset/composition_wizard/04_configure_new_dataset.tsx
@@ -9,7 +9,7 @@ import { Button, Checkbox, Col, Form, FormInstance, Input, List, Modal, Row, Too
 import { FormItemWithInfo } from "dashboard/dataset/helper_components";
 import FolderSelection from "dashboard/folders/folder_selection";
 import { estimateAffineMatrix4x4 } from "libs/estimate_affine";
-import Toast from "libs/toast";
+import Toast, { guardedWithErrorToast } from "libs/toast";
 import * as Utils from "libs/utils";
 import _ from "lodash";
 import messages from "messages";
@@ -209,11 +209,7 @@ export function ConfigureNewDataset(props: WizardComponentProps) {
     // Using Forms here only to validate fields and for easy layout
     <div style={{ padding: 5 }}>
       <p>Please configure the dataset that is about to be created.</p>
-      <Form
-        form={form}
-        layout="vertical"
-        onFinish={() => Utils.guardedWithErrorToast(handleSubmit)}
-      >
+      <Form form={form} layout="vertical" onFinish={() => guardedWithErrorToast(handleSubmit)}>
         <Row gutter={8}>
           <Col span={12}>
             <DatasetNameFormItem activeUser={activeUser} />
diff --git a/frontend/javascripts/libs/toast.tsx b/frontend/javascripts/libs/toast.tsx
index 4afbc5664c1..e8e210397a1 100644
--- a/frontend/javascripts/libs/toast.tsx
+++ b/frontend/javascripts/libs/toast.tsx
@@ -35,6 +35,19 @@ type ToastParams = {
   details?: string;
 };
 
+export async function guardedWithErrorToast(fn: () => Promise<any>) {
+  try {
+    await fn();
+  } catch (error) {
+    import("libs/error_handling").then((_ErrorHandling) => {
+      const ErrorHandling = _ErrorHandling.default;
+      Toast.error("An unexpected error occurred. Please check the console for details");
+      console.error(error);
+      ErrorHandling.notify(error as Error);
+    });
+  }
+}
+
 const Toast = {
   // The notificationAPI is designed to be a singleton spawned by the ToastContextMountRoot
   // mounted in the GlobalThemeProvider.
diff --git a/frontend/javascripts/libs/utils.ts b/frontend/javascripts/libs/utils.ts
index 0128578f401..dd146d2277e 100644
--- a/frontend/javascripts/libs/utils.ts
+++ b/frontend/javascripts/libs/utils.ts
@@ -16,8 +16,6 @@ import type {
 import window, { document, location } from "libs/window";
 import { ArbitraryObject, Comparator } from "types/globals";
 import dayjs from "dayjs";
-import Toast from "./toast";
-import ErrorHandling from "libs/error_handling";
 
 type UrlParams = Record<string, string>;
 // Fix JS modulo bug
@@ -1302,13 +1300,3 @@ export function generateRandomId(length: number) {
   }
   return result;
 }
-
-export async function guardedWithErrorToast(fn: () => Promise<any>) {
-  try {
-    await fn();
-  } catch (error) {
-    Toast.error("An unexpected error occurred. Please check the console for details");
-    console.error(error);
-    ErrorHandling.notify(error as Error);
-  }
-}