From 071bd28934c06f4003f763bee5e88f6ef103ed02 Mon Sep 17 00:00:00 2001
From: Jo-Byr <jonathanbouyer24@gmail.com>
Date: Thu, 3 Jul 2025 16:02:53 +0200
Subject: [PATCH 1/5] Add multi-segment nifti export support

Modify nifti exporter to create an additional nifti file that contains
all segments of the annotated volume
---
 darwin/exporter/formats/nifti.py              |  13 +-
 .../coronal_LAS_pixdim_0.1_0.2_0.5.json       | 257 ++++++++++++++++++
 .../nifti/multi_segment/ground_truth.nii.gz   | Bin 0 -> 670 bytes
 .../exporter/formats/export_darwin_test.py    |  37 ++-
 4 files changed, 305 insertions(+), 2 deletions(-)
 create mode 100644 tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5.json
 create mode 100644 tests/darwin/data/nifti/multi_segment/ground_truth.nii.gz

diff --git a/darwin/exporter/formats/nifti.py b/darwin/exporter/formats/nifti.py
index 396f49743..b7c80854c 100644
--- a/darwin/exporter/formats/nifti.py
+++ b/darwin/exporter/formats/nifti.py
@@ -58,13 +58,18 @@ class Volume:
     primary_plane: str
 
 
+# Unique ID and file suffix for the "All segments" volume
+multi_segments_label = "0"
+multi_segments_name = "Segments"
+
+
 def export(
     annotation_files: Iterable[dt.AnnotationFile],
     output_dir: Path,
 ) -> None:
     """
     Exports the given ``AnnotationFile``\\s into nifti format inside of the given
-    ``output_dir``. Deletes everything within ``output_dir/masks`` before writting to it.
+    ``output_dir``. Deletes everything within ``output_dir/masks`` before writing to it.
 
     Parameters
     ----------
@@ -146,6 +151,8 @@ def export(
                     for ann in slot_annotations
                     if ann.annotation_class.annotation_type == "mask"
                 }
+                # Add a unique ID for the "All segments" volume
+                mask_id_to_classname[multi_segments_label] = multi_segments_name
                 raster_output_volumes = build_output_volumes(
                     slot,
                     class_names_to_export=list(mask_id_to_classname.values()),
@@ -497,6 +504,10 @@ def populate_output_volumes_from_raster_layer(
             volume[class_name].pixel_array = np.where(
                 multilabel_volume == global_id, 1, volume[class_name].pixel_array
             )
+        elif mask_id == multi_segments_label:
+            # Unique ID for "All segments":
+            volume = output_volumes[series_instance_uid]
+            volume[multi_segments_name].pixel_array = multilabel_volume
 
     return volume
 
diff --git a/tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5.json b/tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5.json
new file mode 100644
index 000000000..13e182cb1
--- /dev/null
+++ b/tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5.json
@@ -0,0 +1,257 @@
+{
+  "version": "2.0",
+  "schema_ref": "https://darwin-public.s3.eu-west-1.amazonaws.com/darwin_json/2.0/schema.json",
+  "item": {
+    "name": "coronal_LAS_pixdim_0.1_0.2_0.5.dcm",
+    "path": "/",
+    "source_info": {
+      "item_id": "01951442-3873-46c2-7373-30e56050d853",
+      "dataset": {
+        "name": "dicom_test_data",
+        "slug": "dicom_test_data",
+        "dataset_management_url": "https://darwin.v7labs.com/datasets/1643259/dataset-management"
+      },
+      "team": {
+        "name": "V7 John",
+        "slug": "v7-john"
+      },
+      "workview_url": "https://darwin.v7labs.com/workview?dataset=1643259&item=01951442-3873-46c2-7373-30e56050d853"
+    },
+    "slots": [
+      {
+        "type": "dicom",
+        "slot_name": "0",
+        "width": 128,
+        "height": 128,
+        "fps": null,
+        "thumbnail_url": "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/thumbnail?token=642eedac-c980-4747-8dca-cba51e52dec1",
+        "source_files": [
+          {
+            "file_name": "coronal_LAS_pixdim_0.1_0.2_0.5.dcm",
+            "url": "https://darwin.v7labs.com/api/v2/teams/v7-john/uploads/100f98aa-6917-42a0-891e-bdd692950e49?token=642eedac-c980-4747-8dca-cba51e52dec1"
+          }
+        ],
+        "frame_count": 16,
+        "frame_urls": [
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/0?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/1?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/2?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/3?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/4?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/5?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/6?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/7?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/8?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/9?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/10?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/11?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/12?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/13?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/14?token=642eedac-c980-4747-8dca-cba51e52dec1",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/15?token=642eedac-c980-4747-8dca-cba51e52dec1"
+        ],
+        "metadata": {
+          "handler": "MONAI",
+          "shape": [
+            1,
+            128,
+            16,
+            128
+          ],
+          "SeriesInstanceUID": "1.2.826.0.1.3680043.8.498.10392093638286046303269310577715221690",
+          "affine": "[[-0.1, 0.0, 0.0, 0.0], [0.0, -1.0, 0.0, 0.0], [0.0, 0.0, -0.25, 31.75], [0.0, 0.0, 0.0, 1.0]]",
+          "colorspace": "RG16",
+          "original_affine": [
+            [
+              "-0.1",
+              "0.0",
+              "0.0",
+              "0.0"
+            ],
+            [
+              "0.0",
+              "0.0",
+              "-1.0",
+              "0.0"
+            ],
+            [
+              "0.0",
+              "0.25",
+              "0.0",
+              "0.0"
+            ],
+            [
+              "0.0",
+              "0.0",
+              "0.0",
+              "1.0"
+            ]
+          ],
+          "pixdim": "(0.1, 1.0, 0.25)",
+          "plane_map": {
+            "0": "CORONAL"
+          },
+          "primary_plane": "CORONAL"
+        }
+      }
+    ]
+  },
+  "annotations": [
+    {
+      "frames": {
+        "15": {
+          "keyframe": true,
+          "mask": {}
+        }
+      },
+      "id": "cce036e7-dcc2-46de-ab71-4e20beb94459",
+      "interpolate_algorithm": "linear-1.1",
+      "name": "mask1",
+      "only_keyframes": true,
+      "properties": [],
+      "ranges": [
+        [
+          15,
+          16
+        ]
+      ],
+      "slot_names": [
+        "0"
+      ]
+    },
+    {
+      "frames": {
+        "15": {
+          "keyframe": true,
+          "mask": {}
+        }
+      },
+      "id": "beffc847-da35-4937-b4a1-a1e16994cfc8",
+      "interpolate_algorithm": "linear-1.1",
+      "name": "mask2",
+      "only_keyframes": true,
+      "properties": [],
+      "ranges": [
+        [
+          15,
+          16
+        ]
+      ],
+      "slot_names": [
+        "0"
+      ]
+    },
+    {
+      "frames": {
+        "15": {
+          "keyframe": true,
+          "raster_layer": {
+            "dense_rle": [
+              0,
+              6184,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              7736
+            ],
+            "mask_annotation_ids_mapping": {
+              "81b795d7-0f12-4951-a2dc-0bd06af0aa6e": 1,
+              "dec395da-9478-476e-921e-4a4750ba413f": 2
+            },
+            "total_pixels": 16384
+          }
+        }
+      },
+      "id": "7fe1310e-8a4d-457c-815a-e34276366d0d",
+      "name": "__raster_layer__",
+      "only_keyframes": true,
+      "properties": [],
+      "ranges": [
+        [
+          0,
+          16
+        ]
+      ],
+      "slot_names": [
+        "0"
+      ]
+    }
+  ],
+  "properties": []
+}
\ No newline at end of file
diff --git a/tests/darwin/data/nifti/multi_segment/ground_truth.nii.gz b/tests/darwin/data/nifti/multi_segment/ground_truth.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..5e0eddacbb2f3e8d969e7d73bee1d66db519b132
GIT binary patch
literal 670
zcmb2|=3oE=?ziU;@-`VTI9zPvc_25>rXqxI-9sL^ISZ6`HY766ImW6Z82G4_#YW&>
z_ADpwhWb;77^ZLFGVCoqaqD9ElF4ps-j(k4f30}-(|6nJkFVF+JvsgV%exAZ-J52<
zG}>moq%Zn+#P;t|$zONoTkYOF?{k{<&;Lvin@7pv9|C7Q?TXIKt^51y>+9?5<Nsg!
gwRvLlyDuR2exTs=Yy3z-;Pal7(c&<30wV_l0M<xXApigX

literal 0
HcmV?d00001

diff --git a/tests/darwin/exporter/formats/export_darwin_test.py b/tests/darwin/exporter/formats/export_darwin_test.py
index 487145269..d2dd7557a 100644
--- a/tests/darwin/exporter/formats/export_darwin_test.py
+++ b/tests/darwin/exporter/formats/export_darwin_test.py
@@ -1,13 +1,17 @@
+import shutil
 import tempfile
 import zipfile
 from pathlib import Path
+import nibabel as nib
+import numpy as np
 
 from darwin.datatypes import Annotation, AnnotationClass, AnnotationFile
 from darwin.exporter.formats.darwin import (
     _build_v2_annotation_data,
     build_image_annotation,
 )
-from darwin.utils import get_annotation_files_from_dir
+from darwin.exporter.formats.nifti import export
+from darwin.utils import get_annotation_files_from_dir, parse_darwin_json
 
 
 def test_empty_annotation_file_v2():
@@ -142,3 +146,34 @@ def test_properties_metadata_is_ignored_when_reading_annotations_directory():
         for annotation_filepath in annotation_filepaths:
             assert "./v7/" not in annotation_filepath
             assert "\\.v7\\" not in annotation_filepath
+
+
+def test_multi_segment_nifti_export():
+    work_dir = Path("tests/darwin/data/nifti/multi_segment")
+    ground_truth_path = work_dir.joinpath("ground_truth.nii.gz")
+    darwin_json_path = work_dir.joinpath("coronal_LAS_pixdim_0.1_0.2_0.5.json")
+    target_output_directory = work_dir.joinpath("output")
+    target_output_path = target_output_directory.joinpath(
+        "coronal_LAS_pixdim_0.1_0.2_0.5",
+        "0",
+        "coronal_LAS_pixdim_0.1_0.2_0_Segments_m.nii.gz"
+    )
+
+    try:
+        # Convert darwin json to nifti
+        annotation_file = parse_darwin_json(darwin_json_path)
+        assert annotation_file is not None
+        export([annotation_file], target_output_directory)
+
+        # Compare exported nifti to ground truth
+        ground_truth = nib.load(ground_truth_path.absolute().as_posix())
+        ground_truth_array = ground_truth.get_fdata()
+
+        nifti = nib.load(target_output_path)
+        nifti_array = nifti.get_fdata()
+
+        assert np.array_equal(nifti_array, ground_truth_array)
+
+    finally:
+        # Delete produced nifti
+        shutil.rmtree(target_output_directory.absolute().as_posix())

From b83955c3b4d0cc210a302aa3b06c5a39f61dbcdf Mon Sep 17 00:00:00 2001
From: Jo-Byr <jonathanbouyer24@gmail.com>
Date: Wed, 9 Jul 2025 10:04:45 +0200
Subject: [PATCH 2/5] Fix pixel offset in test data and add tests

Fix pixel offset in anisotropic test data
Add sagittal and axial test data
---
 .../axial_RPI_pixdim_1.0_1.0_1.0/darwin.json  | 259 ++++++++++++++++++
 .../ground_truth.nii.gz                       | Bin 0 -> 653 bytes
 .../darwin.json}                              |  58 ++--
 .../ground_truth.nii.gz                       | Bin
 .../darwin.json                               | 259 ++++++++++++++++++
 .../ground_truth.nii.gz                       | Bin 0 -> 664 bytes
 .../exporter/formats/export_darwin_test.py    |  62 +++--
 7 files changed, 582 insertions(+), 56 deletions(-)
 create mode 100644 tests/darwin/data/nifti/multi_segment/axial_RPI_pixdim_1.0_1.0_1.0/darwin.json
 create mode 100644 tests/darwin/data/nifti/multi_segment/axial_RPI_pixdim_1.0_1.0_1.0/ground_truth.nii.gz
 rename tests/darwin/data/nifti/multi_segment/{coronal_LAS_pixdim_0.1_0.2_0.5.json => coronal_LAS_pixdim_0.1_0.2_0.5/darwin.json} (71%)
 rename tests/darwin/data/nifti/multi_segment/{ => coronal_LAS_pixdim_0.1_0.2_0.5}/ground_truth.nii.gz (100%)
 create mode 100644 tests/darwin/data/nifti/multi_segment/sagittal_LPI_pixdim_0.1_0.2_0.5/darwin.json
 create mode 100644 tests/darwin/data/nifti/multi_segment/sagittal_LPI_pixdim_0.1_0.2_0.5/ground_truth.nii.gz

diff --git a/tests/darwin/data/nifti/multi_segment/axial_RPI_pixdim_1.0_1.0_1.0/darwin.json b/tests/darwin/data/nifti/multi_segment/axial_RPI_pixdim_1.0_1.0_1.0/darwin.json
new file mode 100644
index 000000000..7c64e0c0b
--- /dev/null
+++ b/tests/darwin/data/nifti/multi_segment/axial_RPI_pixdim_1.0_1.0_1.0/darwin.json
@@ -0,0 +1,259 @@
+{
+  "version": "2.0",
+  "schema_ref": "https://darwin-public.s3.eu-west-1.amazonaws.com/darwin_json/2.0/schema.json",
+  "item": {
+    "name": "axial_RPI_pixdim_1.0_1.0_1.0.dcm",
+    "path": "/",
+    "source_info": {
+      "item_id": "0197ee1d-591e-a61b-82e2-e6f1e5c30cf2",
+      "dataset": {
+        "name": "dicom_test_data_new",
+        "slug": "dicom_test_data_new",
+        "dataset_management_url": "https://darwin.v7labs.com/datasets/1856922/dataset-management"
+      },
+      "team": {
+        "name": "V7 John",
+        "slug": "v7-john"
+      },
+      "workview_url": "https://darwin.v7labs.com/workview?dataset=1856922&item=0197ee1d-591e-a61b-82e2-e6f1e5c30cf2"
+    },
+    "slots": [
+      {
+        "type": "dicom",
+        "slot_name": "0",
+        "width": 128,
+        "height": 128,
+        "fps": null,
+        "thumbnail_url": "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/thumbnail?token=590de404-3490-4dde-90f9-d13136b0d14f",
+        "source_files": [
+          {
+            "file_name": "axial_RPI_pixdim_1.0_1.0_1.0.dcm",
+            "url": "https://darwin.v7labs.com/api/v2/teams/v7-john/uploads/d4f4e7cd-e8a8-407f-9ff3-0a1f3298c84c?token=590de404-3490-4dde-90f9-d13136b0d14f"
+          }
+        ],
+        "frame_count": 16,
+        "frame_urls": [
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/0?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/1?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/2?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/3?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/4?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/5?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/6?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/7?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/8?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/9?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/10?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/11?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/12?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/13?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/14?token=590de404-3490-4dde-90f9-d13136b0d14f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/243d7c36-d767-4e3c-adb0-44324ebd14fe/sections/15?token=590de404-3490-4dde-90f9-d13136b0d14f"
+        ],
+        "metadata": {
+          "handler": "MONAI",
+          "shape": [
+            1,
+            128,
+            128,
+            16
+          ],
+          "SeriesInstanceUID": "1.2.826.0.1.3680043.8.498.37180825650614764423282910493086149224",
+          "affine": "[[-1.0, 0.0, 0.0, 127.0], [0.0, -1.0, 0.0, 0.0], [0.0, 0.0, -1.0, 15.0], [0.0, 0.0, 0.0, 1.0]]",
+          "colorspace": "RG16",
+          "original_affine": [
+            [
+              "1.0",
+              "0.0",
+              "0.0",
+              "0.0"
+            ],
+            [
+              "0.0",
+              "-1.0",
+              "0.0",
+              "0.0"
+            ],
+            [
+              "0.0",
+              "0.0",
+              "1.0",
+              "0.0"
+            ],
+            [
+              "0.0",
+              "0.0",
+              "0.0",
+              "1.0"
+            ]
+          ],
+          "pixdim": "(1.0, 1.0, 1.0)",
+          "plane_map": {
+            "0": "AXIAL"
+          },
+          "primary_plane": "AXIAL"
+        }
+      }
+    ]
+  },
+  "annotations": [
+    {
+      "frames": {
+        "15": {
+          "keyframe": true,
+          "mask": {}
+        }
+      },
+      "global_sub_types": {},
+      "id": "02c693fa-97f5-4a3c-9c45-e1d9eebb0731",
+      "interpolate_algorithm": "linear-1.1",
+      "name": "mask1",
+      "only_keyframes": true,
+      "properties": [],
+      "ranges": [
+        [
+          15,
+          16
+        ]
+      ],
+      "slot_names": [
+        "0"
+      ]
+    },
+    {
+      "frames": {
+        "15": {
+          "keyframe": true,
+          "mask": {}
+        }
+      },
+      "global_sub_types": {},
+      "id": "d212f8a6-8e09-4901-a44b-77745626edc9",
+      "interpolate_algorithm": "linear-1.1",
+      "name": "mask2",
+      "only_keyframes": true,
+      "properties": [],
+      "ranges": [
+        [
+          15,
+          16
+        ]
+      ],
+      "slot_names": [
+        "0"
+      ]
+    },
+    {
+      "frames": {
+        "15": {
+          "keyframe": true,
+          "raster_layer": {
+            "dense_rle": [
+              0,
+              2104,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              11816
+            ],
+            "mask_annotation_ids_mapping": {
+              "02c693fa-97f5-4a3c-9c45-e1d9eebb0731": 1,
+              "d212f8a6-8e09-4901-a44b-77745626edc9": 2
+            },
+            "total_pixels": 16384
+          }
+        }
+      },
+      "id": "a15c3b3e-89af-4733-b6c7-10f01e2c0b57",
+      "name": "__raster_layer__",
+      "only_keyframes": true,
+      "properties": [],
+      "ranges": [
+        [
+          0,
+          16
+        ]
+      ],
+      "slot_names": [
+        "0"
+      ]
+    }
+  ],
+  "properties": []
+}
\ No newline at end of file
diff --git a/tests/darwin/data/nifti/multi_segment/axial_RPI_pixdim_1.0_1.0_1.0/ground_truth.nii.gz b/tests/darwin/data/nifti/multi_segment/axial_RPI_pixdim_1.0_1.0_1.0/ground_truth.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..be0895e8903618749dfe854a37224cb063fcdddc
GIT binary patch
literal 653
zcmb2|=3oE=?ziX9avm~}Xn459s-e1~h>3sQLms&~3d%bj!;Swg?ClCzA?G#kxpKfI
zhfi_I5f9|b6rWnQSe#p3`|q-6Zrt<Az11;Yf74E${clq8<-O<Quvz<;|4k~by}UDE
z&hG;2d38U6fc7j<D}0(Wx9;z+udlDKkFU@Dd-l{#D=2UOzgxc;A&wa(M@|Urt7MvU
L&~9S_BL@QjIF(PO

literal 0
HcmV?d00001

diff --git a/tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5.json b/tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5/darwin.json
similarity index 71%
rename from tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5.json
rename to tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5/darwin.json
index 13e182cb1..e42e9e8d3 100644
--- a/tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5.json
+++ b/tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5/darwin.json
@@ -5,17 +5,17 @@
     "name": "coronal_LAS_pixdim_0.1_0.2_0.5.dcm",
     "path": "/",
     "source_info": {
-      "item_id": "01951442-3873-46c2-7373-30e56050d853",
+      "item_id": "0197ee1d-591e-7d19-bb01-65d27fb0bcdd",
       "dataset": {
-        "name": "dicom_test_data",
-        "slug": "dicom_test_data",
-        "dataset_management_url": "https://darwin.v7labs.com/datasets/1643259/dataset-management"
+        "name": "dicom_test_data_new",
+        "slug": "dicom_test_data_new",
+        "dataset_management_url": "https://darwin.v7labs.com/datasets/1856922/dataset-management"
       },
       "team": {
         "name": "V7 John",
         "slug": "v7-john"
       },
-      "workview_url": "https://darwin.v7labs.com/workview?dataset=1643259&item=01951442-3873-46c2-7373-30e56050d853"
+      "workview_url": "https://darwin.v7labs.com/workview?dataset=1856922&item=0197ee1d-591e-7d19-bb01-65d27fb0bcdd"
     },
     "slots": [
       {
@@ -24,31 +24,31 @@
         "width": 128,
         "height": 128,
         "fps": null,
-        "thumbnail_url": "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/thumbnail?token=642eedac-c980-4747-8dca-cba51e52dec1",
+        "thumbnail_url": "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/thumbnail?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
         "source_files": [
           {
             "file_name": "coronal_LAS_pixdim_0.1_0.2_0.5.dcm",
-            "url": "https://darwin.v7labs.com/api/v2/teams/v7-john/uploads/100f98aa-6917-42a0-891e-bdd692950e49?token=642eedac-c980-4747-8dca-cba51e52dec1"
+            "url": "https://darwin.v7labs.com/api/v2/teams/v7-john/uploads/bbf2147d-e328-4a93-a624-90f9c474a071?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f"
           }
         ],
         "frame_count": 16,
         "frame_urls": [
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/0?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/1?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/2?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/3?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/4?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/5?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/6?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/7?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/8?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/9?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/10?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/11?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/12?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/13?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/14?token=642eedac-c980-4747-8dca-cba51e52dec1",
-          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b9d93da4-37dc-4af4-825e-41b9899bf799/sections/15?token=642eedac-c980-4747-8dca-cba51e52dec1"
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/0?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/1?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/2?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/3?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/4?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/5?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/6?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/7?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/8?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/9?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/10?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/11?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/12?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/13?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/14?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/b33547f6-c281-4766-97cf-1623f00353f5/sections/15?token=971b08d7-a0d7-4d95-a22f-f1f7429b207f"
         ],
         "metadata": {
           "handler": "MONAI",
@@ -104,7 +104,8 @@
           "mask": {}
         }
       },
-      "id": "cce036e7-dcc2-46de-ab71-4e20beb94459",
+      "global_sub_types": {},
+      "id": "0a8b3cfb-d6ff-427a-8b3e-a31410f10331",
       "interpolate_algorithm": "linear-1.1",
       "name": "mask1",
       "only_keyframes": true,
@@ -126,7 +127,8 @@
           "mask": {}
         }
       },
-      "id": "beffc847-da35-4937-b4a1-a1e16994cfc8",
+      "global_sub_types": {},
+      "id": "0e845870-995b-4cb7-982e-741c1e54109e",
       "interpolate_algorithm": "linear-1.1",
       "name": "mask2",
       "only_keyframes": true,
@@ -231,14 +233,14 @@
               7736
             ],
             "mask_annotation_ids_mapping": {
-              "81b795d7-0f12-4951-a2dc-0bd06af0aa6e": 1,
-              "dec395da-9478-476e-921e-4a4750ba413f": 2
+              "0a8b3cfb-d6ff-427a-8b3e-a31410f10331": 1,
+              "0e845870-995b-4cb7-982e-741c1e54109e": 2
             },
             "total_pixels": 16384
           }
         }
       },
-      "id": "7fe1310e-8a4d-457c-815a-e34276366d0d",
+      "id": "1af4d613-c4c4-41cd-a53a-2e8905f90b95",
       "name": "__raster_layer__",
       "only_keyframes": true,
       "properties": [],
diff --git a/tests/darwin/data/nifti/multi_segment/ground_truth.nii.gz b/tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5/ground_truth.nii.gz
similarity index 100%
rename from tests/darwin/data/nifti/multi_segment/ground_truth.nii.gz
rename to tests/darwin/data/nifti/multi_segment/coronal_LAS_pixdim_0.1_0.2_0.5/ground_truth.nii.gz
diff --git a/tests/darwin/data/nifti/multi_segment/sagittal_LPI_pixdim_0.1_0.2_0.5/darwin.json b/tests/darwin/data/nifti/multi_segment/sagittal_LPI_pixdim_0.1_0.2_0.5/darwin.json
new file mode 100644
index 000000000..b757dee96
--- /dev/null
+++ b/tests/darwin/data/nifti/multi_segment/sagittal_LPI_pixdim_0.1_0.2_0.5/darwin.json
@@ -0,0 +1,259 @@
+{
+  "version": "2.0",
+  "schema_ref": "https://darwin-public.s3.eu-west-1.amazonaws.com/darwin_json/2.0/schema.json",
+  "item": {
+    "name": "sagittal_LPI_pixdim_0.1_0.2_0.5.dcm",
+    "path": "/",
+    "source_info": {
+      "item_id": "0197ee1d-5920-c9f8-017f-987b38e38f5f",
+      "dataset": {
+        "name": "dicom_test_data_new",
+        "slug": "dicom_test_data_new",
+        "dataset_management_url": "https://darwin.v7labs.com/datasets/1856922/dataset-management"
+      },
+      "team": {
+        "name": "V7 John",
+        "slug": "v7-john"
+      },
+      "workview_url": "https://darwin.v7labs.com/workview?dataset=1856922&item=0197ee1d-5920-c9f8-017f-987b38e38f5f"
+    },
+    "slots": [
+      {
+        "type": "dicom",
+        "slot_name": "0",
+        "width": 128,
+        "height": 128,
+        "fps": null,
+        "thumbnail_url": "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/thumbnail?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+        "source_files": [
+          {
+            "file_name": "sagittal_LPI_pixdim_0.1_0.2_0.5.dcm",
+            "url": "https://darwin.v7labs.com/api/v2/teams/v7-john/uploads/54adbf48-0129-44ea-978c-313aeb35627b?token=4ca42b77-ad16-42ce-82e1-e9c762085012"
+          }
+        ],
+        "frame_count": 16,
+        "frame_urls": [
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/0?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/1?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/2?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/3?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/4?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/5?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/6?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/7?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/8?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/9?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/10?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/11?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/12?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/13?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/14?token=4ca42b77-ad16-42ce-82e1-e9c762085012",
+          "https://darwin.v7labs.com/api/v2/teams/v7-john/files/c160652a-9d74-4a27-91f5-158bd68eab2c/sections/15?token=4ca42b77-ad16-42ce-82e1-e9c762085012"
+        ],
+        "metadata": {
+          "handler": "MONAI",
+          "shape": [
+            1,
+            16,
+            128,
+            128
+          ],
+          "SeriesInstanceUID": "1.2.826.0.1.3680043.8.498.16951377570626244557338024182864652772",
+          "affine": "[[-1.0, 0.0, 0.0, 15.0], [0.0, -0.1, 0.0, 0.0], [0.0, 0.0, -0.25, 0.0], [0.0, 0.0, 0.0, 1.0]]",
+          "colorspace": "RG16",
+          "original_affine": [
+            [
+              "0.0",
+              "0.0",
+              "1.0",
+              "0.0"
+            ],
+            [
+              "-0.1",
+              "0.0",
+              "0.0",
+              "0.0"
+            ],
+            [
+              "0.0",
+              "-0.25",
+              "0.0",
+              "0.0"
+            ],
+            [
+              "0.0",
+              "0.0",
+              "0.0",
+              "1.0"
+            ]
+          ],
+          "pixdim": "(1.0, 0.1, 0.25)",
+          "plane_map": {
+            "0": "SAGITTAL"
+          },
+          "primary_plane": "SAGITTAL"
+        }
+      }
+    ]
+  },
+  "annotations": [
+    {
+      "frames": {
+        "15": {
+          "keyframe": true,
+          "mask": {}
+        }
+      },
+      "global_sub_types": {},
+      "id": "2d12dc2e-5cc5-4bb7-89ce-5f010fc0f184",
+      "interpolate_algorithm": "linear-1.1",
+      "name": "mask1",
+      "only_keyframes": true,
+      "properties": [],
+      "ranges": [
+        [
+          15,
+          16
+        ]
+      ],
+      "slot_names": [
+        "0"
+      ]
+    },
+    {
+      "frames": {
+        "15": {
+          "keyframe": true,
+          "mask": {}
+        }
+      },
+      "global_sub_types": {},
+      "id": "97117be2-ae2e-4431-bcd3-5dd724121489",
+      "interpolate_algorithm": "linear-1.1",
+      "name": "mask2",
+      "only_keyframes": true,
+      "properties": [],
+      "ranges": [
+        [
+          15,
+          16
+        ]
+      ],
+      "slot_names": [
+        "0"
+      ]
+    },
+    {
+      "frames": {
+        "15": {
+          "keyframe": true,
+          "raster_layer": {
+            "dense_rle": [
+              0,
+              2088,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              1,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              96,
+              2,
+              32,
+              0,
+              11832
+            ],
+            "mask_annotation_ids_mapping": {
+              "2d12dc2e-5cc5-4bb7-89ce-5f010fc0f184": 1,
+              "97117be2-ae2e-4431-bcd3-5dd724121489": 2
+            },
+            "total_pixels": 16384
+          }
+        }
+      },
+      "id": "c41d3017-793b-41f8-b9be-fa95d2e505ef",
+      "name": "__raster_layer__",
+      "only_keyframes": true,
+      "properties": [],
+      "ranges": [
+        [
+          0,
+          16
+        ]
+      ],
+      "slot_names": [
+        "0"
+      ]
+    }
+  ],
+  "properties": []
+}
\ No newline at end of file
diff --git a/tests/darwin/data/nifti/multi_segment/sagittal_LPI_pixdim_0.1_0.2_0.5/ground_truth.nii.gz b/tests/darwin/data/nifti/multi_segment/sagittal_LPI_pixdim_0.1_0.2_0.5/ground_truth.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..6d281de98974061c08b594ef51c189f7b33520a5
GIT binary patch
literal 664
zcmb2|=3oE=?ziU;@-`VrG+Y#uJz#5N*-%u#oBrVei|k3(E35_T-75u?Jv=TjKiq4-
zq(yD%eZ@9LzeK^Hd7&MtcDkSaw6A_&cJo>3^?mj8i|>{13wQqa$A9VLY4dljS!wfd
zuig9EMc0>Z{(o!tx4E@3`E@nXKr0jU9-WwJ_4n7;*Vos_@Bg>+Yq)ayt1n<q-QQo&
Zukl0NHA;@05V-K1@ss3=xCBNH1^^69Q@{WK

literal 0
HcmV?d00001

diff --git a/tests/darwin/exporter/formats/export_darwin_test.py b/tests/darwin/exporter/formats/export_darwin_test.py
index d2dd7557a..395606a19 100644
--- a/tests/darwin/exporter/formats/export_darwin_test.py
+++ b/tests/darwin/exporter/formats/export_darwin_test.py
@@ -149,31 +149,37 @@ def test_properties_metadata_is_ignored_when_reading_annotations_directory():
 
 
 def test_multi_segment_nifti_export():
-    work_dir = Path("tests/darwin/data/nifti/multi_segment")
-    ground_truth_path = work_dir.joinpath("ground_truth.nii.gz")
-    darwin_json_path = work_dir.joinpath("coronal_LAS_pixdim_0.1_0.2_0.5.json")
-    target_output_directory = work_dir.joinpath("output")
-    target_output_path = target_output_directory.joinpath(
-        "coronal_LAS_pixdim_0.1_0.2_0.5",
-        "0",
-        "coronal_LAS_pixdim_0.1_0.2_0_Segments_m.nii.gz"
-    )
-
-    try:
-        # Convert darwin json to nifti
-        annotation_file = parse_darwin_json(darwin_json_path)
-        assert annotation_file is not None
-        export([annotation_file], target_output_directory)
-
-        # Compare exported nifti to ground truth
-        ground_truth = nib.load(ground_truth_path.absolute().as_posix())
-        ground_truth_array = ground_truth.get_fdata()
-
-        nifti = nib.load(target_output_path)
-        nifti_array = nifti.get_fdata()
-
-        assert np.array_equal(nifti_array, ground_truth_array)
-
-    finally:
-        # Delete produced nifti
-        shutil.rmtree(target_output_directory.absolute().as_posix())
+    root_dir = Path("tests/darwin/data/nifti/multi_segment")
+    for subdir in root_dir.iterdir():
+        if not subdir.is_dir():
+            continue
+        print(subdir)
+        
+        ground_truth_path = subdir.joinpath("ground_truth.nii.gz")
+        darwin_json_path = subdir.joinpath("darwin.json")
+        target_output_directory = subdir.joinpath("output")
+        volume_name = subdir.parts[-1]
+        target_output_path = target_output_directory.joinpath(
+            "darwin",
+            "0",
+            f"{volume_name[:-2]}_Segments_m.nii.gz"
+        )
+
+        try:
+            # Convert darwin json to nifti
+            annotation_file = parse_darwin_json(darwin_json_path)
+            assert annotation_file is not None
+            export([annotation_file], target_output_directory)
+
+            # Compare exported nifti to ground truth
+            ground_truth = nib.load(ground_truth_path.absolute().as_posix())
+            ground_truth_array = ground_truth.get_fdata()
+
+            nifti = nib.load(target_output_path)
+            nifti_array = nifti.get_fdata()
+
+            assert np.array_equal(nifti_array, ground_truth_array)
+
+        finally:
+            # Delete produced nifti
+            shutil.rmtree(target_output_directory.absolute().as_posix())

From 5afdfceac1c88b1c0958c500a5c01825bb78cd67 Mon Sep 17 00:00:00 2001
From: Jo-Byr <jonathanbouyer24@gmail.com>
Date: Thu, 10 Jul 2025 16:10:48 +0200
Subject: [PATCH 3/5] Add multi-label nifti import test

Add test ensuring correct import of multi-label nifti file, by asserting
no error is produced in the process, and that the number of unique
values in the produced array is coherent with the nifti file
---
 .../darwin/importer/formats/import_nifti_test.py  | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/tests/darwin/importer/formats/import_nifti_test.py b/tests/darwin/importer/formats/import_nifti_test.py
index 11632ec58..44bdbb4dc 100644
--- a/tests/darwin/importer/formats/import_nifti_test.py
+++ b/tests/darwin/importer/formats/import_nifti_test.py
@@ -610,3 +610,18 @@ def test_parse_path_nifti_without_legacy_scaling():
             parsed_annotation, decimal_places=4
         )
         assert expected_annotation_rounded == parsed_annotation_rounded
+
+
+def test_image_annotation_nifti_multi_label():
+    root_dir = Path("tests/darwin/data/nifti/multi_segment")
+    for subdir in root_dir.iterdir():
+        if not subdir.is_dir():
+            continue
+        print(subdir)
+
+        nifti_file_path = subdir.joinpath("ground_truth.nii.gz")
+        nifti_image = nib.load(nifti_file_path)
+        data_array = process_nifti(nifti_image)
+
+        # Assert correct conversion with presence of 3 values (background and 2 labels)
+        assert data_array is not None and len(np.unique(data_array)) == 3

From ef78db4b1f28aa46eba7d01ed57242ee103aea33 Mon Sep 17 00:00:00 2001
From: Valentin Vikhorev <vvihorevv@gmail.com>
Date: Thu, 24 Jul 2025 16:29:13 +0200
Subject: [PATCH 4/5] black formatting

---
 tests/darwin/exporter/formats/export_darwin_test.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/darwin/exporter/formats/export_darwin_test.py b/tests/darwin/exporter/formats/export_darwin_test.py
index 395606a19..b3e2f2e0a 100644
--- a/tests/darwin/exporter/formats/export_darwin_test.py
+++ b/tests/darwin/exporter/formats/export_darwin_test.py
@@ -154,15 +154,13 @@ def test_multi_segment_nifti_export():
         if not subdir.is_dir():
             continue
         print(subdir)
-        
+
         ground_truth_path = subdir.joinpath("ground_truth.nii.gz")
         darwin_json_path = subdir.joinpath("darwin.json")
         target_output_directory = subdir.joinpath("output")
         volume_name = subdir.parts[-1]
         target_output_path = target_output_directory.joinpath(
-            "darwin",
-            "0",
-            f"{volume_name[:-2]}_Segments_m.nii.gz"
+            "darwin", "0", f"{volume_name[:-2]}_Segments_m.nii.gz"
         )
 
         try:

From c734056d89497cea13171ff13ca4be4418ece02b Mon Sep 17 00:00:00 2001
From: Valentin Vikhorev <vvihorevv@gmail.com>
Date: Thu, 24 Jul 2025 16:58:22 +0200
Subject: [PATCH 5/5] Drop print statements

---
 tests/darwin/exporter/formats/export_darwin_test.py | 1 -
 tests/darwin/importer/formats/import_nifti_test.py  | 1 -
 2 files changed, 2 deletions(-)

diff --git a/tests/darwin/exporter/formats/export_darwin_test.py b/tests/darwin/exporter/formats/export_darwin_test.py
index b3e2f2e0a..1c61ee8cd 100644
--- a/tests/darwin/exporter/formats/export_darwin_test.py
+++ b/tests/darwin/exporter/formats/export_darwin_test.py
@@ -153,7 +153,6 @@ def test_multi_segment_nifti_export():
     for subdir in root_dir.iterdir():
         if not subdir.is_dir():
             continue
-        print(subdir)
 
         ground_truth_path = subdir.joinpath("ground_truth.nii.gz")
         darwin_json_path = subdir.joinpath("darwin.json")
diff --git a/tests/darwin/importer/formats/import_nifti_test.py b/tests/darwin/importer/formats/import_nifti_test.py
index 44bdbb4dc..41dc0cb33 100644
--- a/tests/darwin/importer/formats/import_nifti_test.py
+++ b/tests/darwin/importer/formats/import_nifti_test.py
@@ -617,7 +617,6 @@ def test_image_annotation_nifti_multi_label():
     for subdir in root_dir.iterdir():
         if not subdir.is_dir():
             continue
-        print(subdir)
 
         nifti_file_path = subdir.joinpath("ground_truth.nii.gz")
         nifti_image = nib.load(nifti_file_path)