From 071e3c02c7c6d8c825d4a4dc2c4ab997321ebccc Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 9 Oct 2024 16:00:56 -0500
Subject: [PATCH 1/2] Add example script to export webknossos volume
 annotations

---
 scripts/export_annotation.py | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 scripts/export_annotation.py

diff --git a/scripts/export_annotation.py b/scripts/export_annotation.py
new file mode 100644
index 00000000..bb6c20a7
--- /dev/null
+++ b/scripts/export_annotation.py
@@ -0,0 +1,35 @@
+import os
+import numpy as np
+import webknossos as wk
+from tifffile import imwrite
+
+ANNOTATION_ID = '<annotation_id>'
+SEGMENT_IDS = [1,2]
+MAG = wk.Mag('8-8-1')
+annotation_directory='~/example_export'
+
+with wk.client.context.webknossos_context(url=os.environ.get('WK_URL'),token=os.environ.get('WK_TOKEN')):
+    dataset = wk.Annotation.open_as_remote_dataset(
+        ANNOTATION_ID, 
+        annotation_type='Volume',
+        webknossos_url=os.environ.get('WK_URL')
+    )
+    mag_view = dataset.get_segmentation_layers()[0].get_mag(MAG)
+
+z = mag_view.bounding_box.topleft.z
+with mag_view.get_buffered_slice_reader() as reader:
+    for slice_data in reader:
+        print(slice_data)
+        slice_data = slice_data[0]  # First channel only
+        for segment_id in SEGMENT_IDS:
+            segment_mask = (slice_data == segment_id).astype(
+                np.uint8
+            ) * 255  # Make a binary mask 0=empty, 255=segment
+            segment_mask = segment_mask.T  # Tiff likes the data transposed
+            imwrite(
+                f"{annotation_directory}/seg{segment_id:04d}_mag{MAG}_z{z:04d}.tiff",
+                segment_mask,
+            )
+
+        print(f'Downloaded z={z:04d}')
+        z += MAG.z
\ No newline at end of file

From 453a60ecb42bafff1960bc8b53feea006adb5347 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Wed, 9 Oct 2024 16:07:32 -0500
Subject: [PATCH 2/2] Remove print statement

---
 scripts/export_annotation.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/export_annotation.py b/scripts/export_annotation.py
index bb6c20a7..e0666837 100644
--- a/scripts/export_annotation.py
+++ b/scripts/export_annotation.py
@@ -19,7 +19,6 @@
 z = mag_view.bounding_box.topleft.z
 with mag_view.get_buffered_slice_reader() as reader:
     for slice_data in reader:
-        print(slice_data)
         slice_data = slice_data[0]  # First channel only
         for segment_id in SEGMENT_IDS:
             segment_mask = (slice_data == segment_id).astype(