From 034b879e3f73fcc525577dd01ff455b8e9829e32 Mon Sep 17 00:00:00 2001
From: Wim Pomp <w.pomp@nki.nl>
Date: Sun, 4 Jan 2026 16:49:12 +0100
Subject: [PATCH] - change all Option<Vec<_>> into Vec<_> - add
 multi-channel.ome test

---
 Cargo.toml                  |  2 +-
 src/lib.rs                  |  1 +
 src/ome.rs                  | 60 ++++++++++++++++++-------------------
 tests/multi-channel.ome.xml |  1 +
 4 files changed, 33 insertions(+), 31 deletions(-)
 create mode 100644 tests/multi-channel.ome.xml

diff --git a/Cargo.toml b/Cargo.toml
index 167fc3f..2165e65 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "ome-metadata"
-version = "0.3.3"
+version = "0.4.0"
 edition = "2024"
 rust-version = "1.85.1"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
diff --git a/src/lib.rs b/src/lib.rs
index cfaa233..34ccd7f 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -48,5 +48,6 @@ mod tests {
         i: "beads_2023_05_04__19_00_22"
         j: "20230511-p53-4x-CMV-1min-4h-01-Airyscan Processing-01"
         k: "YTL1849A131_2023_05_04__13_36_36"
+        l: "multi-channel.ome"
     );
 }
diff --git a/src/ome.rs b/src/ome.rs
index 3fb00e1..c68a29c 100644
--- a/src/ome.rs
+++ b/src/ome.rs
@@ -1584,30 +1584,30 @@ pub struct Ome {
     pub creator: Option<String>,
     #[serde(rename = "Rights")]
     pub rights: Option<Rights>,
-    #[serde(rename = "Project")]
-    pub project: Option<Vec<Project>>,
-    #[serde(rename = "Dataset")]
-    pub dataset: Option<Vec<Dataset>>,
-    #[serde(rename = "Folder")]
-    pub folder: Option<Vec<Folder>>,
-    #[serde(rename = "Experiment")]
-    pub experiment: Option<Vec<Experiment>>,
-    #[serde(rename = "Plate")]
-    pub plate: Option<Vec<Plate>>,
-    #[serde(rename = "Screen")]
-    pub screen: Option<Vec<Screen>>,
-    #[serde(rename = "Experimenter")]
-    pub experimenter: Option<Vec<Experimenter>>,
-    #[serde(rename = "ExperimenterGroup")]
-    pub experimenter_group: Option<Vec<ExperimenterGroup>>,
-    #[serde(rename = "Instrument")]
-    pub instrument: Option<Vec<Instrument>>,
-    #[serde(rename = "Image")]
-    pub image: Option<Vec<Image>>,
+    #[serde(default, rename = "Project")]
+    pub project: Vec<Project>,
+    #[serde(default, rename = "Dataset")]
+    pub dataset: Vec<Dataset>,
+    #[serde(default, rename = "Folder")]
+    pub folder: Vec<Folder>,
+    #[serde(default, rename = "Experiment")]
+    pub experiment: Vec<Experiment>,
+    #[serde(default, rename = "Plate")]
+    pub plate: Vec<Plate>,
+    #[serde(default, rename = "Screen")]
+    pub screen: Vec<Screen>,
+    #[serde(default, rename = "Experimenter")]
+    pub experimenter: Vec<Experimenter>,
+    #[serde(default, rename = "ExperimenterGroup")]
+    pub experimenter_group: Vec<ExperimenterGroup>,
+    #[serde(default, rename = "Instrument")]
+    pub instrument: Vec<Instrument>,
+    #[serde(default, rename = "Image")]
+    pub image: Vec<Image>,
     #[serde(rename = "StructuredAnnotations")]
     pub structured_annotations: Option<StructuredAnnotations>,
-    #[serde(rename = "ROI")]
-    pub roi: Option<Vec<Roi>>,
+    #[serde(default, rename = "ROI")]
+    pub roi: Vec<Roi>,
     #[serde(rename = "BinaryOnly")]
     pub binary_only: Option<OmeBinaryOnly>,
 }
@@ -1812,16 +1812,16 @@ pub struct Pixels {
         rename = "@TimeIncrementUnit"
     )]
     pub time_increment_unit: UnitsTime,
-    #[serde(rename = "Channel")]
-    pub channel: Option<Vec<Channel>>,
-    #[serde(rename = "BinData")]
-    pub bin_data: Option<Vec<BinData>>,
-    #[serde(rename = "TiffData")]
-    pub tiff_data: Option<Vec<TiffData>>,
+    #[serde(default, rename = "Channel")]
+    pub channel: Vec<Channel>,
+    #[serde(default, rename = "BinData")]
+    pub bin_data: Vec<BinData>,
+    #[serde(default, rename = "TiffData")]
+    pub tiff_data: Vec<TiffData>,
     #[serde(rename = "MetadataOnly")]
     pub metadata_only: Option<MetadataOnly>,
-    #[serde(rename = "Plane")]
-    pub plane: Option<Vec<Plane>>,
+    #[serde(default, rename = "Plane")]
+    pub plane: Vec<Plane>,
 }
 impl Pixels {
     pub fn default_physical_size_x_unit() -> UnitsLength {
diff --git a/tests/multi-channel.ome.xml b/tests/multi-channel.ome.xml
new file mode 100644
index 0000000..475176d
--- /dev/null
+++ b/tests/multi-channel.ome.xml
@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="multi-channel.ome.tif"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="439" SizeY="167" SizeZ="1" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData></Pixels></Image></OME>
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