- read ome xml tiff
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Wim Pomp committed
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7f07f82fdb
commit
4815690621
3 files changed
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-163
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Submodule image-tiff updated: 96d37bb087...9b452e93b7.
@@ -33,7 +33,7 @@ libczirw-sys = { version = "0.5", optional = true }
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ndarray = { version = "0.17", features = ["serde"] }
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num = "0.4"
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numpy = { version = "0.29", optional = true }
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ome-metadata = "0.5"
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ome-metadata = "0.6"
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ordered-float = { version = "5", optional = true }
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phf = { version = "0.14", features = ["macros"] }
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postcard = { version = "1", features = ["use-std"], optional = true }
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+184
-161
@@ -156,47 +156,61 @@ impl Reader for TiffReader {
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.unwrap_or(1)
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== 2;
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let imagej_bytes = reader
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.current_ifd()
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.get_tag(Tag::Unknown(50839))
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.or_else(|_| reader.current_ifd().get_tag(Tag::ImageDescription))?;
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let imagej_bytes = match imagej_bytes {
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Value::Ascii(s) => s.into_bytes(),
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other => other.into_u8_vec()?,
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};
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let metadata_str = String::from_utf8_lossy(&imagej_bytes);
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let metadata_map = parse_imagej_metadata(&metadata_str);
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let image_description = reader.current_ifd().get_tag(Tag::ImageDescription);
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let p_ndim = if n_samples > 1 { 3u8 } else { 2u8 };
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let size_c = if p_ndim == 3 {
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n_samples
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let (size_c, size_t, size_z) = if let Ok(Value::Ascii(xml)) = image_description
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&& xml.starts_with("<?xml")
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{
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let ome = Ome::from_xml(xml)?;
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(
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ome.image[0].pixels.size_c as usize,
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ome.image[0].pixels.size_t as usize,
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ome.image[0].pixels.size_z as usize,
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)
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} else {
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metadata_map
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.get("channels")
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let imagej_bytes = reader
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.current_ifd()
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.get_tag(Tag::Unknown(50839))
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.or_else(|_| reader.current_ifd().get_tag(Tag::ImageDescription))?;
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let imagej_bytes = match imagej_bytes {
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Value::Ascii(s) => s.into_bytes(),
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other => other.into_u8_vec()?,
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};
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let metadata_str = String::from_utf8_lossy(&imagej_bytes);
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let metadata_map = parse_imagej_metadata(&metadata_str);
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let size_c = if p_ndim == 3 {
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n_samples
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} else {
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metadata_map
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.get("channels")
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.and_then(|v| v.parse::<usize>().ok())
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.unwrap_or(1)
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};
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let size_z = metadata_map
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.get("slices")
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.and_then(|v| v.parse::<usize>().ok())
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.unwrap_or(1)
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};
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let size_z = metadata_map
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.get("slices")
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.and_then(|v| v.parse::<usize>().ok())
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.unwrap_or(1);
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let size_t = metadata_map
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.get("frames")
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.and_then(|v| v.parse::<usize>().ok())
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.unwrap_or(1);
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.unwrap_or(1);
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let size_t = metadata_map
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.get("frames")
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.and_then(|v| v.parse::<usize>().ok())
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.unwrap_or(1);
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let mult = if p_ndim == 3 { n_samples } else { 1 };
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let expected = size_c * size_z * size_t / mult;
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let mult = if p_ndim == 3 { n_samples } else { 1 };
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let expected = size_c * size_z * size_t / mult;
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let mut n_ifds = 1;
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while reader.more_images() {
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reader.next_directory()?;
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n_ifds += 1;
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}
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let mut n_ifds = 1;
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while reader.more_images() {
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reader.next_directory()?;
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n_ifds += 1;
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}
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let size_z = if n_ifds != expected && n_ifds > 0 {
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n_ifds / (size_c * size_t / mult).max(1)
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} else {
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size_z
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let size_z = if n_ifds != expected && n_ifds > 0 {
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n_ifds / (size_c * size_t / mult).max(1)
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} else {
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size_z
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};
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(size_c, size_t, size_z)
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};
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drop(reader);
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@@ -220,139 +234,146 @@ impl Reader for TiffReader {
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fn metadata(&self) -> Result<Ome, Error> {
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let mut reader = self.get_reader()?;
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let imagej_bytes = reader
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.current_ifd()
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.get_tag(Tag::Unknown(50839))
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.or_else(|_| reader.current_ifd().get_tag(Tag::ImageDescription))?;
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let imagej_bytes = match imagej_bytes {
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Value::Ascii(s) => s.into_bytes(),
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other => other.into_u8_vec()?,
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};
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let metadata_str = String::from_utf8_lossy(&imagej_bytes);
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let metadata_map = parse_imagej_metadata(&metadata_str);
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let image_description = reader.current_ifd().get_tag(Tag::ImageDescription);
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if let Ok(Value::Ascii(xml)) = image_description
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&& xml.starts_with("<?xml")
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{
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Ok(Ome::from_xml(xml)?)
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} else {
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let imagej_bytes = reader
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.current_ifd()
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.get_tag(Tag::Unknown(50839))
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.or_else(|_| reader.current_ifd().get_tag(Tag::ImageDescription))?;
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let imagej_bytes = match imagej_bytes {
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Value::Ascii(s) => s.into_bytes(),
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other => other.into_u8_vec()?,
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};
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let metadata_str = String::from_utf8_lossy(&imagej_bytes);
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let metadata_map = parse_imagej_metadata(&metadata_str);
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let interval_t = metadata_map
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.get("interval")
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.and_then(|v| v.parse::<f64>().ok());
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let ru = reader
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.current_ifd()
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.get_tag(Tag::ResolutionUnit)
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.ok()
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.and_then(|i| i.into_u16().ok())
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.unwrap_or(2);
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let pixel_size = reader
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.current_ifd()
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.get_tag(Tag::XResolution)
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.ok()
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.and_then(|i| i.into_u64_vec().ok())
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.and_then(|i| {
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i.first()
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.and_then(|&n| i.get(1).map(|&d| (n as f64) / (d as f64)))
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})
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.and_then(|i| {
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if i <= 0.0 {
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None
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} else if ru == 3 {
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Some(1e4 / i)
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} else if ru == 2 {
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Some(25400.0 / i)
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} else {
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Some(1.0 / i)
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}
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});
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let interval_z = metadata_map
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.get("spacing")
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.and_then(|v| v.parse::<f64>().ok());
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let interval_t = metadata_map
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.get("interval")
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.and_then(|v| v.parse::<f64>().ok());
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let ru = reader
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.current_ifd()
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.get_tag(Tag::ResolutionUnit)
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.ok()
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.and_then(|i| i.into_u16().ok())
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.unwrap_or(2);
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let pixel_size = reader
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.current_ifd()
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.get_tag(Tag::XResolution)
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.ok()
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.and_then(|i| i.into_u64_vec().ok())
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.and_then(|i| {
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i.first()
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.and_then(|&n| i.get(1).map(|&d| (n as f64) / (d as f64)))
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})
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.and_then(|i| {
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if i <= 0.0 {
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None
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} else if ru == 3 {
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Some(1e4 / i)
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} else if ru == 2 {
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Some(25400.0 / i)
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} else {
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Some(1.0 / i)
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}
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});
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let interval_z = metadata_map
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.get("spacing")
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.and_then(|v| v.parse::<f64>().ok());
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let ome_pixel_type = match self.pixel_type {
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PixelType::I8 => ome::PixelType::Int8,
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PixelType::U8 => ome::PixelType::Uint8,
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PixelType::I16 => ome::PixelType::Int16,
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PixelType::U16 => ome::PixelType::Uint16,
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PixelType::I32 => ome::PixelType::Int32,
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PixelType::U32 => ome::PixelType::Uint32,
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PixelType::F32 => ome::PixelType::Float,
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PixelType::F64 => ome::PixelType::Double,
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_ => ome::PixelType::Uint16,
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};
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let ome_pixel_type = match self.pixel_type {
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PixelType::I8 => ome::PixelType::Int8,
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PixelType::U8 => ome::PixelType::Uint8,
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PixelType::I16 => ome::PixelType::Int16,
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PixelType::U16 => ome::PixelType::Uint16,
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PixelType::I32 => ome::PixelType::Int32,
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PixelType::U32 => ome::PixelType::Uint32,
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PixelType::F32 => ome::PixelType::Float,
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PixelType::F64 => ome::PixelType::Double,
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_ => ome::PixelType::Uint16,
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};
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let mut pixels = ome::Pixels {
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id: "Pixels:0".to_string(),
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size_x: self.shape.x as i32,
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size_y: self.shape.y as i32,
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size_z: self.shape.z as i32,
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size_c: self.shape.c as i32,
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size_t: self.shape.t as i32,
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dimension_order: ome::PixelsDimensionOrderType::Xyczt,
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r#type: ome_pixel_type,
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physical_size_x: pixel_size.map(|v| v as f32),
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physical_size_x_unit: ome::UnitsLength::um,
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physical_size_y: pixel_size.map(|v| v as f32),
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physical_size_y_unit: ome::UnitsLength::um,
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physical_size_z: interval_z.map(|v| v as f32),
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physical_size_z_unit: ome::UnitsLength::um,
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time_increment: interval_t.map(|v| v as f32),
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time_increment_unit: ome::UnitsTime::s,
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significant_bits: None,
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interleaved: None,
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big_endian: None,
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channel: Vec::new(),
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bin_data: Vec::new(),
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tiff_data: Vec::new(),
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metadata_only: None,
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plane: Vec::new(),
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};
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let mut pixels = ome::Pixels {
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id: "Pixels:0".to_string(),
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size_x: self.shape.x as i32,
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size_y: self.shape.y as i32,
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size_z: self.shape.z as i32,
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size_c: self.shape.c as i32,
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size_t: self.shape.t as i32,
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dimension_order: ome::PixelsDimensionOrderType::Xyczt,
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r#type: ome_pixel_type,
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physical_size_x: pixel_size.map(|v| v as f32),
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physical_size_x_unit: ome::UnitsLength::um,
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physical_size_y: pixel_size.map(|v| v as f32),
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physical_size_y_unit: ome::UnitsLength::um,
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physical_size_z: interval_z.map(|v| v as f32),
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physical_size_z_unit: ome::UnitsLength::um,
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time_increment: interval_t.map(|v| v as f32),
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time_increment_unit: ome::UnitsTime::s,
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significant_bits: None,
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interleaved: None,
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big_endian: None,
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channel: Vec::new(),
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bin_data: Vec::new(),
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tiff_data: Vec::new(),
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metadata_only: None,
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plane: Vec::new(),
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};
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for c in 0..self.shape.c {
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pixels.channel.push(ome::Channel {
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id: format!("Channel:{}", c),
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name: Some(format!("Channel {}", c)),
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..Default::default()
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});
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}
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for c in 0..self.shape.c {
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pixels.channel.push(ome::Channel {
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id: format!("Channel:{}", c),
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name: Some(format!("Channel {}", c)),
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..Default::default()
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});
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}
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for c in 0..self.shape.c {
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for z in 0..self.shape.z {
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for t in 0..self.shape.t {
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pixels.plane.push(ome::Plane {
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the_c: Some(c as i32),
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the_z: Some(z as i32),
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the_t: Some(t as i32),
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delta_t: interval_t.and_then(|v| {
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if v > 0.0 {
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Some((t as f64 * v) as f32)
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} else {
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None
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}
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}),
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..Default::default()
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});
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for c in 0..self.shape.c {
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for z in 0..self.shape.z {
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for t in 0..self.shape.t {
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pixels.plane.push(ome::Plane {
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the_c: Some(c as i32),
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the_z: Some(z as i32),
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the_t: Some(t as i32),
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delta_t: interval_t.and_then(|v| {
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if v > 0.0 {
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Some((t as f64 * v) as f32)
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} else {
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None
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}
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}),
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..Default::default()
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});
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}
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}
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}
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}
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let mut ome = Ome::default();
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ome.image.push(ome::Image {
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id: "Image:0".to_string(),
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name: self
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.path
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.file_name()
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.map(|n| n.to_string_lossy().to_string()),
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pixels,
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instrument_ref: None,
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objective_settings: None,
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acquisition_date: None,
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description: None,
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experimenter_ref: None,
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experiment_ref: None,
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experimenter_group_ref: None,
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imaging_environment: None,
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stage_label: None,
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roi_ref: Vec::new(),
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microbeam_manipulation_ref: Vec::new(),
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annotation_ref: Vec::new(),
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});
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Ok(ome)
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let mut ome = Ome::default();
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ome.image.push(ome::Image {
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id: "Image:0".to_string(),
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name: self
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.path
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.file_name()
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.map(|n| n.to_string_lossy().to_string()),
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pixels,
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instrument_ref: None,
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objective_settings: None,
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acquisition_date: None,
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description: None,
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experimenter_ref: None,
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experiment_ref: None,
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experimenter_group_ref: None,
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imaging_environment: None,
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stage_label: None,
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roi_ref: Vec::new(),
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microbeam_manipulation_ref: Vec::new(),
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annotation_ref: Vec::new(),
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});
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Ok(ome)
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}
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}
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fn get_frame(&self, c: usize, z: usize, t: usize) -> Result<Frame, Error> {
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@@ -521,6 +542,8 @@ mod tests {
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metadata_e: "tiff/1xp53-01-AP1.tiff",
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metadata_f: "tiff/test.tif",
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metadata_g: "tiff/YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.tif",
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metadata_h: "tiff/Wapl-AID_C46_13_tagRFPt_MCP_well1_video1_1_max.tif"
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metadata_h: "tiff/Wapl-AID_C46_13_tagRFPt_MCP_well1_video1_1_max.tif",
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metadata_i: "tiff/R1_NRF1_Gtf3a500nM_REAL_20260731_25pct_500ms_001_MMStack_PosR1_NRF1_Gtf3a500nM_REAL_20260731_25pct_500ms_001.ome.tif"
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metadata_j: "tiff/20260922_Pos0_max.tif"
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}
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}
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