- repo link fix

Upgrade zstd to 0.14

.gitignore

@@ -1,5 +1,6 @@
-
 /target/
 **/*.rs.bk
 Cargo.lock
 tests/benches/corpus/
+.idea
+.agentbridge

Cargo.toml

@@ -1,8 +1,7 @@
 [package]
-name = "tiff"
+name = "ndbioimage-tiff"
 version = "0.11.3"
 edition = "2021"
-resolver = "2"
 
 # note: when changed, also update test runner in `.github/workflows/rust.yml`
 rust-version = "1.88.0"
@@ -11,30 +10,33 @@ license = "MIT"
 description = "TIFF decoding and encoding library in pure Rust"
 authors = ["The image-rs Developers"]
 
-repository = "https://github.com/image-rs/image-tiff"
+repository = "https://git.pomppervova.nl/wim/image-tiff"
 categories = ["multimedia::images", "multimedia::encoding"]
 
 exclude = ["tests/images/*", "tests/fuzz_images/*", "tests/**/*.tif"]
 
+[lib]
+name = "tiff"
+
 [dependencies]
 half = { version = "2.4.1" }
 quick-error = "2.0.1"
 
 # Rename to avoid confusion with the feature name.
-fax34 = { package = "fax", version = "0.2.6", optional = true }
+fax34 = { package = "fax", version = "0.3", optional = true }
-flate2 = { version = "1.0.20", optional = true }
+flate2 = { version = "1", optional = true }
-weezl = { version = "0.2.1", optional = true }
+weezl = { version = "0.2", optional = true }
-zstd = { version = "0.13", optional = true }
+zstd = { version = "0.14", optional = true }
-zrip-decode = { version = "0.8.2", features = ["paranoid"], optional = true }
+zrip-decode = { version = "0.8", features = ["paranoid"], optional = true }
-zune-jpeg = { version = "0.5.1", optional = true }
+zune-jpeg = { version = "0.5", optional = true }
-image-webp = {version = "0.2.4", optional = true }
+image-webp = {version = "0.2", optional = true }
 
 [dev-dependencies]
-criterion = "0.3.1"
+criterion = "0.3"
 # We may already depend on this via flate2
-crc32fast = "1.5"
+crc32fast = "1"
-libtest-mimic = "0.8.1"
+libtest-mimic = "0.8"
-walkdir = "2.5"
+walkdir = "2"
 
 [features]
 default = ["deflate", "fax", "jpeg", "lzw"]

README.md

@@ -5,6 +5,8 @@
 
 TIFF decoding and encoding library in pure Rust
 
+Forked from https://github.com/image-rs/image-tiff. Changes: read images containing RGBPalette frames, ignoring colormaps.
+
 ## Supported
 
 ### Features

src/decoder/ifd.rs

@@ -599,8 +599,10 @@ impl Entry {
                 self.decode_values(self.count, self.type_, reader, |bytes| {
                     v.extend(
                         bytes
-                            .chunks_exact(2)
+                            .as_chunks::<2>()
-                            .map(|ch| Short(u16::from_ne_bytes(ch.try_into().unwrap()))),
+                            .0
+                            .iter()
+                            .map(|&ch| Short(u16::from_ne_bytes(ch))),
                     )
                 })
             }
@@ -609,8 +611,10 @@ impl Entry {
                 self.decode_values(self.count, self.type_, reader, |bytes| {
                     v.extend(
                         bytes
-                            .chunks_exact(2)
+                            .as_chunks::<2>()
-                            .map(|ch| SignedShort(i16::from_ne_bytes(ch.try_into().unwrap()))),
+                            .0
+                            .iter()
+                            .map(|&ch| SignedShort(i16::from_ne_bytes(ch))),
                     )
                 })
             }
@@ -619,8 +623,10 @@ impl Entry {
                 self.decode_values(self.count, self.type_, reader, |bytes| {
                     v.extend(
                         bytes
-                            .chunks_exact(4)
+                            .as_chunks::<4>()
-                            .map(|ch| Unsigned(u32::from_ne_bytes(ch.try_into().unwrap()))),
+                            .0
+                            .iter()
+                            .map(|&ch| Unsigned(u32::from_ne_bytes(ch))),
                     )
                 })
             }
@@ -629,8 +635,10 @@ impl Entry {
                 self.decode_values(self.count, self.type_, reader, |bytes| {
                     v.extend(
                         bytes
-                            .chunks_exact(4)
+                            .as_chunks::<4>()
-                            .map(|ch| Signed(i32::from_ne_bytes(ch.try_into().unwrap()))),
+                            .0
+                            .iter()
+                            .map(|&ch| Signed(i32::from_ne_bytes(ch))),
                     )
                 })
             }
@@ -639,8 +647,10 @@ impl Entry {
                 self.decode_values(self.count, self.type_, reader, |bytes| {
                     v.extend(
                         bytes
-                            .chunks_exact(4)
+                            .as_chunks::<4>()
-                            .map(|ch| Float(f32::from_ne_bytes(ch.try_into().unwrap()))),
+                            .0
+                            .iter()
+                            .map(|&ch| Float(f32::from_ne_bytes(ch))),
                     )
                 })
             }
@@ -649,15 +659,17 @@ impl Entry {
                 self.decode_values(self.count, self.type_, reader, |bytes| {
                     v.extend(
                         bytes
-                            .chunks_exact(8)
+                            .as_chunks::<8>()
-                            .map(|ch| Double(f64::from_ne_bytes(ch.try_into().unwrap()))),
+                            .0
+                            .iter()
+                            .map(|&ch| Double(f64::from_ne_bytes(ch))),
                     )
                 })
             }
             Type::RATIONAL => {
                 v = Self::vec_with_capacity(self.count, self.type_, limits)?;
                 self.decode_values(self.count, self.type_, reader, |bytes| {
-                    v.extend(bytes.chunks_exact(8).map(|ch| {
+                    v.extend(bytes.as_chunks::<8>().0.iter().map(|ch| {
                         Rational(
                             u32::from_ne_bytes(ch[..4].try_into().unwrap()),
                             u32::from_ne_bytes(ch[4..].try_into().unwrap()),
@@ -668,7 +680,7 @@ impl Entry {
             Type::SRATIONAL => {
                 v = Self::vec_with_capacity(self.count, self.type_, limits)?;
                 self.decode_values(self.count, self.type_, reader, |bytes| {
-                    v.extend(bytes.chunks_exact(8).map(|ch| {
+                    v.extend(bytes.as_chunks::<8>().0.iter().map(|ch| {
                         SRational(
                             i32::from_ne_bytes(ch[..4].try_into().unwrap()),
                             i32::from_ne_bytes(ch[4..].try_into().unwrap()),
@@ -681,8 +693,10 @@ impl Entry {
                 self.decode_values(self.count, self.type_, reader, |bytes| {
                     v.extend(
                         bytes
-                            .chunks_exact(8)
+                            .as_chunks::<8>()
-                            .map(|ch| UnsignedBig(u64::from_ne_bytes(ch.try_into().unwrap()))),
+                            .0
+                            .iter()
+                            .map(|&ch| UnsignedBig(u64::from_ne_bytes(ch))),
                     )
                 })
             }
@@ -691,8 +705,10 @@ impl Entry {
                 self.decode_values(self.count, self.type_, reader, |bytes| {
                     v.extend(
                         bytes
-                            .chunks_exact(8)
+                            .as_chunks::<8>()
-                            .map(|ch| SignedBig(i64::from_ne_bytes(ch.try_into().unwrap()))),
+                            .0
+                            .iter()
+                            .map(|&ch| SignedBig(i64::from_ne_bytes(ch))),
                     )
                 })
             }
@@ -701,8 +717,10 @@ impl Entry {
                 self.decode_values(self.count, self.type_, reader, |bytes| {
                     v.extend(
                         bytes
-                            .chunks_exact(4)
+                            .as_chunks::<4>()
-                            .map(|ch| Ifd(u32::from_ne_bytes(ch.try_into().unwrap()))),
+                            .0
+                            .iter()
+                            .map(|&ch| Ifd(u32::from_ne_bytes(ch))),
                     )
                 })
             }
@@ -711,8 +729,10 @@ impl Entry {
                 self.decode_values(self.count, self.type_, reader, |bytes| {
                     v.extend(
                         bytes
-                            .chunks_exact(8)
+                            .as_chunks::<8>()
-                            .map(|ch| IfdBig(u64::from_ne_bytes(ch.try_into().unwrap()))),
+                            .0
+                            .iter()
+                            .map(|&ch| IfdBig(u64::from_ne_bytes(ch))),
                     )
                 })
             }

src/decoder/image.rs

@@ -36,6 +36,9 @@ impl TileAttributes {
     pub fn tiles_down(&self) -> usize {
         self.image_height.div_ceil(self.tile_length)
     }
+    pub fn tiles_per_plane(&self) -> usize {
+        self.tiles_across() * self.tiles_down()
+    }
     fn padding_right(&self) -> usize {
         (self.tile_width - self.image_width % self.tile_width) % self.tile_width
     }
@@ -176,7 +179,7 @@ impl Image {
             .map(Value::into_u16)
             .transpose()?
             .and_then(PhotometricInterpretation::from_u16)
-            .ok_or(TiffUnsupportedError::UnknownInterpretation)?;
+            .unwrap_or(PhotometricInterpretation::BlackIsZero);
 
         // Try to parse both the compression method and the number, format, and bits of the included samples.
         // If they are not explicitly specified, those tags are reset to their default values and not carried from previous images.
@@ -467,11 +470,11 @@ impl Image {
                     }
                     Some(map)
                 }
-                None => {
+                // A missing palette is not an error. The pixel values of an indexed image are just
-                    return Err(TiffError::FormatError(
+                // indices into the palette, and the palette itself is only display information, so
-                        TiffFormatError::RequiredTagNotFound(Tag::ColorMap),
+                // the image still decodes. Callers observe the absence as `None` from
-                    ));
+                // `Decoder::color_map`.
-                }
+                None => None,
             }
         } else {
             None
@@ -1016,7 +1019,15 @@ impl Image {
             }
             ChunkType::Tile => {
                 let tile_attrs = self.tile_attributes.as_ref().unwrap();
-                let (padding_right, padding_down) = tile_attrs.get_padding(chunk_index as usize);
+                // The chunk index counts the tiles of all planes, but the tile grid repeats per
+                // plane, so only the position within the plane decides the padding.
+                let tiles_per_plane = tile_attrs.tiles_per_plane();
+                let tile = if tiles_per_plane == 0 {
+                    0
+                } else {
+                    chunk_index as usize % tiles_per_plane
+                };
+                let (padding_right, padding_down) = tile_attrs.get_padding(tile);
 
                 let tile_width = tile_attrs.tile_width - padding_right;
                 let tile_length = tile_attrs.tile_length - padding_down;

src/decoder/mod.rs

@@ -294,8 +294,8 @@ fn one_byte_predict<const N: usize>(buf: &mut [u8]) {
     acc.copy_from_slice(&buf[..N]);
 
     // Process N bytes per iteration. Each channel's prefix sum is independent.
-    let mut chunks = buf[N..].chunks_exact_mut(N);
+    let chunks = buf[N..].as_chunks_mut::<N>();
-    for chunk in &mut chunks {
+    for chunk in &mut chunks.0.iter_mut() {
         for c in 0..N {
             acc[c] = chunk[c].wrapping_add(acc[c]);
             chunk[c] = acc[c];
@@ -303,7 +303,7 @@ fn one_byte_predict<const N: usize>(buf: &mut [u8]) {
     }
 
     // Handle trailing bytes (when buf.len() - N is not a multiple of N).
-    for (c, byte) in chunks.into_remainder().iter_mut().enumerate() {
+    for (c, byte) in chunks.1.iter_mut().enumerate() {
         *byte = byte.wrapping_add(acc[c]);
     }
 }
@@ -1288,7 +1288,7 @@ impl<R: Read + Seek> Decoder<R> {
     /// Utility to create a reader like [`Self::read_entry`], from the current IFD.
     ///
     /// Returns an `Ok(None)` if the tag is not found in the current directory. See
-    /// [`Self::read_entry´] of which this is a simple wrapper.
+    /// [`Self::read_entry`] of which this is a simple wrapper.
     pub fn read_tag(&mut self, tag: Tag) -> TiffResult<Option<EntryBytesReader<'_, R>>> {
         match self.current_ifd().find_entry(tag) {
             None => Ok(None),

src/decoder/stream.rs

@@ -294,7 +294,7 @@ pub struct Group4Reader<R: Read> {
     decoder: fax34::decoder::Group4Decoder<FaxBytes<R>>,
     line_buf: io::Cursor<Vec<u8>>,
     height: u32,
-    width: u16,
+    width: u32,
     y: u32,
 }
 
@@ -306,7 +306,7 @@ impl<R: Read> Group4Reader<R> {
         compressed_length: u64,
         fill_order: u16,
     ) -> crate::TiffResult<Self> {
-        let width = u16::try_from(dimensions.0)?;
+        let width = dimensions.0;
         let height = dimensions.1;
 
         Ok(Self {
@@ -314,7 +314,7 @@ impl<R: Read> Group4Reader<R> {
                 fax_byte_iter(reader, compressed_length, fill_order),
                 width,
             )?,
-            line_buf: io::Cursor::new(Vec::with_capacity(width.into())),
+            line_buf: io::Cursor::new(Vec::with_capacity(width as usize)),
             width,
             height,
             y: 0,
@@ -344,7 +344,7 @@ impl<R: Read> Read for Group4Reader<R> {
                     let transitions = fax34::decoder::pels(self.decoder.transition(), self.width);
 
                     let buffer = self.line_buf.get_mut();
-                    buffer.resize(usize::from(self.width).div_ceil(8), 0u8);
+                    buffer.resize((self.width as usize).div_ceil(8), 0u8);
 
                     let target = &mut buffer[..];
 
@@ -409,7 +409,7 @@ pub struct Group3Reader {
     reader: OwnedBitReader,
     line_buf: io::Cursor<Vec<u8>>,
     height: u32,
-    width: u16,
+    width: u32,
     y: u32,
 }
 
@@ -421,7 +421,7 @@ impl Group3Reader {
         compressed_length: u64,
         fill_order: u16,
     ) -> crate::TiffResult<Self> {
-        let width = u16::try_from(dimensions.0)?;
+        let width = dimensions.0;
         let height = dimensions.1;
 
         // Buffer all compressed data and apply FillOrder bit reversal
@@ -442,7 +442,7 @@ impl Group3Reader {
 
         Ok(Self {
             reader: bit_reader,
-            line_buf: io::Cursor::new(Vec::with_capacity(width.into())),
+            line_buf: io::Cursor::new(Vec::with_capacity(width as usize)),
             width,
             height,
             y: 0,
@@ -463,10 +463,10 @@ impl Group3Reader {
     fn with_markup<R: fax34::BitReader>(
         decoder: fn(&mut R) -> Option<u16>,
         reader: &mut R,
-    ) -> Option<u16> {
+    ) -> Option<u32> {
-        let mut sum = 0u16;
+        let mut sum = 0u32;
         while let Some(n) = decoder(reader) {
-            sum = sum.checked_add(n)?;
+            sum = sum.checked_add(n as u32)?;
             if n < 64 {
                 return Some(sum);
             }
@@ -483,7 +483,7 @@ impl Read for Group3Reader {
         {
             // Decode one line of alternating white/black run-lengths
             let mut transitions = Vec::new();
-            let mut a0 = 0u16;
+            let mut a0 = 0u32;
             let mut is_white = true;
             loop {
                 let run = if is_white {
@@ -507,7 +507,7 @@ impl Read for Group3Reader {
             self.y += 1;
 
             // Convert transitions to packed bilevel output
-            let bytes_per_line = usize::from(self.width).div_ceil(8);
+            let bytes_per_line = (self.width as usize).div_ceil(8);
             let buffer = self.line_buf.get_mut();
             buffer.clear();
             buffer.resize(bytes_per_line, 0u8);

src/directory.rs

@@ -171,7 +171,7 @@ mod tests {
             dir.get(Tag::Unknown(1))
                 .expect("tag 1 should be present after this chain")
                 .count(),
-            u16::MAX.into()
+            u64::from(u16::MAX)
         );
     }
 

src/tags.rs

@@ -617,26 +617,22 @@ impl ByteOrder {
             return;
         }
 
-        // FIXME: at MSRV 1.89 or higher use `slice::as_chunks_mut`.
         match cls {
             EndianBytes::One => {
                 // No change needed
             }
             EndianBytes::Two => {
-                for chunk in buffer.chunks_exact_mut(2) {
+                for chunk in buffer.as_chunks_mut::<2>().0 {
-                    let chunk: &mut [u8; 2] = chunk.try_into().unwrap();
                     *chunk = u16::from_be_bytes(*chunk).to_le_bytes();
                 }
             }
             EndianBytes::Four => {
-                for chunk in buffer.chunks_exact_mut(4) {
+                for chunk in buffer.as_chunks_mut::<4>().0 {
-                    let chunk: &mut [u8; 4] = chunk.try_into().unwrap();
                     *chunk = u32::from_be_bytes(*chunk).to_le_bytes();
                 }
             }
             EndianBytes::Eight => {
-                for chunk in buffer.chunks_exact_mut(8) {
+                for chunk in buffer.as_chunks_mut::<8>().0 {
-                    let chunk: &mut [u8; 8] = chunk.try_into().unwrap();
                     *chunk = u64::from_be_bytes(*chunk).to_le_bytes();
                 }
             }

tests/decode_images.rs

@@ -506,6 +506,47 @@ fn test_tiled_extra_samples_border_u8() {
     assert_eq!(data, expected);
 }
 
+#[test]
+fn test_tiled_planar_border_u16() {
+    // A planar (separate) tiled image whose dimensions are not multiples of the tile size.
+    // The tile grid repeats for every plane, but the chunk (tile) index counts all planes, so
+    // the border padding of the second plane used to be looked up with the wrong tile index.
+    // The bottom-right tile of plane 1 then claimed a full tile height, and the decoder ran
+    // past the end of the output buffer.
+    //
+    // Note that `read_image` only decodes the first plane, so this has to go through
+    // `read_image_to_buffer` to reach the tiles that were mis-sized.
+    let path = PathBuf::from(TEST_IMAGE_DIR).join("tiled-planar-2c-16b.tif");
+    let img_file = File::open(path).expect("Cannot find test image!");
+    let mut decoder = Decoder::open(img_file).expect("Cannot create decoder");
+    decoder.next_image().expect("Cannot read image IFD");
+    assert_eq!(decoder.dimensions().unwrap(), (30, 20));
+    assert_eq!(
+        decoder.colortype().unwrap(),
+        ColorType::Multiband {
+            bit_depth: 16,
+            num_samples: 2
+        }
+    );
+
+    let mut buffer = DecodingSampleBuffer::U16(Vec::new());
+    decoder.read_image_to_buffer(&mut buffer).unwrap();
+    let DecodingSampleBuffer::U16(data) = buffer else {
+        panic!("Wrong bit depth")
+    };
+    assert_eq!(data.len(), 2 * 20 * 30);
+
+    let mut expected = Vec::with_capacity(2 * 20 * 30);
+    for plane in 0..2u16 {
+        for y in 0..20u16 {
+            for x in 0..30u16 {
+                expected.push(1000 * plane + 10 * y + x);
+            }
+        }
+    }
+    assert_eq!(data, expected);
+}
+
 #[test]
 fn test_inner_access() {
     let path = PathBuf::from(TEST_IMAGE_DIR).join("tiled-rect-rgb-u8.tif");
@@ -898,22 +939,22 @@ fn test_image_bytes(
 }
 
 fn byte_order_u16(bytes: &mut [u8]) {
-    for chunk in bytes.chunks_exact_mut(2) {
+    for chunk in bytes.as_chunks_mut::<2>().0 {
-        let n = u16::from_ne_bytes(chunk.try_into().unwrap());
+        let n = u16::from_ne_bytes(*chunk);
         chunk.copy_from_slice(&n.to_le_bytes());
     }
 }
 
 fn byte_order_u32(bytes: &mut [u8]) {
-    for chunk in bytes.chunks_exact_mut(4) {
+    for chunk in bytes.as_chunks_mut::<4>().0 {
-        let n = u32::from_ne_bytes(chunk.try_into().unwrap());
+        let n = u32::from_ne_bytes(*chunk);
         chunk.copy_from_slice(&n.to_le_bytes());
     }
 }
 
 fn byte_order_u64(bytes: &mut [u8]) {
-    for chunk in bytes.chunks_exact_mut(8) {
+    for chunk in bytes.as_chunks_mut::<8>().0 {
-        let n = u64::from_ne_bytes(chunk.try_into().unwrap());
+        let n = u64::from_ne_bytes(*chunk);
         chunk.copy_from_slice(&n.to_le_bytes());
     }
 }