ENH: Add reading and writing adapters for deflated TS

object/src/lib.rs

@@ -151,6 +151,7 @@ pub use dicom_dictionary_std::StandardDataDictionary;
 pub type DefaultDicomObject<D = StandardDataDictionary> = FileDicomObject<mem::InMemDicomObject<D>>;
 
 use dicom_core::header::{GroupNumber, Header};
+use dicom_encoding::Codec;
 use dicom_encoding::adapters::{PixelDataObject, RawPixelData};
 use dicom_encoding::transfer_syntax::TransferSyntaxIndex;
 use dicom_parser::dataset::{DataSetWriter, IntoTokens};
@@ -475,21 +476,34 @@ where
             .with_context(|| WriteUnsupportedTransferSyntaxSnafu {
                 uid: self.meta.transfer_syntax.clone(),
             })?;
-        let mut dset_writer = DataSetWriter::with_ts(to, ts).context(CreatePrinterSnafu)?;
+        if let Codec::Dataset(Some(adapter))= ts.codec() {
+            let adapter = adapter.adapt_writer(Box::new(to));
+            let mut dset_writer = DataSetWriter::with_ts(adapter, ts).context(CreatePrinterSnafu)?;
 
-        // We use the default options, because only the inner object knows if something needs to change
-        dset_writer
-            .write_sequence((&self.obj).into_tokens())
-            .context(PrintDataSetSnafu)?;
+            // write object
+            dset_writer
+                .write_sequence((&self.obj).into_tokens())
+                .context(PrintDataSetSnafu)?;
 
-        Ok(())
+            Ok(())
+
+        } else {
+            let mut dset_writer = DataSetWriter::with_ts(to, ts).context(CreatePrinterSnafu)?;
+
+            // write object
+            dset_writer
+                .write_sequence((&self.obj).into_tokens())
+                .context(PrintDataSetSnafu)?;
+
+            Ok(())
+        }
     }
 
     /// Write the entire object as a DICOM file
     /// into the given writer.
     /// Preamble, magic code, and file meta group will be included
     /// before the inner object.
-    pub fn write_all<W: Write>(&self, to: W) -> Result<(), WriteError> {
+    pub fn write_all<W: Write + 'static>(&self, to: W) -> Result<(), WriteError> {
         let mut to = BufWriter::new(to);
 
         // write preamble
@@ -507,14 +521,27 @@ where
             .with_context(|| WriteUnsupportedTransferSyntaxSnafu {
                 uid: self.meta.transfer_syntax.clone(),
             })?;
-        let mut dset_writer = DataSetWriter::with_ts(to, ts).context(CreatePrinterSnafu)?;
+        if let Codec::Dataset(Some(adapter))= ts.codec() {
+            let adapter = adapter.adapt_writer(Box::new(to));
+            let mut dset_writer = DataSetWriter::with_ts(adapter, ts).context(CreatePrinterSnafu)?;
+
+            // write object
+            dset_writer
+                .write_sequence((&self.obj).into_tokens())
+                .context(PrintDataSetSnafu)?;
+
+            Ok(())
 
-        // We use the default options, because only the inner object knows if something needs to change
-        dset_writer
-            .write_sequence((&self.obj).into_tokens())
-            .context(PrintDataSetSnafu)?;
+        } else {
+            let mut dset_writer = DataSetWriter::with_ts(to, ts).context(CreatePrinterSnafu)?;
 
-        Ok(())
+            // write object
+            dset_writer
+                .write_sequence((&self.obj).into_tokens())
+                .context(PrintDataSetSnafu)?;
+
+            Ok(())
+        }
     }
 
     /// Write the file meta group set into the given writer.
@@ -528,7 +555,7 @@ where
     /// without preamble, magic code, nor file meta group.
     ///
     /// The transfer syntax is selected from the file meta table.
-    pub fn write_dataset<W: Write>(&self, to: W) -> Result<(), WriteError> {
+    pub fn write_dataset<W: Write + 'static>(&self, to: W) -> Result<(), WriteError> {
         let to = BufWriter::new(to);
 
         // prepare encoder
@@ -537,14 +564,27 @@ where
             .with_context(|| WriteUnsupportedTransferSyntaxSnafu {
                 uid: self.meta.transfer_syntax.clone(),
             })?;
-        let mut dset_writer = DataSetWriter::with_ts(to, ts).context(CreatePrinterSnafu)?;
+        if let Codec::Dataset(Some(adapter))= ts.codec() {
+            let adapter = adapter.adapt_writer(Box::new(to));
+            let mut dset_writer = DataSetWriter::with_ts(adapter, ts).context(CreatePrinterSnafu)?;
+
+            // write object
+            dset_writer
+                .write_sequence((&self.obj).into_tokens())
+                .context(PrintDataSetSnafu)?;
 
-        // write object
-        dset_writer
-            .write_sequence((&self.obj).into_tokens())
-            .context(PrintDataSetSnafu)?;
+            Ok(())
 
-        Ok(())
+        } else {
+            let mut dset_writer = DataSetWriter::with_ts(to, ts).context(CreatePrinterSnafu)?;
+
+            // write object
+            dset_writer
+                .write_sequence((&self.obj).into_tokens())
+                .context(PrintDataSetSnafu)?;
+
+            Ok(())
+        }
     }
 }
 

object/src/mem.rs

@@ -238,7 +238,7 @@ impl InMemDicomObject<StandardDataDictionary> {
         cs: SpecificCharacterSet,
     ) -> Result<Self, ReadError>
     where
-        S: Read,
+        S: Read + 'static,
     {
         Self::read_dataset_with_dict_ts_cs(from, StandardDataDictionary, ts, cs)
     }
@@ -252,7 +252,7 @@ impl InMemDicomObject<StandardDataDictionary> {
     #[inline]
     pub fn read_dataset_with_ts<S>(from: S, ts: &TransferSyntax) -> Result<Self, ReadError>
     where
-        S: Read,
+        S: Read + 'static,
     {
         Self::read_dataset_with_dict_ts_cs(
             from,
@@ -662,7 +662,7 @@ where
         ts: &TransferSyntax,
     ) -> Result<Self, ReadError>
     where
-        S: Read,
+        S: Read + 'static,
         D: DataDictionary,
     {
         Self::read_dataset_with_dict_ts_cs(from, dict, ts, SpecificCharacterSet::default())
@@ -682,12 +682,19 @@ where
         cs: SpecificCharacterSet,
     ) -> Result<Self, ReadError>
     where
-        S: Read,
+        S: Read + 'static,
         D: DataDictionary,
     {
         let from = BufReader::new(from);
-        let mut dataset = DataSetReader::new_with_ts_cs(from, ts, cs).context(CreateParserSnafu)?;
-        InMemDicomObject::build_object(&mut dataset, dict, false, Length::UNDEFINED, None)
+        if let Codec::Dataset(Some(adapter)) = ts.codec() {
+            let adapter = adapter.adapt_reader(Box::new(from));
+            let mut dataset =
+                DataSetReader::new_with_ts_cs(adapter, ts, cs).context(CreateParserSnafu)?;
+            InMemDicomObject::build_object(&mut dataset, dict, false, Length::UNDEFINED, None)
+        } else {
+            let mut dataset = DataSetReader::new_with_ts_cs(from, ts, cs).context(CreateParserSnafu)?;
+            InMemDicomObject::build_object(&mut dataset, dict, false, Length::UNDEFINED, None)
+        }
     }
 
     // Standard methods follow. They are not placed as a trait implementation
@@ -1768,7 +1775,9 @@ where
     /// in which then that character set will be used.
     ///
     /// Note: [`write_dataset_with_ts`] and [`write_dataset_with_ts_cs`]
-    /// may be easier to use.
+    /// may be easier to use and _will_ apply a dataset adapter (such as
+    /// DeflatedExplicitVRLittleEndian (1.2.840.10008.1.2.99)) whereas this
+    /// method will _not_
     ///
     /// [`write_dataset_with_ts`]: #method.write_dataset_with_ts
     /// [`write_dataset_with_ts_cs`]: #method.write_dataset_with_ts_cs
@@ -1802,18 +1811,30 @@ where
         cs: SpecificCharacterSet,
     ) -> Result<(), WriteError>
     where
-        W: Write,
+        W: Write + 'static,
     {
-        // prepare data set writer
-        let mut dset_writer = DataSetWriter::with_ts_cs(to, ts, cs).context(CreatePrinterSnafu)?;
-        let required_options = IntoTokensOptions::new(self.charset_changed);
+        if let Codec::Dataset(Some(adapter)) = ts.codec() {
+            let adapter = adapter.adapt_writer(Box::new(to));
+            // prepare data set writer
+            let mut dset_writer = DataSetWriter::with_ts(adapter, ts).context(CreatePrinterSnafu)?;
 
-        // write object
-        dset_writer
-            .write_sequence(self.into_tokens_with_options(required_options))
-            .context(PrintDataSetSnafu)?;
+            // write object
+            dset_writer
+                .write_sequence(self.into_tokens())
+                .context(PrintDataSetSnafu)?;
 
-        Ok(())
+            Ok(())
+        } else {
+            // prepare data set writer
+            let mut dset_writer = DataSetWriter::with_ts_cs(to, ts, cs).context(CreatePrinterSnafu)?;
+
+            // write object
+            dset_writer
+                .write_sequence(self.into_tokens())
+                .context(PrintDataSetSnafu)?;
+
+            Ok(())
+        }
     }
 
     /// Write this object's data set into the given writer,
@@ -1825,7 +1846,7 @@ where
     /// after which the text encoder is overridden accordingly.
     pub fn write_dataset_with_ts<W>(&self, to: W, ts: &TransferSyntax) -> Result<(), WriteError>
     where
-        W: Write,
+        W: Write + 'static,
     {
         self.write_dataset_with_ts_cs(to, ts, SpecificCharacterSet::default())
     }

transfer-syntax-registry/Cargo.toml

@@ -100,3 +100,5 @@ features = ["native"]
 
 [dev-dependencies]
 dicom-test-files = "0.3"
+dicom-object = { path = "../object" }
+dicom-pixeldata = { path = "../pixeldata" }

transfer-syntax-registry/tests/deflate.rs

@@ -1,20 +1,38 @@
 
-use std::{io::BufReader, fs::File};
+use std::{io::BufReader, fs::{metadata, File}};
 
-// use dicom_object::OpenFileOptions;
-// use dicom_pixeldata::PixelDecoder;
 
-// #[test]
-// fn test_read_data_with_preamble() {
-//     let path = dicom_test_files::path("pydicom/image_dfl.dcm").expect("test DICOM file should exist");
-//     let source = BufReader::new(File::open(path).unwrap());
+use dicom_object::OpenFileOptions;
+use dicom_pixeldata::PixelDecoder;
 
-//     // should read preamble even though it's from a reader
-//     let object = OpenFileOptions::new()
-//         .from_reader(source)
-//         .expect("Should read from source successfully");
+#[test]
+fn test_read_data_deflated() {
+    let path = dicom_test_files::path("pydicom/image_dfl.dcm").expect("test DICOM file should exist");
+    let source = BufReader::new(File::open(path).unwrap());
 
-//     let res = object.decode_pixel_data();
-//     println!("{:?}", res);
+    // should read preamble even though it's from a reader
+    let object = OpenFileOptions::new()
+        .from_reader(source)
+        .expect("Should read from source successfully");
 
-// }
+    let res = object.decode_pixel_data().unwrap();
+    assert_eq!((
+        res.rows() as usize * 
+        res.columns() as usize *
+        res.number_of_frames() as usize), res.data().len() as usize);
+}
+
+#[test]
+fn write_deflated(){
+    let path = dicom_test_files::path("pydicom/image_dfl.dcm").expect("test DICOM file should exist");
+    let source = BufReader::new(File::open(path.clone()).unwrap());
+
+    // should read preamble even though it's from a reader
+    let object = OpenFileOptions::new()
+        .from_reader(source)
+        .expect("Should read from source successfully");
+
+    let mut buf = Vec::<u8>::new();
+    object.write_all(&mut buf).unwrap();
+    assert_eq!(buf.len(), metadata(path).unwrap().len() as usize);
+}