From cb72c736fbbbd9e20abcd19cfcd45bbc6b5ab044 Mon Sep 17 00:00:00 2001
From: Nathan Richman <naterichman@flywheel.io>
Date: Tue, 21 Nov 2023 10:24:57 -0600
Subject: [PATCH 01/10] [dicom-dump] Add json output format

---
 Cargo.lock       | 25 ++++++++++++++++++++++++-
 dump/Cargo.toml  |  3 +++
 dump/src/lib.rs  | 38 ++++++++++++++++++++++----------------
 dump/src/main.rs | 31 +++++++++++++++++++++++++------
 4 files changed, 74 insertions(+), 23 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index de36e3e3e..981446bd0 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -80,6 +80,17 @@ version = "1.0.75"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6"
 
+[[package]]
+name = "atty"
+version = "0.2.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8"
+dependencies = [
+ "hermit-abi 0.1.19",
+ "libc",
+ "winapi",
+]
+
 [[package]]
 name = "autocfg"
 version = "1.1.0"
@@ -394,13 +405,16 @@ dependencies = [
 name = "dicom-dump"
 version = "0.6.2"
 dependencies = [
+ "atty",
  "clap",
  "dicom-core",
  "dicom-dictionary-std",
  "dicom-encoding",
+ "dicom-json",
  "dicom-object",
  "dicom-transfer-syntax-registry",
  "owo-colors",
+ "serde_json",
  "snafu",
  "term_size",
 ]
@@ -978,6 +992,15 @@ version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
 
+[[package]]
+name = "hermit-abi"
+version = "0.1.19"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33"
+dependencies = [
+ "libc",
+]
+
 [[package]]
 name = "hermit-abi"
 version = "0.3.3"
@@ -1061,7 +1084,7 @@ version = "0.4.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "cb0889898416213fab133e1d33a0e5858a48177452750691bde3666d0fdbaf8b"
 dependencies = [
- "hermit-abi",
+ "hermit-abi 0.3.3",
  "rustix",
  "windows-sys 0.48.0",
 ]
diff --git a/dump/Cargo.toml b/dump/Cargo.toml
index d165e1b3d..b9a3f4e8e 100644
--- a/dump/Cargo.toml
+++ b/dump/Cargo.toml
@@ -34,3 +34,6 @@ dicom-object = { path = "../object/", version = "0.6.3" }
 dicom-transfer-syntax-registry = { path = "../transfer-syntax-registry/", version = "0.6.2", default-features = false }
 dicom-dictionary-std = { path = "../dictionary-std/", version = "0.6.1" }
 owo-colors = { version = "4.0.0-rc.1", features = ["supports-colors"] }
+dicom-json = { version = "0.1.0", path = "../json" }
+serde_json = "1.0.108"
+atty = "0.2.14"
diff --git a/dump/src/lib.rs b/dump/src/lib.rs
index 724d6dbcf..121f7b096 100644
--- a/dump/src/lib.rs
+++ b/dump/src/lib.rs
@@ -32,6 +32,7 @@
 //! options.width(100).dump_file(&obj)?;
 //! # Result::<(), Box<dyn std::error::Error>>::Ok(())
 //! ```
+use clap::ValueEnum;
 #[cfg(feature = "sop-class")]
 use dicom_core::dictionary::UidDictionary;
 use dicom_core::dictionary::{DataDictionary, DataDictionaryEntry};
@@ -41,6 +42,7 @@ use dicom_core::VR;
 #[cfg(feature = "sop-class")]
 use dicom_dictionary_std::StandardSopClassDictionary;
 use dicom_encoding::transfer_syntax::TransferSyntaxIndex;
+use dicom_json::DicomJson;
 use dicom_object::mem::{InMemDicomObject, InMemElement};
 use dicom_object::{FileDicomObject, FileMetaTable, StandardDataDictionary};
 use dicom_transfer_syntax_registry::TransferSyntaxRegistry;
@@ -50,12 +52,10 @@ use std::fmt::{self, Display, Formatter};
 use std::io::{stdout, Result as IoResult, Write};
 use std::str::FromStr;
 
-/// An enum of all supported output formats for dumping DICOM data.
-#[derive(Debug, Copy, Clone, Eq, Hash, PartialEq)]
-#[non_exhaustive]
+#[derive(ValueEnum, Clone, Debug, PartialEq, Default)]
 pub enum DumpFormat {
-    /// The main DICOM dump format adopted by the project.
-    ///
+    /// Text dump of DICOM file
+    /// 
     /// It is primarily designed to be human readable,
     /// although its output can be used to recover the original object
     /// in its uncut form (no limit width).
@@ -64,15 +64,12 @@ pub enum DumpFormat {
     ///
     /// Note that this format is not stabilized,
     /// and may change with subsequent versions of the crate.
-    Main,
+    #[default]
+    Text,
+    /// Dicom part 18 chapter F json format provided by the json crate
+    Json,
 }
 
-/// The [main output format](DumpFormat::Main) is used by default.
-impl Default for DumpFormat {
-    fn default() -> Self {
-        DumpFormat::Main
-    }
-}
 
 /// Options and flags to configure how to dump a DICOM file or object.
 ///
@@ -227,14 +224,23 @@ impl DumpOptions {
         } else {
             (true, true)
         };
+        match self.format {
+            DumpFormat::Text => {
+                meta_dump(&mut to, meta, if no_limit { u32::MAX } else { width })?;
 
-        meta_dump(&mut to, meta, if no_limit { u32::MAX } else { width })?;
+                writeln!(to, "{:-<58}", "")?;
 
-        writeln!(to, "{:-<58}", "")?;
+                dump(&mut to, obj, width, 0, no_text_limit, no_limit)?;
 
-        dump(&mut to, obj, width, 0, no_text_limit, no_limit)?;
+                Ok(())
+            },
+            DumpFormat::Json => {
+                let json_obj = DicomJson::from(obj);
+                println!("{}", serde_json::to_string_pretty(&json_obj)?);
+                Ok(())
+            }
+        }
 
-        Ok(())
     }
 
     /// Dump the contents of a DICOM object to standard output.
diff --git a/dump/src/main.rs b/dump/src/main.rs
index aa374fccb..aeba91fff 100644
--- a/dump/src/main.rs
+++ b/dump/src/main.rs
@@ -1,7 +1,7 @@
 //! A CLI tool for inspecting the contents of a DICOM file
 //! by printing it in a human readable format.
 use clap::Parser;
-use dicom_dump::{ColorMode, DumpOptions};
+use dicom_dump::{ColorMode, DumpOptions, DumpFormat};
 use dicom_object::open_file;
 use snafu::{Report, Whatever};
 use std::io::ErrorKind;
@@ -12,6 +12,7 @@ const ERROR_READ: i32 = -2;
 /// Exit code for when an error emerged while dumping the file.
 const ERROR_PRINT: i32 = -3;
 
+
 /// Dump the contents of DICOM files
 #[derive(Debug, Parser)]
 #[command(version)]
@@ -20,7 +21,10 @@ struct App {
     #[clap(required = true)]
     files: Vec<PathBuf>,
     /// Print text values to the end
-    /// (limited to `width` by default)
+    /// (limited to `width` by default).
+    /// 
+    /// Does not apply if output is not a tty 
+    /// or if output type is json
     #[clap(long = "no-text-limit")]
     no_text_limit: bool,
     /// Print all values to the end
@@ -28,7 +32,10 @@ struct App {
     #[clap(long = "no-limit")]
     no_limit: bool,
     /// The width of the display
-    /// (default is to check automatically)
+    /// (default is to check automatically).
+    /// 
+    /// Does not apply if output is not a tty 
+    /// or if output type is json
     #[clap(short = 'w', long = "width")]
     width: Option<u32>,
     /// The color mode
@@ -37,6 +44,14 @@ struct App {
     /// Fail if any errors are encountered
     #[clap(long = "fail-first")]
     fail_first: bool,
+    /// Output format
+    #[arg(value_enum)]
+    #[clap(short = 'o', long = "output", default_value = "text")]
+    output_type: DumpFormat
+}
+
+fn is_terminal() -> bool {
+    atty::is(atty::Stream::Stdout)
 }
 
 fn main() {
@@ -54,6 +69,7 @@ fn run() -> Result<(), Whatever> {
         width,
         color,
         fail_first,
+        output_type,
     } = App::parse();
 
     let width = width
@@ -63,14 +79,17 @@ fn run() -> Result<(), Whatever> {
     let mut options = DumpOptions::new();
     options
         .no_text_limit(no_text_limit)
-        .no_limit(no_limit)
+        // No limit when output is not a terminal
+        .no_limit(if !is_terminal() { true } else {no_limit})
         .width(width)
-        .color_mode(color);
+        .color_mode(color)
+        .format(output_type);
     let fail_first = filenames.len() == 1 || fail_first;
     let mut errors: i32 = 0;
 
     for filename in &filenames {
-        println!("{}: ", filename.display());
+        // Write filename to stderr to make piping easier, i.e. dicom-dump -o json file.dcm | jq
+        eprintln!("{}: ", filename.display());
         match open_file(filename) {
             Err(e) => {
                 eprintln!("{}", Report::from_error(e));

From a61b2dced066d2fe4d5de5cd3128d2f9d2213de5 Mon Sep 17 00:00:00 2001
From: Nathan Richman <naterichman@flywheel.io>
Date: Tue, 21 Nov 2023 14:55:31 -0600
Subject: [PATCH 02/10] MAIN: Review suggestions

* Change option from output to format
* Pretty print to writer instead of to string
---
 dump/src/lib.rs  | 2 +-
 dump/src/main.rs | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/dump/src/lib.rs b/dump/src/lib.rs
index 121f7b096..843bfe801 100644
--- a/dump/src/lib.rs
+++ b/dump/src/lib.rs
@@ -236,7 +236,7 @@ impl DumpOptions {
             },
             DumpFormat::Json => {
                 let json_obj = DicomJson::from(obj);
-                println!("{}", serde_json::to_string_pretty(&json_obj)?);
+                serde_json::to_writer_pretty(stdout(), &json_obj)?;
                 Ok(())
             }
         }
diff --git a/dump/src/main.rs b/dump/src/main.rs
index aeba91fff..841d32900 100644
--- a/dump/src/main.rs
+++ b/dump/src/main.rs
@@ -46,8 +46,8 @@ struct App {
     fail_first: bool,
     /// Output format
     #[arg(value_enum)]
-    #[clap(short = 'o', long = "output", default_value = "text")]
-    output_type: DumpFormat
+    #[clap(short = 'f', long = "format", default_value = "text")]
+    format: DumpFormat
 }
 
 fn is_terminal() -> bool {
@@ -69,7 +69,7 @@ fn run() -> Result<(), Whatever> {
         width,
         color,
         fail_first,
-        output_type,
+        format,
     } = App::parse();
 
     let width = width
@@ -83,7 +83,7 @@ fn run() -> Result<(), Whatever> {
         .no_limit(if !is_terminal() { true } else {no_limit})
         .width(width)
         .color_mode(color)
-        .format(output_type);
+        .format(format);
     let fail_first = filenames.len() == 1 || fail_first;
     let mut errors: i32 = 0;
 

From 9da65af79cb0fb9711346d6f994797bfc25a70c0 Mon Sep 17 00:00:00 2001
From: Eduardo Pinho <enet4mikeenet@gmail.com>
Date: Sat, 24 Feb 2024 11:04:58 +0000
Subject: [PATCH 03/10] [dump] Improve doc comment in DumpFormat::Json

---
 dump/src/lib.rs | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dump/src/lib.rs b/dump/src/lib.rs
index 843bfe801..a4ea03a26 100644
--- a/dump/src/lib.rs
+++ b/dump/src/lib.rs
@@ -66,7 +66,8 @@ pub enum DumpFormat {
     /// and may change with subsequent versions of the crate.
     #[default]
     Text,
-    /// Dicom part 18 chapter F json format provided by the json crate
+    /// DICOM part 18 chapter F JSON format,
+    /// provided via [`dicom_json`]
     Json,
 }
 

From 1eb4cf83a8ea4da93d71caa384f12d73ef7e21f8 Mon Sep 17 00:00:00 2001
From: Eduardo Pinho <enet4mikeenet@gmail.com>
Date: Sat, 24 Feb 2024 11:13:47 +0000
Subject: [PATCH 04/10] [dump] Make dump_object work for Json output

+ add dump_json test
---
 dump/src/lib.rs | 66 ++++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 52 insertions(+), 14 deletions(-)

diff --git a/dump/src/lib.rs b/dump/src/lib.rs
index a4ea03a26..dd4b50c63 100644
--- a/dump/src/lib.rs
+++ b/dump/src/lib.rs
@@ -271,24 +271,33 @@ impl DumpOptions {
     where
         D: DataDictionary,
     {
-        match (self.color, to_stdout) {
-            (ColorMode::Never, _) => colored::control::set_override(false),
-            (ColorMode::Always, _) => colored::control::set_override(true),
-            (ColorMode::Auto, false) => colored::control::set_override(false),
-            (ColorMode::Auto, true) => colored::control::unset_override(),
-        }
+        match self.format {
+            DumpFormat::Text => {
+                match (self.color, to_stdout) {
+                    (ColorMode::Never, _) => colored::control::set_override(false),
+                    (ColorMode::Always, _) => colored::control::set_override(true),
+                    (ColorMode::Auto, false) => colored::control::set_override(false),
+                    (ColorMode::Auto, true) => colored::control::unset_override(),
+                }
 
-        let width = determine_width(self.width);
+                let width = determine_width(self.width);
 
-        let (no_text_limit, no_limit) = if to_stdout {
-            (self.no_text_limit, self.no_limit)
-        } else {
-            (true, true)
-        };
+                let (no_text_limit, no_limit) = if to_stdout {
+                    (self.no_text_limit, self.no_limit)
+                } else {
+                    (true, true)
+                };
 
-        dump(&mut to, obj, width, 0, no_text_limit, no_limit)?;
+                dump(&mut to, obj, width, 0, no_text_limit, no_limit)?;
 
-        Ok(())
+                Ok(())
+            }
+            DumpFormat::Json => {
+                let json_obj = DicomJson::from(obj);
+                serde_json::to_writer_pretty(to, &json_obj)?;
+                Ok(())
+            }
+        }
     }
 }
 
@@ -1103,4 +1112,33 @@ mod tests {
             assert_eq!(value, expected.3);
         }
     }
+
+    #[test]
+    fn dump_json() {
+        // create object
+        let obj = InMemDicomObject::from_element_iter(vec![DataElement::new(
+            tags::SOP_INSTANCE_UID,
+            VR::UI,
+            PrimitiveValue::from("1.2.888.123"),
+        )]);
+
+        let mut out = Vec::new();
+        DumpOptions::new()
+            .color_mode(ColorMode::Never)
+            .format(crate::DumpFormat::Json)
+            .dump_object_to(&mut out, &obj)
+            .unwrap();
+
+        let json = std::str::from_utf8(&out).expect("output is not valid UTF-8");
+        assert_eq!(
+            json,
+            r#"{
+  "00080018": {
+    "vr": "UI",
+    "Value": [
+      "1.2.888.123"
+    ]
+  }
+}"#);
+    }
 }

From 7f0704a45f69ed37bd3947952e3a8ded793e7da1 Mon Sep 17 00:00:00 2001
From: Eduardo Pinho <enet4mikeenet@gmail.com>
Date: Sat, 24 Feb 2024 11:21:39 +0000
Subject: [PATCH 05/10] [dump] derive ValueEnum conditionally on "cli" cargo
 feature

---
 dump/src/lib.rs | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/dump/src/lib.rs b/dump/src/lib.rs
index dd4b50c63..6f864f3c2 100644
--- a/dump/src/lib.rs
+++ b/dump/src/lib.rs
@@ -32,6 +32,7 @@
 //! options.width(100).dump_file(&obj)?;
 //! # Result::<(), Box<dyn std::error::Error>>::Ok(())
 //! ```
+#[cfg(feature = "cli")]
 use clap::ValueEnum;
 #[cfg(feature = "sop-class")]
 use dicom_core::dictionary::UidDictionary;
@@ -52,7 +53,8 @@ use std::fmt::{self, Display, Formatter};
 use std::io::{stdout, Result as IoResult, Write};
 use std::str::FromStr;
 
-#[derive(ValueEnum, Clone, Debug, PartialEq, Default)]
+#[derive(Clone, Debug, PartialEq, Default)]
+#[cfg_attr(feature = "cli", derive(ValueEnum))]
 pub enum DumpFormat {
     /// Text dump of DICOM file
     /// 

From cacc762300c5b207f158d95e2803452601e73d4e Mon Sep 17 00:00:00 2001
From: Eduardo Pinho <enet4mikeenet@gmail.com>
Date: Fri, 1 Mar 2024 08:13:07 +0000
Subject: [PATCH 06/10] [echoscu] Tweak msg_id check to avoid type inference
 bug

---
 echoscu/src/main.rs | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/echoscu/src/main.rs b/echoscu/src/main.rs
index 16856eca8..40ac7a9c7 100644
--- a/echoscu/src/main.rs
+++ b/echoscu/src/main.rs
@@ -158,15 +158,13 @@ fn run() -> Result<(), Whatever> {
             }
 
             // msg ID response, should be equal to sent msg ID
-            let msg_id_elem = obj
+            let got_msg_id: u16 = obj
                 .element(tags::MESSAGE_ID_BEING_RESPONDED_TO)
-                .whatever_context("Could not retrieve Message ID from response")?;
+                .whatever_context("Could not retrieve Message ID from response")?
+                .to_int()
+                .whatever_context("Message ID is not a valid integer")?;
 
-            if message_id
-                != msg_id_elem
-                    .to_int()
-                    .whatever_context("Message ID is not a valid integer")?
-            {
+            if message_id != got_msg_id {
                 whatever!("Message ID mismatch");
             }
         }

From eb10e305635a40b672a4c5b556a1fb809f42c2d6 Mon Sep 17 00:00:00 2001
From: Eduardo Pinho <enet4mikeenet@gmail.com>
Date: Fri, 1 Mar 2024 08:28:42 +0000
Subject: [PATCH 07/10] [dump] Drop atty in favor of std::io::IsTerminal

---
 Cargo.lock       | 23 +----------------------
 dump/Cargo.toml  |  1 -
 dump/src/main.rs |  4 ++--
 3 files changed, 3 insertions(+), 25 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 981446bd0..8c27565de 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -80,17 +80,6 @@ version = "1.0.75"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6"
 
-[[package]]
-name = "atty"
-version = "0.2.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8"
-dependencies = [
- "hermit-abi 0.1.19",
- "libc",
- "winapi",
-]
-
 [[package]]
 name = "autocfg"
 version = "1.1.0"
@@ -405,7 +394,6 @@ dependencies = [
 name = "dicom-dump"
 version = "0.6.2"
 dependencies = [
- "atty",
  "clap",
  "dicom-core",
  "dicom-dictionary-std",
@@ -992,15 +980,6 @@ version = "0.4.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8"
 
-[[package]]
-name = "hermit-abi"
-version = "0.1.19"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33"
-dependencies = [
- "libc",
-]
-
 [[package]]
 name = "hermit-abi"
 version = "0.3.3"
@@ -1084,7 +1063,7 @@ version = "0.4.9"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "cb0889898416213fab133e1d33a0e5858a48177452750691bde3666d0fdbaf8b"
 dependencies = [
- "hermit-abi 0.3.3",
+ "hermit-abi",
  "rustix",
  "windows-sys 0.48.0",
 ]
diff --git a/dump/Cargo.toml b/dump/Cargo.toml
index b9a3f4e8e..56a063100 100644
--- a/dump/Cargo.toml
+++ b/dump/Cargo.toml
@@ -36,4 +36,3 @@ dicom-dictionary-std = { path = "../dictionary-std/", version = "0.6.1" }
 owo-colors = { version = "4.0.0-rc.1", features = ["supports-colors"] }
 dicom-json = { version = "0.1.0", path = "../json" }
 serde_json = "1.0.108"
-atty = "0.2.14"
diff --git a/dump/src/main.rs b/dump/src/main.rs
index 841d32900..bafb5aff2 100644
--- a/dump/src/main.rs
+++ b/dump/src/main.rs
@@ -4,7 +4,7 @@ use clap::Parser;
 use dicom_dump::{ColorMode, DumpOptions, DumpFormat};
 use dicom_object::open_file;
 use snafu::{Report, Whatever};
-use std::io::ErrorKind;
+use std::io::{ErrorKind, IsTerminal};
 use std::path::PathBuf;
 
 /// Exit code for when an error emerged while reading the DICOM file.
@@ -51,7 +51,7 @@ struct App {
 }
 
 fn is_terminal() -> bool {
-    atty::is(atty::Stream::Stdout)
+    std::io::stdout().is_terminal()
 }
 
 fn main() {

From fdedb0fccd04d57ad1b737b239096093c4370cd3 Mon Sep 17 00:00:00 2001
From: Nate Richman <naterichman@flywheel.io>
Date: Mon, 5 Aug 2024 11:46:32 -0500
Subject: [PATCH 08/10] MAIN: Add serialization for encapsulated pixel data

---
 json/src/ser/mod.rs | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/json/src/ser/mod.rs b/json/src/ser/mod.rs
index f9a9fd1e4..bfb433fd1 100644
--- a/json/src/ser/mod.rs
+++ b/json/src/ser/mod.rs
@@ -3,7 +3,7 @@
 use std::io::Write;
 
 use crate::DicomJson;
-use dicom_core::{header::Header, DicomValue, PrimitiveValue, Tag, VR};
+use dicom_core::{header::Header, value::PixelFragmentSequence, DicomValue, PrimitiveValue, Tag, VR};
 use dicom_dictionary_std::StandardDataDictionary;
 use dicom_object::{mem::InMemElement, DefaultDicomObject, InMemDicomObject};
 use serde::{ser::SerializeMap, Serialize, Serializer};
@@ -216,8 +216,8 @@ impl<D> Serialize for DicomJson<&'_ InMemElement<D>> {
             DicomValue::Sequence(seq) => {
                 serializer.serialize_entry("Value", &DicomJson(seq.items()))?;
             }
-            DicomValue::PixelSequence(_seq) => {
-                panic!("serialization of encapsulated pixel data is not supported")
+            DicomValue::PixelSequence(seq) => {
+                serializer.serialize_entry("Value", &DicomJson(seq))?;
             }
             DicomValue::Primitive(PrimitiveValue::Empty) => {
                 // no-op
@@ -281,6 +281,20 @@ impl<D> Serialize for DicomJson<InMemElement<D>> {
     }
 }
 
+impl Serialize for DicomJson<&PixelFragmentSequence<Vec<u8>>> {
+    fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
+    where
+        S: Serializer,
+    {
+        let offset_table = self.inner().offset_table();
+        let fragments = self.inner().fragments();
+        let mut map = serializer.serialize_map(Some(2))?;
+        map.serialize_entry("Offset Table", offset_table)?;
+        map.serialize_entry("Pixel Fragments", fragments)?;
+        map.end()
+    }
+}
+
 impl From<Tag> for DicomJson<Tag> {
     fn from(value: Tag) -> Self {
         Self(value)

From e59af6cf713832e53a5029f98c8f079911d77274 Mon Sep 17 00:00:00 2001
From: Nate Richman <naterichman@flywheel.io>
Date: Mon, 5 Aug 2024 11:57:17 -0500
Subject: [PATCH 09/10] MAIN: Remove unused import

---
 json/src/ser/mod.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/json/src/ser/mod.rs b/json/src/ser/mod.rs
index 208a8b87b..03c11ec32 100644
--- a/json/src/ser/mod.rs
+++ b/json/src/ser/mod.rs
@@ -7,7 +7,7 @@ use dicom_core::{header::Header, value::PixelFragmentSequence, DicomValue, Primi
 use dicom_dictionary_std::StandardDataDictionary;
 use dicom_object::{mem::InMemElement, DefaultDicomObject, InMemDicomObject};
 use serde::{
-    ser::{Error as _, SerializeMap},
+    ser::SerializeMap,
     Serialize, Serializer,
 };
 

From 69c49a3387bddb4a225d86b1651916971cf46762 Mon Sep 17 00:00:00 2001
From: Nate Richman <naterichman@flywheel.io>
Date: Wed, 7 Aug 2024 10:56:04 -0500
Subject: [PATCH 10/10] MAIN: Ignore encapsulated pixel data in json output

---
 dump/src/main.rs    | 14 ++++++++++++--
 json/src/ser/mod.rs |  4 ++--
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/dump/src/main.rs b/dump/src/main.rs
index cded31be7..ea860a19a 100644
--- a/dump/src/main.rs
+++ b/dump/src/main.rs
@@ -1,6 +1,7 @@
 //! A CLI tool for inspecting the contents of a DICOM file
 //! by printing it in a human readable format.
 use clap::Parser;
+use dicom_dictionary_std::tags;
 use dicom_dump::{ColorMode, DumpOptions, DumpFormat};
 use dicom_object::open_file;
 use snafu::{Report, Whatever};
@@ -47,7 +48,7 @@ struct App {
     /// Output format
     #[arg(value_enum)]
     #[clap(short = 'f', long = "format", default_value = "text")]
-    format: DumpFormat
+    format: DumpFormat,
 }
 
 fn is_terminal() -> bool {
@@ -98,7 +99,16 @@ fn run() -> Result<(), Whatever> {
                 }
                 errors += 1;
             }
-            Ok(obj) => {
+            Ok(mut obj) => {
+                if options.format == DumpFormat::Json {
+                    // JSON output doesn't currently support encapsulated pixel data
+                    if let Ok(elem) = obj.element(tags::PIXEL_DATA){
+                        if let dicom_core::value::Value::PixelSequence(_) = elem.value(){
+                            eprintln!("[WARN] Encapsulated pixel data not supported in JSON output, skipping");
+                            obj.remove_element(tags::PIXEL_DATA);
+                        }
+                    }
+                }
                 if let Err(ref e) = options.dump_file(&obj) {
                     if e.kind() == ErrorKind::BrokenPipe {
                         // handle broken pipe separately with a no-op
diff --git a/json/src/ser/mod.rs b/json/src/ser/mod.rs
index 03c11ec32..525743f64 100644
--- a/json/src/ser/mod.rs
+++ b/json/src/ser/mod.rs
@@ -219,8 +219,8 @@ impl<D> Serialize for DicomJson<&'_ InMemElement<D>> {
             DicomValue::Sequence(seq) => {
                 serializer.serialize_entry("Value", &DicomJson(seq.items()))?;
             }
-            DicomValue::PixelSequence(seq) => {
-                serializer.serialize_entry("Value", &DicomJson(seq))?;
+            DicomValue::PixelSequence(_seq) => {
+                //serializer.serialize_entry("Value", &DicomJson(seq))?;
             }
             DicomValue::Primitive(PrimitiveValue::Empty) => {
                 // no-op