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Merge pull request #532 from Enet4/chore/toimage/cli-tweaks
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Tweak toimage
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@Enet4
Enet4 authored Jul 6, 2024
2 parents 493e03c + f11d4fd commit 89c4f1c
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Showing 2 changed files with 107 additions and 56 deletions.
9 changes: 5 additions & 4 deletions toimage/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -11,20 +11,21 @@ This tool is part of the [DICOM-rs](https://github.com/Enet4/dicom-rs) project.
## Usage

```none
dicom-toimage [OPTIONS] [FILES]...
dicom-toimage [OPTIONS] <FILES>...
Arguments:
[FILES]... Path to the DICOM file to convert
<FILES>... Paths to the DICOM files (or directories) to convert
Options:
-r, --recursive Parse directory recursively
-o, --out <OUTPUT> Path to the output image, this should include the file extension (default is to replace input extension with `.png`)
-d, --outdir <OUTDIR> Path to the output directory if multiple files are given Conflicts with `output`
-o, --out <OUTPUT> Path to the output image, including file extension (replaces input extension with `.png` by default)
-d, --outdir <OUTDIR> Path to the output directory in bulk conversion mode, conflicts with `output`
-e, --ext <EXT> Extension when converting multiple files (default is to replace input extension with `.png`)
-F, --frame <FRAME_NUMBER> Frame number (0-indexed) [default: 0]
--8bit Force output bit depth to 8 bits per sample
--16bit Force output bit depth to 16 bits per sample
--unwrap Output the raw pixel data instead of decoding it
--fail-first Stop on the first failed conversion
-v, --verbose Print more information about the image and the output file
-h, --help Print help
-V, --version Print version
Expand Down
154 changes: 102 additions & 52 deletions toimage/src/main.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -10,24 +10,25 @@ use dicom_pixeldata::{ConvertOptions, PixelDecoder};
use snafu::{OptionExt, Report, ResultExt, Snafu, Whatever};
use tracing::{error, warn, Level};

/// Convert a DICOM file into an image file
/// Convert DICOM files into image files
#[derive(Debug, Parser)]
#[command(version)]
struct App {
/// Path to the DICOM file to convert
/// A directory or multiple paths to the DICOM files to convert
#[arg(required(true))]
files: Vec<PathBuf>,

/// Parse directory recursively
/// Parse the given directory recursively
#[arg(short = 'r', long = "recursive")]
recursive: bool,

/// Path to the output image, this should include the file extension
/// (default is to replace input extension with `.png`)
/// Path to the output image, including file extension
/// (replaces input extension with `.png` by default)
#[arg(short = 'o', long = "out")]
output: Option<PathBuf>,

/// Path to the output directory if multiple files are given
/// Conflicts with `output`
/// Path to the output directory in bulk conversion mode,
/// conflicts with `output`
#[arg(short = 'd', long = "outdir", conflicts_with = "output")]
outdir: Option<PathBuf>,

Expand All @@ -43,6 +44,10 @@ struct App {
#[clap(flatten)]
image_options: ImageOptions,

/// Stop on the first failed conversion
#[arg(long)]
fail_first: bool,

/// Print more information about the image and the output file
#[arg(short = 'v', long = "verbose")]
verbose: bool,
Expand All @@ -68,7 +73,6 @@ struct ImageOptions {
unwrap: bool,
}


#[derive(Debug, Snafu)]
enum Error {
#[snafu(display("could not read DICOM file {}", path.display()))]
Expand Down Expand Up @@ -165,6 +169,7 @@ fn run(args: App) -> Result<(), Error> {
ext,
frame_number,
image_options,
fail_first,
verbose,
} = args;

Expand All @@ -184,73 +189,97 @@ fn run(args: App) -> Result<(), Error> {
}

dicoms.iter().for_each(|file| {
convert_single_file(
&file.0,
let output = build_output_path(
false,
file.1.clone(),
outdir.clone(),
ext.clone(),
image_options.unwrap,
);

convert_single_file(
&file.0,
false,
output,
frame_number,
image_options,
verbose,
)
.unwrap();
.unwrap_or_else(|_| {
if fail_first {
std::process::exit(-2);
}
});
});
}
false => {
let file =
open_file(file).with_context(|_| ReadFileSnafu { path: file.clone() })?;

let output_is_set = output.is_some();
let output = build_output_path(
output_is_set,
output.unwrap_or(files[0].clone()),
outdir.clone(),
ext.clone(),
image_options.unwrap,
);

convert_single_file(
&file,
output.is_some(),
output.unwrap_or(files[0].clone()),
outdir,
ext,
output_is_set,
output,
frame_number,
image_options,
verbose,
)?;
)
.or_else(|e| if fail_first { Err(e) } else { Ok(()) })?;
}
}
} else {
files.iter().for_each(|file| {
let dicom_file = open_file(file)
.with_context(|_| ReadFileSnafu { path: file.clone() })
.unwrap();
convert_single_file(
&dicom_file,
for file in files.iter() {
let dicom_file =
match open_file(file).with_context(|_| ReadFileSnafu { path: file.clone() }) {
Ok(file) => file,
Err(e) => {
if fail_first {
return Err(e);
} else {
continue;
}
}
};

let output = build_output_path(
false,
file.clone(),
outdir.clone(),
ext.clone(),
image_options.unwrap,
);

convert_single_file(
&dicom_file,
false,
output,
frame_number,
image_options,
verbose,
)
.unwrap();
});
.or_else(|e| if fail_first { Err(e) } else { Ok(()) })?;
}
}

Ok(())
}

fn convert_single_file(
file: &FileDicomObject<InMemDicomObject>,
fn build_output_path(
output_is_set: bool,
mut output: PathBuf,
outdir: Option<PathBuf>,
ext: Option<String>,
frame_number: u32,
image_options: ImageOptions,
verbose: bool,
) -> Result<(), Error> {
let ImageOptions {
force_8bit,
force_16bit,
unwrap,
} = image_options;

unwrap: bool,
) -> PathBuf {
// check if there is a .dcm extension, otherwise, add it
if output.extension() != Some("dcm".as_ref()) && !output_is_set {
let pathstr = output.to_str().unwrap();
Expand All @@ -263,6 +292,31 @@ fn convert_single_file(
output = outdir.join(output.file_name().unwrap());
}

if !unwrap && !output_is_set {
if let Some(extension) = ext {
output.set_extension(extension);
} else {
output.set_extension("png");
}
}

output
}

fn convert_single_file(
file: &FileDicomObject<InMemDicomObject>,
output_is_set: bool,
mut output: PathBuf,
frame_number: u32,
image_options: ImageOptions,
verbose: bool,
) -> Result<(), Error> {
let ImageOptions {
force_8bit,
force_16bit,
unwrap,
} = image_options;

if unwrap {
if !output_is_set {
match file.meta().transfer_syntax() {
Expand All @@ -284,10 +338,10 @@ fn convert_single_file(
}
}

let pixeldata = file.get(tags::PIXEL_DATA).unwrap_or_else(|| {
error!("DICOM file has no pixel data");
std::process::exit(-2);
});
let pixeldata = file.get(tags::PIXEL_DATA).with_context(|| {
error!("{}: DICOM file has no pixel data", output.display());
MissingPropertySnafu { name: "PixelData" }
})?;

let out_data = match pixeldata.value() {
DicomValue::PixelSequence(seq) => {
Expand All @@ -306,10 +360,14 @@ fn convert_single_file(
let fragment =
seq.fragments()
.get(frame_number as usize)
.unwrap_or_else(|| {
error!("Frame number {} is out of range", frame_number);
std::process::exit(-2);
});
.with_context(|| {
error!(
"{}: Frame number {} is out of range",
output.display(),
frame_number
);
FrameOutOfBoundsSnafu { frame_number }
})?;

Cow::Borrowed(&fragment[..])
} else {
Expand Down Expand Up @@ -386,14 +444,6 @@ fn convert_single_file(
std::fs::create_dir_all(output.parent().unwrap()).unwrap();
std::fs::write(output, out_data).context(SaveDataSnafu)?;
} else {
if !output_is_set {
if let Some(extension) = ext {
output.set_extension(extension);
} else {
output.set_extension("png");
}
}

let pixel = file
.decode_pixel_data_frame(frame_number)
.context(DecodePixelDataSnafu)?;
Expand Down

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