An easy-to-use Grassroots DICOM Library wrapper designed to convert DICOM files transfer syntaxes and photometric interpretation.

Usage

You need CMake to build GDCM Library.

Linux Ubuntu:

sudo apt-get install cmake

Windows & MacOS:

Download CMake directly from www.cmake.org/download page.

Quickstart

Copy this code and make sure you have a DICOM file to test (DICOM file samples).

use std::io::prelude::*;
use std::fs::File;
use gdcm_conv::{TransferSyntax, PhotometricInterpretation};

// Read input file
let mut ibuffer = Vec::new();
let mut ifile = File::open("test.dcm").unwrap();    
ifile.read_to_end(&mut ibuffer).unwrap();

// Transcode DICOM file
let obuffer = match gdcm_conv::pipeline(
// Input DICOM file buffer
ibuffer,
// Estimated Length
None,
// First Transfer Syntax conversion
TransferSyntax::JPEG2000Lossless,
// Photometric conversion
PhotometricInterpretation::None,
// Second Transfer Syntax conversion
TransferSyntax::None,
) {
Ok(t) => t,
Err(e) => {
eprintln!("{}", e);
return;
}
};

// Create output file and save
let mut ofile = File::create("output.dcm").unwrap();
ofile.write_all(&obuffer).unwrap();

How it works

The gdcm_conv library takes as input the content of the DICOM file. It reuse the source vector allocating an estimated size to avoid cloned memory. The default estimad length is 3 times the input file size, the worst case, changing from a compressed image (like JPEG2000) to raw. Is recommended to use an estimated calculation, to minimize memory allocation.

If the allocated size is not enough, the library will re-allocate to the correct size and execute the FFI function again.

To estimate the output length you could use this aproximation:

(0028,0100) bits_allocated (0028,0004) photometric_interpretation (0028,0008) number_of_frames (0028,0010) rows (0028,0011) columns

// MAX HEADER SIZE const MAX_HEADER_SIZE: usize = 5000;

let a = match bits_allocated { 8 => 1, 16 => 2, };

let b = match photometric_interpretation { "MONOCHROME1" => 1, "MONOCHROME2" => 1, _ => 3, };

let estimad_length = (a * b * rows * columns * number_of_frames) + MAX_HEADER_SIZE;

The library works as a pipeline with a first transfer syntax conversion (PRE-TRANSFER), a photometric conversion and a final transfer syntax conversion (POST-TRANSFER). If you set to None it don't execute the step. Usually, you will use only the first and/or second step.

I setup this way because in some cases is needed two transfer syntax transcoding like this example:

The conversion from JPEG Baseline (Process 1) 1.2.840.10008.1.2.4.50 with YBR_FULL or YBR_FULL_422 to JPEG2000 lossles, you need to change to Explicit Little Endian transfer syntax, then to an RGB photometric interpretation and finally to JPG2000, to avoid GDCM color interpretation issue.