Crate gdcm_conv

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.

Enums

Error

GDCMError

PhotometricInterpretation

TransferSyntax

Functions

pipeline