README
¶
dicom
High Performance Golang DICOM Medical Image Parser
👀 Note: please tell me more about how you use this tool here (or how you plan to use it).
This is a (hard-ish) fork of work I did at gradienthealth which built on top of go-dicom--a golang DICOM image parsing library and command line tool. We have been working on this package with the goal of building a full-featured and high-performance dicom parser in Golang with major new features and improvements. I will continue to add some (potentially API breaking) improvements on my repository fork here, and have added many such improvements (and general maintenance) to date.
👀 Note: there is a fairly significant rewrite and refactor I am exploring that's in progress at branch s/1.0-rewrite, which further cleans up the API, rewrites critical sections of the code, improves performance, and more.
So far, improvements that have made on top of go-dicom include:
- parsing and extracting multi-frame DICOM imagery (both encapsulated and native pixel data)
- exposing a
Parsergolang interface to make mock-based testing easier for clients - Channel-based streaming of
Frames to a client as they are parsed out of the dicom - Parsing performance improvements
- General refactors to the go-dicom code (though there's more work to be done here) for maintainability an readability.
Usage
To use this in your golang project, import github.com/suyashkumar/dicom and then you can use dicom.Parser for your parsing needs:
p, err := dicom.NewParserFromFile("myfile.dcm", nil)
opts := dicom.ParseOptions{DropPixelData: true}
element := p.ParseNext(opts) // parse and return the next dicom element
// or
dataset, err := p.Parse(opts) // parse whole dicom
More details about the package can be found in the godoc
CLI Tool
A CLI tool that uses this package to parse imagery and metadata out of DICOMs is provided in the dicomutil package. All dicom tags present are printed to STDOUT by default.
Installation
You can download the prebuilt binaries from the releases tab, or use the following to download the binary at the command line using my getbin tool:
wget -qO- "https://getbin.io/suyashkumar/dicom" | tar xvz
(This attempts to infer your OS and 301 redirects wget to the latest github release asset for your system. Downloads come from GitHub releases).
Usage
dicomutil --extract-images-stream myfile.dcm
Note: for some dicoms (with native pixel data) no automatic intensity scaling is applied yet (this is coming). You can apply this in your image viewer if needed (in Preview on mac, go to Tools->Adjust Color).
Docker build
To build the tool for all platforms (Mac, Windows, Linux) from source using docker, execute the following in the cloned repo:
docker build . -t godicom
docker run -it -v $PWD/build:/go/src/github.com/suyashkumar/dicom/build godicom make release
You can then use the binaries that will show up in the build folder in your current working directory
Build manually
To build manually, ensure you have make, golang, and dep installed on your machine. Clone (or go get) this repo into your gopath then:
make
Acknowledgements
- Original go-dicom
- Grailbio go-dicom -- commits from their fork were applied to ours
- GradientHealth for supporting work I did on this while there gradienthealth/dicom
- Innolitics DICOM browser
- DICOM Specification
Documentation
¶
Index ¶
- type DirectoryRecord
- type ParseOptions
- type Parser
- func NewParser(in io.Reader, bytesToRead int64, frameChannel chan *frame.Frame) (Parser, error)
- func NewParserFromBytes(data []byte, frameChannel chan *frame.Frame) (Parser, error)
- func NewParserFromDecoder(decoder *dicomio.Decoder, frameChannel chan *frame.Frame) (Parser, error)
- func NewParserFromFile(path string, frameChannel chan *frame.Frame) (Parser, error)
- func NewUninitializedParserFromDecoder(decoder *dicomio.Decoder, frameChannel chan *frame.Frame) Parser
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
This section is empty.
Types ¶
type DirectoryRecord ¶
type DirectoryRecord struct {
Path string
}
DirectoryRecord contains info about one DICOM file mentioned in DICOMDIR.
func ParseDICOMDIR ¶
func ParseDICOMDIR(in io.Reader) (recs []DirectoryRecord, err error)
ParseDICOMDIR parses contents of a "DICOMDIR" stored in "in".
http://dicom.nema.org/medical/Dicom/2016b/output/chtml/part03/sect_F.2.2.2.html
type ParseOptions ¶
type ParseOptions struct {
// DropPixelData will cause the parser to skip the PixelData element
// (bulk images) in ReadDataSet.
DropPixelData bool
// ReturnTags is a whitelist of tags to return.
ReturnTags []dicomtag.Tag
// StopAtag defines a tag at which when read (or a tag with a greater
// value than it is read), the program will stop parsing the dicom file.
StopAtTag *dicomtag.Tag
}
ParseOptions defines how DataSets and Elements are parsed.
type Parser ¶
type Parser interface {
// Parse DICOM data
Parse(options ParseOptions) (*element.DataSet, error)
// ParseNext reads and parses the next element
ParseNext(options ParseOptions) *element.Element
// DecoderError fetches an error (if exists) from the dicomio.Decoder
DecoderError() error // This should go away as we continue refactors
// Finish should be called after manually parsing elements using ParseNext (instead of Parse)
Finish() error // This should maybe go away as we continue refactors
}
Parser represents an entity that can read and parse DICOMs
func NewParserFromBytes ¶
NewParserFromBytes initializes and returns a new Parser from []byte
func NewParserFromDecoder ¶ added in v0.4.0
NewParserFromDecoder returns parser from a decoder TODO: remove or cleanup, currently needed for testing
func NewParserFromFile ¶
NewParserFromFile initializes and returns a new dicom Parser from a file path
Source Files
Directories
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| Path | Synopsis |
|---|---|
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cmd
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dicomutil
command
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Package dicomio provides utility functions for encoding and decoding low-level DICOM data types, such as integers and strings.
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Package dicomio provides utility functions for encoding and decoding low-level DICOM data types, such as integers and strings. |
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Package dicomlog performs logging for go-dicom or go-netdicom.
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Package dicomlog performs logging for go-dicom or go-netdicom. |
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Package dicomtag enumerates element tags defined in the DICOM standard.
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Package dicomtag enumerates element tags defined in the DICOM standard. |
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Package dicomuid defines standard UIDs, as defined in P3.6.
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Package dicomuid defines standard UIDs, as defined in P3.6. |
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legacy
module
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