gdcm

GDCM

A ruby wrapper for GDCM tools

Information

Inspired by MiniMagick ruby gem, this realization was created based on same DSL structure (but for GDCM tools).

Requirements

GDCM command-line tool has to be installed. You can check if you have it installed by running

$ gdcminfo --version
gdcminfo: gdcm 3.0.10

Installation

Add the gem to your Gemfile:

gem "gdcm"

Usage

Let's first see a basic example.

require "gdcm"

package = GDCM::Package.open("original.dcm")

package.convert do |convert|
  convert.raw
  convert.verbose
end

package.path
package.write "output.dcm"

GDCM::Package.open makes a copy of the package, and further methods modify that copy (the original stays untouched). The writing part is necessary because the copy is just temporary, it gets garbage collected when we lose reference to the package.

On the other hand, if we want the original package to actually get modified, we can use GDCM::Package.new.

package = GDCM::Package.new("original.dcm")
package.path

package.convert do |convert|
  convert.raw
  convert.verbose
end
# Not calling #write, because it's not a copy

Attributes

To get the all information about the package, GDCM gives you a handy method which returns the output from gdcminfo in hash format:

package.info.data #=>
#{"MediaStorage"=>"1.2.840.10008.5.1.4.1.1.77.1.5.1",                             
# "TransferSyntax"=>"1.2.840.10008.1.2.4.70",                                     
# "NumberOfDimensions"=>"2",                                                      
# "Dimensions"=>"(4000,4000,1)",                                                  
# "SamplesPerPixel"=>"3",                                                         
# "BitsAllocated"=>"8",                                                           
# "BitsStored"=>"8",                                                              
# "HighBit"=>"7",                                                                 
# "PixelRepresentation"=>"0",                                                     
# "ScalarType found"=>"UINT8",                                                    
# "PhotometricInterpretation"=>"RGB",                                             
# "PlanarConfiguration"=>"0",                                                     
# "Origin"=>"(0,0,0)",                                                            
# "Spacing"=>"(1,1,1)",
# "DirectionCosines"=>"(1,0,0,0,1,0)",
# "Rescale Intercept/Slope"=>"(0,1)",
# "Orientation Label"=>"AXIAL"}

Configuration

GDCM.configure do |config|
  config.timeout = 5
end

Package validation

By default, GDCM validates package each time it's opening them. It validates them by running gdcminfo on them, and see if GDCM tools finds them valid. This adds slight overhead to the whole processing. Sometimes it's safe to assume that all input and output packages are valid by default and turn off validation:

GDCM.configure do |config|
  config.validate_on_create = false
end

You can test whether an package is valid:

package.valid?
package.validate! # raises GDCM::Invalid if package is invalid

Logging

You can choose to log GDCM commands and their execution times:

GDCM.logger.level = Logger::DEBUG

D, [2022-04-11T12:07:39.240238 #59063] DEBUG -- : [0.11s] gdcminfo /var/folders/4d/k113_9r544nfj8k0bfxtjx0m0000gn/T/gdcm20220411-59063-8yvk5s.dcm

In Rails you'll probably want to set GDCM.logger = Rails.logger.

Metal

If you want to be close to the metal, you can use GDCM's command-line tools directly.

GDCM::Tool::Convert.new do |convert|
  convert.raw
  convert.verbose
  convert << "input.dcm"
  convert << "output.dcm"
end #=> `gdcmconv --raw --verbose input.dcm output.dcm`

# OR

convert = GDCM::Tool::Convert.new
convert.raw
convert.verbose
convert << "input.dcm"
convert << "output.dcm"
convert.call #=> `gdcmconv --raw --verbose input.dcm output.dcm`

Troubleshooting

Errors being raised when they shouldn't

If you're using the tool directly, you can pass whiny: false value to the constructor:

GDCM::Tool::Identify.new(whiny: false) do |b|
  b.help
end