metamri 0.2.20 → 0.2.21

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checksums.yaml CHANGED
@@ -1,15 +1,15 @@
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@@ -42,7 +42,7 @@ def convert_visit(raw_directory, scan_procedure_codename, output_directory = nil
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  output_directory = output_directory ||= v.default_preprocess_directory
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  begin
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- default_options = {:ignore_patterns => [/vipr/,/pfiles/,/raw/,/$Processed-Images$/,/900$/,/901$/,/999$/]} # seems to like number , not like string
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+ default_options = {:ignore_patterns => [[/vipr/,/raw$/,/pfiles/,/Processed-Images/,/900$/,/901$/,/999$/,/\/01300\./,/\/01301\./,/\/01001\./,/\/01002\./,/\/01000\./,/\/00600\./]} # does not like "raw" because in dir path
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  #options = default_options.merge(options)
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  v.scan(default_options)
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  v.to_nifti!(output_directory)
@@ -11,7 +11,8 @@ class DicomGroup
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  # Initialize with an array of strings or DICOM::DObjects to aggregate
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  def initialize(dicomgroup)
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  if dicomgroup.select {|dcm| dcm.is_a? DICOM::DObject }.empty?
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- @dobjects = dicomgroup.collect {|dcm| DICOM::DObject.new(dcm)}
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+ @dobjects = dicomgroup.collect {|dcm| DICOM::DObject.read(dcm)}
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+ #@dobjects = dicomgroup.collect {|dcm| DICOM::DObject.new(dcm)} # changing from dicom 0.8.0 to 0.9.5
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  else
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  @dobjects = dicomgroup
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  end
@@ -127,7 +127,8 @@ class RawImageDatasetThumbnail
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  end
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  dicom_file = Pathname(dicom_files[(dicom_files.size/2)+1])
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  dicom_file.local_copy do |lc|
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- dcm = DICOM::DObject.new(lc.to_s)
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+ #dcm = DICOM::DObject.new(lc.to_s) # changing from dicom 0.8.0 to 0.9.5
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+ dcm = DICOM::DObject.read(lc.to_s)
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  raise ScriptError, "Could not read dicom #{dicom_file.to_s}" unless dcm.read_success
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  v_call = "dcmj2pnm -v +Wi 1 --write-png "+lc.to_s+" "+output_file
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  v_results = %x[#{v_call}]
@@ -159,7 +160,8 @@ class RawImageDatasetThumbnail
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  end
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  dicom_file = Pathname(dicom_files[dicom_files.size/2])
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  dicom_file.local_copy do |lc|
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- dcm = DICOM::DObject.new(lc.to_s)
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+ #dcm = DICOM::DObject.new(lc.to_s) # changing from dicom 0.8.0 to 0.9.5
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+ dcm = DICOM::DObject.read(lc.to_s)
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  raise ScriptError, "Could not read dicom #{dicom_file.to_s}" unless dcm.read_success
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  image = dcm.get_image_magick(:rescale => true)
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  raise ScriptError, "RubyDicom did not return an image array (this is probably a color image)." unless image.kind_of? Magick::Image
@@ -300,7 +300,9 @@ private
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  else
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  # Try reading with RubyDICOM
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  @current_hdr_reader = RUBYDICOM_HDR
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- header = DICOM::DObject.new(absfilepath)
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+ ####header = DICOM::DObject.new(absfilepath) # changing from dicom 0.8.0 to 0.9.5
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+ header = DICOM::DObject.read(absfilepath)
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+
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  if defined? header.read_success && header.read_success
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  @current_hdr_reader = nil
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  return [header, RUBYDICOM_HDR]
@@ -1,3 +1,3 @@
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  module Metamri
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- VERSION = "0.2.20"
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+ VERSION = "0.2.21"
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  end
@@ -17,7 +17,8 @@ Gem::Specification.new do |s|
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  s.executables = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
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  s.require_paths = ["lib"]
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- s.add_runtime_dependency('dicom', "~> 0.8.0")
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+ s.add_runtime_dependency('dicom', "~> 0.9.5") # fixed issue with multi row dicom values
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+ #s.add_runtime_dependency('dicom', "~> 0.8.0")
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  s.add_runtime_dependency('activeresource', "~> 3.0")
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  # s.add_runtime_dependency('rmagick')
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  s.add_runtime_dependency('hirb', "~> 0.4")
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: metamri
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  version: !ruby/object:Gem::Version
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- version: 0.2.20
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+ version: 0.2.21
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  platform: ruby
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  authors:
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  - Kristopher J. Kosmatka
@@ -9,7 +9,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-04-02 00:00:00.000000000 Z
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+ date: 2014-05-01 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: dicom
@@ -17,14 +17,14 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 0.8.0
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+ version: 0.9.5
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 0.8.0
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+ version: 0.9.5
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  - !ruby/object:Gem::Dependency
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  name: activeresource
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  requirement: !ruby/object:Gem::Requirement