metamri 0.2.20 → 0.2.21

checksums.yaml

@@ -1,15 +1,15 @@
 ---
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   metadata.gz: !binary |-
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   data.tar.gz: !binary |-
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 SHA512:
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data/bin/convert_visit.rb

@@ -42,7 +42,7 @@ def convert_visit(raw_directory, scan_procedure_codename, output_directory = nil
   output_directory = output_directory ||= v.default_preprocess_directory
 
   begin
-    default_options = {:ignore_patterns => [/vipr/,/pfiles/,/raw/,/$Processed-Images$/,/900$/,/901$/,/999$/]}  # seems to like number , not like string
+    default_options = {:ignore_patterns => [[/vipr/,/raw$/,/pfiles/,/Processed-Images/,/900$/,/901$/,/999$/,/\/01300\./,/\/01301\./,/\/01001\./,/\/01002\./,/\/01000\./,/\/00600\./]}  # does not like "raw" because in dir path
     #options = default_options.merge(options)
     v.scan(default_options)
     v.to_nifti!(output_directory)

data/lib/metamri/dicom_additions.rb

@@ -11,7 +11,8 @@ class DicomGroup
   # Initialize with an array of strings or DICOM::DObjects to aggregate
   def initialize(dicomgroup)
     if dicomgroup.select {|dcm| dcm.is_a? DICOM::DObject }.empty?
-      @dobjects = dicomgroup.collect {|dcm| DICOM::DObject.new(dcm)}
+      @dobjects = dicomgroup.collect {|dcm| DICOM::DObject.read(dcm)} 
+      #@dobjects = dicomgroup.collect {|dcm| DICOM::DObject.new(dcm)}  # changing from dicom 0.8.0  to 0.9.5
     else 
       @dobjects = dicomgroup
     end

data/lib/metamri/raw_image_dataset_thumbnail.rb

@@ -127,7 +127,8 @@ class RawImageDatasetThumbnail
     end
     dicom_file = Pathname(dicom_files[(dicom_files.size/2)+1])
     dicom_file.local_copy do |lc|
-      dcm = DICOM::DObject.new(lc.to_s)
+      #dcm = DICOM::DObject.new(lc.to_s) # changing from dicom 0.8.0  to 0.9.5
+      dcm = DICOM::DObject.read(lc.to_s)
       raise ScriptError, "Could not read dicom #{dicom_file.to_s}" unless dcm.read_success
       v_call = "dcmj2pnm -v +Wi 1 --write-png "+lc.to_s+" "+output_file
       v_results = %x[#{v_call}]
@@ -159,7 +160,8 @@ class RawImageDatasetThumbnail
     end
     dicom_file = Pathname(dicom_files[dicom_files.size/2])
     dicom_file.local_copy do |lc|
-      dcm = DICOM::DObject.new(lc.to_s)
+      #dcm = DICOM::DObject.new(lc.to_s) # changing from dicom 0.8.0  to 0.9.5
+      dcm = DICOM::DObject.read(lc.to_s)
       raise ScriptError, "Could not read dicom #{dicom_file.to_s}" unless dcm.read_success
       image = dcm.get_image_magick(:rescale => true)
       raise ScriptError, "RubyDicom did not return an image array (this is probably a color image)." unless image.kind_of? Magick::Image

data/lib/metamri/raw_image_file.rb

@@ -300,7 +300,9 @@ private
     else
       # Try reading with RubyDICOM
       @current_hdr_reader = RUBYDICOM_HDR
-      header = DICOM::DObject.new(absfilepath)
+      ####header = DICOM::DObject.new(absfilepath) # changing from dicom 0.8.0  to 0.9.5
+      header = DICOM::DObject.read(absfilepath)
+
       if defined? header.read_success && header.read_success
         @current_hdr_reader = nil
         return [header, RUBYDICOM_HDR] 

data/lib/metamri/version.rb

@@ -1,3 +1,3 @@
 module Metamri
-  VERSION = "0.2.20"
+  VERSION = "0.2.21"
 end

data/metamri.gemspec

@@ -17,7 +17,8 @@ Gem::Specification.new do |s|
   s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
   s.require_paths = ["lib"]
 
-  s.add_runtime_dependency('dicom', "~> 0.8.0")
+  s.add_runtime_dependency('dicom', "~> 0.9.5") # fixed issue with multi row dicom values
+  #s.add_runtime_dependency('dicom', "~> 0.8.0")
   s.add_runtime_dependency('activeresource', "~> 3.0")
   # s.add_runtime_dependency('rmagick') 
   s.add_runtime_dependency('hirb', "~> 0.4")

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: metamri
 version: !ruby/object:Gem::Version
-  version: 0.2.20
+  version: 0.2.21
 platform: ruby
 authors:
 - Kristopher J. Kosmatka
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-02 00:00:00.000000000 Z
+date: 2014-05-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: dicom
@@ -17,14 +17,14 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.8.0
+        version: 0.9.5
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.8.0
+        version: 0.9.5
 - !ruby/object:Gem::Dependency
   name: activeresource
   requirement: !ruby/object:Gem::Requirement