metamri 0.2.15 → 0.2.16

data/Gemfile

@@ -1,4 +1,5 @@
 source "http://rubygems.org"
 
+
 # Specify your gem's dependencies in metamri.gemspec
 gemspec

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/,/900$/,/901$/,/999$/]}  # seems to like number , not like string ??? /raw/,
+    default_options = {:ignore_patterns => [/vipr/,/900$/,/901$/,/999$/]}  # seems to like number , not like string
     #options = default_options.merge(options)
     v.scan(default_options)
     v.to_nifti!(output_directory)

data/lib/metamri/raw_image_dataset_thumbnail.rb

@@ -1,6 +1,6 @@
 require 'tmpdir'
 begin
-  %W{dicom RMagick}.each do |lib|
+  %W{dicom }.each do |lib|     #####RMagick
     require lib unless defined?(lib)
   end
 rescue LoadError => e
@@ -86,10 +86,12 @@ class RawImageDatasetThumbnail
     default_name = @dataset.series_description.escape_filename
     filepath ||= File.join(output_directory, default_name + '.png')
     
+
     begin
       case @processor
       when :rubydicom
-        @path = create_thumbnail_with_rubydicom(filepath)
+        @path = create_thumbnail_with_rubydicom_dcmtk(filepath)
+        #@path = create_thumbnail_with_rubydicom(filepath)
       when :slicer
         @path = create_thumbnail_with_fsl_slicer(filepath)
       end
@@ -108,6 +110,38 @@ class RawImageDatasetThumbnail
   end
   
   private
+
+    # Creates a thumbnail using RubyDicom and dcmtk
+  # Pass in an absolute or relative filepath, including filename and extension.
+  # Returns an absolute path to the created thumbnail image.
+  def create_thumbnail_with_rubydicom_dcmtk(output_file)
+    output_file = File.expand_path(output_file)
+
+    dicom_files = Dir.glob(File.join(dataset.directory, dataset.glob))
+    if dicom_files.empty?  # Try the glob again with a zipped extension.
+      dicom_files = Dir.glob(File.join(dataset.directory, dataset.glob) + '*.bz2')
+    end
+    if dicom_files.empty? # If still empty...
+      raise StandardError, "Could not find dicom files using #{dataset.glob} in #{dataset.directory}"
+    end
+    dicom_file = Pathname(dicom_files[(dicom_files.size/2)+1])
+    dicom_file.local_copy do |lc|
+      dcm = DICOM::DObject.new(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}]
+      puts "results= "+v_results
+      puts "dicom_file= "+dicom_file.to_s
+      puts "output_file= "+output_file
+      ####    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
+      #### image.write(output_file)
+    end
+
+    raise(ScriptError, "Error creating thumbnail #{output_file}") unless File.exist?(output_file)
+
+    return output_file
+  end
   
   # Creates a thumbnail using RubyDicom
   # Pass in an absolute or relative filepath, including filename and extension.

data/lib/metamri/version.rb

@@ -1,3 +1,3 @@
 module Metamri
-  VERSION = "0.2.15"
+  VERSION = "0.2.16"
 end

data/lib/metamri/visit_raw_data_directory.rb

@@ -4,7 +4,7 @@ require 'tempfile'
 require 'yaml'
 require 'tmpdir'
 require 'fileutils'
-require 'sqlite3'
+require 'sqlite3'  # being used in code with inserts and things?????
 require 'logger'
 require 'pp'
 require 'metamri/raw_image_file'

data/lib/metamri.rb

@@ -8,7 +8,7 @@ begin
   require 'hirb'
   require 'rspec'
   require 'dicom'
-  require 'rmagick'   
+  ##### require 'rmagick'
   require 'sqlite'
 rescue LoadError
 end

data/metamri.gemspec

@@ -19,7 +19,7 @@ Gem::Specification.new do |s|
 
   s.add_runtime_dependency('dicom', "~> 0.8.0")
   s.add_runtime_dependency('activeresource', "~> 3.0")
-  s.add_runtime_dependency('rmagick', "~> 2.13.1")  # rmagick is used by the panda snapshots, so should not be needed on a machine only doing convert visit
+  ##### s.add_runtime_dependency('rmagick', "~> 2.13.1") 
   s.add_runtime_dependency('hirb', "~> 0.4")
   s.add_runtime_dependency('sqlite3', "~>1.3.4")
   s.add_development_dependency('rspec', "~> 2.5")

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  hash: 9
+  hash: 55
   prerelease: 
   segments: 
   - 0
   - 2
-  - 15
-  version: 0.2.15
+  - 16
+  version: 0.2.16
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -16,7 +16,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2013-02-18 00:00:00 Z
+date: 2013-03-25 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: dicom
@@ -49,26 +49,10 @@ dependencies:
         version: "3.0"
   type: :runtime
   version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: rmagick
-  prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 57
-        segments: 
-        - 2
-        - 13
-        - 1
-        version: 2.13.1
-  type: :runtime
-  version_requirements: *id003
 - !ruby/object:Gem::Dependency 
   name: hirb
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -79,11 +63,11 @@ dependencies:
         - 4
         version: "0.4"
   type: :runtime
-  version_requirements: *id004
+  version_requirements: *id003
 - !ruby/object:Gem::Dependency 
   name: sqlite3
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -95,11 +79,11 @@ dependencies:
         - 4
         version: 1.3.4
   type: :runtime
-  version_requirements: *id005
+  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: rspec
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -110,11 +94,11 @@ dependencies:
         - 5
         version: "2.5"
   type: :development
-  version_requirements: *id006
+  version_requirements: *id005
 - !ruby/object:Gem::Dependency 
   name: escoffier
   prerelease: false
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  requirement: &id006 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -124,7 +108,7 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  version_requirements: *id007
+  version_requirements: *id006
 description: Extraction of MRI metadata.
 email: ekk@medicine.wisc.edu
 executables: