metamri 0.2.1 → 0.2.2

data/VERSION

@@ -1 +1 @@
-0.2.1
+0.2.2

data/lib/metamri/raw_image_dataset.rb

@@ -42,6 +42,8 @@ class RawImageDataset
   attr_reader :dicom_series_uid
   # DICOM Study UID
   attr_reader :dicom_study_uid
+  # Array of Read Error Strings
+  attr_reader :read_errors
   
   # * dir: The directory containing the files.
   # * files: An array of #RawImageFile objects that compose the complete data set.
@@ -51,6 +53,7 @@ class RawImageDataset
   # * any of the raw image files is not actually a RawImageFile => IndexError
   # * series description, rmr number, or timestamp cannot be extracted from the first RawImageFile => IndexError
   def initialize(directory, raw_image_files)    
+    @read_errors = Array.new
     @directory = File.expand_path(directory)
     raise(IOError, "#{@directory} not found.") if not File.directory?(@directory)
     raise(IOError, "No raw image files supplied.") unless raw_image_files
@@ -90,7 +93,7 @@ class RawImageDataset
     validates_metainfo_for :protocol_name, :msg => "No protocol name found" if dicom?
     
     @operator_name = @raw_image_files.first.operator_name
-    validates_metainfo_for :operator_name if dicom?
+    validates_metainfo_for :operator_name, :optional => true if dicom?
     
     @patient_name = @raw_image_files.first.patient_name
     validates_metainfo_for :patient_name if dicom?
@@ -104,6 +107,15 @@ class RawImageDataset
     $LOG ||= Logger.new(STDOUT)
   end
   
+  # Prints a "success" dot or error mesage if any errors in @read_errors.
+  def print_scan_status
+    if @read_errors.empty?
+      print "."; STDOUT.flush
+    else
+      puts @read_errors.join("; ")
+    end
+  end
+  
 
 
   # Generates an SQL insert statement for this dataset that can be used to
@@ -330,7 +342,8 @@ private
   def validates_metainfo_for(info_variable, options = {})
     raise StandardError, "#{info_variable} must be a symbol" unless info_variable.kind_of? Symbol
     if self.instance_variable_get("@" + info_variable.to_s).nil?
-      raise IndexError, options[:msg] ||= "Couldn't find #{info_variable.to_s}"
+      @read_errors << options[:msg] ||= "Couldn't find #{info_variable.to_s}"
+      raise IndexError, message unless options[:optional]
     end
   end
 

data/lib/metamri/raw_image_dataset_resource.rb

@@ -108,7 +108,7 @@ class RawImageDatasetResource < ActiveResource::Base
     unless image_dataset_quality_checks.empty?
       image_dataset_quality_checks.each do |qc|
         qc.failed_checks.each do |check|
-          output << "* #{check[:name].capitalize.gsub("_", " ")} (#{check[:value]}): #{check[:comment]}."
+          output << "* #{check[:name].capitalize.gsub("_", " ") } (#{check[:value]}): #{(check[:comment] + ".") if check[:comment]}"
         end
 
         output << "Concerns: #{qc.other_issues}" if qc.other_issues
@@ -131,7 +131,8 @@ class RawImageDatasetResource < ActiveResource::Base
       datasets.sort_by{ |ds| [ds.timestamp, File.basename(ds.path)] }, 
       :headers => { :relative_dataset_path => 'Dataset', :series_description => 'Series Details', :file_count => "File Count", :image_dataset_quality_checks_tablerow => "Quality Checks"}, 
       :fields => [:relative_dataset_path, :series_description, :file_count, :image_dataset_quality_checks_tablerow],
-      :description => false # Turn off rendering row count description at bottom.
+      :description => false, # Turn off rendering row count description at bottom.
+      :resize => false
     )
   rescue NameError => e
     raise e

data/lib/metamri/visit_raw_data_directory.rb

@@ -95,8 +95,8 @@ class VisitRawDataDirectory
       begin
         matches = options[:ignore_patterns].collect {|pat| dd.to_s =~ pat ? dd : nil }.compact
         next unless matches.empty?
-        dd.each_pfile  { |pf| @datasets << import_dataset(pf, dd); (print "."; STDOUT.flush) if $LOG.level == Logger::INFO }
-        dd.first_dicom { |fd| @datasets << import_dataset(fd, dd); (print "."; STDOUT.flush) if $LOG.level == Logger::INFO }
+        dd.each_pfile  { |pf| @datasets << import_dataset(pf, dd); @datasets.last.print_scan_status if $LOG.level == Logger::INFO }
+        dd.first_dicom { |fd| @datasets << import_dataset(fd, dd); @datasets.last.print_scan_status if $LOG.level == Logger::INFO }
       rescue StandardError => e
         raise(e, "There was an error scaning dataset #{dd}: #{e}")
       end

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.2.1"
+  s.version = "0.2.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-11-22}
+  s.date = %q{2011-01-18}
   s.description = %q{Extraction of MRI metadata and insertion into compatible sqlite3 databases.}
   s.email = %q{kk4@medicine.wisc.edu}
   s.executables = ["convert_visit.rb", "import_visit.rb", "import_respiratory_files.rb", "import_study.rb", "list_visit"]
@@ -57,7 +57,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = %q{http://github.com/brainmap/metamri}
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.6}
+  s.rubygems_version = %q{1.4.1}
   s.summary = %q{MRI metadata}
   s.test_files = [
     "spec/helper_spec.rb",
@@ -73,10 +73,9 @@ Gem::Specification.new do |s|
   ]
 
   if s.respond_to? :specification_version then
-    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
     s.specification_version = 3
 
-    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<sqlite3-ruby>, [">= 0"])
       s.add_runtime_dependency(%q<dicom>, [">= 0"])
       s.add_development_dependency(%q<rspec>, [">= 0"])

metadata

@@ -1,12 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  prerelease: false
+  hash: 19
+  prerelease: 
   segments: 
   - 0
   - 2
-  - 1
-  version: 0.2.1
+  - 2
+  version: 0.2.2
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -14,16 +15,18 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-11-22 00:00:00 -06:00
+date: 2011-01-18 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: sqlite3-ruby
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 3
         segments: 
         - 0
         version: "0"
@@ -33,9 +36,11 @@ dependencies:
   name: dicom
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 3
         segments: 
         - 0
         version: "0"
@@ -45,9 +50,11 @@ dependencies:
   name: rspec
   prerelease: false
   requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 3
         segments: 
         - 0
         version: "0"
@@ -113,23 +120,27 @@ rdoc_options: []
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      hash: 3
       segments: 
       - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      hash: 3
       segments: 
       - 0
       version: "0"
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.6
+rubygems_version: 1.4.1
 signing_key: 
 specification_version: 3
 summary: MRI metadata