metamri 0.2.0 → 0.2.1

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.2.1

data/bin/list_visit

@@ -36,6 +36,7 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
 require 'pathname'
 require 'logger'
 require 'metamri'
+require 'optparse'
 
 def run!
   options = parse_options
@@ -82,7 +83,7 @@ def list_visit(raw_directory, options = {})
     
     raise IOError.new("Could not lookup visit using path #{lookup_path}.") unless visit
     raise IOError.new("Returned visit's path #{visit.path} does not match path.") unless visit.path == File.expand_path(lookup_path)
-  rescue ScriptError, IOError => e
+  rescue ActiveResource::ConnectionError, ScriptError, IOError => e
     puts e unless options[:verbose] == false
     visit = VisitRawDataDirectory.new(raw_directory)
     begin

data/lib/metamri.rb

@@ -13,6 +13,7 @@ require 'metamri/raw_image_dataset'
 require 'metamri/visit_raw_data_directory'
 require 'metamri/raw_image_dataset_resource'
 require 'metamri/visit_raw_data_directory_resource'
+require 'metamri/image_dataset_quality_check_resource'
 
 # require 'metamri/raw_image_dataset_thumbnail'
 # TODO Move raw_image_dataset_thumbnail out of metamri.  

data/lib/metamri/core_additions.rb

@@ -57,7 +57,7 @@ class Pathname
   def first_dicom
     entries.each do |leaf|
       branch = self + leaf
-      if leaf.to_s =~ /^I\.(\.bz2)?$|\.dcm(\.bz2)?$|[A-Za-z^P]\.[0-9]+(\.bz2)?$/
+      if leaf.to_s =~ /^I\..*(\.bz2)?$|\.dcm(\.bz2)?$|\.[0-9]{2,}(\.bz2)?$/
         lc = branch.local_copy
         begin
           yield lc

data/lib/metamri/image_dataset_quality_check_resource.rb

@@ -22,5 +22,25 @@ class ImageDatasetQualityCheckResource < ActiveResource::Base
   self.site = VisitRawDataDirectory::DATAPANDA_SERVER
   self.element_name = "image_dataset_quality_check"
   
+  PASSING_STATUSES = Set.new(%w(complete pass))
+  FAILING_STATUSES = Set.new( ["Incomplete","Mild","Moderate","Severe","Limited Activation","No activation","No pass"] )
   
+  # Returns an array of hashes for failed checks.
+  def failed_checks
+    failed_checks = Array.new
+    self.attribute_names.each_pair do |name, value|
+      unless name.blank?
+        if FAILING_STATUSES.include?(value)
+          comment = instance_values['attributes']["#{name}_comment"]
+          failed_checks << {:name => name, :value => value, :comment => comment }
+        end
+      end
+    end
+    return failed_checks
+  end
+  
+  def attribute_names
+    instance_values['attributes']
+  end
+    
 end

data/lib/metamri/raw_image_dataset_resource.rb

@@ -98,8 +98,30 @@ class RawImageDatasetResource < ActiveResource::Base
     return relative_dataset_path
   end
   
-  def image_quality_checks
-    
+  # Queries ActiveResource for an array of ImageDatasetQualityCheckResources 
+  def image_dataset_quality_checks
+    @image_dataset_quality_checks ||= ImageDatasetQualityCheckResource.find(:all, :params => {:image_dataset_id => id })
+  end
+  
+  def image_dataset_quality_checks_tablerow
+    output = []
+    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]}."
+        end
+
+        output << "Concerns: #{qc.other_issues}" if qc.other_issues
+
+        if output.empty? 
+          output << "Good"
+        end
+      
+        # Add QC date at end.
+        output << "[#{qc.attribute_names['created_at'].strftime('%D')}]"
+      end
+    end
+    return output.join(" ")
   end
   
   # Creates an Hirb Table for pretty output of dataset info.
@@ -107,12 +129,12 @@ class RawImageDatasetResource < ActiveResource::Base
   def self.to_table(datasets)
     Hirb::Helpers::AutoTable.render(
       datasets.sort_by{ |ds| [ds.timestamp, File.basename(ds.path)] }, 
-      :headers => { :relative_dataset_path => 'Dataset', :series_description => 'Series Details', :file_count => "File Count", }, 
-      :fields => [:relative_dataset_path, :series_description, :file_count],
+      :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.
     )
   rescue NameError => e
-    puts e
+    raise e
 
     # Header Line
     printf "\t%-15s %-30s [%s]\n", "Directory", "Series Description", "Files"
@@ -125,6 +147,6 @@ class RawImageDatasetResource < ActiveResource::Base
     # Reminder Line
     puts "(This would be much prettier if you installed hirb.)"
     return
-  end   
+  end
   
 end

data/lib/metamri/visit_raw_data_directory.rb

@@ -59,7 +59,7 @@ class VisitRawDataDirectory
   
   PREPROCESS_REPOSITORY_DIRECTORY = '/Data/vtrak1/preprocessed/visits'
   # DATAPANDA_SERVER = 'http://localhost:3000'
-  DATAPANDA_SERVER = 'http://144.92.151.228'
+  DATAPANDA_SERVER = 'http://nelson'
 
   
   # A new Visit instance needs to know the path to its raw data and scan_procedure name.  The scan_procedure
@@ -95,7 +95,7 @@ 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.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 }
       rescue StandardError => e
         raise(e, "There was an error scaning dataset #{dd}: #{e}")

data/lib/metamri/visit_raw_data_directory_resource.rb

@@ -39,6 +39,7 @@ class VisitRawDataDirectoryResource < ActiveResource::Base
     # puts "#{@scan_procedure_name}"
     puts RawImageDatasetResource.to_table(datasets)
     puts "Notes: " + notes unless notes.nil? or notes.empty?
+    puts "#{VisitRawDataDirectory::DATAPANDA_SERVER}/visits/#{id}"
   end
   
 end

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.2.0"
+  s.version = "0.2.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-11-19}
+  s.date = %q{2010-11-22}
   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"]

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 2
-  - 0
-  version: 0.2.0
+  - 1
+  version: 0.2.1
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-11-19 00:00:00 -06:00
+date: 2010-11-22 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency