metamri 0.2.3 → 0.2.4

data/VERSION

@@ -1 +1 @@
-0.2.3
+0.2.4

data/bin/list_visit

@@ -51,7 +51,12 @@ def run!
   
   unless input_directories.empty?
     input_directories.each do |raw_directory|
-      list_visit raw_directory, options
+      begin
+        list_visit raw_directory, options
+      rescue StandardError => e
+        puts e
+        next
+      end
     end
   else
     raise IOError, "No input directories specified."
@@ -79,7 +84,7 @@ def list_visit(raw_directory, options = {})
     raise ScriptError, "Scaning filesystem directly..." if options[:force_scan]
     
     lookup_path = File.dirname(raw_directory).split(File::Separator).last == "dicoms" ?  File.join(raw_directory, '..') : raw_directory
-    visit = VisitRawDataDirectoryResource.find(:first, :params => {:search => {:path => File.expand_path(lookup_path)}})
+    visit = VisitRawDataDirectoryResource.find(:first, :params => {:search => {:path_contains => File.expand_path(lookup_path)}})
     
     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)

data/lib/metamri/raw_image_dataset.rb

@@ -164,11 +164,18 @@ class RawImageDataset
   # Returns a hash of attributes used for insertion into active record.
   # Options:  :thumb => FileHandle to thumbnail includes a thumbnail.
   def attributes_for_active_record(options = {})
-    thumbnail = options.has_key?(:thumb) ? options[:thumb] : nil
+    attrs = {}
     
-    unless (thumbnail.class == File || thumbnail == nil)
-      raise(IOError, "Thumbnail #{options[:thumb]} must be a #File instead of #{thumbnail.class}.")
+    # If the thumbnail is present and valid, add it to the hash.
+    # Otherwise don't add the key, or paperclip will delete the attachments (it deletes when given nil)
+    if options.has_key?(:thumb)
+      thumbnail = options[:thumb]
+      unless (thumbnail.class == File || thumbnail == nil)
+        raise(IOError, "Thumbnail #{options[:thumb]} must be a #File instead of #{thumbnail.class}.")
+      end
+      attrs[:thumbnail] = thumbnail
     end
+
     { :rmr => @rmr_number,
       :series_description => @series_description,
       :path => @directory,
@@ -178,10 +185,9 @@ class RawImageDataset
       :bold_reps => @raw_image_files.first.bold_reps,
       :slices_per_volume => @raw_image_files.first.num_slices,
       :scanned_file => @scanned_file,
-      :thumbnail => thumbnail,
       :dicom_series_uid => @dicom_series_uid,
       :dicom_taghash => @dicom_taghash
-    }
+    }.merge attrs
   end
   
   def create_thumbnail
@@ -272,7 +278,7 @@ Returns a path to the created dataset as a string if successful.
   
   def file_count
     unless @file_count
-      if @raw_image_files.first.dicom?
+      if @raw_image_files.first.dicom? or @raw_image_files.first.geifile?
         @file_count = Dir.open(@directory).reject{ |branch| /(^\.|.yaml$)/.match(branch) }.length
       elsif @raw_image_files.first.pfile?
         @file_count = 1
@@ -305,7 +311,7 @@ Returns a path to the created dataset as a string if successful.
   def relative_dataset_path(visit_dir = nil)
     image_file = @raw_image_files.first
     case image_file.file_type
-      when 'dicom'
+      when 'dicom', 'geifile'
         relative_dataset_path = File.basename(directory)
       when 'pfile'
         full_dataset_path = Pathname.new(File.join(directory, image_file.filename))

data/lib/metamri/raw_image_dataset_thumbnail.rb

@@ -19,6 +19,8 @@ class RawImageDatasetThumbnail
   attr_reader :path
   # The processor for creating the thumbnail (:rubydicom or :slicer)
   attr_reader :processor
+  # An array of errors encountered during the reading process.
+  attr_reader :errors
 
   # Creates a RawImageDatasetThumbnail instance by passing in a parent dataset to thumbnail.
   def initialize(dataset)

data/lib/metamri/raw_image_file.rb

@@ -143,6 +143,10 @@ class RawImageFile
     return @file_type == "dicom"
   end
   
+  def geifile?
+    return @file_type == "geifile"
+  end
+  
   
   # Returns a yaml string based on a subset of the attributes.  Specifically,
   # the @hdr_data is not included.  This is used to generate .yaml files that are 
@@ -294,8 +298,9 @@ private
   # file a "pfile" if it is an image and the file name is of the form P*.7
   # All other images are called "dicom".
   def determine_file_type
-    return "pfile" if image? and (@filename =~ /^P.....\.7/) != nil
-    return "dicom" if image? and (@filename =~ /^P.....\.7/) == nil
+    return "pfile"    if image? and (@filename =~ /^P.....\.7/) != nil
+    return "geifile"  if image? and (@filename =~ /^I\.\d*/) != nil
+    return "dicom"    if image? and (@filename =~ /^P.....\.7/) == nil
     return nil
   end
 

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.2.3"
+  s.version = "0.2.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2011-02-25}
+  s.date = %q{2011-03-07}
   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

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  hash: 17
+  hash: 31
   prerelease: 
   segments: 
   - 0
   - 2
-  - 3
-  version: 0.2.3
+  - 4
+  version: 0.2.4
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-02-25 00:00:00 -06:00
+date: 2011-03-07 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency