metamri 0.1.13 → 0.1.14

data/.gitignore

@@ -4,4 +4,4 @@
 .idea
 *~
 test/fixtures/visit_raw_data_directory
-
+doc/*

data/README.rdoc

@@ -1,6 +1,8 @@
 == ImageData
 
-A small library that can be used to extract metadata from large collections of research MR imaging data sets.  Support is also provided to insert the metadata into a Wisconsin ADRC Imaging Core compatible database.  Several 
+A small library that can be used to extract metadata from large collections of research MR imaging data sets.  
+
+Support is also provided to insert the metadata into a Wisconsin ADRC Imaging Core compatible database.  Several 
 command line utilities are provided as well as a minimal API that is useful for building ruby on rails rake tasks.
 
 You will most likely be interested in either:

data/VERSION

@@ -1 +1 @@
-0.1.13
+0.1.14

data/bin/list_visit

@@ -9,17 +9,18 @@
 #
 # == Examples
 #
-#   list_visit /Data/vtrak1/raw/ries.aware.visit1/awr001_7854_02102009
+#   %> list_visit /Data/vtrak1/raw/ries.aware.visit1/awr001_7854_02102009
 #
-#   cd /Data/vtrak1/raw/ries.aware.visit1/awr001_7854_02102009
+#   
 #   list_visit
 #
 #   If no raw data directory is given, the current directory will be assumed.
-#     list_visit
+#     %> cd /Data/vtrak1/raw/ries.aware.visit1/awr001_7854_02102009
+#     %> list_visit
 #
 # == Usage 
-#   list_visit <raw_data_directory>
-#
+#   %> list_visit <raw_data_directory>
+# 
 #   For help use: list_vist -h
 #
 # == Options
@@ -38,18 +39,19 @@ require 'rdoc/usage'
 # require 'logger'
 
 def list_visit(raw_directory)
-  # $LOG = Logger.new(STDOUT)
-  # $LOG.level = Logger::INFO
+  unless $LOG
+    $LOG = Logger.new(STDOUT)
+    $LOG.level = Logger::INFO
+  end
   
   # First try to lookup Visit and Datasets through active_resource
-  # Then fall back to scanning them fresh.
+  # Then fall back to scanning them fresh using the metamri classes.
   
   begin
-    # raise
     visit = VisitRawDataDirectoryResource.find(:first, :params => {:search => {:path => raw_directory}})
-    raise "Could not lookup visit using path." unless visit
-    raise "Incorrect visit found." unless visit.path == raw_directory
-  rescue Exception => e
+    raise IOError.new("Could not lookup visit using path.") unless visit
+    raise IOError.new("Returned visit does not match path.") unless visit.path == raw_directory
+  rescue IOError => e
     puts e
     visit = VisitRawDataDirectory.new(raw_directory)
     begin
@@ -60,15 +62,9 @@ def list_visit(raw_directory)
     end
   end
 
-  # begin
-  # rescue Exception => e
-  #   $LOG.error "There was a problem scanning a dataset in #{visit.visit_directory}... skipping."
-  #   $LOG.error "Exception message: #{e.message}"
-  #   raise e
-  # end
-  
-  # Visit is Either a RawVisitDataDirectory or a RawVisitDataDirectoryResource
-  # Either can handle printing to_s
+  # Output a pretty version of the visit details.
+  # Visit is Either a RawVisitDataDirectory or a RawVisitDataDirectoryResource,
+  # and either should respond to to_s
   visit.to_s
 
 end

data/lib/metamri/core_additions.rb

@@ -48,6 +48,10 @@ class Pathname
     end
   end
   
+  # def first_pfile(&block)
+  #   Pathname.new(filename).local_copy { block }
+  # end
+  
   def first_dicom
     entries.each do |leaf|
       branch = self + leaf
@@ -87,7 +91,14 @@ class Pathname
     return
   end
   
-  def local_copy(tempdir = Dir.tmpdir)
+=begin
+  Creates a local, unzipped copy of a file for use in scanning.
+  Will return a pathname to the local copy if called directly, or can also be 
+  passed a block.  If it is passed a block, it will create the local copy
+  and ensure the local copy is deleted.
+=end
+
+  def local_copy(tempdir = Dir.tmpdir, &block)
     tfbase = self.to_s =~ /\.bz2$/ ? self.basename.to_s.chomp(".bz2") : self.basename.to_s
     tfbase.escape_filename
     tmpfile = File.join(tempdir, tfbase)
@@ -96,7 +107,19 @@ class Pathname
     else
       FileUtils.cp(self.to_s, tmpfile)
     end
-    return Pathname.new(tmpfile)
+
+    lc = Pathname.new(tmpfile)
+    
+    if block
+      begin
+        yield lc
+      ensure
+        lc.delete
+      end
+
+    else
+      return lc
+    end
   end
   
 end

data/lib/metamri/raw_image_dataset_resource.rb

@@ -9,10 +9,39 @@ class RawImageDatasetResource < ActiveResource::Base
   # so check the current schema.rb file for those.
   def to_metamri_raw_image_dataset
     # A Metamri Class requires at least one valid image file.
-    # This is a little tricky since we really only care about the variables, not rescanning them.
+    # This is a little wasteful since we really only care about the variables, 
+    # not rescanning them.
     
-    Pathname.new(path).first_dicom do |fd|
-      @dataset = RawImageDataset.new( path, [RawImageFile.new(fd)] )
+    filename = Pathname.new(File.join(path, scanned_file))
+    filename_matches = /P\d{5}.7(.bz2)?/.match(filename)
+    
+    if filename_matches    # Pfile
+      if filename_matches[1] # '.bz2' if present, nil if otherwise.
+        filename = Pathname.new(File.join(filename, '.bz2'))
+      end
+            
+      # The scanned file is always reported in unzipped format, so we don't
+      # have to worry about stripping a .bz2 extension.
+      # The actual file on the filesystem may be zipped or unzipped 
+      # (although it Should! be zipped.  Check for that or return IOError.
+      zipped_filename = filename.to_s.chomp + '.bz2'
+
+      if filename.file?
+        image_file = filename
+      elsif Pathname.new(zipped_filename).file?
+        image_file = Pathname.new(zipped_filename)
+      else 
+        raise IOError, "Could not find #{filename} or it's bz2 zipped equivalent #{zipped_filename}."
+      end
+      
+      image_file.local_copy do |local_pfile| 
+        @dataset = RawImageDataset.new( path, [RawImageFile.new(local_pfile)])
+      end
+
+    else # Dicom      
+      Pathname.new(path).first_dicom do |fd|
+        @dataset = RawImageDataset.new( path, [RawImageFile.new(fd)] )
+      end
     end
     
     return @dataset
@@ -29,4 +58,71 @@ class RawImageDatasetResource < ActiveResource::Base
   #     super
   #   end
   # end
+  
+  # def file_count
+  #   unless @file_count
+  #     if @raw_image_files.first.dicom?
+  #       @file_count = Dir.open(@directory).reject{ |branch| /^\./.match(branch) }.length
+  #     elsif @raw_image_files.first.pfile?
+  #       @file_count = 1
+  #     else raise "File not recognized as dicom or pfile."
+  #     end
+  #   end
+  #   return @file_count
+  # end
+  
+  def pfile?
+    scanned_file =~ /^P.*.7$/
+  end
+  
+  
+  
+  def file_count
+    if pfile?
+      file_count = 1
+    else
+      file_count = Dir.open(path).reject{ |branch| /(^\.|.yaml$)/.match(branch) }.length
+    end
+    return file_count
+  end
+  
+  # Returns a relative filepath to the dataset.  Handles dicoms by returning the
+  # dataset directory, and pfiles by returning either the pfile filename or,
+  # if passed a visit directory, the relative path from the visit directory to 
+  # the pfile (i.e. P00000.7 or raw/P00000.7).
+  def relative_dataset_path(visit_dir = nil)
+    if pfile?
+      relative_dataset_path = scanned_file
+    else # Then it's a dicom.
+      relative_dataset_path = File.basename(path)
+    end
+    
+    return relative_dataset_path
+  end
+  
+  # Creates an Hirb Table for pretty output of dataset info.
+  # It takes an array of either RawImageDatasets or RawImageDatasetResources
+  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],
+      :description => false # Turn off rendering row count description at bottom.
+    )
+  rescue NameError => e
+    puts e
+
+    # Header Line
+    printf "\t%-15s %-30s [%s]\n", "Directory", "Series Description", "Files"
+
+    # Dataset Lines
+    datasets.sort_by{|ds| [ds.timestamp, File.basename(ds.path)] }.each do |dataset|
+      printf "\t%-15s %-30s [%s]\n", dataset.relative_dataset_path, dataset.series_description, dataset.file_count
+    end
+
+    # Reminder Line
+    puts "(This would be much prettier if you installed hirb.)"
+    return
+  end   
+  
 end

data/lib/metamri/visit_raw_data_directory_resource.rb

@@ -8,8 +8,9 @@ class VisitRawDataDirectoryResource < ActiveResource::Base
   self.element_name = "visit"
   
   # Creates a Backwards Transfer to go from ActiveRecord to Metamri Classes
-  # ActiveResource will provide :attr methods for column names from the database, 
-  # so check the current schema.rb file for those.
+  #
+  # ActiveResource will provide :attr methods for column names from the 
+  # database, so check the current schema.rb file for those.
   def to_metamri_visit_raw_data_directory    
     @visit = VisitRawDataDirectory.new(path)
     @visit.timestamp = date
@@ -23,10 +24,23 @@ class VisitRawDataDirectoryResource < ActiveResource::Base
     @datasets ||= RawImageDatasetResource.find(:all, :from => "/visits/#{id}/image_datasets.xml" )
   end
   
+  # Convert a Resource and its datasets to a VisitRawDataDirectory and 
+  # RawImageDataset, respectively, then pretty print it using
+  # VisitRawDataDirectory.to_s
+  # def to_s
+  #   metamri_visit = to_metamri_visit_raw_data_directory
+  #   metamri_visit.datasets = datasets.collect { |ds| ds.to_metamri_raw_image_dataset}
+  #   metamri_visit.to_s
+  # end
+  
   def to_s
-    metamri_visit = to_metamri_visit_raw_data_directory
-    metamri_visit.datasets = datasets.collect { |ds| ds.to_metamri_raw_image_dataset}
-    metamri_visit.to_s
+    puts; path.length.times { print "-" }; puts
+    puts "#{path}"
+    puts "#{rmr} - #{date} - #{scanner_source}"
+    puts
+    # puts "#{@scan_procedure_name}"
+    puts RawImageDatasetResource.to_table(datasets)
+    puts "Notes: " + notes unless notes.nil? or notes.empty?
   end
+  
 end
-

data/lib/metamri.rb

@@ -9,7 +9,7 @@ require 'metamri/visit_raw_data_directory_resource'
 
 begin
   require 'hirb'
-rescue LoadError => e
+rescue LoadError
   puts "Hirb must be installed for pretty output. Use 'sudo gem install hirb'"
 end
 

data/lib/nifti_builder.rb

@@ -28,4 +28,10 @@ module UnknownImageDataset
 
     return nifti_conversion_command, nifti_output_file
   end
+end
+
+module DTIDataset
+  def dataset_to_nifti(nifti_output_directory, nifti_filename, input_options = {} )
+    
+  end
 end

data/lib/raw_image_dataset.rb

@@ -179,7 +179,15 @@ have more component files than shell commands can handle.
   
   
   def file_count
-    @file_count ||= Dir.open(@directory).reject{ |branch| /^\./.match(branch) }.length
+    unless @file_count
+      if @raw_image_files.first.dicom?
+        @file_count = Dir.open(@directory).reject{ |branch| /(^\.|.yaml$)/.match(branch) }.length
+      elsif @raw_image_files.first.pfile?
+        @file_count = 1
+      else raise "File not recognized as dicom or pfile."
+      end
+    end
+    return @file_count
   end
   
   # Creates an Hirb Table for pretty output of dataset info.
@@ -191,11 +199,41 @@ have more component files than shell commands can handle.
     
     Hirb::Helpers::AutoTable.render(
       datasets.sort_by{ |ds| [ds.timestamp, File.basename(ds.directory)] }, 
-      :headers => { :directory_basename => 'Directory', :series_description => 'Series Description', :file_count => 'File Count'}, 
-      :fields => [:directory_basename, :series_description, :file_count]
+      :headers => { :relative_dataset_path => 'Dataset', :series_details => 'Series Details', :file_count => 'File Count'}, 
+      :fields => [:relative_dataset_path, :series_details, :file_count],
+      :description => false # Turn off rendering row count description at bottom.
     )
       
   end
+
+  # Returns a relative filepath to the dataset.  Handles dicoms by returning the
+  # dataset directory, and pfiles by returning either the pfile filename or,
+  # if passed a visit directory, the relative path from the visit directory to 
+  # the pfile (i.e. P00000.7 or raw/P00000.7).
+  def relative_dataset_path(visit_dir = nil)
+    image_file = @raw_image_files.first
+    case image_file.file_type
+      when 'dicom'
+        relative_dataset_path = File.basename(directory)
+      when 'pfile'
+        full_dataset_path = Pathname.new(File.join(directory, image_file.filename))
+        if visit_dir
+          relative_dataset_path = full_dataset_path.relative_path_from(visit_dir)
+        else
+          relative_dataset_path = image_file.filename
+        end
+      else raise "Cannot identify #{@raw_image_files.first.filename}"
+    end
+    
+    return relative_dataset_path
+  end
+  
+  # Reports series details, including description and possilby image quality
+  # check comments.  
+  def series_details
+    @series_description
+  end
+  
 private
 
   # Gets the earliest timestamp among the raw image files in this dataset.

data/lib/visit_raw_data_directory.rb

@@ -184,12 +184,19 @@ Returns an array of the created nifti files.
   def to_s
     puts; @visit_directory.length.times { print "-" }; puts
     puts "#{@visit_directory}"
-    puts "#{@rmr_number} - #{@scanner_source}"
-    puts "#{@scan_procedure_name}"
-    puts "#{@scanid}"
+    puts "#{@rmr_number} - #{@timestamp.strftime('%F')} - #{@scanner_source}"
+    puts
     puts RawImageDataset.to_table(@datasets)
     return
   rescue NameError => e
+    puts e
+    if @datasets.first.class.to_s == "RawImageDatasetResource"
+      @datasets = @datasets.map { |ds| ds.to_metamri_image_dataset }
+    end
+    
+    # puts @datasets.first.class.to_s
+    # puts @datasets
+    
     # Header Line
     printf "\t%-15s %-30s [%s]\n", "Directory", "Series Description", "Files"
     

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.13"
+  s.version = "0.1.14"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-02-04}
+  s.date = %q{2010-03-11}
   s.description = %q{Extraction of MRI metadata and insertion into compatible sqlite3 databases.}
   s.email = %q{kk4@medicine.wisc.edu}
   s.executables = ["import_study.rb", "import_visit.rb", "import_respiratory_files.rb", "list_visit", "convert_visit.rb"]
@@ -48,7 +48,7 @@ Gem::Specification.new do |s|
   s.homepage = %q{http://github.com/brainmap/metamri}
   s.rdoc_options = ["--charset=UTF-8"]
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.5}
+  s.rubygems_version = %q{1.3.6}
   s.summary = %q{MRI metadata}
   s.test_files = [
     "test/nifti_builder_spec.rb",

metadata

@@ -1,7 +1,12 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  version: 0.1.13
+  prerelease: false
+  segments: 
+  - 0
+  - 1
+  - 14
+  version: 0.1.14
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -9,29 +14,33 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-02-04 00:00:00 -06:00
+date: 2010-03-11 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: sqlite3-ruby
-  type: :runtime
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        segments: 
+        - 0
         version: "0"
-    version: 
+  type: :runtime
+  version_requirements: *id001
 - !ruby/object:Gem::Dependency 
   name: rspec
-  type: :development
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        segments: 
+        - 0
         version: "0"
-    version: 
+  type: :development
+  version_requirements: *id002
 description: Extraction of MRI metadata and insertion into compatible sqlite3 databases.
 email: kk4@medicine.wisc.edu
 executables: 
@@ -85,18 +94,20 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      segments: 
+      - 0
       version: "0"
-  version: 
 required_rubygems_version: !ruby/object:Gem::Requirement 
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      segments: 
+      - 0
       version: "0"
-  version: 
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.5
+rubygems_version: 1.3.6
 signing_key: 
 specification_version: 3
 summary: MRI metadata