metamri 0.1.10 → 0.1.11

data/VERSION

@@ -1 +1 @@
-0.1.10
+0.1.11

data/bin/convert_visit.rb

@@ -36,7 +36,8 @@ require 'logger'
 #   
 # 
 # == Usage
-#   
+#
+#   convert_visit.rb /Data/vtrak1/raw/ries.aware.visit1/awr001_9999_010110/ ries.aware.visit1 /tmp/awr001
 #
 # == Example
 #   
@@ -66,9 +67,13 @@ if File.basename(__FILE__) == File.basename($PROGRAM_NAME)
   RDoc::usage() if (ARGV[0] == '-h')
   raw_directory = ARGV[0]
 
-  # This is required for now, will be inferred from path in the future.
-  scan_procedure_codename = ARGV[1] 
+
+  # Optional Scan Procdedure Codename
+  # If not given this is inferred by VisitRawDataDirectory#get_scan_procedure_based_on_raw_directory
+  scan_procedure_codename = ARGV[1] ? ARGV[1] : nil
   
+  # Optional Output Directory
+  # If not given this is inferred by  VisitRawDataDirectory#default_preprocess_directory
   output_directory = ARGV[2] ? ARGV[2] : nil
 
   convert_visit(raw_directory, scan_procedure_codename, output_directory)

data/bin/import_visit.rb

@@ -1,10 +1,12 @@
 #!/usr/bin/env ruby
 #
 # == Synopsis 
-#   A simple utility for importing imaging data collected during one visit into the WADRC Data Tools web
-#   application.  Data from a visit is contained in one big directory that may have many subdirectories.
-#   Each individual imaging scan may be composed of an entire directory of dicom files or one single p-file.
-#   This utility scans through all of the image data sets and retrieved meta-data about the scans from their
+#   A simple utility for importing imaging data collected during one 
+#   visit into the WADRC Data Tools web application.  Data from a visit
+#   is contained in one large directory that may have many subdirectories.
+#   Each individual imaging scan may be composed of an entire directory 
+#   of dicom files or one single p-file.  This utility scans through all
+#   of the image data sets and retrieved meta-data about the scans from their
 #   header information.
 #
 # == Examples

data/bin/list_visit

@@ -0,0 +1,69 @@
+#!/usr/bin/env ruby
+#
+# == Synopsis 
+#   A simple utility for listing visit details and scan acquistion
+#   information from the terminal, either through freshly scanning
+#   the filesystem or connecting to an imaging database and looking
+#   up information through there (for Image Quality Checks, for 
+#   example.
+#
+# == Examples
+#
+#   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
+#
+# == Usage 
+#   list_visit <raw_data_directory>
+#
+#   For help use: list_vist -h
+#
+# == Options
+#   -h, --help          Displays help message
+#
+# == Author
+#   Erik Kastman
+#   WADRC Imaging Core
+#
+
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'metamri'
+require 'pathname'
+require 'rdoc/usage'
+require 'logger'
+
+def list_visit(raw_directory)
+  $LOG = Logger.new(STDOUT)  
+  $LOG.level = Logger::INFO
+  visit = VisitRawDataDirectory.new(raw_directory)
+  # visit = VisitRawDataDirectoryResource.find(:all, :from => '/visits/found.xml', :params => {:visit_search => {:rmr => 'rmr'}})
+
+  begin
+    visit.scan
+    # visit.datasets = RawImageDatasetResource.find(:all, :from => "/visits/#{visit.database_id}/image_datasets.xml" )
+  rescue IndexError => e
+    $LOG.error "Are you sure #{raw_directory} is a valid raw visit directory?"
+    raise e
+  rescue Exception => e
+    $LOG.error "There was a problem scanning a dataset in #{visit.visit_directory}... skipping."
+    $LOG.error "Exception message: #{e.message}"
+    raise e
+  end
+  
+  visit.to_s
+
+end
+
+if File.basename(__FILE__) == File.basename($PROGRAM_NAME)
+  RDoc::usage() if (ARGV[0] == '-h')
+
+  # Default to scanning the current directory if no argument was given.
+  raw_directory = ARGV[0] ||= File.expand_path('.')
+
+  list_visit(raw_directory)
+end

data/lib/metamri.rb

@@ -4,6 +4,14 @@ require 'raw_image_file'
 require 'raw_image_dataset'
 require 'visit_raw_data_directory'
 require 'metamri/core_additions'
+require 'metamri/raw_image_dataset_resource'
+require 'metamri/visit_raw_data_directory_resource'
+
+begin
+  require 'hirb'
+rescue LoadError => e
+  puts "Hirb must be installed for pretty output. Use 'sudo gem install hirb'"
+end
 
 module Metamri
 end

data/lib/metamri/core_additions.rb

@@ -14,4 +14,89 @@ Does same basic string replacements to ensure valid filenames.
     end
   end
   
+end
+
+class Pathname
+  MIN_PFILE_SIZE = 10_000_000
+  
+  def each_subdirectory
+    each_entry do |leaf|
+      next if leaf.to_s =~ /^\./
+      branch = self + leaf
+      next if not branch.directory?
+      next if branch.symlink?
+      branch.each_subdirectory { |subbranch| yield subbranch }
+      yield branch
+    end
+  end
+  
+  def each_pfile(min_file_size = MIN_PFILE_SIZE)
+    entries.each do |leaf|
+      next unless leaf.to_s =~ /^P.*\.7|^P.*\.7\.bz2/
+      branch = self + leaf
+      next if branch.symlink?
+      if branch.size >= min_file_size
+        lc = branch.local_copy
+        begin
+          yield lc
+        rescue Exception => e
+          puts "#{e}"
+        ensure
+          lc.delete
+        end
+      end
+    end
+  end
+  
+  def first_dicom
+    entries.each do |leaf|
+      branch = self + leaf
+      if leaf.to_s =~ /^I\.|\.dcm(\.bz2)?$|\.0[0-9]+(\.bz2)?$/
+        lc = branch.local_copy
+        begin
+          yield lc
+        rescue Exception => e
+          puts "#{e}"
+        ensure
+          lc.delete
+        end
+        return
+      end 
+    end
+  end
+  
+  def all_dicoms
+    local_copies = []
+    Dir.mktmpdir do |tempdir|
+      begin
+      
+        entries.each do |leaf|
+          branch = self + leaf
+          if leaf.to_s =~ /^I\.|\.dcm(\.bz2)?$|\.0[0-9]+(\.bz2)?$/
+            local_copies << branch.local_copy(tempdir)
+          end
+        end
+
+        yield local_copies
+
+      ensure
+        local_copies.each { |lc| lc.delete }
+      end
+    end
+    
+    return
+  end
+  
+  def local_copy(tempdir = Dir.tmpdir)
+    tfbase = self.to_s =~ /\.bz2$/ ? self.basename.to_s.chomp(".bz2") : self.basename.to_s
+    tfbase.escape_filename
+    tmpfile = File.join(tempdir, tfbase)
+    if self.to_s =~ /\.bz2$/
+      `bunzip2 -k -c '#{self.to_s}' >> '#{tmpfile}'`
+    else
+      FileUtils.cp(self.to_s, tmpfile)
+    end
+    return Pathname.new(tmpfile)
+  end
+  
 end

data/lib/metamri/raw_image_dataset_resource.rb

@@ -0,0 +1,20 @@
+require 'active_resource'
+
+class RawImageDatasetResource < ActiveResource::Base
+  self.site = VisitRawDataDirectory::DATAPANDA_SERVER
+  self.element_name = "image_dataset"
+  
+  # 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.
+  def to_metamri_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.
+    
+    Pathname.new(path).first_dicom do |fd|
+      @dataset = RawImageDataset.new( path, [RawImageFile.new(fd)] )
+    end
+    
+    return @dataset
+  end
+end

data/lib/metamri/visit_raw_data_directory_resource.rb

@@ -0,0 +1,20 @@
+require 'active_resource'
+
+DATAPANDA_SERVER = 'http://144.92.151.228'
+
+class VisitRawDataDirectoryResource < ActiveResource::Base
+  self.site = VisitRawDataDirectory::DATAPANDA_SERVER
+  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.
+  def to_metamri_visit_raw_data_directory    
+    @visit = VisitRawDataDirectory.new(path)
+    @visit.timestamp = date
+    @visit.rmr_number = rmr
+    @visit.scanner_source = scanner_source
+    @visit.database_id = id
+    return @visit
+  end
+end

data/lib/raw_image_dataset.rb

@@ -177,14 +177,36 @@ have more component files than shell commands can handle.
     end
   end
   
-
   
+  def file_count
+    @file_count ||= Dir.open(@directory).reject{ |branch| /^\./.match(branch) }.length
+  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)
+    if datasets.first.class.to_s == "RawImageDatasetResource"
+      datasets = datasets.map { |ds| ds.to_metamri_image_dataset }
+    end
+    
+    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]
+    )
+      
+  end
 private
 
   # Gets the earliest timestamp among the raw image files in this dataset.
   def get_earliest_timestamp
     @timestamp = (@raw_image_files.sort_by { |i| i.timestamp }).first.timestamp
   end
+  
+  # Directory Basename is hardcoded for Pretty Printing using Hirb, which takes symbols as method names for its columns.
+  def directory_basename
+    File.basename(@directory)
+  end
 
 end
 #### END OF CLASS ####

data/lib/visit_raw_data_directory.rb

@@ -7,17 +7,20 @@ require 'fileutils'
 require 'raw_image_file'
 require 'raw_image_dataset'
 require 'sqlite3'
+require 'logger'
 
 
 # A shared function that displays a message and the date/time to standard output.
 def flash(msg)
+  flash_size =msg.size + 20
+  
   puts
-  puts "+" * 120
+  puts "+" * flash_size
   printf "\t%s\n", msg
   printf "\t%s\n", Time.now
-  puts "+" * 120
+  puts "+" * flash_size
   puts
-  $LOG.info msg if $LOG
+  $LOG.debug msg if $LOG
 end
 
 
@@ -37,21 +40,25 @@ class VisitRawDataDirectory
   # The absolute path of the visit directory, as a string.
   attr_reader :visit_directory
   # An array of :RawImageDataset objects acquired during this visit.
-  attr_reader :datasets
+  attr_accessor :datasets
   # Timestamp for this visit, obtained from the first :RawImageDataset
-  attr_reader :timestamp
+  attr_accessor :timestamp
   # RMR number for this visit.
-  attr_reader :rmr_number
+  attr_accessor :rmr_number
   # scan_procedure name
   attr_reader :scan_procedure_name
   # scanner source
-  attr_reader :scanner_source
+  attr_accessor :scanner_source
   #
   attr_accessor :db
   # Scan ID is the short name for the scan (tbiva018, tbiva018b)
   attr_accessor :scanid
+  # The id of the visit to be used when doing reverse-lookup in data panda.
+  attr_accessor :database_id
   
   PREPROCESS_REPOSITORY_DIRECTORY = '/Data/vtrak1/preprocessed/visits'
+  # DATAPANDA_SERVER = 'http://localhost:3000'
+  DATAPANDA_SERVER = 'http://144.92.151.228'
 
   
   # A new Visit instance needs to know the path to its raw data and scan_procedure name.  The scan_procedure
@@ -65,6 +72,7 @@ class VisitRawDataDirectory
     @rmr_number = nil
     @scan_procedure_name = scan_procedure_name.nil? ? get_scan_procedure_based_on_raw_directory : scan_procedure_name
     @db = nil
+    initialize_log
   end
   
   # Recursively walks the filesystem inside the visit directory.  At each subdirectory, any and all
@@ -72,7 +80,7 @@ class VisitRawDataDirectory
   # @datasets will hold an array of ImageDataset instances.  Setting the rmr here can raise an 
   # exception if no valid rmr is found in the datasets, be prepared to catch it.
   def scan
-    flash "Scanning visit raw data directory #{@visit_directory}"
+    flash "Scanning visit raw data directory #{@visit_directory}" if $LOG.level <= Logger::INFO
     d = Pathname.new(@visit_directory)
     d.each_subdirectory do |dd|
       begin 
@@ -87,7 +95,7 @@ class VisitRawDataDirectory
       @timestamp = get_visit_timestamp
       @rmr_number = get_rmr_number
       @scanner_source = get_scanner_source
-      flash "Completed scanning #{@visit_directory}"
+      flash "Completed scanning #{@visit_directory}" if $LOG.level <= Logger::DEBUG
     else
       raise(IndexError, "No datasets could be scanned for directory #{@visit_directory}")
     end
@@ -173,6 +181,30 @@ Returns an array of the created nifti files.
     @scanid ||= File.basename(visit_directory).split('_')[0]
   end
   
+  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 RawImageDataset.to_table(@datasets)
+    return
+  rescue NameError => e
+    # Header Line
+    printf "\t%-15s %-30s [%s]\n", "Directory", "Series Description", "Files"
+    
+    # Dataset Lines
+    @datasets.sort_by{|ds| [ds.timestamp, File.basename(ds.directory)] }.each do |dataset|
+      printf "\t%-15s %-30s [%s]\n", File.basename(dataset.directory), dataset.series_description, dataset.file_count
+    end
+    
+    # Reminder Line
+    puts "(This would be much prettier if you installed hirb.)"
+    
+    return
+  end
+  
+  
   private
   
   def get_existing_dataset_id(ds)
@@ -273,7 +305,7 @@ generates an sql insert statement to insert this visit with a given participant
   end
   
   def import_dataset(rawfile, original_parent_directory)
-    puts "Importing scan session: #{original_parent_directory.to_s} using raw data file: #{rawfile.basename}"
+    puts "Importing scan session: #{original_parent_directory.to_s} using raw data file: #{rawfile.basename}" if $LOG.level <= Logger::DEBUG
     
     begin
       rawimagefile = RawImageFile.new(rawfile.to_s)
@@ -381,103 +413,21 @@ generates an sql insert statement to insert this visit with a given participant
       
     when /ries.aware.visit1/
       return 'ries.aware.visit1'
+      
+    when /carlson.sharp.visit1/
+      return 'carlson.sharp.visit1'
     
     else
       return 'unknown.scan_procedure'
     end
   end
   
-
-
-end
-
-
-
-
-
-class Pathname
-  MIN_PFILE_SIZE = 10_000_000
-  
-  def each_subdirectory
-    each_entry do |leaf|
-      next if leaf.to_s =~ /^\./
-      branch = self + leaf
-      next if not branch.directory?
-      next if branch.symlink?
-      branch.each_subdirectory { |subbranch| yield subbranch }
-      yield branch
-    end
-  end
-  
-  def each_pfile(min_file_size = MIN_PFILE_SIZE)
-    entries.each do |leaf|
-      next unless leaf.to_s =~ /^P.*\.7|^P.*\.7\.bz2/
-      branch = self + leaf
-      next if branch.symlink?
-      if branch.size >= min_file_size
-        lc = branch.local_copy
-        begin
-          yield lc
-        rescue Exception => e
-          puts "#{e}"
-        ensure
-          lc.delete
-        end
-      end
+  def initialize_log
+    # If a log hasn't been created, catch that here and go to STDOUT.
+    unless $LOG
+      $LOG = Logger.new(STDOUT)
+      $LOG.level = Logger::DEBUG
     end
   end
-  
-  def first_dicom
-    entries.each do |leaf|
-      branch = self + leaf
-      if leaf.to_s =~ /^I\.|\.dcm(\.bz2)?$|\.0[0-9]+(\.bz2)?$/
-        lc = branch.local_copy
-        begin
-          yield lc
-        rescue Exception => e
-          puts "#{e}"
-        ensure
-          lc.delete
-        end
-        return
-      end 
-    end
-  end
-  
-  def all_dicoms
-    local_copies = []
-    Dir.mktmpdir do |tempdir|
-      begin
-      
-        entries.each do |leaf|
-          branch = self + leaf
-          if leaf.to_s =~ /^I\.|\.dcm(\.bz2)?$|\.0[0-9]+(\.bz2)?$/
-            local_copies << branch.local_copy(tempdir)
-          end
-        end
 
-        yield local_copies
-
-      ensure
-        local_copies.each { |lc| lc.delete }
-      end
-    end
-    
-    return
-  end
-  
-  
-  
-  def local_copy(tempdir = Dir.tmpdir)
-    tfbase = self.to_s =~ /\.bz2$/ ? self.basename.to_s.chomp(".bz2") : self.basename.to_s
-    tfbase.escape_filename
-    tmpfile = File.join(tempdir, tfbase)
-    if self.to_s =~ /\.bz2$/
-      `bunzip2 -k -c '#{self.to_s}' >> '#{tmpfile}'`
-    else
-      FileUtils.cp(self.to_s, tmpfile)
-    end
-    return Pathname.new(tmpfile)
-  end
-  
-end
+end

data/metamri.gemspec

@@ -5,14 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.10"
+  s.version = "0.1.11"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2010-01-25}
+  s.date = %q{2010-02-03}
   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_study.rb", "import_visit.rb", "import_respiratory_files.rb"]
+  s.executables = ["import_study.rb", "import_visit.rb", "import_respiratory_files.rb", "list_visit", "convert_visit.rb"]
   s.extra_rdoc_files = [
     "README.rdoc"
   ]
@@ -26,8 +26,11 @@ Gem::Specification.new do |s|
      "bin/import_respiratory_files.rb",
      "bin/import_study.rb",
      "bin/import_visit.rb",
+     "bin/list_visit",
      "lib/metamri.rb",
      "lib/metamri/core_additions.rb",
+     "lib/metamri/raw_image_dataset_resource.rb",
+     "lib/metamri/visit_raw_data_directory_resource.rb",
      "lib/mysql_tools.rb",
      "lib/nifti_builder.rb",
      "lib/raw_image_dataset.rb",

data/test/nifti_builder_spec.rb

@@ -4,6 +4,7 @@ require 'rubygems'
 require 'spec'
 require 'fileutils'
 require 'tmpdir'
+require 'metamri/core_additions'
 require 'visit_raw_data_directory'
 require 'raw_image_dataset'
 require 'raw_image_file'
@@ -17,20 +18,24 @@ VISIT_FIXTURE_UNZIPPED = File.join(Dir.tmpdir, 'fixtures/visit_raw_data_director
 describe "Convert Unknown Dicoms to Nifti Files" do  
   before(:all) do
     # Initialize a local scratch directory to hold fixtures for testing if it doesn't already exist.
-    #unless File.directory?(VISIT_FIXTURE)
-      #FileUtils.mkdir_p(File.dirname(VISIT_FIXTURE))
-      #FileUtils.cp_r(VISIT_FIXTURE_SRC, VISIT_FIXTURE)
-      #FileUtils.cp_r(VISIT_FIXTURE, VISIT_FIXTURE_UNZIPPED)
+    unless File.directory?(VISIT_FIXTURE)
+      FileUtils.mkdir_p(File.dirname(VISIT_FIXTURE))
+      FileUtils.cp_r(VISIT_FIXTURE_SRC, VISIT_FIXTURE)
+    end
+    unless File.directory?(VISIT_FIXTURE_UNZIPPED)
+      FileUtils.cp_r(VISIT_FIXTURE, VISIT_FIXTURE_UNZIPPED)
       `find #{VISIT_FIXTURE_UNZIPPED} -name '*.bz2' -exec bunzip2 {} \\;`
-    #end
+    end
   end
   
   before(:each) do
     @visit = VisitRawDataDirectory.new(VISIT_FIXTURE, 'johnson.tbi-va.visit1')
-    @dataset = RawImageDataset.new(
-      File.join(VISIT_FIXTURE, '001'), 
-      [RawImageFile.new(File.join(VISIT_FIXTURE, '001/I0001.dcm.bz2'))]
-    )
+    Pathname.new(File.join(@visit.visit_directory, '001')).first_dicom do |fd|
+      @dataset = RawImageDataset.new(
+        File.join(VISIT_FIXTURE, '001'), 
+        [RawImageFile.new(fd)]
+      )
+    end
     
     @visit_unzipped = VisitRawDataDirectory.new(VISIT_FIXTURE_UNZIPPED, 'johnson.tbi-va.visit1')
     @dataset_unzipped = RawImageDataset.new(

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  version: 0.1.10
+  version: 0.1.11
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -9,17 +9,18 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-01-25 00:00:00 -06:00
+date: 2010-02-03 00:00:00 -06:00
 default_executable: 
 dependencies: []
 
 description: Extraction of MRI metadata and insertion into compatible sqlite3 databases.
 email: kk4@medicine.wisc.edu
 executables: 
-- convert_visit.rb
 - import_study.rb
 - import_visit.rb
 - import_respiratory_files.rb
+- list_visit
+- convert_visit.rb
 extensions: []
 
 extra_rdoc_files: 
@@ -34,8 +35,11 @@ files:
 - bin/import_respiratory_files.rb
 - bin/import_study.rb
 - bin/import_visit.rb
+- bin/list_visit
 - lib/metamri.rb
 - lib/metamri/core_additions.rb
+- lib/metamri/raw_image_dataset_resource.rb
+- lib/metamri/visit_raw_data_directory_resource.rb
 - lib/mysql_tools.rb
 - lib/nifti_builder.rb
 - lib/raw_image_dataset.rb