metamri 0.2.9 → 0.2.10

data/bin/import_study.rb

@@ -75,6 +75,11 @@ STUDIES = {
                      :filter => /^pd..._/,
                      :codename => 'gallagher.pd.visit1' 
   },
+  :pc_4000  =>     { :dir => '/Data/vtrak1/raw/pc_4000',
+                     :logfile => 'pc_4000.scan.log',
+                     :filter => /^pc001/,
+                     :codename => 'johnson.pc4000.visit1' 
+  },
   :pib_pilot =>    { :dir => '/Data/vtrak1/raw/pib_pilot_mri',
                      :logfile => 'pib.mri.pilot.scan.log',
                      :filter => /^cpr0/,
@@ -148,6 +153,8 @@ def import_study(study, dbfile)
       puts "Exception message: #{e.message}"
       log.error "There was a problem scanning a dataset in #{visitdir}... skipping."
       log.error "Exception message: #{e.message}"
+      log.error e.backtrace
+      raise e
     ensure
       v = nil
     end

data/lib/metamri.rb

@@ -9,6 +9,7 @@ begin
   require 'rspec'
   require 'dicom'
   require 'rmagick'
+  require 'sqlite'
 rescue LoadError
 end
 

data/lib/metamri/raw_image_dataset.rb

@@ -21,7 +21,7 @@ class RawImageDataset
   # From the first raw image file in the dataset
   attr_reader :timestamp
   # From the first raw image file in the dataset
-  attr_reader :study_id
+  attr_reader :exam_number
   # A key string unique to a dataset composed of the rmr number and the timestamp.
   attr_reader :dataset_key
   # the file scanned
@@ -86,8 +86,8 @@ class RawImageDataset
     @scanner_source = @raw_image_files.first.source
     raise(IndexError, "No scanner source found") if @scanner_source.nil?
         
-    @study_id = @raw_image_files.first.study_id.nil? ? nil : @raw_image_files.first.study_id
-    # raise(IndexError, "No study id / exam number found") if @study_id.nil?
+    @exam_number = @raw_image_files.first.exam_number.nil? ? nil : @raw_image_files.first.exam_number
+    validates_metainfo_for :exam_number, :msg => "No study id / exam number found", :optional => true
     
     @study_description = @raw_image_files.first.study_description
     validates_metainfo_for :study_description, :msg => "No study description found" if dicom?
@@ -109,7 +109,10 @@ class RawImageDataset
     
     @dicom_taghash = @raw_image_files.first.dicom_taghash
     validates_metainfo_for :dicom_taghash if dicom?
-        
+    
+    @image_uid  = @raw_image_files.first.image_uid
+    validates_metainfo_for :image_uid if pfile?
+    
     $LOG ||= Logger.new(STDOUT)
   end
   
@@ -132,10 +135,10 @@ class RawImageDataset
   def db_insert(visit_id)
     "INSERT INTO image_datasets
     (rmr, series_description, path, timestamp, created_at, updated_at, visit_id, 
-    glob, rep_time, bold_reps, slices_per_volume, scanned_file)
+    glob, rep_time, bold_reps, slices_per_volume, scanned_file, 'dicom_study_uid')
     VALUES ('#{@rmr_number}', '#{@series_description}', '#{@directory}', '#{@timestamp.to_s}', '#{DateTime.now}', 
     '#{DateTime.now}', '#{visit_id}', '#{self.glob}', '#{@raw_image_files.first.rep_time}', 
-    '#{@raw_image_files.first.bold_reps}', '#{@raw_image_files.first.num_slices}', '#{@scanned_file}')"
+    '#{@raw_image_files.first.bold_reps}', '#{@raw_image_files.first.num_slices}', '#{@scanned_file}' )"
   end
   
   def db_update(dataset_id)
@@ -186,7 +189,8 @@ class RawImageDataset
       :slices_per_volume => @raw_image_files.first.num_slices,
       :scanned_file => @scanned_file,
       :dicom_series_uid => @dicom_series_uid,
-      :dicom_taghash => @dicom_taghash
+      :dicom_taghash => @dicom_taghash,
+      :image_uid => @image_uid
     }.merge attrs
   end
   
@@ -361,6 +365,15 @@ private
   def directory_basename
     File.basename(@directory)
   end
+  
+  # Metamri will return both dicom_series_uid and image_uid for ActiveRecord
+  # Correct UID choosing will happen in the Panda.
+  # But, here's a shortcut to a pfile?/dicom? ternary for correct uid for dataset
+  def dataset_uid
+    @raw_image_files.first.dicom_series_uid ? 
+      @raw_image_files.first.dicom_series_uid : @raw_image_files.first.image_uid
+  end
+  
 
   # Ensure that metadata is present in instance variables.
   #

data/lib/metamri/raw_image_file.rb

@@ -41,7 +41,7 @@ class RawImageFile
   # An identifier unique to a 'visit', these are assigned by the scanner techs at scan time.
   attr_reader :rmr_number
   # An identifier unique to a Study Session - AKA Exam Number
-  attr_reader :study_id
+  attr_reader :exam_number
   # A short string describing the acquisition sequence. These come from the scanner.
   # code and are used to initialise SeriesDescription objects to find related attributes.
   attr_reader :series_description
@@ -73,6 +73,8 @@ class RawImageFile
   attr_reader :dicom_header
   # Hash of all DICOM Tags including their Names and Values (See #dicom_taghash for more information on the structure)
   attr_reader :dicom_taghash
+  # DICOM SOP Instance UID (from the scanned file)
+  attr_reader :dicom_image_uid
   # DICOM Series UID
   attr_reader :dicom_series_uid
   # DICOM Study UID
@@ -235,8 +237,16 @@ class RawImageFile
     return db_row
   end
   
-
-
+  # The series ID (dicom_series_uid [dicom] or series_uid [pfile/ifile])
+  # This is unique for DICOM datasets, but not for PFiles
+  def series_uid
+    @dicom_series_uid || @series_uid
+  end
+  
+  # The UID unique to the raw image file scanned
+  def image_uid
+    @dicom_image_uid || @image_uid
+  end
 
 private
 
@@ -325,6 +335,7 @@ private
   #   0008,0030 Study Time                           TM      6 101538
   #   0008,0080 Institution Name                     LO      4 Institution
   #   0008,1010 Station Name                         SH      8 Station
+  #   0008,0018 SOP Instance UID                            12 1.2.840.113619.2.155.3596.6906438.17031.1121881958.942
   #   0008,1030 Study Description                    LO     12 PILOT Study
   #   0008,103E Series Description                   LO     12 3pl loc FGRE
   #   0008,1070 Operators' Name                      PN      2 SP
@@ -386,9 +397,10 @@ private
       :software_version => "0018,1020",
       :protocol_name => "0018,1030",
       :bold_reps => "0020,0105",
-      :dicom_series_uid => "0020,000E",
+      :dicom_image_uid => "0008,0018",    # Each DICOM Image (i.e. raw image file) has a unique SOP Instance UID
+      :dicom_series_uid => "0020,000E",   # Series UID (shared by all dicoms in the same series)
       :dicom_study_uid => "0020,000D",
-      :study_id => "0020,0010",
+      :exam_number => "0020,0010",
       :num_slices => "0020,1002",
       :acquisition_matrix_x => "0028,0010",
       :acquisition_matrix_y => "0028,0011"
@@ -461,7 +473,7 @@ private
       :pat => /[ID Accession Number|ID Study Description]\/\/(RMR.*)\n/i, 
       :required => true 
     }
-    dicom_tag_templates[:study_id] = {
+    dicom_tag_templates[:exam_number] = {
       :type => :string,
       :pat => /STUDY ID\/\/([0-9]+)/i,
       :required => true 
@@ -580,6 +592,7 @@ private
     rep_time_pat =             /Pulse repetition time \(usec\): ([0-9]+)/i
     study_uid_pat =            /Study entity unique ID: ([[:graph:]]+)/i
     series_uid_pat =           /Series entity unique ID: ([[:graph:]]+)/i
+    image_uid_pat =            /Image unique ID: ([[:graph:]]+)/i    
 
     rmr_number_pat =~ @hdr_data
     @rmr_number = ($1).nil? ? "rmr not found" : ($1).strip.chomp
@@ -620,10 +633,14 @@ private
     @rep_time = ($1).to_f / 1000000
     
     study_uid_pat =~ @hdr_data
-    @dicom_study_uid = ($1).strip.chomp unless $1.nil?
+    @study_uid = ($1).strip.chomp unless $1.nil?
     
     series_uid_pat =~ @hdr_data
-    @dicom_series_uid = ($1).strip.chomp
+    @series_uid = ($1).strip.chomp unless $1.nil?
+    
+    image_uid_pat =~ @hdr_data
+    @image_uid = ($1).strip.chomp unless $1.nil?
+    
   end
  
 end

data/lib/metamri/version.rb

@@ -1,3 +1,3 @@
 module Metamri
-  VERSION = "0.2.9"
+  VERSION = "0.2.10"
 end

data/lib/metamri/visit_raw_data_directory.rb

@@ -4,7 +4,7 @@ require 'tempfile'
 require 'yaml'
 require 'tmpdir'
 require 'fileutils'
-# require 'sqlite3'
+require 'sqlite3'
 require 'logger'
 require 'pp'
 require 'metamri/raw_image_file'
@@ -49,7 +49,7 @@ class VisitRawDataDirectory
   # scanner source
   attr_accessor :scanner_source
   # scanner-defined study id / exam number
-  attr_accessor :study_id
+  attr_accessor :exam_number
   #
   attr_accessor :db
   # Scan ID is the short name for the scan (tbiva018, tbiva018b)
@@ -67,7 +67,7 @@ class VisitRawDataDirectory
   # A new Visit instance needs to know the path to its raw data and scan_procedure name.  The scan_procedure
   # name must match a name in the database, if not a new scan_procedure entry will be inserted.
   def initialize(directory, scan_procedure_name=nil)
-    raise(IOError, "Visit directory not found: #{directory}") unless File.exist?(File.expand_path(directory))
+    raise(IOError, "Visit directory not found: #{directory}") unless File.directory? File.expand_path(directory)
     @visit_directory = File.expand_path(directory)
     @working_directory = Dir.tmpdir
     @datasets = Array.new
@@ -75,7 +75,7 @@ class VisitRawDataDirectory
     @rmr_number = nil
     @scan_procedure_name = scan_procedure_name.nil? ? get_scan_procedure_based_on_raw_directory : scan_procedure_name
     @db = nil
-    @study_id = nil
+    @exam_number = nil
     initialize_log
   end
   
@@ -84,8 +84,10 @@ 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.
   #
-  # Run a scan with the following options:
-  # - :ignore_patterns - An array of Regular Expressions that will be used to skip heavy directories.
+  # === Options
+  # 
+  # * <tt>:ignore_patterns</tt> -- Array of Regex'es. An array of Regular Expressions that will be used to skip heavy directories.
+  # 
   def scan(options = {})
     flash "Scanning visit raw data directory #{@visit_directory}" if $LOG.level <= Logger::INFO
     default_options = {:ignore_patterns => []}
@@ -110,8 +112,8 @@ class VisitRawDataDirectory
       @timestamp = get_visit_timestamp
       @rmr_number = get_rmr_number
       @scanner_source = get_scanner_source
-      @study_id = get_study_id
-      @dicom_study_uid = get_dicom_study_uid unless dicom_datasets.empty?
+      @exam_number = get_exam_number
+      @study_uid = get_study_uid unless dicom_datasets.empty?
       flash "Completed scanning #{@visit_directory}" if $LOG.level <= Logger::DEBUG
     else
       raise(IndexError, "No datasets could be scanned for directory #{@visit_directory}")
@@ -125,8 +127,8 @@ class VisitRawDataDirectory
       :rmr => @rmr_number, 
       :path => @visit_directory, 
       :scanner_source => @scanner_source ||= get_scanner_source,
-      :scan_number => @study_id,
-      :dicom_study_uid => @dicom_study_uid
+      :scan_number => @exam_number,
+      :dicom_study_uid => @study_uid
     }
   end
   
@@ -161,6 +163,7 @@ class VisitRawDataDirectory
       end
     rescue Exception => e
       puts e.message
+      puts e.backtrace
     ensure
       @db.close
       @db = nil
@@ -203,7 +206,7 @@ Returns an array of the created nifti files.
   def to_s
     puts; @visit_directory.length.times { print "-" }; puts
     puts "#{@visit_directory}"
-    puts "#{@rmr_number} - #{@timestamp.strftime('%F')} - #{@scanner_source} - #{@study_id unless @study_id.nil?}"
+    puts "#{@rmr_number} - #{@timestamp.strftime('%F')} - #{@scanner_source} - #{@exam_number unless @exam_number.nil?}"
     puts
     puts RawImageDataset.to_table(@datasets)
     return
@@ -260,18 +263,24 @@ Returns an array of the created nifti files.
   end
   
   def insert_new_visit(p_id)
-    puts sql_insert_visit(p_id)
-    @db.execute(sql_insert_visit(p_id))
-    return @db.last_insert_row_id
+    puts sql_insert_visit
+    @db.execute(sql_insert_visit)
+    visit_id = @db.last_insert_row_id
+    puts sql_insert_scan_procedures_visits(p_id, visit_id)
+    @db.execute(sql_insert_scan_procedures_visits(p_id, visit_id))
+    return visit_id
   end
   
   def get_existing_visit_id
     return @db.execute(sql_fetch_visit_matches).first['id']
   end
   
+  # ScanProcedure now in a separate table
+  # Ignore it for now. BAD! 
+  # Note: wtf
   def update_existing_visit(v_id, p_id)
-    puts sql_update_visit(v_id, p_id)
-    @db.execute(sql_update_visit(v_id, p_id))
+    puts sql_update_visit(v_id)
+    @db.execute(sql_update_visit(v_id))
   end
   
   def fetch_or_insert_scan_procedure
@@ -284,12 +293,11 @@ Returns an array of the created nifti files.
     return scan_procedure_matches.empty? ? new_scan_procedure_id : scan_procedure_matches.first['id']
   end
   
-  def sql_update_visit(v_id, p_id)
+  def sql_update_visit(v_id)
     "UPDATE visits SET 
     date = '#{@timestamp.to_s}',
     rmr = '#{@rmr_number}',
     path = '#{@visit_directory}',
-    scan_procedure_id = '#{p_id.to_s}',
     scanner_source = '#{@scanner_source}'
     WHERE id = '#{v_id}'"
   end
@@ -298,6 +306,10 @@ Returns an array of the created nifti files.
     "INSERT INTO scan_procedures (codename) VALUES ('#{@scan_procedure_name}')"
   end
   
+  def sql_insert_scan_procedures_visits(scan_procedure_id, visit_id)
+    "INSERT INTO scan_procedures_visits (scan_procedure_id, visit_id) VALUES('#{scan_procedure_id}', '#{visit_id}')"
+  end
+  
   def sql_insert_series_description(sd)
     "INSERT INTO series_descriptions (long_description) VALUES ('#{sd}')"
   end
@@ -307,7 +319,7 @@ Returns an array of the created nifti files.
   end
   
   def sql_fetch_scan_procedure_name
-    "SELECT * FROM scan_procedures WHERE codename = '#{@scan_procedure_name}'"
+    "SELECT * FROM scan_procedures WHERE codename = '#{@scan_procedure_name}' LIMIT 1"
   end
   
   def sql_fetch_series_description(sd)
@@ -320,13 +332,13 @@ Returns an array of the created nifti files.
   
 
   # generates an sql insert statement to insert this visit with a given participant id
-  def sql_insert_visit(scan_procedure_id=0)
+  def sql_insert_visit
     "INSERT INTO visits 
-    (date, scan_procedure_id, scan_number, initials, rmr, radiology_outcome, notes, transfer_mri, transfer_pet,
+    (date, scan_number, initials, rmr, radiology_outcome, notes, transfer_mri, transfer_pet,
     conference, compile_folder, dicom_dvd, user_id, path, scanner_source, created_at, updated_at) 
     VALUES 
-    ('#{@timestamp.to_s}', '#{scan_procedure_id.to_s}', '', '', '#{@rmr_number}', 'no', '', 'no', 'no', 
-    'no', 'no', 'no', NULL, '#{@visit_directory}', '#{@scanner_source}', '#{DateTime.now}', '#{DateTime.now}')"
+    ('#{@timestamp.to_s}', '', '', '#{@rmr_number}', 'no', '', 'yes', 'no', 
+    'no', 'no', '', NULL, '#{@visit_directory}', '#{@scanner_source}', '#{DateTime.now}', '#{DateTime.now}')"
   end
 
   # Build a new RawImageDataset from a path to the rawfile and parent directory.
@@ -386,6 +398,7 @@ Returns an array of the created nifti files.
   
   # retrieves a scanner source from the collection of datasets, raises Exception of none is found
   def get_scanner_source
+    raise IOError, "No datasets available, can't look for a scanner source" if @datasets.empty?
     @datasets.each do |ds|
       return ds.scanner_source unless ds.scanner_source.nil?
     end
@@ -393,15 +406,15 @@ Returns an array of the created nifti files.
   end
   
   # retrieves exam number / scan id from first #RawImageDataset
-  def get_study_id
+  def get_exam_number
     @datasets.each do |ds|
-      return ds.study_id unless ds.study_id.nil?
+      return ds.exam_number unless ds.exam_number.nil?
     end
     # raise(IOError, "No valid study id / exam number found.")
   end
   
   # retrieves exam number / scan id from first #RawImageDataset
-  def get_dicom_study_uid
+  def get_study_uid
     @datasets.each do |ds|
       return ds.dicom_study_uid unless ds.dicom_study_uid.nil?
     end

data/spec/unit/raw_image_dataset_spec.rb

@@ -22,7 +22,7 @@ describe RawImageDataset, "for a single valid DICOM file" do
     ds.scanned_file.should == @valid_dicom_basename
     ds.scanner_source.should == "Institution"
     ds.series_description.should == "Ax FSPGR BRAVO T1"
-    ds.study_id.should == "1405"
+    ds.exam_number.should == "1405"
     ds.timestamp.should == DateTime.parse("Wed, 10 Nov 2010 00:00:00 +0000")
     ds.study_description.should == "RMRMABRAVOTEST"
     ds.dicom?.should be true

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  hash: 5
+  hash: 3
   prerelease: 
   segments: 
   - 0
   - 2
-  - 9
-  version: 0.2.9
+  - 10
+  version: 0.2.10
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -16,7 +16,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-08-18 00:00:00 -05:00
+date: 2011-08-26 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency