brainmap-metamri 0.1.1 → 0.1.2

data/bin/import_study.rb

@@ -27,7 +27,7 @@
 #   Copyright (c) 2009 WADRC Imaging Core.
 #
 
-$:.unshift File.join(File.dirname(__FILE__),'..')
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
 require 'visit_raw_data_directory'
 require 'pathname'
@@ -65,7 +65,7 @@ STUDIES = {
                      :filter => /^esp3/,
                      :codename => 'carlsson.esprit.visit2.9month' 
   },
-  :gallagher_pd => { :dir => '/Data/vtrak1/raw/gallagher_pd',
+  :gallagher_pd => { :dir => '/Data/vtrak1/raw/gallagher.pd',
                      :logfile => 'gallagher.scan.log',
                      :filter => /^pd..._/,
                      :codename => 'gallagher.pd.visit1' 
@@ -95,7 +95,7 @@ STUDIES = {
                      :filter => /^tbi..._2/,
                      :codename => 'johnson.tbi1000.visit2' 
   },
-  :tbi1000_3 =>    { :dir => '/Data/vtrak1/raw/tbi_aware',
+  :tbi1000_3 =>    { :dir => '/Data/vtrak1/raw/johnson.tbi.aware.visit3',
                      :logfile => 'tbiaware.visit3.scan.log',
                      :filter => /^tbi..._3$/,
                      :codename => 'johnson.tbiaware.visit3' 
@@ -141,8 +141,8 @@ def import_study(study, dbfile)
     rescue Exception => e
       puts "There was a problem scanning a dataset in #{visitdir}... skipping."
       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 "There was a problem scanning a dataset in #{visitdir}... skipping."
+      log.error "Exception message: #{e.message}"
     ensure
       v = nil
     end

data/bin/import_visit.rb

@@ -29,12 +29,12 @@
 #   Copyright (c) 2009 WADRC Imaging Core.
 #
 
-$:.unshift File.join(File.dirname(__FILE__),'..')
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
 
 require 'visit_raw_data_directory'
 require 'pathname'
 require 'rdoc/usage'
-
+require 'logger'
 
 # == Function
 #   Imports imaging data collected during a single visit into the WADRC Data Tools web application database.
@@ -46,17 +46,17 @@ require 'rdoc/usage'
 #   import_visit('/Data/vtrak1/raw/alz_2000/alz001','johnson.alz.visit1','/path/to/the/rails/db/production.sqlite3')
 #
 def import_visit(raw_directory, scan_procedure_codename, database)
+  log = Logger.new(File.basename(raw_directory))  
   v = VisitRawDataDirectory.new(raw_directory, scan_procedure_codename)
   puts "+++ Importing #{v.visit_directory} as part of #{v.scan_procedure_name} +++"
   begin
     v.scan
-    puts v
     v.db_insert!(database)
   rescue Exception => e
-    puts "There was a problem scanning a dataset in #{visitdir}... skipping."
+    puts "There was a problem scanning a dataset in #{v.visit_directory}... skipping."
     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 "There was a problem scanning a dataset in #{v.visit_directory}... skipping."
+    log.error "Exception message: #{e.message}"
   ensure
     v = nil
   end

data/lib/raw_image_file.rb

@@ -69,15 +69,18 @@ unzip a file to a temporary location, be sure to keep the same filename for the
 temporary file.
 =end
   def initialize(pathtofile)
-    
     # raise an error if the file doesn't exist
     absfilepath = File.expand_path(pathtofile)
     raise(IOError, "File not found.") if not File.exists?(absfilepath)
     @filename = File.basename(absfilepath)
     
     # try to read the header, raise an ioerror if unsuccessful
-    @hdr_data, @hdr_reader = read_header(absfilepath)
-    raise(IOError, "Header not readable.") if @hdr_reader.nil?
+    begin
+      @hdr_data, @hdr_reader = read_header(absfilepath)
+      #puts "@hdr_data: #{@hdr_data}; @hdr_reader: #{@hdr_reader}"
+    rescue Exception => e
+      raise(IOError, "Header not readable. #{e}")
+    end
     
     # file type is based on file name but only if the header was read successfully
     @file_type = determine_file_type
@@ -86,8 +89,8 @@ temporary file.
     # are not found
     begin
       import_hdr
-    rescue
-      raise(IOError, "Header import failed.")
+    rescue Exception => e
+      raise(IOError, "Header import failed. #{e}")
     end
     
     # deallocate the header data to save memory space.
@@ -242,15 +245,19 @@ private
 Reads the file header using one of the available header reading utilities. 
 Returns both the header data as a one big string, and the name of the utility 
 used to read it.
+
+Note: The rdgehdr is a binary file; the correct version for your architecture must be installed in the path.
 =end
   def read_header(absfilepath)
     header = `#{DICOM_HDR} #{absfilepath} 2> /dev/null`
+    #header = `#{DICOM_HDR} #{absfilepath}`
     if ( header.index("ERROR") == nil and 
          header.chomp != "" and 
          header.length > MIN_HDR_LENGTH )
       return [ header, DICOM_HDR ]
     end
     header = `#{RDGEHDR} #{absfilepath} 2> /dev/null`
+    #header = `#{RDGEHDR} #{absfilepath}`
     if ( header.chomp != "" and
          header.length > MIN_HDR_LENGTH )
       return [ header, RDGEHDR ]
@@ -277,7 +284,7 @@ Parses the header data and extracts a collection of instance variables.  If
 @hdr_data and @hdr_reader are not already availables, this function does nothing.
 =end
   def import_hdr
-    return if @hdr_data == nil
+    raise(IndexError, "No Header Data Available.") if @hdr_data == nil
     dicom_hdr_import if (@hdr_reader == "dicom_hdr")
     rdgehdr_import if (@hdr_reader == "rdgehdr")
   end

data/lib/visit_raw_data_directory.rb

@@ -68,13 +68,22 @@ class VisitRawDataDirectory
     flash "Scanning visit raw data directory #{@visit_directory}"
     d = Pathname.new(@visit_directory)
     d.each_subdirectory do |dd|
-      dd.each_pfile { |pf| @datasets << import_dataset(pf, dd) }
-      dd.first_dicom { |fd| @datasets << import_dataset(fd, dd) }
+      begin 
+        dd.each_pfile { |pf| @datasets << import_dataset(pf, dd) }
+        dd.first_dicom { |fd| @datasets << import_dataset(fd, dd) }
+      rescue Exception => e
+        raise(IndexError, "There was an error scaning dataset #{dd}: #{e}")
+      end
+    end
+    
+    unless @datasets.size == 0
+      @timestamp = get_visit_timestamp
+      @rmr_number = get_rmr_number
+      @scanner_source = get_scanner_source
+      flash "Completed scanning #{@visit_directory}"
+    else
+      raise(IndexError, "No datasets could be scanned for directory #{@visit_directory}")
     end
-    @timestamp = get_visit_timestamp
-    @rmr_number = get_rmr_number
-    @scanner_source = get_scanner_source
-    flash "Completed scanning #{@visit_directory}"
   end
   
   # use this to initialize Visit objects in the rails app
@@ -219,12 +228,19 @@ class VisitRawDataDirectory
     enter_info_in_db, 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', 'no', 'no', 'no', 'no', 'no', 'no', 'no', 'no', NULL, '#{@visit_directory}', #{@scanner_source}, '#{DateTime.now}', '#{DateTime.now}')"
+    'no', 'no', 'no', 'no', 'no', 'no', 'no', 'no', 'no', 'no', 'no', NULL, '#{@visit_directory}', '#{@scanner_source}', '#{DateTime.now}', '#{DateTime.now}')"
   end
   
   def import_dataset(rawfile, original_parent_directory)
     puts "Importing scan session: #{original_parent_directory.to_s} using raw data file: #{rawfile.basename}"
-    return RawImageDataset.new(original_parent_directory.to_s, [RawImageFile.new(rawfile.to_s)])
+    
+    begin
+      rawimagefile = RawImageFile.new(rawfile.to_s)
+    rescue Exception => e
+      raise(IOError, "Trouble reading raw image file #{rawfile}. #{e}")
+    end
+    
+    return RawImageDataset.new(original_parent_directory.to_s, [rawimagefile])
   end
   
   def get_visit_timestamp
@@ -340,8 +356,8 @@ class Pathname
         lc = branch.local_copy
         begin
           yield lc
-        rescue
-          # Do nothing
+        rescue Exception => e
+          puts "#{e}"
         ensure
           lc.delete
         end
@@ -356,8 +372,8 @@ class Pathname
         lc = branch.local_copy
         begin
           yield lc
-        rescue
-          # Do nothing
+        rescue Exception => e
+          puts "#{e}"
         ensure
           lc.delete
         end

data/metamri.gemspec

@@ -2,7 +2,7 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 1.2") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: brainmap-metamri
 version: !ruby/object:Gem::Version 
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -49,7 +49,6 @@ files:
 - metamri.gemspec
 has_rdoc: true
 homepage: http://github.com/brainmap/metamri
-licenses: 
 post_install_message: 
 rdoc_options: 
 - --line-numbers
@@ -75,7 +74,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: metamri
-rubygems_version: 1.3.5
+rubygems_version: 1.2.0
 signing_key: 
 specification_version: 2
 summary: Extraction of MRI metadata and insertion into compatible sqlite3 databases.