metamri 0.2.22 → 0.2.24

checksums.yaml

@@ -1,15 +1,15 @@
 ---
 !binary "U0hBMQ==":
   metadata.gz: !binary |-
-    ZjFhMjkxMTIxODJjYzk4MjQ3NTZhZDQ4MjNkMTRhNzgxN2RiMWJmYQ==
+    ZWY3NWY2MWZkMDY2ZGEwOTc1YTU0OGZmM2Q0YzBjMWQ4ZTExZTkyNQ==
   data.tar.gz: !binary |-
-    ZjIzODliNzRlMTY4MThiNGYwODc0YzY5ZWFiYjc2NjIyNDk4MmQ5Mw==
+    NDgyNWE5ZjJkMDkxYzRkM2VmNWJiMjdiZWZiZWI5MWEzZWM1NWY3ZQ==
 SHA512:
   metadata.gz: !binary |-
-    OWY2YzQ2OGI1NWE2NzJjNTdkOTk4YTY1Yzc5ZWFiNDkyZTk1MmYyZjc4MTI3
-    YThhOGFiYzhjZDZmMDM5YWUzMjVkNjY3OGRhNzlkMDVhZjE2MDg0MzdjMTkx
-    NjBkMGUzNGE5YjY1YjZmMTcyMWNiY2FmZmI5MTBlM2I4YTA1Yjk=
+    NDNkNTA3ZDY1ZjFhZWVlMzk1NWY4ZmM5OTZjMTRlNTJkMzUwYjc5MzEzNzZj
+    YzA2YmZlMDA4N2UyMjU2N2UxZTJjZDVhMWZkMzdmMzRjYjRlM2M2NzNkZGM1
+    YWFhM2U5MjQ5YzMwOWNiM2JhMTZjYjFkZjRiZDBlNDQzZWJiYzU=
   data.tar.gz: !binary |-
-    NWE0NjkyZGExMzkwNzE5ZjY4NTI2N2JjZmZlMjFlNzE5MjBkMjE0Y2RjZjI0
-    OWIwZjhlZDJhZDNjZmYyY2Q1YWM3NjM3NWNmMTdjYWNkYjBlYTZlMjhhZjNk
-    Y2IyOTU3NzUwOTgyMzU0Zjk3OWJiMTZjNGMyMzZiMmNjYzc1ZmU=
+    M2Q1NjY2OGFmZGQzZTFiODI3MWU5MmQwNTM4OWZhOWE3OGQ2MzI2OWE0Yjhh
+    NWRmZWMwZWMyMWJiZDRiZDA0ZjQyOGE1NTRhODgxODIzN2UzMmI0YWM5YzRj
+    MDhkMDYwZmQzNDhkZDQzMjRhOTUxOGVkYWQzNjRlOWQyNDA3ZDA=

data/VERSION

@@ -1 +1 @@
-0.2.8
+0.2.24

data/bin/convert_visit.rb

@@ -42,7 +42,9 @@ def convert_visit(raw_directory, scan_procedure_codename, output_directory = nil
   output_directory = output_directory ||= v.default_preprocess_directory
 
   begin
-    default_options = {:ignore_patterns => [/vipr/,/ge_physios/,/raw$/,/pfiles/,/Processed-Images/,/900$/,/901$/,/999$/,/\/01300\./,/\/01301\./,/\/01001\./,/\/01002\./,/\/01000\./,/\/00600\./]}  # does not like "raw" because in dir path
+   ##  default_options = {:ignore_patterns => [/vipr/,/ge_physios/,/raw$/,/pfiles/,/Processed-Images/,/900$/,/901$/,/999$/,/\/01300\./,/\/01301\./,/\/01001\./,/\/01002\./,/\/01000\./,/\/00600\./]}  # does not like "raw" because in dir path
+   ## new flair has numbers in name and should not be skipped - removing
+    default_options = {:ignore_patterns => [/vipr/,/ge_physios/,/raw$/,/pfiles/,/Processed-Images/]}  # does not like "raw" because in dir path
     #options = default_options.merge(options)
     v.scan(default_options)
     v.to_nifti!(output_directory)

data/lib/metamri/core_additions.rb

@@ -38,12 +38,24 @@ class Pathname
   end
   
   def each_pfile(min_file_size = MIN_PFILE_SIZE)
+    #puts "in each_pfile"
+    #puts "core_additions each_pfile ==> local_copy"
     entries.each do |leaf|
       next unless leaf.to_s =~ /^P.{5}\.7(\.bz2)/
       branch = self + leaf
       next if branch.symlink?
       if branch.size >= min_file_size
+        # check for P*.7.summary 
+        # if there, skip local_copy of P*.7.bz2
+       leaf_summary_s = (leaf.to_s).gsub(/\.bz2/,"")+".summary"
+       branch_summary_s = self.to_s+"/"+leaf_summary_s
+       if File.exist?(branch_summary_s)
+            branch_summary_pn = Pathname.new(branch_summary_s)
+            lc = branch_summary_pn.local_copy
+           # summary_lc.delete
+       else
         lc = branch.local_copy
+       end
         begin
           yield lc
         rescue StandardError => e
@@ -59,6 +71,55 @@ class Pathname
       end
     end
   end
+
+    def each_pfile_non_bz2(min_file_size = MIN_PFILE_SIZE)
+      # not using the P*.7.summary --- should be bzip2'ed
+    entries.each do |leaf|
+      next unless leaf.to_s =~ /^P.{5}(\.7)$/
+      branch = self + leaf
+      next if branch.symlink?
+      if branch.size >= min_file_size
+        lc = branch.local_copy
+        begin
+          yield lc
+        rescue StandardError => e
+          case $LOG.level
+          when Logger::DEBUG
+            raise e
+          else
+            puts "#{e}"
+          end
+        ensure
+          lc.delete
+        end
+      end
+    end
+  end
+
+
+    def each_pfile_summary(min_file_size = MIN_PFILE_SIZE)
+    entries.each do |leaf|
+      next unless leaf.to_s =~ /^P.{5}(\.7\.summary)/
+      branch = self + leaf
+      next if branch.symlink?
+      if branch.size >= min_file_size
+        lc = branch.local_copy
+        begin
+          yield lc
+        rescue StandardError => e
+          case $LOG.level
+          when Logger::DEBUG
+            raise e
+          else
+            puts "#{e}"
+          end
+        ensure
+          lc.delete
+        end
+      end
+    end
+  end
+
   
   def first_dicom
     entries.each do |leaf|

data/lib/metamri/nifti_builder.rb

@@ -12,7 +12,7 @@ module UnknownImageDataset
       input_files = "#{input_options[:input_directory]}/'#{glob}'"
     else input_files = "#{Dir.tmpdir}/'#{glob}'"
     end
-    
+
     if @raw_image_files.first.rep_time && @raw_image_files.first.bold_reps && @raw_image_files.first.num_slices && !input_options[:no_timing_options]
       slice_order = "altplus"
       functional_args = "-time:zt #{@raw_image_files.first.num_slices} #{@raw_image_files.first.bold_reps} #{@raw_image_files.first.rep_time} #{slice_order}"

data/lib/metamri/raw_image_dataset_resource.rb

@@ -11,8 +11,13 @@ class RawImageDatasetResource < ActiveResource::Base
     # This is a little wasteful since we really only care about the variables, 
     # not rescanning them.
     
+    # need to stop loading bz2 P files - 15 GB nmprage pfiles taking to long to bunzip2
+    # load just P*.7 and have routine job to pbzip2 things up later
     filename = Pathname.new(File.join(path, scanned_file))
+flash "wwwwwwwwwwww filename= #{filename}" if $LOG.level <= Logger::INFO
     filename_matches = /P\d{5}.7(.bz2)?/.match(filename)
+    filename_matches_non_bz2 = /P\d{5}(.7)?/.match(filename)
+    filename_matches_summary = /P\d{5}(.7.summary)?/.match(filename)
     
     if filename_matches    # Pfile
       if filename_matches[1] # '.bz2' if present, nil if otherwise.
@@ -24,7 +29,7 @@ class RawImageDatasetResource < ActiveResource::Base
       # 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'
-
+      summary_filename = filename.to_s.chomp + '.summary'
       if filename.file?
         image_file = filename
       elsif Pathname.new(zipped_filename).file?
@@ -32,10 +37,59 @@ class RawImageDatasetResource < ActiveResource::Base
       else 
         raise IOError, "Could not find #{filename} or it's bz2 zipped equivalent #{zipped_filename}."
       end
-      
+      puts "raw_image_dataset_resource  before check for P*.7.summary"
+      if  Pathname.new(summary_filename).file?
+         puts "raw_image_dataset_resource   THERE IS A SUMMARY P*.7.summary file"
+         # skiplocal copy 
+         # make @dataset
+      end
+
       image_file.local_copy do |local_pfile| 
         @dataset = RawImageDataset.new( path, [RawImageFile.new(local_pfile)])
       end
+    elsif filename_matches_non_bz2 # non-compressed Pfile
+      puts "raw_image_dataset_resource  matches non_bz2"
+      if filename_matches_non_bz2[1] 
+       # filename = Pathname.new(File.join(filename, '.bz2'))
+      else
+        filename = nil
+      end
+      if filename.file?
+        image_file = filename
+      else 
+        raise IOError, "Could not find #{filename}."
+      end
+      # if non-bz2  P*.7 file , the pfile header reader is pulling file from /mounts/data/raw/...
+      # but the there is still a local copy being made - ? for the pfile reader?
+      # not sure if better to copy a bz2 file over to tmp, bunzip2, then cp to local, again?, for the pfile header reader
+      @dataset = RawImageDataset.new( path, [RawImageFile.new(filename)] )
+
+    #  image_file.local_copy do |local_pfile| 
+    #    @dataset = RawImageDataset.new( path, [RawImageFile.new(local_pfile)])
+    #  end
+    elsif filename_matches_summary # 3 line summary of Pfile
+      # not do anything - check in P*.7 and P*.7.bz2 if P*.7.summary exists
+      puts "raw_image_dataset_resource P*.7.summary match"
+     # if filename_matches_summary[1] 
+       # filename = Pathname.new(File.join(filename, '.bz2'))
+    #    puts " summary file name="+filename
+     # else
+     #   filename = nil
+    #  end
+    #  if filename.file?
+    #    image_file = filename
+    #  else 
+    #    raise IOError, "Could not find #{filename}."
+    #  end
+      # if non-bz2  P*.7 file , the pfile header reader is pulling file from /mounts/data/raw/...
+      # but the there is still a local copy being made - ? for the pfile reader?
+      # not sure if better to copy a bz2 file over to tmp, bunzip2, then cp to local, again?, for the pfile header reader
+     # @dataset = RawImageDataset.new( path, [RawImageFile.new(filename)] )
+
+    #  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|

data/lib/metamri/raw_image_file.rb

@@ -18,11 +18,13 @@ require 'dicom'
 class RawImageFile
   #:stopdoc:
   MIN_HDR_LENGTH = 400
+  MIN_HDR_SUMMARY_LENGTH = 100
   DICOM_HDR = "dicom_hdr"
   RDGEHDR = "rdgehdr"
   PRINTRAW = "printraw"
+  PRINTRAW_SUMMARY = "cat"   #"printraw_summary"
   RUBYDICOM_HDR = "rubydicom"
-  VALID_HEADERS = [DICOM_HDR, PRINTRAW, RDGEHDR, RUBYDICOM_HDR]
+  VALID_HEADERS = [DICOM_HDR, PRINTRAW, RDGEHDR, RUBYDICOM_HDR,PRINTRAW_SUMMARY]
   MONTHS = {
     :jan => "01", :feb => "02", :mar => "03", :apr => "04", :may => "05", 
     :jun => "06", :jul => "07", :aug => "08", :sep => "09", :oct => "10", 
@@ -97,13 +99,21 @@ class RawImageFile
   def initialize(pathtofile)
     # raise an error if the file doesn't exist
     absfilepath = File.expand_path(pathtofile)
+     puts "initialize raw image file ="+absfilepath
     raise(IOError, "File not found at #{absfilepath}.") if not File.exists?(absfilepath)
     @filename = File.basename(absfilepath)
     @warnings = []
-    
+
+    #if P*.7.summary need different read_header_summary
+    if @filename =~ /^P*\.summary/
+       @hdr_reader = PRINTRAW_SUMMARY
+    end
     # try to read the header, raise an IOError if unsuccessful
     begin
       @hdr_data, @hdr_reader = read_header(absfilepath)
+      if @hdr_reader == nil
+           puts " hdr_reader is nil"
+      end
     rescue Exception => e
       raise(IOError, "Header not readable for file #{@filename} using #{@current_hdr_reader ? @current_hdr_reader : "unknown header reader."}. #{e}")
     end
@@ -268,24 +278,36 @@ private
   # 
   # Note: The rdgehdr is a binary file; the correct version for your architecture must be installed in the path.
   def read_header(absfilepath)
+    tmp_filename= File.basename(absfilepath)
 
     case File.basename(absfilepath)
     when /^P.{5}\.7$|^I\..{3}/
+         # check for 
             # Try reading Pfiles or Genesis I-Files with GE's printraw
             # printraw works on the new waisman p-files
             # rdgehdr works on wimr p-files, and old waisman p-files 
          @current_hdr_reader = PRINTRAW
-      puts "aaaaaaa absfilepath="+absfilepath
+        #puts "aaaaaaa absfilepath="+absfilepath
          header = `#{PRINTRAW} '#{absfilepath}' 2> /dev/null`
          #header = `#{RDGEHDR} #{absfilepath}`
-      #puts "bbbbb header="+header
+        # puts "bbbbb pfile header="+header
          header = header.encode("UTF-8", :invalid => :replace, :undef => :replace, :replace => "").force_encoding('UTF-8')
          if ( header.chomp != "" and
               header.length > MIN_HDR_LENGTH )
             @current_hdr_reader = nil
             return [ header, PRINTRAW ]
          end
-
+    when /^P.{5}\.7\.summary/
+         # check for 
+         @current_hdr_reader = PRINTRAW_SUMMARY
+         # puts "aaaaaaa summary absfilepath="+absfilepath
+         header = `#{PRINTRAW_SUMMARY} '#{absfilepath}' 2> /dev/null`
+         header = header.encode("UTF-8", :invalid => :replace, :undef => :replace, :replace => "").force_encoding('UTF-8')
+         if ( header.chomp != "" and
+              header.length > MIN_HDR_SUMMARY_LENGTH )
+            @current_hdr_reader = nil
+            return [ header, PRINTRAW_SUMMARY ]
+         end
 
       # Try reading Pfiles or Genesis I-Files with GE's rdgehdr -- rdgehdr newer version needs macos 10.8, adrcdev2 = 10.7.5 - 
       # works on old headers, not on new header format
@@ -331,6 +353,7 @@ private
   # All other images are called "dicom".
   def determine_file_type
     return "pfile"    if image? and (@filename =~ /^P.....\.7/) != nil
+    return "pfile"    if (@filename =~ /^P.....\.7\.summary/) != nil
     return "geifile"  if image? and (@filename =~ /^I\.\d*/) != nil
     return "dicom"    if image? and (@filename =~ /^P.....\.7/) == nil
     return nil
@@ -340,13 +363,21 @@ private
   # Parses the header data and extracts a collection of instance variables.  If 
   # @hdr_data and @hdr_reader are not already available, this function does nothing.
   def import_hdr
-    raise(IndexError, "No Header Data Available.") if @hdr_data == nil
-    case @hdr_reader
-      when "rubydicom" then rubydicom_hdr_import
-      when "dicom_hdr" then dicom_hdr_import
-      when "printraw" then printraw_import
-      when "rdgehdr" then rdgehdr_import
-    end
+
+    if @hdr_reader == nil
+      case @file_type
+          when "pfile" then printraw_summary_import
+     end
+    else
+      raise(IndexError, "No Header Data Available.") if @hdr_data == nil
+      case @hdr_reader
+        when "rubydicom" then rubydicom_hdr_import
+        when "dicom_hdr" then dicom_hdr_import
+        when "printraw" then printraw_import
+        when "rdgehdr" then rdgehdr_import
+        when "cat" then printraw_summary_import
+      end
+     end
   end
 
 
@@ -626,11 +657,8 @@ private
      hdr_data_bak = @hdr_data
      @hdr_data.encode!("ISO-8859-1", :invalid => :replace).encode("UTF-8")  #Attribute was supposed to be a Hash, but was a String
 
-     puts "aaaaaaaaaaa"
-
     rmr_number_pat =~ @hdr_data
     @rmr_number = ($1).nil? ? "rmr not found" : ($1).strip.chomp
-    puts "bbbbbbbb "
 
     source_pat =~ @hdr_data
     @source = ($1).nil? ? "source not found" : ($1).strip.chomp
@@ -676,7 +704,90 @@ private
     image_uid_pat =~ @hdr_data
     @image_uid = ($1).strip.chomp unless $1.nil?
 
-puts "rrrrrr @image_uid ="+@image_uid .to_s
+puts "printraw_import rrrrrr @image_uid ="+@image_uid .to_s
+    @hdr_data = nil
+
+  end
+
+  def printraw_summary_import
+    source_pat =               /hospital [Nn]ame: ([[:graph:]\t ]+)/i
+    num_slices_pat =           /rdb_hdr_nslices = ([0-9]+)/i
+    slice_thickness_pat =      /slthick = ([[:graph:]]+)/i
+    slice_spacing_pat =        /scanspacing = ([[:graph:]]+)/i
+    date_pat =                 /ex_datetime = (.*)\n/i
+    gender_pat =               /patsex = (1|2)/i
+    acquisition_matrix_x_pat = /imatrix_X = ([0-9]+)/i
+    acquisition_matrix_y_pat = /imatrix_Y = ([0-9]+)/i
+    series_description_pat =   /se_desc = ([[:graph:] \t]+)/i
+    recon_diam_pat =           /dfov = ([0-9]+)/i
+    rmr_number_pat =           /Patient ID for this exam: ([[:graph:]]+)/i
+    bold_reps_pat =            /nex = ([0-9]+)/i
+    rep_time_pat =             /reptime = ([0-9]+)/i      # not sure ifg this is right
+    study_uid_pat =            /Ssop_uid = ([[:graph:]]+)/i
+    series_uid_pat =           /series_uid = ([[:graph:]]+)/i
+    image_uid_pat =            /image_uid = (.*)/i #([[:graph:]]+)/i   
+
+     # @hdr_data = @hdr_data.encode("UTF-8", :invalid => :replace, :undef => :replace, :replace => "").force_encoding('UTF-8')
+    #@hdr_data = @hdr_data.encode!('UTF-8', 'UTF-8', :invalid => :replace)
+     #@hdr_data_2 = @hdr_data.encode("UTF-8") 
+     #@hdr_data.encode!("ISO-8859-1", :invalid => :replace).encode("UTF-8")
+     #@hdr_data.encode("UTF-8", :invalid => :replace, :replace => "") ==  invalid byte sequence in UTF-8
+     #@hdr_data.encode!("UTF-8", :invalid => :replace, :replace => "")  invalid byte sequence in UTF-8
+     #@hdr_data.encode("ISO-8859-1", :invalid => :replace)  invalid byte sequence in UTF-8
+     #@hdr_data = @hdr_data.encode('UTF-8','binary', :invalid => :replace,:undef => :replace, :replace =>'') #Attribute was supposed to be a Hash, but was a String
+     #@hdr_data = @hdr_data.encode('UTF-8','UTF-8', :invalid => :replace,:undef => :replace, :replace =>'') # invalid byte sequence in UTF-8
+     #@hdr_data.encode('UTF-8','UTF-8', :invalid => :replace,:undef => :replace, :replace =>'') # invalid byte sequence in UTF-8
+     hdr_data_bak = @hdr_data
+     @hdr_data.encode!("ISO-8859-1", :invalid => :replace).encode("UTF-8")  #Attribute was supposed to be a Hash, but was a String
+
+    rmr_number_pat =~ @hdr_data
+    @rmr_number = ($1).nil? ? "rmr not found" : ($1).strip.chomp
+
+    source_pat =~ @hdr_data
+    @source = ($1).nil? ? "source not found" : ($1).strip.chomp
+    
+    num_slices_pat =~ @hdr_data
+    @num_slices = ($1).to_i
+    
+    slice_thickness_pat =~ @hdr_data
+    @slice_thickness = ($1).to_f
+    
+    slice_spacing_pat =~ @hdr_data
+    @slice_spacing = ($1).to_f
+    
+    date_pat =~ @hdr_data
+    #@timestamp = Time.at($1.to_i).to_datetime   # thought summary date was 1969
+    @timestamp = DateTime.parse($1) # --- 2 rows- same start of line- first since epoch, 2nd date stamnp
+    
+    gender_pat =~ @hdr_data
+    @gender = $1 == 1 ? "M" : "F"
+    
+    acquisition_matrix_x_pat =~ @hdr_data
+    @acquisition_matrix_x = ($1).to_i
+    acquisition_matrix_y_pat =~ @hdr_data
+    @acquisition_matrix_y = ($1).to_i
+    
+    series_description_pat =~ @hdr_data
+    @series_description = ($1).strip.chomp
+    
+    recon_diam_pat =~ @hdr_data
+    @reconstruction_diameter = ($1).to_i
+    
+    bold_reps_pat =~ @hdr_data
+    @bold_reps = ($1).to_i
+    
+    rep_time_pat =~ @hdr_data
+    @rep_time = ($1).to_f / 1000000
+    
+    study_uid_pat =~ @hdr_data
+    @study_uid = ($1).strip.chomp unless $1.nil?
+    
+    series_uid_pat =~ @hdr_data
+    @series_uid = ($1).strip.chomp unless $1.nil?  
+    image_uid_pat =~ @hdr_data
+    @image_uid = ($1).strip.chomp unless $1.nil?
+
+puts "printraw_summary_import rrrrrr @image_uid ="+@image_uid .to_s
     @hdr_data = nil
 
   end

data/lib/metamri/version.rb

@@ -1,3 +1,3 @@
 module Metamri
-  VERSION = "0.2.22"
+  VERSION = "0.2.24"
 end

data/lib/metamri/visit_raw_data_directory.rb

@@ -61,7 +61,7 @@ class VisitRawDataDirectory
   attr_reader :dicom_study_uid
   
   PREPROCESS_REPOSITORY_DIRECTORY = '/Data/vtrak1/preprocessed/visits' unless defined?(PREPROCESS_REPOSITORY_DIRECTORY)
-  DATAPANDA_SERVER = 'http://nelson' unless defined?(DATAPANDA_SERVER)
+  DATAPANDA_SERVER = 'https://adrcdev2.dom.wisc.edu' unless defined?(DATAPANDA_SERVER)
   # DATAPANDA_SERVER = 'http://localhost:3000' unless defined?(DATAPANDA_SERVER)
 
   
@@ -99,10 +99,14 @@ class VisitRawDataDirectory
     
     d = Pathname.new(@visit_directory)
     d.each_subdirectory do |dd|
+      flash "ppppppppp #{dd}" if $LOG.level <= Logger::INFO
       begin
         matches = options[:ignore_patterns].collect {|pat| dd.to_s =~ pat ? dd : nil }.compact
-        next unless matches.empty?
-        dd.each_pfile  { |pf| @datasets << import_dataset(pf, dd); @datasets.last.print_scan_status if $LOG.level == Logger::INFO }
+        next unless matches.empty?  
+        # if dd is P*.7.bz2 or P*.7 , check for P*.7.summary 
+        dd.each_pfile_non_bz2  { |pf| @datasets << import_dataset(pf, dd);  @datasets.last.print_scan_status if $LOG.level == Logger::INFO }
+        dd.each_pfile  { |pf|  # check for p*.7.summary
+              @datasets << import_dataset(pf, dd); @datasets.last.print_scan_status if $LOG.level == Logger::INFO }
         dd.first_dicom { |fd| @datasets << import_dataset(fd, dd); @datasets.last.print_scan_status if $LOG.level == Logger::INFO }
       rescue StandardError => e
         raise(e, "There was an error scaning dataset #{dd}: #{e}")
@@ -362,14 +366,23 @@ Returns an array of the created nifti files.
   # Returns a RawImageDataset built from the directory and single rawfile.
   def import_dataset(rawfile, original_parent_directory)
     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)
+      # if summary, change rawfile to /mounts/data/raw/[s]/[enum_exam_date]/mri/dir/P*.summary for 
+      tmp_filename = File.basename rawfile.to_s
+      tmp_filname_summary_s = (tmp_filename).gsub(/\.bz2/,"").gsub(/\.summary/,"")+".summary"
+      tmp_branch_summary_s = original_parent_directory.to_s+"/"+tmp_filname_summary_s
+       if File.exist?(tmp_branch_summary_s)
+            #branch_summary_pn = Pathname.new(branch_summary_s)
+         rawimagefile = RawImageFile.new(tmp_branch_summary_s)
+        else
+            rawimagefile = RawImageFile.new(rawfile.to_s)
+        end
+
     # rescue StandardError => e
       # puts e.backtrace
       # raise(e, "+++ Trouble reading raw image file #{rawfile}. #{e}")
     end
-    
+
     return RawImageDataset.new(original_parent_directory.to_s, [rawimagefile])
   end
   

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: metamri
 version: !ruby/object:Gem::Version
-  version: 0.2.22
+  version: 0.2.24
 platform: ruby
 authors:
 - Kristopher J. Kosmatka
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-10 00:00:00.000000000 Z
+date: 2016-01-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: dicom