metamri 0.2.17 → 0.2.18

checksums.yaml

@@ -1,15 +1,15 @@
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data/lib/metamri/core_additions.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 require 'tmpdir'
 
 class String

data/lib/metamri/dicom_additions.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 # Dicom Additions is a test extension of DICOM to allow for gathering common tags
 class DicomGroup
   # Array of DObjects to aggregate

data/lib/metamri/image_dataset_quality_check_resource.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 # An ImageQualityCheckResource is a ruby object that represents a quality check
 # pulled down from the DataPanda database.  It contains notes on the quality of
 # specific images, with a note for each possible problem, and an overall note.

data/lib/metamri/mysql_tools.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 require 'mysql'
 
 class Mysql

data/lib/metamri/nifti_builder.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 # Builds Nifti files from Dicoms.
 module UnknownImageDataset
   # Always set AFNI GE DICOM Fix to "No" before conversion with to3d.

data/lib/metamri/raw_image_dataset.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 require 'rubygems'
 # require 'sqlite3'
 require 'fileutils'

data/lib/metamri/raw_image_dataset_resource.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 class RawImageDatasetResource < ActiveResource::Base
   self.site = VisitRawDataDirectory::DATAPANDA_SERVER
   self.element_name = "image_dataset"

data/lib/metamri/raw_image_dataset_thumbnail.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 require 'tmpdir'
 begin
   %W{dicom }.each do |lib|     #####RMagick

data/lib/metamri/raw_image_file.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 require 'pp'
 require 'rubygems';
 require 'yaml';
@@ -31,7 +32,7 @@ class RawImageFile
 
   # The file name that the instance represents.
   attr_reader :filename
-  # Which header reading utility reads this file, currently 'rdgehdr' or 'dicom_hdr'.
+  # Which header reading utility reads this file, currently 'rdgehdr'(old p-files&wimr) or 'dicom_hdr' or 'printraw'(new p-files->waisman).
   attr_reader :hdr_reader
   # File types are either 'dicom' or 'pfile'.
   attr_reader :file_type
@@ -271,14 +272,21 @@ private
     case File.basename(absfilepath)
     when /^P.{5}\.7$|^I\..{3}/
             # Try reading Pfiles or Genesis I-Files with GE's printraw
-      @current_hdr_reader = PRINTRAW
-      header = `#{PRINTRAW} '#{absfilepath}' 2> /dev/null`
-      #header = `#{RDGEHDR} #{absfilepath}`
-      if ( header.chomp != "" and
-           header.length > MIN_HDR_LENGTH )
-        @current_hdr_reader = nil
-        return [ header, PRINTRAW ]
-      end
+            # 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
+         header = `#{PRINTRAW} '#{absfilepath}' 2> /dev/null`
+         #header = `#{RDGEHDR} #{absfilepath}`
+      #puts "bbbbb 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
+
+
       # 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
       ###@current_hdr_reader = RDGEHDR
@@ -349,7 +357,7 @@ private
   #   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
+  #   0008,103E Series Description                   LO     12 3pl loc FGR
   #   0008,1070 Operators' Name                      PN      2 SP
   #   0008,1090 Manufacturer's Model Name            LO     16 DISCOVERY MR750
   #   0010,0010 Patient's Name                       PN     12 mosPilot
@@ -603,10 +611,25 @@ private
     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
+
+     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
     
@@ -634,7 +657,6 @@ private
     series_description_pat =~ @hdr_data
     @series_description = ($1).strip.chomp
     
-    
     recon_diam_pat =~ @hdr_data
     @reconstruction_diameter = ($1).to_i
     
@@ -643,17 +665,18 @@ private
     
     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?
-    
+    @series_uid = ($1).strip.chomp unless $1.nil?  
     image_uid_pat =~ @hdr_data
     @image_uid = ($1).strip.chomp unless $1.nil?
 
+puts "rrrrrr @image_uid ="+@image_uid .to_s
+    @hdr_data = nil
+
   end
 
   # Extracts a collection of metadata from @hdr_data retrieved using the rdgehdr

data/lib/metamri/series_description_parameters.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 =begin rdoc
 Provides a mapping between series descriptions that are extracted from raw image
 headers and some associated attributes.

data/lib/metamri/version.rb

@@ -1,3 +1,3 @@
 module Metamri
-  VERSION = "0.2.17"
+  VERSION = "0.2.18"
 end

data/lib/metamri/visit_raw_data_directory.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 require 'rubygems'
 require 'pathname'
 require 'tempfile'

data/lib/metamri/visit_raw_data_directory_resource.rb

@@ -1,3 +1,4 @@
+# encoding: utf-8
 $:.unshift File.dirname(__FILE__)
 require 'raw_image_dataset_resource'
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: metamri
 version: !ruby/object:Gem::Version
-  version: 0.2.17
+  version: 0.2.18
 platform: ruby
 authors:
 - Kristopher J. Kosmatka
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-22 00:00:00.000000000 Z
+date: 2013-11-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: dicom
@@ -168,7 +168,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.4
+rubygems_version: 2.1.10
 signing_key: 
 specification_version: 4
 summary: MRI metadata