metamri 0.2.16 → 0.2.17

checksums.yaml

@@ -0,0 +1,15 @@
+---
+!binary "U0hBMQ==":
+  metadata.gz: !binary |-
+    ZGQ1ZTRjNjZkY2E3NmVkNDgyYmNhM2Y3MGYyZDcwNGQzOTc4Y2UxNA==
+  data.tar.gz: !binary |-
+    NWUxZDA4ZjQ1N2ExYTk0NjI3OGI1ZWMyZDk5ZTEyNGQxODg0MTM3MQ==
+SHA512:
+  metadata.gz: !binary |-
+    NjEyYmJkMjdjMDBlZjM1M2Y0OGM3NGEwNjQ1MTczMWViYzJlNTI1MzcwZTEw
+    YTBjYTljMjE4ZmNlMWQ4YTAwNjFhMTc5ZDZjOThhN2JhMDZmODI5ZjhjOTYz
+    NWVhZGY2NmM2MDRhYzE4NjY4MzMwMWQ4MDczYjFhZDNkNjNjZWE=
+  data.tar.gz: !binary |-
+    YTAwMWRiOTgzNDA2OTY5YTBjMDhlZjIxYWQzZDgwZmY3YTgxNGI0NzU2ZTEy
+    MzRlY2RmZTRiYjNiZWU2OWYyYTFhNzM1YjEzZjJmNDMxZWE4YjQ4M2JjMWVi
+    ZWQ5OTliNTY3OGY1NTQ0NzMxMDE4NmFmZmFjNTcyMGZlYzZkNTg=

data/Gemfile

@@ -1,5 +1,4 @@
 source "http://rubygems.org"
 
-
 # Specify your gem's dependencies in metamri.gemspec
 gemspec

data/bin/convert_visit.rb

@@ -42,7 +42,7 @@ 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/,/900$/,/901$/,/999$/]}  # seems to like number , not like string
+    default_options = {:ignore_patterns => [/vipr/,/$Processed-Images$/,/900$/,/901$/,/999$/]}  # seems to like number , not like string
     #options = default_options.merge(options)
     v.scan(default_options)
     v.to_nifti!(output_directory)

data/lib/metamri/raw_image_file.rb

@@ -19,8 +19,9 @@ class RawImageFile
   MIN_HDR_LENGTH = 400
   DICOM_HDR = "dicom_hdr"
   RDGEHDR = "rdgehdr"
+  PRINTRAW = "printraw"
   RUBYDICOM_HDR = "rubydicom"
-  VALID_HEADERS = [DICOM_HDR, RDGEHDR, RUBYDICOM_HDR]
+  VALID_HEADERS = [DICOM_HDR, PRINTRAW, RDGEHDR, RUBYDICOM_HDR]
   MONTHS = {
     :jan => "01", :feb => "02", :mar => "03", :apr => "04", :may => "05", 
     :jun => "06", :jul => "07", :aug => "08", :sep => "09", :oct => "10", 
@@ -269,15 +270,25 @@ private
 
     case File.basename(absfilepath)
     when /^P.{5}\.7$|^I\..{3}/
-      # Try reading Pfiles or Genesis I-Files with GE's rdgehdr
-      @current_hdr_reader = RDGEHDR
-      header = `#{RDGEHDR} '#{absfilepath}' 2> /dev/null`
+            # 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, RDGEHDR ]
+        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
+      ###header = `#{RDGEHDR} '#{absfilepath}' 2> /dev/null`
+      #header = `#{RDGEHDR} #{absfilepath}`
+      ###if ( header.chomp != "" and
+      ###     header.length > MIN_HDR_LENGTH )
+      ###  @current_hdr_reader = nil
+      ###  return [ header, RDGEHDR ]
+      ### end
     else
       # Try reading with RubyDICOM
       @current_hdr_reader = RUBYDICOM_HDR
@@ -323,6 +334,7 @@ private
     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
   end
@@ -573,6 +585,76 @@ private
     
   end
   
+  def printraw_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   
+
+
+    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
+    # @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?
+
+  end
 
   # Extracts a collection of metadata from @hdr_data retrieved using the rdgehdr
   # utility. 
@@ -631,6 +713,7 @@ 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?

data/lib/metamri/version.rb

@@ -1,3 +1,3 @@
 module Metamri
-  VERSION = "0.2.16"
+  VERSION = "0.2.17"
 end

data/metamri.gemspec

@@ -19,7 +19,7 @@ Gem::Specification.new do |s|
 
   s.add_runtime_dependency('dicom', "~> 0.8.0")
   s.add_runtime_dependency('activeresource', "~> 3.0")
-  ##### s.add_runtime_dependency('rmagick', "~> 2.13.1") 
+  # s.add_runtime_dependency('rmagick') 
   s.add_runtime_dependency('hirb', "~> 0.4")
   s.add_runtime_dependency('sqlite3', "~>1.3.4")
   s.add_development_dependency('rspec', "~> 2.5")

metadata

@@ -1,127 +1,111 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: metamri
-version: !ruby/object:Gem::Version 
-  hash: 55
-  prerelease: 
-  segments: 
-  - 0
-  - 2
-  - 16
-  version: 0.2.16
+version: !ruby/object:Gem::Version
+  version: 0.2.17
 platform: ruby
-authors: 
+authors:
 - Kristopher J. Kosmatka
 - Erik Kastman
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2013-03-25 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2013-10-22 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: dicom
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 63
-        segments: 
-        - 0
-        - 8
-        - 0
+      - !ruby/object:Gem::Version
         version: 0.8.0
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: activeresource
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.8.0
+- !ruby/object:Gem::Dependency
+  name: activeresource
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 7
-        segments: 
-        - 3
-        - 0
-        version: "3.0"
+      - !ruby/object:Gem::Version
+        version: '3.0'
   type: :runtime
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: hirb
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: hirb
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        - 4
-        version: "0.4"
+      - !ruby/object:Gem::Version
+        version: '0.4'
   type: :runtime
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: sqlite3
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 19
-        segments: 
-        - 1
-        - 3
-        - 4
+      - !ruby/object:Gem::Version
+        version: '0.4'
+- !ruby/object:Gem::Dependency
+  name: sqlite3
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
         version: 1.3.4
   type: :runtime
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: rspec
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.4
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 9
-        segments: 
-        - 2
-        - 5
-        version: "2.5"
+      - !ruby/object:Gem::Version
+        version: '2.5'
   type: :development
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  name: escoffier
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.5'
+- !ruby/object:Gem::Dependency
+  name: escoffier
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  version_requirements: *id006
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Extraction of MRI metadata.
 email: ekk@medicine.wisc.edu
-executables: 
+executables:
 - convert_visit.rb
 - import_respiratory_files.rb
 - import_study.rb
 - import_visit.rb
 - list_visit
 extensions: []
-
 extra_rdoc_files: []
-
-files: 
+files:
 - .gitignore
 - .rspec
 - Gemfile
@@ -167,38 +151,28 @@ files:
 - test/visit_test.rb
 homepage: http://github.com/brainmap/metamri
 licenses: []
-
+metadata: {}
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 2.1.4
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: MRI metadata
-test_files: 
+test_files:
 - spec/helper_spec.rb
 - spec/unit/dicom_additions_spec.rb
 - spec/unit/nifti_builder_spec.rb