metamri 0.2.4 → 0.2.5

data/VERSION

@@ -1 +1 @@
-0.2.4
+0.2.5

data/lib/metamri/nifti_builder.rb

@@ -1,10 +1,4 @@
-#!/usr/bin/env ruby
-
-=begin rdoc
-Builds Nifti files from Dicoms.
-=end
-
-
+# Builds Nifti files from Dicoms.
 module UnknownImageDataset
   # Always set AFNI GE DICOM Fix to "No" before conversion with to3d.
   ENV['AFNI_SLICE_SPACING_IS_GAP'] = "NO"
@@ -26,7 +20,7 @@ module UnknownImageDataset
     
     nifti_output_file = File.join(nifti_output_directory, nifti_filename)
     
-    File.makedirs(nifti_output_directory) unless File.directory?(nifti_output_directory)
+    FileUtils.makedirs(nifti_output_directory) unless File.directory?(nifti_output_directory)
     raise(IOError, "Cannot write to #{nifti_output_directory}") unless File.writable?(nifti_output_directory)
         
     nifti_conversion_command = "to3d -session #{nifti_output_directory} -prefix #{[nifti_filename, functional_args, input_files].compact.join(' ')}"

data/lib/metamri/raw_image_dataset.rb

@@ -338,6 +338,18 @@ Returns a path to the created dataset as a string if successful.
     @raw_image_files.first.dicom?
   end
   
+  # Helper predicate method to check whether the dataset is a DICOM dataset or not.
+  # This just sends dicom? to the first raw file in the dataset.
+  def pfile?
+    @raw_image_files.first.pfile?
+  end
+  
+  # Helper predicate method to check whether the dataset is a DICOM dataset or not.
+  # This just sends dicom? to the first raw file in the dataset.
+  def geifile?
+    @raw_image_files.first.geifile?
+  end
+  
 private
 
   # Gets the earliest timestamp among the raw image files in this dataset.

data/lib/metamri/raw_image_file.rb

@@ -577,6 +577,8 @@ private
     rmr_number_pat =           /Patient ID for this exam: ([[:graph:]]+)/i
     bold_reps_pat =            /Number of excitations: ([0-9]+)/i
     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
 
     rmr_number_pat =~ @hdr_data
     @rmr_number = ($1).nil? ? "rmr not found" : ($1).strip.chomp
@@ -615,6 +617,12 @@ private
     
     rep_time_pat =~ @hdr_data
     @rep_time = ($1).to_f / 1000000
+    
+    study_uid_pat =~ @hdr_data
+    @dicom_study_uid = ($1).strip.chomp
+    
+    series_uid_pat =~ @hdr_data
+    @dicom_series_uid = ($1).strip.chomp
   end
  
 end

data/lib/metamri/visit_raw_data_directory.rb

@@ -111,7 +111,7 @@ class VisitRawDataDirectory
       @rmr_number = get_rmr_number
       @scanner_source = get_scanner_source
       @study_id = get_study_id
-      @dicom_study_uid = get_dicom_study_uid
+      @dicom_study_uid = get_dicom_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}")
@@ -472,6 +472,12 @@ Returns an array of the created nifti files.
     end
   end
   
+  def dicom_datasets
+    dicom_sets ||= []
+    datasets.each {|ds| dicom_sets << ds if ds.dicom?}
+    return dicom_sets
+  end
+    
   def initialize_log
     # If a log hasn't been created, catch that here and go to STDOUT.
     unless $LOG

data/lib/metamri.rb

@@ -15,6 +15,7 @@ require 'metamri/raw_image_dataset_resource'
 require 'metamri/visit_raw_data_directory_resource'
 require 'metamri/image_dataset_quality_check_resource'
 require 'metamri/dicom_additions'
+require 'fileutils'
 
 # require 'metamri/raw_image_dataset_thumbnail'
 # TODO Move raw_image_dataset_thumbnail out of metamri.  

data/metamri.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{metamri}
-  s.version = "0.2.4"
+  s.version = "0.2.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Kristopher J. Kosmatka"]
-  s.date = %q{2011-03-07}
+  s.date = %q{2011-03-14}
   s.description = %q{Extraction of MRI metadata and insertion into compatible sqlite3 databases.}
   s.email = %q{kk4@medicine.wisc.edu}
   s.executables = ["convert_visit.rb", "import_visit.rb", "import_respiratory_files.rb", "import_study.rb", "list_visit"]

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: metamri
 version: !ruby/object:Gem::Version 
-  hash: 31
+  hash: 29
   prerelease: 
   segments: 
   - 0
   - 2
-  - 4
-  version: 0.2.4
+  - 5
+  version: 0.2.5
 platform: ruby
 authors: 
 - Kristopher J. Kosmatka
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-07 00:00:00 -06:00
+date: 2011-03-14 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency