Class: RawImageDataset

Inherits:
Object
  • Object
show all
Defined in:
lib/raw_image_dataset.rb

Overview

A #Dataset defines a single 3D or 4D image, i.e. either a volume or a time series of volumes. This encapsulation will provide easy manipulation of groups of raw image files including basic reconstruction.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(directory, raw_image_files) ⇒ RawImageDataset

  • dir: The directory containing the files.

    • files: An array of #RawImageFile objects that compose the complete data set.

    Initialization raises errors in several cases:

    • directory doesn’t exist => IOError

    • any of the raw image files is not actually a RawImageFile => IndexError

    • series description, rmr number, or timestamp cannot be extracted from the first RawImageFile => IndexError

Raises:

  • (IOError) 


38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
 
# File 'lib/raw_image_dataset.rb', line 38

def initialize(directory, raw_image_files)
  @directory = File.expand_path(directory)
  raise(IOError, "#{@directory} not found.") if not File.directory?(@directory)
  raise(IOError, "No raw image files supplied.") if (raw_image_files.nil? or raw_image_files.empty?)
  raw_image_files.each do |im|
    raise(IndexError, im.to_s + " is not a RawImageFile") if im.class.to_s != "RawImageFile"
  end
  @raw_image_files = raw_image_files
  @series_description = @raw_image_files.first.series_description
  raise(IndexError, "No series description found") if @series_description.nil?
  @rmr_number = @raw_image_files.first.rmr_number
  raise(IndexError, "No rmr found") if @rmr_number.nil?
  @timestamp = get_earliest_timestamp
  raise(IndexError, "No timestamp found") if @timestamp.nil?
  @dataset_key = @rmr_number + "::" + @timestamp.to_s
  @scanned_file = @raw_image_files.first.filename
  raise(IndexError, "No scanned file found") if @scanned_file.nil?
end

Instance Attribute Details

#dataset_key ⇒ Object (readonly)

A key string unique to a dataset composed of the rmr number and the timestamp.



24
25
26
 
# File 'lib/raw_image_dataset.rb', line 24

def dataset_key
  @dataset_key
end

#directory ⇒ Object (readonly)

The directory that contains all the raw images and related files that make up this data set.



14
15
16
 
# File 'lib/raw_image_dataset.rb', line 14

def directory
  @directory
end

#raw_image_files ⇒ Object (readonly)

An array of #RawImageFile objects that compose the complete data set.



16
17
18
 
# File 'lib/raw_image_dataset.rb', line 16

def raw_image_files
  @raw_image_files
end

#rmr_number ⇒ Object (readonly)

From the first raw image file in the dataset



20
21
22
 
# File 'lib/raw_image_dataset.rb', line 20

def rmr_number
  @rmr_number
end

#scanned_file ⇒ Object (readonly)

the file scanned



26
27
28
 
# File 'lib/raw_image_dataset.rb', line 26

def scanned_file
  @scanned_file
end

#series_description ⇒ Object (readonly)

From the first raw image file in the dataset



18
19
20
 
# File 'lib/raw_image_dataset.rb', line 18

def series_description
  @series_description
end

#timestamp ⇒ Object (readonly)

From the first raw image file in the dataset



22
23
24
 
# File 'lib/raw_image_dataset.rb', line 22

def timestamp
  @timestamp
end

Instance Method Details

#db_fetch ⇒ Object 



87
88
89
90
91
92
 
# File 'lib/raw_image_dataset.rb', line 87

def db_fetch
  "SELECT * FROM image_datasets 
   WHERE rmr = '#{@rmr_number}' 
   AND path = '#{@directory}' 
   AND timestamp LIKE '#{@timestamp.to_s.split(/\+|Z/).first}%'"
end

#db_insert(visit_id) ⇒ Object

Generates an SQL insert statement for this dataset that can be used to populate the Johnson Lab rails TransferScans application database backend. The motivation for this is that many dataset inserts can be collected into one db transaction at the visit level, or even higher when doing a whole file system scan.



63
64
65
66
67
68
69
70
 
# File 'lib/raw_image_dataset.rb', line 63

def db_insert(visit_id)
  "INSERT INTO image_datasets
  (rmr, series_description, path, timestamp, created_at, updated_at, visit_id, 
  glob, rep_time, bold_reps, slices_per_volume, scanned_file)
  VALUES ('#{@rmr_number}', '#{@series_description}', '#{@directory}', '#{@timestamp.to_s}', '#{DateTime.now}', 
  '#{DateTime.now}', '#{visit_id}', '#{self.glob}', '#{@raw_image_files.first.rep_time}', 
  '#{@raw_image_files.first.bold_reps}', '#{@raw_image_files.first.num_slices}', '#{@scanned_file}')"
end

#db_update(dataset_id) ⇒ Object 



72
73
74
75
76
77
78
79
80
81
82
83
84
85
 
# File 'lib/raw_image_dataset.rb', line 72

def db_update(dataset_id)
  "UPDATE image_datasets SET
   rmr = '#{@rmr_number}',
   series_description = '#{@series_description}',
   path = '#{@directory}',
   timestamp = '#{@timestamp.to_s}',
   updated_at = '#{DateTime.now.to_s}',
   glob = '#{self.glob}',
   rep_time = '#{@raw_image_files.first.rep_time}',
   bold_reps = '#{@raw_image_files.first.bold_reps}',
   slices_per_volume = '#{@raw_image_files.first.num_slices}',
   scanned_file = '#{@scanned_file}'
   WHERE id = '#{dataset_id}'"
end

#glob ⇒ Object

Returns a globbing wildcard that is used by to3D to gather files for reconstruction. If no compatible glob is found for the data set, nil is returned. This is always the case for pfiles. For example if the first file in a data set is I.001, then: dataset.glob => "I.*" including the quotes, which are necessary becuase some data sets (functional dicoms) have more component files than shell commands can handle.



105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
 
# File 'lib/raw_image_dataset.rb', line 105

def glob
  case @raw_image_files.first.filename
  when /^E.*dcm$/
    return 'E*.dcm'
  when /\.dcm$/
    return '*.dcm'
  when /^I\./
    return 'I.*'
  when /^I/
    return 'I*.dcm'
  when /\.0/
    return '*.0*'
  else
    return nil
  end
end