metamri 0.1.9 → 0.1.10
Sign up to get free protection for your applications and to get access to all the features.
- data/VERSION +1 -1
- data/lib/metamri/core_additions.rb +17 -0
- data/lib/metamri.rb +3 -0
- data/lib/raw_image_dataset.rb +1 -16
- data/lib/raw_image_file.rb +2 -2
- data/lib/visit_raw_data_directory.rb +2 -1
- data/metamri.gemspec +3 -2
- data/test/nifti_builder_spec.rb +27 -14
- metadata +3 -2
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.1.
|
1
|
+
0.1.10
|
@@ -0,0 +1,17 @@
|
|
1
|
+
class String
|
2
|
+
|
3
|
+
=begin rdoc
|
4
|
+
Does same basic string replacements to ensure valid filenames.
|
5
|
+
=end
|
6
|
+
def escape_filename
|
7
|
+
mgsub([[/[\s\:\)\(\/\?]+/, "-"], [/\*/, "star"]])
|
8
|
+
end
|
9
|
+
|
10
|
+
def mgsub(key_value_pairs=[].freeze)
|
11
|
+
regexp_fragments = key_value_pairs.collect { |k,v| k }
|
12
|
+
gsub(Regexp.union(*regexp_fragments)) do |match|
|
13
|
+
key_value_pairs.detect { |k,v| k =~ match}[1]
|
14
|
+
end
|
15
|
+
end
|
16
|
+
|
17
|
+
end
|
data/lib/metamri.rb
CHANGED
data/lib/raw_image_dataset.rb
CHANGED
@@ -177,12 +177,7 @@ have more component files than shell commands can handle.
|
|
177
177
|
end
|
178
178
|
end
|
179
179
|
|
180
|
-
|
181
|
-
Does same basic string replacements to ensure valid filenames.
|
182
|
-
=end
|
183
|
-
def escape_filename(filename)
|
184
|
-
filename.mgsub([[/[\s\:\)\(\/]+/, "-"], [/\*/, "star"]])
|
185
|
-
end
|
180
|
+
|
186
181
|
|
187
182
|
private
|
188
183
|
|
@@ -191,15 +186,5 @@ private
|
|
191
186
|
@timestamp = (@raw_image_files.sort_by { |i| i.timestamp }).first.timestamp
|
192
187
|
end
|
193
188
|
|
194
|
-
|
195
189
|
end
|
196
190
|
#### END OF CLASS ####
|
197
|
-
|
198
|
-
class String
|
199
|
-
def mgsub(key_value_pairs=[].freeze)
|
200
|
-
regexp_fragments = key_value_pairs.collect { |k,v| k }
|
201
|
-
gsub(Regexp.union(*regexp_fragments)) do |match|
|
202
|
-
key_value_pairs.detect { |k,v| k =~ match}[1]
|
203
|
-
end
|
204
|
-
end
|
205
|
-
end
|
data/lib/raw_image_file.rb
CHANGED
@@ -79,7 +79,7 @@ temporary file.
|
|
79
79
|
@hdr_data, @hdr_reader = read_header(absfilepath)
|
80
80
|
#puts "@hdr_data: #{@hdr_data}; @hdr_reader: #{@hdr_reader}"
|
81
81
|
rescue Exception => e
|
82
|
-
raise(IOError, "Header not readable. #{e}")
|
82
|
+
raise(IOError, "Header not readable for file #{@filename}. #{e}")
|
83
83
|
end
|
84
84
|
|
85
85
|
# file type is based on file name but only if the header was read successfully
|
@@ -90,7 +90,7 @@ temporary file.
|
|
90
90
|
begin
|
91
91
|
import_hdr
|
92
92
|
rescue Exception => e
|
93
|
-
raise(IOError, "Header import failed. #{e}")
|
93
|
+
raise(IOError, "Header import failed for file #{@filename}. #{e}")
|
94
94
|
end
|
95
95
|
|
96
96
|
# deallocate the header data to save memory space.
|
@@ -157,7 +157,7 @@ Returns an array of the created nifti files.
|
|
157
157
|
|
158
158
|
@datasets.each do |dataset|
|
159
159
|
nifti_output_path = output_directory
|
160
|
-
nifti_filename = "#{scanid}_#{dataset.escape_filename
|
160
|
+
nifti_filename = "#{scanid}_#{dataset.series_description.escape_filename}_#{File.basename(dataset.directory).escape_filename}.nii"
|
161
161
|
|
162
162
|
Pathname.new(dataset.directory).all_dicoms do |dicom_files|
|
163
163
|
nifti_input_path = File.dirname(dicom_files.first)
|
@@ -470,6 +470,7 @@ class Pathname
|
|
470
470
|
|
471
471
|
def local_copy(tempdir = Dir.tmpdir)
|
472
472
|
tfbase = self.to_s =~ /\.bz2$/ ? self.basename.to_s.chomp(".bz2") : self.basename.to_s
|
473
|
+
tfbase.escape_filename
|
473
474
|
tmpfile = File.join(tempdir, tfbase)
|
474
475
|
if self.to_s =~ /\.bz2$/
|
475
476
|
`bunzip2 -k -c '#{self.to_s}' >> '#{tmpfile}'`
|
data/metamri.gemspec
CHANGED
@@ -5,11 +5,11 @@
|
|
5
5
|
|
6
6
|
Gem::Specification.new do |s|
|
7
7
|
s.name = %q{metamri}
|
8
|
-
s.version = "0.1.
|
8
|
+
s.version = "0.1.10"
|
9
9
|
|
10
10
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
11
11
|
s.authors = ["Kristopher J. Kosmatka"]
|
12
|
-
s.date = %q{2010-01-
|
12
|
+
s.date = %q{2010-01-25}
|
13
13
|
s.description = %q{Extraction of MRI metadata and insertion into compatible sqlite3 databases.}
|
14
14
|
s.email = %q{kk4@medicine.wisc.edu}
|
15
15
|
s.executables = ["convert_visit.rb", "import_study.rb", "import_visit.rb", "import_respiratory_files.rb"]
|
@@ -27,6 +27,7 @@ Gem::Specification.new do |s|
|
|
27
27
|
"bin/import_study.rb",
|
28
28
|
"bin/import_visit.rb",
|
29
29
|
"lib/metamri.rb",
|
30
|
+
"lib/metamri/core_additions.rb",
|
30
31
|
"lib/mysql_tools.rb",
|
31
32
|
"lib/nifti_builder.rb",
|
32
33
|
"lib/raw_image_dataset.rb",
|
data/test/nifti_builder_spec.rb
CHANGED
@@ -3,54 +3,67 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib')
|
|
3
3
|
require 'rubygems'
|
4
4
|
require 'spec'
|
5
5
|
require 'fileutils'
|
6
|
+
require 'tmpdir'
|
6
7
|
require 'visit_raw_data_directory'
|
7
8
|
require 'raw_image_dataset'
|
8
9
|
require 'raw_image_file'
|
9
10
|
|
10
|
-
VISIT_FIXTURE = File.join(Dir.tmpdir, 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009')
|
11
11
|
VISIT_FIXTURE_SRC = '/Data/vtrak1/raw/johnson.tbi-va.visit1/tbiva018b_9336_12022009'
|
12
|
+
VISIT_FIXTURE = File.join(Dir.tmpdir, 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009')
|
13
|
+
VISIT_FIXTURE_UNZIPPED = File.join(Dir.tmpdir, 'fixtures/visit_raw_data_directory/tbiva018b_9336_12022009_unzipped')
|
14
|
+
|
15
|
+
|
12
16
|
|
13
17
|
describe "Convert Unknown Dicoms to Nifti Files" do
|
14
18
|
before(:all) do
|
15
19
|
# Initialize a local scratch directory to hold fixtures for testing if it doesn't already exist.
|
16
|
-
unless File.directory?(VISIT_FIXTURE)
|
17
|
-
FileUtils.mkdir_p(File.dirname(VISIT_FIXTURE))
|
18
|
-
FileUtils.cp_r(VISIT_FIXTURE_SRC, VISIT_FIXTURE)
|
19
|
-
|
20
|
+
#unless File.directory?(VISIT_FIXTURE)
|
21
|
+
#FileUtils.mkdir_p(File.dirname(VISIT_FIXTURE))
|
22
|
+
#FileUtils.cp_r(VISIT_FIXTURE_SRC, VISIT_FIXTURE)
|
23
|
+
#FileUtils.cp_r(VISIT_FIXTURE, VISIT_FIXTURE_UNZIPPED)
|
24
|
+
`find #{VISIT_FIXTURE_UNZIPPED} -name '*.bz2' -exec bunzip2 {} \\;`
|
25
|
+
#end
|
20
26
|
end
|
21
27
|
|
22
28
|
before(:each) do
|
23
29
|
@visit = VisitRawDataDirectory.new(VISIT_FIXTURE, 'johnson.tbi-va.visit1')
|
24
30
|
@dataset = RawImageDataset.new(
|
25
31
|
File.join(VISIT_FIXTURE, '001'),
|
26
|
-
[RawImageFile.new(File.join(VISIT_FIXTURE, '001/I0001.dcm'))]
|
32
|
+
[RawImageFile.new(File.join(VISIT_FIXTURE, '001/I0001.dcm.bz2'))]
|
33
|
+
)
|
34
|
+
|
35
|
+
@visit_unzipped = VisitRawDataDirectory.new(VISIT_FIXTURE_UNZIPPED, 'johnson.tbi-va.visit1')
|
36
|
+
@dataset_unzipped = RawImageDataset.new(
|
37
|
+
File.join(VISIT_FIXTURE_UNZIPPED, '001'),
|
38
|
+
[RawImageFile.new(File.join(VISIT_FIXTURE_UNZIPPED, '001/I0001.dcm'))]
|
27
39
|
)
|
40
|
+
|
28
41
|
@test_niftis = Array.new
|
29
42
|
@output_directories = Array.new
|
30
43
|
end
|
31
44
|
|
32
45
|
it "should Convert an anatomical from dicom to nifti using original, unzipped files." do
|
33
|
-
@
|
34
|
-
nifti_conversion_command, nifti_output_file = @
|
35
|
-
nifti_conversion_command.should == "to3d -session /tmp/ -prefix filename.nii #{@
|
46
|
+
@dataset_unzipped.to_nifti('/tmp/', 'filename.nii', :input_directory => @dataset_unzipped.directory)[0].should == "to3d -session /tmp/ -prefix filename.nii #{@dataset_unzipped.directory}/'*.dcm'"
|
47
|
+
nifti_conversion_command, nifti_output_file = @dataset_unzipped.to_nifti!('/tmp/', 'filename.nii', :input_directory => @dataset_unzipped.directory)
|
48
|
+
nifti_conversion_command.should == "to3d -session /tmp/ -prefix filename.nii #{@dataset_unzipped.directory}/'*.dcm'"
|
36
49
|
@test_niftis << nifti_output_file
|
37
50
|
@output_directories << '/tmp'
|
38
51
|
end
|
39
52
|
|
40
53
|
it "should convert all anatomicals in a visit raw directory using original, unzipped files." do
|
41
|
-
@
|
54
|
+
@visit_unzipped.scan
|
42
55
|
|
43
|
-
@
|
56
|
+
@visit_unzipped.datasets.each do |ds|
|
44
57
|
begin
|
45
|
-
nifti_filename = "#{@
|
46
|
-
nifti_conversion_commmand, nifti_output_file = ds.to_nifti!(File.join(Dir.tmpdir, @
|
58
|
+
nifti_filename = "#{@visit_unzipped.scanid}_#{ds.series_description.escape_filename}_#{File.basename(ds.directory)}.nii"
|
59
|
+
nifti_conversion_commmand, nifti_output_file = ds.to_nifti!(File.join(Dir.tmpdir, @visit_unzipped.default_preprocess_directory), nifti_filename, :input_directory => ds.directory, :append_modality_directory => true )
|
47
60
|
@test_niftis << nifti_output_file
|
48
61
|
rescue IOError => e
|
49
62
|
puts "-- Error: #{e.message}"
|
50
63
|
end
|
51
64
|
end
|
52
65
|
|
53
|
-
@output_directories = File.join(@
|
66
|
+
@output_directories = File.join(@visit_unzipped.default_preprocess_directory, 'unknown')
|
54
67
|
end
|
55
68
|
|
56
69
|
it "should convert all anatomicals in a visit raw directory using local copy." do
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: metamri
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.1.
|
4
|
+
version: 0.1.10
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Kristopher J. Kosmatka
|
@@ -9,7 +9,7 @@ autorequire:
|
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
11
|
|
12
|
-
date: 2010-01-
|
12
|
+
date: 2010-01-25 00:00:00 -06:00
|
13
13
|
default_executable:
|
14
14
|
dependencies: []
|
15
15
|
|
@@ -35,6 +35,7 @@ files:
|
|
35
35
|
- bin/import_study.rb
|
36
36
|
- bin/import_visit.rb
|
37
37
|
- lib/metamri.rb
|
38
|
+
- lib/metamri/core_additions.rb
|
38
39
|
- lib/mysql_tools.rb
|
39
40
|
- lib/nifti_builder.rb
|
40
41
|
- lib/raw_image_dataset.rb
|