metamri 0.2.15 → 0.2.16
Sign up to get free protection for your applications and to get access to all the features.
- data/Gemfile +1 -0
- data/bin/convert_visit.rb +1 -1
- data/lib/metamri/raw_image_dataset_thumbnail.rb +36 -2
- data/lib/metamri/version.rb +1 -1
- data/lib/metamri/visit_raw_data_directory.rb +1 -1
- data/lib/metamri.rb +1 -1
- data/metamri.gemspec +1 -1
- metadata +12 -28
data/Gemfile
CHANGED
data/bin/convert_visit.rb
CHANGED
@@ -42,7 +42,7 @@ def convert_visit(raw_directory, scan_procedure_codename, output_directory = nil
|
|
42
42
|
output_directory = output_directory ||= v.default_preprocess_directory
|
43
43
|
|
44
44
|
begin
|
45
|
-
default_options = {:ignore_patterns => [/vipr/,/900$/,/901$/,/999$/]} # seems to like number , not like string
|
45
|
+
default_options = {:ignore_patterns => [/vipr/,/900$/,/901$/,/999$/]} # seems to like number , not like string
|
46
46
|
#options = default_options.merge(options)
|
47
47
|
v.scan(default_options)
|
48
48
|
v.to_nifti!(output_directory)
|
@@ -1,6 +1,6 @@
|
|
1
1
|
require 'tmpdir'
|
2
2
|
begin
|
3
|
-
%W{dicom
|
3
|
+
%W{dicom }.each do |lib| #####RMagick
|
4
4
|
require lib unless defined?(lib)
|
5
5
|
end
|
6
6
|
rescue LoadError => e
|
@@ -86,10 +86,12 @@ class RawImageDatasetThumbnail
|
|
86
86
|
default_name = @dataset.series_description.escape_filename
|
87
87
|
filepath ||= File.join(output_directory, default_name + '.png')
|
88
88
|
|
89
|
+
|
89
90
|
begin
|
90
91
|
case @processor
|
91
92
|
when :rubydicom
|
92
|
-
@path =
|
93
|
+
@path = create_thumbnail_with_rubydicom_dcmtk(filepath)
|
94
|
+
#@path = create_thumbnail_with_rubydicom(filepath)
|
93
95
|
when :slicer
|
94
96
|
@path = create_thumbnail_with_fsl_slicer(filepath)
|
95
97
|
end
|
@@ -108,6 +110,38 @@ class RawImageDatasetThumbnail
|
|
108
110
|
end
|
109
111
|
|
110
112
|
private
|
113
|
+
|
114
|
+
# Creates a thumbnail using RubyDicom and dcmtk
|
115
|
+
# Pass in an absolute or relative filepath, including filename and extension.
|
116
|
+
# Returns an absolute path to the created thumbnail image.
|
117
|
+
def create_thumbnail_with_rubydicom_dcmtk(output_file)
|
118
|
+
output_file = File.expand_path(output_file)
|
119
|
+
|
120
|
+
dicom_files = Dir.glob(File.join(dataset.directory, dataset.glob))
|
121
|
+
if dicom_files.empty? # Try the glob again with a zipped extension.
|
122
|
+
dicom_files = Dir.glob(File.join(dataset.directory, dataset.glob) + '*.bz2')
|
123
|
+
end
|
124
|
+
if dicom_files.empty? # If still empty...
|
125
|
+
raise StandardError, "Could not find dicom files using #{dataset.glob} in #{dataset.directory}"
|
126
|
+
end
|
127
|
+
dicom_file = Pathname(dicom_files[(dicom_files.size/2)+1])
|
128
|
+
dicom_file.local_copy do |lc|
|
129
|
+
dcm = DICOM::DObject.new(lc.to_s)
|
130
|
+
raise ScriptError, "Could not read dicom #{dicom_file.to_s}" unless dcm.read_success
|
131
|
+
v_call = "dcmj2pnm -v +Wi 1 --write-png "+lc.to_s+" "+output_file
|
132
|
+
v_results = %x[#{v_call}]
|
133
|
+
puts "results= "+v_results
|
134
|
+
puts "dicom_file= "+dicom_file.to_s
|
135
|
+
puts "output_file= "+output_file
|
136
|
+
#### image = dcm.get_image_magick(:rescale => true)
|
137
|
+
#### raise ScriptError, "RubyDicom did not return an image array (this is probably a color image)." unless image.kind_of? Magick::Image
|
138
|
+
#### image.write(output_file)
|
139
|
+
end
|
140
|
+
|
141
|
+
raise(ScriptError, "Error creating thumbnail #{output_file}") unless File.exist?(output_file)
|
142
|
+
|
143
|
+
return output_file
|
144
|
+
end
|
111
145
|
|
112
146
|
# Creates a thumbnail using RubyDicom
|
113
147
|
# Pass in an absolute or relative filepath, including filename and extension.
|
data/lib/metamri/version.rb
CHANGED
data/lib/metamri.rb
CHANGED
data/metamri.gemspec
CHANGED
@@ -19,7 +19,7 @@ Gem::Specification.new do |s|
|
|
19
19
|
|
20
20
|
s.add_runtime_dependency('dicom', "~> 0.8.0")
|
21
21
|
s.add_runtime_dependency('activeresource', "~> 3.0")
|
22
|
-
s.add_runtime_dependency('rmagick', "~> 2.13.1")
|
22
|
+
##### s.add_runtime_dependency('rmagick', "~> 2.13.1")
|
23
23
|
s.add_runtime_dependency('hirb', "~> 0.4")
|
24
24
|
s.add_runtime_dependency('sqlite3', "~>1.3.4")
|
25
25
|
s.add_development_dependency('rspec', "~> 2.5")
|
metadata
CHANGED
@@ -1,13 +1,13 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: metamri
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
hash:
|
4
|
+
hash: 55
|
5
5
|
prerelease:
|
6
6
|
segments:
|
7
7
|
- 0
|
8
8
|
- 2
|
9
|
-
-
|
10
|
-
version: 0.2.
|
9
|
+
- 16
|
10
|
+
version: 0.2.16
|
11
11
|
platform: ruby
|
12
12
|
authors:
|
13
13
|
- Kristopher J. Kosmatka
|
@@ -16,7 +16,7 @@ autorequire:
|
|
16
16
|
bindir: bin
|
17
17
|
cert_chain: []
|
18
18
|
|
19
|
-
date: 2013-
|
19
|
+
date: 2013-03-25 00:00:00 Z
|
20
20
|
dependencies:
|
21
21
|
- !ruby/object:Gem::Dependency
|
22
22
|
name: dicom
|
@@ -49,26 +49,10 @@ dependencies:
|
|
49
49
|
version: "3.0"
|
50
50
|
type: :runtime
|
51
51
|
version_requirements: *id002
|
52
|
-
- !ruby/object:Gem::Dependency
|
53
|
-
name: rmagick
|
54
|
-
prerelease: false
|
55
|
-
requirement: &id003 !ruby/object:Gem::Requirement
|
56
|
-
none: false
|
57
|
-
requirements:
|
58
|
-
- - ~>
|
59
|
-
- !ruby/object:Gem::Version
|
60
|
-
hash: 57
|
61
|
-
segments:
|
62
|
-
- 2
|
63
|
-
- 13
|
64
|
-
- 1
|
65
|
-
version: 2.13.1
|
66
|
-
type: :runtime
|
67
|
-
version_requirements: *id003
|
68
52
|
- !ruby/object:Gem::Dependency
|
69
53
|
name: hirb
|
70
54
|
prerelease: false
|
71
|
-
requirement: &
|
55
|
+
requirement: &id003 !ruby/object:Gem::Requirement
|
72
56
|
none: false
|
73
57
|
requirements:
|
74
58
|
- - ~>
|
@@ -79,11 +63,11 @@ dependencies:
|
|
79
63
|
- 4
|
80
64
|
version: "0.4"
|
81
65
|
type: :runtime
|
82
|
-
version_requirements: *
|
66
|
+
version_requirements: *id003
|
83
67
|
- !ruby/object:Gem::Dependency
|
84
68
|
name: sqlite3
|
85
69
|
prerelease: false
|
86
|
-
requirement: &
|
70
|
+
requirement: &id004 !ruby/object:Gem::Requirement
|
87
71
|
none: false
|
88
72
|
requirements:
|
89
73
|
- - ~>
|
@@ -95,11 +79,11 @@ dependencies:
|
|
95
79
|
- 4
|
96
80
|
version: 1.3.4
|
97
81
|
type: :runtime
|
98
|
-
version_requirements: *
|
82
|
+
version_requirements: *id004
|
99
83
|
- !ruby/object:Gem::Dependency
|
100
84
|
name: rspec
|
101
85
|
prerelease: false
|
102
|
-
requirement: &
|
86
|
+
requirement: &id005 !ruby/object:Gem::Requirement
|
103
87
|
none: false
|
104
88
|
requirements:
|
105
89
|
- - ~>
|
@@ -110,11 +94,11 @@ dependencies:
|
|
110
94
|
- 5
|
111
95
|
version: "2.5"
|
112
96
|
type: :development
|
113
|
-
version_requirements: *
|
97
|
+
version_requirements: *id005
|
114
98
|
- !ruby/object:Gem::Dependency
|
115
99
|
name: escoffier
|
116
100
|
prerelease: false
|
117
|
-
requirement: &
|
101
|
+
requirement: &id006 !ruby/object:Gem::Requirement
|
118
102
|
none: false
|
119
103
|
requirements:
|
120
104
|
- - ">="
|
@@ -124,7 +108,7 @@ dependencies:
|
|
124
108
|
- 0
|
125
109
|
version: "0"
|
126
110
|
type: :development
|
127
|
-
version_requirements: *
|
111
|
+
version_requirements: *id006
|
128
112
|
description: Extraction of MRI metadata.
|
129
113
|
email: ekk@medicine.wisc.edu
|
130
114
|
executables:
|