metamri 0.2.20 → 0.2.21
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +8 -8
- data/bin/convert_visit.rb +1 -1
- data/lib/metamri/dicom_additions.rb +2 -1
- data/lib/metamri/raw_image_dataset_thumbnail.rb +4 -2
- data/lib/metamri/raw_image_file.rb +3 -1
- data/lib/metamri/version.rb +1 -1
- data/metamri.gemspec +2 -1
- metadata +4 -4
checksums.yaml
CHANGED
@@ -1,15 +1,15 @@
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---
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!binary "U0hBMQ==":
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metadata.gz: !binary |-
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-
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4
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+
ZDcxZTM0MmRiYWY0OTk5Nzg3YjllNmFmNGIyZmM3OWRmNGZjYThiMA==
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data.tar.gz: !binary |-
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6
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-
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6
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+
YTU5Y2MzODk5Yjk1ODI4MzY3YWUyNzI5ZWYzMTE0MjFkMTdiYWRlYQ==
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SHA512:
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metadata.gz: !binary |-
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-
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-
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-
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9
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+
NjhmMTVjYWIzYjUwYmI4ZmE3YjNmY2FjYTdhM2U2ZDJkOGY5Y2QzNzY4YWI1
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+
NjdkYjU0NDNlZGY2YmQ2MWY0YTQ5MGRlZjVmMDdmMjcxZTAwZDg3ZDAxYmVj
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N2RjMWNlNGQ3ZjE2OWZhOTkyNTNlY2FmZDYyMjc3YTE4NjRiMmE=
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data.tar.gz: !binary |-
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-
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-
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+
NWU2NTgyNWQ4NGNlZDI0YzY5ODRiOGU0MGIzYmIxMWI0MDMwODQzYjBjZGIw
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+
ODk3YmRmNWQyZDhhYTI2MjY1ZDNmYTdkOWRiMDM5NzEyMzljMzgyMDVjMmM3
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+
ZWM0YjY4NTQxZjBiYTgzYjM3YmRjMjgwMTBjMTAyMTQ2MjcxMmI=
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data/bin/convert_visit.rb
CHANGED
@@ -42,7 +42,7 @@ def convert_visit(raw_directory, scan_procedure_codename, output_directory = nil
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output_directory = output_directory ||= v.default_preprocess_directory
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begin
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-
default_options = {:ignore_patterns => [/vipr/,/pfiles/,/
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+
default_options = {:ignore_patterns => [[/vipr/,/raw$/,/pfiles/,/Processed-Images/,/900$/,/901$/,/999$/,/\/01300\./,/\/01301\./,/\/01001\./,/\/01002\./,/\/01000\./,/\/00600\./]} # does not like "raw" because in dir path
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#options = default_options.merge(options)
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v.scan(default_options)
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v.to_nifti!(output_directory)
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@@ -11,7 +11,8 @@ class DicomGroup
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# Initialize with an array of strings or DICOM::DObjects to aggregate
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def initialize(dicomgroup)
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if dicomgroup.select {|dcm| dcm.is_a? DICOM::DObject }.empty?
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-
@dobjects = dicomgroup.collect {|dcm| DICOM::DObject.
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@dobjects = dicomgroup.collect {|dcm| DICOM::DObject.read(dcm)}
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#@dobjects = dicomgroup.collect {|dcm| DICOM::DObject.new(dcm)} # changing from dicom 0.8.0 to 0.9.5
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else
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@dobjects = dicomgroup
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end
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@@ -127,7 +127,8 @@ class RawImageDatasetThumbnail
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end
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dicom_file = Pathname(dicom_files[(dicom_files.size/2)+1])
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dicom_file.local_copy do |lc|
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-
dcm = DICOM::DObject.new(lc.to_s)
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#dcm = DICOM::DObject.new(lc.to_s) # changing from dicom 0.8.0 to 0.9.5
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dcm = DICOM::DObject.read(lc.to_s)
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raise ScriptError, "Could not read dicom #{dicom_file.to_s}" unless dcm.read_success
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v_call = "dcmj2pnm -v +Wi 1 --write-png "+lc.to_s+" "+output_file
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v_results = %x[#{v_call}]
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@@ -159,7 +160,8 @@ class RawImageDatasetThumbnail
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end
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dicom_file = Pathname(dicom_files[dicom_files.size/2])
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dicom_file.local_copy do |lc|
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-
dcm = DICOM::DObject.new(lc.to_s)
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#dcm = DICOM::DObject.new(lc.to_s) # changing from dicom 0.8.0 to 0.9.5
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dcm = DICOM::DObject.read(lc.to_s)
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raise ScriptError, "Could not read dicom #{dicom_file.to_s}" unless dcm.read_success
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image = dcm.get_image_magick(:rescale => true)
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raise ScriptError, "RubyDicom did not return an image array (this is probably a color image)." unless image.kind_of? Magick::Image
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@@ -300,7 +300,9 @@ private
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else
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# Try reading with RubyDICOM
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@current_hdr_reader = RUBYDICOM_HDR
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-
header = DICOM::DObject.new(absfilepath)
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####header = DICOM::DObject.new(absfilepath) # changing from dicom 0.8.0 to 0.9.5
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header = DICOM::DObject.read(absfilepath)
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+
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if defined? header.read_success && header.read_success
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@current_hdr_reader = nil
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return [header, RUBYDICOM_HDR]
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data/lib/metamri/version.rb
CHANGED
data/metamri.gemspec
CHANGED
@@ -17,7 +17,8 @@ Gem::Specification.new do |s|
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s.executables = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
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s.require_paths = ["lib"]
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-
s.add_runtime_dependency('dicom', "~> 0.
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s.add_runtime_dependency('dicom', "~> 0.9.5") # fixed issue with multi row dicom values
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#s.add_runtime_dependency('dicom', "~> 0.8.0")
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s.add_runtime_dependency('activeresource', "~> 3.0")
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# s.add_runtime_dependency('rmagick')
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s.add_runtime_dependency('hirb', "~> 0.4")
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metadata
CHANGED
@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: metamri
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version: !ruby/object:Gem::Version
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-
version: 0.2.
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version: 0.2.21
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platform: ruby
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authors:
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- Kristopher J. Kosmatka
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2014-
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+
date: 2014-05-01 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: dicom
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@@ -17,14 +17,14 @@ dependencies:
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.
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version: 0.9.5
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 0.
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version: 0.9.5
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- !ruby/object:Gem::Dependency
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name: activeresource
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requirement: !ruby/object:Gem::Requirement
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