metamri 0.2.24 → 0.2.25

checksums.yaml

@@ -1,15 +1,7 @@
 ---
-!binary "U0hBMQ==":
-  metadata.gz: !binary |-
-    ZWY3NWY2MWZkMDY2ZGEwOTc1YTU0OGZmM2Q0YzBjMWQ4ZTExZTkyNQ==
-  data.tar.gz: !binary |-
-    NDgyNWE5ZjJkMDkxYzRkM2VmNWJiMjdiZWZiZWI5MWEzZWM1NWY3ZQ==
+SHA1:
+  metadata.gz: 92932063e1a8a63e45c8b74c92adfbd4def00b09
+  data.tar.gz: 467f2328d0aee4538b0cd03c68e98b8a8599c7b9
 SHA512:
-  metadata.gz: !binary |-
-    NDNkNTA3ZDY1ZjFhZWVlMzk1NWY4ZmM5OTZjMTRlNTJkMzUwYjc5MzEzNzZj
-    YzA2YmZlMDA4N2UyMjU2N2UxZTJjZDVhMWZkMzdmMzRjYjRlM2M2NzNkZGM1
-    YWFhM2U5MjQ5YzMwOWNiM2JhMTZjYjFkZjRiZDBlNDQzZWJiYzU=
-  data.tar.gz: !binary |-
-    M2Q1NjY2OGFmZGQzZTFiODI3MWU5MmQwNTM4OWZhOWE3OGQ2MzI2OWE0Yjhh
-    NWRmZWMwZWMyMWJiZDRiZDA0ZjQyOGE1NTRhODgxODIzN2UzMmI0YWM5YzRj
-    MDhkMDYwZmQzNDhkZDQzMjRhOTUxOGVkYWQzNjRlOWQyNDA3ZDA=
+  metadata.gz: 9de4f0f131ad11edd2c8a9e99c22efeb8c0e243e14fb8a23ec3c373e7fa537cceabc3dc837310dd35704c7d77a674b8f136fc455adf490e4227c2d1ced991419
+  data.tar.gz: bf1ade09fe6571e22d4c6f71efb3305e28bb01b528e87e5c9212bf6e8aab3fd8f2d5d4289c3d45323c941a2f77fb394b73b7e42a0fffa7329c24e3651b465542

data/VERSION

@@ -1 +1 @@
-0.2.24
+0.2.25

data/lib/metamri/core_additions.rb

@@ -44,7 +44,15 @@ class Pathname
       next unless leaf.to_s =~ /^P.{5}\.7(\.bz2)/
       branch = self + leaf
       next if branch.symlink?
-      if branch.size >= min_file_size
+      v_pfile_small_but_summary_flag ="N"
+      if branch.size < min_file_size
+        leaf_summary_s = (leaf.to_s).gsub(/\.bz2/,"")+".summary"
+        branch_summary_s = self.to_s+"/"+leaf_summary_s
+        if File.exist?(branch_summary_s)
+           v_pfile_small_but_summary_flag ="Y"
+        end
+      end
+      if branch.size >= min_file_size or v_pfile_small_but_summary_flag == "Y"
         # check for P*.7.summary 
         # if there, skip local_copy of P*.7.bz2
        leaf_summary_s = (leaf.to_s).gsub(/\.bz2/,"")+".summary"

data/lib/metamri/raw_image_dataset_thumbnail.rb

@@ -125,7 +125,7 @@ class RawImageDatasetThumbnail
     if dicom_files.empty? # If still empty...
       raise StandardError, "Could not find dicom files using #{dataset.glob} in #{dataset.directory}"
     end
-    dicom_file = Pathname(dicom_files[(dicom_files.size/2)+1])
+    dicom_file = Pathname(dicom_files[(dicom_files.size/3)+1])   # 2 => 3 to keep asl in first half of set --> delay time
     dicom_file.local_copy do |lc|
       #dcm = DICOM::DObject.new(lc.to_s) # changing from dicom 0.8.0  to 0.9.5
       dcm = DICOM::DObject.read(lc.to_s)

data/lib/metamri/raw_image_file.rb

@@ -196,14 +196,15 @@ class RawImageFile
   # compatible database (sqlite3).  This is intended for inserting into the rails
   # backend database.
   def db_insert(image_dataset_id)
-    "INSERT INTO raw_image_files
-    (filename, header_reader, file_type, timestamp, source, rmr_number, series_description, 
-    gender, num_slices, slice_thickness, slice_spacing, reconstruction_diameter, 
-    acquisition_matrix_x, acquisition_matrix_y, rep_time, bold_reps, created_at, updated_at, image_dataset_id)
-    VALUES ('#{@filename}', '#{@hdr_reader}', '#{@file_type}', '#{@timestamp.to_s}', '#{@source}', '#{@rmr_number}', 
-    '#{@series_description}', '#{@gender}', #{@num_slices}, #{@slice_thickness}, #{@slice_spacing}, 
-    #{@reconstruction_diameter}, #{@acquisition_matrix_x}, #{@acquisition_matrix_y}, #{@rep_time}, 
-    #{@bold_reps}, '#{DateTime.now}', '#{DateTime.now}', #{image_dataset_id})"
+    ####"INSERT INTO raw_image_files
+    ####(filename, header_reader, file_type, timestamp, source, rmr_number, series_description, 
+    ####gender, num_slices, slice_thickness, slice_spacing, reconstruction_diameter, 
+    ####acquisition_matrix_x, acquisition_matrix_y, rep_time, bold_reps, created_at, updated_at, image_dataset_id)
+    ####VALUES ('#{@filename}', '#{@hdr_reader}', '#{@file_type}', '#{@timestamp.to_s}', '#{@source}', '#{@rmr_number}', 
+    ####'#{@series_description}', '#{@gender}', #{@num_slices}, #{@slice_thickness}, #{@slice_spacing}, 
+   #### #{@reconstruction_diameter}, #{@acquisition_matrix_x}, #{@acquisition_matrix_y}, #{@rep_time}, 
+   #### #{@bold_reps}, '#{DateTime.now}', '#{DateTime.now}', #{image_dataset_id})"  
+     puts "Old no raw_image_files table"
   end
 
   # Returns an SQL statement to select this image file row from the raw_image_files table
@@ -222,31 +223,35 @@ class RawImageFile
   # Uses the db_insert method to actually perform the database insert using the 
   # specified database file.
   def db_insert!( db_file )
-    db = SQLite3::Database.new( db_file )
-    db.transaction do |database|
-      if not database.execute( db_fetch ).empty?
-        raise(IndexError, "Entry exists for #{filename}, #{@rmr_number}, #{@timestamp.to_s}... Skipping.")
-      end
-      database.execute( db_insert )
-    end
-    db.close
+    ####db = SQLite3::Database.new( db_file )
+    ####db.transaction do |database|
+    ####  if not database.execute( db_fetch ).empty?
+    ####    raise(IndexError, "Entry exists for #{filename}, #{@rmr_number}, #{@timestamp.to_s}... Skipping.")
+    ####  end
+    ####  database.execute( db_insert )
+    ####end
+    ####db.close
+    puts "SQLite3"
   end
 
   # Removes this instance from the raw_image_files table of the specified database.
   def db_remove!( db_file )
-    db = SQLite3::Database.new( db_file )
-    db.execute( db_remove )
-    db.close
+    ####db = SQLite3::Database.new( db_file )
+    ####db.execute( db_remove )
+    ####db.close  
+    puts "SQLite3"
   end
   
   # Finds the row in the raw_image_files table of the given db file that matches this object.
   # ORM is based on combination of rmr_number, timestamp, and filename.  The row is returned 
   # as an array of values (see 'sqlite3' gem docs).
   def db_fetch!( db_file )
-    db = SQLite3::Database.new( db_file )
-    db_row = db.execute( db_fetch )
-    db.close
-    return db_row
+    ####db = SQLite3::Database.new( db_file )
+    ####db_row = db.execute( db_fetch )
+    ####db.close
+    ####return db_row
+    puts "SQLite" 
+    return nil
   end
   
   # The series ID (dicom_series_uid [dicom] or series_uid [pfile/ifile])

data/lib/metamri/version.rb

@@ -1,3 +1,3 @@
 module Metamri
-  VERSION = "0.2.24"
+  VERSION = "0.2.25"
 end

data/lib/metamri.rb

@@ -9,7 +9,7 @@ begin
   require 'rspec'
   require 'dicom'
   ##### require 'rmagick'
-  require 'sqlite'
+  ####require 'sqlite'
 rescue LoadError
 end
 

data/metamri.gemspec

@@ -17,14 +17,14 @@ Gem::Specification.new do |s|
   s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
   s.require_paths = ["lib"]
 
-  s.add_runtime_dependency('dicom', "~> 0.9.5") # fixed issue with multi row dicom values
+  s.add_runtime_dependency('dicom') ####, "~> 0.9.5") # fixed issue with multi row dicom values
   #s.add_runtime_dependency('dicom', "~> 0.8.0")
-  s.add_runtime_dependency('activeresource', "~> 3.0")
+  s.add_runtime_dependency('activeresource') #####, "~> 3.0")
   # s.add_runtime_dependency('rmagick') 
-  s.add_runtime_dependency('hirb', "~> 0.4")
-  s.add_runtime_dependency('sqlite3', "~>1.3.4")
-  s.add_development_dependency('rspec', "~> 2.5")
-  s.add_development_dependency('escoffier', ">= 0")
+  s.add_runtime_dependency('hirb') #####, "~> 0.4")
+  s.add_runtime_dependency('sqlite3') #####, "~>1.3.4")
+  s.add_development_dependency('rspec') ####, "~> 2.5")
+  ####s.add_development_dependency('escoffier', ">= 0")
   
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: metamri
 version: !ruby/object:Gem::Version
-  version: 0.2.24
+  version: 0.2.25
 platform: ruby
 authors:
 - Kristopher J. Kosmatka
@@ -9,90 +9,76 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-01-27 00:00:00.000000000 Z
+date: 2017-04-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: dicom
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.9.5
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.9.5
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: activeresource
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '3.0'
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '3.0'
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: hirb
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '0.4'
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '0.4'
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: sqlite3
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.3.4
+        version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.3.4
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '2.5'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '2.5'
-- !ruby/object:Gem::Dependency
-  name: escoffier
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 description: Extraction of MRI metadata.
@@ -106,8 +92,8 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
-- .gitignore
-- .rspec
+- ".gitignore"
+- ".rspec"
 - Gemfile
 - Manifest
 - README.rdoc
@@ -158,17 +144,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.10
+rubygems_version: 2.4.5.1
 signing_key: 
 specification_version: 4
 summary: MRI metadata