rimageanalysistools 5.1.3.1-java → 5.1.4.1-java

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 4c7d48f0ed9ddeb04036796490373e3ba01b4801
+  data.tar.gz: 902959cd4e6552ab1fc53c3d9fa229f3d254085a
+SHA512:
+  metadata.gz: 7e0058d24160cfbd535afbe59f08a872eb6f57e4958d10292918158e2eb9e925ef729c0ab2dc6379db5ec5e0f4cc461c1337d746a47d6001623513fdea42e552
+  data.tar.gz: d1fc10d700d36f01093b2891cbd2db43af8ff9184cb7c76d853c57f55de171473d7e8cb02c9b5ec21e36c2bbf2046a273421b74ac7bd8e5c5d8f3ab283f49cb6

data/lib/rimageanalysistools/centroids.rb

@@ -31,8 +31,20 @@ java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageCoordinate
 
 module RImageAnalysisTools
 
-  class Centroids
-
+  ##
+  # Methods for calculating the geometric centroids of regions in an image
+  #
+  module Centroids
+
+    ##
+    # Calculates the centroid of all 2d regions in a mask.  A region is
+    # defined as all pixels having the same nonzero greylevel in an image.
+    #
+    # @param [Image] mask the mask containing the regions
+    #
+    # @return [Hash] a hash mapping the greylevel of each region to its
+    #  2d centroid stored as an array [x,y]
+    #
     def self.calculate_centroids_2d(mask)
 
       centroids = {}

data/lib/rimageanalysistools/create_parameters.rb

@@ -30,10 +30,25 @@ java_import Java::edu.stanford.cfuller.imageanalysistools.meta.parameters.Parame
 
 class ParameterDictionary
 
+  ##
+  # Adds hash-like getter access to ParameterDictionary objects
+  #
+  # @param key an object whose to_s method returns the name of a parameter
+  # 
+  # @return [String] the value of the parameter as returned by ParameterDictionary#getValueForKey
+  #
   def [](key)
     getValueForKey(key.to_s)
   end
 
+  ##
+  # Adds hash-like setter access to ParameterDictionary objects
+  #
+  # @param key an object whose to_s method returns the name of a parameter
+  # @param value an object whose to_s method returns the parameter value being set
+  # 
+  # @return [void]
+  #
   def []=(key, value)
     setValueForKey(key.to_s, value.to_s)
   end
@@ -42,7 +57,13 @@ end
 
 module RImageAnalysisTools
 
-
+  ##
+  # Creates a ParameterDictionary from a hash of parameters.
+  #
+  # @param [Hash] parameter_hash a hash mapping parameters to values
+  #
+  # @return [ParameterDictionary] a parameter dictionary now containing the specified parameters
+  #
   def self.create_parameter_dictionary(parameter_hash)
 
     p = ParameterDictionary.emptyDictionary

data/lib/rimageanalysistools/drawing.rb

@@ -31,6 +31,21 @@ java_import Java::edu.stanford.cfuller.imageanalysistools.image.ReadOnlyImageImp
 
 class ReadOnlyImageImpl
 
+  ##
+  # Allows setting a region of interest of an image along only some dimenions, preserving any
+  # current region of interest along other dimenions.
+  #
+  # @param [Hash, ImageCoordinate] lower a hash or ImageCoordinate mapping dimensions to the lower
+  #  bound of the box (inclusive) along the specified dimensions.  Can contain extra dimenions not boxed;
+  #  only the boxing on the dimenions specified in the dims parameter will be changed.
+  # @param [Hash, ImageCoordinate] upper a hash or ImageCoordinate mapping dimensions to the upper
+  #  bound of the box (exclusive) along the specified dimensions.  Can contain extra dimenions not boxed;
+  #  only the boxing on the dimenions specified in the dims parameter will be changed.
+  # @param [Enumerable] dims an enumeration of the dimensions to be boxed (these should be the symbol shortcuts
+  #  to the dimensions; e.g. :x, :y)
+  #
+  # @return [void]
+  #
   def box_conservative(lower, upper, dims)
 
     low_curr = nil
@@ -57,10 +72,27 @@ class ReadOnlyImageImpl
 
 end
 
+
 module RImageAnalysisTools
 
+
+  ##
+  # A collection of methods for drawing into an existing image.
+  #
   class Drawing
 
+    ##
+    # A basic drawing method that iterates through an entire image.  At each coordinate,
+    # an attached block is evaluated for a boolean response that determines whether that
+    # coordinate is overwritten with a specified value.  The attached block will be given
+    # a single parameter, which is the current ImageCoordinate.
+    #
+    # @param [WritableImage] im the image being drawn on
+    # @param [Numeric] draw_value the value to which a pixel will be set if the block
+    #  evaluates to a true value at that coordinate
+    #
+    # @return [void]
+    #
     def draw(im, draw_value = 255.0)
 
       im.each do |ic|
@@ -75,6 +107,19 @@ module RImageAnalysisTools
 
     end
     
+    ##
+    # Draws a specified shape into an image.
+    # 
+    # @param [WritableImage] im the image into which to draw
+    # @param [Array] location an array containing the coordinates of the shape to draw.
+    #  The exact meaning of this parameter depends on which shape is being drawn.
+    # @param [Symbol] shape_name the name of the shape to draw.  This should correspond
+    #  to one of the methods of this class.
+    # @param shape_parameters the parameters for drawing the specified shape;
+    #  the meaning of this parameter depends on the shape.
+    #
+    # @return [void]
+    #
     def draw_shape(im, location, shape_name=:circle, shape_parameters= 10)
 
       if self.respond_to?(shape_name) then
@@ -85,6 +130,15 @@ module RImageAnalysisTools
 
     end
     
+    ##
+    # Draws a circle into an image.
+    #
+    # @param [WritableImage] im the image into which to draw
+    # @param [Array] center an array containing the x,y coordinates of the circle's center
+    # @param [Numeric] radius the radius of the circle in pixels
+    #
+    # @return [void]
+    #
     def circle(im, center, radius)
 
       lower = ImageCoordinate[center[0]-radius-1, center[1]-radius-1, 0,0,0]
@@ -110,6 +164,18 @@ module RImageAnalysisTools
         
     end
 
+    ##
+    # Draws an ellipse into an image.
+    #
+    # @param [WritableImage] im the image into which to draw
+    # @param [Array] foci an array containing two arrays, each of which contains the x,y
+    #  coordinates of one focus of the ellipse
+    # @param [Numeric] radius_inc the extra amount of distance (in pixels) beyond the
+    #  distance between the foci that the ellipse should be drawn.  (2*radius_inc + dist
+    #  between foci = major axis length)
+    #
+    # @return [void]
+    #
     def ellipse(im, foci, radius_inc)
 
       min_x = foci[0][0]

data/lib/rimageanalysistools/get_image.rb

@@ -25,14 +25,22 @@
 #++
 
 require 'rimageanalysistools/initjava'
+require 'rimageanalysistools/image/io/url_image_reader'
+require 'uri'
 
 java_import Java::edu.stanford.cfuller.imageanalysistools.image.io.ImageReader
 
 module RImageAnalysisTools
     
   def self.get_image(filename)
-    
-    ir = ImageReader.new
+
+    ir = nil
+
+    if filename.is_a? URI then
+      ir = URLImageReader.new
+    else
+      ir = ImageReader.new
+    end
     
     ir.read(filename)
         

data/lib/rimageanalysistools/image/io/url_image_reader.rb

@@ -0,0 +1,61 @@
+#--
+# Copyright (c) 2013 Colin J. Fuller
+# 
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the Software), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+# 
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+# 
+# THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+#++
+
+require 'open-uri'
+require 'tempfile'
+require 'rimageanalysistools/get_image'
+
+module RImageAnalysisTools
+
+	class URLImageReader
+
+		def read(url)
+
+			data = nil
+			im = nil
+
+			open(url) do |f|
+				data = f.read
+			end
+
+			tf = Tempfile.new('url_image_reader')
+
+			begin
+
+				tf.write(data)
+				im = RImageAnalysisTools.get_image(tf.path)
+
+			ensure
+
+				tf.close
+				tf.unlink
+
+			end
+
+			im
+
+		end
+
+	end
+
+end
+

metadata

@@ -1,17 +1,17 @@
 --- !ruby/object:Gem::Specification
 name: rimageanalysistools
 version: !ruby/object:Gem::Version
-  version: 5.1.3.1
-  prerelease:
+  version: 5.1.4.1
 platform: java
 authors:
 - Colin J. Fuller
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
 date: 2013-01-25 00:00:00.000000000 Z
 dependencies: []
-description: Helper code and some extensions for the ImageAnalysisTools package at http://cjfuller.github.com/imageanalysistools/
+description: Helper code and some extensions for the ImageAnalysisTools package at
+  http://cjfuller.github.com/imageanalysistools/
 email: cjfuller@gmail.com
 executables: []
 extensions: []
@@ -27,42 +27,40 @@ files:
 - lib/rimageanalysistools/get_image.rb
 - lib/rimageanalysistools/skeletonizer.rb
 - lib/rimageanalysistools/get_filter.rb
-- lib/rimageanalysistools/centroids.rb
-- lib/rimageanalysistools/drawing.rb
-- lib/rimageanalysistools/image_shortcuts.rb
 - lib/rimageanalysistools/fitting/bisquare_linear_fit.rb
 - lib/rimageanalysistools/method/centromere_finding_method.rb
 - lib/rimageanalysistools/method/method.rb
+- lib/rimageanalysistools/image/io/url_image_reader.rb
 - lib/rimageanalysistools/image/io/image_writer.rb
+- lib/rimageanalysistools/centroids.rb
+- lib/rimageanalysistools/drawing.rb
+- lib/rimageanalysistools/image_shortcuts.rb
 - extlib/ImageAnalysisTools.jar
 homepage: https://github.com/cjfuller/rimageanalysistools/
 licenses:
 - MIT
-post_install_message:
+metadata: {}
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 - extlib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
-      version: !binary |-
-        MA==
-  none: false
+      version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
-      version: !binary |-
-        MA==
-  none: false
+      version: '0'
 requirements:
 - jruby
-rubyforge_project:
-rubygems_version: 1.8.24
-signing_key:
-specification_version: 3
+rubyforge_project: 
+rubygems_version: 2.0.0
+signing_key: 
+specification_version: 4
 summary: JRuby extensions to the ImageAnalysisTools java package
 test_files: []
-has_rdoc:
+has_rdoc: