find_beads 0.9.4-java → 0.9.5-java

data/lib/find_beads/bead_clumps.rb

@@ -0,0 +1,226 @@
+#--
+# 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 'set'
+
+module FindBeads
+
+	module BeadClumping
+
+		class Edge
+
+			def initialize(v0, v1)
+				@v0 = v0
+				@v1 = v1
+			end
+
+			attr_accessor :v0, :v1
+
+			def connected_to?(v)
+				v == @v0 or v == @v1
+			end
+
+			def ==(e)
+				(e.v0 == @v0 and e.v1 == @v1) or (e.v1 == @v0 and e.v0 == @v1)
+			end
+
+			alias eql? ==
+
+		end
+
+		class Vertex
+
+			def initialize(label)
+				@edges = Set.new
+				@label = label
+			end
+
+			def connect(v)
+				e = Edge.new(self, v)
+				@edges << e
+			end
+
+			def add_edge(e)
+				@edges << e if (e.v0 == self or e.v1 == self)
+			end
+
+			def connected_to?(v)
+				e.Edge.new(self, v)
+				@edges.include?(e)
+			end
+
+			def include?(e)
+				@edges.include?(e)
+			end
+
+			def each(&b)
+				@edges.each &b
+			end
+
+			attr_accessor :edges, :label
+
+		end
+
+		class Graph
+
+			def initialize
+				@vertices = {}
+			end
+
+			def add_vertex(v)
+				@vertices[v.label]= v
+			end
+
+			def new_vertex(l)
+				@vertices[l] = Vertex.new(l)
+			end
+
+			def vertex(label)
+				@vertices[label]
+			end
+
+			def each(&b)
+				@vertices.each &b
+			end
+
+			alias [] vertex
+
+			def direct_connected?(l0, l1)
+				self[l0].connected_to? self[l1]
+			end
+
+			def add_edge_between(l0, l1)
+				self[l0].connect(self[l1])
+			end
+
+			def connected?(l0, l1)
+				sg = get_connected_subgraph(l0)
+				sg.include?(self[l1])
+			end
+
+			def build_connected_dfs(current, visited)
+
+				visited << current
+
+				current.each do |e|
+
+					[:v0, :v1].each do |vi|
+
+						v = e.send(vi)
+
+						if v.nil?
+
+							puts e.inspect
+
+							raise
+
+						end
+
+						unless visited.include?(v) then
+
+							build_connected_dfs(v, visited)
+
+						end
+
+					end
+
+				end
+
+				visited
+
+			end
+
+			def get_connected_subgraph(l0)
+
+				build_connected_dfs(self[l0], Set.new)
+
+			end
+
+		end
+
+
+		def self.get_points_within_distance(point, points_list, distance_cutoff)
+
+			close = []
+
+			points_list.each do |p|
+
+				next if point == p
+
+				if (Vector[*point] - Vector[*p]).norm < distance_cutoff then
+
+					close << p
+
+				end
+
+			end
+
+			close
+
+		end
+
+		def self.construct_adjacency_graph(points, distance_cutoff)
+
+			g = Graph.new
+
+			points.each_with_index do |p, i|
+
+				g.new_vertex(i+1)
+
+			end
+
+			points.each_with_index do |p, i|
+
+				close = get_points_within_distance(p, points, distance_cutoff)
+
+				close.each do |c|
+
+					g.add_edge_between(i+1, points.index(c) + 1)
+
+				end
+
+			end
+
+			g
+
+		end
+
+
+		def self.count_disjoint_subgraphs(graph)
+
+			subgraphs = Set.new
+
+			graph.each do |l, vert|
+
+				subgraphs << graph.get_connected_subgraph(l)
+
+			end
+
+			subgraphs.size
+
+		end
+
+	end
+
+end
+
+

data/lib/find_beads/version.rb

@@ -26,7 +26,7 @@
 
 module FindBeads
 
-  VERSION = '0.9.4'
+  VERSION = '0.9.5'
 
 end
 

data/lib/find_beads.rb

@@ -56,6 +56,7 @@ module FindBeads
   DEFAULT_SEG_CH = 2
   DEFAULT_SEG_PL = 8
   DEFAULT_BEAD_RADIUS = 24.0
+  DEFAULT_THREADS = 1
 
   ##
   # Finds the centroid of each unique-greylevel region in a mask.
@@ -501,6 +502,7 @@ module FindBeads
       opt :file, "File to process", :type => :string
       opt :segchannel, "Channel on which to segment (0-indexed)", :type => :integer, :default => DEFAULT_SEG_CH
       opt :segplane, "Plane on which to segment (0-indexed)", :type => :integer, :default => DEFAULT_SEG_PL
+      opt :max_threads, "Maximum number of paralell execution threads", :type => :integer, :default => DEFAULT_THREADS
       opt :beadradius, "Radius of the bead in pixels", :type => :float, :default => DEFAULT_BEAD_RADIUS
 
     end
@@ -509,15 +511,26 @@ module FindBeads
 
       fod = opts[:dir]
 
+      sleep_time_s = 0.5
+      threads = []
+
       Dir.foreach(fod) do |f|
 
+        until threads.count { |t| t.alive? } < opts[:max_threads] do
+          sleep sleep_time_s
+        end
+
         fn = File.expand_path(f, fod)
 
         if File.file?(fn) then
 
           begin
 
-            process_file(fn, opts)
+            threads << Thread.new do 
+
+              process_file(fn, opts)
+
+            end
 
           rescue Exception => e
 
@@ -530,8 +543,12 @@ module FindBeads
 
       end
 
+      threads.each { |t| t.join }
+
     end
 
+
+
     if opts[:file] then
 
       process_file(opts[:file], opts)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: find_beads
 version: !ruby/object:Gem::Version
-  version: 0.9.4
+  version: 0.9.5
   prerelease:
 platform: java
 authors:
@@ -56,6 +56,7 @@ extra_rdoc_files: []
 files:
 - lib/find_beads.rb
 - lib/find_beads/version.rb
+- lib/find_beads/bead_clumps.rb
 - bin/find_beads
 homepage: http://github.com/cjfuller/find_beads
 licenses: