rimageanalysistools 5.1.2-java

data/lib/rimageanalysistools/method/method.rb

@@ -0,0 +1,38 @@
+#--
+# /* ***** BEGIN LICENSE BLOCK *****
+#  * 
+#  * Copyright (c) 2012 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.
+#  * 
+#  * ***** END LICENSE BLOCK ***** */
+#++
+
+
+module RImageAnalysisTools
+
+  class Method
+    
+    attr_accessor :parameters, :metadata, :input_images, :output_images, :quantification
+
+  end
+  
+
+end
+

data/lib/rimageanalysistools/simple_output.rb

@@ -0,0 +1,74 @@
+#--
+# /* ***** BEGIN LICENSE BLOCK *****
+#  * 
+#  * Copyright (c) 2012 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.
+#  * 
+#  * ***** END LICENSE BLOCK ***** */
+#++
+
+require 'rimageanalysistools/initjava'
+
+java_import Java::edu.stanford.cfuller.imageanalysistools.frontend.LocalAnalysis
+
+module RImageAnalysisTools
+
+  IM_OUTPUT_DIR = "output_images"
+  QUANT_OUTPUT_DIR = "quantification"
+
+  def self.handle_output(original_filename, output_image, quant)
+    
+    fn_parts = File.split(original_filename)
+
+    im_dir = File.expand_path(IM_OUTPUT_DIR, fn_parts[0])
+
+    quant_dir = File.expand_path(QUANT_OUTPUT_DIR, fn_parts[0])
+
+    Dir.mkdir(im_dir) unless Dir.exist?(im_dir)
+    Dir.mkdir(quant_dir) unless Dir.exist?(quant_dir)
+
+    mask_fn = fn_parts[1] + "_output.ome.tif"
+
+    quant_fn = fn_parts[1] + "_quant.txt"
+
+    unless quant.nil? then
+
+      quant_str = LocalAnalysis.generateDataOutputString(quant, nil)
+
+      File.open(File.expand_path(quant_fn, quant_dir), 'w') do |f|
+        f.puts quant_str
+      end
+
+    end
+
+    unless output_image.nil? then
+
+      output_image.writeToFile(File.expand_path(mask_fn, im_dir))
+
+    end
+
+  end
+
+  
+
+end
+
+
+

data/lib/rimageanalysistools/skeletonizer.rb

@@ -0,0 +1,250 @@
+#--
+# /* ***** BEGIN LICENSE BLOCK *****
+#  * 
+#  * Copyright (c) 2012 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.
+#  * 
+#  * ***** END LICENSE BLOCK ***** */
+#++
+
+require 'rimageanalysistools'
+require 'rimageanalysistools/image_shortcuts'
+
+java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageCoordinate
+
+module RImageAnalysisTools
+
+  class Skeletonizer
+
+    #implementation of skeletonization algorithm presented in Gonzalez & Woods, p 651-652
+
+    def initialize(im)
+
+      @im = im
+
+    end
+
+    def compute_n(ic)
+
+      temp_ic = ImageCoordinate.cloneCoord(ic)
+
+      n = -1  # compensate for 0,0 case
+
+      x_off = [-1,0,1]
+      y_off = [-1,0,1]
+
+      x_off.each do |x|
+        y_off.each do |y|
+
+          temp_ic[:x] = ic[:x] + x
+          temp_ic[:y] = ic[:y] + y
+
+          if @im.inBounds(temp_ic) and @im[temp_ic] == @im[ic] then
+            n += 1
+          end
+
+        end
+
+      end
+
+      temp_ic.recycle
+
+      n
+
+    end
+
+    def compute_t(ic)
+
+      temp_ic1 = ImageCoordinate.cloneCoord(ic)
+      temp_ic2 = ImageCoordinate.cloneCoord(ic)
+
+      pixel_offsets = [[0, -1], [1, -1], [1, 0], [1, 1], [0, 1], [-1, 1], [-1, 0], [-1, -1], [0, -1]]
+
+      t = 0
+
+      0.upto(pixel_offsets.length - 2) do |i|
+        
+        p1 = pixel_offsets[i]
+        p2 = pixel_offsets[i+1]
+
+        temp_ic1[:x] = ic[:x] + p1[0]
+        temp_ic2[:x] = ic[:x] + p2[0]
+
+        temp_ic1[:y] = ic[:y] + p1[1]
+        temp_ic2[:y] = ic[:y] + p2[1]
+
+        v1 = 0
+        v2 = 0
+
+        v1 = 1 if @im.inBounds(temp_ic1) and @im[ic] == @im[temp_ic1]
+        v2 = 1 if @im.inBounds(temp_ic2) and @im[ic] == @im[temp_ic2]
+
+        t += 1 if v2 - v1 == 1
+
+      end
+
+      temp_ic1.recycle
+      temp_ic2.recycle
+
+      t
+
+    end
+
+    def compute_pixel_product(ic, pixel_offsets)
+
+      temp_ic = ImageCoordinate.cloneCoord(ic)
+
+      pixel_offsets.each do |po|
+
+        temp_ic[:x]= ic[:x] + po[0]
+        temp_ic[:y]= ic[:y] + po[1]
+        
+        unless @im.inBounds(temp_ic) and @im[temp_ic] == @im[ic] then
+          temp_ic.recycle
+          return 0
+        end
+
+      end
+
+      temp_ic.recycle
+
+      1
+
+    end
+
+    def pass1(ic)
+
+      n = compute_n(ic)
+      
+      return false if n < 2 or n > 6
+
+      t = compute_t(ic)
+
+      return false unless t == 1
+
+      pixels246 = [[0, -1], [1, 0], [0, 1]]
+
+      p246 = compute_pixel_product(ic, pixels246)
+
+      return false unless p246 == 0
+
+      pixels468 = [[1, 0], [0, 1], [-1, 0]]
+
+      p468 = compute_pixel_product(ic, pixels468)
+
+      return false unless p468 == 0
+
+      true
+
+    end
+
+    def pass2(ic)
+
+      n = compute_n(ic)
+      
+      return false if n < 2 or n > 6
+
+      t = compute_t(ic)
+
+      return false unless t == 1
+
+      pixels248 = [[0, -1], [1, 0], [-1, 0]]
+
+      p248 = compute_pixel_product(ic, pixels248)
+
+      return false unless p248 == 0
+
+      pixels268 = [[0, -1], [0, 1], [-1, 0]]
+
+      p268 = compute_pixel_product(ic, pixels268)
+
+      return false unless p268 == 0
+
+      true
+
+    end
+
+    def do_iteration
+
+      flagged1 = []
+
+      @im.each do |ic|
+
+        next if @im[ic] == 0
+
+        should_flag = pass1(ic)
+
+        if should_flag then
+          flagged1 << ImageCoordinate.cloneCoord(ic)
+        end
+
+      end
+
+      flagged1.each do |ic|
+
+        @im[ic]= 0
+
+        ic.recycle
+
+      end
+
+      flagged2 = []
+
+      @im.each do |ic|
+        
+        next if @im[ic] == 0
+
+        should_flag = pass2(ic)
+
+        if should_flag then
+
+          flagged2 << ImageCoordinate.cloneCoord(ic)
+
+        end
+
+      end
+
+      flagged2.each do |ic|
+        
+        @im[ic]= 0
+
+        ic.recycle
+
+      end
+
+      changed = (not (flagged1.empty? and flagged2.empty?))
+
+      changed
+
+    end
+
+    def skeletonize
+
+      while do_iteration do
+        
+      end
+
+    end
+
+
+  end
+
+end
+

data/lib/rimageanalysistools/thread_queue.rb

@@ -0,0 +1,140 @@
+#--
+# /* ***** BEGIN LICENSE BLOCK *****
+#  * 
+#  * Copyright (c) 2012 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.
+#  * 
+#  * ***** END LICENSE BLOCK ***** */
+#++
+
+
+module RImageAnalysisTools
+
+  class ThreadQueue
+    
+    def self.new_scope_with_vars(*args)
+      
+      yield *args
+      
+    end
+
+    def initialize
+      @threads = Array.new
+      @waiting = Array.new
+      @mut = Mutex.new
+      @max_threads = 4
+      @running = false
+      @results = []
+    end
+    
+    attr_reader :running
+
+    def enqueue(&b)
+
+      @mut.synchronize do
+        @waiting << b
+      end
+
+    end
+    
+    def start_queue
+      
+      return nil if @running
+      
+      @running = true
+      
+      Thread.new do 
+        
+        until empty? do
+          
+          run_thread_if_space
+        
+          sleep 0.2
+        
+        end
+        
+        @running = false
+        
+      end
+      
+    end
+
+    def run_thread_if_space
+      
+      @mut.synchronize do 
+        while (not @threads.size >= @max_threads) and (not @waiting.empty?) do
+          next_task = @waiting.pop
+          @threads << Thread.new(next_task) do |task| 
+            task.call
+          end
+        end
+      end
+
+    end
+
+    def remove_completed_threads
+
+      dead = Array.new
+
+      @threads.each do |t|
+        if not t.alive? then
+          dead << t
+        end
+      end
+
+      @mut.synchronize do
+        dead.each do |d|
+          @results << d.value
+          @threads.delete(d)
+        end
+      end
+                  
+    end
+
+    def finish
+      until empty? do
+        remove_completed_threads
+        sleep 0.5
+      end
+      @results 
+    end
+
+
+
+    attr_accessor :max_threads 
+    
+    def has_running_threads?
+      remove_completed_threads
+      not @threads.empty?
+    end
+    
+    
+    def empty?
+      @mut.synchronize do
+        @threads.empty? and @waiting.empty?
+      end
+    end
+
+  end
+
+end
+
+
+