rimageanalysistools 5.1.2-java

data/lib/rimageanalysistools.rb

@@ -0,0 +1,33 @@
+#--
+# /* ***** 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'
+
+require 'edu/stanford/cfuller/imageanalysistools/resources/common_methods'
+
+
+
+

data/lib/rimageanalysistools/centroids.rb

@@ -0,0 +1,72 @@
+#--
+# /* ***** 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 Centroids
+
+    def self.calculate_centroids_2d(mask)
+
+      centroids = {}
+      counts = {}
+
+      mask.each do |ic|
+
+        next unless mask[ic] > 0
+
+        unless centroids[mask[ic]] then
+          
+          centroids[mask[ic]]= [0.0,0.0]
+          counts[mask[ic]]= 0
+
+        end
+
+        centroids[mask[ic]][0]+= ic.get(ImageCoordinate::X)
+        centroids[mask[ic]][1]+= ic.get(ImageCoordinate::Y)
+
+        counts[mask[ic]]+= 1
+
+      end
+
+      centroids.each_key do |k|
+
+        centroids[k].map! { |e| e/counts[k] }
+
+      end
+
+      centroids
+
+    end
+
+  end
+
+end
+

data/lib/rimageanalysistools/create_parameters.rb

@@ -0,0 +1,61 @@
+#--
+# /* ***** 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.meta.parameters.ParameterDictionary
+
+class ParameterDictionary
+
+  def [](key)
+    getValueForKey(key.to_s)
+  end
+
+  def []=(key, value)
+    setValueForKey(key.to_s, value.to_s)
+  end
+
+end
+
+module RImageAnalysisTools
+
+
+  def self.create_parameter_dictionary(parameter_hash)
+
+    p = ParameterDictionary.emptyDictionary
+
+    parameter_hash.each do |k,v|
+      p[k]= v
+    end
+
+    p
+
+  end
+
+
+
+end
+

data/lib/rimageanalysistools/dir_walker.rb

@@ -0,0 +1,65 @@
+#--
+# /* ***** 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 DirWalker
+    
+    include Enumerable
+    
+    def initialize(base_path, exclude_hidden = true)
+      
+      @base_path = base_path
+      @exclude_hidden = exclude_hidden
+      
+    end
+    
+    def each
+      
+      walk_path("") do |ext, f|
+        
+        yield @base_path + ext + f
+        
+      end
+      
+    end
+    
+    def walk_path(extra)
+
+      Dir.foreach(@base_path + extra) do |f|
+        if @exclude_hidden and f.start_with?(".") then
+          next
+        end
+        if File.directory?(@base_path + extra + f) then
+          walk_path(@base_path, extra + f + File::Separator) do |ext_rec, f_rec|
+            yield ext_rec, f_rec
+          end
+        else
+          yield extra, f
+        end
+      end
+
+    end

data/lib/rimageanalysistools/drawing.rb

@@ -0,0 +1,158 @@
+#--
+# /* ***** 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.ReadOnlyImageImpl
+
+class ReadOnlyImageImpl
+
+  def box_conservative(lower, upper, dims)
+
+    low_curr = nil
+    up_curr = nil
+
+    if getIsBoxed then
+
+      low_curr = getBoxMin
+      up_curr = getBoxMax
+
+    else
+
+      low_curr = ImageCoordinate[0,0,0,0,0]
+      up_curr = ImageCoordinate.cloneCoord(getDimensionSizes)
+
+    end
+
+    dims.each do |d|
+      low_curr[d]= lower[d]
+      up_curr[d]= upper[d]
+    end
+
+  end
+
+end
+
+module RImageAnalysisTools
+
+  class Drawing
+
+    def draw(im, draw_value = 255.0)
+
+      im.each do |ic|
+
+        if (yield ic) then
+
+          im.setValue(ic, draw_value)
+
+        end
+
+      end
+
+    end
+    
+    def draw_shape(im, location, shape_name=:circle, shape_parameters= 10)
+
+      if self.respond_to?(shape_name) then
+
+        self.send(shape_name, im, location, shape_parameters)
+
+      end
+
+    end
+    
+    def circle(im, center, radius)
+
+      lower = ImageCoordinate[center[0]-radius-1, center[1]-radius-1, 0,0,0]
+      upper = ImageCoordinate[center[0]+radius+1, center[1]+radius+1, 0,0,0]
+
+      im.box_conservative(lower, upper, [:x, :y])
+
+      draw(im) do |ic|
+        
+        xdiff = ic[:x] - center[0]
+        ydiff = ic[:y] - center[1]
+
+        if (Math.hypot(xdiff, ydiff) - radius).abs <= Math.sqrt(2) then
+          true
+        else
+          false
+        end
+
+      end
+
+      lower.recycle
+      upper.recycle
+        
+    end
+
+    def ellipse(im, foci, radius_inc)
+
+      min_x = foci[0][0]
+      max_x = foci[1][0]
+      min_y = foci[0][1]
+      max_y = foci[1][1]
+
+      if foci[1][0] < min_x then
+        min_x = foci[1][0]
+        max_x = foci[0][0]
+      end
+
+      if foci[1][1] < min_y then
+        min_y = foci[1][1]
+        max_y = foci[0][1]
+      end
+
+      radius = radius_inc + Math.hypot(max_x-min_x, max_y-min_y)
+      
+      lower = ImageCoordinate[min_x-radius-1, min_y-radius-1, 0,0,0]
+      upper = ImageCoordinate[max_x+radius+1, max_y+radius+1, 0,0,0]
+
+      im.box_conservative(lower, upper, [:x, :y])
+      
+      draw(im) do |ic|
+        
+        xdiff0 = ic[:x] - foci[0][0]
+        ydiff0 = ic[:y] - foci[0][1]
+        xdiff1 = ic[:x] - foci[1][0]
+        ydiff1 = ic[:y] - foci[1][1]
+
+        if (Math.hypot(xdiff0, ydiff0) + Math.hypot(xdiff1, ydiff1) - radius).abs <= Math.sqrt(2) then
+          true
+        else
+          false
+        end
+
+      end
+
+
+    end
+    
+
+  end
+
+end

data/lib/rimageanalysistools/fitting/bisquare_linear_fit.rb

@@ -0,0 +1,45 @@
+#--
+# /* ***** BEGIN LICENSE BLOCK *****
+#  * 
+#  * 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.
+#  * 
+#  * ***** END LICENSE BLOCK ***** */
+#++
+
+require 'rimageanalysistools'
+
+java_import Java::edu.stanford.cfuller.imageanalysistools.fitting.BisquareLinearFit
+
+java_import Java::org.apache.commons.math3.linear.ArrayRealVector
+
+class BisquareLinearFit
+
+  def fit_rb(x, y)
+
+    x_vec = ArrayRealVector.new(x.to_a.to_java(:double))
+    y_vec = ArrayRealVector.new(y.to_a.to_java(:double))
+
+    fit(x_vec, y_vec)
+
+  end
+
+end
+

data/lib/rimageanalysistools/get_filter.rb

@@ -0,0 +1,43 @@
+#--
+# /* ***** 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.filter.Filter
+
+module RImageAnalysisTools
+  
+  Filter_package_name = "edu.stanford.cfuller.imageanalysistools.filter."
+  
+  def self.get_filter(filter_name)
+    
+    java_import (Filter_package_name + filter_name.to_s)
+    
+    const_get(filter_name).new
+        
+  end
+  
+  
+end