rimageanalysistools 5.1.2-java
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- data/extlib/ImageAnalysisTools.jar +0 -0
- data/lib/rimageanalysistools.rb +33 -0
- data/lib/rimageanalysistools/centroids.rb +72 -0
- data/lib/rimageanalysistools/create_parameters.rb +61 -0
- data/lib/rimageanalysistools/dir_walker.rb +65 -0
- data/lib/rimageanalysistools/drawing.rb +158 -0
- data/lib/rimageanalysistools/fitting/bisquare_linear_fit.rb +45 -0
- data/lib/rimageanalysistools/get_filter.rb +43 -0
- data/lib/rimageanalysistools/get_image.rb +55 -0
- data/lib/rimageanalysistools/graythresh.rb +84 -0
- data/lib/rimageanalysistools/image/io/image_writer.rb +94 -0
- data/lib/rimageanalysistools/image_shortcuts.rb +70 -0
- data/lib/rimageanalysistools/initjava.rb +34 -0
- data/lib/rimageanalysistools/method/centromere_finding_method.rb +114 -0
- data/lib/rimageanalysistools/method/method.rb +38 -0
- data/lib/rimageanalysistools/simple_output.rb +74 -0
- data/lib/rimageanalysistools/skeletonizer.rb +250 -0
- data/lib/rimageanalysistools/thread_queue.rb +140 -0
- metadata +66 -0
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#--
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# /* ***** BEGIN LICENSE BLOCK *****
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# *
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# * Copyright (c) 2012 Colin J. Fuller
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# *
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# * Permission is hereby granted, free of charge, to any person obtaining a copy
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# * of this software and associated documentation files (the Software), to deal
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# * in the Software without restriction, including without limitation the rights
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# * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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# * copies of the Software, and to permit persons to whom the Software is
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# * furnished to do so, subject to the following conditions:
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# *
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# * The above copyright notice and this permission notice shall be included in
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# * all copies or substantial portions of the Software.
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# *
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# * THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# * SOFTWARE.
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# *
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# * ***** END LICENSE BLOCK ***** */
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#++
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require 'rimageanalysistools/initjava'
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require 'edu/stanford/cfuller/imageanalysistools/resources/common_methods'
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#--
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# /* ***** BEGIN LICENSE BLOCK *****
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# *
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# * Copyright (c) 2012 Colin J. Fuller
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# *
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# * Permission is hereby granted, free of charge, to any person obtaining a copy
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# * of this software and associated documentation files (the Software), to deal
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# * in the Software without restriction, including without limitation the rights
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# * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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# * copies of the Software, and to permit persons to whom the Software is
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# * furnished to do so, subject to the following conditions:
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# *
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# * The above copyright notice and this permission notice shall be included in
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# * all copies or substantial portions of the Software.
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# *
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# * THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# * SOFTWARE.
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# *
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# * ***** END LICENSE BLOCK ***** */
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#++
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require 'rimageanalysistools'
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require 'rimageanalysistools/image_shortcuts'
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java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageCoordinate
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module RImageAnalysisTools
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class Centroids
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def self.calculate_centroids_2d(mask)
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centroids = {}
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counts = {}
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mask.each do |ic|
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next unless mask[ic] > 0
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unless centroids[mask[ic]] then
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centroids[mask[ic]]= [0.0,0.0]
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counts[mask[ic]]= 0
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end
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centroids[mask[ic]][0]+= ic.get(ImageCoordinate::X)
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centroids[mask[ic]][1]+= ic.get(ImageCoordinate::Y)
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counts[mask[ic]]+= 1
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end
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centroids.each_key do |k|
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centroids[k].map! { |e| e/counts[k] }
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end
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centroids
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end
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end
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end
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#--
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# /* ***** BEGIN LICENSE BLOCK *****
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# *
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# * Copyright (c) 2012 Colin J. Fuller
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# *
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# * Permission is hereby granted, free of charge, to any person obtaining a copy
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# * of this software and associated documentation files (the Software), to deal
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# * in the Software without restriction, including without limitation the rights
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# * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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# * copies of the Software, and to permit persons to whom the Software is
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# * furnished to do so, subject to the following conditions:
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# *
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# * The above copyright notice and this permission notice shall be included in
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# * all copies or substantial portions of the Software.
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# *
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# * THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# * SOFTWARE.
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# *
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# * ***** END LICENSE BLOCK ***** */
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#++
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require 'rimageanalysistools/initjava'
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java_import Java::edu.stanford.cfuller.imageanalysistools.meta.parameters.ParameterDictionary
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class ParameterDictionary
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def [](key)
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getValueForKey(key.to_s)
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end
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def []=(key, value)
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setValueForKey(key.to_s, value.to_s)
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end
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end
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module RImageAnalysisTools
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def self.create_parameter_dictionary(parameter_hash)
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p = ParameterDictionary.emptyDictionary
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parameter_hash.each do |k,v|
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p[k]= v
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end
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p
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end
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end
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#--
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# /* ***** BEGIN LICENSE BLOCK *****
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# *
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# * Copyright (c) 2012 Colin J. Fuller
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# *
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# * Permission is hereby granted, free of charge, to any person obtaining a copy
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# * of this software and associated documentation files (the Software), to deal
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# * in the Software without restriction, including without limitation the rights
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# * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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# * copies of the Software, and to permit persons to whom the Software is
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# * furnished to do so, subject to the following conditions:
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# *
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# * The above copyright notice and this permission notice shall be included in
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# * all copies or substantial portions of the Software.
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# *
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# * THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# * SOFTWARE.
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# *
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# * ***** END LICENSE BLOCK ***** */
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#++
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module RImageAnalysisTools
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class DirWalker
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include Enumerable
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def initialize(base_path, exclude_hidden = true)
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@base_path = base_path
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@exclude_hidden = exclude_hidden
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end
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def each
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walk_path("") do |ext, f|
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yield @base_path + ext + f
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end
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end
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def walk_path(extra)
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Dir.foreach(@base_path + extra) do |f|
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if @exclude_hidden and f.start_with?(".") then
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next
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end
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if File.directory?(@base_path + extra + f) then
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walk_path(@base_path, extra + f + File::Separator) do |ext_rec, f_rec|
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yield ext_rec, f_rec
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end
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else
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yield extra, f
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end
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end
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end
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#--
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# /* ***** BEGIN LICENSE BLOCK *****
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# *
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# * Copyright (c) 2012 Colin J. Fuller
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# *
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# * Permission is hereby granted, free of charge, to any person obtaining a copy
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# * of this software and associated documentation files (the Software), to deal
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# * in the Software without restriction, including without limitation the rights
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# * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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# * copies of the Software, and to permit persons to whom the Software is
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# * furnished to do so, subject to the following conditions:
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# *
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# * The above copyright notice and this permission notice shall be included in
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# * all copies or substantial portions of the Software.
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# *
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# * THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# * SOFTWARE.
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# *
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# * ***** END LICENSE BLOCK ***** */
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#++
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require 'rimageanalysistools'
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require 'rimageanalysistools/image_shortcuts'
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java_import Java::edu.stanford.cfuller.imageanalysistools.image.ReadOnlyImageImpl
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class ReadOnlyImageImpl
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def box_conservative(lower, upper, dims)
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low_curr = nil
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up_curr = nil
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if getIsBoxed then
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low_curr = getBoxMin
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up_curr = getBoxMax
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else
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low_curr = ImageCoordinate[0,0,0,0,0]
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up_curr = ImageCoordinate.cloneCoord(getDimensionSizes)
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end
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dims.each do |d|
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low_curr[d]= lower[d]
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up_curr[d]= upper[d]
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end
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end
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end
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module RImageAnalysisTools
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class Drawing
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def draw(im, draw_value = 255.0)
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im.each do |ic|
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if (yield ic) then
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im.setValue(ic, draw_value)
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end
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end
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end
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def draw_shape(im, location, shape_name=:circle, shape_parameters= 10)
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if self.respond_to?(shape_name) then
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self.send(shape_name, im, location, shape_parameters)
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end
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end
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def circle(im, center, radius)
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lower = ImageCoordinate[center[0]-radius-1, center[1]-radius-1, 0,0,0]
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upper = ImageCoordinate[center[0]+radius+1, center[1]+radius+1, 0,0,0]
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im.box_conservative(lower, upper, [:x, :y])
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draw(im) do |ic|
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xdiff = ic[:x] - center[0]
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ydiff = ic[:y] - center[1]
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if (Math.hypot(xdiff, ydiff) - radius).abs <= Math.sqrt(2) then
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true
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else
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false
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end
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end
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lower.recycle
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upper.recycle
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end
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def ellipse(im, foci, radius_inc)
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min_x = foci[0][0]
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max_x = foci[1][0]
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min_y = foci[0][1]
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max_y = foci[1][1]
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if foci[1][0] < min_x then
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min_x = foci[1][0]
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max_x = foci[0][0]
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end
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if foci[1][1] < min_y then
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min_y = foci[1][1]
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max_y = foci[0][1]
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end
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radius = radius_inc + Math.hypot(max_x-min_x, max_y-min_y)
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lower = ImageCoordinate[min_x-radius-1, min_y-radius-1, 0,0,0]
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upper = ImageCoordinate[max_x+radius+1, max_y+radius+1, 0,0,0]
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im.box_conservative(lower, upper, [:x, :y])
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draw(im) do |ic|
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xdiff0 = ic[:x] - foci[0][0]
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ydiff0 = ic[:y] - foci[0][1]
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xdiff1 = ic[:x] - foci[1][0]
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ydiff1 = ic[:y] - foci[1][1]
|
143
|
+
|
144
|
+
if (Math.hypot(xdiff0, ydiff0) + Math.hypot(xdiff1, ydiff1) - radius).abs <= Math.sqrt(2) then
|
145
|
+
true
|
146
|
+
else
|
147
|
+
false
|
148
|
+
end
|
149
|
+
|
150
|
+
end
|
151
|
+
|
152
|
+
|
153
|
+
end
|
154
|
+
|
155
|
+
|
156
|
+
end
|
157
|
+
|
158
|
+
end
|
@@ -0,0 +1,45 @@
|
|
1
|
+
#--
|
2
|
+
# /* ***** BEGIN LICENSE BLOCK *****
|
3
|
+
# *
|
4
|
+
# * Copyright (c) 2013 Colin J. Fuller
|
5
|
+
# *
|
6
|
+
# * Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
+
# * of this software and associated documentation files (the Software), to deal
|
8
|
+
# * in the Software without restriction, including without limitation the rights
|
9
|
+
# * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
+
# * copies of the Software, and to permit persons to whom the Software is
|
11
|
+
# * furnished to do so, subject to the following conditions:
|
12
|
+
# *
|
13
|
+
# * The above copyright notice and this permission notice shall be included in
|
14
|
+
# * all copies or substantial portions of the Software.
|
15
|
+
# *
|
16
|
+
# * THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
17
|
+
# * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
18
|
+
# * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
19
|
+
# * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
20
|
+
# * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
21
|
+
# * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
22
|
+
# * SOFTWARE.
|
23
|
+
# *
|
24
|
+
# * ***** END LICENSE BLOCK ***** */
|
25
|
+
#++
|
26
|
+
|
27
|
+
require 'rimageanalysistools'
|
28
|
+
|
29
|
+
java_import Java::edu.stanford.cfuller.imageanalysistools.fitting.BisquareLinearFit
|
30
|
+
|
31
|
+
java_import Java::org.apache.commons.math3.linear.ArrayRealVector
|
32
|
+
|
33
|
+
class BisquareLinearFit
|
34
|
+
|
35
|
+
def fit_rb(x, y)
|
36
|
+
|
37
|
+
x_vec = ArrayRealVector.new(x.to_a.to_java(:double))
|
38
|
+
y_vec = ArrayRealVector.new(y.to_a.to_java(:double))
|
39
|
+
|
40
|
+
fit(x_vec, y_vec)
|
41
|
+
|
42
|
+
end
|
43
|
+
|
44
|
+
end
|
45
|
+
|
@@ -0,0 +1,43 @@
|
|
1
|
+
#--
|
2
|
+
# /* ***** BEGIN LICENSE BLOCK *****
|
3
|
+
# *
|
4
|
+
# * Copyright (c) 2012 Colin J. Fuller
|
5
|
+
# *
|
6
|
+
# * Permission is hereby granted, free of charge, to any person obtaining a copy
|
7
|
+
# * of this software and associated documentation files (the Software), to deal
|
8
|
+
# * in the Software without restriction, including without limitation the rights
|
9
|
+
# * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
+
# * copies of the Software, and to permit persons to whom the Software is
|
11
|
+
# * furnished to do so, subject to the following conditions:
|
12
|
+
# *
|
13
|
+
# * The above copyright notice and this permission notice shall be included in
|
14
|
+
# * all copies or substantial portions of the Software.
|
15
|
+
# *
|
16
|
+
# * THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
17
|
+
# * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
18
|
+
# * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
19
|
+
# * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
20
|
+
# * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
21
|
+
# * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
22
|
+
# * SOFTWARE.
|
23
|
+
# *
|
24
|
+
# * ***** END LICENSE BLOCK ***** */
|
25
|
+
#++
|
26
|
+
|
27
|
+
require 'rimageanalysistools/initjava'
|
28
|
+
java_import Java::edu.stanford.cfuller.imageanalysistools.filter.Filter
|
29
|
+
|
30
|
+
module RImageAnalysisTools
|
31
|
+
|
32
|
+
Filter_package_name = "edu.stanford.cfuller.imageanalysistools.filter."
|
33
|
+
|
34
|
+
def self.get_filter(filter_name)
|
35
|
+
|
36
|
+
java_import (Filter_package_name + filter_name.to_s)
|
37
|
+
|
38
|
+
const_get(filter_name).new
|
39
|
+
|
40
|
+
end
|
41
|
+
|
42
|
+
|
43
|
+
end
|