rimageanalysistools 5.1.2-java
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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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java_import Java::edu.stanford.cfuller.imageanalysistools.image.io.ImageReader
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module RImageAnalysisTools
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def self.get_image(filename)
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ir = ImageReader.new
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ir.read(filename)
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end
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def self.read_image_directory(dirname)
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ir = ImageReader.new
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images = []
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Dir.foreach(dirname) do |f|
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images << ir.read(File.expand_path(f, dirname))
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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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module RImageAnalysisTools
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##
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# Thresholds the values in an array according to Otsu's method (Otsu, 1979, DOI: 10.1109/TSMC.1979.4310076).
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# @param [Array] arr an array (1-D) containing the values to be thresholded.
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# @return [Numeric] the threshold value; values <= to this number are below the threshold.
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#
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def self.graythresh(arr)
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num_steps = 1000.0
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min = arr.reduce(Float::MAX) { |a,e| e < a ? e : a }
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max = arr.reduce(-1.0*Float::MAX) { |a,e| e > a ? e : a }
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mean = arr.reduce(0.0) { |a,e| a + e } / arr.length
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sorted = arr.sort
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step_size = (max - min)/(num_steps)
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best_eta = 0.0
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best_threshold_value = 0.0
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counts_upto_k = 0
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mu = 0
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min.step(max, step_size) do |k|
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last_count_upto_k = counts_upto_k
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last_count_upto_k.upto(sorted.length-1) do |i|
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if sorted[i] > k then
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break
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end
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counts_upto_k += 1
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mu += sorted[i]*1.0/sorted.length
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end
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omega = counts_upto_k*1.0 / sorted.length
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eta = omega*(1-omega) * ((mean - mu)/(1-omega) - mu/omega)**2
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if eta > best_eta then
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best_eta = eta
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best_threshold_value = k
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end
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end
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best_threshold_value
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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 ImageWriter
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java_import Java::loci.formats.ImageWriter
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java_import Java::ome.xml.model.enums.DimensionOrder
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java_import Java::ome.xml.model.enums.PixelType
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java_import Java::loci.formats.FormatTools
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java_import Java::java.nio.ByteBuffer
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def initialize
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end
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def write(filename, image_to_write)
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wr = ImageWriter.new
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m = image_to_write.getMetadata
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pixels = image_to_write.getPixelData
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pixel_array = pixels.toImagePlus.getProcessor.getPixels
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m.setPixelsDimensionOrder(DimensionOrder.fromString(pixels.getDimensionOrder.upcase), 0)
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m.setPixelsType(PixelType.fromString(FormatTools.getPixelTypeString(pixels.getDataType)), 0)
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wr.setMetadataRetrieve(m)
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File.unlink(filename) if File.exist?(filename)
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wr.setId(filename)
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pixels.getNumPlanes.times do |i|
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c = i % pixels::size_c
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z = ((i - c)/pixels::size_c) % pixels::size_z
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t = (i - c - pixels::size_c * z)/(pixels::size_z * pixels::size_c)
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conv_index = pixels.toImagePlus.getStackIndex(c+1, z+1, t+1)
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pixels.toImagePlus.setSliceWithoutUpdate(conv_index)
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pixelData = pixels.toImagePlus.getProcessor.getPixels
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size_to_allocate = pixels::size_x * pixels::size_y * FormatTools.getBytesPerPixel(pixels::dataType)
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out = ByteBuffer.allocate(size_to_allocate)
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out.asFloatBuffer.put(pixelData)
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wr.savePlane(i, out.array)
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end
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wr.close
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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.image.ReadOnlyImageImpl
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java_import Java::edu.stanford.cfuller.imageanalysistools.image.WritableImageImpl
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java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageCoordinate
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class ReadOnlyImageImpl
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def [](ic)
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getValue(ic)
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end
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end
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class WritableImageImpl
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def []=(ic, value)
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setValue(ic, value)
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end
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end
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class ImageCoordinate
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Lookups = {x: X, y: Y, z: Z, c: C, t: T}
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def [](dim)
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get(Lookups[dim])
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end
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def []=(dim, value)
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set(Lookups[dim], value)
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end
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def self.[](*values)
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createCoordXYZCT(*values)
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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 'java'
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require 'ImageAnalysisTools.jar'
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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/method/method'
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java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageFactory
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java_import Java::edu.stanford.cfuller.imageanalysistools.metric.IntensityPerPixelMetric
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java_import Java::edu.stanford.cfuller.imageanalysistools.filter.LocalMaximumSeparabilityThresholdingFilter
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java_import Java::edu.stanford.cfuller.imageanalysistools.filter.LabelFilter
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java_import Java::edu.stanford.cfuller.imageanalysistools.filter.RecursiveMaximumSeparabilityFilter
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java_import Java::edu.stanford.cfuller.imageanalysistools.filter.RelabelFilter
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java_import Java::edu.stanford.cfuller.imageanalysistools.filter.SizeAbsoluteFilter
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java_import Java::edu.stanford.cfuller.imageanalysistools.filter.RenormalizationFilter
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java_import Java::edu.stanford.cfuller.imageanalysistools.filter.BandpassFilter
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module RImageAnalysisTools
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class CentromereFindingMethod < Method
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def centromere_finding(im)
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im = ImageFactory.createWritable(im)
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filters = []
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filters << LocalMaximumSeparabilityThresholdingFilter.new
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filters << LabelFilter.new
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filters << RecursiveMaximumSeparabilityFilter.new
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filters << RelabelFilter.new
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filters << SizeAbsoluteFilter.new
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filters << RelabelFilter.new
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filters.each do |f|
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f.setParameters(parameters)
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f.setReferenceImage(input_images.getMarkerImage)
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f.apply(im)
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end
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im
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end
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def normalize_input_image(im)
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rnf = RenormalizationFilter.new
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rnf.setParameters(parameters)
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rnf.apply(im)
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end
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def go
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mask = ImageFactory.createWritable(input_images.getMarkerImage)
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normalize_input_image(mask)
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bf = BandpassFilter.new
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bf.setParameters(parameters)
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band_lower = 3.0
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band_upper = 4.0
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bf.setBand(band_lower, band_upper)
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bf.apply(mask)
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mask = centromere_finding(mask)
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m = IntensityPerPixelMetric.new
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q = m.quantify(mask, input_images)
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self.quantification= q
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mask
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end
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end
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end
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