rimageanalysistools 5.1.2-java

data/lib/rimageanalysistools/get_image.rb

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+#--
+# /* ***** 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.image.io.ImageReader
+
+module RImageAnalysisTools
+    
+  def self.get_image(filename)
+    
+    ir = ImageReader.new
+    
+    ir.read(filename)
+        
+  end
+
+  def self.read_image_directory(dirname)
+
+    ir = ImageReader.new
+
+    images = []
+
+    Dir.foreach(dirname) do |f|
+
+      images << ir.read(File.expand_path(f, dirname))
+  
+    end
+    
+  end
+
+end

data/lib/rimageanalysistools/graythresh.rb

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+#--
+# /* ***** 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
+
+  ##
+  # Thresholds the values in an array according to Otsu's method (Otsu, 1979, DOI: 10.1109/TSMC.1979.4310076).
+  # @param [Array] arr an array (1-D) containing the values to be thresholded.
+  # @return [Numeric] the threshold value; values <= to this number are below the threshold.
+  #
+  def self.graythresh(arr)
+
+    num_steps = 1000.0
+
+    min = arr.reduce(Float::MAX) { |a,e| e < a ? e : a }
+    max = arr.reduce(-1.0*Float::MAX) { |a,e| e > a ? e : a }
+    mean = arr.reduce(0.0) { |a,e| a + e } / arr.length
+
+    sorted = arr.sort
+
+    step_size = (max - min)/(num_steps)
+
+    best_eta = 0.0
+    best_threshold_value = 0.0
+
+    counts_upto_k = 0
+
+    mu = 0
+
+    min.step(max, step_size) do |k|
+
+      last_count_upto_k = counts_upto_k
+
+      last_count_upto_k.upto(sorted.length-1) do |i|
+
+        if sorted[i] > k then
+          break
+        end
+
+        counts_upto_k += 1
+        mu += sorted[i]*1.0/sorted.length
+
+      end
+
+      omega = counts_upto_k*1.0 / sorted.length
+
+      eta = omega*(1-omega) * ((mean - mu)/(1-omega) - mu/omega)**2
+
+      if eta > best_eta then
+        best_eta = eta
+        best_threshold_value = k
+      end
+
+    end
+
+    best_threshold_value
+
+  end
+
+end

data/lib/rimageanalysistools/image/io/image_writer.rb

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+#--
+# /* ***** 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 ImageWriter
+
+    java_import Java::loci.formats.ImageWriter
+    java_import Java::ome.xml.model.enums.DimensionOrder
+    java_import Java::ome.xml.model.enums.PixelType
+    java_import Java::loci.formats.FormatTools
+    java_import Java::java.nio.ByteBuffer
+
+
+    def initialize
+      
+    end
+
+    def write(filename, image_to_write)
+
+      wr = ImageWriter.new
+
+      m = image_to_write.getMetadata
+
+      pixels = image_to_write.getPixelData
+
+      pixel_array = pixels.toImagePlus.getProcessor.getPixels
+
+      m.setPixelsDimensionOrder(DimensionOrder.fromString(pixels.getDimensionOrder.upcase), 0)
+
+      m.setPixelsType(PixelType.fromString(FormatTools.getPixelTypeString(pixels.getDataType)), 0)
+
+      wr.setMetadataRetrieve(m)
+
+      File.unlink(filename) if File.exist?(filename)
+
+      wr.setId(filename)
+
+      pixels.getNumPlanes.times do |i|
+
+        c = i % pixels::size_c
+        z = ((i - c)/pixels::size_c) % pixels::size_z
+        t = (i - c - pixels::size_c * z)/(pixels::size_z * pixels::size_c)
+
+        conv_index = pixels.toImagePlus.getStackIndex(c+1, z+1, t+1)
+
+        pixels.toImagePlus.setSliceWithoutUpdate(conv_index)
+        pixelData = pixels.toImagePlus.getProcessor.getPixels
+
+        size_to_allocate = pixels::size_x * pixels::size_y * FormatTools.getBytesPerPixel(pixels::dataType)
+
+        out = ByteBuffer.allocate(size_to_allocate)
+    
+        out.asFloatBuffer.put(pixelData)
+
+        wr.savePlane(i, out.array)
+  
+      end
+
+      wr.close
+
+    end
+
+  end
+
+end
+
+
+
+
+

data/lib/rimageanalysistools/image_shortcuts.rb

@@ -0,0 +1,70 @@
+#--
+# /* ***** 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.image.ReadOnlyImageImpl
+java_import Java::edu.stanford.cfuller.imageanalysistools.image.WritableImageImpl
+java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageCoordinate
+
+class ReadOnlyImageImpl
+
+  def [](ic)
+    getValue(ic)
+  end
+  
+end
+
+class WritableImageImpl
+
+  def []=(ic, value)
+    setValue(ic, value)
+  end
+
+end
+
+class ImageCoordinate
+
+  Lookups = {x: X, y: Y, z: Z, c: C, t: T}
+
+  def [](dim)
+    get(Lookups[dim])
+  end
+
+  def []=(dim, value)
+    set(Lookups[dim], value)
+  end
+
+  def self.[](*values)
+
+    createCoordXYZCT(*values)
+
+  end
+
+end
+
+
+

data/lib/rimageanalysistools/initjava.rb

@@ -0,0 +1,34 @@
+#--
+# /* ***** 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 'java'
+require 'ImageAnalysisTools.jar'
+
+
+
+
+
+

data/lib/rimageanalysistools/method/centromere_finding_method.rb

@@ -0,0 +1,114 @@
+#--
+# /* ***** 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/method/method'
+
+java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageFactory
+java_import Java::edu.stanford.cfuller.imageanalysistools.metric.IntensityPerPixelMetric
+java_import Java::edu.stanford.cfuller.imageanalysistools.filter.LocalMaximumSeparabilityThresholdingFilter
+java_import Java::edu.stanford.cfuller.imageanalysistools.filter.LabelFilter
+java_import Java::edu.stanford.cfuller.imageanalysistools.filter.RecursiveMaximumSeparabilityFilter
+java_import Java::edu.stanford.cfuller.imageanalysistools.filter.RelabelFilter
+java_import Java::edu.stanford.cfuller.imageanalysistools.filter.SizeAbsoluteFilter
+java_import Java::edu.stanford.cfuller.imageanalysistools.filter.RenormalizationFilter
+java_import Java::edu.stanford.cfuller.imageanalysistools.filter.BandpassFilter
+
+module RImageAnalysisTools
+
+  class CentromereFindingMethod < Method
+  
+    def centromere_finding(im)
+
+      im = ImageFactory.createWritable(im)
+
+      filters = []
+
+      filters << LocalMaximumSeparabilityThresholdingFilter.new
+      filters << LabelFilter.new
+      filters << RecursiveMaximumSeparabilityFilter.new
+      filters << RelabelFilter.new
+      filters << SizeAbsoluteFilter.new
+      filters << RelabelFilter.new
+
+      filters.each do |f|
+
+        f.setParameters(parameters)
+        f.setReferenceImage(input_images.getMarkerImage)
+        f.apply(im)
+
+      end
+      
+      im
+
+    end
+
+    def normalize_input_image(im)
+
+      rnf = RenormalizationFilter.new
+      rnf.setParameters(parameters)
+      rnf.apply(im)
+
+    end
+    
+
+    def go
+      
+      mask = ImageFactory.createWritable(input_images.getMarkerImage)
+
+      normalize_input_image(mask)
+
+      bf = BandpassFilter.new
+      
+      bf.setParameters(parameters)
+
+      band_lower = 3.0
+      band_upper = 4.0
+
+      bf.setBand(band_lower, band_upper)
+
+      bf.apply(mask)
+
+      mask = centromere_finding(mask)
+
+      m = IntensityPerPixelMetric.new
+
+      q = m.quantify(mask, input_images)
+      
+      self.quantification= q
+
+      mask
+
+    end
+    
+    
+  end
+
+end
+    
+
+
+