Module: RImageAnalysisTools

Defined in:
lib/rimageanalysistools/image/io/image_writer.rb,
lib/rimageanalysistools/drawing.rb,
lib/rimageanalysistools/centroids.rb,
lib/rimageanalysistools/get_image.rb,
lib/rimageanalysistools/get_filter.rb,
lib/rimageanalysistools/graythresh.rb,
lib/rimageanalysistools/skeletonizer.rb,
lib/rimageanalysistools/thread_queue.rb,
lib/rimageanalysistools/method/method.rb,
lib/rimageanalysistools/simple_output.rb,
lib/rimageanalysistools/create_parameters.rb,
lib/rimageanalysistools/image/io/url_image_reader.rb,
lib/rimageanalysistools/method/centromere_finding_method.rb

Overview

– /* ***** 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 ***** */

++

Defined Under Namespace

Modules: Centroids Classes: CentromereFindingMethod, Drawing, ImageWriter, Method, Skeletonizer, ThreadQueue, URLImageReader

Constant Summary collapse

Filter_package_name = 
"edu.stanford.cfuller.imageanalysistools.filter."
IM_OUTPUT_DIR = 
"output_images"
QUANT_OUTPUT_DIR = 
"quantification"

Class Method Summary collapse

Class Method Details

.create_parameter_dictionary(parameter_hash) ⇒ ParameterDictionary

Creates a ParameterDictionary from a hash of parameters.

Parameters:

  • parameter_hash (Hash) —

    a hash mapping parameters to values

Returns:



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# File 'lib/rimageanalysistools/create_parameters.rb', line 73

def self.create_parameter_dictionary(parameter_hash)

  p = ParameterDictionary.emptyDictionary

  parameter_hash.each do |k,v|
    p[k]= v
  end

  p

end

.get_filter(filter_name) ⇒ Object 



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# File 'lib/rimageanalysistools/get_filter.rb', line 34

def self.get_filter(filter_name)
  
  java_import (Filter_package_name + filter_name.to_s)
  
  const_get(filter_name).new
      
end

.get_image(filename) ⇒ Object 



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# File 'lib/rimageanalysistools/get_image.rb', line 35

def self.get_image(filename)

  ir = nil

  if filename.is_a? URI then
    ir = URLImageReader.new
  else
    ir = ImageReader.new
  end
  
  ir.read(filename)
      
end

.graythresh(arr) ⇒ Numeric

Thresholds the values in an array according to Otsu’s method (Otsu, 1979, DOI: 10.1109/TSMC.1979.4310076).

Parameters:

  • arr (Array) —

    an array (1-D) containing the values to be thresholded.

Returns:

  • (Numeric) —

    the threshold value; values <= to this number are below the threshold.



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# File 'lib/rimageanalysistools/graythresh.rb', line 35

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

  return min if step_size == 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

.handle_output(original_filename, output_image, quant) ⇒ Object 



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# File 'lib/rimageanalysistools/simple_output.rb', line 36

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

.read_image_directory(dirname) ⇒ Object 



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# File 'lib/rimageanalysistools/get_image.rb', line 49

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