cicada 0.9.0-java

data/lib/cicada/mutable_matrix.rb

@@ -0,0 +1,133 @@
+#--
+# /* ***** 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 'matrix'
+
+##
+# Extension to the standard library Matrix class making them mutable.
+#
+#class MMatrix < Matrix #disabled until the bug fix for the issue in the standard library that prevents useful subclasses is released
+
+class MMatrix < Matrix
+end
+
+class Matrix 
+  ##
+  # Replaces a row in this matrix by copying the entries from another vector.
+  # 
+  # @param [Integer] i the index of the row to replace
+  # @param [Vector, Array] other the vector or array whose contents will be copied
+  #  to the specified row.
+  #
+  def replace_row(i, other)
+
+    column_size.times do |j|
+
+      self[i, j]= other[j]
+
+    end
+
+  end
+
+  ##
+  # Replaces a column in this matrix by copying the entries from another vector.
+  # 
+  # @param [Integer] j the index of the column to replace
+  # @param [Vector, Array] other the vector or array whose contents will be copied
+  #  to the specified column.
+  #
+  def replace_column(j, other)
+
+    row_size.times do |i|
+
+      self[i, j]= other[i]
+
+    end
+
+  end
+  
+  public :[]=
+
+end
+
+##
+# Extension to the standard library Vector class making them mutable and adding 
+# some additional functionality.
+#
+class MVector < Vector
+
+  ##
+  # Generates a zero vector of specified size.
+  #
+  # @param [Integer] size the size of the zero vector
+  #
+  # @return [MVector] a mutable vector of specified size containing all 0.0
+  #
+  def MVector.zero(size)
+
+    elements(Array.new(size, 0.0), false)
+
+  end
+
+  ##
+  # Generates a unit vector of specified size.
+  #
+  # @param [Integer] size the size of the unit vector
+  # 
+  # @return [MVector] a mutable vector of specified size containing all 1.0
+  #
+  def MVector.unit(size)
+
+    MVector.elements(Array.new(size, 1.0), false)
+
+  end
+
+  ##
+  # Replaces the contents of this vector with the contents of another vector.  This will not
+  # change the size of the current vector and will replace entries only up to the current size.
+  #
+  # @param [Vector<Numeric>, Array<Numeric>] other a vector (or array, or other indexable 
+  #  collection) with at least as many elements as this vector; its entries will replace
+  #  this vector's entries
+  #
+  # @return [void]
+  #
+  def replace(other)
+
+    self.each_with_index do |e,i|
+
+      self[i] = other[i]
+    
+    end
+
+  end
+
+
+  public :[]=
+
+
+end
+

data/lib/cicada/version.rb

@@ -0,0 +1,33 @@
+#--
+# /* ***** 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 ***** */
+#++
+
+module Cicada
+
+  VERSION = "0.9.0"
+
+end
+
+

data/spec/cicada/correction/correction_spec.rb

@@ -0,0 +1,114 @@
+#--
+# /* ***** 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 'cicada/correction/correction'
+
+require 'spec_helper'
+
+describe Cicada::Correction do
+
+  XY_SIZE_NM = 80.0
+  Z_SIZE_NM = 100.0
+
+  DISTANCE_CONVERSIONS = Vector[XY_SIZE_NM, XY_SIZE_NM, Z_SIZE_NM]
+  
+  def expected_aberr(x,y)
+
+    x_aberr = (1024 - (x)*4 -1)*0.01/80.0/4
+    y_aberr = (1024 - (y)*4 -1)*0.01/80.0/4
+    z_aberr = (((x)*4+1)*0.04 + (1024 - (y)*4-1)*0.04)/100.0/2
+
+    Vector[x_aberr, y_aberr, z_aberr]
+
+  end
+
+  def get_diff_from_expected(x_test, y_test, c)
+    
+    corr = c.correct_position(x_test, y_test)
+
+    exp = expected_aberr(x_test, y_test)
+
+    corr = corr.map2(DISTANCE_CONVERSIONS) { |e1, e2| e1*e2 }
+
+    exp = exp.map2(DISTANCE_CONVERSIONS) { |e1, e2| e1*e2 }
+
+    (corr - exp).norm
+
+  end
+
+  it "should calculate the right correction given a position" do
+
+    c = Cicada::Correction.read_from_file(CORR_FN)
+
+    x = [99.75, 20.0, 122.0, 37.98, 200.0, 223.44]
+    y = [54.75, 90.0, 220.0, 77.43, 189.0, 120.30]
+
+    expected_error = [1.671, 
+                      1.103,
+                      0.459,
+                      1.286,
+                      1.243,
+                      2.385] #values based on java implementation
+
+
+    allowed_error = 0.001
+
+    diffs = []
+
+    x.each_index do |i|
+
+      diffs << get_diff_from_expected(x[i], y[i], c)
+
+    end
+
+    remaining_error = expected_error.ewise - diffs
+
+    remaining_error.map! { |e| e.abs }
+
+    remaining_error.each do |e|
+
+      e.should be < allowed_error
+
+    end
+    
+  end
+
+
+  it "should be the same after writing to and reading from XML" do
+
+    c = Cicada::Correction.read_from_file(CORR_FN)
+
+    xml_string = c.write_to_xml
+    
+    ref_string = Cicada::Correction.read_from_xml(xml_string).write_to_xml
+  
+    xml_string.should == ref_string
+
+  end
+
+
+end
+

data/spec/cicada/correction/position_corrector_spec.rb

@@ -0,0 +1,169 @@
+#--
+# /* ***** 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 'spec_helper'
+
+require 'cicada/correction/position_corrector'
+require 'cicada/cicada_main'
+
+require 'rimageanalysistools/create_parameters'
+
+require 'ostruct'
+
+describe Cicada::PositionCorrector do 
+  
+  before :each do 
+
+    @p = {reference_channel: 0, channel_to_correct: 1, half_box_size: 3, half_z_size: 5, pixelsize_nm: 80, z_sectionsize_nm: 100, num_points: 36, num_wavelengths: 3, log_detailed_messages: true, max_threads: 10, photons_per_greylevel: 0.125, determine_correction: true, fit_error_cutoff: 10, correct_images: true}
+
+  end
+
+  it "should generate a correction correctly" do
+
+    pc = Cicada::PositionCorrector.new(@p)
+
+    iobjs = load_iobjs
+
+    c = pc.generate_correction(iobjs)
+   
+    xml_string = c.write_to_xml
+
+    c_ref = load_correction
+
+    ref_string = c_ref.write_to_xml
+
+    xml_string.should == ref_string
+
+  end
+
+
+  it "should be able to correct image objects" do
+
+    iobjs = load_iobjs
+
+    iobjs_orig = iobjs
+
+    iobjs = iobjs.select { |e| e.getLabel % 10 == 0 }
+
+    pc = Cicada::PositionCorrector.new(@p)
+
+    c = load_correction
+
+    diffs = pc.apply_correction(c, iobjs)
+    
+    expected = [0.9648537061749035,
+                0.5709395379024668,
+                0.8858793228753269,
+                1.0188179855284514,
+                0.9905469052645519,
+                1.5904787247607233,
+                0.7160781864125757,
+                0.6880017962144355,
+                0.6415597673221431] #this is based on matching values to the java implementation
+
+    expected.each_index do |i|
+
+      expected[i].should == diffs[i]
+
+    end
+   
+  end
+
+
+  it "should correctly calculate the target registration error (TRE)" do
+
+    pc = Cicada::PositionCorrector.new(@p)
+
+    tre = pc.determine_tre(load_iobjs)
+
+    expected_tre = 1.407 #value from java implementation
+
+    allowed_error = 0.001
+
+    (tre - expected_tre).abs.should be < allowed_error
+
+  end
+
+  it "should be able to calculate coefficients for the in situ correction" do
+
+    @p[:correct_images] = false
+    @p[:channel_to_correct] = 2
+    @p[:in_situ_aberr_corr_channel] = 1
+
+    pc = Cicada::PositionCorrector.new(@p)
+
+    corr = pc.generate_in_situ_correction_from_iobjs(load_iobjs)
+
+    x_corr = corr[0]
+    y_corr = corr[1]
+    z_corr = corr[2]
+
+    #these values match the java implementation; input values for image generation (pre-noise) were 1.32 slope and 0.05625 x,y intercept and 0.1125 z intercept
+    expected_x = [1.28, 0.057]
+    expected_y = [1.15, 0.058]
+    expected_z = [1.32, 0.119]
+
+    allowed_err = [0.01, 0.001]
+
+    (expected_x[0] - x_corr[0]).abs.should be < allowed_err[0]
+    (expected_x[1] - x_corr[1]).abs.should be < allowed_err[1]
+    (expected_y[0] - y_corr[0]).abs.should be < allowed_err[0]
+    (expected_y[1] - y_corr[1]).abs.should be < allowed_err[1]
+    (expected_z[0] - z_corr[0]).abs.should be < allowed_err[0]
+    (expected_z[1] - z_corr[1]).abs.should be < allowed_err[1]
+
+  end
+
+  
+  it "should be able to apply the in situ correction" do 
+    
+    @p[:correct_images] = false
+    @p[:channel_to_correct] = 2
+    @p[:in_situ_aberr_corr_channel] = 1
+
+    pc = Cicada::PositionCorrector.new(@p)
+
+    corr = pc.generate_in_situ_correction_from_iobjs(load_iobjs)
+
+    corrected = pc.apply_in_situ_correction(load_iobjs, corr)
+
+    corrected.map! { |c| pc.apply_scale(c) }
+
+    averages = [0, 0, 0]
+
+    averages = corrected.reduce(averages) { |a, e| a.ewise + e.to_a }
+
+    averages.map! { |e| e/corrected.length }
+
+    Vector[*averages].norm.should be < 0.5
+
+  end
+    
+  
+
+
+end
+