cicada 0.9.4-java → 0.9.5-java

data/lib/cicada/correction/unable_to_correct_error.rb

@@ -0,0 +1,30 @@
+#--
+# 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.
+#++
+
+module Cicada
+  ##
+  # An error indicating that a position cannot be corrected (possibly due to incomplete
+  # coverage in the correction dataset).
+  class UnableToCorrectError < StandardError
+  end
+end
+

data/lib/cicada/file_interaction.rb

@@ -55,28 +55,18 @@ module Cicada
     #  image objects.
     #
     def self.serialize_image_objects(image_objects)
-
       doc = REXML::Document.new
-
-
       doc.add_element "root"
 
       image_objects.each do |iobj|
-
         in_doc = REXML::Document.new iobj.writeToXMLString
-
         in_doc.root.elements[1, "serialized_form"].text = Base64.encode64(Marshal.dump(iobj))
-
         doc.root.add in_doc.elements[1,"image_object"]
-
       end
 
       output = ""
-
       doc.write(output, 2)
-
       output
-
     end
 
     ##
@@ -89,15 +79,7 @@ module Cicada
     # @return [ImageObject] the encoded ImageObject
     #
     def self.image_object_from_bytes(bin_data)
-
       Marshal.load(bin_data)
-
-      #j_bytes = bin_data.to_java_bytes
-
-      #oi = Java::java.io.ObjectInputStream.new(Java::java.io.ByteArrayInputStream.new(j_bytes))
-
-      #oi.readObject
-
     end
 
     ##
@@ -109,23 +91,16 @@ module Cicada
     # @return [Array<ImageObject>] the image objects encoded in the string
     #
     def self.unserialize_image_objects(data)
-
       objs = []
-
       doc = REXML::Document.new data
 
       doc.elements.each("*/image_object/serialized_form") do |el|
-
         bin_data = Base64.decode64(el.text)
-
         objs << image_object_from_bytes(bin_data)
-
       end
 
       objs
-
     end
-
   end
 
 
@@ -133,7 +108,6 @@ module Cicada
   # A collection of methods for interacting with input and output files for cicada.
   # 
   class FileInteraction
-
     # parameters required by the methods in this class
     REQUIRED_PARAMETERS = [:dirname_set, :basename_set, :mask_relative_dirname, :mask_extra_extension, :data_directory, :correction_date, :output_positions_to_directory]
 
@@ -155,7 +129,6 @@ module Cicada
     # separator used in the parameter file for multiple files, directories, etc.
     MULTI_NAME_SEP = ","
 
-
     ##
     # Loads an image from the specified file.
     #
@@ -164,12 +137,9 @@ module Cicada
     # @return [ReadOnlyImage] the image at the specified filename
     #
     def self.load_image(image_fn)
-
       RImageAnalysisTools.get_image(image_fn)
-
     end
 
-
     ##
     # Gets the filename to which / from which image object positions will be written / 
     # read from a parameter dictionary.
@@ -182,7 +152,6 @@ module Cicada
       File.expand_path(p[:basename_set].split(MULTI_NAME_SEP)[0] + POS_XML_EXTENSION, dir)
     end
 
-
     ##
     # Gets the filename to which human-friendly-formatted object positions will be written.
     #
@@ -195,7 +164,6 @@ module Cicada
       File.expand_path(p[:basename_set].split(MULTI_NAME_SEP)[0] + POS_HUMAN_EXTENSION, dir)
     end
 
-
     ##
     # Gets the filename of data to use for in situ correction from a parameter dictionary.
     #
@@ -205,7 +173,7 @@ module Cicada
     # @return [String] the absolute path to the in situ correction data file
     #
     def self.in_situ_corr_data_filename(p)
-      dir = [:data_directory]
+      dir = p[:data_directory]
       File.expand_path(p[:in_situ_aberr_corr_basename_set].split(MULTI_NAME_SEP)[0] + POS_XML_EXTENSION, dir)
     end
 
@@ -229,15 +197,11 @@ module Cicada
     # @return [Array<ImageObject>] the image objects contained in the file.
     #
     def self.unserialize_position_data_file(fn)
-
       data_str = nil
-
       File.open(fn) do |f|
         data_str = f.read
       end
-
       Serialization.unserialize_image_objects(data_str)
-
     end
 
     ##
@@ -248,11 +212,8 @@ module Cicada
     # @return [Array<ImageObject>] the image objects associated with the analysis
     #
     def self.read_position_data(p)
-      
       fn = FileInteraction.position_data_filename(p)
-
       FileInteraction.unserialize_position_data_file(fn)
-
     end
 
     ##
@@ -265,11 +226,8 @@ module Cicada
     # @return [Array<ImageObject>] the image objects for in situ correction associated with the analysis
     #
     def self.read_in_situ_corr_data(p)
-
       fn = FileInteraction.in_situ_corr_data_filename(p)
-
       FileInteraction.unserialize_position_data_file(fn)
-
     end
 
     ##
@@ -281,35 +239,22 @@ module Cicada
     #  which return each image's filename and its paired mask's filename respectively.
     #
     def self.list_files(p)
-
       dirnames = p[:dirname_set].split(MULTI_NAME_SEP)
       basenames = p[:basename_set].split(MULTI_NAME_SEP)
-
       image_sets = []
 
       dirnames.each do |d|
-
         mask_dirname = File.join(d, p[:mask_relative_dirname])
-
         Dir.foreach(d) do |f|
-
-          if basenames.any? { |e| f.match(e) } then
-            
+          if basenames.any? { |e| f.match(e) } then    
             im = File.expand_path(f, d)
             msk = File.expand_path(f + p[:mask_extra_extension], mask_dirname)
-
-            current = OpenStruct.new(image_fn: im, mask_fn: msk)
-            
+            current = OpenStruct.new(image_fn: im, mask_fn: msk)    
             image_sets << current
-
           end          
-
         end
-
-      end
-      
+      end    
       image_sets
-
     end
 
     ##
@@ -321,15 +266,10 @@ module Cicada
     # @return [void]
     #
     def self.write_position_data(image_objects, p)
-
       fn = position_data_filename(p)
-      
       write_position_data_file(image_objects,fn)
-
       fn2 = human_friendly_position_data_filename(p)
-
-      write_human_friendly_position_data_file(image_objects, fn2)      
-
+      write_human_friendly_position_data_file(image_objects, fn2)
     end
 
     ##
@@ -341,13 +281,9 @@ module Cicada
     # @return [void]
     #
     def self.write_position_data_file(image_objects, fn)
-
       File.open(fn, 'w') do |f|
-
         f.write(Serialization.serialize_image_objects(image_objects))
-
       end
-
     end
 
     ##
@@ -357,39 +293,25 @@ module Cicada
     # @see write_position_data_file
     #
     def self.write_human_friendly_position_data_file(image_objects, fn)
-
       CSV.open(fn, 'wb') do |csv|
-
         obj = image_objects[0]
-
         n_channels = obj.getFitParametersByChannel.size
-
         headers = ["object_id"]
         n_channels.times do |i|
           headers.concat(["pos#{i}_x", "pos#{i}_y", "pos#{i}_z"])
         end
-
         csv << headers
 
         image_objects.each do |im_obj|
-
           row = [im_obj.getLabel]
-
           n_channels.times do |i|
-
             row.concat(im_obj.getPositionForChannel(i).toArray)
-
           end
-
           csv << row
-
         end
-
       end
-
     end
 
-
     ##
     # Gets the filename for storing/reading the correction based upon the supplied parameter dictionary.
     #
@@ -398,12 +320,9 @@ module Cicada
     # @return [String] the filename for the correction file.
     #
     def self.correction_filename(p)
-
       dir = p[:data_directory]
       fn = p[:correction_date]
-
       File.expand_path(fn + CORR_XML_EXTENSION, dir)
-
     end
 
     ##
@@ -415,25 +334,13 @@ module Cicada
     # @return [void]
     #
     def self.write_differences(diffs, p)
-
       dirname = p[:output_positions_to_directory]
-      
       fn = File.expand_path(p[:basename_set] + DIFFS_TXT_EXTENSION, dirname)
-
       File.open(fn, 'w') do |f|
-
         diffs.each do |d|
-
           f.puts(d.to_s)
-
         end
-
       end
-
     end
-
   end
-
 end
-
-

data/lib/cicada/fitting/p3d_fitter.rb

@@ -23,7 +23,6 @@
 #  * ***** END LICENSE BLOCK ***** */
 
 require 'rimageanalysistools'
-
 require 'facets/math/mean'
 require 'facets/math/std'
 
@@ -34,7 +33,6 @@ module Cicada
   # to some distribution.
   #
   class DistributionFitter
-
     attr_accessor :parameters
 
     ##
@@ -44,9 +42,7 @@ module Cicada
     # @param [ParameterDictionary, Hash] params a hash-like object containing the parameters
     #
     def initialize(params)
-
       @parameters = params
-
     end
 
     ##
@@ -63,7 +59,6 @@ module Cicada
     def fit(objects, diffs)
       nil
     end
-    
   end
 
   ##
@@ -74,24 +69,20 @@ module Cicada
   #
   #
   class P3DObjectiveFunction
-
     include Java::edu.stanford.cfuller.imageanalysistools.fitting.ObjectiveFunction
 
     ##
     # Constructs an empty P3DObjectiveFunction.
     #
     def initialize
-
       @r = nil
       @s = nil
       @min_prob = nil
       @use_min_prob = false
       @should_fit_s = true
-
     end
 
     attr_accessor :r, :use_min_prob, :should_fit_s
-
     attr_reader :s, :min_prob
     
     ##
@@ -117,10 +108,8 @@ module Cicada
     # @return [void]
     #
     def min_prob=(min_prob)
-
       @min_prob = min_prob
       @use_min_prob = true
-
     end
 
     ##
@@ -133,9 +122,7 @@ module Cicada
     # @return [Float] the probability density at the given point
     #
     def p3d(r, m, s)
-
       (Math.sqrt(2.0/Math::PI)*r/(2*m*s))*(Math.exp(-1 * (m-r)**2/(2*s**2)) - Math.exp( -1 * (m+r)**2/(2*s**2)))
-
     end
 
     ##
@@ -148,47 +135,32 @@ module Cicada
     # @return [Float] the negative log-likelihood of the data.
     #
     def evaluate(point)
-
       point = point.toArray unless point.is_a? Array
-
       m = point[0]
       s = point[1]
       s = @s unless @should_fit_s
-
       return Float::MAX if (m < 0 or s < 0)
 
       r.reduce(0.0) do |sum, ri|
-
         temp_neg_log_p = -1.0*Math.log( p3d(ri, m, s))
-
-        if (@use_min_prob and temp_neg_log_p > @min_prob) then
-          
+        if (@use_min_prob and temp_neg_log_p > @min_prob) then    
           sum + @min_prob
-
         else
-
           sum + temp_neg_log_p
-
         end
-
-      end
-        
+      end       
     end
-
   end
-  
 
   ##
   # A distribution fitter that fits data to a P3D distribution.
   #
   class P3DFitter < DistributionFitter
-
     # parameters required by the methods in this class
     REQUIRED_PARAMETERS =  []
 
     # parmeters used but not required in this class or only required for optional functionality
     OPTIONAL_PARAMETERS = [:robust_p3d_fit_cutoff]
-    
 
     ##
     # Fits the P3D mean- and standard-deviation-like parameters to the data.
@@ -199,36 +171,22 @@ module Cicada
     # @return [Array] a two-element array containing the mean- and standard-deviation-like parameters.
     #
     def fit(objects, diffs)
-
       of = P3DObjectiveFunction.new
-
       of.r = diffs
-
       tol = 1e-12
-
       nmm = Java::edu.stanford.cfuller.imageanalysistools.fitting.NelderMeadMinimizer.new(tol)
-
       initial_mean = Math.mean(diffs)
-
       initial_width = Math.std(diffs)
-
       starting_point = Java::org.apache.commons.math3.linear.ArrayRealVector.new(2, 0.0)
-
       starting_point.setEntry(0, initial_mean)
       starting_point.setEntry(1, initial_width)
-
-      if @parameters[:robust_p3d_fit_cutoff] then
-        
+      if @parameters[:robust_p3d_fit_cutoff] then  
         of.min_prob= @parmaeters[:robust_p3d_fit_cutoff].to_f
-
       end
 
       nmm.optimize(of, starting_point).toArray.to_a
-
     end
-  
   end
-
 end