cicada 0.9.0-java → 0.9.1-java

data/lib/cicada/cicada_main.rb

@@ -293,7 +293,7 @@ module Cicada
         y = fp.getPosition(ImageCoordinate::Y)
         z = fp.getPosition(ImageCoordinate::Z)
 
-        ok = (range_x.include?(x) and range_y.include?(y) and range_z.include?(z))
+        ok = (range_x.include?(x) and range_y.include?(y) and (range_z.include?(z) or toCheck.getParent.getDimensionSizes[:z] == 1))
 
         unless ok then
           
@@ -538,6 +538,7 @@ module Cicada
       FileInteraction.write_position_data(image_objects, @parameters)
 
       pc = PositionCorrector.new(@parameters)
+      pc.logger= @logger
 
       c = pc.generate_correction(image_objects)
 
@@ -545,7 +546,7 @@ module Cicada
 
       if @parameters[:determine_tre] and @parameters[:determine_correction] then
         
-        puts "calculating tre"
+        self.logger.info("calculating tre")
         
         tre = pc.determine_tre(image_objects)
 

data/lib/cicada/correction/correction.rb

@@ -117,46 +117,69 @@ module Cicada
 
     end
 
+
     ##
-    # Writes the correction to a string in XML format
-    # 
-    # @return [String] the correction data encoded as XML
+    # Writes all the points used for correction to XML within a supplied correction
+    #  XML element
     #
-    def write_to_xml
-      
-      doc = REXML::Document.new
+    # @param [REXML::Element] correction_element the XML element representing the correction
+    #
+    # @return [void]
+    #
+    def write_all_correction_point_xml(correction_element)
 
-      ce = doc.add_element XML_STRINGS[:correction_element]
+      @distance_cutoffs.each_with_index do |e,i|
 
-      ce.attributes[XML_STRINGS[:n_points_attr]] = @distance_cutoffs.size
+        write_correction_point_xml(correction_element, i)
 
-      ce.attributes[XML_STRINGS[:ref_channel_attr]] = @reference_channel
+      end
 
-      ce.attributes[XML_STRINGS[:corr_channel_attr]] = @correction_channel
-      
-      @distance_cutoffs.each_with_index do |e, i|
+    end
 
-        cp = ce.add_element XML_STRINGS[:correction_point_element]
 
-        cp.attributes[XML_STRINGS[:x_pos_attr]]= @positions_for_correction[i,0]
-        cp.attributes[XML_STRINGS[:y_pos_attr]]= @positions_for_correction[i,1]
-        cp.attributes[XML_STRINGS[:z_pos_attr]]= @positions_for_correction[i,2]
+    ##
+    # Writes a single point used for correction to XML within a supplied correction
+    #  XML element
+    #
+    # @param [REXML::Element] correction_element the XML element representing the correction
+    # @param [Integer] i the index of the point to write
+    #
+    # @return [void]
+    #
+    def write_correction_point_xml(correction_element, i)
+
+      cp = correction_element.add_element XML_STRINGS[:correction_point_element]
+
+      cp.attributes[XML_STRINGS[:x_pos_attr]]= @positions_for_correction[i,0]
+      cp.attributes[XML_STRINGS[:y_pos_attr]]= @positions_for_correction[i,1]
+      cp.attributes[XML_STRINGS[:z_pos_attr]]= @positions_for_correction[i,2]
 
-        xp = cp.add_element XML_STRINGS[:x_param_element]
+      point_dims_to_corr = {XML_STRINGS[:x_param_element] => @correction_x,
+                            XML_STRINGS[:y_param_element] => @correction_y,
+                            XML_STRINGS[:z_param_element] => @correction_z}
 
-        xp.text = @correction_x[i].to_a.join(", ")
 
-        yp = cp.add_element XML_STRINGS[:y_param_element]
+      point_dims_to_corr.each do |dim_el, corr_txt|
 
-        yp.text = @correction_y[i].to_a.join(", ")
+        p = cp.add_element dim_el
+
+        p.text = corr_txt[i].to_a.join(", ")
 
-        zp = cp.add_element XML_STRINGS[:z_param_element]
-        
-        zp.text = @correction_z[i].to_a.join(", ")
-        
       end
 
-      bd = ce.add_element XML_STRINGS[:binary_data_element]
+    end
+
+    ##
+    # Writes the internal binary representation of the correction into
+    #  an XML element.
+    #
+    # @param [REXML::Element] correction_element the XML element representing the correction
+    #
+    # @return [void]
+    #
+    def write_correction_binary_data_element(correction_element)
+
+      bd = correction_element.add_element XML_STRINGS[:binary_data_element]
 
       bd.attributes[XML_STRINGS[:encoding_attr]]= XML_STRINGS[:encoding_name]
 
@@ -164,6 +187,29 @@ module Cicada
 
       bd.text = bin_data
 
+    end
+
+    ##
+    # Writes the correction to a string in XML format
+    # 
+    # @return [String] the correction data encoded as XML
+    #
+    def write_to_xml
+      
+      doc = REXML::Document.new
+
+      ce = doc.add_element XML_STRINGS[:correction_element]
+
+      ce.attributes[XML_STRINGS[:n_points_attr]] = @distance_cutoffs.size
+
+      ce.attributes[XML_STRINGS[:ref_channel_attr]] = @reference_channel
+
+      ce.attributes[XML_STRINGS[:corr_channel_attr]] = @correction_channel
+      
+      write_all_correction_point_xml(ce)
+
+      write_correction_binary_data_element(ce)
+
       doc_string = ""
 
       doc.write doc_string, 2

data/lib/cicada/correction/position_corrector.rb

@@ -29,6 +29,7 @@ require 'cicada/mutable_matrix'
 require 'cicada/correction/correction'
 
 require 'ostruct'
+require 'logger'
 
 require 'pqueue'
 
@@ -59,7 +60,7 @@ module Cicada
     # for a 2d quadratic fit)
     NUM_CORR_PARAM = 6
 
-    attr_accessor :parameters, :pixel_to_distance_conversions
+    attr_accessor :parameters, :pixel_to_distance_conversions, :logger
 
     ##
     # Constructs a new position corrector with the specified parameters
@@ -69,6 +70,7 @@ module Cicada
     def initialize(p)
       @parameters = p
       @pixel_to_distance_conversions = Vector[p[:pixelsize_nm].to_f, p[:pixelsize_nm].to_f, p[:z_sectionsize_nm].to_f]
+      @logger = Logger.new(STDOUT)
     end
 
 
@@ -281,12 +283,10 @@ module Cicada
 
       mean_corr_vec.map! { |e| e / corrected_vec_diffs.length }
 
-      #TODO - logging
-
-      puts "mean components uncorrected: [#{mean_uncorr_vec.join(', ')}]"
-      puts "mean distance uncorrected: #{Vector[*mean_uncorr_vec].norm}"
-      puts "mean components corrected: [#{mean_corr_vec.join(', ')}]"
-      puts "mean distance corrected: #{Vector[*mean_corr_vec].norm}"
+      self.logger.info("mean components uncorrected: [#{mean_uncorr_vec.join(', ')}]")
+      self.logger.info("mean distance uncorrected: #{Vector[*mean_uncorr_vec].norm}")
+      self.logger.info("mean components corrected: [#{mean_corr_vec.join(', ')}]")
+      self.logger.info("mean distance corrected: #{Vector[*mean_corr_vec].norm}")
 
     end
 
@@ -426,7 +426,7 @@ module Cicada
           
           tq.submit do 
             
-            puts "Calculating TRE.  Progress: #{ii} of #{objs.length}" if ii.modulo(10) == 0
+            self.logger.debug("Calculating TRE.  Progress: #{ii} of #{objs.length}") if ii.modulo(10) == 0
 
             temp_objs = objs.select { |e| e != obj }
 
@@ -486,10 +486,8 @@ module Cicada
       
       tre_2d = Math.mean(tre_values) { |e| e.tre_xy }
 
-      #TODO logging
-
-      puts "TRE: #{tre_3d}"
-      puts "X-Y TRE: #{tre_2d}"
+      self.logger.info("TRE: #{tre_3d}")
+      self.logger.info("X-Y TRE: #{tre_2d}")
 
       tre_3d
 

data/lib/cicada/version.rb

@@ -26,7 +26,7 @@
 
 module Cicada
 
-  VERSION = "0.9.0"
+  VERSION = "0.9.1"
 
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cicada
 version: !ruby/object:Gem::Version
-  version: 0.9.0
+  version: 0.9.1
   prerelease:
 platform: java
 authors: