cicada 0.9.2-java → 0.9.3-java

data/bin/cicada_fit_only

@@ -0,0 +1,37 @@
+#!/usr/bin/env ruby
+
+#--
+# /* ***** 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'
+
+p = Cicada::CicadaMain.parse_parameter_file(ARGV[0])
+
+c = Cicada::CicadaMain.new(p)
+
+c.do_and_save_fits
+
+

data/bin/cicada_generate_map

@@ -0,0 +1,52 @@
+#!/usr/bin/env ruby
+
+#--
+# /* ***** 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 'trollop'
+
+require 'cicada'
+require 'cicada/file_interaction'
+require 'cicada/aberration_map'
+require 'cicada/correction/correction'
+
+opts = Trollop.options do
+	opt :parameter_file, "Parameter file", type: :string
+	opt :size_x, "Width of map in pixels", type: :integer, default: 256
+	opt :size_y, "Height of map in pixels", type: :integer, default: 256
+	opt :output_file, "Map output filename", type: :string
+end
+
+p = Cicada::CicadaMain.parse_parameter_file(opts[:parameter_file])
+
+corr_file_fn = Cicada::FileInteraction.correction_filename(p)
+
+c = Cicada::Correction.read_from_file(corr_file_fn)
+
+ab_map = Cicada::AberrationMap.generate(c, [0, opts[:size_x]], [0, opts[:size_y]], p)
+
+ab_map.write_to_file(opts[:output_file])
+

data/lib/cicada/aberration_map.rb

@@ -0,0 +1,75 @@
+#--
+# /* ***** 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/position_corrector'
+require 'rimageanalysistools'
+require 'rimageanalysistools/image_shortcuts'
+require 'rimageanalysistools/create_parameters'
+
+java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageFactory
+
+module Cicada
+
+	class AberrationMap
+
+		def self.generate(c, bounds_x, bounds_y, params)
+
+			size_x = bounds_x[1] - bounds_x[0]
+			size_y = bounds_y[1] - bounds_y[0]
+
+			ab_map = ImageFactory.createWritable(ImageCoordinate[size_x, size_y, 3,1, 1], 0.0)
+
+			ab_map.setBoxOfInterest(ImageCoordinate[0,0,0,0,0], ImageCoordinate[size_x, size_y, 1, 1, 1])
+
+			ic2 = ImageCoordinate[0,0,0,0,0]
+
+			dist_conv = [params[:pixelsize_nm].to_f, params[:pixelsize_nm].to_f, params[:z_sectionsize_nm].to_f]
+
+			ab_map.each do |ic|
+
+				ic2.setCoord(ic)
+
+				corr = c.correct_position(ic[:x] + bounds_x[0], ic[:y] + bounds_y[0])
+
+				0.upto(2) do |dim|
+
+					ic2[:z] = dim
+
+					ab_map[ic2] = corr[dim] * dist_conv[dim]
+
+				end
+
+			end
+
+			ab_map
+
+		end
+
+	end
+
+end
+
+

data/lib/cicada/cicada_main.rb

@@ -157,7 +157,15 @@ module Cicada
         
           @logger.debug { "Processing object #{obj.getLabel}" }
 
-          obj.fitPosition(@parameters)
+          begin
+
+            obj.fitPosition(@parameters)
+
+          rescue => e
+
+            logger.error { "error while processing object #{obj.label}: #{e.message}" }
+
+          end
 
       end
 
@@ -503,6 +511,8 @@ module Cicada
         
       end
 
+      puts "number of image objects: #{image_objects.size}"
+
       image_objects
 
     end
@@ -526,6 +536,25 @@ module Cicada
     end
 
 
+    ##
+    # Fits all objects in an image or loads objects from disk if they have already
+    # been fit and refitting has not been requested.
+    #
+    # Saves fits to disk in the parameter-specified data directory.
+    #
+    # @return [List<ImageObject>] the fitted or loaded image objects
+    #
+    def do_and_save_fits
+
+      image_objects = load_or_fit_image_objects
+
+      FileInteraction.write_position_data(image_objects, @parameters)
+
+      image_objects
+
+    end
+
+
     ##
     # Runs the analysis.
     #
@@ -533,10 +562,8 @@ module Cicada
     #
     def go
 
-      image_objects = load_or_fit_image_objects
+      image_objects = do_and_save_fits
       
-      FileInteraction.write_position_data(image_objects, @parameters)
-
       pc = PositionCorrector.new(@parameters)
       pc.logger= @logger
 
@@ -632,20 +659,34 @@ module Cicada
 
     end
 
+
     ##
-    # Runs analysis using a specified parameter file.
+    # Reads a parameters file and creates a parameter dictionary.
     #
-    # @param [String] fn  the filename of the parameter file
+    # @param [String] fn the filename of the parameter file
     #
-    # @return [void]
+    # @return [ParameterDictionary] the parsed parameters
     #
-    def self.run_from_parameter_file(fn)
+    def self.parse_parameter_file(fn)
 
       java_import Java::edu.stanford.cfuller.imageanalysistools.meta.AnalysisMetadataParserFactory
 
       parser = AnalysisMetadataParserFactory.createParserForFile(fn)
 
-      p = parser.parseFileToParameterDictionary(fn)
+      parser.parseFileToParameterDictionary(fn)
+
+    end
+
+    ##
+    # Runs analysis using a specified parameter file.
+    #
+    # @param [String] fn  the filename of the parameter file
+    #
+    # @return [void]
+    #
+    def self.run_from_parameter_file(fn)
+
+      p = parse_parameter_file(fn)
 
       c = new(p)
 

data/lib/cicada/file_interaction.rb

@@ -27,6 +27,7 @@
 require 'ostruct'
 require 'base64'
 require 'rexml/document'
+require 'csv'
 
 require 'rimageanalysistools'
 require 'rimageanalysistools/get_image'
@@ -142,6 +143,9 @@ module Cicada
     # extension on position data (image object) files.
     POS_XML_EXTENSION = "_position_data.xml"
 
+    # extension on human-friendly position data (image object) files.
+    POS_HUMAN_EXTENSION = "_position_data.csv"
+
     # extension on the correction files
     CORR_XML_EXTENSION = "_correction.xml"
 
@@ -178,6 +182,20 @@ 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.
+    #
+    # @param [ParameterDictionary, Hash] p a hash-like object specifying the filename for the positions.
+    #
+    # @return [String] the absolute path to the position file.
+    #
+    def self.human_friendly_position_data_filename(p)
+      dir = p[:data_directory]
+      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.
     #
@@ -308,6 +326,10 @@ module Cicada
       
       write_position_data_file(image_objects,fn)
 
+      fn2 = human_friendly_position_data_filename(p)
+
+      write_human_friendly_position_data_file(image_objects, fn2)      
+
     end
 
     ##
@@ -328,6 +350,46 @@ module Cicada
 
     end
 
+    ##
+    # Writes the provided image objects to a human-readable file 
+    # at the location specified.
+    #
+    # @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.
     #

data/lib/cicada/version.rb

@@ -26,7 +26,7 @@
 
 module Cicada
 
-  VERSION = "0.9.2"
+  VERSION = "0.9.3"
 
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cicada
 version: !ruby/object:Gem::Version
-  version: 0.9.2
+  version: 0.9.3
   prerelease:
 platform: java
 authors:
@@ -65,6 +65,24 @@ dependencies:
     none: false
   prerelease: false
   type: :runtime
+- !ruby/object:Gem::Dependency
+  name: trollop
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  prerelease: false
+  type: :runtime
 - !ruby/object:Gem::Dependency
   name: rspec
   version_requirements: !ruby/object:Gem::Requirement
@@ -87,11 +105,13 @@ description: CICADA (Colocalization and In-situ Correction of Aberration for Dis
 email: cjfuller@gmail.com
 executables:
 - cicada
+- cicada_fit_only
 extensions: []
 extra_rdoc_files: []
 files:
 - lib/cicada.rb
 - lib/cicada/cicada_main.rb
+- lib/cicada/aberration_map.rb
 - lib/cicada/file_interaction.rb
 - lib/cicada/mutable_matrix.rb
 - lib/cicada/version.rb
@@ -105,6 +125,8 @@ files:
 - spec/cicada/correction/correction_spec.rb
 - spec/cicada/fitting/p3d_fitter_spec.rb
 - bin/cicada
+- bin/cicada_generate_map
+- bin/cicada_fit_only
 homepage: http://github.com/cjfuller/cicada
 licenses:
 - MIT