cicada 0.9.4-java → 0.9.5-java

data/lib/cicada/mutable_matrix.rb

@@ -43,13 +43,9 @@ class Matrix
   #  to the specified row.
   #
   def replace_row(i, other)
-
     column_size.times do |j|
-
       self[i, j]= other[j]
-
     end
-
   end
 
   ##
@@ -60,17 +56,12 @@ class Matrix
   #  to the specified column.
   #
   def replace_column(j, other)
-
     row_size.times do |i|
-
       self[i, j]= other[i]
-
     end
-
   end
   
   public :[]=
-
 end
 
 ##
@@ -87,9 +78,7 @@ class MVector < 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
 
   ##
@@ -100,9 +89,7 @@ class MVector < 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
 
   ##
@@ -116,18 +103,10 @@ class MVector < Vector
   # @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

@@ -25,9 +25,5 @@
 #++
 
 module Cicada
-
-  VERSION = "0.9.4"
-
+  VERSION = "0.9.5"
 end
-
-

data/spec/cicada/cicada_main_spec.rb

@@ -0,0 +1,62 @@
+#--
+# 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.
+#++
+
+require 'logger'
+
+require 'spec_helper'
+
+require 'cicada/correction/position_corrector'
+require 'cicada/correction/correction'
+require 'cicada/correction/in_situ_correction'
+require 'cicada/cicada_main'
+require 'cicada/file_interaction'
+
+describe Cicada do
+
+  before :each do 
+    @p = {}
+    setup_default_parameters(@p)
+  end
+
+  it "should not give an error when trying not to perform any correction and the correction file does not exist on disk" do
+    @p[:determine_correction] = false
+    @p[:correct_images] = false
+    cic = Cicada::CicadaMain.new(@p)
+
+    cic.class.class_eval do
+      define_method :do_and_save_fits do
+        load_iobjs
+      end
+    end
+
+    Cicada::FileInteraction.class_eval do
+      def self.write_position_data(iobjs, params)
+        nil
+      end
+    end
+
+    expect { cic.go }.not_to raise_exception
+
+  end
+end
+
+

data/spec/cicada/correction/position_corrector_spec.rb

@@ -36,9 +36,8 @@ 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}
-
+    @p = {}
+    setup_default_parameters(@p)
   end
 
   it "should generate a correction correctly" do
@@ -115,7 +114,7 @@ describe Cicada::PositionCorrector do
 
     pc = Cicada::PositionCorrector.new(@p)
 
-    corr = pc.generate_in_situ_correction_from_iobjs(load_iobjs)
+    corr = pc.generate_in_situ_correction_from_iobjs(load_iobjs).corr_parameters.transpose
 
     x_corr = corr[0]
     y_corr = corr[1]

data/spec/spec_helper.rb

@@ -35,16 +35,14 @@ OBJ_FN = "./spec/resources/beads_sim_data.xml"
 CORR_FN = "./spec/resources/sim_correction.xml"
 
 def load_correction
-
   Cicada::Correction.read_from_file(CORR_FN)
-
 end
 
-
 def load_iobjs
-
   Cicada::FileInteraction.unserialize_position_data_file(OBJ_FN)
-
 end
 
+def setup_default_parameters(var)
+  var.merge!({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
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cicada
 version: !ruby/object:Gem::Version
-  version: 0.9.4
+  version: 0.9.5
   prerelease:
 platform: java
 authors:
@@ -15,17 +15,15 @@ dependencies:
   name: pqueue
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
+        version: '0'
     none: false
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
+        version: '0'
     none: false
   prerelease: false
   type: :runtime
@@ -33,17 +31,15 @@ dependencies:
   name: facets
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
+        version: '0'
     none: false
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
+        version: '0'
     none: false
   prerelease: false
   type: :runtime
@@ -51,17 +47,15 @@ dependencies:
   name: rimageanalysistools
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
+        version: '0'
     none: false
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
+        version: '0'
     none: false
   prerelease: false
   type: :runtime
@@ -69,17 +63,15 @@ dependencies:
   name: trollop
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
+        version: '0'
     none: false
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
+        version: '0'
     none: false
   prerelease: false
   type: :runtime
@@ -87,17 +79,15 @@ dependencies:
   name: rspec
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
+        version: '0'
     none: false
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
+        version: '0'
     none: false
   prerelease: false
   type: :development
@@ -118,10 +108,13 @@ files:
 - lib/cicada/version.rb
 - lib/cicada/correction/position_corrector.rb
 - lib/cicada/correction/correction.rb
+- lib/cicada/correction/in_situ_correction.rb
+- lib/cicada/correction/unable_to_correct_error.rb
 - lib/cicada/fitting/p3d_fitter.rb
 - spec/spec_helper.rb
 - spec/cicada/file_interaction_spec.rb
 - spec/cicada/mutable_matrix_spec.rb
+- spec/cicada/cicada_main_spec.rb
 - spec/cicada/correction/position_corrector_spec.rb
 - spec/cicada/correction/correction_spec.rb
 - spec/cicada/fitting/p3d_fitter_spec.rb
@@ -137,17 +130,15 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
-      version: !binary |-
-        MA==
+      version: '0'
   none: false
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
-      version: !binary |-
-        MA==
+      version: '0'
   none: false
 requirements:
 - jruby