cicada 0.9.0-java

data/spec/cicada/file_interaction_spec.rb

@@ -0,0 +1,58 @@
+#--
+# /* ***** 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/file_interaction'
+
+describe Cicada::Serialization do 
+
+  it "should be able to serialize and unserialize a set of image objects" do
+
+    iobjs = load_iobjs
+
+    to_ser = iobjs[0,3]
+
+    ser_str = Cicada::Serialization.serialize_image_objects(to_ser)
+
+    objs_out = Cicada::Serialization.unserialize_image_objects(ser_str)
+
+    objs_out[0].getPositionForChannel(0).getEntry(0).should == to_ser[0].getPositionForChannel(0).getEntry(0)
+
+    objs_out[1].getPositionForChannel(0).getEntry(0).should == to_ser[1].getPositionForChannel(0).getEntry(0)
+
+    objs_out[2].getPositionForChannel(0).getEntry(0).should == to_ser[2].getPositionForChannel(0).getEntry(0)
+
+    objs_out[0].nil?.should be false
+
+    objs_out[1].nil?.should be false
+
+    objs_out[2].nil?.should be false
+
+  end
+
+end
+
+
+

data/spec/cicada/fitting/p3d_fitter_spec.rb

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+# /* ***** 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/fitting/p3d_fitter'
+
+
+describe Cicada::P3DFitter do
+
+  before :each do 
+    @fitter = Cicada::P3DFitter.new({})
+  end
+
+  it "should calculate p3d probability densities correctly" do
+
+    r = 10.0
+    m = 5.0
+    s = 10.0
+
+    expected = 0.04451
+
+    allowed_error = 0.00001
+
+    fct = Cicada::P3DObjectiveFunction.new
+
+    (fct.p3d(r, m, s) - expected).abs.should be < allowed_error
+    
+
+  end
+
+  it "should fit a p3d distribution correctly" do
+
+    data = nil
+
+    File.open("spec/resources/test_p3d_data.txt") do |f|
+      data = f.readlines
+    end
+
+    data.map! { |e| e.to_f }
+
+    result = @fitter.fit(nil, data)
+
+    expected_m = 30.0
+    expected_s = 10.0
+
+    allowed_error = 1.0
+    
+    m = result[0]
+    s = result[1]
+
+    (m - expected_m).abs.should be < allowed_error
+    (s - expected_s).abs.should be < allowed_error
+
+  end
+  
+
+end
+
+

data/spec/cicada/mutable_matrix_spec.rb

@@ -0,0 +1,89 @@
+#--
+# /* ***** 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/mutable_matrix'
+
+describe MMatrix do
+
+  before :each do
+
+    @mat = MMatrix[[1,2], [3,4]]
+
+  end
+
+  it "should allow setting of individual entries" do
+
+    @mat[0,1] = 5
+
+    @mat[0,1].should == 5
+    @mat[0,0].should == 1
+    @mat[1,1].should == 4
+
+  end
+
+  it "should allow replacement of rows" do
+
+    @mat.replace_row(0, [5,6])
+
+    @mat[0,0].should == 5
+    @mat[0,1].should == 6
+    @mat[1,0].should == 3
+
+  end
+
+  it "should allow replacement of columns" do
+
+    @mat.replace_column(0, [5,6])
+
+    @mat[0,0].should == 5
+    @mat[1,0].should == 6
+    @mat[0,1].should == 2
+
+  end
+
+end
+
+describe MVector do
+
+  before :each do
+
+    @vec = MVector.zero(3)
+
+  end
+
+  it "should allow setting of individual entries" do
+
+    @vec[0] = 1
+
+    @vec[0].should == 1
+
+    @vec[1].should == 0
+
+  end
+
+end
+
+

data/spec/spec_helper.rb

@@ -0,0 +1,50 @@
+#--
+# /* ***** 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 ***** */
+#++
+
+#resource locations for test data
+
+CORR_IMAGE = "./spec/resources/beads_sim.ome.tif"
+
+CORR_MASK = "./spec/resources/beads_sim_mask.ome.tif"
+
+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
+
+

metadata

@@ -0,0 +1,137 @@
+--- !ruby/object:Gem::Specification
+name: cicada
+version: !ruby/object:Gem::Version
+  version: 0.9.0
+  prerelease:
+platform: java
+authors:
+- Colin J. Fuller
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2013-01-29 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: pqueue
+  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: facets
+  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: rimageanalysistools
+  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
+    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: :development
+description: CICADA (Colocalization and In-situ Correction of Aberration for Distance Analysis) implementation; see Fuller and Straight J. Microscopy (2012) doi:10.1111/j.1365-2818.2012.03654.x
+email: cjfuller@gmail.com
+executables:
+- cicada
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/cicada.rb
+- lib/cicada/cicada_main.rb
+- lib/cicada/file_interaction.rb
+- lib/cicada/mutable_matrix.rb
+- lib/cicada/version.rb
+- lib/cicada/correction/position_corrector.rb
+- lib/cicada/correction/correction.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/correction/position_corrector_spec.rb
+- spec/cicada/correction/correction_spec.rb
+- spec/cicada/fitting/p3d_fitter_spec.rb
+- bin/cicada
+homepage: http://github.com/cjfuller/cicada
+licenses:
+- MIT
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: !binary |-
+        MA==
+  none: false
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: !binary |-
+        MA==
+  none: false
+requirements:
+- jruby
+rubyforge_project:
+rubygems_version: 1.8.24
+signing_key:
+specification_version: 3
+summary: CICADA implementation
+test_files: []
+has_rdoc: