panelize 1.0.0-java

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in panelize.gemspec
+gemspec

data/LICENSE.txt

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+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.

data/README.md

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+# Panelize
+
+Panelize is a script for arranging microscopy images into a grid with constant leveling for making figures.  Multiple channels are supported with up to three-channel RGB merge.  An arbitrary number of treatments is supported; each channel is scaled the same across all treatments.  Adds a scalebar to the lower left image in the grid.
+
+## Installation
+
+Panelize requires jruby as it uses java libraries.
+
+Execute:
+
+    $ gem install panelize
+
+Or for an application using bundler, add this line to your application's Gemfile:
+
+    gem 'panelize'
+
+And then execute:
+
+    $ bundle
+
+
+## Usage
+
+Run `panelize` from the command prompt and answer the prompts it prints out (which will ask for input images, etc.).
+
+When asked for the channels to display, these should be provided as numbers (with the first channel having index 0) where each number refers to the order the channels are stored in the image file.  The order in which you list the channels will be the order they are displayed in the grid from left to right, and these will appear in the merge as red, green, and blue in that order.  More than three channels can be displayed, but only the first three will appear in the merge.
+
+Additional options are available at the command line; run `panelize --help` for a description.
+
+Panelizer expects that the input images will be multi-channel images in a format that the [bio-formats library](http://www.openmicroscopy.org/site/products/bio-formats) can read and recognize as having multiple channels.  If the images have multiple axial or time planes, only the final one will be used for display.
+
+The final set of panels will be saved with a unique filename (which will be printed out) to the directory from which you ran the script.
+
+If you want to tweak the scaling of the images, you should adjust the command line parameters scalesat and scaleundersat (run `panelize --help` to see the syntax for using these).  If both these parameters are set to zero, in each channel, the images will be scaled between the min and max value appearing in that channel in any of the images.  Setting these to a larger value will narrow the display range by the value supplied (in percent) from either the upper end (the scalesat parameter) or the lower end (scaleundersat), making the image appear brighter or the background dimmer, respectively.
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request
+
+## License
+
+Panelize is distributed under the MIT/X11 license (see LICENSE.txt for the full license).

data/Rakefile

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+require "bundler/gem_tasks"

data/bin/panelize

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+#!/usr/bin/env ruby
+
+require 'panelize'
+
+Panelize.go
+

data/lib/panelize/version.rb

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+module Panelize
+  VERSION = "1.0.0"
+end

data/lib/panelize.rb

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+#--
+# 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 "panelize/version"
+require 'rimageanalysistools'
+require 'rimageanalysistools/get_image'
+require 'rimageanalysistools/image_shortcuts'
+require 'trollop'
+require 'highline/import'
+
+module Panelize
+
+	java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageCoordinate
+	java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageFactory
+	java_import Java::edu.stanford.cfuller.imageanalysistools.image.Histogram
+	java_import Java::ij.process.ColorProcessor
+	java_import Java::ij.ImagePlus
+	java_import Java::ij.io.FileSaver
+
+	class << self
+
+		def box_channel(im, ch)
+			lower = ImageCoordinate[0,0,0,0,0]
+			upper = ImageCoordinate.cloneCoord(im.getDimensionSizes)
+			lower[:c] = ch
+			upper[:c] = ch+1
+			im.setBoxOfInterest(lower, upper)
+			lower.recycle
+			upper.recycle
+			nil
+		end
+
+		def display(im, params)
+			box_channel(im, params[:col_chs][0])
+			max = Histogram.findMaxVal(im)
+			im.clearBoxOfInterest
+			imp = im.toImagePlus
+			imp.setOpenAsHyperStack true
+			imp.updatePosition(params[:col_chs][0]+1, 1, 1)
+			imp.setDisplayRange(0, max)
+			imp.setRoi 0,0, params[:size], params[:size]
+			imp.show
+			ask("Move the region of interest to where you want to crop and press enter when done.")
+			ul = [imp.getRoi.getPolygon.xpoints[0], imp.getRoi.getPolygon.ypoints[0]]
+		end
+
+		def crop(im, ul, params)
+			sizes = ImageCoordinate.cloneCoord(im.getDimensionSizes)
+			sizes[:x] = params[:size]
+			sizes[:y] = params[:size]
+			ul_coord = ImageCoordinate[ul[0], ul[1], 0,0,0]
+			im_crop = im.subImage(sizes, ul_coord)
+			im.toImagePlus.close
+			sizes.recycle
+			ul_coord.recycle
+			im_crop
+		end
+
+		def load_and_crop(fn, params)
+			im = RImageAnalysisTools.get_image(fn)
+			ul = display(im, params)
+			crop(im, ul, params)
+		end
+
+		def calculate_channel_scale(ims, params)
+			scale = {}
+
+			params[:col_chs].each do |ch|
+				min = Float::MAX
+				max = -1.0*Float::MAX
+
+				ims.each do |im|
+					box_channel(im, ch)
+
+					h = Histogram.new(im)
+					min = h.getMinValue if h.getMinValue < min
+					max = h.getMaxValue if h.getMaxValue > max
+				end
+
+				scale[ch] = [min + params[:scaleundersat]/100*(max-min), max - params[:scalesat]/100*(max-min)]
+			end
+
+			scale
+		end
+
+		def scale_to_8_bit(value, scale)
+			value = 255*(value - scale[0])/(scale[1]-scale[0])
+			value = 0 if value < 0
+			value = 255 if value > 255
+			value
+		end
+
+		def add_scalebar(panel_image, params)
+			scalebar_length_px = params[:scalebar]/params[:mpp]
+
+			y_start = calculate_height(params) - 2*params[:spacing]
+			x_start = params[:spacing]
+
+			x_start.upto(x_start + scalebar_length_px - 1) do |x|
+				y_start.upto(y_start + params[:spacing] - 1) do |y|
+					panel_image.putPixel(x, y, [255, 255, 255].to_java(:int))
+				end
+			end
+		end
+
+
+		def place_panel(panel_image, start_coord, image, channel, rgb_chs, scales)
+			box_channel(image, channel)
+
+			rgb_mult = [0, 0, 0]
+			rgb_mult[0] = 1 if rgb_chs.include? :r
+			rgb_mult[1] = 1 if rgb_chs.include? :g
+			rgb_mult[2] = 1 if rgb_chs.include? :b
+
+			image.each do |ic|
+				v = scale_to_8_bit(image[ic], scales[ic[:c]])
+				curr_val = panel_image.getPixel(ic[:x] + start_coord[:x], ic[:y] + start_coord[:y], nil)
+				panel_image.putPixel(ic[:x] + start_coord[:x], ic[:y] + start_coord[:y], rgb_mult.map.with_index { |e, i| e*v + (1-e)*curr_val[i]}.to_java(:int))
+			end
+
+			nil
+		end
+
+		def calculate_width(params)
+			(params[:col_chs].size + 1)*params[:size] + params[:col_chs].size*params[:spacing]
+		end
+
+		def calculate_height(params)
+			(params[:n_rows])*params[:size] + (params[:n_rows]-1)*params[:spacing]
+		end
+
+		def calculate_row_pos(n, params)
+			n*params[:size] + n*params[:spacing]
+		end
+
+		def calculate_col_pos(n, params)
+			n*params[:size] + n*params[:spacing]
+		end
+
+		def initialize_panel(params)
+			w = calculate_width(params)
+			h = calculate_height(params)
+
+			im = ColorProcessor.new(w, h)
+			w.times do |x|
+				h.times do |y|
+					im.putPixel(x, y, [255, 255, 255].to_java(:int))
+				end
+			end
+
+			im
+		end
+
+
+		def make_panels(ims, scale, params)
+			panels = initialize_panel(params)
+
+			params[:n_rows].times do |row|
+				params[:col_chs].size.times do |col|
+					place_panel(panels, {y: calculate_row_pos(row, params), x: calculate_col_pos(col, params)}, ims[row], params[:col_chs][col], [:r, :g, :b], scale)
+				end
+
+				zero_im = ImageFactory.createWritable(ims[0])
+				zero_im.each { |ic| zero_im[ic] = 0.0 }
+
+				[:r, :g, :b].each_with_index do |ch, i|
+					if params[:col_chs].size > i then
+						place_panel(panels, {y:calculate_row_pos(row, params), x: calculate_col_pos(params[:col_chs].size, params)}, ims[row], params[:col_chs][i], [ch], scale)
+					else 
+						place_panel(panels, {y:calculate_row_pos(row, params), x: calculate_col_pos(params[:col_chs].size, params)}, zero_im, params[:col_chs][0], [ch], scale)
+					end
+				end
+			end
+
+			panels
+		end
+
+		def save_image(panels)
+			fs = FileSaver.new(ImagePlus.new("panels", panels))
+			fn = "panels_#{Time.now.to_i}.tif"
+			fs.saveAsTiff(fn)
+			puts "Panels saved as #{fn}"
+		end
+
+		def ask_for_params(params)
+			params[:n_rows] = ask("Enter the number of treatments (rows) to panelize: ", Integer)
+			params[:col_chs] = ask("Enter the channel numbers to display (comma-separated): ", lambda { |str| str.split(/,\s*/).map(&:to_i) })
+			params[:fns] = []
+			params[:n_rows].times do |i|
+				params[:fns] << ask("Enter the filename for treatment #{i+1}: ").gsub("'", "") #remove quotes if drag and drop fn insertion in the terminal puts them in
+			end
+			params[:mpp] = ask("Enter the number of microns per pixel (for calculating the length of a scalebar): ", Float)
+
+		end
+
+		def go
+			params = Trollop::options do 
+				opt :spacing, "Spacing between image panels in pixels", type: :integer, default: 5
+				opt :size, "Size of the image in pixels", type: :integer, default: 256
+				opt :scalebar, "Size of the scalebar in microns", type: :float, default: 5.0
+				opt :scalesat, "Amount in percent by which to saturate images", type: :float, default: 15.0
+				opt :scaleundersat, "Amount in percent by which to undersaturate images", type: :float, default: 5.0
+			end
+
+			ask_for_params(params)
+
+			ims = []
+			params[:fns].each do |fn|
+				ims << load_and_crop(fn, params)
+			end
+
+			scale = calculate_channel_scale(ims, params)
+			panels = make_panels(ims, scale, params)
+			add_scalebar(panels, params)
+			save_image(panels)
+		end
+	end
+end
+

data/panelize.gemspec

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+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'panelize/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = "panelize"
+  gem.version       = Panelize::VERSION
+  gem.authors       = ["Colin J. Fuller"]
+  gem.email         = ["cjfuller@gmail.com"]
+  gem.description   = %q{Script for arranging microscopy images into a grid with constant leveling for making figures.}
+  gem.summary       = %q{Script for arranging microscopy images into a grid with constant leveling for making figures.  Multiple channels are supported with up to three-channel merge.  An arbitrary number of treatments is supported; each channel is scaled the same across all treatments.  Adds a scalebar to the lower left image in the grid.}
+  gem.homepage      = "https://github.com/cjfuller/panelize"
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ["lib"]
+
+  gem.add_dependency('rimageanalysistools', '>= 5.1.4.2')
+  gem.add_dependency('trollop')
+  gem.add_dependency('highline')
+
+  gem.platform = 'java'
+  gem.requirements = 'jruby'
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: panelize
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+  prerelease:
+platform: java
+authors:
+- Colin J. Fuller
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2013-05-13 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rimageanalysistools
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 5.1.4.2
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 5.1.4.2
+    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: highline
+  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
+description: Script for arranging microscopy images into a grid with constant leveling for making figures.
+email:
+- cjfuller@gmail.com
+executables:
+- panelize
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/panelize
+- lib/panelize.rb
+- lib/panelize/version.rb
+- panelize.gemspec
+homepage: https://github.com/cjfuller/panelize
+licenses: []
+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: Script for arranging microscopy images into a grid with constant leveling for making figures.  Multiple channels are supported with up to three-channel merge.  An arbitrary number of treatments is supported; each channel is scaled the same across all treatments.  Adds a scalebar to the lower left image in the grid.
+test_files: []
+has_rdoc: