panelize 1.0.0-java → 1.1.0-java

data/lib/panelize.rb

@@ -29,210 +29,217 @@ 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
+  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 }
+
+        #zero out merge first in case not all channels are being used
+        [:r, :g, :b].each do |ch, i|
+          next if params[:col_chs].include? ch
+          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
+        
+        params[:col_order].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[:col_order] = ask ("Enter the channel order (comma-separated) (default r,g,b if no order given): "), lambda { |str| str.empty? ? [:r, :g, :b] : str.split(/,\s*/).map(&:to_sym) }
+      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/lib/panelize/version.rb

@@ -1,3 +1,3 @@
 module Panelize
-  VERSION = "1.0.0"
+  VERSION = "1.1.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: panelize
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.1.0
   prerelease:
 platform: java
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2013-05-13 00:00:00.000000000 Z
+date: 2013-05-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rimageanalysistools