panelize 1.0.0-java → 1.1.0-java
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- data/lib/panelize.rb +212 -205
- data/lib/panelize/version.rb +1 -1
- metadata +2 -2
data/lib/panelize.rb
CHANGED
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@@ -29,210 +29,217 @@ require 'highline/import'
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module Panelize
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java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageCoordinate
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java_import Java::edu.stanford.cfuller.imageanalysistools.image.ImageFactory
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java_import Java::edu.stanford.cfuller.imageanalysistools.image.Histogram
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java_import Java::ij.process.ColorProcessor
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java_import Java::ij.ImagePlus
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java_import Java::ij.io.FileSaver
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class << self
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def box_channel(im, ch)
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lower = ImageCoordinate[0,0,0,0,0]
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upper = ImageCoordinate.cloneCoord(im.getDimensionSizes)
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lower[:c] = ch
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upper[:c] = ch+1
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im.setBoxOfInterest(lower, upper)
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lower.recycle
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upper.recycle
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nil
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end
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def display(im, params)
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box_channel(im, params[:col_chs][0])
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max = Histogram.findMaxVal(im)
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im.clearBoxOfInterest
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imp = im.toImagePlus
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imp.setOpenAsHyperStack true
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imp.updatePosition(params[:col_chs][0]+1, 1, 1)
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imp.setDisplayRange(0, max)
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imp.setRoi 0,0, params[:size], params[:size]
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imp.show
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ask("Move the region of interest to where you want to crop and press enter when done.")
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ul = [imp.getRoi.getPolygon.xpoints[0], imp.getRoi.getPolygon.ypoints[0]]
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end
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def crop(im, ul, params)
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sizes = ImageCoordinate.cloneCoord(im.getDimensionSizes)
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sizes[:x] = params[:size]
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sizes[:y] = params[:size]
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ul_coord = ImageCoordinate[ul[0], ul[1], 0,0,0]
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im_crop = im.subImage(sizes, ul_coord)
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im.toImagePlus.close
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sizes.recycle
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ul_coord.recycle
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im_crop
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end
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def load_and_crop(fn, params)
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im = RImageAnalysisTools.get_image(fn)
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ul = display(im, params)
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crop(im, ul, params)
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end
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def calculate_channel_scale(ims, params)
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scale = {}
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params[:col_chs].each do |ch|
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min = Float::MAX
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max = -1.0*Float::MAX
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ims.each do |im|
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box_channel(im, ch)
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h = Histogram.new(im)
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min = h.getMinValue if h.getMinValue < min
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max = h.getMaxValue if h.getMaxValue > max
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end
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scale[ch] = [min + params[:scaleundersat]/100*(max-min), max - params[:scalesat]/100*(max-min)]
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end
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scale
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end
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def scale_to_8_bit(value, scale)
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value = 255*(value - scale[0])/(scale[1]-scale[0])
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value = 0 if value < 0
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value = 255 if value > 255
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value
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end
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def add_scalebar(panel_image, params)
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scalebar_length_px = params[:scalebar]/params[:mpp]
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y_start = calculate_height(params) - 2*params[:spacing]
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x_start = params[:spacing]
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x_start.upto(x_start + scalebar_length_px - 1) do |x|
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y_start.upto(y_start + params[:spacing] - 1) do |y|
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panel_image.putPixel(x, y, [255, 255, 255].to_java(:int))
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end
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end
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end
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def place_panel(panel_image, start_coord, image, channel, rgb_chs, scales)
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box_channel(image, channel)
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rgb_mult = [0, 0, 0]
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rgb_mult[0] = 1 if rgb_chs.include? :r
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rgb_mult[1] = 1 if rgb_chs.include? :g
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rgb_mult[2] = 1 if rgb_chs.include? :b
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image.each do |ic|
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v = scale_to_8_bit(image[ic], scales[ic[:c]])
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curr_val = panel_image.getPixel(ic[:x] + start_coord[:x], ic[:y] + start_coord[:y], nil)
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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))
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end
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nil
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end
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def calculate_width(params)
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(params[:col_chs].size + 1)*params[:size] + params[:col_chs].size*params[:spacing]
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end
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def calculate_height(params)
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(params[:n_rows])*params[:size] + (params[:n_rows]-1)*params[:spacing]
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end
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def calculate_row_pos(n, params)
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n*params[:size] + n*params[:spacing]
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end
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def calculate_col_pos(n, params)
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n*params[:size] + n*params[:spacing]
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end
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def initialize_panel(params)
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w = calculate_width(params)
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h = calculate_height(params)
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im = ColorProcessor.new(w, h)
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w.times do |x|
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h.times do |y|
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im.putPixel(x, y, [255, 255, 255].to_java(:int))
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end
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end
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im
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end
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def make_panels(ims, scale, params)
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panels = initialize_panel(params)
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params[:n_rows].times do |row|
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params[:col_chs].size.times do |col|
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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)
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end
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zero_im = ImageFactory.createWritable(ims[0])
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zero_im.each { |ic| zero_im[ic] = 0.0 }
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#zero out merge first in case not all channels are being used
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[:r, :g, :b].each do |ch, i|
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next if params[:col_chs].include? ch
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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)
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end
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params[:col_order].each_with_index do |ch, i|
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if params[:col_chs].size > i then
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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)
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else
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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)
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end
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end
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end
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panels
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end
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def save_image(panels)
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fs = FileSaver.new(ImagePlus.new("panels", panels))
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fn = "panels_#{Time.now.to_i}.tif"
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fs.saveAsTiff(fn)
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puts "Panels saved as #{fn}"
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end
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def ask_for_params(params)
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params[:n_rows] = ask("Enter the number of treatments (rows) to panelize: ", Integer)
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params[:col_chs] = ask("Enter the channel numbers to display (comma-separated): ", lambda { |str| str.split(/,\s*/).map(&:to_i) })
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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) }
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params[:fns] = []
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params[:n_rows].times do |i|
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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
|
|
217
|
+
end
|
|
218
|
+
params[:mpp] = ask("Enter the number of microns per pixel (for calculating the length of a scalebar): ", Float)
|
|
219
|
+
|
|
220
|
+
end
|
|
221
|
+
|
|
222
|
+
def go
|
|
223
|
+
params = Trollop::options do
|
|
224
|
+
opt :spacing, "Spacing between image panels in pixels", type: :integer, default: 5
|
|
225
|
+
opt :size, "Size of the image in pixels", type: :integer, default: 256
|
|
226
|
+
opt :scalebar, "Size of the scalebar in microns", type: :float, default: 5.0
|
|
227
|
+
opt :scalesat, "Amount in percent by which to saturate images", type: :float, default: 15.0
|
|
228
|
+
opt :scaleundersat, "Amount in percent by which to undersaturate images", type: :float, default: 5.0
|
|
229
|
+
end
|
|
230
|
+
|
|
231
|
+
ask_for_params(params)
|
|
232
|
+
|
|
233
|
+
ims = []
|
|
234
|
+
params[:fns].each do |fn|
|
|
235
|
+
ims << load_and_crop(fn, params)
|
|
236
|
+
end
|
|
237
|
+
|
|
238
|
+
scale = calculate_channel_scale(ims, params)
|
|
239
|
+
panels = make_panels(ims, scale, params)
|
|
240
|
+
add_scalebar(panels, params)
|
|
241
|
+
save_image(panels)
|
|
242
|
+
end
|
|
243
|
+
end
|
|
237
244
|
end
|
|
238
245
|
|
data/lib/panelize/version.rb
CHANGED
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: panelize
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 1.
|
|
4
|
+
version: 1.1.0
|
|
5
5
|
prerelease:
|
|
6
6
|
platform: java
|
|
7
7
|
authors:
|
|
@@ -9,7 +9,7 @@ authors:
|
|
|
9
9
|
autorequire:
|
|
10
10
|
bindir: bin
|
|
11
11
|
cert_chain: []
|
|
12
|
-
date: 2013-05-
|
|
12
|
+
date: 2013-05-24 00:00:00.000000000 Z
|
|
13
13
|
dependencies:
|
|
14
14
|
- !ruby/object:Gem::Dependency
|
|
15
15
|
name: rimageanalysistools
|