Create new templates

Added new sample Ruby scripts based off the examples in
http://imagej.net/JRuby_Scripting

Author: hinerm

src/main/resources/script-templates/Ruby/Batch_Convert.rb

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+# Convert a directory of LSM files to BioRad .PIC
+java_import "ij.IJ"
+java_import "ij.process.StackConverter"
+
+input_directory  = "/home/mark/lsm-examples/"
+output_directory = "/home/mark/lsm-examples/biorad/"
+
+include_class 'util.BatchOpener'
+include_class 'Biorad_Writer'
+
+# Check that the input directory exists:
+unless FileTest.directory? input_directory
+  ij.IJ.error "Input directory '#{input_directory} was not found"
+  exit(-1)
+end
+
+# Create the output directory if it doesn't exist:
+unless FileTest.exist? output_directory
+  Dir.mkdir output_directory
+end
+
+# Biorad filenames have a standard format, which we generate with
+# this function.  ('channel' should be 1-indexed):
+def make_biorad_filename(lsm_filename,channel)
+  lsm_filename.gsub(/.lsm$/,sprintf("%02d.pic",channel))
+end
+
+Dir.entries(input_directory).each do |e|
+  # Skip anything that doesn't have a '.lsm' extension:
+  next unless e =~ /\.lsm$/
+  puts "Converting: #{e}"
+  # Open the image file to an array of ImagePlus objects:
+  a = BatchOpener.open("#{input_directory}#{e}")
+  # Create the writer plugin object:
+  writer = Biorad_Writer.new
+  # Now, for each channel in the input image, write out
+  index = 0
+  a.each do |image|
+    # The Biorad_Writer doesn't like COLOR_256 images, so convert to
+    # GRAY8:
+    ij.process.StackConverter.new(image).convertToGray8
+    biorad_filename = make_biorad_filename e, index + 1
+    puts "    Writing: #{biorad_filename}"
+    writer.save image, output_directory, biorad_filename
+    index += 1
+    image.close
+  end
+end
+
+ij.IJ.showMessage("Finished converting to Biorad format!")

src/main/resources/script-templates/Ruby/Invert_image.rb

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+# @ImagePlus i
+# A basic script that inverts the current image.
+# NB: this requires that an image is already open.
+# The ImagePlus is populated automatically via the
+# scripting framework.
+# We explicitly import the java ij.ImagePlus class,
+# but this may not be necessary if you already have
+# an imagej.rb required into this script.
+java_import "ij.ImagePlus"
+
+# Invert the image and redraw it
+$i.getProcessor.invert
+$i.updateAndDraw

src/main/resources/script-templates/Ruby/Plasma_Cloud.rb

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+# Manually create and display a color ImagePlus
+java_import "ij.process.ColorProcessor"
+java_import "ij.ImagePlus"
+
+w = 800
+h = 600
+
+# Create an ImagePlus
+cp = ColorProcessor.new(w, h)
+i = ij.ImagePlus.new "Plasma Cloud", cp
+
+# Set Image's pixels
+pixels = cp.getPixels;
+java.util.Arrays.fill(pixels, 0, w*h/2 - 1, 0x0000FF00)
+
+# Display the image
+i.show