Make a json of list of images of MicroManager

mk_list.rb

#!/usr/bin/env ruby

# 

require 'rubygems'
require 'json'
require 'find'
require 'csv'

def parent(f)
	f.split(File::SEPARATOR)[0...-1].join(File::SEPARATOR)
end

# A folder with display_and_comments.txt is a unit of acquisition.
# It may have multiple metadata.txt
def search(f)
	num_pos = 0
	chs = []
	frames = []
	slices = []
	Find.find(f){|mf|
		next if not mf =~ /metadata\.txt$/
		num_pos += 1
		obj = JSON.parse(IO.read(mf))
		s = obj["Summary"]
		if s["ChNames"] == ["Default"]
			chs << [obj[obj.keys[1]]["Channel"]]
		else
			chs << s["ChNames"]
		end
		slices << s["Slices"]
		frames << Dir.glob(parent(mf)+'/*.tif').length
	}
	chs = chs.flatten.uniq
	{:folder => f.split(File::SEPARATOR).last, :ch => chs, :pos => num_pos, :slice => slices.max, :frames => frames.max}
end

top_folders = Dir.glob('../../*/')
rr = []
top_folders.map{|folder|
	r = []
	Find.find(folder){|f|
		next if not f =~ /display_and_comments\.txt$/
		puts parent(f)
		r << search(parent(f))
	}
	rr << {:folder => folder.split(File::SEPARATOR).last, :sets =>r}
}

def write_csv(obj)
	CSV.open("list.csv", "wb") do |csv|
		csv << ["Flowcell", "Acquisition", "Positions", "Channels", "Frames", "Slices"]
		for fc in obj
			csv << [fc[:folder]]
			for s in fc[:sets]
				csv << ["",s[:folder],s[:pos],s[:ch].join(", "), s[:frames], s[:slice]]
			end
		end
	end
end

write_csv(rr)

IO.write("list.json",JSON.pretty_generate(rr))