DDSM数据库转换图像格式——LJPEG转为PNG格式

Digital Database for Screening Mammography (DDSM)数据库是一个非常大的乳腺图像数据库，有一万多张图像，但是图像格式是LJPEG，现有的图像软件（如photoshop、ACCDsee、windows自带的图像查看软件）以及编程软件（如matlab）都无法读取，需要将其转换成其他常见的格式才能使用。我从网上搜到了很多方法，试过之后都不成功，其中包括该数据库的创建者——南佛罗里达大学自己写的一个程序[1]，一个医学图像格式转换软件XMedCon[2]。最后成功的方法是使用曼彻斯特大学的Dr. Chris Rose写的一个完整的程序，在他的程序基础上做了些修改，成功的将图像格式转换成了PNG格式。他的程序链接见http://microserf.org.uk/academic/Software.html （PS. 最近发现此链接地址已失效，所以我把源程序放在了我的github上，地址：https://github.com/hd11224/DDSM，包括了所有需要的工具和软件）

从上面给出的链接下载到的程序中，有用户手册告诉你怎么使用这个程序。这个程序是用Ruby语言写的，需要在Cygwin下运行，用户手册中有介绍如何安装Cygwin及其他需要的工具。程序工作流程是使用者手动输入图像名称，程序先从FTP上下载该图像，然后经过几步转换，最终转换为PNG格式。我在按照用户手册运行这个程序时没有成功，用VS2013打开get-ddsm-mammo文件查看源码，发现是从FTP上下载图像环节出了问题，做了修改后，最终运行成功。我修改后的程序如下：

#!/usr/bin/ruby# This program gets a specified mammogram from the DDSM website and
# converts it to a PNG image. See the help message for full details.require 'net/ftp'# Specify the name of the info-file.
def info_file_name'info-file.txt'
enddef image_names'image_name.txt'
end# Get an FTP file as specified by a DDSM path (e.g.,
# /pub/DDSM/cases/cancers/cancer_06/case1141/A-1141-1.ics) and return the
# local path to the file, or return nil if the file could not be dowloaded.
def get_file_via_ftp(ddsm_path)ftp = Net::FTP.new('figment.csee.usf.edu')ftp.passive = trueftp.login  ftp.chdir(File.dirname(ddsm_path))  puts File.basename(ddsm_path)  ftp.getbinaryfile(File.basename(ddsm_path))#ftp.getbinaryfile(ddsm_path)# Will be stored local to this program, under the same file name# Check to make sure that we managed to get the file.if !FileTest.exist?(File.basename(ddsm_path))puts "Could not get the file #{File.basename(ddsm_path)} from the DDSM FTP server; perhaps the server is busy."exit(-1)end  return File.basename(ddsm_path)
end# Return the string input with the system's filesep at the end; if there
# is one there already then return input.
def ensure_filesep_terminated(input)if input[input.length-1].chr != File::SEPARATORinput += File::SEPARATORendreturn input
end# Check program input; input is the program input (i.e ARGV).
def check_inputs(input)if input.length != 1puts get_helpexit(-1)end# See if the user wanted the help docs.if input[0] == '--help'puts get_helpexit(-1)end# Check to make sure that the info file exists.if !FileTest.exist?(info_file_name)puts "The file #{info_file_name} does not exist; use catalogue-ddsm-ftp-server.rb"exit(-1)endend# Given the name of a DDSM image, return the path to the
# .ics file associated with the image name. If we can't find the
# path, then we return nil.
def get_ics_path_for_image(image_name)# Does image_name look right?if image_name[/._\d{4,4}_.\..+/].nil?raise 'image_name seems to be wrong. It is: ' + image_nameend# Edit the image name, as .ics files have the format 'A-0384-1.ics';# there is no '.RIGHT_CC' (for example).image_name = image_name[0..(image_name.rindex('.')-1)] # Strip everything after and including the last '.'.image_name[1] = '-'image_name[6] = '-' # Change the '_'s to '-'s (better regexp-based approach?).image_name+='.ics' # Add the file suffix.# Get the path to the .ics file for the specified image.File.open(info_file_name) do |file|file.each_line do |line|# Does this line specify the .ics file for the specified image name?if !line[/.+#{image_name}/].nil?# If so, we can stop looking       return line     endendend# If we get here, then we did not find a match, so we will return nil.return nil
end# Given a line from a .ics file, return a string that specifies the
# number of rows and cols in the image described by the line. The
# string would be '123 456' if the image has 123 rows and 456 cols.
def get_image_dims(line)rows = line[/.+LINES\s\d+/][/\d+/]cols = line[/.+PIXELS_PER_LINE\s\d+/][/PIXELS_PER_LINE\s\d+/][/\d+/]return rows + ' ' + cols
end# Given an image name and a string representing the location of a
# local .ics file, get the image dimensions and digitizer name for
# image_name. Return a hash which :image_dims maps to a string of the
# image dims (which would be '123 456' if the image has 123 rows and
# 456 cols) and :digitizer maps to the digitizer name. If we can't
# determine the dimensions and/or digitizer name, the corresponding
# entry in the hash will be nil.
def get_image_dims_and_digitizer(image_name, ics_file)# Get the name of the image view (e.g. 'RIGHT_CC')image_view = image_name[image_name.rindex('.')+1..image_name.length-1]image_dims = nildigitizer = nil# Read the image dimensions and digitizer name from the file.File.open(ics_file, 'r') do |file|file.each_line do |line|if !line[/#{image_view}.+/].nil?# Read the image dimensionsimage_dims = get_image_dims(line)endif !line[/DIGITIZER.+/].nil?# Read the digitizer type from the file.digitizer = line.split[1].downcase # Get the second word in the DIGITIZER line.# There are two types of Howtek scanner and they are# distinguished by the first letter in image_name.if digitizer == 'howtek'if image_name[0..0].upcase == 'A'digitizer += '-mgh'elsif image_name[0..0].upcase == 'D'digitizer += '-ismd'elseraise 'Error trying to determine Howtek digitizer variant.'endendendendend# Return an associative array specifying the image dimensions and# digitizer used.return {:image_dims => image_dims, :digitizer =>digitizer}
end# Given the name of a DDSM image, return a string that describes
# the image dimensions and the name of the digitizer that was used to
# capture it. If
def do_get_image_info(image_name)# Get the path to the ics file for image_name.ftp_path = get_ics_path_for_image(image_name)ftp_path.chomp!# Get the ics file; providing us with a string representing# the local location of the file.ics_file = get_file_via_ftp(ftp_path)# Get the image dimensions and digitizer for image_name.image_dims_and_digitizer = get_image_dims_and_digitizer(image_name, ics_file)# Remove the .ics file as we don't need it any more.File.delete(ics_file)return image_dims_and_digitizer
end# Given a mammogram name and the path to the image info file, get the
# image dimensions and digitizer name string.
def get_image_info(image_name)# Get the image dimensions and digitizer type for the specified# image as a string.image_info = do_get_image_info(image_name)# Now output the result to standard output.all_ok = !image_info[:image_dims].nil? && !image_info[:digitizer].nil? # Is everything OK?if all_okret_val = image_info[:image_dims] + ' ' + image_info[:digitizer]endreturn ret_val
end# Return a non-existant random filename.
def get_temp_filenamerand_name = "#{rand(10000000)}" # A longish stringif FileTest.exist?(rand_name)rand_name = get_temp_filenameendreturn rand_name
end# Retrieve the LJPEG file for the mammogram with the specified
# image_name, given the path to the info file. Return the path to the
# local file if successful. If we can't get the file, then return nil.
def get_ljpeg(image_name)# Get the path to the image file on the mirror of the FTP server.path = nilFile.open(info_file_name) do |file|file.each_line do |line|if !line[/.+#{image_name}\.LJPEG/].nil?# We've found it, so get the file.line.chomp!local_path = get_file_via_ftp(line)      return local_pathendendend# If we get here we didn't find where the file is on the server.return nil
end# Given the path to the dir containing the jpeg program, the path to a
# LJPEG file, convert it to a PNM file. Return the path to the PNM
# file.
def ljpeg_to_pnm(ljpeg_file, dims_and_digitizer)# First convert it to raw format.command = "./jpeg.exe -d -s #{ljpeg_file}"`#{command}` # Run it.raw_file = ljpeg_file + '.1' # The jpeg program adds a .1 suffix.# See if the .1 file was created.if !FileTest.exist?(raw_file)raise 'Could not convert from LJPEG to raw.'end# Now convert the raw file to PNM and delete the raw file.command = "./ddsmraw2pnm.exe #{raw_file} #{dims_and_digitizer}"pnm_file = `#{command}`File.delete(raw_file)if $? != 0raise 'Could not convert from raw to PNM.'end# Return the path to the PNM file.return pnm_file.split[0]
end# Convert a PNM file to a PNG file. pnm_file is the path to the pnm file
# and target_png_file is the name of the PNG file that we want created.
def pnm_to_png(pnm_file, target_png_file)command = "convert -depth 16 #{pnm_file} #{target_png_file}"`#{command}`if !FileTest.exist?(target_png_file)raise 'Could not convert from PNM to PNG.'endreturn target_png_file
end#write image_names to image_nama.txt
def write_image_names(name)namefile=File.open(image_names,'a') namefile.puts namenamefile.puts "\r\n"namefile.close
end# The entry point of the program.
def main  # Check to see if the input is sensible.#check_inputs(ARGV)#image_name = ARGV[0]File.open('read_names.txt','r') do |file|file.each_line do |line|image_name = lineimage_name.chomp!# Get the image dimensions and digitizer name string for the# specified image.image_info = get_image_info(image_name)# Get the LJPEG file from the mirror of the FTP site, returning the# path to the local file.ljpeg_file = get_ljpeg(image_name)# Convert the LJPEG file to PNM and delete the original LJPEG.pnm_file = ljpeg_to_pnm(ljpeg_file, image_info)File.delete(ljpeg_file)# Now convert the PNM file to PNG and delete the PNG file.target_png_file = image_name + '.png'png_file = pnm_to_png(pnm_file, target_png_file)File.delete(pnm_file)# Test to see if we got something.if !FileTest.exist?(png_file)raise 'Could not create PNG file.'exit(-1)end# Display the path to the file.puts File.expand_path(png_file)#write image namewrite_image_names(image_name)#exit(0)end  endexit(0)
end# The help message
def get_help<<END_OF_HELPThis program gets a specified mammogram from a local mirror of theDDSM FTP Server, converts it to a PNG image and saves it to a targetdirectory; if the target directory already contains a suitably-namedfile, the download and conversion are skipped.Call this program using:ruby get-ddsm-mammo.rb <image-name>(Note: the '\\' simply indicates that the above command should be onone line.)where:* <image-name> is the name of the DDSM image you want to get andconvert, for example: 'A_1141_1.LEFT_MLO'.If successful, the program will print the path to the PNG file ofthe requested mammogram to standard output and will return a statuscode of 0. If unsuccessful, the program should display auseful error message and return a non-zero status code.END_OF_HELP
end# Call the entry point.
main

很麻烦的一点是，原程序运行需要手动依次输入图像名称，一次只能处理一张图像，一张图像处理完后才能处理下一张，很费时费力，所以在上面贴出的程序中我还做了一点修改，可以批量处理图像。方法是将要处理的图像的名称提前写在一个txt文件里，一行一个，命名为read_names，运行程序只需输入 ./get-ddsm-mammo即可。程序运行界面如下：

每处理完一张图像，程序会将图像的名称写在一个名为image_name的txt文件里，所以在运行程序前要先创建一个名为image_name的txt文件。

最后一点要说明的是，用户手册中提到在安装Cygwin时要同时安装Ruby,因为当时的Cygwin版本较低，Ruby已不在手册中所示位置，而是单独拿出来的，要安装如下图所示的Ruby和rubygems：

和

在ddsm-software文件夹下，会看到已经转为PNG格式的图像：

[1]http://marathon.csee.usf.edu/Mammography/software/heathusf_v1.1.0.html

[2]http://sourceforge.net/projects/xmedcon/

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