cmtkgui.py

'''
cmtkgui module containing helper functions for Fiji CMTK GUI
'''
import os, sys, time, csv
import subprocess, re, urllib2, tempfile
import platform

is_jython = platform.system()=="Java"

if(is_jython):
	import java.io.File

gui_tarball_url='https://github.com/jefferis/fiji-cmtk-gui/tarball/master'

def myExit(err):
	'''Placeholder until I figure out suitable way to break out of jython script'''
	if err==None:
		err=''
	sys.exit(err)

def myErr(err):
	from ij import IJ
	IJ.error(err)
	myExit(err)

def log(msg):
	'''
	logger that chooses simple prints or ImageJ log as appropriate
	'''
	if is_jython:
		from ij import IJ
		if IJ.debugMode:
			print(msg)
	else:
		print(msg)

def which(execname):
	'''
	run system which command to locate an executable
	'''
	return subprocess.Popen(["which", execname], stdout=subprocess.PIPE).communicate()[0].rstrip()

def findExecutable(execname,msg=''):
    '''
    @return full path to a command using the shell's which function
    '''
    execpath=which(execname)
    if execpath == '' :
        import fiji.util.gui.GenericDialogPlus
        gd = fiji.util.gui.GenericDialogPlus(msg)
        if msg == '' :
            msg="Locate the directory containing program "+execname
        gd.addDirectoryField(msg, "")
        gd.showDialog()
        execdir = gd.getNextString()
        execpath = os.path.join(execdir,execname)
        if os.path.exists(execpath) :
            return execpath
        else :
            sys.exit('Unable to locate '+execname+' in directory '+execdir)
    else : return execpath

def relpath(path, basedir = os.curdir):
    ''' @return a relative path from basedir to (sub) path.
    
    basedir defaults to curdir
    Does not work with paths outside basedir
    This is superseded by a builtin in python >=2.6
    '''
    basedir = os.path.abspath(basedir)
    path = os.path.abspath(path)
    
    if basedir == path :
        return '.'
    if basedir in path :
    	# nb joining empty string appends terminal pathsep in platform independent way
        return path.replace(os.path.join(basedir,''),'')
    return (path)

def makescript(cmd,rootdir,outdir):
    '''
    Make a shell script file that can be used to rerun the warp action, using
    chmod to ensure that it is executable.
    
    On MacOS X the file suffix is command so that it can be double clicked in the Finder.
    '''
    if not os.path.exists(outdir): os.mkdir(outdir)
    mtime = time.strftime('%Y-%m-%d_%H.%M.%S')
    suffix='sh'
    if "MacOSX" in os_string():
        suffix='command'
    filename= "munger_%s.%s" %(mtime,suffix)
    filepath=os.path.join(outdir,filename)
    f = open(filepath, 'w')
    f.write('#!/bin/sh\n# %s\ncd \"%s"\n%s' % (mtime, rootdir, cmd))
    f.close()
    os.chmod(filepath,0755)
    return filepath

def downloads():
	'''
	Fetch a list of available tar.gz downloads
	Exclude macports versions or 
	'''
	nitrc_url='http://www.nitrc.org'
	cmtk_dwld_url=nitrc_url+'/frs/?group_id=212'
	response = urllib2.urlopen(cmtk_dwld_url)
	html = response.readlines()

	urls=list()
	for line in html:
		match=re.search('href="(.*tar.gz)".*',line)
		if match is not None:
			badmatch=re.search('(-mp-|-MacPorts-|Source)',line)
			if badmatch == None:
				relpath=match.group(1)
				url=nitrc_url+relpath
				urls.append(url)
	if len(urls)==0:return None
	else: return urls

def os_string():
	'''
	Return a string indicating the current OS formatted according to CMTK filename conventions
	Linux
	MacOSX-10.4
	MacOSX-10.5
	MacOSX-10.6
	CYGWIN
	'''
	from java.lang import System
	osname=System.getProperty("os.name")

	if osname.startswith('Windows'):
		return 'CYGWIN'
	elif osname.startswith('Linux'):
		return 'Linux'
	elif osname.startswith('Mac'):
		osversion=System.getProperty("os.version")
		match=re.match(r'10\.([0-9]+)(\.[0-9])*',osversion)
		if match==None:
			sys.exit('Unable to identify OS version: '+osversion)
		osmajor=match.group(1)
		iosmajor=int(osmajor)
		if iosmajor<4:
			myErr('Sorry CMTK requires MacOSX >=10.4')
		elif iosmajor>6:
			osmajor='6'
		return 'MacOSX-10.'+osmajor
	else:
		return None

def recommended_file(files):
	'''
	Pick the recommended download file based on current OS
	'''
	osname=os_string()
	if osname==None:
		return None
	for f in files:
		match=re.search(osname,f)
		if match:
			return f
	return None

def install_dir():
	'''return sensible location to install cmtk'''
	from ij import IJ
	ijdir=IJ.getDirectory('imagej')
	return os.path.join(ijdir,'bin','cmtk')

def gui_install_dir():
	'''return sensible location to install CMTK GUI'''
	from ij import IJ
	pluginsdir=IJ.getDirectory('plugins')
	return os.path.join(pluginsdir,'CMTK_Registration')

def bin_dir():
	'''
	Return path to cmtk binaries
	Currently the same as install dir
	'''
	return install_dir()

def system_cmtk_bin_dir(cmtktool='streamxform'):
	'''
	return path to the system folder containing CMTK binaries
	'''
	extradirs=('/usr/local/bin', '/opt/local/bin', '/usr/local/lib/cmtk/bin', '/opt/local/lib/cmtk/bin')
	cmtktoolpath=which(cmtktool)
	if(cmtktoolpath!=''):
		return os.path.dirname(cmtktoolpath)
	cmtkwrapperpath=which("cmtkk")
	if(cmtkwrapperpath!=''):
		return os.path.abspath(os.path.join(os.path.dirname(cmtkwrapperpath),"..","lib", "cmtk","bin"))
	return dir_containing_file(extradirs, cmtktool)

def dir_containing_file(dirs, filename):
	'''
	return absolute path to directory containing a file
	'''
	for d in dirs:
		filepath=os.path.join(d, filename)
		if os.path.exists(filepath):
			return os.path.abspath(d)
	return None

def tool_path(tool):
	'''path to a CMTK tool'''
	return os.path.join(bin_dir(),tool)

def installed_version():
	'''Return current version of CMTK installed in Fiji bin dir'''
	ver=run_tool_stdout('warpx','--version')
	if ver:
		return ver
	else: return ""

def run_tool_stdout(tool,args):
	'''Return stdout after running CMTK tool with args'''
	toolp=tool_path(tool)
	if not os.path.exists(toolp):
		return None
	arglist=[toolp]
	if isinstance(args,list):
		arglist+=args
	elif args is None:
		arglist+=['']
	else:
		arglist+=[args]
	return subprocess.Popen(arglist, stdout=subprocess.PIPE).communicate()[0].rstrip()

def nitrc_version():
	'''Check NITRC website to see what version is available'''
	match=re.search(r"CMTK-([0-9]+\.[0-9]+\.[0-9]+)",os.path.basename(downloads()[0]))
	if match:
		return match.group(1)
	else:
		return None

def parse_version_string(ver_string):
	'''
	Parse a CMTK version string into major,minor and patch numbers (integers)
	'''
	if ver_string is None:
		return None
	v=re.match(r"(?P<major>[0-9]+)\.(?P<minor>[0-9]+)\.(?P<patch>[0-9]+)",ver_string)
	if v:
		ver_list=(v.group('major'),v.group('minor'),v.group('patch'))
		return map(int,ver_list)
	else:
		return None

def update_available():
	'''
	Check if NITRC version is newer than current version.
	Assumes that NITRC version can never be older than current version.
	'''
	r=parse_version_string(nitrc_version())
	l=parse_version_string(installed_version())
	if r is None: return None
	if l is None: return True
	if l[0]<r[0]: return True
	elif l[1]<r[1]: return True
	elif l[2]<r[2]: return True
	else: return False

def gui_github_versioninfo():
	'''
	Create a dictionary containing version information for current
	github code
	'''
	try:
		u = urllib2.urlopen(gui_tarball_url)
		headers = u.info()
		date = headers['date']
		size = int(headers['Content-Length'])
		filename = re.sub(".*filename=","",headers['Content-Disposition'])
		u.close()
		abbrev_sha1 = re.sub(".*-([a-f0-9]+).tar.gz","\\1",filename)
		return {'abbrev_sha1':abbrev_sha1, 'filename':filename, 'date':date, 'size':size}
	except IOError, e:
		myErr("Unable to read github repository")
	except :
		myErr("Trouble parsing github return information")

def gui_local_versioninfo():
	'''	
	Read a csv file containing the version information for current
	CMTK GUI code
	'''
	version_file = os.path.join(gui_install_dir(),"CMTKGUIVersion.csv")
	if not os.path.exists(version_file):
		return {}
	versioninfo = {}
	for key, val in csv.reader(open(version_file)):
		versioninfo[key] = val
	return(versioninfo)

def gui_write_local_versioninfo(versioninfo):
	'''
	Write a csv file containing the version information for current
	CMTK GUI code
	'''
	version_file = os.path.join(gui_install_dir(),"CMTKGUIVersion.csv")
	myfile = open(version_file, "w")
	
	w = csv.writer(myfile)
	for key, val in versioninfo.items():
		w.writerow([key, val])
	myfile.close()

def gui_update_available(github_versioninfo=None):
	'''
	Check if an update is available on github
	optionally using a cached copy of the versioninfo dictionary
	'''
	lvi=gui_local_versioninfo()
	if not lvi.has_key('abbrev_sha1'):
		return True
	if github_versioninfo is None:
		github_versioninfo=gui_github_versioninfo()
	if lvi['abbrev_sha1']==github_versioninfo['abbrev_sha1']:
		return(False)
	else:
		return(True)

def download_and_untar_url(download_url,target_dir,untarfun,download_file=None,
	download_msg=None):
	'''
	download file in temporary location
	untar to target_dir using untarfun
	clean up download
	'''
	# open url and set up using header information
	u = urllib2.urlopen(download_url)
	headers = u.info()
	download_size = int(headers['Content-Length'])
	if download_file == None:
		if headers.has_key('Content-Disposition'):
			download_file = re.sub(".*filename=","",headers['Content-Disposition'])
		else:
			myErr("No filename specified for download and none in http header!")
	if download_msg==None:
		download_msg='Downloading: %s' % (download_file)
	tf=tempfile.NamedTemporaryFile(suffix=download_file)
	print 'Downloading '+download_url+' to '+ tf.name
	print "Download size should be %d" % (download_size)
	
	from ij import IJ
	
	# Now for the download
	block_size=100000
	if download_size>block_size:
		bytes_read=0
		while bytes_read<download_size:
			IJ.showStatus("%s (%.1f/%.1f Mb)" % 
				(download_msg,(bytes_read/1000000.0),(download_size/1000000.0)))
			IJ.showProgress(bytes_read,download_size)
			tf.file.write(u.read(block_size))
			bytes_read+=block_size
		IJ.showProgress(1.0)
	else:
		tf.file.write(u.read())
	u.close()
	tf.file.close()
	print ('Downloaded file has size %d')%(os.path.getsize(tf.name))
	untarfun(tf.name,target_dir)
	IJ.showStatus('Cleaning up!')
	tf.close()

def movefile(frompath, todir):
	'''
	move a file to a new location (renaming) using Java calls
	needed because jython shutil.move has bugs
	'''
	if is_jython:
		fromf=java.io.File(frompath)
		tof=java.io.File(os.path.join(todir,os.path.basename(frompath)))
		fromf.renameTo(tof)
	else:
		shutil.move(frompath, to)