import sys

from ij import IJ as ij

from ij.plugin.frame import RoiManager

from ij.gui import Roi, PolygonRoi

from loci.plugins import BF

from loci.common import Region

from loci.plugins.in import ImporterOptions

from loci.formats import ImageReader, ImageWriter

from loci.formats import MetadataTools

from ome.xml.meta import OMEXMLMetadata

file = "%s"

options = ImporterOptions()

options.setId(file)

imps = BF.openImagePlus(options)

reader = ImageReader()

omeMeta = MetadataTools.createOMEXMLMetadata()

reader.setMetadataStore(omeMeta)

reader.setId(file)

roiCount = omeMeta.getROICount()

if roiCount > 1:

sys.exit(0)

omeMetaStr = omeMeta.dumpXML()

shape = omeMeta.getShapeType(0,0)

if 'Polygon' not in shape:

sys.exit(0)

prefix = omeMetaStr.index(shape)

stop = omeMetaStr.find('/',prefix,-1) - 1

start = len(shape + " " + "points=") + 1

pts = omeMetaStr[start+prefix:stop]

new_pts_str =pts.replace(" ",",")

new_pts = [int(p) for p in new_pts_str.split(",")]

xs = new_pts[0::2]

ys = new_pts[1::2]

proi = PolygonRoi(xs, ys, len(xs), Roi.POLYGON)

imp = imps[0]

imp.setRoi(proi)

# create a writer and set metadata

writer = ImageWriter()

writer.setMetadataRetrieve(omeMeta)

writer.setId('%s')

# get the stack

planes = imp.getStack()

for p in range(planes.getSize()):

# get the plane

plane = planes.getProcessor(p+1)

# fill outside

plane.fillOutside(proi)

pixels = plane.convertToByte(True).getPixels()

writer.saveBytes(p,pixels)

reader.close()

writer.close()

imp.flush()