from __future__ import absolute_import, division, print_function from six.moves import range # -*- mode: python; coding: utf-8; indent-tabs-mode: nil; python-indent: 2 -*- # # LIBTBX_SET_DISPATCHER_NAME cxi.make_mar_mask # # $Id: # # This code dumps a flex array containing masked out pixels given certain specifications # The result is an image with all pixels which are valid for use set to 0, and # those that are invalid set to -2 by default, or the value of the option passed in # to mask_pix_val. # from scitbx.array_family import flex import sys from libtbx import easy_pickle from xfel.cxi.cspad_ana.cspad_tbx import dpack, dwritef2 def point_in_polygon(point, poly): """ Determine if a point is inside a given polygon or not. Polygon is a list of (x,y) pairs. Code adapted from a dials polygon clipping test algorithm""" if len(poly) < 3: return False inside = False for i in range(len(poly)): j = (i+1) % len(poly) if (((poly[i][1] > point[1]) != (poly[j][1] > point[1])) and (point[0] < (poly[j][0] - poly[i][0]) * (point[1] - poly[i][1]) / (poly[j][1] - poly[i][1]) + poly[i][0])): inside = not inside return inside def point_inside_circle(x,y,center_x,center_y,radius): """Determine if a given point (x,y) is inside a circle whose center is at (center_x,center_y) with radius x.""" return (x-center_x)**2 + (y - center_y)**2 < radius**2 def run(argv=None): import libtbx.option_parser if (argv is None): argv = sys.argv command_line = (libtbx.option_parser.option_parser( usage="%s [-v] [-p poly_mask] [-c circle_mask] [-x mask_pix_val] [-o output] -W mask_width -H mask_height" % libtbx.env.dispatcher_name) .option(None, "--verbose", "-v", action="store_true", default=False, dest="verbose", help="Print more information about progress") .option(None, "--poly_mask", "-p", type="string", default=None, dest="poly_mask", help="Polygon to mask out. Comma-seperated string of xy pairs.") .option(None, "--circle_mask", "-c", type="string", default=None, dest="circle_mask", help="Circle to mask out. Comma-seperated string of x, y, and radius.") .option(None, "--mask_pix_val", "-x", type="int", default=-2, dest="mask_pix_val", help="Value for masked out pixels") .option(None, "--mask_width", "-W", type="int", default=None, dest="mask_width", help="Width of output mask") .option(None, "--mask_height", "-H", type="int", default=None, dest="mask_height", help="Height of output mask") .option(None, "--output", "-o", type="string", default="mask.pickle", dest="destpath", help="Output file path, should be *.pickle") .option(None, "--pixel_size", "-s", type="float", default=None, dest="pixel_size", help="Pixel size for detector") ).process(args=argv[1:]) # Must have width and height set if command_line.options.mask_height is None or command_line.options.mask_width is None: command_line.parser.print_usage(file=sys.stderr) return poly_mask = None if not command_line.options.poly_mask == None: poly_mask = [] poly_mask_tmp = command_line.options.poly_mask.split(",") if len(poly_mask_tmp) % 2 != 0: command_line.parser.print_usage(file=sys.stderr) return odd = True for item in poly_mask_tmp: try: if odd: poly_mask.append(int(item)) else: poly_mask[-1] = (poly_mask[-1],int(item)) except ValueError: command_line.parser.print_usage(file=sys.stderr) return odd = not odd circle_mask = None if command_line.options.circle_mask is not None: circle_mask_tmp = command_line.options.circle_mask.split(",") if len(circle_mask_tmp) != 3: command_line.parser.print_usage(file=sys.stderr) return try: circle_mask = (int(circle_mask_tmp[0]),int(circle_mask_tmp[1]),int(circle_mask_tmp[2])) except ValueError: command_line.parser.print_usage(file=sys.stderr) return mask = flex.int(flex.grid(command_line.options.mask_width, command_line.options.mask_height)) if poly_mask is not None or circle_mask is not None: minx = miny = 0 maxx = mask.focus()[0] maxy = mask.focus()[1] if poly_mask is not None: minx = min([x[0] for x in poly_mask]) miny = min([y[1] for y in poly_mask]) maxx = max([x[0] for x in poly_mask]) maxy = max([y[1] for y in poly_mask]) if circle_mask is not None: circle_x, circle_y, radius = circle_mask if circle_x - radius < minx: minx = circle_x - radius if circle_y - radius < miny: miny = circle_y - radius if circle_x + radius > maxx: maxx = circle_x + radius if circle_y + radius > maxy: maxy = circle_y + radius sel = mask == command_line.options.mask_pix_val for j in range(miny, maxy): for i in range(minx, maxx): idx = j * mask.focus()[0] + i if not sel[idx]: if poly_mask is not None and point_in_polygon((i,j),poly_mask): sel[idx] = True elif circle_mask is not None and point_inside_circle(i,j,circle_x,circle_y,radius): sel[idx] = True mask.set_selected(sel,command_line.options.mask_pix_val) masked_out = len(mask.as_1d().select((mask == command_line.options.mask_pix_val).as_1d())) print("Masked out %d pixels out of %d (%.2f%%)"% \ (masked_out,len(mask),(masked_out)*100/(len(mask)))) easy_pickle.dump(command_line.options.destpath, mask) d = dpack( active_areas=[0,0,command_line.options.mask_width,command_line.options.mask_height], address=None, beam_center_x=None, beam_center_y=None, data=mask, distance=None, timestamp=None, wavelength=1, xtal_target=None, pixel_size=command_line.options.pixel_size, saturated_value=None) dwritef2(d, command_line.options.destpath) if (__name__ == "__main__"): sys.exit(run())