def _combine_exclude_mask(self, mask):
# create masks from exclude/include regions and combine it with the
# input DQ mask:
#
regmask = None
if self.src_find_filters is not None and \
'region_file' in self.src_find_filters:
reg_file_name = self.src_find_filters['region_file']
if not os.path.isfile(reg_file_name):
raise IOError(
"The 'exclude' region file '{:s}' does not exist.".format(
reg_file_name))
else:
return mask
# get data image size:
(img_ny, img_nx) = self.source.shape
# find out if user provided a region file or a mask FITS file:
reg_file_ext = os.path.splitext(reg_file_name)[-1]
if reg_file_ext.lower().strip() in ['.fits', '.fit'] and \
basicFITScheck(reg_file_name):
# likely we are dealing with a FITS file.
# check that the file is a simple with 2 axes:
hdulist = fits.open(reg_file_name, memmap=False)
extlist = get_extver_list(hdulist, extname=None)
for ext in extlist:
usermask = hdulist[ext].data
if usermask.shape == (img_ny, img_nx):
regmask = usermask.astype(np.bool)
break
hdulist.close()
if regmask is None:
raise ValueError("None of the image-like extensions in the "
"user-provided exclusion mask '{}' has a "
"correct shape".format(reg_file_name))
else:
# we are dealing with a region file:
reglist = pyregion.open(reg_file_name)
## check that regions are in image-like coordinates:
##TODO: remove the code below once 'pyregion' package can correctly
## (DS9-like) convert sky coordinates to image coordinates for all
## supported shapes.
#if not all([ (x.coord_format == 'image' or \
# x.coord_format == 'physical') for x in reglist]):
# print("WARNING: Some exclusion regions are in sky coordinates.\n"
# " These regions will be ignored.")
# # filter out regions in sky coordinates:
# reglist = pyregion.ShapeList(
# [x for x in reglist if x.coord_format == 'image' or \
# x.coord_format == 'physical']
# )
#TODO: comment out next lines if we do not support region files
# in sky coordinates and uncomment previous block:
# Convert regions from sky coordinates to image coordinates:
auxwcs = _AuxSTWCS(self.wcs)
reglist = reglist.as_imagecoord(auxwcs, rot_wrt_axis=2)
# if all regions are exclude regions, then assume that the entire image
# should be included and that exclude regions exclude from this
# rectangular region representing the entire image:
if all([x.exclude for x in reglist]):
# we slightly widen the box to make sure that
# the entire image is covered:
imreg = pyregion.parse(
"image;box({:.1f},{:.1f},{:d},{:d},0)".format(
(img_nx + 1) / 2.0, (img_ny + 1) / 2.0, img_nx + 1,
img_ny + 1))
reglist = pyregion.ShapeList(imreg + reglist)
# create a mask from regions:
regmask = np.asarray(reglist.get_mask(shape=(img_ny, img_nx)),
dtype=np.bool)
if mask is not None and regmask is not None:
mask = np.logical_and(regmask, mask)
else:
mask = regmask
#DEBUG:
if mask is not None:
fn = os.path.splitext(self.fname)[0] + '_srcfind_mask.fits'
fits.writeto(fn, mask.astype(dtype=np.uint8), overwrite=True)
return mask
def map_region_files(input_reg,
images,
img_wcs_ext='sci',
refimg=None,
ref_wcs_ext='sci',
chip_reg=None,
outpath='./regions',
filter=None,
catfname=None,
iteractive=False,
append=False,
verbose=True):
# Check that output directory exists:
if outpath in [None, ""]:
outpath = os.path.curdir + os.path.sep
elif not os.path.isdir(outpath):
raise IOError("The output directory \'%s\' does not exist." % outpath)
if filter is not None and filter.lower() not in ["fast", "precise"]:
raise TypeError("The 'filter' argument can be None, 'fast', " \
"or 'precise'.")
#TODO: Implement the "precise" checking of region intersection
# with the image's bounding box.
if filter is not None and filter.lower() == "precise":
_print_warning("\"precise\" filter option is not yet supported. "\
"Reverting to filter = \"fast\" instead.")
filter = "fast"
# create a 2D list of region - header (with WCS) pairs:
# [[reg1,ref_wcs_header1],[reg2,ref_wcs_header2],...]
regheaders = build_reg_refwcs_header_list(input_reg, refimg, ref_wcs_ext,
verbose)
# create a list of input files *without* extensions (if present) and
# a 2D list of "chip" region - image extension pairs:
# [[reg1, ext1], [reg2,ext2],...]
imgfnames, cregext = build_img_ext_reg_list(images, chip_reg, img_wcs_ext,
verbose)
# build a "master" list of regions in sky coordinates:
all_sky_regions = []
for p in regheaders:
if p[1] is None: # Already in sky WCS
all_sky_regions += p[0]
else:
all_sky_regions += shapes_img2sky(
p[0], p[1]) #TODO: implement shapes_img2sky
all_sky_regions = pyregion.ShapeList(list(all_sky_regions))
cattb = []
# create a region file (with regions in image coordinates) for each
# image extension from the input_reg and chip_reg regions
for fname in imgfnames:
imghdu = None
imghdu = fits.open(fname, memmap=False)
catreg = []
try:
for extp in cregext:
ext = extp[1]
# check that the extension is of supported type:
if not _is_supported_hdu(imghdu[ext].header):
raise RuntimeError("Extension {} is of unsupported " \
"type.".format(ext))
# Remove references to non-SIP distortions from the header
#TODO: remove this line of code as well as the remove_header_tdd
# function once publicly available release of pyregion uses
# all_world2pix and all_pix2world functions and does this header
# cleanup itself.
# remove_header_tdd(imghdu[ext].header)
####### added to pass hstwcs instead of header to pyregion
# if isinstance(ext, str):
# ext = findExtname(imghdu, extname = ext, extver = 1)
# elif isinstance(ext, tuple):
# ext = findExtname(imghdu, extname = ext[0], extver = ext[1])
# wcs = stwcs.wcsutil.HSTWCS(imghdu, ext=ext)
wcs = _AuxSTWCS(imghdu, ext=ext)
extreg = all_sky_regions.as_imagecoord(wcs, rot_wrt_axis=2)
#######
#extreg = all_sky_regions.as_imagecoord(imghdu[ext].header, rot_wrt_axis=2)
if extp[0]: # add "fixed" regions if any
extreg = pyregion.ShapeList(extreg + extp[0])
# filter out regions outside the image:
if filter and filter.lower() == 'fast':
fast_filter_outer_regions(extreg,
imghdu[ext].header['NAXIS1'],
imghdu[ext].header['NAXIS2'],
origin=1)
if len(extreg) < 1: # do not create empty region files
catreg.append('None')
continue
# generate output region file name:
extsuffix = _ext2str_suffix(ext)
basefname, fext = os.path.splitext(os.path.basename(fname))
regfname = basefname + extsuffix + os.extsep + "reg"
fullregfname = os.path.join(outpath, regfname)
catreg.append(regfname)
# save regions to a file:
if append and os.path.isfile(fullregfname):
old_extreg = pyregion.open(fullregfname)
extreg = pyregion.ShapeList(old_extreg + extreg)
#TODO: pyregion.write does not work well. For now use _regwite
# (until the bug fixes get to the pyregion project).
#TODO: we replaced pyregion.write with our implementation
# of the write (code from _regwrite) in the locally maintained
# pyregion until these changes get to be implemented in the
# publicly available release of pyregion.
#
_regwrite(extreg, fullregfname)
#extreg.write(fullregfname) # <- use this instead of _regwrite
# once the pyregion bugs are fixed.
cattb.append([fname, catreg])
except:
if imghdu:
imghdu.close()
raise
# create exclusions catalog file:
if catfname:
catfh = open(os.path.join(outpath, catfname), 'w')
for catentry in cattb:
catfh.write(catentry[0]) # image file name
for reg in catentry[1]:
catfh.write(' ' + reg) # region file name
catfh.write('\n')
catfh.close()
reg_name = "test.reg"
r = stregion.open(reg_name).as_imagecoord(header=f_xray[0].header)
from stregion.mpl_helper import properties_func_default
# Use custom function for patch attribute
def fixed_color(shape, saved_attrs):
attr_list, attr_dict = saved_attrs
attr_dict["color"] = "red"
kwargs = properties_func_default(shape, (attr_list, attr_dict))
return kwargs
# select region shape with tag=="Group 1"
r1 = stregion.ShapeList([rr for rr in r if rr.attr[1].get("tag") == "Group 1"])
patch_list1, artist_list1 = r1.get_mpl_patches_texts(fixed_color)
r2 = stregion.ShapeList([rr for rr in r if rr.attr[1].get("tag") != "Group 1"])
patch_list2, artist_list2 = r2.get_mpl_patches_texts()
for p in patch_list1 + patch_list2:
ax.add_patch(p)
for t in artist_list1 + artist_list2:
ax.add_artist(t)
plt.show()