def mosaic(input_dir, output_dir, header=None, mpi=False, n_proc=8,
background_match=False, imglist=None, combine="mean",
exact_size=False, cleanup=True, bitpix=-32, level_only=True,
work_dir=None):
if not combine in ['mean', 'median', 'count']:
raise Exception("combine should be one of mean/median/count")
# Check that there are files in the input directory
if len(glob.glob('%s/*' % input_dir)) == 0:
raise Exception("No files in input directory")
# Find path to input and output directory
input_dir = os.path.abspath(input_dir) + "/"
output_dir = os.path.abspath(output_dir) + "/"
# Make work directory
if work_dir:
work_dir = os.path.abspath(work_dir) + '/'
if os.path.exists(work_dir):
raise Exception("Work directory already exists")
os.mkdir(work_dir)
else:
work_dir = tempfile.mkdtemp() + '/'
images_raw_all_tbl = work_dir + 'images_raw_all.tbl'
images_raw_tbl = work_dir + 'images_raw.tbl'
images_projected_tbl = work_dir + 'images_projected.tbl'
images_corrected_tbl = work_dir + 'images_corrected.tbl'
corrections_tbl = work_dir + 'corrections.tbl'
diffs_tbl = work_dir + 'diffs.tbl'
stats_tbl = work_dir + 'stats.tbl'
fits_tbl = work_dir + 'fits.tbl'
raw_dir = work_dir + 'raw'
projected_dir = work_dir + 'projected'
corrected_dir = work_dir + 'corrected'
diffs_dir = work_dir + 'diffs'
header_hdr = work_dir + 'header.hdr'
# Find path to header file if specified
if header:
header = os.path.abspath(header)
# Find path to image list if specified
if imglist:
imglist = os.path.abspath(imglist)
# Create output dir
if os.path.exists(output_dir):
raise Exception("Output directory already exists")
else:
os.mkdir(output_dir)
# Create symbolic links
os.symlink(input_dir, raw_dir)
if header:
os.symlink(header, header_hdr)
# Create temporary directories for Montage
os.mkdir(projected_dir)
if background_match:
os.mkdir(diffs_dir)
os.mkdir(corrected_dir)
# List frames to mosaic
print "Listing raw frames"
m.mImgtbl(raw_dir, images_raw_all_tbl, img_list=imglist, corners=True)
# Compute header if needed
if not header:
print "Computing optimal header"
m.mMakeHdr(images_raw_all_tbl, header_hdr)
images_raw_tbl = images_raw_all_tbl
else:
print "Checking for coverage"
m.mCoverageCheck(images_raw_all_tbl, images_raw_tbl, mode='header', header=header_hdr)
# Projecting raw frames
print "Projecting raw frames"
m.mProjExec(images_raw_tbl, header_hdr, projected_dir, stats_tbl,
raw_dir=raw_dir, mpi=mpi, n_proc=n_proc, exact=exact_size)
# List projected frames
m.mImgtbl(projected_dir, images_projected_tbl)
if background_match:
# Modeling background
print "Modeling background"
m.mOverlaps(images_projected_tbl, diffs_tbl)
m.mDiffExec(diffs_tbl, header_hdr, diffs_dir, proj_dir=projected_dir,
mpi=mpi, n_proc=n_proc)
m.mFitExec(diffs_tbl, fits_tbl, diffs_dir)
m.mBgModel(images_projected_tbl, fits_tbl, corrections_tbl,
n_iter=32767, level_only=level_only)
# Matching background
print "Matching background"
m.mBgExec(images_projected_tbl, corrections_tbl, corrected_dir,
proj_dir=projected_dir)
sh.copy(corrections_tbl, output_dir)
# Mosaicking frames
print "Mosaicking frames"
m.mImgtbl(corrected_dir, images_corrected_tbl)
m.mAdd(images_corrected_tbl, header_hdr, output_dir + 'mosaic64.fits',
img_dir=corrected_dir, type=combine, exact=exact_size)
sh.copy(images_projected_tbl, output_dir)
sh.copy(images_corrected_tbl, output_dir)
else:
# Mosaicking frames
print "Mosaicking frames"
m.mAdd(images_projected_tbl, header_hdr, output_dir + 'mosaic64.fits',
img_dir=projected_dir, type=combine, exact=exact_size)
sh.copy(images_projected_tbl, output_dir)
m.mConvert(output_dir + 'mosaic64.fits', output_dir + 'mosaic.fits',
bitpix=bitpix)
m.mConvert(output_dir + 'mosaic64_area.fits',
output_dir + 'mosaic_area.fits', bitpix=bitpix)
os.remove(output_dir + "mosaic64.fits")
os.remove(output_dir + "mosaic64_area.fits")
_finalize(cleanup, work_dir)
return
def mosaic(input_dir,
output_dir,
header=None,
mpi=False,
n_proc=8,
background_match=False,
imglist=None,
combine="mean",
exact_size=False,
cleanup=True,
bitpix=-32,
level_only=True,
work_dir=None):
if not combine in ['mean', 'median', 'count']:
raise Exception("combine should be one of mean/median/count")
# Check that there are files in the input directory
if len(glob.glob('%s/*' % input_dir)) == 0:
raise Exception("No files in input directory")
# Find path to input and output directory
input_dir = os.path.abspath(input_dir) + "/"
output_dir = os.path.abspath(output_dir) + "/"
# Make work directory
if work_dir:
work_dir = os.path.abspath(work_dir) + '/'
if os.path.exists(work_dir):
raise Exception("Work directory already exists")
os.mkdir(work_dir)
else:
work_dir = tempfile.mkdtemp() + '/'
images_raw_all_tbl = work_dir + 'images_raw_all.tbl'
images_raw_tbl = work_dir + 'images_raw.tbl'
images_projected_tbl = work_dir + 'images_projected.tbl'
images_corrected_tbl = work_dir + 'images_corrected.tbl'
corrections_tbl = work_dir + 'corrections.tbl'
diffs_tbl = work_dir + 'diffs.tbl'
stats_tbl = work_dir + 'stats.tbl'
fits_tbl = work_dir + 'fits.tbl'
raw_dir = work_dir + 'raw'
projected_dir = work_dir + 'projected'
corrected_dir = work_dir + 'corrected'
diffs_dir = work_dir + 'diffs'
header_hdr = work_dir + 'header.hdr'
# Find path to header file if specified
if header:
header = os.path.abspath(header)
# Find path to image list if specified
if imglist:
imglist = os.path.abspath(imglist)
# Create output dir
if os.path.exists(output_dir):
raise Exception("Output directory already exists")
else:
os.mkdir(output_dir)
# Create symbolic links
os.symlink(input_dir, raw_dir)
if header:
os.symlink(header, header_hdr)
# Create temporary directories for Montage
os.mkdir(projected_dir)
if background_match:
os.mkdir(diffs_dir)
os.mkdir(corrected_dir)
# List frames to mosaic
print "Listing raw frames"
m.mImgtbl(raw_dir, images_raw_all_tbl, img_list=imglist, corners=True)
# Compute header if needed
if not header:
print "Computing optimal header"
m.mMakeHdr(images_raw_all_tbl, header_hdr)
images_raw_tbl = images_raw_all_tbl
else:
print "Checking for coverage"
m.mCoverageCheck(images_raw_all_tbl,
images_raw_tbl,
mode='header',
header=header_hdr)
# Projecting raw frames
print "Projecting raw frames"
m.mProjExec(images_raw_tbl,
header_hdr,
projected_dir,
stats_tbl,
raw_dir=raw_dir,
mpi=mpi,
n_proc=n_proc,
exact=exact_size)
# List projected frames
m.mImgtbl(projected_dir, images_projected_tbl)
if background_match:
# Modeling background
print "Modeling background"
m.mOverlaps(images_projected_tbl, diffs_tbl)
m.mDiffExec(diffs_tbl,
header_hdr,
diffs_dir,
proj_dir=projected_dir,
mpi=mpi,
n_proc=n_proc)
m.mFitExec(diffs_tbl, fits_tbl, diffs_dir)
m.mBgModel(images_projected_tbl,
fits_tbl,
corrections_tbl,
n_iter=32767,
level_only=level_only)
# Matching background
print "Matching background"
m.mBgExec(images_projected_tbl,
corrections_tbl,
corrected_dir,
proj_dir=projected_dir)
sh.copy(corrections_tbl, output_dir)
# Mosaicking frames
print "Mosaicking frames"
m.mImgtbl(corrected_dir, images_corrected_tbl)
m.mAdd(images_corrected_tbl,
header_hdr,
output_dir + 'mosaic64.fits',
img_dir=corrected_dir,
type=combine,
exact=exact_size)
sh.copy(images_projected_tbl, output_dir)
sh.copy(images_corrected_tbl, output_dir)
else:
# Mosaicking frames
print "Mosaicking frames"
m.mAdd(images_projected_tbl,
header_hdr,
output_dir + 'mosaic64.fits',
img_dir=projected_dir,
type=combine,
exact=exact_size)
sh.copy(images_projected_tbl, output_dir)
m.mConvert(output_dir + 'mosaic64.fits',
output_dir + 'mosaic.fits',
bitpix=bitpix)
m.mConvert(output_dir + 'mosaic64_area.fits',
output_dir + 'mosaic_area.fits',
bitpix=bitpix)
os.remove(output_dir + "mosaic64.fits")
os.remove(output_dir + "mosaic64_area.fits")
_finalize(cleanup, work_dir)
return
def reproject(in_images, out_images, header=None, bitpix=None,
north_aligned=False, system=None, equinox=None, factor=None, common=False,
exact_size=False, cleanup=True, silent_cleanup=False):
'''
General-purpose reprojection routine.
If one input/output image is specified, and the header argument is set,
the routine is equivalent to using mProject or mProjectPP. If header= is
not set, a new header is computed by taking into account the
north_aligned, system, and equinox arguments (if set).
If tuples of input/output images are specified, the tuples need to have
the same number of elements. If header= is specified, all images are
projected to this common projection. If header= is not specified, then a
new header is computed a new header is computed by taking into account the
north_aligned, system, and equinox arguments (if set). If common=False,
then a header is computed for each individual image, whereas if
common=True, an optimal header is computed for all images.
Required Arguments
*in_images* [ string | tuple or list of strings ]
Path(s) of input FITS file(s) to be reprojected.
*out_images* [ string | tuple or list of strings ]
Path(s) of output FITS file(s) to be created.
Optional Arguments
*header* [ string ]
Path to the header file to use for re-projection.
*bitpix* [ value ]
BITPIX value for the ouput FITS file (default is -64). Possible
values are: 8 (character or unsigned binary integer), 16 (16-bit
integer), 32 (32-bit integer), -32 (single precision floating
point), -64 (double precision floating point).
*north_aligned* [ True | False ]
Align the pixel y-axis with North
*system* [ value ]
Specifies the coordinate system
Possible values are: EQUJ EQUB ECLJ ECLB GAL SGAL
*equinox* [ value ]
If a coordinate system is specified, the equinox can also be given
in the form YYYY. Default is J2000.
*factor* [ value ]
Drizzle factor (see mProject)
*exact_size* [ True | False ]
Whether to reproject the image(s) to the exact header specified
(i.e. whether cropping is unacceptable).
*silent_cleanup* [ True | False ] (default False)
Hide messages related to tmp directory removal
Optional Arguments (multiple files only)
*common* [ string ]
Compute a common optimal header for all images (only used if
header=None)
'''
if type(in_images) == str and type(out_images) == str:
in_images = (in_images, )
out_images = (out_images, )
elif type(in_images) in [tuple, list] and type(out_images) in [tuple, list]:
pass
else:
raise Exception("Inconsistent type for in_images (%s) and out_images (%s)" % (type(in_images), type(out_images)))
if header:
if north_aligned or system or equinox:
warnings.warn("header= is set, so north_aligned=, system=, and equinox= will be ignored")
if common and len(in_images) == 1:
warnings.warn("only one image is being reprojected, so common= will be ignored")
# Find path to input and output file
in_images = [os.path.abspath(in_image) for in_image in in_images]
out_images = [os.path.abspath(out_image) for out_image in out_images]
if len(in_images) > 1 and not header and not common:
for i, in_image in enumerate(in_images):
reproject(in_images[i], out_images[i], bitpix=bitpix,
north_aligned=north_aligned, system=system,
equinox=equinox, factor=factor,
exact_size=exact_size, cleanup=cleanup,
silent_cleanup=silent_cleanup)
return
# Make work directory
work_dir = tempfile.mkdtemp() + '/'
# Set paths
raw_dir = work_dir + 'raw/'
final_dir = work_dir + 'final/'
if header:
header_hdr = os.path.abspath(header)
else:
header_hdr = work_dir + 'header.hdr'
images_raw_tbl = work_dir + 'images_raw.tbl'
images_tmp_tbl = work_dir + 'images_tmp.tbl'
# Create raw directory
os.mkdir(raw_dir)
os.mkdir(final_dir)
# Link to images
for i, in_image in enumerate(in_images):
os.mkdir(raw_dir + '%i' % i)
os.symlink(in_image, raw_dir + '%i/image.fits' % i)
# Make image table
m.mImgtbl(raw_dir, images_raw_tbl, corners=True, recursive=True)
# Make new header
if not header:
m.mMakeHdr(images_raw_tbl, header_hdr, north_aligned=north_aligned,
system=system, equinox=equinox)
for i, in_image in enumerate(in_images):
os.mkdir(final_dir + '%i' % i)
mProject_auto(in_images[i], final_dir + '%i/image_tmp.fits' % i,
header_hdr)
if exact_size:
m.mImgtbl(final_dir + '%i' % i, images_tmp_tbl, corners=True)
m.mAdd(images_tmp_tbl, header_hdr,
final_dir + '%i/image.fits' % i,
img_dir=final_dir + '%i' % i, exact=True)
else:
os.symlink(final_dir + '%i/image_tmp.fits' % i,
final_dir + '%i/image.fits' % i)
m.mConvert(final_dir + '%i/image.fits' % i, out_images[i],
bitpix=bitpix)
_finalize(cleanup, work_dir, silence=silent_cleanup)
return
def reproject(in_images,
out_images,
header=None,
bitpix=None,
north_aligned=False,
system=None,
equinox=None,
factor=None,
common=False,
exact_size=False,
hdu=None,
cleanup=True,
silent_cleanup=False):
'''
General-purpose reprojection routine.
If one input/output image is specified, and the header argument is set,
the routine is equivalent to using mProject or mProjectPP. If header= is
not set, a new header is computed by taking into account the
north_aligned, system, and equinox arguments (if set).
If tuples of input/output images are specified, the tuples need to have
the same number of elements. If header= is specified, all images are
projected to this common projection. If header= is not specified, then a
new header is computed a new header is computed by taking into account the
north_aligned, system, and equinox arguments (if set). If common=False,
then a header is computed for each individual image, whereas if
common=True, an optimal header is computed for all images.
Required Arguments
*in_images* [ string | tuple or list of strings ]
Path(s) of input FITS file(s) to be reprojected.
*out_images* [ string | tuple or list of strings ]
Path(s) of output FITS file(s) to be created.
Optional Arguments
*header* [ string ]
Path to the header file to use for re-projection.
*bitpix* [ value ]
BITPIX value for the ouput FITS file (default is -64). Possible
values are: 8 (character or unsigned binary integer), 16 (16-bit
integer), 32 (32-bit integer), -32 (single precision floating
point), -64 (double precision floating point).
*north_aligned* [ True | False ]
Align the pixel y-axis with North
*system* [ value ]
Specifies the coordinate system
Possible values are: EQUJ EQUB ECLJ ECLB GAL SGAL
*equinox* [ value ]
If a coordinate system is specified, the equinox can also be given
in the form YYYY. Default is J2000.
*factor* [ value ]
Drizzle factor (see mProject)
*exact_size* [ True | False ]
Whether to reproject the image(s) to the exact header specified
(i.e. whether cropping is unacceptable).
*hdu* [ value ]
The HDU to use in the file(s)
*silent_cleanup* [ True | False ] (default False)
Hide messages related to tmp directory removal
Optional Arguments (multiple files only)
*common* [ string ]
Compute a common optimal header for all images (only used if
header=None)
'''
if type(in_images) == str and type(out_images) == str:
in_images = (in_images, )
out_images = (out_images, )
elif type(in_images) in [tuple, list
] and type(out_images) in [tuple, list]:
pass
else:
raise Exception(
"Inconsistent type for in_images (%s) and out_images (%s)" %
(type(in_images), type(out_images)))
if header:
if north_aligned or system or equinox:
warnings.warn(
"header= is set, so north_aligned=, system=, and equinox= will be ignored"
)
if common and len(in_images) == 1:
warnings.warn(
"only one image is being reprojected, so common= will be ignored")
# Find path to input and output file
in_images = [os.path.abspath(in_image) for in_image in in_images]
out_images = [os.path.abspath(out_image) for out_image in out_images]
if len(in_images) > 1 and not header and not common:
for i, in_image in enumerate(in_images):
reproject(in_images[i],
out_images[i],
bitpix=bitpix,
north_aligned=north_aligned,
system=system,
equinox=equinox,
factor=factor,
exact_size=exact_size,
cleanup=cleanup,
silent_cleanup=silent_cleanup)
return
# Make work directory
work_dir = tempfile.mkdtemp() + '/'
# Set paths
raw_dir = work_dir + 'raw/'
final_dir = work_dir + 'final/'
if header:
header_hdr = os.path.abspath(header)
else:
header_hdr = work_dir + 'header.hdr'
images_raw_tbl = work_dir + 'images_raw.tbl'
images_tmp_tbl = work_dir + 'images_tmp.tbl'
# Create raw directory
os.mkdir(raw_dir)
os.mkdir(final_dir)
# Link to images
for i, in_image in enumerate(in_images):
os.mkdir(raw_dir + '%i' % i)
os.symlink(in_image, raw_dir + '%i/image.fits' % i)
# Make image table
m.mImgtbl(raw_dir, images_raw_tbl, corners=True, recursive=True)
# Make new header
if not header:
m.mMakeHdr(images_raw_tbl,
header_hdr,
north_aligned=north_aligned,
system=system,
equinox=equinox)
for i, in_image in enumerate(in_images):
os.mkdir(final_dir + '%i' % i)
mProject_auto(in_images[i],
final_dir + '%i/image_tmp.fits' % i,
header_hdr,
hdu=hdu)
if exact_size:
m.mImgtbl(final_dir + '%i' % i, images_tmp_tbl, corners=True)
m.mAdd(images_tmp_tbl,
header_hdr,
final_dir + '%i/image.fits' % i,
img_dir=final_dir + '%i' % i,
exact=True)
else:
os.symlink(final_dir + '%i/image_tmp.fits' % i,
final_dir + '%i/image.fits' % i)
m.mConvert(final_dir + '%i/image.fits' % i,
out_images[i],
bitpix=bitpix)
_finalize(cleanup, work_dir, silence=silent_cleanup)
return
