def bg_model(reprojected_dir,
bg_model_dir,
diff_dir,
corr_dir,
template_header,
im_type='intbgsub',
level_only=True):
"""
Model the background for the mosaiced image
Parameters
----------
reprojected_dir : str
Path to temp directory containing reprojected images
bg_model_dir : str
Path to directory inside gal_dir to hold the background modeling information
diff_dir : str
Path to directory inside bg_model_dir to hold the difference images
corr_dir : str
Path to directory inside bg_model_dir to hold the background corrected images
template_header : ascii file
Path to file containing the WCS to which we want to reproject our images
im_type : str
Type of image used (Default: intbgsub)
level_only : bool, optional
Montage argument: Adjust background levels only, don't try to fit the slope (Default: True)
"""
# FIND OVERLAPS
diff_dir = os.path.join(diff_dir, im_type)
os.makedirs(diff_dir)
reprojected_table = os.path.join(reprojected_dir,
im_type + '_reprojected.tbl')
diffs_table = os.path.join(diff_dir, 'differences.tbl')
montage.mOverlaps(reprojected_table, diffs_table)
# CALCULATE DIFFERENCES BETWEEN OVERLAPPING IMAGES
montage.mDiffExec(diffs_table,
template_header,
diff_dir,
proj_dir=reprojected_dir)
# BEST-FIT PLANE COEFFICIENTS
fits_table = os.path.join(diff_dir, 'fits.tbl')
montage.mFitExec(diffs_table, fits_table, diff_dir)
# CALCULATE CORRECTIONS
corr_dir = os.path.join(corr_dir, im_type)
os.makedirs(corr_dir)
corrections_table = os.path.join(corr_dir, 'corrections.tbl')
montage.mBgModel(reprojected_table,
fits_table,
corrections_table,
level_only=level_only)
# APPLY CORRECTIONS
montage.mBgExec(reprojected_table,
corrections_table,
corr_dir,
proj_dir=reprojected_dir)
def bg_model(gal_dir, reprojected_dir, template_header, level_only=False):
bg_model_dir = os.path.join(gal_dir, 'background_model')
os.makedirs(bg_model_dir)
# FIND OVERLAPS
diff_dir = os.path.join(bg_model_dir, 'differences')
os.makedirs(diff_dir)
reprojected_table = os.path.join(reprojected_dir, 'int_reprojected.tbl')
diffs_table = os.path.join(diff_dir, 'differences.tbl')
montage.mOverlaps(reprojected_table, diffs_table)
# CALCULATE DIFFERENCES BETWEEN OVERLAPPING IMAGES
montage.mDiffExec(diffs_table,
template_header,
diff_dir,
proj_dir=reprojected_dir)
# BEST-FIT PLANE COEFFICIENTS
fits_table = os.path.join(diff_dir, 'fits.tbl')
montage.mFitExec(diffs_table, fits_table, diff_dir)
# CALCULATE CORRECTIONS
corr_dir = os.path.join(bg_model_dir, 'corrected')
os.makedirs(corr_dir)
corrections_table = os.path.join(corr_dir, 'corrections.tbl')
montage.mBgModel(reprojected_table,
fits_table,
corrections_table,
level_only=level_only)
# APPLY CORRECTIONS
montage.mBgExec(reprojected_table,
corrections_table,
corr_dir,
proj_dir=reprojected_dir)
return corr_dir
def mosaic(input_files, mosaic_file, work_dir, ext=0, background_match=False,
cdelt=None, density=False, equinox=None, header=None,
level_only=False, north_aligned=False, postprocess=None,
preprocess=None, system=None, weights_file=None):
"""Make a mosiac.
High-level wrapper around several Montage operations similar to
`montage_wrapper.mosaic`. The main differences are 1) added support for
preprocessing the input images before reprojection and postprocessing
the final image after mosaicking, 2) options for using images in total
flux units instead of flux density (as assumed by Montage), 3) more of
the `montage_wrapper.mMakeHdr` keywords available for header creation,
and 4) the `whole` keyword for `montage_wrapper.mProjExec` is
automatically set to True when `background_match` is True. The latter
is important since backround matching behaves unreliably otherwise.
Parameters
----------
input_files : list or string
List of paths to the input images. This may also be the path to a
directory containing all input images, in which case `input_files`
will automatically be set to a list of all files in the directory
ending with ".fits".
mosaic_file : str
Path to the output mosaic file. The final mosaic always has the
same units as the `input_files` images.
work_dir : str
Path to the working directory for all intermediate files produced
by Montage. The directory has the following structure::
work_dir/
input/
Contains either symlinks to `input_files` or new files
depending on the `preprocess` and `density` keywords.
Assuming the `density` keyword has been set correctly, these
images will always be in flux density units.
reprojected/
The reprojected images.
differences/
Difference calculations for background matching (only if
`background_match` is True).
corrected/
Background-matched images (only if `background_match` is
True).
output/
The intermediate mosiac used to produce the final mosaic
file, depending on the `density` and `postprocess` keywords.
background_match : bool, optional
If True, match the background levels of the reprojected images
before mosaicking. Automatically sets ``whole = True`` in
`montage_wrapper.mProjExec`. Default is False.
cdelt : float, optional
See `header` and `montage_wrapper.mMakeHdr`. Default is None.
density : bool, optional
If True, the input images are in flux density units (i.e., signal
per unit pixel area). If False (default), the input images are
assumed to be in units of total flux, and are automatically scaled
to flux density before reprojection.
equinox : str, optional
See `header` and `montage_wrapper.mMakeHdr`. Default is None.
header : str, optional
Path to the template header file describing the output mosaic.
Default is None, in which case a template header is created
automatically using `montage_wrapper.mMakeHdr` and the `cdelt`,
`equinox`, `north_aligned`, and `system` keyword arguments.
level_only : bool, optional
See `montage_wrapper.mBgModel`. Ignored if `background_match` is
False. Default is False.
north_aligned : bool, optional
See `header` and `montage_wrapper.mMakeHdr`. Default is None.
postprocess, preprocess : function, optional
Functions for processing the raw input images before the input
density images are created (`preprocess`) and after the final
mosaic is created (`postprocess`). The function arguments should be
the image data array and the image header
(`astropy.io.fits.Header`), and the return values should be the
same. Default is None.
system : str, optional
See `header` and `montage_wrapper.mMakeHdr`. Default is None.
weights_file : str, optional
Path to output pixel weights file. Pixel weights are derived from
the final mosaic area file. Weights are normalized to 1, and
represent coverage of the mosaic area by the input images. Unlike
Montage area files, regions where the input images overlap are not
considered. Default is None.
Returns
-------
None
"""
# Get list of files if input_files is a directory name
if isinstance(input_files, basestring):
dirname = os.path.dirname(input_files)
input_files = [os.path.join(dirname, basename)
for basename in os.listdir(dirname)
if os.path.splitext(basename)[1] == '.fits']
# Create working directory
try:
os.makedirs(work_dir)
except OSError:
shutil.rmtree(work_dir)
os.makedirs(work_dir)
# Create input directory, populate it, and get image metadata
input_dir = os.path.join(work_dir, 'input')
os.mkdir(input_dir)
if preprocess or not density or ext>0:
# Create new input files
for input_file in input_files:
data, hdr = astropy.io.fits.getdata(input_file, header=True,
ext=ext)
if preprocess:
data, hdr = preprocess(data, hdr)
if not density:
# Convert total flux into flux density
dx, dy = wcs.calc_pixscale(hdr, ref='crpix').arcsec
pixarea = dx * dy # arcsec2
data /= pixarea
# Write
basename = os.path.basename(input_file)
basename = '_density'.join(os.path.splitext(basename))
new_input_file = os.path.join(input_dir, basename)
hdu = astropy.io.fits.PrimaryHDU(data=data, header=hdr)
hdu.writeto(new_input_file, output_verify='ignore')
else:
# Symlink existing files
for input_file in input_files:
basename = os.path.basename(input_file)
new_input_file = os.path.join(input_dir, basename)
os.symlink(input_file, new_input_file)
input_table = os.path.join(input_dir, 'input.tbl')
montage.mImgtbl(input_dir, input_table, corners=True)
# Template header
if header is None:
template_header = os.path.join(work_dir, 'template.hdr')
montage.mMakeHdr(input_table, template_header, cdelt=cdelt,
equinox=equinox, north_aligned=north_aligned,
system=system)
else:
template_header = header
# Create reprojection directory, reproject, and get image metadata
proj_dir = os.path.join(work_dir, 'reprojected')
os.makedirs(proj_dir)
whole = True if background_match else False
stats_table = os.path.join(proj_dir, 'mProjExec_stats.log')
montage.mProjExec(input_table, template_header, proj_dir, stats_table,
raw_dir=input_dir, whole=whole)
reprojected_table = os.path.join(proj_dir, 'reprojected.tbl')
montage.mImgtbl(proj_dir, reprojected_table, corners=True)
# Background matching
if background_match:
diff_dir = os.path.join(work_dir, 'differences')
os.makedirs(diff_dir)
# Find overlaps
diffs_table = os.path.join(diff_dir, 'differences.tbl')
montage.mOverlaps(reprojected_table, diffs_table)
# Calculate differences between overlapping images
montage.mDiffExec(diffs_table, template_header, diff_dir,
proj_dir=proj_dir)
# Find best-fit plane coefficients
fits_table = os.path.join(diff_dir, 'fits.tbl')
montage.mFitExec(diffs_table, fits_table, diff_dir)
# Calculate corrections
corr_dir = os.path.join(work_dir, 'corrected')
os.makedirs(corr_dir)
corrections_table = os.path.join(corr_dir, 'corrections.tbl')
montage.mBgModel(reprojected_table, fits_table, corrections_table,
level_only=level_only)
# Apply corrections
montage.mBgExec(reprojected_table, corrections_table, corr_dir,
proj_dir=proj_dir)
img_dir = corr_dir
else:
img_dir = proj_dir
# Make mosaic
output_dir = os.path.join(work_dir, 'output')
os.makedirs(output_dir)
out_image = os.path.join(output_dir, 'mosaic.fits')
montage.mAdd(reprojected_table, template_header, out_image,
img_dir=img_dir, exact=True)
# Pixel areas and weights
if weights_file or not density:
area_file = '_area'.join(os.path.splitext(out_image))
area, hdr = astropy.io.fits.getdata(area_file, header=True) # steradians
area *= (180/np.pi*3600)**2 # arcsec2
dx, dy = wcs.calc_pixscale(hdr, ref='crpix').arcsec
pixarea = dx * dy # arcsec2
area = np.clip(area, 0, pixarea) # Don't care about overlaps
if weights_file:
weights = area / pixarea # Normalize to 1
hdu = astropy.io.fits.PrimaryHDU(weights, header=hdr)
try:
hdu.writeto(weights_file)
except IOError:
os.remove(weights_file)
hdu.writeto(weights_file)
# Write final mosaic
dirname = os.path.dirname(mosaic_file)
try:
os.makedirs(dirname)
except OSError:
pass
if postprocess or not density:
# Create new file
data, hdr = astropy.io.fits.getdata(out_image, header=True)
if not density:
# Convert flux density into total flux
data *= pixarea
if postprocess:
data, hdr = postprocess(data, hdr)
# Write
hdu = astropy.io.fits.PrimaryHDU(data, header=hdr)
try:
hdu.writeto(mosaic_file)
except IOError:
os.remove(mosaic_file)
hdu.writeto(mosaic_file)
else:
# Move existing file
os.rename(out_image, mosaic_file)
return
def _montage_test():
# create density images
input_dir = os.path.dirname(density_files[0])
# image metadata
meta1_file = os.path.join(input_dir, 'meta1.tbl')
montage.mImgtbl(input_dir, meta1_file, corners=True)
# make header
#lon, lat = [], []
#for density_file in density_files:
# data, hdr = astropy.io.fits.getdata(density_file, header=True)
# wcs = astropy.wcs.WCS(hdr)
# x1, y1 = 0.5, 0.5
# y2, x2 = data.shape
# x2, y2 = x2 + 0.5, y2 + 0.5
# x, y = [x1, x2, x2, x1], [y1, y1, y2, y2]
# ln, lt = wcs.wcs_pix2world(x, y, 1)
# lon += list(ln)
# lat += list(lt)
#lon1, lon2 = np.min(lon), np.max(lon)
#lat1, lat2 = np.min(lat), np.max(lat)
hdr_file = os.path.join(os.path.dirname(input_dir), 'test.hdr')
montage.mMakeHdr(meta1_file, hdr_file)
# reproject
proj_dir = os.path.dirname(proj_files[0])
safe_mkdir(proj_dir)
stats_file = os.path.join(proj_dir, 'stats.tbl')
montage.mProjExec(meta1_file, hdr_file, proj_dir, stats_file,
raw_dir=input_dir, exact=True)
# image metadata
meta2_file = os.path.join(proj_dir, 'meta2.tbl')
montage.mImgtbl(proj_dir, meta2_file, corners=True)
# Background modeling
diff_dir = os.path.join(os.path.dirname(proj_dir), 'difference')
safe_mkdir(diff_dir)
diff_file = os.path.join(diff_dir, 'diffs.tbl')
montage.mOverlaps(meta2_file, diff_file)
montage.mDiffExec(diff_file, hdr_file, diff_dir, proj_dir)
fits_file = os.path.join(diff_dir, 'fits.tbl')
montage.mFitExec(diff_file, fits_file, diff_dir)
# Background matching
corr_dir = os.path.join(os.path.dirname(proj_dir), 'correct')
safe_mkdir(corr_dir)
corr_file = os.path.join(corr_dir, 'corrections.tbl')
montage.mBgModel(meta2_file, fits_file, corr_file, level_only=False)
montage.mBgExec(meta2_file, corr_file, corr_dir, proj_dir=proj_dir)
# Native mosaic
projadd_file = config.path('{:s}.reproject.add'.format(kind))
projadd_dir, filename = os.path.split(projadd_file)
filename, ext = os.path.splitext(filename)
filename = '{0:s}_native{1:s}'.format(filename, ext)
projaddnative_file = os.path.join(projadd_dir, filename)
safe_mkdir(projadd_dir)
montage.mAdd(meta2_file, hdr_file, projaddnative_file, img_dir=corr_dir, exact=True)
# Reproject to final header
header_file = config.path('{:s}.hdr'.format(kind))
montage.mProject(projaddnative_file, projadd_file, header_file)
# Postprocess
data, hdr = astropy.io.fits.getdata(projaddnative_file, header=True)
x1, x2 = 900, 1900
y1, y2 = 3000, 4500
val = np.mean(data[y1:y2,x1:x2])
data, hdr = astropy.io.fits.getdata(projadd_file, header=True)
data = data - val
areaadd_file = config.path('{:s}.area.add'.format(kind))
area = astropy.io.fits.getdata(areaadd_file) * (180/np.pi*3600)**2 # arcsec2
data = data * area
add_file = config.path('{:s}.add'.format(kind))
dirname = os.path.dirname(add_file)
safe_mkdir(dirname)
if os.path.exists(add_file):
os.remove(add_file)
hdu = astropy.io.fits.PrimaryHDU(data, header=hdr)
hdu.writeto(add_file)
os.path.getsize("diffdir/"+os.listdir("diffdir")[1]) < 10000) or
(len(os.listdir("diffdir")) < 1)) :
listPro = os.listdir('projected')
listPro = np.array(listPro)
fileSize = np.array(range(len(listPro)))
for ifile in range(len(listPro)):
fileSize[ifile] = os.path.getsize('projected/'+listPro[ifile])
proTable = Table([listPro, fileSize], names = ["Name", "size"])
proTable.sort(["size", "Name"])
shutil.copy('projected/'+proTable['Name'][-2],
'../'+sour_name+'_'+bands+'.fits')
shutil.copy('projected/'+proTable['Name'][-1],
'../'+sour_name+'_'+bands+'_area.fits')
else:
mt.mBgModel('pimages.tbl', 'fits.tbl', 'corrections.tbl')
mt.mBgExec('pimages.tbl', 'corrections.tbl', 'corrdir',
proj_dir = 'projected')
mt.mAdd('pimages.tbl', '../'+bands+'.hdr',
'../'+sour_name+'_'+bands+'.fits', img_dir = 'corrdir')
os.chdir('..')
shutil.rmtree(bands)
os.remove(bands+'.hdr')
os.remove(sour_name+'_'+bands+'_area.fits')
os.chdir('..')
print(pfmt %(isour+1, sour_name, ((isour+1.0) / len(sourList)*100)))
stop = time.time()
dure = stop - start
print("Run time = ",dure, "seconds")
