def reproject_images(template_header,
input_dir,
reprojected_dir,
imtype,
whole=False,
exact=True,
img_list=None):
input_table = os.path.join(input_dir, imtype + '_input.tbl')
montage.mImgtbl(input_dir, input_table, corners=True, img_list=img_list)
# Create reprojection directory, reproject, and get image metadata
stats_table = os.path.join(reprojected_dir,
imtype + '_mProjExec_stats.log')
montage.mProjExec(input_table,
template_header,
reprojected_dir,
stats_table,
raw_dir=input_dir,
whole=whole,
exact=exact)
reprojected_table = os.path.join(reprojected_dir,
imtype + '_reprojected.tbl')
montage.mImgtbl(reprojected_dir, reprojected_table, corners=True)
def reproject_images(template_header, int_images, rrhr_images, flag_images, input_dir, reprojected_dir, whole=True, exact=True):
# MASK IMAGES
for i in range(len(int_images)):
image_infile = int_images[i]
wt_infile = rrhr_images[i]
flg_infile = flag_images[i]
image_outfile = os.path.join(input_dir, os.path.basename(image_infile).replace('.fits', '_masked.fits'))
wt_outfile = os.path.join(input_dir, os.path.basename(wt_infile).replace('.fits', '_masked.fits'))
#mask_galex_edges(image_infile, flg_infile, outfile=image_outfile)
#mask_galex_edges(wt_infile, flg_infile, outfile=wt_outfile)
mask_galex(image_infile, wt_infile, flg_infile, out_intfile=image_outfile, out_wtfile=wt_outfile)
# REPROJECT IMAGES
input_table = os.path.join(input_dir, 'input.tbl')
montage.mImgtbl(input_dir, input_table, corners=True)
# Create reprojection directory, reproject, and get image metadata
#whole = True #if background_match else False
stats_table = os.path.join(reprojected_dir, 'mProjExec_stats.log')
montage.mProjExec(input_table, template_header, reprojected_dir, stats_table, raw_dir=input_dir, whole=whole, exact=exact)
reprojected_table = os.path.join(reprojected_dir, 'reprojected.tbl')
montage.mImgtbl(reprojected_dir, reprojected_table, corners=True)
def reproject_images(template_header,
input_dir,
reproj_dir,
imtype,
whole=True,
exact=True,
corners=True,
img_list=None):
"""
Reproject input images to a new WCS as given by a template header
Parameters
----------
template_header : ascii file
ASCII file containing the WCS to which you want to reproject. This is what Montage requires.
input_dir : str
Path to directory containing input data
reproj_imtype_dir :
Path to new directory for storing reprojected data
imtype : str
The type of image you are reprojecting; one of [int, rrhr]
whole : bool, optional
Montage argument: Force reprojection of whole images, even if they exceed the area of the FITS
header template (Default: True)
exact : bool, optional
Montage argument: Flag indicating output image should exactly match the FITS header template,
and not crop off blank pixels (Default: True)
corners : bool, optional
Montage argument: Adds 8 columns for the RA and Dec of the image corners to the output metadata table
(Default: True)
img_list : list of strs, optional
Montage argument: only process files with names specified in table img_list, ignoring any other files
in the directory. (Default: None)
"""
# get image metadata from input images
input_table = os.path.join(input_dir, imtype + '_input.tbl')
montage.mImgtbl(input_dir, input_table, corners=corners, img_list=img_list)
# reproject images
stats_table = os.path.join(reproj_dir, imtype + '_mProjExec_stats.log')
montage.mProjExec(input_table,
template_header,
reproj_dir,
stats_table,
raw_dir=input_dir,
whole=whole,
exact=exact)
# get new image metadata with new header information
reprojected_table = os.path.join(reproj_dir, imtype + '_reprojected.tbl')
montage.mImgtbl(reproj_dir, reprojected_table, corners=corners)
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)
def mosaic_band(self,band,ra,dec,margin,radius,pgc):#,clean=True):
'''
Input: source info param
Create a mosaic fit file for the specified band.
Return: String filename of resulting mosaic
'''
print ("------------------mosaic_band----------------------")
DEBUG = True
# output = open("rc3_galaxies_outside_SDSS_footprint.txt",'a') # 'a' for append #'w')
# unclean = open("rc3_galaxies_unclean","a")
# filename = "{},{}".format(str(ra),str(dec))
filename = str(ra)+str(dec)
#print (margin/radius)
if (DEBUG) : print ("Querying data that lies inside margin")
#result = sqlcl.query( "SELECT distinct run,camcol,field FROM PhotoObj WHERE ra between {0}-{1} and {0}+{1}and dec between {2}-{3} and {2}+{3}".format(str(ra),str(margin),str(dec),str(margin))).readlines()
result = sqlcl.query( "SELECT distinct run,camcol,field FROM PhotoObj WHERE ra between "+str(ra)+"-"+str(margin)+" and " +str(ra)+"+"+str(margin)+"and dec between "+str(dec)+"-"+str(margin)+" and "+ str(dec)+"+"+str(margin)).readlines()
clean_result = sqlcl.query( "SELECT distinct run,camcol,field FROM PhotoObj WHERE CLEAN =1 and ra between "+str(ra)+"-"+str(margin)+" and " +str(ra)+"+"+str(margin)+"and dec between "+str(dec)+"-"+str(margin)+" and "+ str(dec)+"+"+str(margin)).readlines()
# clean_result = sqlcl.query( "SELECT distinct run,camcol,field FROM PhotoObj WHERE CLEAN =1 and ra between {0}-{1} and {0}+{1}and dec between {2}-{3} and {2}+{3}".format(str(ra),str(margin),str(dec),str(margin))) .readlines()
clean = True
print (result)
print (clean_result)
if (result[0][5:]=="<html>"):
print("strange error from SQL server")
return -1
if (result[1]=='error_message\n' or clean_result[1]=='error_message\n'):
#Case where doing more than 60 queries in 1 minute
time.sleep(60)
#results are messed up, need to re-query
result = sqlcl.query( "SELECT distinct run,camcol,field FROM PhotoObj WHERE ra between "+str(ra)+"-"+str(margin)+" and " +str(ra)+"+"+str(margin)+"and dec between "+str(dec)+"-"+str(margin)+" and "+ str(dec)+"+"+str(margin)).readlines()
clean_result = sqlcl.query( "SELECT distinct run,camcol,field FROM PhotoObj WHERE CLEAN =1 and ra between "+str(ra)+"-"+str(margin)+" and " +str(ra)+"+"+str(margin)+"and dec between "+str(dec)+"-"+str(margin)+" and "+ str(dec)+"+"+str(margin)).readlines()
if (len(result)!=len(clean_result) and band=='u'):
#only print this once in the u band. If it is unclean in u band (ex. cosmic ray, bright star..etc) then it must be unclean in the other bands too.
print ("Data contain unclean images")
clean=False
unclean.write(str(ra)+" "+str(dec)+" "+str(radius)+" "+pgc)
# unclean.write("{} {} {} {} \n".format(str(ra),str(dec),str(radius),pgc))
data =[]
count =0
for i in result:
if count>1:
list =i.split(',')
list[2]= list[2][:-1]
data.append(list)
count += 1
print (data)
if (len(data)==0 and band=='r'): #you will only evounter non-footprint galaxy inint run , because after that we just take the footprint gaalxy already mosaiced (init) from rfits
if (DEBUG): print ('The given ra, dec of this galaxy does not lie in the SDSS footprint. Onto the next galaxy!')#Exit Program.'
output.write(str(ra)+ " "+ str(dec)+" "+str(radius)+"\n")
# output.write("{} {} {} {} \n".format(str(ra),str(dec),str(radius),pgc))
output.write(str(ra)+" "+str(dec)+" "+str(radius)+" "+pgc)
#sys.exit()
return -1 #special value reserved for not in SDSS footprint galaxies
else :
if (DEBUG):
print ( "Complete Query. These data lies within margin: ")
print (data)
# os.mkdir(filename)
# os.chdir(filename)
#if (os.path.exists(band)):
#os.system("rm -r "+band)
os.mkdir(band)
os.chdir(band)
os.mkdir ("raw")
os.mkdir ("projected")
os.chdir("raw")
if (DEBUG): print ("Retrieving data from SDSS SAS server for "+ band +"band")
for i in data :
out = "frame-"+str(band)+"-"+str(i[0]).zfill(6)+"-"+str(i[1])+"-"+str(i[2]).zfill(4)
os.system("wget http://mirror.sdss3.org/sas/dr10/boss/photoObj/frames/301/"+str(i[0])+"/"+str(i[1])+"/"+out+".fits.bz2")
os.system("bunzip2 "+out+".fits.bz2")
os.chdir("../")
if (DEBUG) : print("Creating mosaic for "+band+" band.")
outfile_r="SDSS_"+band+"_"+str(ra)+"_"+str(dec)+"r.fits"
outfile="SDSS_"+band+"_"+str(ra)+"_"+str(dec)+".fits"
if (len(data)==1):
#With header info, len of processed result list is 1 if there is only 1 field lying in the margin, simply do mSubImage without mosaicing
#This patch should not be necessary but the program is aparently not mosaicing for the case where there is only one field.
print ("Only one field in region of interest")
os.chdir("raw")
montage.mSubimage(out+".fits",outfile,ra,dec,2*margin) # mSubImage takes xsize which should be twice the margin (margin measures center to edge of image)
#os.chdir("../..")
hdulist = pyfits.open(outfile)
shutil.move(outfile,"../..")
os.chdir("../..")
else:
montage.mImgtbl("raw","images.tbl")
montage.mHdr(str(ra)+" "+str(dec),margin,out+".hdr")
if (DEBUG): print ("Reprojecting images")
os.chdir("raw")
montage.mProjExec("../images.tbl","../"+out+".hdr","../projected", "../stats.tbl")
os.chdir("..")
montage.mImgtbl("projected","pimages.tbl")
os.chdir("projected")
montage.mAdd("../pimages.tbl","../"+out+".hdr","SDSS_"+out+".fits")
# outfile_r="SDSS_{}_{}_{}r.fits".format(band,str(ra),str(dec))
#outfile_r="SDSS_"+band+"_"+str(ra)+"_"+str(dec)+"r.fits"
montage.mSubimage("SDSS_"+out+".fits",outfile_r,ra,dec,2*margin) # mSubImage takes xsize which should be twice the margin (margin measures center to edge of image)
shutil.move(outfile_r,os.getcwd()[:-11] )#if change to :-11 then move out of u,g,r,i,z directory, may be more convenient for mJPEG
if (DEBUG) : print ("Completed Mosaic for " + band)
os.chdir("../..")
hdulist = pyfits.open(outfile_r)
hdulist[0].header['RA']=ra
hdulist[0].header['DEC']=dec
hdulist[0].header['RADIUS']=radius
hdulist[0].header['PGC']=pgc
hdulist[0].header['NED']=("http://ned.ipac.caltech.edu/cgi-bin/objsearch?objname="+ str(hdulist[0].header['PGC'])+"&extend=no&hconst=73&omegam=0.27&omegav=0.73&corr_z=1&out_csys=Equatorial&out_equinox=J2000.0&obj_sort=RA+or+Longitude&of=pre_text&zv_breaker=30000.0&list_limit=5&img_stamp=YES")
hdulist[0].header['CLEAN']=clean
hdulist[0].header['MARGIN']=margin
#if (os.path.exists(outfile)):
#os.system("rm "+ outfile)
hdulist.writeto(outfile)
if (os.path.exists(outfile_r)):
os.system("rm "+outfile_r)
#print("Deleting")
os.system("rm -r "+band+"/")
print ("Completed Mosaic")
return outfile
os.chdir("raw")
if (DEBUG): print ("Retrieving data from SDSS SAS server for "+ band +"band")
for i in data :
out = "frame-"+str(band)+"-"+str(i[0]).zfill(6)+"-"+str(i[1])+"-"+str(i[2]).zfill(4)
os.system("wget http://data.sdss3.org/sas/dr10/boss/photoObj/frames/301/"+str(i[0])+"/"+ str(i[1]) +"/"+out+".fits.bz2")
os.system("bunzip2 "+out+".fits.bz2")
# print (os.getcwd())
os.chdir("../")
if (DEBUG) : print("Creating mosaic for " +" "+ band + " band.")
montage.mImgtbl("raw","images.tbl")
montage.mHdr(str(ra)+" "+str(dec),radius,out+".hdr")
if (DEBUG): print ("Reprojecting images")
#Sometimes you can't find the files and result in images.tbl => empty doc
#need to put data file inside raw AND unzip it so that Montage detect that it is a fit file
os.chdir("raw")
montage.mProjExec("../images.tbl","../"+out+".hdr","../projected", "../stats.tbl")
os.chdir("..")
montage.mImgtbl("projected","pimages.tbl")
#mAdd coadds the reprojected images using the FITS header template and mImgtbl list.
os.chdir("projected")
montage.mAdd("../pimages.tbl","../"+out+".hdr","SDSS_"+out+".fits")
montage.mSubimage("SDSS_"+out+".fits","SDSS_"+ele+"_"+str(trunc(ra))+"_"+str(trunc(dec))+".fits",ra,dec,2*margin) # mSubImage takes xsize which should be twice the margin (margin measures center to edge of image)
shutil.move("SDSS_"+ele+"_"+str(trunc(ra))+"_"+str(trunc(dec))+".fits",os.getcwd()[:-11] )#if change to :-11 then move out of u,g,r,i,z directory, may be more convenient for mJPEG
if (DEBUG) : print ("Completed Mosaic for " + band)
os.chdir("../..")
# Superimposing R,G,B image mosaics into TIFF using STIFF
os.system("stiff "+" SDSS_i_"+str(trunc(ra))+"_"+str(trunc(dec))+ ".fits "+ " SDSS_r_"+str(trunc(ra))+"_"+str(trunc(dec))+ ".fits "+" SDSS_g_"+str(trunc(ra))+"_"+str(trunc(dec))+ ".fits "+ " -c stiff.conf " +" -OUTFILE_NAME "+str(trunc(ra))+"_"+str(trunc(dec))+"_COLORSAT_5_MAX_MAN_3 -COLOUR_SAT 5 -MAX_TYPE MANUAL -MAX_LEVEL 3")
# for b in bands:
# os.system("rm -r "+b+"/")
#we want to keep the fit files, but for testing purposes Python will throw file-already-exist error , if we dont delete them.
#os.system("rm -r " + "SDSS_frame-"+b+"-"+str(run).zfill(6)+"-"+str(camcol)+"-"+str(field).zfill(4)+ ".fits" )
hdr_out.close()
os.mkdir(bands)
os.mkdir(bands+'/raw')
coor = ascii.read(list_dir+'list_'+bands+'.txt')
for icoor in range(len(coor)):
if (l_0+1.5 > coor['l'][icoor]/10.0 and l_0-1.5 < coor['l'][icoor]/10.0):
shutil.copy(data_dir+coor['Name'][icoor],
bands+'/raw/'+coor['Name'][icoor])
os.chdir(bands)
os.mkdir('projected')
os.mkdir('diffdir')
os.mkdir('corrdir')
mt.mImgtbl('raw','rimages.tbl')
mt.mProjExec('rimages.tbl', '../'+bands+'.hdr', 'projected', 'stats.tbl',
raw_dir='raw')
mt.mImgtbl('projected', 'pimages.tbl')
len_dir = len(os.listdir('projected'))
if len_dir < 3 :
mt.mAdd('pimages.tbl', '../'+bands+'.hdr',
'../'+sour_name+'_'+bands+'.fits',
img_dir='projected')
else:
mt.mOverlaps('pimages.tbl', 'diffs.tbl')
mt.mDiffExec('diffs.tbl', '../'+bands+'.hdr', 'diffdir',
proj_dir = 'projected')
mt.mFitExec('diffs.tbl', 'fits.tbl', 'diffdir')
if ((len(os.listdir("diffdir")) > 1 and
os.path.getsize("diffdir/"+os.listdir("diffdir")[1]) < 10000) or
(len(os.listdir("diffdir")) < 1)) :
listPro = os.listdir('projected')
def mosaic_band(self,band,ra,dec,margin,radius,pgc,survey,remove_bkgrd=False):
'''
Input: source info param
Create a mosaic fit file for the specified band.
Return: String filename of resulting mosaic
'''
print ("------------------mosaic_band----------------------")
print ("Now mosaic_band on {}".format(pgc))
output = open("../rc3_galaxies_outside_{}_footprint".format(survey.name),'a') # 'a' for append #'w')
unclean = open("../rc3_galaxies_unclean_{}".format(survey.name),"a")
filename = str(ra)+str(dec)
if (DEBUG) : print ("Querying data that lies inside margin")
print (ra,dec,margin)
result = survey.data_server.surveyFieldConverter(float(ra),float(dec),float(margin))
clean_result = survey.data_server.surveyFieldConverter(float(ra),float(dec),float(margin),True)
clean = True
if(DEBUG):print ("result: "+str(result))
if(DEBUG):print ("clean_result: "+str(clean_result))
if (len(result)!=len(clean_result)and band=='u'):
# Only print this once in the u band.
# Assume that if it is unclean in u band (ex. cosmic ray, bright star..etc) then it must be unclean in the other bands too.
print ("Data contain unclean images")
clean=False
unclean.write("{} {} {} {} \n".format(self.rc3_ra,self.rc3_dec,self.rc3_radius,self.pgc))
if (len(result)==0):
if (DEBUG): print ('The given ra, dec of this galaxy does not lie in the survey footprint. Onto the next galaxy!')#Exit Program.'
output.write("{} {} {} {} \n".format(str(ra),str(dec),str(radius),str(pgc)))
return -1 #special value reserved for not in survey footprint galaxies
else :
if (DEBUG):
print ( "Complete Query. These data lies within margin: ")
print (result)
os.mkdir(band)
os.chdir(band)
os.mkdir ("rawdir")
os.mkdir ("projdir")
if (remove_bkgrd):
os.mkdir ("diffdir")
os.mkdir ("corrdir")
# os.mkdir("final")
if (DEBUG): print ("Retrieving data from server for "+ band +"band")
os.chdir("rawdir")
out=""
# Raw Imaging Data naming
for i in result :
if (survey.data_server.name=='Gator'):
survey.data_server.getData(band,ra,dec,margin,survey)
out = i # 2MASS designation
print out
elif (survey.data_server.name=='SkyServer'):
survey.data_server.getData(band,str(i[0]), str(i[1]),str(i[2]))
# run-camcol-field
out = "frame-"+str(band)+"-"+str(i[0]).zfill(6)+"-"+str(i[1])+"-"+str(i[2]).zfill(4)
elif (survey.data_server.name=='DSSServer'):
survey.data_server.getData(band,ra,dec,margin)
# Patch for when we can not pass in th pgc number in getData of dssServer class, we rename the file here to conform with RC3's filename expectation for the imaging data
raw_data = glob.glob("raw_*.fits")
print (raw_data)
for i in raw_data:
os.rename(i,"DSS_{}_{}.fits".format(band, self.pgc))
out = "raw_{}_{}".format(band,self.pgc)
print ("dss_out: "+out)
else:
raise TypeError("Missing implementation for data retrieval")
os.chdir("../")
if (DEBUG) : print("Creating mosaic for "+band+" band.")
outfile_r = "{}_{}_{}r.fits".format(survey.name,band,self.pgc)
outfile = "{}_{}_{}.fits".format(survey.name,band,self.pgc)
if (len(result)==1):
#With header info, len of processed result list is 1 if there is only 1 field lying in the margin, simply do mSubImage without mosaicing
print ("Only one field in region of interest")
os.chdir("rawdir")
if (DEBUG):print ("m:{}".format(margin))
try:
if (DEBUG):print ("2m:{}".format(2*margin))
if (DEBUG):print ([outfile_r,outfile,ra,dec,2*margin])
montage.mSubimage(outfile,outfile,ra,dec,2*margin) # mSubImage takes xsize which should be twice the margin (margin measures center to edge of image)
except(montage.status.MontageError):
print ("montage_wrapper.status.MontageError: mSubimage: Region outside image.")
try :#give it one last chance
if (DEBUG):print ("lastchancem:{}".format(margin))
montage.mSubimage(out+".fits",outfile,ra,dec,margin)
except(montage.status.MontageError):
print("Doesn't work after trying half the margin, just keep the raw FITS file")
if (DEBUG):print (out+".fits")
if (DEBUG):print (outfile)
shutil.move(out+".fits","../..")
os.chdir("../../")
os.rename(out+".fits",outfile)
os.system("rm -r {}".format(survey.best_band))
return outfile
if (DEBUG):print (os.getcwd())
os.chdir("../../") #Get out of directory for that galaxy and move on
os.system("rm -r {}".format(survey.best_band))
if (DEBUG):print(os.getcwd())
failed_msubimage = open ("failed_msubimage","a")
failed_msubimage.write("{} {} {} {} \n".format(str(ra),str(dec),str(radius),str(pgc)))
return -1 # masking with special value reserved for not in survey footprint galaxies
hdulist = pyfits.open(outfile)
if (os.path.exists("../../"+outfile)):
os.system("rm ../../"+outfile)
shutil.move(outfile,"../..")
os.chdir("../..")
else:
imgtbl="images-rawdir.tbl"
hdr="template.hdr"
montage.mImgtbl("rawdir",imgtbl)
# montage.mHdr(str(ra)+" "+str(dec),margin,out+".hdr")
montage.mMakeHdr(imgtbl,hdr)
if (DEBUG): print ("Reprojecting images")
# os.chdir("rawdir")
if (DEBUG):print(os.getcwd())
montage.mProjExec(imgtbl,hdr,"projdir", "stats.tbl",raw_dir="rawdir")#, mpi=enable_mpi,debug=True)
if os.listdir("projdir") == []:
print "Projection Failed. No projected images produced. Skip to the next galaxy"
os.chdir("../") #Get out of directory for that galaxy and move on
os.system("rm -r {}".format(survey.best_band))
failed_projection = open ("failed_projection","a")
failed_projection.write("{} {} {} {} \n".format(str(ra),str(dec),str(radius),str(pgc)))
return -1 # masking with special value reserved for not in survey footprint galaxies
if (remove_bkgrd):
if (DEBUG): print "Calling the bash script containing Montage routines to rectify the background"
if os.getcwd()[-4:-2]==str(pgc):
os.system("bash ../../mosaic.sh")
else:
os.system("bash ../mosaic.sh")
print "mSubimage"
montage.mSubimage("mosaic.fits" ,"mosaic.fits",ra,dec,2*margin) # mSubImage takes xsize which should be twice the margin (margin measures center to edge of image)
shutil.move("mosaic.fits","../{}".format(outfile_r))#if change to :-11 then move out of u,g,r,i,z directory, may be more convenient for mJPEG
if (DEBUG) : print ("Completed Mosaic for " + band)
else:
montage.mImgtbl("projdir","pimages.tbl")
os.chdir("projdir")
montage.mAdd("../pimages.tbl","../"+hdr,"{}_{}.fits".format(survey.name,out))#, mpi=enable_mpi)
montage.mSubimage("{}_{}.fits".format(survey.name,out),outfile_r,ra,dec,2*margin) # mSubImage takes xsize which should be twice the margin (margin measures center to edge of image)
shutil.move(outfile_r,"../../{}".format(outfile_r) )#if change to :-11 then move out of u,g,r,i,z directory, may be more convenient for mJPEG
if (DEBUG) : print ("Completed Mosaic for " + band)
os.chdir("..")
os.chdir("../")
hdulist = pyfits.open(outfile_r)
hdulist[0].header['RA']=float(ra)
hdulist[0].header['DEC']=float(dec)
hdulist[0].header['RADIUS']=radius
if (DEBUG):print ("Finished mosaic_band on {}".format(pgc))
hdulist[0].header['PGC']=pgc
hdulist[0].header['NED']=("http://ned.ipac.caltech.edu/cgi-bin/objsearch?objname="+ str(hdulist[0].header['PGC'])+"&extend=no&hconst=73&omegam=0.27&omegav=0.73&corr_z=1&out_csys=Equatorial&out_equinox=J2000.0&obj_sort=RA+or+Longitude&of=pre_text&zv_breaker=30000.0&list_limit=5&img_stamp=YES")
hdulist[0].header['CLEAN']=clean
hdulist[0].header['MARGIN']=margin
if (os.path.exists(outfile)):
os.system("rm "+ outfile)
hdulist.writeto(outfile)
if (os.path.exists(outfile_r)):
os.system("rm "+outfile_r)
os.system("rm -r {}".format(band))
return outfile
def re_project(orig_dir,
Name_f0,
proj_dir,
Name_f1,
para,
exact=True,
clear_files=True):
'''
To re-project fits files using montage_wrapper.
Inputs
orig_dir: directory of fits to be re-projected, should omit
unnecessary '/'
Name_f0: list of fits names before re-projection
proj_dir: directory of re-projected fits, DO NOT LET proj_dir=orig_dir!
Name_f1: list of fits names after re-projection, ordered like Name_f0
para: list of parameters defining the framework of re-projected image,
which includes:
NAXIS1: integer
NAXIS2: integer
projection: 3-letter string, e.g. 'TAN'
CRVAL1
CRVAL2
CRPIX1
CRPIX2
CD1_1
CD1_2
CD2_1
CD2_2
exact: whether the output shape exactly match the FITS header
clear_files: whether to delete intermediate files
Outputs
re-projected fits in proj_dir
Caveats
1. This code is still in test.
2. Only tested for 2D fits with one hdu.
3. It's quite often that "exact=True" doesn't work, try to use mAdd.
Sometimes mAdd gives fits with zero file sizes. Maybe mAdd can't
handle single fits.
'''
# create a folder containing the original fits
raw_dir = orig_dir + '/fits_orig'
os.mkdir(raw_dir)
for name_f in Name_f0:
shutil.copy('%s/%s' % (orig_dir, name_f), raw_dir)
# make images_table
images_table = raw_dir + '/images_table.txt'
mw.mImgtbl(raw_dir, images_table)
# create header file
(NAXIS1, NAXIS2, projection, CRVAL1, CRVAL2, CRPIX1, CRPIX2, CD1_1, CD1_2,
CD2_1, CD2_2) = para
f = open(raw_dir + '/header.txt', 'w')
f.write('SIMPLE = T\n')
f.write('BITPIX = -64\n')
f.write('BUNIT = none\n')
f.write('NAXIS = 2\n')
f.write('NAXIS1 = %d\n' % NAXIS1)
f.write('NAXIS2 = %d\n' % NAXIS2)
f.write("CTYPE1 = 'RA---%s'\n" % projection)
f.write("CTYPE2 = 'DEC--%s'\n" % projection)
f.write('CRPIX1 = %d\n' % CRPIX1)
f.write('CRPIX2 = %d\n' % CRPIX2)
f.write('CRVAL1 = %f\n' % CRVAL1)
f.write('CRVAL2 = %f\n' % CRVAL2)
f.write('CD1_1 = %f\n' % CD1_1)
f.write('CD1_2 = %f\n' % CD1_2)
f.write('CD2_1 = %f\n' % CD2_1)
f.write('CD2_2 = %f\n' % CD2_2)
f.write('HISTORY = By Yue Cao\n')
f.write('END')
f.close()
# re-project
stats_table = raw_dir + '/stats_table.txt'
mw.mProjExec(images_table=images_table,
template_header=raw_dir + '/header.txt',
raw_dir=raw_dir,
proj_dir=proj_dir,
stats_table=stats_table,
exact=exact)
# delete intermediate files
if clear_files:
shutil.rmtree(raw_dir)
for name_f in Name_f0:
n_f = name_f.split('.')[0]
os.remove('%s/hdu0_%s_area.fits' % (proj_dir, n_f))
# rename the re-projected fits
for i in range(len(Name_f0)):
os.rename('%s/hdu0_%s' % (proj_dir, Name_f0[i]),
'%s/%s' % (proj_dir, Name_f1[i]))
# def re_project(orig_dir,proj_dir,header,exact=True,clear_files=True):
'''
