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coadd.py
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coadd.py
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from __future__ import division, print_function
import numpy as np, argparse, os
from enlib import enmap, array_ops, utils, mpi
from scipy import ndimage
parser = argparse.ArgumentParser()
parser.add_argument("imaps_and_hits", nargs="+", help="map map map ... hits hits hits ... unless --transpose, in which case it's map hits map hits map hits ...")
parser.add_argument("omap")
parser.add_argument("ohit")
parser.add_argument("-v", "--verbose", action="store_true")
parser.add_argument("-a", "--apod", type=str, default=None)
parser.add_argument("-e", "--edge", type=int, default=0)
parser.add_argument("-t", "--trim", type=int, default=0, help="Amount to trim maps that need to be interplated by, in pixels on each side.")
parser.add_argument("--fslice", type=str, default="")
parser.add_argument("-c", "--cont", action="store_true")
parser.add_argument("-M", "--allow-missing", action="store_true")
parser.add_argument("-T", "--transpose", action="store_true")
parser.add_argument("-W", "--warn", action="store_true")
parser.add_argument("-N", "--ncomp", type=int, default=-1)
args = parser.parse_args()
comm = mpi.COMM_WORLD
n = len(args.imaps_and_hits)//2
if not args.transpose:
imaps = args.imaps_and_hits[:n]
ihits = args.imaps_and_hits[n:]
else:
imaps = args.imaps_and_hits[0::2]
ihits = args.imaps_and_hits[1::2]
imaps = eval("imaps" + args.fslice)
ihits = eval("ihits" + args.fslice)
apod_params = [float(w) for w in args.apod.split(":")] if args.apod else None
def read_helper(fname, shape=None, wcs=None):
if shape is None: return enmap.read_map(fname)
mshape, mwcs = enmap.read_map_geometry(fname)
pixbox = enmap.pixbox_of(mwcs, shape, wcs)
return enmap.read_map(fname, pixbox=pixbox)
def read_map(fname, shape=None, wcs=None, ncomp=3):
m = nonan(read_helper(fname, shape, wcs))
#return m.preflat[:1]
m = m.reshape(-1, m.shape[-2], m.shape[-1])
if ncomp == 0: return m[0]
if len(m) == 1:
res = enmap.zeros((ncomp,)+m.shape[1:],m.wcs,m.dtype)
res[0] = m
return res
else: return m
def read_div(fname, shape=None, wcs=None, ncomp=3):
m = nonan(read_helper(fname, shape, wcs))*1.0
if ncomp == 0: return m.preflat[0]
#return m.preflat[:1][None]
if m.ndim == 2:
res = enmap.zeros((ncomp,ncomp)+m.shape[-2:], m.wcs, m.dtype)
for i in range(ncomp):
res[i,i] = m
return res
elif m.ndim == 3:
res = enmap.zeros((ncomp,ncomp)+m.shape[-2:], m.wcs, m.dtype)
for i in range(ncomp):
res[i,i] = m[i]
return res
elif m.ndim == 4: return m
else: raise ValueError("Wrong number of dimensions in div %s" % fname)
def get_tilenames(dir):
return sorted([name for name in os.listdir(dir) if name.endswith(".fits") or name.endswith(".hdf")])
def mul(w,m):
if w.ndim < 4: return m*w
elif w.ndim == 4: return enmap.samewcs(array_ops.matmul(w,m, axes=[0,1]),m)
else: raise NotImplementedError("Only 2d, 3d or 4d weight maps understood")
def add(m1,m2):
ndim = min(m1.ndim,m2.ndim)
if m1.ndim == m2.ndim or ndim < 4: return m1+m2
elif ndim == 4:
if m1.ndim < m2.ndim: m1,m2 = m2,m1
res = m1.copy()
for i in range(len(m1)):
res[i,i] += (m2 if m2.ndim == 2 else m2[i])
return res
else: raise NotImplementedError("Only 2d, 3d or 4d maps understood")
def solve(w,m):
if w.ndim < 4: return m/w
elif w.ndim == 4:
# This is slower, but handles low-hit areas near the edge better
iw = array_ops.eigpow(w,-1,axes=[0,1])
return enmap.samewcs(array_ops.matmul(iw,m,axes=[0,1]), m)
#return array_ops.solve_masked(w,m,axes=[0,1])
else: raise NotImplementedError("Only 2d, 3d or 4d weight maps understood")
def nonan(a):
res = a.copy()
res[~np.isfinite(res)] = 0
return res
def apply_apod(div):
if apod_params is None: return div
weight = div.preflat[0]
moo = enmap.downgrade(weight,50)
maxval = np.max(enmap.downgrade(weight,50))
apod = np.minimum(1,weight/maxval/apod_params[0])**apod_params[1]
return div*apod
def apply_trim(div):
t = args.trim
if t <= 0: return div
div[...,range(t)+range(-t,0),:] = 0
div[...,:,range(t)+range(-t)] = 0
return div
#fdiv = div.reshape((-1,)+div.shape[-2:])
#dists= ndimage.distance_transform_edt(np.any(fdiv!=0,0))
#mask = (dists>0)&(dists<args.trim)
#apod = dists[mask]*float(args.trim)**-1
#for cdiv in fdiv:
# print "A"
# cdiv[mask] *= apod
return div
def apply_edge(div):
if args.edge == 0: return div
w = div.preflat[0]*0+1
w[[0,-1],:] = 0
w[:,[0,-1]] = 0
dists = ndimage.distance_transform_edt(w)
apod = np.minimum(1,dists/float(args.edge))
return div*apod
def coadd_maps(imaps, ihits, omap, ohit, cont=False, ncomp=-1):
# The first map will be used as a reference. All subsequent maps
# must fit in its boundaries.
if cont and os.path.exists(omap): return
if args.verbose: print("Reading %s" % imaps[0])
if ncomp < 0:
shape, wcs = enmap.read_map_geometry(imaps[0])
ncomp = 0 if len(shape) == 2 else shape[0]
m = read_map(imaps[0], ncomp=ncomp)
if args.verbose: print("Reading %s" % ihits[0])
w = apply_edge(apply_apod(apply_trim(read_div(ihits[0], ncomp=ncomp))))
if args.warn and np.any(w.preflat[0]<0):
print("Negative weight in %s" % ihits[0])
wm = mul(w,m)
for i, (mif,wif) in enumerate(zip(imaps[1:],ihits[1:])):
if args.verbose: print("Reading %s" % mif)
try:
mi = read_map(mif, m.shape, m.wcs, ncomp=ncomp)
except (IOError, OSError):
if args.allow_missing:
print("Can't read %s. Skipping" % mif)
continue
else: raise
if args.verbose: print("Reading %s" % wif)
wi = apply_edge(apply_apod(apply_trim(read_div(wif, m.shape, m.wcs, ncomp=ncomp))))
if args.warn and np.any(wi.preflat[0]<0):
print("Negative weight in %s" % ihits[i+1])
## We may need to reproject maps
#if mi.shape != m.shape or str(mi.wcs.to_header()) != str(m.wcs.to_header()):
# mi = enmap.extract(mi, m.shape, m.wcs)
# wi = enmap.extract(wi, w.shape, w.wcs)
w = add(w,wi)
wm = add(wm,mul(wi,mi))
if args.verbose: print("Solving")
m = solve(w,wm)
if args.verbose: print("Writing %s" % omap)
enmap.write_map(omap, m)
if args.verbose: print("Writing %s" % ohit)
enmap.write_map(ohit, w)
# Two cases: Normal enmaps or dmaps
if not os.path.isdir(imaps[0]):
# Normal monotlithic map
coadd_maps(imaps, ihits, args.omap, args.ohit, cont=args.cont, ncomp=args.ncomp)
else:
# Dmap. Each name is actually a directory, but they
# all have compatible tile names.
tilenames = get_tilenames(imaps[0])
utils.mkdir(args.omap)
utils.mkdir(args.ohit)
for tilename in tilenames[comm.rank::comm.size]:
timaps = ["%s/%s" % (imap,tilename) for imap in imaps]
tihits = ["%s/%s" % (ihit,tilename) for ihit in ihits]
print("%3d %s" % (comm.rank, tilename))
coadd_maps(timaps, tihits, args.omap + "/" + tilename, args.ohit + "/" + tilename, cont=args.cont, ncomp=args.ncomp)
if args.verbose: print("Done")