def main():
parser = getparser()
args = parser.parse_args()
fn = args.fn
if not iolib.fn_check(fn):
sys.exit("Unable to locate input file: %s" % fn)
#Need some checks on these
param = args.param
print("Loading input raster into masked array")
ds = iolib.fn_getds(fn)
#Currently supports only single band operations
r = iolib.ds_getma(ds, 1)
#May need to cast input ma as float32 so np.nan filling works
#r = r.astype(np.float32)
#Want function that checks and returns float32 if necessary
#Should filter, then return original dtype
r_fltr = r
#Loop through all specified input filters
#for filt in args.filt:
filt = args.filt[0]
if len(param) == 1:
param = param[0]
param_str = ''
if filt == 'range':
#Range filter
param = [float(i) for i in param[1:]]
r_fltr = filtlib.range_fltr(r_fltr, param)
param_str = '_{0:0.2f}-{1:0.2f}'.format(*param)
elif filt == 'absrange':
#Range filter of absolute values
param = [float(i) for i in param[1:]]
r_fltr = filtlib.absrange_fltr(r_fltr, param)
param_str = '_{0:0.2f}-{1:0.2f}'.format(*param)
elif filt == 'perc':
#Percentile filter
param = [float(i) for i in param[1:]]
r_fltr = filtlib.perc_fltr(r, perc=param)
param_str = '_{0:0.2f}-{1:0.2f}'.format(*param)
elif filt == 'med':
#Median filter
param = int(param)
r_fltr = filtlib.rolling_fltr(r_fltr, f=np.nanmedian, size=param)
#r_fltr = filtlib.median_fltr(r_fltr, fsize=param, origmask=True)
#r_fltr = filtlib.median_fltr_skimage(r_fltr, radius=4, origmask=True)
param_str = '_%ipx' % param
elif filt == 'gauss':
#Gaussian filter (default)
param = int(param)
r_fltr = filtlib.gauss_fltr_astropy(r_fltr,
size=param,
origmask=False,
fill_interior=False)
param_str = '_%ipx' % param
elif filt == 'highpass':
#High pass filter
param = int(param)
r_fltr = filtlib.highpass(r_fltr, size=param)
param_str = '_%ipx' % param
elif filt == 'sigma':
#n*sigma filter, remove outliers
param = int(param)
r_fltr = filtlib.sigma_fltr(r_fltr, n=param)
param_str = '_n%i' % param
elif filt == 'mad':
#n*mad filter, remove outliers
#Maybe better to use a percentile filter
param = int(param)
r_fltr = filtlib.mad_fltr(r_fltr, n=param)
param_str = '_n%i' % param
elif filt == 'dz':
#Difference filter, need to specify ref_fn and range
#Could let the user compute their own dz, then just run a standard range or absrange filter
ref_fn = param[0]
ref_ds = warplib.memwarp_multi_fn([
ref_fn,
],
res=ds,
extent=ds,
t_srs=ds)[0]
ref = iolib.ds_getma(ref_ds)
param = [float(i) for i in param[1:]]
r_fltr = filtlib.dz_fltr_ma(r, ref, rangelim=param)
#param_str = '_{0:0.2f}-{1:0.2f}'.format(*param)
param_str = '_{0:0.0f}_{1:0.0f}'.format(*param)
else:
sys.exit("No filter type specified")
#Compute and print stats before/after
if args.stats:
print("Input stats:")
malib.print_stats(r)
print("Filtered stats:")
malib.print_stats(r_fltr)
#Write out
dst_fn = os.path.splitext(fn)[0] + '_%sfilt%s.tif' % (filt, param_str)
if args.outdir is not None:
outdir = args.outdir
if not os.path.exists(outdir):
os.makedirs(outdir)
dst_fn = os.path.join(outdir, os.path.split(dst_fn)[-1])
print("Writing out filtered raster: %s" % dst_fn)
iolib.writeGTiff(r_fltr, dst_fn, ds)
def sample_stack(ex, ey, geoid_offset=False, pad=3):
if ex > m.shape[2]-1 or ey > m.shape[1]-1:
print "Input coordinates are outside stack extent:"
print ex, ey
print m.shape
v = None
else:
print "Sampling with pad: %i" % pad
if pad == 0:
v = m[:,ey,ex]
else:
window_x = np.around(np.clip([ex-pad, ex+pad+1], 0, m.shape[2]-1)).astype(int)
window_y = np.around(np.clip([ey-pad, ey+pad+1], 0, m.shape[1]-1)).astype(int)
print window_x
print window_y
v = m[:,window_y[0]:window_y[1],window_x[0]:window_x[1]].reshape(m.shape[0], np.ptp(window_x)*np.ptp(window_y))
#v = v.mean(axis=1)
v = np.ma.median(v, axis=1)
if v.count() == 0:
print "No valid values"
else:
mx, my = geolib.pixelToMap(ex, ey, gt)
print ex, ey, mx, my
print "Count: %i" % v.count()
#Hack to get elevations relative to geoid
#Note: this can be added multiple times if clicked quickly
if geoid_offset:
#geoid_offset = geolib.sps2geoid(mx, my, 0.0)[2]
geoid_offset = geolib.nps2geoid(mx, my, 0.0)[2]
print "Removing geoid offset: %0.1f" % geoid_offset
v += geoid_offset
#Should filter here
#RS1 has some values that are many 1000s of m/yr below neighbors
if filter_outliers:
if True:
med = malib.fast_median(v)
mad = malib.mad(v)
min_v = med - mad*4
f_idx = (v < min_v).filled(False)
if np.any(f_idx):
print med, mad
print "Outliers removed by absolute filter: (val < %0.1f)" % min_v
print timelib.o2dt(d[f_idx])
print v[f_idx]
v[f_idx] = np.ma.masked
if True:
v_idx = (~np.ma.getmaskarray(v)).nonzero()[0]
#This tries to maintain fixed window in time
f = filtlib.rolling_fltr(v, size=7)
#This uses fixed number of neighbors
f = filtlib.rolling_fltr(v[v_idx], size=7)
#f_diff = np.abs(f - v)
#Note: the issue is usually that the velocity values are too low
#f_diff = f - v
f_diff = f - v[v_idx]
diff_thresh = 2000
#f_idx = (f_diff > diff_thresh).filled(False)
#f_idx = (f_diff < diff_thresh).filled(False)
f_idx = np.zeros_like(v.data).astype(bool)
f_idx[v_idx] = (f_diff > diff_thresh)
if np.any(f_idx):
print "Outliers removed by rolling median filter: (val < %0.1f)" % diff_thresh
print timelib.o2dt(d[f_idx])
print v[f_idx]
v[f_idx] = np.ma.masked
return v
if args.density is None:
#Attempt to extract from nearby SNOTEL sites for dem_ts
#Attempt to use model
#Last resort, use constant value
rho_s = 0.5
#rho_s = 0.4
#rho_s = 0.36
#Convert snow depth to swe
swe = dz * rho_s
if args.filter:
print("Filtering SWE map")
#Median filter to remove artifacts
swe_f = filtlib.rolling_fltr(swe, size=5)
#Gaussian filter to smooth over gaps
swe_f = filtlib.gauss_fltr_astropy(swe, size=9)
swe = swe_f
swe_clim = list(malib.calcperc(swe, (1,99)))
swe_clim[0] = 0
swe_clim = (0, 8)
prism = None
nax = 2
figsize = (8, 4)
if args.prism:
#This is PRISM 30-year normal winter PRECIP
prism_fn = '/Users/dshean/data/PRISM_ppt_30yr_normal_800mM2_10-05_winter_cum.tif'
if os.path.exists(prism_fn):
print("Input pixel count: %s" % trend.count())
#Outlier filter
#This can remove valid pixels for larger glaciers (e.g. Baltoro) with negative dh/dt - could scale based on pixel count
#trend_filt = filtlib.mad_fltr(trend, n=4)
#trend_filt = filtlib.sigma_fltr(trend, n=3)
#print("Output pixel count: %s" % trend_filt.count())
#Remove islands
#trend_filt = filtlib.remove_islands(trend, iterations=1)
#Erode edges near nodata
trend_filt = filtlib.erode_edge(trend, iterations=1)
print("Output pixel count: %s" % trend_filt.count())
#Rolling median filter (remove noise) - can use a slightly larger window here
trend_filt = filtlib.rolling_fltr(trend_filt, size=size, circular=True, origmask=True)
print("Output pixel count: %s" % trend_filt.count())
#Gaussian filter (smooth)
#trend_filt = filtlib.gauss_fltr_astropy(trend_filt, size=size, origmask=True, fill_interior=True)
trend_filt = filtlib.gauss_fltr_astropy(trend_filt, size=size)
print("Output pixel count: %s" % trend_filt.count())
trend_fn=out_fn+'_trend_%spx_filt.tif' % size
print("Writing out: %s" % trend_fn)
iolib.writeGTiff(trend_filt*365.25, trend_fn, trend_ds)
#Update intercept using new filtered slope values
#Need to update for different periods?
#dt_pivot = timelib.mean_date(datetime(2000,5,31), datetime(2009,5,31))
#dt_pivot = timelib.mean_date(datetime(2009,5,31), datetime(2018,5,31))