def tsx_near_time(time, glacier, just_filename=False):
'''
x,y,vx,vy,v,time = tsx_near_time(time,glacier,just_filename = False)
Find TSX data closest to "time".
Inputs:
time: time that you want data
glacier: glacier name (Kanger or Helheim)
just_filename: option to only return the filename
Outputs:
x,y: grid coordinates
vx,vy: x and y velocities
v: velocity magnitudes for gird
time: time of transect
'''
DIR_TSX = os.path.join(os.getenv("DATA_HOME"),
"Velocity/TSX/" + glacier + "/")
DIRs = os.listdir(DIR_TSX)
tpt = []
best_track = []
min_diff = 1.0
for DIR in DIRs:
if DIR.startswith('track'):
tsx_time, interval = geodatlib.readtime(DIR_TSX + DIR +
"/mosaicOffsets")
if abs(tsx_time - time) < min_diff:
min_diff = abs(tsx_time - time)
best_time = tsx_time
best_track = DIR
if just_filename:
year, month, day = datelib.fracyear_to_date(best_time)
return DIR_TSX + 'TIF/' + best_track + '_' + "%04d%02d%02d" % (
year, month, day), best_time
else:
# Return the closest velocity profile
x, y, v, vx, vy, ex, ey, time, interval = geodatlib.readvelocity(
DIR_TSX, best_track, "/mosaicOffsets")
return x, y, vx, vy, v, time
def readvelocity(DIR, track, file):
'''
x,y,v,vx,vy,ex,ey,time,interval = readvelocity(DIR,track,file)
'''
# Filename
filename = DIR + track + "/" + file
# Get time
if os.path.exists(filename + ".meta"):
time, interval = readtime(filename)
year, month, day = datelib.fracyear_to_date(time)
date = "%04d%02d%02d" % (year, month, day)
else:
time = float('NaN')
interval = float('NaN')
date = float('NaN')
if os.path.isfile(DIR + "TIF/" + track + "_v.tif"):
x, y, v = geotifflib.read(DIR + "TIF/" + track + "_v.tif")
x, y, vx = geotifflib.read(DIR + "TIF/" + track + "_vx.tif")
x, y, vy = geotifflib.read(DIR + "TIF/" + track + "_vy.tif")
x, y, ex = geotifflib.read(DIR + "TIF/" + track + "_ex.tif")
x, y, ey = geotifflib.read(DIR + "TIF/" + track + "_ey.tif")
# Check to see if there are geotiff files in the subdirectory. If not, read the binary data.
elif os.path.isfile(DIR + "TIF/" + track + "_" + date + "_v.tif"):
x, y, v = geotifflib.read(DIR + "TIF/" + track + "_" + date + "_v.tif")
x, y, vx = geotifflib.read(DIR + "TIF/" + track + "_" + date +
"_vx.tif")
x, y, vy = geotifflib.read(DIR + "TIF/" + track + "_" + date +
"_vy.tif")
x, y, ex = geotifflib.read(DIR + "TIF/" + track + "_" + date +
"_ex.tif")
x, y, ey = geotifflib.read(DIR + "TIF/" + track + "_" + date +
"_ey.tif")
else:
print "Unpacking binary velocity file ", track
x, y, v, vx, vy, ex, ey, time, interval = readbinary(filename)
return (x, y, v, vx, vy, ex, ey, time, interval)
def load_extent_timeseries(glacier,time1,time2,dt,nofront_shapefile='glacier_extent_nofront',datatypes=['Landsat','TSX','WV']):
'''
time, xextents, yxextents, bounds = load_extent_timeseries(glacier,time1,
time2,dt,nofront_shapefile='glacier_extent_nofront',
datatypes=['Landsat','TSX','WV'])
Interpolates ice-front positions from picked ice-front positions to create
a timeseries of meshes to be used in the terminus-driven model.
Inputs:
glacier : glacier name (Helheim, Kanger)
time1 : fractional start time for timeseries
time2 : fractional end time for timeseries
dt : timestep
nofront_shapefile : nofront shapefile name for mesh extent
datatypes : satellite image types for picked ice fronts
Outputs:
time : interpolated time between time1,time2 with timestep dt
xextents : 2-d array of x-coordinates of extents
yextents : 2-d array of y-coordinates of extents
bounds : boundary numbers for extents
'''
# Glacier extent with no ice front
extent = meshlib.shp_to_xy(os.path.join(os.getenv("DATA_HOME"),"ShapeFiles/Glaciers/3D/"+glacier+"/"+nofront_shapefile))
if extent[1,1] > extent[0,1]:
extent = np.flipud(extent)
xextent = extent[:,0]
yextent = extent[:,1]
bound_extent = extent[:,2]
# Interpolate glacier extent to a finer grid to make ice-front interpolation easier
dextent = distlib.transect(xextent,yextent)
#dextent = np.arange(0,dold[-1],20.0)
#xextent = np.interp(dextent,dold,xextent)
#yextent = np.interp(dextent,dold,yextent)
#f = scipy.interpolate.interp1d(dold,bound,kind='nearest')
#bound = f(dextent)
extent = LineString(np.column_stack([extent[:,0:2]]))
# Load all ice front positions for that time period
termx,termy,termt = icefrontlib.load_all(time1-0.5,time2+0.5,glacier,type='icefront',datatypes=datatypes)
# In case we have multiple ice front picks for the same day, we want to
# use only one of those for continuity
[junk,ind] = np.unique(termt,return_index=True)
termt = np.array(termt)[ind]
termx = termx[:,ind]
termy = termy[:,ind]
# Load a velocity profile to use as interpolation direction to figure out ice-front position
# on timesteps that fall between picked ice fronts
x,y,u = geotifflib.read(os.path.join(os.getenv("DATA_HOME"),"Velocity/TSX/"+glacier+"/TIF/all-2008-2016_vx.tif"))
x,y,v = geotifflib.read(os.path.join(os.getenv("DATA_HOME"),"Velocity/TSX/"+glacier+"/TIF/all-2008-2016_vy.tif"))
fu = scipy.interpolate.RegularGridInterpolator((y,x),u)
fv = scipy.interpolate.RegularGridInterpolator((y,x),v)
# Get ice-front position for each timestep
time = np.arange(time1,time2+dt,dt)
timeseries_x = np.zeros([len(termx[:,0]),len(time)])
timeseries_y = np.zeros([len(termx[:,0]),len(time)])
timeseries_advance = np.zeros([len(termx[:,0]),len(time)])
timeseries_dist = np.zeros([len(termx[:,0]),len(time)])
timeseries_x[:,:] = float('nan')
timeseries_y[:,:] = float('nan')
timeseries_advance[:,:] = float('nan')
timeseries_dist[:,:] = float('nan')
xextents = np.zeros([len(termx[:,0])+len(xextent),len(time)])
yextents = np.zeros([len(termx[:,0])+len(xextent),len(time)])
bounds = np.zeros([len(termx[:,0])+len(xextent),len(time)])
for i in range(0,len(time)):
# Find picked ice-front positions for before and after timestep for the interpolation
ind = np.argmin(abs(time[i]-termt))
if termt[ind] < time[i]:
ind1 = ind
ind2 = ind+1
else:
ind1 = ind-1
ind2 = ind
# Fractional time between ind1,ind2 to use for interpolation
frac = (time[i]-termt[ind1])/(termt[ind2]-termt[ind1])
# Get picked ice-front positions that we will use for the interpolation
nonnan = np.where(~(np.isnan(termx[:,ind1])))[0]
termx1 = termx[nonnan,ind1]
termy1 = termy[nonnan,ind1]
nonnan = np.where(~(np.isnan(termx[:,ind2])))[0]
termx2 = termx[nonnan,ind2]
termy2 = termy[nonnan,ind2]
if termy1[-1] > termy1[0]:
termx1 = np.flipud(termx1)
termy1 = np.flipud(termy1)
if termy2[-1] > termy2[0]:
termx2 = np.flipud(termx2)
termy2 = np.flipud(termy2)
# Get locations where interpolate ice front intersects the glacier extent
# First, get intersection pts for two closest ice-front positions in time
term1 = LineString(np.column_stack([termx1,termy1]))
intersect = extent.intersection(term1)
try:
if len(intersect) == 2:
if intersect[0].y > intersect[1].y:
top1 = [intersect[0].x,intersect[0].y]
bot1 = [intersect[1].x,intersect[1].y]
else:
top1 = [intersect[1].x,intersect[1].y]
bot1 = [intersect[0].x,intersect[0].y]
else:
print "Need to look at date ", datelib.fracyear_to_date(termt[ind1])
except:
print "Need to look at date ", datelib.fracyear_to_date(termt[ind1])
term2 = LineString(np.column_stack([termx2,termy2]))
intersect = extent.intersection(term2)
try:
if len(intersect) == 2:
if intersect[0].y > intersect[1].y:
top2 = [intersect[0].x,intersect[0].y]
bot2 = [intersect[1].x,intersect[1].y]
else:
top2 = [intersect[1].x,intersect[1].y]
bot2 = [intersect[0].x,intersect[0].y]
else:
print "Need to look at date ", datelib.fracyear_to_date(termt[ind2])
except:
print "Need to look at date ", datelib.fracyear_to_date(termt[ind2])
# Now find new intersection points
if top1[0] < top2[0]: # advancing on this side
ind_top = np.where((xextent > top1[0]) & (xextent < top2[0]) & (abs(top1[1]-yextent) < 500.))[0]
sortind = np.argsort(xextent[ind_top])
xtops = np.r_[top1[0],xextent[ind_top[sortind]],top2[0]]
ytops = np.r_[top1[1],yextent[ind_top[sortind]],top2[1]]
dtops = distlib.transect(xtops,ytops)
dtop = dtops[-1]*frac
elif top1[0] > top2[0]: # retreating on this side
ind_top = np.where((xextent < top1[0]) & (xextent > top2[0]) & (abs(top1[1]-yextent) < 500.))[0]
sortind = np.argsort(xextent[ind_top])
xtops = np.r_[top2[0],xextent[ind_top[sortind]],top1[0]]
ytops = np.r_[top2[1],yextent[ind_top[sortind]],top1[1]]
dtops = distlib.transect(xtops,ytops)
dtop = dtops[-1]*(1-frac)
else:
print "not advancing or retreating on top"
xtop = np.interp(dtop,dtops,xtops)
ytop = np.interp(dtop,dtops,ytops)
if bot1[0] < bot2[0]: # advancing on this side
ind_bot = np.where((xextent > bot1[0]) & (xextent < bot2[0]) & (abs(bot1[1]-yextent) < 500.))[0]
sortind = np.argsort(xextent[ind_bot])
xbots = np.r_[bot1[0],xextent[ind_bot[sortind]],bot2[0]]
ybots = np.r_[bot1[1],yextent[ind_bot[sortind]],bot2[1]]
dbots= distlib.transect(xbots,ybots)
dbot = (dbots[-1])*frac
elif bot1[0] > bot2[0]: # retreating on this side
ind_bot = np.where((xextent < bot1[0]) & (xextent > bot2[0]) & (abs(bot1[1]-yextent) < 500.))[0]
sortind = np.argsort(xextent[ind_bot])
xbots = np.r_[bot2[0],xextent[ind_bot[sortind]],bot1[0]]
ybots = np.r_[bot2[1],yextent[ind_bot[sortind]],bot1[1]]
dbots= distlib.transect(xbots,ybots)
dbot = (dbots[-1])*(1-frac)
else:
print "not advancing or retreating on bot"
xbot = np.interp(dbot,dbots,xbots)
ybot = np.interp(dbot,dbots,ybots)
# Now that we know the bottom and top points (extent of the ice front), we can start
# calculating the shape, again based on linear interpolation
# May need to change next expression to find indices between the sidewalls for Kanger,
# but this should work for Helheim
ind_term1 = np.where((termy1 > bot1[1]) & (termy1 < top1[1]))[0]
icefront_x = []
icefront_y = []
advance = []
icefront_x.append(xtop)
icefront_y.append(ytop)
if i > 0:
nonnan = np.where(~(np.isnan(xextents[:,i-1])))[0]
extentpath = Path(np.column_stack([xextents[nonnan,i-1],yextents[nonnan,i-1]]))
if extentpath.contains_point([xtop,ytop]) or (xtop < xtop_old):
sign = -1
else:
sign = 1
advance.append(sign*distlib.between_pts(xtop,ytop,xtop_old,ytop_old))
else:
advance.append(0)
for j in ind_term1:
# Get velocities to create a line, to interpolate between ice fronts
uj = fu((termy1[j],termx1[j]))
vj = fv((termy1[j],termx1[j]))
# Create flowline that intersects that point of the ice front
xunit = uj/(np.sqrt(uj**2+vj**2))
yunit = vj/(np.sqrt(uj**2+vj**2))
b = termy1[j] - (yunit/xunit)*termx1[j]
flowlinex = np.arange(-3000.,3005.,10) + termx1[j]
flowliney = (yunit/xunit)*flowlinex + b
flowline = LineString(np.column_stack([flowlinex,flowliney]))
# Find where flowline intersects the next ice-front position
intersect = flowline.intersection(term2)
add = False
try:
if len(intersect) > 0:
ind = np.argmin(abs([intersect[k].x for k in range(0,len(intersect))]-termx1[j]))
term2_flowline = [intersect[ind].x,intersect[ind].y]
add = True
except:
try:
term2_flowline = [intersect.x,intersect.y]
add = True
except:
pass
dflow = distlib.between_pts(termx1[j],termy1[j],term2_flowline[0],term2_flowline[1])
dmid = frac*dflow
xmid = np.interp(dmid,[0,dflow],[termx1[j],term2_flowline[0]])
ymid = np.interp(dmid,[0,dflow],[termy1[j],term2_flowline[1]])
if (add == True) and (ymid > ybot) and (ymid < ytop):
icefront_x.append(xmid)
icefront_y.append(ymid)
if i > 0:
nonnan = np.where(~(np.isnan(timeseries_x[:,i-1])))[0]
front_lasttime = LineString(np.column_stack([timeseries_x[nonnan,i-1],timeseries_y[nonnan,i-1]]))
intersect = flowline.intersection(front_lasttime)
try:
diff = distlib.between_pts(xmid,ymid,intersect.x,intersect.y)
except:
try:
diff = 1000.0
for pt in intersect:
newdiff = distlib.between_pts(xmid,ymid,pt.x,pt.y)
if newdiff < diff:
diff = newdiff
if diff == 1000.0:
diff = 0
except:
diff = 0
if extentpath.contains_point([xmid,ymid]):
sign = -1
else:
sign = 1
advance.append(sign*diff)
else:
advance.append(0)
icefront_x.append(xbot)
icefront_y.append(ybot)
if i > 0:
if extentpath.contains_point([xbot,ybot]) or (xbot < xbot_old):
sign = -1
else:
sign = 1
advance.append(sign*distlib.between_pts(xbot,ybot,xbot_old,ybot_old))
else:
advance.append(0)
# Try sorting icefront to get rid of potential tangles
icefront_x_old = np.asarray(icefront_x)
icefront_y_old = np.asarray(icefront_y)
advance_old = np.asarray(advance)
icefront_x = np.zeros_like(icefront_x_old)
icefront_y = np.zeros_like(icefront_y_old)
advance = np.zeros_like(advance_old)
icefront_x[0] = icefront_x_old[0]
icefront_y[0] = icefront_y_old[0]
advance[0] = advance_old[0]
ind = range(1,len(icefront_x_old))
for k in range(1,len(icefront_x_old)):
mindist = 10000.
for j in range(0,len(ind)):
dist = distlib.between_pts(icefront_x[k-1],icefront_y[k-1],icefront_x_old[ind[j]],icefront_y_old[ind[j]])
if dist < mindist:
mindist = dist
minind = ind[j]
icefront_x[k] = icefront_x_old[minind]
icefront_y[k] = icefront_y_old[minind]
advance[k] = advance_old[minind]
ind.remove(minind)
# Save icefront in timeseries
timeseries_x[0:len(icefront_x),i] = icefront_x
timeseries_y[0:len(icefront_y),i] = icefront_y
timeseries_dist[0:len(icefront_x),i] = distlib.transect(icefront_x,icefront_y)
timeseries_advance[0:len(icefront_x),i] = advance
# Now create mesh extent and BC numbers using the interpolated ice front
boundterminus = np.ones(len(icefront_x))*2.0
ind1 = np.where((xextent > xbot) & (abs(yextent - ybot) < 1.0e3))[0][0]
ind2 = np.where((xextent > xtop) & (abs(yextent - ytop) < 1.0e3))[0][-1]
extent_x = np.r_[xextent[0:ind1],np.flipud(icefront_x),xextent[ind2+1:]]
extent_y = np.r_[yextent[0:ind1],np.flipud(icefront_y),yextent[ind2+1:]]
bound = np.r_[bound_extent[0:ind1],boundterminus,bound_extent[ind2+1:]]
xextents[0:len(extent_x),i] = extent_x
yextents[0:len(extent_x),i] = extent_y
bounds[0:len(extent_x),i] = bound
xtop_old = float(xtop)
ytop_old = float(ytop)
xbot_old = float(xbot)
ybot_old = float(ybot)
return time, xextents, yextents, bounds, timeseries_x, timeseries_y, timeseries_advance
method='linear',
fill_value=float('nan'))
plt.plot(dists / 1e3, floatlib.height(zb), 'k:')
plt.plot(dists / 1e3, f((y, x)), 'b', lw=1.5)
plt.plot(dists / 1e3, floatlib.shelfbase(f(((y, x)))), 'b', lw=1.5)
if glacier == 'Helheim':
plt.ylim([-1200, 220])
plt.xticks(range(-10, 5, 2), fontsize=10)
plt.yticks(np.arange(-1200, 400, 200), fontsize=10)
plt.xlim([-7, 4])
elif glacier == 'Kanger':
plt.ylim([-1200, 220])
plt.xticks(np.arange(-10, 5, 2), fontsize=10)
plt.yticks(np.arange(-1200, 400, 200), fontsize=10)
plt.xlim([-7, 4])
year, month, day = datelib.fracyear_to_date(timedem[i])
plt.title(str(year) + '-' + str(month) + '-' + str(int(day)))
plt.tight_layout()
plt.subplots_adjust(hspace=10, wspace=0)
plt.savefig(os.path.join(
os.getenv("HOME"),
"Bigtmp/model_movie/" + '{0:02g}'.format(i) + '.png'),
format='PNG',
dpi=400)
plt.close()
##############
# Make movie #
##############
p = np.polyfit(model_time[ind[nonnan]],
model_grid_zs[j, ind[nonnan]].T, 1) / 365.25
model_grid_dhdt[j, k] = p[0]
vel_model_11day[k, :] = np.mean(vel_model[ind, :], axis=0)
dhdt = np.reshape(model_grid_dhdt, [len(ygrid), len(xgrid), len(model_time)])
print "Making plots..."
cx = cubehelix.cmap(start=1.0, rot=-1.1, reverse=True, minLight=0.05, sat=2)
colors = ['r', 'b', 'g', 'limegreen', 'gold', 'k']
for i in range(1, len(model_time)):
fig = plt.figure(figsize=(5.5, 4.2))
gs = matplotlib.gridspec.GridSpec(6, 2)
year, month, day = datelib.fracyear_to_date(model_time[i])
plt.subplot(gs[0:3, 0])
ax = plt.gca()
p = plt.imshow(model_grid['velocity'][:,:,i]/365.25,extent=[np.min(xgrid),np.max(xgrid),\
np.min(ygrid),np.max(ygrid)],origin='lower',cmap=cx,clim=[0,22])
plt.contour(model_grid['velocity'][:,:,i]/365.25,extent=[np.min(xgrid),np.max(xgrid),\
np.min(ygrid),np.max(ygrid)],origin='lower',levels=np.arange(0,25,5),cmap=cx,linewidths=1)
plt.plot(model_gl['x'][:, i], model_gl['y'][:, i], 'w.', markersize=0.5)
plt.plot(np.r_[mesh_hole1[:, 0], mesh_hole1[0, 0]],
np.r_[mesh_hole1[:, 1], mesh_hole1[0, 1]],
'k',
linewidth=0.75,
zorder=2)
plt.plot(np.r_[mesh_hole2[:, 0], mesh_hole2[0, 0]],
np.r_[mesh_hole2[:, 1], mesh_hole2[0, 1]],
# Find dimensions for plot
ncol = 0
for year in years:
ndem = len(np.where(np.floor(timewv)==year)[0])
if ndem > ncol:
ncol = ndem
nrow = len(years)
# Make plot
plt.figure(figsize=(ncol*2.8,nrow*3))
cmap = matplotlib.cm.get_cmap('gray_r',4)
gs = matplotlib.gridspec.GridSpec(nrow,ncol)
gs.update(right=0.94,left=0.02,wspace=0.04,hspace=0.04)
for j in range(0,nrow):
year = years[j]
for i in range(0,len(np.where(np.floor(timewv)==year)[0])):
plt.subplot(gs[j,i])
wvind = np.where(np.floor(timewv)==year)[0][i]
date = datelib.fracyear_to_date(timewv[wvind])
shadeddem = demshadelib.set_shade(zwv[:,:,wvind],0,220)
plt.imshow(shadeddem,extent=[np.min(xwv),np.max(xwv),np.min(ywv),np.max(ywv)],clim=[0,200],origin='lower')
#plt.scatter(xf,yf,c=zabovefloat[:,wvind],s=3.0**2.0,cmap='gist_gray_r',edgecolors='none',vmin=-10,vmax=10)
plt.xlim([np.min(xwv),np.max(xwv)])
plt.ylim([np.min(ywv),np.max(ywv)])
plt.xticks([])
plt.yticks([])
plt.text(xmin+500,ymax-1.25e3,str(date[0])+'-'+str(date[1])+'-'+str(int(np.floor(date[2]))),backgroundcolor='w',fontsize=8)
plt.savefig("/Users/kehrl/Bigtmp/"+glacier+"_dems.png",format='PNG',dpi=150)
plt.close()
imageind = np.argmin(abs(imagetimes - zstimedem[zsind[0]]))
ax = plt.gca()
plt.imshow(images[imageind][2],
extent=[
np.min(images[imageind][0]),
np.max(images[imageind][0]),
np.min(images[imageind][1]),
np.max(images[imageind][1])
],
origin='lower',
cmap='Greys_r')
plt.xticks([])
plt.yticks([])
plt.xlim([xmin, xmax])
plt.ylim([ymin, ymax])
year, month, day = datelib.fracyear_to_date(imagetimes[imageind])
path = matplotlib.path.Path(
[[0.02 * (xmax - xmin) + xmin, 0.82 * (ymax - ymin) + ymin],
[0.02 * (xmax - xmin) + xmin, 0.98 * (ymax - ymin) + ymin],
[0.38 * (xmax - xmin) + xmin, 0.98 * (ymax - ymin) + ymin],
[0.38 * (xmax - xmin) + xmin, 0.82 * (ymax - ymin) + ymin],
[0.02 * (xmax - xmin) + xmin, 0.82 * (ymax - ymin) + ymin]])
patch = matplotlib.patches.PathPatch(path,
edgecolor='k',
facecolor='w',
lw=1,
zorder=3)
ax.add_patch(patch)
plt.text(xmin + 0.04 * (xmax - xmin),
0.92 * (ymax - ymin) + ymin,
'{0:4d}-{1:02d}-{2:02d}'.format(year, month, int(np.round(day))),
def inversion_3D(glacier,
x,
y,
time,
dir_velocity_out='none',
blur=False,
dx='none'):
'''
Inputs:
x : list of x coordinates for grid interpolation
y : list of y coordinates for grid interpolation
time : primary time for velocities, which will be filled in with other data
file_velocity_in : velocity file for interpolation
dir_velocity_out : directory for outputting the velocity
Outputs:
u : velocity in x-dir on grid defined by x,y
y : velocity in y-dir on grid defined by x,y
'''
xmin = np.min(x) - 5.0e3
xmax = np.max(x) + 5.0e3
ymin = np.min(y) - 5.0e3
ymax = np.max(y) + 5.0e3
OUTDIR = os.path.join(os.getenv("DATA_HOME"),
"Velocity/MosaicVelocities/" + glacier)
# Large velocity map to fill in gaps in smaller velocity map
file_velocity_all = os.path.join(
os.getenv("DATA_HOME"),
"Velocity/TSX/" + glacier + "/TIF/all-2008-2016")
# If the region is bigger than what is covered by the TSX stripmaps, then we use Ian's big
# inSAR velocity map
file_velocity_global = os.path.join(
os.getenv("DATA_HOME"),
"Velocity/Random/Greenland/AllGLVel/mosaicOffsets")
year, month, day = datelib.fracyear_to_date(time)
date = "%04d%02d%02d" % (year, month, day)
# Individual velocity map for time step
if time <= 2008:
HOWATDIR = os.path.join(os.getenv("DATA_HOME"),
"Velocity/Howat/" + glacier + "/")
# Use Howat velocity maps
print date
if glacier == 'Kanger':
if '200707' in date:
filename1 = HOWATDIR + "OPT_E68.80N_2007-08/OPT_E68.80N_2007-08"
filename2 = HOWATDIR + "OPT_E68.80N_2007-07/OPT_E68.80N_2007-07"
elif '200107' in date:
filename1 = HOWATDIR + "OPT_E68.80N_2001-07/OPT_E68.80N_2001-07"
filename2 = filename1
elif ('200308' in date) or ('200307' in date):
filename1 = HOWATDIR + "OPT_E68.80N_2003-07/OPT_E68.80N_2003-07"
filename2 = HOWATDIR + "OPT_E68.80N_2001-07/OPT_E68.80N_2001-07"
elif '200506' in date:
filename1 = HOWATDIR + "OPT_E68.80N_2005-06/OPT_E68.80N_2005-06"
filename2 = filename1
elif '200508' in date:
filename1 = HOWATDIR + "OPT_E68.80N_2005-08/OPT_E68.80N_2005-08"
filename2 = filename1
elif '200605' in date:
filename2 = HOWATDIR + "OPT_E68.80N_2006-05/OPT_E68.80N_2006-05"
filename1 = HOWATDIR + "OPT_E68.80N_2006-04/OPT_E68.80N_2006-04"
elif '200607' in date:
filename2 = HOWATDIR + "OPT_E68.80N_2006-07/OPT_E68.80N_2006-07"
filename1 = HOWATDIR + "OPT_E68.80N_2006-06/OPT_E68.80N_2006-06"
elif '200609' in date:
filename1 = HOWATDIR + "OPT_E68.80N_2006-09/OPT_E68.80N_2006-09"
filename2 = filename1
elif glacier == 'Helheim':
if '200709' in date:
filename1 = HOWATDIR + "OPT_E66.50N_2007-08/OPT_E66.50N_2007-08"
filename2 = HOWATDIR + "OPT_E66.50N_2007-09/OPT_E66.50N_2007-09"
elif '200408' in date:
filename1 = HOWATDIR + "OPT_E66.50N_2004-08/OPT_E66.50N_2004-08"
filename2 = HOWATDIR + "OPT_E66.50N_2004-07/OPT_E66.50N_2004-07"
elif '200508' in date:
filename1 = HOWATDIR + "OPT_E66.50N_2005-09/OPT_E66.50N_2005-09"
filename2 = HOWATDIR + "OPT_E66.50N_2005-07/OPT_E66.50N_2005-07"
elif '200608' in date:
filename1 = HOWATDIR + "OPT_E66.50N_2006-09/OPT_E66.50N_2006-09"
filename2 = HOWATDIR + "OPT_E66.50N_2006-07/OPT_E66.50N_2006-07"
files_vx = ' '+filename1+'.vx.tif '+filename2+'.vx.tif '+\
file_velocity_all+'_vx.tif'+' '+file_velocity_global+'_vx.tif'
files_vy = ' '+filename1+'.vy.tif '+filename2+'.vy.tif '+\
file_velocity_all+'_vy.tif'+' '+file_velocity_global+'_vy.tif'
else:
# Use TSX velocity maps
filename1, time1 = tsx_near_time(time, glacier, just_filename=True)
filename2, time2 = tsx_near_time(time - 11 / 365.,
glacier,
just_filename=True)
filename3, time3 = tsx_near_time(time + 11 / 365.,
glacier,
just_filename=True)
if abs(time - time2) < abs(time - time3):
files_vx = ' '+filename1+'_vx.tif'+' '+filename2+'_vx.tif'+\
' '+filename3+'_vx.tif'+' '+file_velocity_all+'_vx.tif'+' '+file_velocity_global+'_vx.tif'
files_vy = ' '+filename1+'_vy.tif'+' '+filename2+'_vy.tif'+\
' '+filename3+'_vy.tif'+' '+file_velocity_all+'_vy.tif'+' '+file_velocity_global+'_vy.tif'
else:
files_vx = ' '+filename1+'_vx.tif'+' '+filename3+'_vx.tif'+\
' '+filename2+'_vx.tif'+' '+file_velocity_all+'_vx.tif'+' '+file_velocity_global+'_vx.tif'
files_vy = ' '+filename1+'_vy.tif'+' '+filename3+'_vy.tif'+\
' '+filename2+'_vy.tif'+' '+file_velocity_all+'_vy.tif'+' '+file_velocity_global+'_vy.tif'
CURRENTDIR = os.getcwd()
os.chdir(OUTDIR)
filename_vx = 'mosaic-' + date + '-vx'
filename_vy = 'mosaic-' + date + '-vy'
if dx == 'none':
os.system('dem_mosaic --hole-fill-length 5 --t_projwin '+str(xmin)+' '+str(ymin)+' '+str(xmax)+\
' '+str(ymax)+' --priority-blending-length 10 -o'+filename_vx+files_vx)
os.system('dem_mosaic --hole-fill-length 5 --t_projwin '+str(xmin)+' '+str(ymin)+' '+str(xmax)+\
' '+str(ymax)+' --priority-blending-length 10 -o'+filename_vy+files_vy)
else:
os.system('dem_mosaic --hole-fill-length 5 --t_projwin '+str(xmin)+' '+str(ymin)+' '+str(xmax)+\
' '+str(ymax)+' --tr '+str(dx)+' --priority-blending-length 10 -o'+filename_vx+files_vx)
os.system('dem_mosaic --hole-fill-length 5 --t_projwin '+str(xmin)+' '+str(ymin)+' '+str(xmax)+\
' '+str(ymax)+' --tr '+str(dx)+' --priority-blending-length 10 -o'+filename_vy+files_vy)
xu, yu, uu = geotifflib.read(filename_vx + "-tile-0.tif")
xv, yv, vv = geotifflib.read(filename_vy + "-tile-0.tif")
if (blur == True) and (dx == 'none'):
print "Blurring DEM over 17 pixels (roughly 1.5km in each direction)..."
# 17 pixel gaussian blur
vx_blur = scipy.ndimage.filters.gaussian_filter(uu,
sigma=2,
truncate=4)
vy_blur = scipy.ndimage.filters.gaussian_filter(vv,
sigma=2,
truncate=4)
else:
vx_blur = uu
vy_blur = vv
os.chdir(CURRENTDIR)
# Calculate velocity magnitude
vmag = np.sqrt(vx_blur**2 + vy_blur**2)
######################################################
# Write out velocities to files for inversion solver #
######################################################
# Interpolate to input grid
xgrid, ygrid = np.meshgrid(x, y)
fu = scipy.interpolate.RegularGridInterpolator((yu, xu),
vx_blur,
method='linear')
vx = fu((ygrid, xgrid))
fv = scipy.interpolate.RegularGridInterpolator((yv, xv),
vy_blur,
method='linear')
vy = fv((ygrid, xgrid))
if dir_velocity_out != 'none':
#files = os.listdir(OUTDIR):
#for file in files:
# if file.startswith('mosaic-'+date):
# shutil.copy(file,dir_velocity_out)
# File for velocity in x-dir
fidu = open(dir_velocity_out + "/udem.xy", "w")
fidu.write('{}\n{}\n'.format(len(x), len(y)))
# File for velocity in y-dir
fidv = open(dir_velocity_out + "/vdem.xy", "w")
fidv.write('{}\n{}\n'.format(len(x), len(y)))
for i in range(0, len(x)):
for j in range(0, len(y)):
fidu.write('{} {} {}\n'.format(x[i], y[j], vx[j, i]))
fidv.write('{} {} {}\n'.format(x[i], y[j], vy[j, i]))
fidv.close()
fidu.close()
return vx, vy
def variability(glacier, time1, time2):
''
''
DIR_TSX = os.path.join(os.getenv("DATA_HOME"),
"Velocity/TSX/" + glacier + "/")
if glacier == 'Helheim':
xmin = 270000.0
xmax = 354900.0
ymin = -2601000.0
ymax = -2541000.0
elif glacier == 'Kanger':
xmin = 457000.0
xmax = 517000.0
ymin = -2319100.0
ymax = -2247100.0
dx = dy = 100.
nx = int(np.ceil((xmax - xmin) / dx) + 1)
x = np.linspace(xmin, (nx - 1) * dx + xmin, nx)
ny = int(np.ceil((ymax - ymin) / dx) + 1)
y = np.linspace(ymin, (ny - 1) * dy + ymin, ny)
xgrid, ygrid = np.meshgrid(x, y)
coords = np.column_stack([ygrid.flatten(), xgrid.flatten()])
#################
# LOAD TSX Data #
#################
DIRs = os.listdir(DIR_TSX)
# Get number of velocity files
nt = 0
for DIR in DIRs:
if DIR.startswith('track'):
nt = nt + 1
# Set up variables
velgrid = np.zeros([ny, nx, nt])
mask = np.zeros([ny, nx, nt])
velgrid_mask = np.zeros([ny, nx, nt])
time = np.zeros(nt)
ergrid = np.zeros([ny, nx, nt])
# Load velocity and mask
count = 0
for j in range(0, len(DIRs)):
DIR = DIRs[j]
if DIR.startswith('track'):
# Load velocity
x1, y1, v1, vx1, vy1, ex1, ey1, time_file, interval1 = geodatlib.readvelocity(
DIR_TSX, DIR, "mosaicOffsets")
time[count] = time_file
year, month, day = datelib.fracyear_to_date(time_file)
xind1 = np.argmin(abs(x1 - xmin))
xind2 = np.argmin(abs(x1 - xmax)) + 1
yind1 = np.argmin(abs(y1 - ymin))
yind2 = np.argmin(abs(y1 - ymax)) + 1
# Load velocity
try:
# If the input and output grids have the same dimensions...
velgrid[:, :, count] = v1[yind1:yind2, xind1:xind2]
except:
# Otherwise interpolate onto output grid
f_dem = scipy.interpolate.RegularGridInterpolator(
[y1, x1],
v1,
bounds_error=False,
method='linear',
fill_value=float('nan'))
v_flatten = f_dem(coords)
# Reshape to grid
velgrid[:, :, count] = np.reshape(v_flatten, (ny, nx))
# Load mask
date = "%04d%02d%02d" % (year, month, day)
maskfile = DIR_TSX + 'TIF/' + DIR + '_' + date + '_' + 'mask.tif'
if os.path.isfile(maskfile):
xmask, ymask, mask[:, :, count] = geotifflib.read(maskfile)
else:
xmask, ymask, mask[:, :, count] = masklib.load_grid(
glacier, xmin, xmax, ymin, ymax, dx, icefront_time=time1)
geotifflib.write_from_grid(xmask, ymask,
np.flipud(mask[:, :, count]),
float('nan'), maskfile)
velgrid_mask[:, :, count] = np.array(velgrid[:, :, count])
velgrid_mask[mask[:, :, count] == 1, count] = float('nan')
count = count + 1
del count, maskfile, date, xind1, yind1, xind2, yind2, year, month, x1, y1, vx1, vy1, ex1, ey1, time_file, interval1
# Throw out obvious outliers
ind = np.where(velgrid > 16.0e3)
velgrid[ind[0], ind[1], ind[2]] = float('nan')
velgrid_mask[ind[0], ind[1], ind[2]] = float('nan')
print "Throwing out velocities above 16 km/yr to deal with outliers in Kanger record"
# Only keep data that falls between time1 and time2, and sort that data by time
sortind = np.argsort(time)
time = time[sortind]
velgrid_mask = velgrid_mask[:, :, sortind]
velgrid = velgrid[:, :, sortind]
ind = np.where((time > time1) & (time < time2))[0]
velgrid_mask = velgrid_mask[:, :, ind]
time = time[ind]
velgrid = velgrid[:, :, ind]
# Get average and std values
velmean = np.nanmean(velgrid_mask, axis=2)
# Get linear trends
veltrend = np.zeros_like(velmean)
veltrend_time1 = np.zeros_like(velmean)
veltrend_time2 = np.zeros_like(velmean)
veltrend_count = np.zeros_like(velmean)
veltrend_p = np.zeros_like(velmean)
veltrend_error = np.zeros_like(velmean)
veltrend_r = np.zeros_like(velmean)
veltrend_intercept = np.zeros_like(velmean)
veltrend_p[:, :] = float('nan')
veltrend[:, :] = float('nan')
veltrend_error[:, :] = float('nan')
veltrend_r[:, :] = float('nan')
veltrend_intercept[:, :] = float('nan')
for j in range(0, len(y)):
for i in range(0, len(x)):
nonnan = np.where((~(np.isnan(velgrid_mask[j, i, :]))))[0]
if len(nonnan) > 0.75 * len(time):
if (np.floor(np.min(time[nonnan])) == time1) and np.ceil(
np.max(time[nonnan])) == time2:
slope, intercept, r, p, std_err = stats.linregress(
time[nonnan], velgrid_mask[j, i, nonnan])
veltrend_count[j, i] = len(nonnan)
veltrend[j, i] = slope
veltrend_p[j, i] = p
veltrend_error[j, i] = std_err
veltrend_time1[j, i] = np.min(time[nonnan])
veltrend_time2[j, i] = np.max(time[nonnan])
veltrend_r[j, i] = r
veltrend_intercept[j, i] = intercept
# Detrend velocity timeseries
veldetrend = np.zeros_like(velgrid_mask)
for i in range(0, len(time)):
trend = veltrend_intercept + time[i] * veltrend
veldetrend[:, :, i] = velgrid_mask[:, :, i] - trend
# Calculate range of observed values
velrange = np.zeros_like(velmean)
velrange[:, :] = float('nan')
for i in range(0, len(x)):
for j in range(0, len(y)):
nonnan = np.where(~(np.isnan(veldetrend[j, i, :])))[0]
if len(nonnan) > 1:
velrange[j, i] = np.max(veldetrend[j, i, nonnan]) - np.min(
veldetrend[j, i, nonnan])
# Remove insignifcant trends
ind = np.where(veltrend_p > 0.05)
veltrend[ind] = float('nan')
veltrend_error[ind] = float('nan')
# Get number of nonnan velocities for each pixel
velcount = np.zeros([ny, nx])
for j in range(0, ny):
for i in range(0, nx):
nonnan = len(np.where(~(np.isnan(velgrid_mask[j, i, :])))[0])
velcount[j, i] = nonnan
sortind = np.argsort(time)
velgrid_mask = velgrid_mask[:, :, sortind]
time = time[sortind]
return x, y, velgrid_mask, veltrend, veldetrend, velrange, velcount, veltrend_error, time
def convert_binary_to_geotiff(glacier):
'''
I'm getting tired of unpacking Ian's binary velocity files every time
I need to use them, so I've set up a script to convert all of them to
geotifflib. Then the "geodat" module checks to see if there are geotiffs
before unpacking the binary files.
'''
DIRTOP_TSX = os.path.join(os.getenv("DATA_HOME"),
"Velocity/TSX/" + glacier + "/")
DIRTOP_RADARSAT = os.path.join(os.getenv("DATA_HOME"),
"Velocity/RADARSAT/Greenland/")
# TSX files
files = os.listdir(DIRTOP_TSX)
for file in files:
if file.startswith('track'):
print file
# Load binary data
x, y, v, vx, vy, vz, ex, ey, time, interval = geodatlib.readbinary(
DIRTOP_TSX + file + "/mosaicOffsets",
nodatavalue=-2.0e9,
read_vz=True)
year, month, day = datelib.fracyear_to_date(time)
# Set up date label for geotiff file
date = "%04d%02d%02d" % (year, month, day)
# Save as geotiff
geotifflib.write_from_grid(
x, y, np.flipud(v), -2.0e9,
DIRTOP_TSX + "TIF/" + file + "_" + date + "_v.tif")
geotifflib.write_from_grid(
x, y, np.flipud(vx), -2.0e9,
DIRTOP_TSX + "TIF/" + file + "_" + date + "_vx.tif")
geotifflib.write_from_grid(
x, y, np.flipud(vy), -2.0e9,
DIRTOP_TSX + "TIF/" + file + "_" + date + "_vy.tif")
geotifflib.write_from_grid(
x, y, np.flipud(ex), -2.0e9,
DIRTOP_TSX + "TIF/" + file + "_" + date + "_ex.tif")
geotifflib.write_from_grid(
x, y, np.flipud(ey), -2.0e9,
DIRTOP_TSX + "TIF/" + file + "_" + date + "_ey.tif")
geotifflib.write_from_grid(
x, y, np.flipud(vz), -2.0e9,
DIRTOP_TSX + "TIF/" + file + "_" + date + "_vz.tif")
# RADARSAT files
files = os.listdir(DIRTOP_RADARSAT)
for file in files:
if file.startswith('winter'):
print file
# Load binary data
x, y, v, vx, vy, ex, ey, time, interval = geodatlib.readbinary(
DIRTOP_RADARSAT + file + "/mosaicOffsets")
# Save as geotiff
geotifflib.write_from_grid(
x, y, np.flipud(v), -2.0e9,
DIRTOP_RADARSAT + "TIF/" + file + "_v.tif")
geotifflib.write_from_grid(
x, y, np.flipud(vx), -2.0e9,
DIRTOP_RADARSAT + "TIF/" + file + "_vx.tif")
geotifflib.write_from_grid(
x, y, np.flipud(vy), -2.0e9,
DIRTOP_RADARSAT + "TIF/" + file + "_vy.tif")
geotifflib.write_from_grid(
x, y, np.flipud(ex), -2.0e9,
DIRTOP_RADARSAT + "TIF/" + file + "_ex.tif")
geotifflib.write_from_grid(
x, y, np.flipud(ey), -2.0e9,
DIRTOP_RADARSAT + "TIF/" + file + "_ey.tif")
return 1
def inversion_2D(x, y, d, glacier, time, dir_velocity_out, filt_len='none'):
xmin = np.min(x) - 2.0e3
xmax = np.max(x) + 2.0e3
ymin = np.min(y) - 2.0e3
ymax = np.max(y) + 2.0e3
OUTDIR = os.path.join(os.getenv("DATA_HOME"),
"Velocity/MosaicVelocities/" + glacier)
# Large velocity map to fill in gaps in smaller velocity map
file_velocity_global = os.path.join(
os.getenv("DATA_HOME"),
"Velocity/Random/Greenland/AllGLVel/mosaicOffsets")
# Individual velocity map
filename1, time1 = tsx_near_time(time, glacier, just_filename=True)
filename2, time2 = tsx_near_time(time - 0.1, glacier, just_filename=True)
filename3, time3 = tsx_near_time(time + 0.1, glacier, just_filename=True)
year, month, day = datelib.fracyear_to_date(time1)
date = "%04d%02d%02d" % (year, month, day)
files_vx = ' '+filename1+'_vx.tif'+' '+filename2+'_vx.tif'+\
' '+filename3+'_vx.tif'+' '+file_velocity_global+'_vx.tif'
files_vy = ' '+filename1+'_vy.tif'+' '+filename2+'_vy.tif'+\
' '+filename3+'_vy.tif'+' '+file_velocity_global+'_vy.tif'
CURRENTDIR = os.getcwd()
os.chdir(OUTDIR)
filename_vx = 'mosaic-' + date + '-vx'
if not (os.path.isfile(filename_vx + '-tile-0.tif')):
os.system('dem_mosaic --t_projwin '+str(xmin)+' '+str(ymin)+' '+str(xmax)+\
' '+str(ymax)+' --priority-blending-length 10 -o'+filename_vx+files_vx)
filename_vy = 'mosaic-' + date + '-vy'
if not (os.path.isfile(filename_vy + '-tile-0.tif')):
os.system('dem_mosaic --t_projwin '+str(xmin)+' '+str(ymin)+' '+str(xmax)+\
' '+str(ymax)+' --priority-blending-length 10 -o'+filename_vy+files_vy)
xu, yu, uu = geotifflib.read(filename_vx + "-tile-0.tif")
xv, yv, vv = geotifflib.read(filename_vy + "-tile-0.tif")
fu = scipy.interpolate.RegularGridInterpolator((yu, xu), uu)
vx = fu((y, x))
fv = scipy.interpolate.RegularGridInterpolator((yv, xv), vv)
vy = fv((y, x))
vnonnan = np.sqrt(vx**2 + vy**2)
# Filter velocities
if filt_len != 'none':
cutoff = (1 / filt_len) / (1 / (np.diff(d[1:3]) * 2))
b, a = scipy.signal.butter(4, cutoff, btype='low')
filtered = scipy.signal.filtfilt(b, a, vnonnan)
else:
filtered = np.array(vcomb)
# Write out the velocity data
fid = open(dir_velocity_out + "velocity.dat", 'w')
R = len(filtered)
fid.write('{0}\n'.format(R))
for j in range(0, R):
fid.write('{} {}\n'.format(d[j], filtered[j]))
fid.close()
return filtered
def velocity_grid(glacier,
xmin=-np.Inf,
xmax=np.Inf,
ymin=-np.Inf,
ymax=np.Inf,
resolution=100):
DIR_TSX = os.path.join(os.getenv("DATA_HOME"),
"Velocity/TSX/" + glacier + "/")
dx = dy = float(resolution)
nx = int(np.ceil((xmax - xmin) / dx) + 1)
x = np.linspace(xmin, (nx - 1) * dx + xmin, nx)
ny = int(np.ceil((ymax - ymin) / dx) + 1)
y = np.linspace(ymin, (ny - 1) * dy + ymin, ny)
xgrid, ygrid = np.meshgrid(x, y)
coords = np.column_stack([ygrid.flatten(), xgrid.flatten()])
#################
# LOAD TSX Data #
#################
DIRs = os.listdir(DIR_TSX)
# Get number of velocity files
nt = 0
for DIR in DIRs:
if DIR.startswith('track'):
nt = nt + 1
# Set up variables
velgrid = np.zeros([ny, nx, nt])
time = np.zeros(nt)
ergrid = np.zeros([ny, nx, nt])
# Load velocity and mask
count = 0
for j in range(0, len(DIRs)):
DIR = DIRs[j]
if DIR.startswith('track'):
# Load velocity
x1, y1, v1, vx1, vy1, ex1, ey1, time_file, interval1 = geodatlib.readvelocity(
DIR_TSX, DIR, "mosaicOffsets")
time[count] = time_file
year, month, day = datelib.fracyear_to_date(time_file)
xind1 = np.argmin(abs(x1 - xmin))
xind2 = np.argmin(abs(x1 - xmax)) + 1
yind1 = np.argmin(abs(y1 - ymin))
yind2 = np.argmin(abs(y1 - ymax)) + 1
# Load velocity
try:
# If the input and output grids have the same dimensions...
velgrid[:, :, count] = v1[yind1:yind2, xind1:xind2]
except:
# Otherwise interpolate onto output grid
f_dem = scipy.interpolate.RegularGridInterpolator(
[y1, x1],
v1,
bounds_error=False,
method='linear',
fill_value=float('nan'))
v_flatten = f_dem(coords)
# Reshape to grid
velgrid[:, :, count] = np.reshape(v_flatten, (ny, nx))
count = count + 1
# Sort velocities
sortind = np.argsort(time)
time = time[sortind]
velgrid = velgrid[:, :, sortind]
return x, y, velgrid, time
# Create elmer mesh
call([
"ElmerGrid", "14", "2", file_2d_temp + ".msh", "-autoclean",
"-metis", partitions, "1"
])
# Check to make sure the mesh was created successfully
files = os.listdir(DIRM + file_2d_temp + '/partitioning.' +
str(partitions))
success = False
for file in files:
if file.endswith('header'):
success = True
if success == False:
year, month, day = datelib.fracyear_to_date(time1 + i * dt)
sys.exit('Unsuccessful generation of mesh for date ' + str(year) +
str(month) + str(int(np.round(day))) + ', timesetep ' +
str(i))
os.system("rm mesh2d.geo")
os.system("tar -czf" + file_2d_temp + ".tar.gz" + " " + file_2d_temp)
os.system("rm -r " + file_2d_temp)
os.system("tar -czf mesh_gmsh.tar.gz *.msh")
os.system("rm *.msh")
os.chdir(CURDIR)
del CURDIR, file_2d_temp, exterior_temp, xnew, ynew, zbed_new, zsur_new, zbot_new
##########################################