def plot_with_landsat(landsatfile, rasterfile, title):
raster = ice.Raster(rasterfile=rasterfile)
# Load Landsat 8 raster with same projection window
e = raster.hdr.extent
proj_win = [e[0], e[3], e[1], e[2]]
landsat = ice.Raster(rasterfile=landsatfile, projWin=proj_win)
fig, axs = plt.subplots(figsize=(9, 9))
data = np.flip(raster.data, axis=0)
axs.imshow(landsat.data, extent=e, cmap='binary_r')
axs.imshow(data, extent=e, cmap='Spectral_r', alpha=0.6)
plt.title(title)
plt.show()
def main(args):
# Load the stack
stack = ice.Stack(args.stackfile)
# Check if requested dataset is 2D. If so, view it directly
if stack[args.key].ndim == 2:
mean = stack[args.key][()]
# Otherwise, compute mean
else:
mean = stack.mean(key=args.key)
# Load reference SAR image
if args.ref is not None:
sar = ice.Raster(rasterfile=args.ref)
if sar.hdr != stack.hdr:
sar.resample(stack.hdr)
db = 10.0 * np.log10(sar.data)
low = np.percentile(db.ravel(), 5)
high = np.percentile(db.ravel(), 99.9)
else:
db = None
fig, ax = plt.subplots()
vmin, vmax = args.clim
cmap = ice.get_cmap(args.cmap)
if db is not None:
ref = ax.imshow(db,
aspect='auto',
cmap='gray',
vmin=low,
vmax=high,
extent=stack.hdr.extent)
im = ax.imshow(mean,
aspect='auto',
vmin=vmin,
vmax=vmax,
cmap=cmap,
extent=stack.hdr.extent,
alpha=args.alpha)
cbar = plt.colorbar(im, ax=ax, pad=0.02)
cbar.set_label(args.key)
plt.show()
if args.save is not None:
out = ice.Raster(data=mean, hdr=stack.hdr)
out.write_gdal(args.save, epsg=args.save_epsg)
def main():
stack_path = './data/stacks/'
stack_fname = 'enderlin_velocity_stack.hdf5'
pre_transect_fname = 'landsat_pre_transect.npy'
transect_fname = 'landsat_transect.npy'
landsat8_raster_fname = './data/landsat8/LC08_L1TP_066017_20140224_20170306_01_T1/LC08_L1TP_066017_20140224_20170306_01_T1_B1.TIF'
# Load Stack header
hdr = ice.RasterInfo(stackfile=stack_path + stack_fname)
# Load landsat 8 Raster
e = hdr.extent
proj_win = [e[0], e[3], e[1], e[2]]
raster = ice.Raster(rasterfile=landsat8_raster_fname, projWin=proj_win)
# Get reference x, y points to extract centerline from
x, y = get_transect_points(raster, stack_path + pre_transect_fname)
# plot_transect(raster, x, y, 'Hand crafted transect')
xs, ys = resample_transect(raster, x, y)
# Save transect
s = 100 # Start point along transect (bottom is very noisy)
np.save(stack_path + transect_fname, [xs[s:], ys[s:]])
plot_transect(raster, xs[s:], ys[s:],
'Columbia Manual Centerline Transect')
def get_stack_data(path, rasterfiles, proj_win):
""" Load data from each raster into a single array indexed by slice.
Parameters
----------
path: str
Path to directory storing all rasters
rasterfiles: list
List with the name of each rasterfile in the path
proj_win: list
Projection window to load raster data with
Return
------
stack_data: array_like
Dataset that will back the Stack, stored as (nrasters, nrows, ncols)
"""
data = []
for rasterfile in tqdm(rasterfiles):
raster = ice.Raster(path + rasterfile, projWin=proj_win)
data.append(raster.data)
'''
d = np.array(raster.data)
d[d < 0] = np.nan
nan_mask = np.isnan(d)
d[nan_mask] = np.nanmedian(d)
smooth_data = sgolay2d(d, 51, 3)
smooth_data[nan_mask] = np.nan
data.append(smooth_data)
'''
return np.array(data)
def plot_transect_landsat(mean, hdr, tx, ty):
# Plot centerline transect with data mean
fig, axs = plt.subplots(nrows=1, ncols=2, figsize=(9, 7))
axs[0].imshow(mean, clim=[0, 10], cmap='Spectral_r', extent=hdr.extent)
axs[0].plot(tx, ty)
axs[0].set_title("Discovered Centerline Transect")
axs[0].set_ylabel("Y (m)")
axs[0].set_xlabel("X (m)")
# Plot centerrline transect with landsat 8
landsat8_raster_path = './data/landsat8/LC08_L1TP_066017_20140224_20170306_01_T1/LC08_L1TP_066017_20140224_20170306_01_T1_B1.TIF'
e = hdr.extent
proj_win = [e[0], e[3], e[1], e[2]]
raster = ice.Raster(rasterfile=landsat8_raster_path, projWin=proj_win)
axs[1].imshow(raster.data, cmap='binary_r', extent=raster.hdr.extent)
axs[1].plot(tx, ty)
axs[1].set_ylabel("Y (m)")
axs[1].set_xlabel("X (m)")
axs[1].set_title('Landsat 8 View')
fig.set_tight_layout(True)
# Save to figures file
Path("./figures").mkdir(parents=True, exist_ok=True)
plt.savefig("./figures/columbia_transect_landsat.jpg", dpi=300)
def plot_mean_with_landsat(landsatfile,
stackfile,
title,
lb=float('-inf'),
clim=None,
fname=None):
stack = ice.Stack(stackfile, mode='r')
# Load Landsat 8 raster with same projection window
e = stack.hdr.extent
proj_win = [e[0], e[3], e[1], e[2]]
landsat = ice.Raster(rasterfile=landsatfile, projWin=proj_win)
fig, axs = plt.subplots(figsize=(9, 9))
data = np.array(stack._datasets["data"][0])
# data = np.nanmedian(data, axis=0)
data[data < lb] = np.nan
axs.imshow(landsat.data, extent=e, cmap='binary_r')
im = axs.imshow(data, extent=e, cmap='Spectral_r', alpha=0.6, clim=clim)
plt.title(title)
fig.colorbar(im)
if fname is not None:
plt.savefig('./figures/' + fname, dpi=300)
plt.show()
stack.fid.close()
def create_stack(data_root, dtype, stackfile):
""" Create Stacks for the different data """
hdr = None
# Set a lower bound for valid data
lb = 0
if dtype in ['vx', 'vy']:
lb = -1e6 # m/yr
# Get dates and data from files
data_dict = {}
init_tdec, init_data = [], []
for root, _, files in os.walk(data_root):
if len(files) == 0:
continue
# Get filename (not very elegant, but it works)
rasterfile = ''
for f in files:
if dtype + '.tif' in f:
rasterfile = f
# Get date
date = root.split('/')[-1]
tdec = ice.datestr2tdec(yy=int(date[0:4]),
mm=int(date[4:6]),
dd=int(date[6:8]))
init_tdec.append(tdec)
# Get data
e = [-3130000, -3090000, 642500, 680000]
proj_win = [e[0], e[3], e[1], e[2]]
raster = ice.Raster(rasterfile=root + '/' + rasterfile,
projWin=proj_win)
# Apply data bounds
data = np.array(raster.data)
data[data < lb] = np.nan
# Store in dict so that data can be sorted by date before adding to Stack
data_dict[tdec] = data
# Store the first header
if hdr is None:
hdr = raster.hdr
# Sort data before adding to Stack
init_tdec.sort()
for t in init_tdec:
init_data.append(data_dict[t])
# Create Stack
stack = ice.Stack(stackfile,
mode='w',
init_tdec=np.array(init_tdec),
init_rasterinfo=hdr)
stack.fid.create_dataset("data", data=np.array(init_data))
stack.fid.close()
def create_stack(data_path,
data_table,
stack_path,
stack_fname,
proj_win=None):
""" Build a new Stack from a set of raster files.
Parameters
----------
data_path: str
path to directory storing all downloaded rasters to build Stack from
data_table: dict
table of information for each Raster
stack_path: str
path to directory that Stack will be saved to
stack_fname: str
Stackfile name
proj_win: list
Projection window to load each Raster in the Stack with. If None, the
optimal projection window will be calculated
Return
------
The projection window used for the Stack
"""
Path(stack_path).mkdir(parents=True, exist_ok=True)
# Calculate largest common extent between rasers
if proj_win is None:
proj_win = calc_optimal_proj_win(data_path, data_table['fname'])
print('Using projection window', proj_win)
# Convert date strings to tdec
dates = 'start_date' if 'start_date' in data_table.keys() else 'date'
init_tdec = dates_to_tdec(data_table[dates])
# Get stack data
print('Loading Stack data:')
init_data = get_stack_data(data_path, data_table['fname'], proj_win)
# Smooth data
print('Loaded data has shape,', init_data.shape)
# Get header to init stack with
init_rasterinfo = ice.Raster(data_path + data_table['fname'][0],
projWin=proj_win).hdr
# Initialize stack
print('Initializing Stack and saving to', stack_path + stack_fname)
stack = ice.Stack(stack_path + stack_fname,
mode='w',
init_tdec=init_tdec,
init_rasterinfo=init_rasterinfo)
stack.fid.create_dataset("data", data=init_data)
stack.fid.close()
return proj_win
def resample_landsat():
landsatfile = './data/landsat8/LC08_L1TP_066017_20140224_20170306_01_T1/LC08_L1TP_066017_20140224_20170306_01_T1_B1.TIF'
landsat = ice.Raster(rasterfile=landsatfile)
# Resample raster to new projection
landsat_out = ice.warp(landsat, target_epsg=3413, n_proc=5, cval=np.nan)
# Replace with raster of new projection
landsat_out.write_gdal('./data/landsat8/landsat8_3413.tif', epsg=3413)
def get_stack_mean(stack_path, stack_fname, mean_fname):
""" Calculate the mean for a Stack and save to a file to save
future computational time.
Parameters
----------
stack_path: str
Path to directory containing stackfile
stack_fname:
Name of stackfile
mean_fname:
Name to save derived mean as
Returns
-------
mean: array_like
The loaded Stack mean
"""
if os.path.exists(stack_path + mean_fname):
# Load mean file if found
print('Loading mean from file')
raster = ice.Raster(rasterfile=stack_path + mean_fname)
return raster.data, raster.hdr
else:
# Calculate mean from Stack and save to file
print('Calculating mean from Stack')
stack = ice.Stack(stack_path + stack_fname)
data = np.array(stack._datasets['data'])
data[data < 0] = np.nan
mean = np.nanmean(data, axis=0)
# Save to file for next time
print('Saving mean to Raster for next time')
raster = ice.Raster(data=mean, hdr=stack.hdr)
raster.write_gdal(stack_path + mean_fname)
stack.fid.close()
return mean, raster.hdr
def main(args):
# Load the raster
r = ice.Raster(args.rasterfile, band=args.band)
fig, ax = plt.subplots()
vmin, vmax = args.clim
cmap = ice.get_cmap(args.cmap)
im = ax.imshow(r.data, aspect='auto', vmin=vmin, vmax=vmax, cmap=cmap,
extent=args.xscale*r.hdr.extent)
cbar = plt.colorbar(im, ax=ax, pad=0.02)
plt.tight_layout()
plt.show()
def main(args):
# Load the raster/stack and reference raster/stack
if args.raster.endswith('.h5'):
# Input stack
inobj = ice.Stack(args.raster)
# Reference stack
ref = ice.Stack(args.reference)
# Initialize output stack
outobj = ice.Stack(args.output, mode='w')
outobj.initialize(inobj.tdec, ref.hdr, data=False, weights=False)
# Loop over keys to resample
for key in args.keys:
print('Resampling', key)
inobj.resample(ref.hdr, outobj, key=key)
else:
# Input raster
inobj = ice.Raster(rasterfile=args.raster)
# Reference raster
ref = ice.Raster(rasterfile=args.reference)
# Resample
inobj.resample(ref.hdr)
# Write to disk
if args.epsg is not None:
out_epsg = args.epsg
else:
out_epsg = ref.hdr.epsg
inobj.write_gdal(args.output, epsg=out_epsg, driver=args.driver)
def plot_stream(vx_stackfile, vy_stackfile, v_stackfile, landsatfile, idx=0):
vx_stack = ice.Stack(vx_stackfile)
vy_stack = ice.Stack(vy_stackfile)
v_stack = ice.Stack(v_stackfile)
e = vx_stack.hdr.extent
proj_win = [e[0], e[3], e[1], e[2]]
landsat = ice.Raster(rasterfile=landsatfile, projWin=proj_win)
v = np.array(v_stack._datasets['data'][idx])
vx = np.array(vx_stack._datasets['data'][idx])
vy = np.array(vy_stack._datasets['data'][idx])
dx = vx_stack.hdr.dx
dy = vy_stack.hdr.dy
x0, x1, y0, y1 = vx_stack.hdr.extent
x = np.arange(x0, x0 + len(vx[0]) * dx, dx)
y = np.arange(y1, y1 + len(vx) * dy, dy)
fig, axs = plt.subplots(figsize=(9, 9))
axs.imshow(landsat.data, extent=e, cmap='binary_r')
axs.set_ylim(bottom=y0, top=y1)
axs.set_xlim(left=x0, right=x1)
cmap = copy.copy(cm.get_cmap('plasma'))
cmap.set_under(alpha=0)
stream = axs.streamplot(x,
y,
vx,
vy,
color=v,
cmap=cmap,
norm=Normalize(vmin=150, vmax=5000),
density=5)
fig.colorbar(stream.lines, fraction=0.046, pad=0.04)
plt.tight_layout()
plt.savefig('./figures/streamline.jpg', dpi=300)
plt.show()
def main():
enderlin_data_path = './data/enderlin2018/'
stack_path = './data/stacks/'
stack_fname = 'enderlin_velocity_stack.hdf5'
landsat8_raster_fname = './data/landsat8/LC08_L1TP_066017_20140224_20170306_01_T1/LC08_L1TP_066017_20140224_20170306_01_T1_B1.TIF'
# Get all raster files from manifest
rasterfiles = []
with open(enderlin_data_path + 'MANIFEST.TXT', 'r') as f:
for line in f:
rasterfiles.append(line.split()[0])
# plot_with_landsat(landsat8_raster_fname, enderlin_data_path + rasterfiles[0], 'Enderlin velocity on Landsat 8 Image')
# Get dates and data from files
init_tdec, init_data = [], []
for rasterfile in rasterfiles:
# Parse date from filename
date = rasterfile.split('_')[1]
tdec = ice.datestr2tdec(yy=int(date[0:4]),
mm=int(date[4:6]),
dd=int(date[6:8]))
init_tdec.append(tdec)
# Load file and get data
raster = ice.Raster(rasterfile=enderlin_data_path + rasterfile)
print(raster.hdr.extent)
# Data is flipped - not sure why
init_data.append(np.flip(raster.data, axis=0))
# Create Stack
hdr = ice.RasterInfo(rasterfile=enderlin_data_path + rasterfiles[0])
stack = ice.Stack(stack_path + stack_fname,
mode='w',
init_tdec=np.array(init_tdec),
init_rasterinfo=hdr)
stack.fid.create_dataset("data", data=np.array(init_data))
stack.fid.close()
plot_mean_with_landsat(landsat8_raster_fname, stack_path + stack_fname,
"Mean Velocity")
def main(args):
# Load Stack
stack = ice.Stack(args.stackfile)
# Load reference SAR image
if args.ref is not None:
sar = ice.Raster(rasterfile=args.ref)
if sar.hdr != stack.hdr:
sar.resample(stack.hdr)
db = 10.0 * np.log10(sar.data)
low = np.percentile(db.ravel(), 5)
high = np.percentile(db.ravel(), 99.9)
else:
db = None
# Set up animation
fig, ax = plt.subplots(figsize=args.figsize)
data = stack._datasets[args.key]
cmap = ice.get_cmap(args.cmap)
# Add ref image if using
if db is not None:
ax.imshow(db,
aspect='auto',
cmap='gray',
vmin=low,
vmax=high,
extent=stack.hdr.extent)
# Extract reference frame if index provided
if args.rel_index is not None:
data_ref = data[args.rel_index]
else:
data_ref = 0.0
im = ax.imshow(data[0] - data_ref,
extent=stack.hdr.extent,
cmap=cmap,
clim=args.clim,
alpha=args.alpha)
# Create title
datestr = ice.tdec2datestr(stack.tdec[0])
tx = ax.set_title(args.title + ' ' + datestr, fontweight='bold')
ax.set_xlabel(args.xlabel)
ax.set_ylabel(args.ylabel)
# Add colorbar
div = make_axes_locatable(ax)
cax = div.append_axes('right', '5%', '5%')
cb = fig.colorbar(im, cax=cax)
cb.set_label(args.clabel)
# Update the frame
def animate(i):
im.set_data(data[i] - data_ref)
datestr = ice.tdec2datestr(stack.tdec[i])
tx.set_text(args.title + ' ' + datestr)
fig.set_tight_layout(True)
print('Generating animation and saving to', args.save)
interval = 1000 / args.fps # Convert fps to interval in milliseconds
anim = animation.FuncAnimation(fig,
animate,
interval=interval,
frames=len(data),
repeat=True)
anim.save(args.save, dpi=args.dpi)
if args.show:
plt.show()
def main(args):
# Load the stack
stack = ice.Stack(args.stackfile)
# Get frame
if args.frame == 'initial':
mean = stack.slice(0, key=args.key)
elif args.frame == 'final':
mean = stack.slice(stack.Nt - 1, key=args.key)
elif args.frame == 'mean':
mean = stack.mean(key=args.key)
elif args.frame == 'std':
mean = stack.std(key=args.key)
else:
raise ValueError('Unsupported frame type.')
# If model directory is given, load model stack (full fit)
mstack = None
if args.mfile is not None:
mstack = ice.Stack(args.mfile)
# Load reference SAR image
if args.ref is not None:
sar = ice.Raster(rasterfile=args.ref)
if sar.hdr != stack.hdr:
sar.resample(stack.hdr)
db = 10.0 * np.log10(sar.data.astype(np.float32))
low = np.percentile(db.ravel(), 5)
high = np.percentile(db.ravel(), 99.9)
else:
db = None
# Initialize image plot
fig, ax = plt.subplots()
vmin, vmax = args.clim
cmap = ice.get_cmap(args.cmap)
if db is not None:
ref = ax.imshow(db,
aspect='auto',
cmap='gray',
vmin=low,
vmax=high,
extent=stack.hdr.extent)
im = ax.imshow(mean,
aspect='auto',
vmin=vmin,
vmax=vmax,
cmap=cmap,
extent=stack.hdr.extent,
alpha=args.alpha)
cbar = plt.colorbar(im, ax=ax, pad=0.02)
cbar.set_label(args.key)
# Initialize plot for time series for a given pixel
pts, axts = plt.subplots(figsize=(10, 6))
# Define action for clicking on deformation map
def printcoords(event):
if event.inaxes != ax:
return
# Get cursor coordinates
y, x = event.ydata, event.xdata
# Print out pixel locaton
i, j = stack.hdr.xy_to_imagecoord(x, y)
print('Row: %d Col: %d' % (i, j))
# Get time series for cursor location
d = stack.timeseries(xy=(x, y), key=args.key)
# Plot data and fit
axts.clear()
if args.sigma:
w = stack.timeseries(xy=(x, y), key='weights')
sigma = 1.0 / w
axts.errorbar(stack.tdec, d, yerr=sigma, fmt='o')
else:
axts.plot(stack.tdec, d, 'o')
if mstack is not None:
fit = mstack.timeseries(xy=(x, y), key=args.mkey)
axts.plot(mstack.tdec, fit, 'o')
axts.set_xlabel('Year')
axts.set_ylabel('Velocity')
pts.canvas.draw()
cid = fig.canvas.mpl_connect('button_press_event', printcoords)
plt.show()
fig.canvas.mpl_disconnect(cid)
def main(args):
# Load the raster
raster = ice.Raster(rasterfile=args.rasterfile)
# Load reference SAR image
if args.ref is not None:
sar = ice.Raster(rasterfile=args.ref)
if sar.hdr != raster.hdr:
sar.resample(raster.hdr)
db = 10.0 * np.log10(sar.data)
low = np.percentile(db.ravel(), 5)
high = np.percentile(db.ravel(), 99.9)
else:
db = None
fig, ax = plt.subplots()
vmin, vmax = args.clim
cmap = ice.get_cmap(args.cmap)
if db is not None:
ref = ax.imshow(db, aspect='auto', cmap='gray', vmin=low, vmax=high,
extent=raster.hdr.extent)
im = ax.imshow(raster.data, aspect='auto', vmin=vmin, vmax=vmax, cmap=cmap,
extent=raster.hdr.extent, alpha=args.alpha)
# Define action for clicking on deformation map
xpts = []; ypts = []
def printcoords(event):
global line
if event.inaxes != ax:
return
# Get cursor coordinates if left-click
if event.button == 1:
y, x = event.ydata, event.xdata
xpts.append(x)
ypts.append(y)
if line is None:
line, = ax.plot(xpts, ypts, '-o')
else:
line.set_xdata(xpts)
line.set_ydata(ypts)
# Right-click clear the points
elif event.button == 3:
xpts.clear()
ypts.clear()
line.set_xdata(xpts)
line.set_ydata(ypts)
fig.canvas.draw()
cid = fig.canvas.mpl_connect('button_press_event', printcoords)
plt.show()
fig.canvas.mpl_disconnect(cid)
# Save the points
np.savetxt(args.output, np.column_stack((xpts, ypts)))