def circle_index(atr,circle_par):
## Return Index of Elements within a Circle
## Inputs:
## atr : (dictionary) attributes containging width, length info
## circle_par : (string) center_x,center_y,radius
width = int(atr['WIDTH'])
length = int(atr['FILE_LENGTH'])
cir_par = circle_par.split(',')
try:
c_y = int(cir_par[0])
c_x = int(cir_par[1])
radius = int(float(cir_par[2]))
except:
try:
c_lat = float(cir_par[0])
c_lon = float(cir_par[1])
radius = int(float(cir_par[2]))
c_y = subset.coord_geo2radar(c_lat,atr,'lat')
c_x = subset.coord_geo2radar(c_lon,atr,'lon')
except:
print '\nERROR: Unrecognized circle index format: '+circle_par
print 'Supported format:'
print '--circle 200,300,20 for radar coord input'
print '--circle 31.0214,130.5699,20 for geo coord input\n'
return 0
y,x = np.ogrid[-c_y:length-c_y, -c_x:width-c_x]
idx = x**2 + y**2 <= radius**2
return idx
def circle_index(atr,circle_par):
## Return Index of Elements within a Circle
## Inputs:
## atr : (dictionary) attributes containging width, length info
## circle_par : (string) center_x,center_y,radius
width = int(atr['WIDTH'])
length = int(atr['FILE_LENGTH'])
cir_par = circle_par.split(',')
#import pdb; pdb.set_trace()
try:
c_y = int(cir_par[0])
c_x = int(cir_par[1])
radius = int(float(cir_par[2]))
except:
try:
c_lat = float(cir_par[0])
c_lon = float(cir_par[1])
radius = int(float(cir_par[2]))
c_y = subset.coord_geo2radar(c_lat,atr,'lat')
c_x = subset.coord_geo2radar(c_lon,atr,'lon')
except:
print '\nERROR: Unrecognized circle index format: '+circle_par
print 'Supported format:'
print '--circle 200,300,20 for radar coord input'
print '--circle 31.0214,130.5699,20 for geo coord input\n'
return 0
y,x = np.ogrid[-c_y:length-c_y, -c_x:width-c_x]
idx = x**2 + y**2 <= radius**2
return idx
def read_dis_lalo(lat, lon, dateList, timeseriesFile, radius=0, unit='cm'):
atr = readfile.read_attribute(timeseriesFile)
h5 = h5py.File(timeseriesFile, 'r')
x = subset.coord_geo2radar(lon, atr, 'longitude')
y = subset.coord_geo2radar(lat, atr, 'latitude')
if radius == 0: radius = 3
xsub = [x - radius, x + radius]
ysub = [y - radius, y + radius]
dis, dis_mean, dis_std = read_dis_xy(xsub, ysub, dateList, h5, unit)[0:3]
h5.close()
return dis, dis_mean, dis_std
def main(argv):
inps = cmdLineParse()
inps.file = ut.get_file_list(inps.file)
atr = readfile.read_attribute(inps.file[0])
length = int(atr['FILE_LENGTH'])
width = int(atr['WIDTH'])
if inps.reset:
print '----------------------------------------------------------------------------'
for file in inps.file:
remove_reference_pixel(file)
return
##### Check Input Coordinates
# Read ref_y/x/lat/lon from reference/template
# priority: Direct Input > Reference File > Template File
if inps.template_file:
print 'reading reference info from template: ' + inps.template_file
inps = read_seed_template2inps(inps.template_file, inps)
if inps.reference_file:
print 'reading reference info from reference: ' + inps.reference_file
inps = read_seed_reference2inps(inps.reference_file, inps)
## Do not use ref_lat/lon input for file in radar-coord
#if not 'X_FIRST' in atr.keys() and (inps.ref_lat or inps.ref_lon):
# print 'Lat/lon reference input is disabled for file in radar coord.'
# inps.ref_lat = None
# inps.ref_lon = None
# Convert ref_lat/lon to ref_y/x
if inps.ref_lat and inps.ref_lon:
if 'X_FIRST' in atr.keys():
inps.ref_y = subset.coord_geo2radar(inps.ref_lat, atr, 'lat')
inps.ref_x = subset.coord_geo2radar(inps.ref_lon, atr, 'lon')
else:
# Convert lat/lon to az/rg for radar coord file using geomap*.trans file
inps.ref_y, inps.ref_x = ut.glob2radar(np.array(inps.ref_lat), np.array(inps.ref_lon),\
inps.trans_file, atr)[0:2]
print 'Input reference point in lat/lon: ' + str(
[inps.ref_lat, inps.ref_lon])
print 'Input reference point in y/x : ' + str([inps.ref_y, inps.ref_x])
# Do not use ref_y/x outside of data coverage
if (inps.ref_y and inps.ref_x
and not (0 <= inps.ref_y <= length and 0 <= inps.ref_x <= width)):
inps.ref_y = None
inps.ref_x = None
print 'WARNING: input reference point is OUT of data coverage!'
print 'Continue with other method to select reference point.'
# Do not use ref_y/x in masked out area
if inps.ref_y and inps.ref_x and inps.mask_file:
print 'mask: ' + inps.mask_file
mask = readfile.read(inps.mask_file)[0]
if mask[inps.ref_y, inps.ref_x] == 0:
inps.ref_y = None
inps.ref_x = None
print 'WARNING: input reference point is in masked OUT area!'
print 'Continue with other method to select reference point.'
##### Select method
if inps.ref_y and inps.ref_x:
inps.method = 'input-coord'
elif inps.coherence_file:
if os.path.isfile(inps.coherence_file):
inps.method = 'max-coherence'
else:
inps.coherence_file = None
if inps.method == 'manual':
inps.parallel = False
print 'Parallel processing is disabled for manual seeding method.'
##### Seeding file by file
# check outfile and parallel option
if inps.parallel:
num_cores, inps.parallel, Parallel, delayed = ut.check_parallel(
len(inps.file))
if len(inps.file) == 1:
seed_file_inps(inps.file[0], inps, inps.outfile)
elif inps.parallel:
#num_cores = min(multiprocessing.cpu_count(), len(inps.file))
#print 'parallel processing using %d cores ...'%(num_cores)
Parallel(n_jobs=num_cores)(delayed(seed_file_inps)(file, inps)
for file in inps.file)
else:
for File in inps.file:
seed_file_inps(File, inps)
print 'Done.'
return
def main(argv):
inps = cmdLineParse()
##### 1. Extract the common area of two input files
# Basic info
atr1 = readfile.read_attribute(inps.file[0])
atr2 = readfile.read_attribute(inps.file[1])
if any('X_FIRST' not in i for i in [atr1, atr2]):
sys.exit('ERROR: Not all input files are geocoded.')
k1 = atr1['FILE_TYPE']
print 'Input 1st file is ' + k1
# Common AOI in lalo
west, east, south, north = get_overlap_lalo(atr1, atr2)
lon_step = float(atr1['X_STEP'])
lat_step = float(atr1['Y_STEP'])
width = int(round((east - west) / lon_step))
length = int(round((south - north) / lat_step))
# Read data in common AOI: LOS displacement, heading angle, incident angle
u_los = np.zeros((2, width * length))
heading = []
incidence = []
for i in range(len(inps.file)):
fname = inps.file[i]
print '---------------------'
print 'reading ' + fname
atr = readfile.read_attribute(fname)
[x0, x1] = subset.coord_geo2radar([west, east], atr, 'lon')
[y0, y1] = subset.coord_geo2radar([north, south], atr, 'lat')
V = readfile.read(fname, (x0, y0, x1, y1))[0]
u_los[i, :] = V.flatten(0)
heading_angle = float(atr['HEADING'])
if heading_angle < 0.:
heading_angle += 360.
print 'heading angle: ' + str(heading_angle)
heading_angle *= np.pi / 180.
heading.append(heading_angle)
inc_angle = float(ut.incidence_angle(atr, dimension=0))
#print 'incidence angle: '+str(inc_angle)
inc_angle *= np.pi / 180.
incidence.append(inc_angle)
##### 2. Project displacement from LOS to Horizontal and Vertical components
# math for 3D: cos(theta)*Uz - cos(alpha)*sin(theta)*Ux + sin(alpha)*sin(theta)*Uy = Ulos
# math for 2D: cos(theta)*Uv - sin(alpha-az)*sin(theta)*Uh = Ulos #Uh_perp = 0.0
# This could be easily modified to support multiple view geometry (e.g. two adjcent tracks from asc & desc) to resolve 3D
# Design matrix
A = np.zeros((2, 2))
for i in range(len(inps.file)):
A[i, 0] = np.cos(incidence[i])
A[i, 1] = np.sin(incidence[i]) * np.sin(heading[i] - inps.azimuth)
A_inv = np.linalg.pinv(A)
u_vh = np.dot(A_inv, u_los)
u_v = np.reshape(u_vh[0, :], (length, width))
u_h = np.reshape(u_vh[1, :], (length, width))
##### 3. Output
# Attributes
atr = atr1.copy()
atr['WIDTH'] = str(width)
atr['FILE_LENGTH'] = str(length)
atr['X_FIRST'] = str(west)
atr['Y_FIRST'] = str(north)
atr['X_STEP'] = str(lon_step)
atr['Y_STEP'] = str(lat_step)
print '---------------------'
outname = inps.outfile[0]
print 'writing vertical component to file: ' + outname
writefile.write(u_v, atr, outname)
outname = inps.outfile[1]
print 'writing horizontal component to file: ' + outname
writefile.write(u_h, atr, outname)
print 'Done.'
return
def main(argv):
## Default settings
contour_step = 200.0
contour_sigma = 3.0
demShade = "yes"
demContour = "yes"
global markerSize, markderSize2, markerColor, markerColor2, rectColor
global lineWidth, lineWidth2, edgeWidth, fontSize
# global markerColor_ref, markerColor_ref2
markerSize = 16
markerSize2 = 16
markerColor = "crimson" # g
markerColor2 = "lightgray"
markerColor_ref = "white"
markerColor_ref2 = "lightgray"
rectColor = "black"
lineWidth = 0
lineWidth2 = 0
edgeWidth = 1.5
fontSize = 16
global unit, radius, saveFig, dispFig, fig_dpi
fig_dpi = 300
radius = 0
saveFig = "no"
dispFig = "yes"
unit = "cm"
dispDisplacement = "no"
dispOpposite = "no"
dispContour = "only"
smoothContour = "no"
contour_step = 200
showRef = "yes"
vel_alpha = 1.0
zero_start = "yes"
global ref_xsub, ref_ysub, ref_date
global h5timeseries_2, dates_2, dateList_2
global lbound, hbound
############### Check Inputs ##################
if len(sys.argv) < 2:
Usage()
sys.exit(1)
elif len(sys.argv) == 2:
if argv[0] == "-h":
Usage()
sys.exit(1)
elif os.path.isfile(argv[0]):
timeSeriesFile = argv[0]
h5timeseries = h5py.File(timeSeriesFile)
k = h5timeseries.keys()
if not "timeseries" in k:
print "ERROR: Input file is " + k[0] + ".\n\tOnly timeseries is supported.\n"
sys.exit(1)
else:
Usage()
sys.exit(1)
elif len(sys.argv) > 2:
try:
opts, args = getopt.getopt(
argv,
"f:F:v:a:b:s:m:c:w:u:l:h:D:V:t:T:d:r:x:y:X:Y:o:E:",
[
"save",
"nodisplay",
"unit=",
"exclude=",
"ref-date=",
"rect-color=",
"zero-start=",
"zoom-x=",
"zoom-y=",
"zoom-lon",
"zoom-lat",
"lalo=",
"opposite",
"dem-nocontour",
"dem-noshade",
"displacement",
"contour-step=",
"contour-smooth=",
"LALO=",
],
)
except getopt.GetoptError:
Usage()
sys.exit(1)
for opt, arg in opts:
if opt == "-f":
timeSeriesFile = arg
elif opt == "-F":
timeSeriesFile_2 = arg
elif opt == "-v":
velocityFile = arg
elif opt == "-a":
vmin = float(arg)
elif opt == "-b":
vmax = float(arg)
elif opt == "-s":
fontSize = int(arg)
elif opt == "-m":
markerSize = int(arg)
markerSize2 = int(arg)
elif opt == "-c":
markerColor = arg
elif opt == "-w":
lineWidth = int(arg)
elif opt == "-u":
unit = arg
elif opt == "-l":
lbound = float(arg)
elif opt == "-h":
hbound = float(arg)
elif opt == "-D":
demFile = arg
elif opt == "-V":
contour_step = float(arg)
elif opt == "-t":
minDate = arg
elif opt == "-T":
maxDate = arg
elif opt == "-r":
radius = abs(int(arg))
elif opt == "-x":
xsub = [int(i) for i in arg.split(":")]
xsub.sort()
# dispVelFig='no'
elif opt == "-y":
ysub = [int(i) for i in arg.split(":")]
ysub.sort()
# dispVelFig='no'
elif opt == "-X":
ref_xsub = [int(i) for i in arg.split(":")]
ref_xsub.sort()
elif opt == "-Y":
ref_ysub = [int(i) for i in arg.split(":")]
ref_ysub.sort()
# dispVelFig='no'
elif opt == "--contour-step":
contour_step = float(arg)
elif opt == "--contour-smooth":
contour_sigma = float(arg)
elif opt == "--dem-nocontour":
demContour = "no"
elif opt == "--dem-noshade":
demShade = "no"
elif opt == "--displacement":
dispDisplacement = "yes"
elif opt in ["-E", "--exclude"]:
datesNot2show = arg.split(",")
elif opt in "--lalo":
lalosub = [float(i) for i in arg.split(",")]
elif opt in "--LALO":
ref_lalosub = [float(i) for i in arg.split(",")]
elif opt in ["--rect-color"]:
rectColor = arg
elif opt in ["--ref-date"]:
ref_date = ptime.yyyymmdd(arg)
elif opt in ["-u", "--unit"]:
unit = arg.lower()
elif opt == "--save":
saveFig = "yes"
elif opt == "--nodisplay":
dispFig = "no"
saveFig = "yes"
elif opt == "--opposite":
dispOpposite = "yes"
elif opt == "--zero-start":
zero_start = arg.lower()
elif opt == "--zoom-x":
win_x = [int(i) for i in arg.split(":")]
win_x.sort()
elif opt == "--zoom-y":
win_y = [int(i) for i in arg.split(":")]
win_y.sort()
elif opt == "--zoom-lon":
win_lon = [float(i) for i in arg.split(":")]
win_lon.sort()
elif opt == "--zoom-lat":
win_lat = [float(i) for i in arg.split(":")]
win_lat.sort()
##############################################################
## Read time series file info
if not os.path.isfile(timeSeriesFile):
print "\nERROR: Input time series file does not exist: " + timeSeriesFile + "\n"
sys.exit(1)
h5timeseries = h5py.File(timeSeriesFile)
k = h5timeseries.keys()
# read h5 file and its group type
if not "timeseries" in k:
print "ERROR: Input file is " + k[0] + ".\n\tOnly timeseries is supported.\n"
sys.exit(1)
atr = readfile.read_attributes(timeSeriesFile)
dateList1 = h5timeseries["timeseries"].keys()
dateList1 = sorted(dateList1)
dates1, datevector1 = ptime.date_list2vector(dateList1)
print "\n************ Time Series Display - Point *************"
##### Select Check
try:
lalosub
xsub = subset.coord_geo2radar([lalosub[1]], atr, "longitude")
ysub = subset.coord_geo2radar([lalosub[0]], atr, "latitude")
xsub = [xsub]
ysub = [ysub]
if radius == 0:
radius = 3
except:
pass
try:
ref_lalosub
ref_xsub = subset.coord_geo2radar([ref_lalosub[1]], atr, "longitude")
ref_ysub = subset.coord_geo2radar([ref_lalosub[0]], atr, "latitude")
ref_xsub = [ref_xsub]
ref_ysub = [ref_ysub]
if radius == 0:
radius = 3
except:
pass
##############################################################
global dates, dateList, datevector_all, dateListMinMax
print "*******************"
print "All dates existed:"
print dateList1
print "*******************"
## Check exclude date input
try:
datesNot2show
if os.path.isfile(datesNot2show[0]):
try:
datesNot2show = ptime.read_date_list(datesNot2show[0])
except:
print "Can not read date list file: " + datesNot2show[0]
print "dates not to show: " + str(datesNot2show)
except:
datesNot2show = []
## Check Min / Max Date
dateListMinMax = []
try:
minDate
minDate = ptime.yyyymmdd(minDate)
dateListMinMax.append(minDate)
minDateyy = ptime.yyyymmdd2years(minDate)
print "minimum date: " + minDate
for date in dateList1:
yy = ptime.yyyymmdd2years(date)
if yy < minDateyy:
datesNot2show.append(date)
except:
pass
try:
maxDate
maxDate = ptime.yyyymmdd(maxDate)
dateListMinMax.append(maxDate)
maxDateyy = ptime.yyyymmdd2years(maxDate)
print "maximum date: " + maxDate
for date in dateList1:
yy = ptime.yyyymmdd2years(date)
if yy > maxDateyy:
datesNot2show.append(date)
except:
pass
dateListMinMax = sorted(dateListMinMax)
if not dateListMinMax:
print "no min/max date input."
else:
datesMinMax, dateVecMinMax = ptime.date_list2vector(dateListMinMax)
## Finalize Date List
try:
dateList = []
for date in dateList1:
if date not in datesNot2show:
dateList.append(date)
print "--------------------------------------------"
print "dates used to show time series displacements:"
print dateList
print "--------------------------------------------"
except:
dateList = dateList1
print "using all dates to show time series displacement"
## Read Date Info (x axis for time series display)
dates, datevector = ptime.date_list2vector(dateList)
datevector_all = list(datevector)
## Check reference date input
try:
ref_date
if not ref_date in dateList:
print "Reference date - " + ref_date + " - is not included in date list to show."
sys.exit(1)
else:
print "reference date: " + ref_date
except:
if zero_start == "yes":
ref_date = dateList[0]
print "set the 1st date as reference for displacement display."
else:
pass
##############################################################
##### Plot Fig 1 - Velocity / last epoch of time series / DEM
fig = plt.figure(1)
ax = fig.add_subplot(111)
##### Check subset range
width = int(atr["WIDTH"])
length = int(atr["FILE_LENGTH"])
print "file size: " + str(length) + ", " + str(width)
try:
win_y = subset.coord_geo2radar(win_lat, atr, "latitude")
except:
try:
win_y
except:
win_y = [0, length]
try:
win_x = subset.coord_geo2radar(win_lon, atr, "longitude")
except:
try:
win_x
except:
win_x = [0, width]
win_y, win_x = subset.check_subset_range(win_y, win_x, atr)
try:
velocityFile
try:
vel, vel_atr = readfile.read(velocityFile)
except:
vel, vel_atr = readfile.read(timeSeriesFile, velocityFile)
ax.set_title(velocityFile)
print "display: " + velocityFile
except:
vel, vel_atr = readfile.read(timeSeriesFile, dateList1[-1])
ax.set_title("epoch: " + dateList1[-1])
print "display last epoch"
##### show displacement instead of phase
if vel_atr["FILE_TYPE"] in ["interferograms", ".unw"] and dispDisplacement == "yes":
print "show displacement"
phase2range = -float(vel_atr["WAVELENGTH"]) / (4 * np.pi)
vel *= phase2range
else:
dispDisplacement = "no"
## Reference Point
if showRef == "yes":
try:
ax.plot(int(atr["ref_x"]), int(atr["ref_y"]), "ks", ms=6)
except:
pass
if dispOpposite == "yes":
print "show opposite value in figure/map 1"
vel *= -1
## Flip
try:
flip_lr
except:
try:
flip_ud
except:
flip_lr, flip_ud = view.auto_flip_check(atr)
## Status bar
## Geo coordinate
try:
ullon = float(atr["X_FIRST"])
ullat = float(atr["Y_FIRST"])
lon_step = float(atr["X_STEP"])
lat_step = float(atr["Y_STEP"])
lon_unit = atr["Y_UNIT"]
lat_unit = atr["X_UNIT"]
geocoord = "yes"
print "Input file is Geocoded"
except:
geocoord = "no"
def format_coord(x, y):
col = int(x + 0.5)
row = int(y + 0.5)
if col >= 0 and col <= width and row >= 0 and row <= length:
z = vel[row, col]
try:
lon = ullon + x * lon_step
lat = ullat + y * lat_step
return "x=%.1f, y=%.1f, value=%.4f, lon=%.4f, lat=%.4f" % (x, y, z, lon, lat)
except:
return "x=%.1f, y=%.1f, value=%.4f" % (x, y, z)
ax.format_coord = format_coord
## DEM
try:
demFile
dem, demRsc = readfile.read(demFile)
ax = view.plot_dem_yx(ax, dem, demShade, demContour, contour_step, contour_sigma)
vel_alpha = 0.8
except:
print "No DEM file"
try:
img = ax.imshow(vel, vmin=vmin, vmax=vmax, alpha=vel_alpha)
except:
img = ax.imshow(vel, alpha=vel_alpha)
plt.colorbar(img)
## Zoom In (subset)
if flip_lr == "yes":
ax.set_xlim(win_x[1], win_x[0])
else:
ax.set_xlim(win_x[0], win_x[1])
if flip_ud == "yes":
ax.set_ylim(win_y[0], win_y[1])
else:
ax.set_ylim(win_y[1], win_y[0])
## Flip
# if flip_lr == 'yes': fig.gca().invert_xaxis()
# if flip_ud == 'yes': fig.gca().invert_yaxis()
##########################################
##### Plot Fig 2 - Time series plot
# fig2 = plt.figure(num=2,figsize=(12,6))
fig2 = plt.figure(2, figsize=(12, 6))
ax2 = fig2.add_subplot(111)
try:
timeSeriesFile_2
h5timeseries_2 = h5py.File(timeSeriesFile_2)
dateList_2 = h5timeseries_2["timeseries"].keys()
dateList_2 = sorted(dateList_2)
dates_2, datevector_2 = ptime.date_list2vector(dateList_2)
datevector_all += list(set(datevector_2) - set(datevector_all))
datevector_all = sorted(datevector_all)
except:
pass
################################ Plot Code Package <start> #################################
def plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries):
ax2.cla()
print "\n-------------------------------------------------------------------------------"
disp_min = 0
disp_max = 0
############################# Plot Time Series ##############################
global ref_xsub, ref_ysub
##### 1.1 Plot Reference time series
try:
ref_xsub
ref_ysub
ref_xsub, ref_ysub = check_yx(ref_xsub, ref_ysub, radius, ax, rectColor)
print "----------------------------------------------------"
print "Reference Point:"
print "ref_x=" + str(ref_xsub[0]) + ":" + str(ref_xsub[1])
print "ref_y=" + str(ref_ysub[0]) + ":" + str(ref_ysub[1])
print "-----------------------------"
print "Time series with all dates:"
dis1, dis1_mean, dis1_std, dis1_vel = read_dis(ref_xsub, ref_ysub, dateList1, h5timeseries, unit)
(_, caps, _) = ax2.errorbar(
dates1,
dis1_mean,
yerr=dis1_std,
fmt="-ks",
ms=markerSize2,
lw=0,
alpha=1,
mfc=markerColor_ref,
mew=edgeWidth,
elinewidth=edgeWidth,
ecolor="black",
capsize=markerSize * 0.5,
)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis1_mean, dis1_std)
if not len(dateList) == len(dateList1):
print "-----------------------------"
print "Time series with dates of interest:"
dis12, dis12_mean, dis12_std, dis12_vel = read_dis(ref_xsub, ref_ysub, dateList, h5timeseries, unit)
(_, caps, _) = ax2.errorbar(
dates,
dis12_mean,
yerr=dis12_std,
fmt="-ks",
ms=markerSize2,
lw=0,
alpha=1,
mfc=markerColor_ref2,
mew=edgeWidth,
elinewidth=edgeWidth,
ecolor="black",
capsize=markerSize * 0.5,
)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis12_mean, dis12_std)
except:
pass
##### 1.2.0 Read y/x
print "\n----------------------------------------------------"
print "Point of Interest:"
xsub, ysub = check_yx(xsub, ysub, radius, ax, rectColor)
print "x=" + str(xsub[0]) + ":" + str(xsub[1])
print "y=" + str(ysub[0]) + ":" + str(ysub[1])
##### 1.2.1 Plot 2nd time series
try:
timeSeriesFile_2
print "-----------------------------"
print "2nd Time Series:"
dis2, dis2_mean, dis2_std, dis2_vel = read_dis(xsub, ysub, dateList_2, h5timeseries_2, unit)
(_, caps, _) = ax2.errorbar(
dates_2,
dis2_mean,
yerr=dis2_std,
fmt="-ko",
ms=markerSize2,
lw=0,
alpha=1,
mfc=markerColor2,
elinewidth=0,
ecolor="black",
capsize=0,
)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis2_mean, dis2_std)
except:
pass
##### 1.2.2 Plot 1st time series
print "-----------------------------"
print "Time Series:"
dis, dis_mean, dis_std, dis_vel = read_dis(xsub, ysub, dateList, h5timeseries, unit)
(_, caps, _) = ax2.errorbar(
dates,
dis_mean,
yerr=dis_std,
fmt="-ko",
ms=markerSize,
lw=lineWidth,
alpha=1,
mfc=markerColor,
elinewidth=edgeWidth,
ecolor="black",
capsize=markerSize * 0.5,
)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis_mean, dis_std)
####################### Figure Format #######################
## x axis format
try:
ax2 = ptime.adjust_xaxis_date(ax2, dateVecMinMax, fontSize)
except:
ax2 = ptime.adjust_xaxis_date(ax2, datevector_all, fontSize)
## y axis format
ax2.set_ylabel("Displacement [" + unit + "]", fontsize=fontSize)
try:
lbound
hbound
ax2.set_ylim(lbound, hbound)
except:
disp_buf = 0.2 * (disp_max - disp_min)
ax2.set_ylim(disp_min - disp_buf, disp_max + disp_buf)
for tick in ax2.yaxis.get_major_ticks():
tick.label.set_fontsize(fontSize)
## title
figTitle = "x=" + str(xsub[0]) + ":" + str(xsub[1]) + ", y=" + str(ysub[0]) + ":" + str(ysub[1])
try:
lonc = ullon + (xsub[0] + xsub[1]) / 2.0 * lon_step
latc = ullat + (ysub[0] + ysub[1]) / 2.0 * lat_step
figTitle += ", lalo=" + "%.4f,%.4f" % (latc, lonc)
except:
pass
ax2.set_title(figTitle)
################## Save and Output #####################
if saveFig == "yes":
print "-----------------------------"
Delay = {}
Delay["displacement"] = dis
Delay["unit"] = unit
Delay["time"] = datevector
Delay["velocity"] = dis_vel[0]
Delay["velocity_unit"] = unit + "/yr"
Delay["velocity_std"] = dis_vel[4]
figBase = "x" + str(xsub[0]) + "_" + str(xsub[1] - 1) + "y" + str(ysub[0]) + "_" + str(ysub[1] - 1)
sio.savemat(figBase + "_ts.mat", {"displacement": Delay})
print "saved " + figBase + "_ts.mat"
fig2.savefig(figBase + "_ts.pdf", bbox_inches="tight", transparent=True, dpi=fig_dpi)
print "saved " + figBase + "_ts.pdf"
if dispFig == "no":
fig.savefig(figBase + "_vel.png", bbox_inches="tight", transparent=True, dpi=fig_dpi)
print "saved " + figBase + "_vel.png"
################################ Plot Code Package <end> #################################
########### 1. Plot Time Series with x/y ##########
try:
xsub
ysub
plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries)
except:
print "No x/y input"
pass
########### 2. Plot Time Series with Click ##########
## similar to 1. Plot Time Series with x/y
def onclick(event):
ax2.cla()
xsub = [int(event.xdata)]
ysub = [int(event.ydata)]
plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries)
if dispFig == "yes":
plt.show()
try:
cid = fig.canvas.mpl_connect("button_press_event", onclick)
except:
pass
if dispFig == "yes":
plt.show()
def main(argv):
## Default settings
contour_step = 200.0
contour_sigma = 3.0
demShade = 'yes'
demContour = 'yes'
global markerSize, markderSize2, markerColor, markerColor2, rectColor
global lineWidth, lineWidth2, edgeWidth, fontSize
#global markerColor_ref, markerColor_ref2
markerSize = 16
markerSize2 = 16
markerColor = 'crimson' # g
markerColor2 = 'lightgray'
markerColor_ref = 'white'
markerColor_ref2 = 'lightgray'
rectColor = 'black'
lineWidth = 0
lineWidth2 = 0
edgeWidth = 1.5
fontSize = 16
global unit, radius, saveFig, dispFig, fig_dpi
fig_dpi = 300
radius = 0
saveFig = 'no'
dispFig = 'yes'
unit = 'cm'
dispDisplacement = 'no'
dispOpposite = 'no'
dispContour = 'only'
smoothContour = 'no'
contour_step = 200
showRef = 'yes'
vel_alpha = 1.0
zero_start = 'yes'
global ref_xsub, ref_ysub, ref_date
global h5timeseries_2, dates_2, dateList_2
global lbound, hbound
############### Check Inputs ##################
if len(sys.argv) < 2:
usage()
sys.exit(1)
elif len(sys.argv) == 2:
if argv[0] == '-h':
usage()
sys.exit(1)
elif os.path.isfile(argv[0]):
timeSeriesFile = argv[0]
h5timeseries = h5py.File(timeSeriesFile)
k = h5timeseries.keys()
if not 'timeseries' in k:
print 'ERROR: Input file is ' + k[
0] + '.\n\tOnly timeseries is supported.\n'
sys.exit(1)
else:
usage()
sys.exit(1)
elif len(sys.argv) > 2:
try: opts, args = getopt.getopt(argv,"f:F:v:a:b:s:m:c:w:u:l:h:D:V:t:T:d:r:x:y:X:Y:o:E:",
['save','nodisplay','unit=','exclude=','ref-date=','rect-color=',\
'zero-start=','zoom-x=','zoom-y=','zoom-lon','zoom-lat','lalo=',\
'opposite','dem-nocontour','dem-noshade','displacement','contour-step=',\
'contour-smooth=','LALO='])
except getopt.GetoptError:
usage()
sys.exit(1)
for opt, arg in opts:
if opt == '-f': timeSeriesFile = arg
elif opt == '-F': timeSeriesFile_2 = arg
elif opt == '-v': velocityFile = arg
elif opt == '-a': vmin = float(arg)
elif opt == '-b': vmax = float(arg)
elif opt == '-s': fontSize = int(arg)
elif opt == '-m':
markerSize = int(arg)
markerSize2 = int(arg)
elif opt == '-c':
markerColor = arg
elif opt == '-w':
lineWidth = int(arg)
elif opt == '-u':
unit = arg
elif opt == '-l':
lbound = float(arg)
elif opt == '-h':
hbound = float(arg)
elif opt == '-D':
demFile = arg
elif opt == '-V':
contour_step = float(arg)
elif opt == '-t':
minDate = arg
elif opt == '-T':
maxDate = arg
elif opt == '-r':
radius = abs(int(arg))
elif opt == '-x':
xsub = sorted([int(i) for i in arg.split(':')])
elif opt == '-y':
ysub = sorted([int(i) for i in arg.split(':')])
elif opt == '-X':
ref_xsub = sorted([int(i) for i in arg.split(':')])
elif opt == '-Y':
ref_ysub = sorted([int(i) for i in arg.split(':')])
elif opt == '--contour-step':
contour_step = float(arg)
elif opt == '--contour-smooth':
contour_sigma = float(arg)
elif opt == '--dem-nocontour':
demContour = 'no'
elif opt == '--dem-noshade':
demShade = 'no'
elif opt == '--displacement':
dispDisplacement = 'yes'
elif opt in ['-E', '--exclude']:
datesNot2show = arg.split(',')
elif opt in '--lalo':
lalosub = [float(i) for i in arg.split(',')]
elif opt in '--LALO':
ref_lalosub = [float(i) for i in arg.split(',')]
elif opt in ['--rect-color']:
rectColor = arg
elif opt in ['--ref-date']:
ref_date = ptime.yyyymmdd(arg)
elif opt in ['-u', '--unit']:
unit = arg.lower()
elif opt == '--save':
saveFig = 'yes'
elif opt == '--nodisplay':
dispFig = 'no'
saveFig = 'yes'
elif opt == '--opposite':
dispOpposite = 'yes'
elif opt == '--zero-start':
zero_start = arg.lower()
elif opt == '--zoom-x':
win_x = sorted([int(i) for i in arg.split(':')])
elif opt == '--zoom-y':
win_y = sorted([int(i) for i in arg.split(':')])
elif opt == '--zoom-lon':
win_lon = sorted([float(i) for i in arg.split(':')])
elif opt == '--zoom-lat':
win_lat = sorted([float(i) for i in arg.split(':')])
##############################################################
## Read time series file info
if not os.path.isfile(timeSeriesFile):
print '\nERROR: Input time series file does not exist: ' + timeSeriesFile + '\n'
sys.exit(1)
h5timeseries = h5py.File(timeSeriesFile, 'r')
k = h5timeseries.keys()
# read h5 file and its group type
if not 'timeseries' in k:
print 'ERROR: Input file is ' + k[
0] + '.\n\tOnly timeseries is supported.\n'
sys.exit(1)
atr = readfile.read_attribute(timeSeriesFile)
dateList1 = sorted(h5timeseries['timeseries'].keys())
dates1, datevector1 = ptime.date_list2vector(dateList1)
print '\n************ Time Series Display - Point *************'
##### Select Check
try:
lalosub
xsub = subset.coord_geo2radar([lalosub[1]], atr, 'longitude')
ysub = subset.coord_geo2radar([lalosub[0]], atr, 'latitude')
xsub = [xsub]
ysub = [ysub]
if radius == 0: radius = 3
except:
pass
try:
ref_lalosub
ref_xsub = subset.coord_geo2radar([ref_lalosub[1]], atr, 'longitude')
ref_ysub = subset.coord_geo2radar([ref_lalosub[0]], atr, 'latitude')
ref_xsub = [ref_xsub]
ref_ysub = [ref_ysub]
if radius == 0: radius = 3
except:
pass
##############################################################
global dates, dateList, datevector_all, dateListMinMax
print '*******************'
print 'All dates existed:'
print dateList1
print '*******************'
## Check exclude date input
try:
datesNot2show
if os.path.isfile(datesNot2show[0]):
try:
datesNot2show = ptime.read_date_list(datesNot2show[0])
except:
print 'Can not read date list file: ' + datesNot2show[0]
print 'dates not to show: ' + str(datesNot2show)
except:
datesNot2show = []
## Check Min / Max Date
dateListMinMax = []
try:
minDate
minDate = ptime.yyyymmdd(minDate)
dateListMinMax.append(minDate)
minDateyy = ptime.yyyymmdd2years(minDate)
print 'minimum date: ' + minDate
for date in dateList1:
yy = ptime.yyyymmdd2years(date)
if yy < minDateyy:
datesNot2show.append(date)
except:
pass
try:
maxDate
maxDate = ptime.yyyymmdd(maxDate)
dateListMinMax.append(maxDate)
maxDateyy = ptime.yyyymmdd2years(maxDate)
print 'maximum date: ' + maxDate
for date in dateList1:
yy = ptime.yyyymmdd2years(date)
if yy > maxDateyy:
datesNot2show.append(date)
except:
pass
dateListMinMax = sorted(dateListMinMax)
if not dateListMinMax: print 'no min/max date input.'
else: datesMinMax, dateVecMinMax = ptime.date_list2vector(dateListMinMax)
## Finalize Date List
try:
dateList = []
for date in dateList1:
if date not in datesNot2show:
dateList.append(date)
print '--------------------------------------------'
print 'dates used to show time series displacements:'
print dateList
print '--------------------------------------------'
except:
dateList = dateList1
print 'using all dates to show time series displacement'
## Read Date Info (x axis for time series display)
dates, datevector = ptime.date_list2vector(dateList)
datevector_all = list(datevector)
## Check reference date input
try:
ref_date
if not ref_date in dateList:
print 'Reference date - ' + ref_date + ' - is not included in date list to show.'
sys.exit(1)
else:
print 'reference date: ' + ref_date
except:
if zero_start == 'yes':
ref_date = dateList[0]
print 'set the 1st date as reference for displacement display.'
else:
pass
##############################################################
##### Plot Fig 1 - Velocity / last epoch of time series / DEM
fig = plt.figure(1)
ax = fig.add_subplot(111)
##### Check subset range
width = int(atr['WIDTH'])
length = int(atr['FILE_LENGTH'])
print 'file size: ' + str(length) + ', ' + str(width)
try:
win_y = subset.coord_geo2radar(win_lat, atr, 'latitude')
except:
try:
win_y
except:
win_y = [0, length]
try:
win_x = subset.coord_geo2radar(win_lon, atr, 'longitude')
except:
try:
win_x
except:
win_x = [0, width]
win_box = (win_x[0], win_y[0], win_x[1], win_y[1])
win_box = subset.check_box_within_data_coverage(win_box, atr)
try:
velocityFile
try:
vel, vel_atr = readfile.read(velocityFile)
except:
vel, vel_atr = readfile.read(timeSeriesFile, velocityFile)
ax.set_title(velocityFile)
print 'display: ' + velocityFile
except:
vel, vel_atr = readfile.read(timeSeriesFile, dateList1[-1])
ax.set_title('epoch: ' + dateList1[-1])
print 'display last epoch'
##### show displacement instead of phase
if vel_atr['FILE_TYPE'] in ['interferograms', '.unw'
] and dispDisplacement == 'yes':
print 'show displacement'
phase2range = -float(vel_atr['WAVELENGTH']) / (4 * np.pi)
vel *= phase2range
else:
dispDisplacement = 'no'
## Reference Point
if showRef == 'yes':
try:
ax.plot(int(atr['ref_x']), int(atr['ref_y']), 'ks', ms=6)
except:
pass
if dispOpposite == 'yes':
print 'show opposite value in figure/map 1'
vel *= -1
## Flip
try:
flip_lr
except:
try:
flip_ud
except:
flip_lr, flip_ud = view.auto_flip_direction(atr)
## Status bar
## Geo coordinate
try:
ullon = float(atr['X_FIRST'])
ullat = float(atr['Y_FIRST'])
lon_step = float(atr['X_STEP'])
lat_step = float(atr['Y_STEP'])
lon_unit = atr['Y_UNIT']
lat_unit = atr['X_UNIT']
geocoord = 'yes'
print 'Input file is Geocoded'
except:
geocoord = 'no'
def format_coord(x, y):
col = int(x + 0.5)
row = int(y + 0.5)
if col >= 0 and col <= width and row >= 0 and row <= length:
z = vel[row, col]
try:
lon = ullon + x * lon_step
lat = ullat + y * lat_step
return 'x=%.1f, y=%.1f, value=%.4f, lon=%.4f, lat=%.4f' % (
x, y, z, lon, lat)
except:
return 'x=%.1f, y=%.1f, value=%.4f' % (x, y, z)
ax.format_coord = format_coord
## DEM
try:
demFile
dem, demRsc = readfile.read(demFile)
ax = view.plot_dem_yx(ax, dem, demShade, demContour, contour_step,
contour_sigma)
vel_alpha = 0.8
except:
print 'No DEM file'
try:
img = ax.imshow(vel, vmin=vmin, vmax=vmax, alpha=vel_alpha)
except:
img = ax.imshow(vel, alpha=vel_alpha)
plt.colorbar(img)
## Zoom In (subset)
if flip_lr == 'yes': ax.set_xlim(win_box[2], win_box[0])
else: ax.set_xlim(win_box[0], win_box[2])
if flip_ud == 'yes': ax.set_ylim(win_box[1], win_box[3])
else: ax.set_ylim(win_box[3], win_box[1])
## Flip
#if flip_lr == 'yes': fig.gca().invert_xaxis()
#if flip_ud == 'yes': fig.gca().invert_yaxis()
##########################################
##### Plot Fig 2 - Time series plot
#fig2 = plt.figure(num=2,figsize=(12,6))
fig2 = plt.figure(2, figsize=(12, 6))
ax2 = fig2.add_subplot(111)
try:
timeSeriesFile_2
h5timeseries_2 = h5py.File(timeSeriesFile_2)
dateList_2 = sorted(h5timeseries_2['timeseries'].keys())
dates_2, datevector_2 = ptime.date_list2vector(dateList_2)
datevector_all += list(set(datevector_2) - set(datevector_all))
datevector_all = sorted(datevector_all)
except:
pass
################################ Plot Code Package <start> #################################
def plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries):
ax2.cla()
print '\n-------------------------------------------------------------------------------'
disp_min = 0
disp_max = 0
############################# Plot Time Series ##############################
global ref_xsub, ref_ysub
##### 1.1 Plot Reference time series
try:
ref_xsub
ref_ysub
ref_xsub, ref_ysub = check_yx(ref_xsub, ref_ysub, radius, ax,
rectColor)
print '----------------------------------------------------'
print 'Reference Point:'
print 'ref_x=' + str(ref_xsub[0]) + ':' + str(ref_xsub[1])
print 'ref_y=' + str(ref_ysub[0]) + ':' + str(ref_ysub[1])
print '-----------------------------'
print 'Time series with all dates:'
dis1, dis1_mean, dis1_std, dis1_vel = read_dis_xy(
ref_xsub, ref_ysub, dateList1, h5timeseries, unit)
(_, caps, _)=ax2.errorbar(dates1,dis1_mean,yerr=dis1_std,fmt='-ks',\
ms=markerSize2, lw=0, alpha=1,mfc=markerColor_ref,mew=edgeWidth,\
elinewidth=edgeWidth,ecolor='black',capsize=markerSize*0.5)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis1_mean,
dis1_std)
if not len(dateList) == len(dateList1):
print '-----------------------------'
print 'Time series with dates of interest:'
dis12, dis12_mean, dis12_std, dis12_vel = read_dis_xy(
ref_xsub, ref_ysub, dateList, h5timeseries, unit)
(_, caps, _)=ax2.errorbar(dates,dis12_mean,yerr=dis12_std,fmt='-ks',\
ms=markerSize2, lw=0, alpha=1,mfc=markerColor_ref2,mew=edgeWidth,\
elinewidth=edgeWidth,ecolor='black',capsize=markerSize*0.5)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis12_mean,
dis12_std)
except:
pass
##### 1.2.0 Read y/x
print '\n----------------------------------------------------'
print 'Point of Interest:'
xsub, ysub = check_yx(xsub, ysub, radius, ax, rectColor)
print 'x=' + str(xsub[0]) + ':' + str(xsub[1])
print 'y=' + str(ysub[0]) + ':' + str(ysub[1])
##### 1.2.1 Plot 2nd time series
try:
timeSeriesFile_2
print '-----------------------------'
print '2nd Time Series:'
dis2, dis2_mean, dis2_std, dis2_vel = read_dis_xy(
xsub, ysub, dateList_2, h5timeseries_2, unit)
(_, caps, _)=ax2.errorbar(dates_2,dis2_mean,yerr=dis2_std,fmt='-ko',\
ms=markerSize2, lw=0, alpha=1, mfc=markerColor2,\
elinewidth=0,ecolor='black',capsize=0)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis2_mean,
dis2_std)
except:
pass
##### 1.2.2 Plot 1st time series
print '-----------------------------'
print 'Time Series:'
dis, dis_mean, dis_std, dis_vel = read_dis_xy(xsub, ysub, dateList,
h5timeseries, unit)
(_, caps, _)=ax2.errorbar(dates,dis_mean,yerr=dis_std,fmt='-ko',\
ms=markerSize, lw=lineWidth, alpha=1, mfc=markerColor,\
elinewidth=edgeWidth,ecolor='black',capsize=markerSize*0.5)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis_mean, dis_std)
####################### Figure Format #######################
## x axis format
try:
ax2 = ptime.auto_adjust_xaxis_date(ax2, dateVecMinMax, fontSize)
except:
ax2 = ptime.auto_adjust_xaxis_date(ax2, datevector_all, fontSize)
## y axis format
ax2.set_ylabel('Displacement [' + unit + ']', fontsize=fontSize)
try:
lbound
hbound
ax2.set_ylim(lbound, hbound)
except:
disp_buf = 0.2 * (disp_max - disp_min)
ax2.set_ylim(disp_min - disp_buf, disp_max + disp_buf)
for tick in ax2.yaxis.get_major_ticks():
tick.label.set_fontsize(fontSize)
## title
figTitle = 'x=' + str(xsub[0]) + ':' + str(xsub[1]) + ', y=' + str(
ysub[0]) + ':' + str(ysub[1])
try:
lonc = ullon + (xsub[0] + xsub[1]) / 2.0 * lon_step
latc = ullat + (ysub[0] + ysub[1]) / 2.0 * lat_step
figTitle += ', lalo=' + '%.4f,%.4f' % (latc, lonc)
except:
pass
ax2.set_title(figTitle)
################## Save and Output #####################
if saveFig == 'yes':
print '-----------------------------'
Delay = {}
Delay['displacement'] = dis
Delay['unit'] = unit
Delay['time'] = datevector
Delay['velocity'] = dis_vel[0]
Delay['velocity_unit'] = unit + '/yr'
Delay['velocity_std'] = dis_vel[4]
figBase = 'x' + str(xsub[0]) + '_' + str(xsub[1] - 1) + 'y' + str(
ysub[0]) + '_' + str(ysub[1] - 1)
sio.savemat(figBase + '_ts.mat', {'displacement': Delay})
print 'saved ' + figBase + '_ts.mat'
fig2.savefig(figBase + '_ts.pdf',
bbox_inches='tight',
transparent=True,
dpi=fig_dpi)
print 'saved ' + figBase + '_ts.pdf'
if dispFig == 'no':
fig.savefig(figBase + '_vel.png',
bbox_inches='tight',
transparent=True,
dpi=fig_dpi)
print 'saved ' + figBase + '_vel.png'
################################ Plot Code Package <end> #################################
########### 1. Plot Time Series with x/y ##########
try:
xsub
ysub
plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries)
except:
print 'No x/y input'
pass
########### 2. Plot Time Series with Click ##########
## similar to 1. Plot Time Series with x/y
def onclick(event):
ax2.cla()
xsub = [int(event.xdata)]
ysub = [int(event.ydata)]
plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries)
if dispFig == 'yes': plt.show()
try:
cid = fig.canvas.mpl_connect('button_press_event', onclick)
except:
pass
if dispFig == 'yes': plt.show()
def main(argv):
global method_default
##### Referencing methods
method_default = 'max_coherence'
#method = 'manual'
#method = 'max_coherence' ## Use phase on point with max coherence [default]
#method = 'global_average' ## Use Nan Mean of phase on all pixels
#method = 'random'
#maskFile = 'Mask.h5'
global SeedingDone
############################## Check Inputs ##############################
if len(sys.argv) > 2:
try: opts, args = getopt.getopt(argv,"h:c:f:m:y:x:l:L:t:o:r:",\
['manual','max-coherence','global-average','random'])
except getopt.GetoptError: Usage() ; sys.exit(1)
for opt,arg in opts:
if opt in ("-h","--help"): Usage(); sys.exit()
elif opt == '-f': File = arg
elif opt == '-m': maskFile = arg
elif opt == '-c': corFile = arg
elif opt == '-o': outFile = arg
elif opt == '-y': ry = int(arg)
elif opt == '-x': rx = int(arg)
elif opt == '-l': rlat = float(arg)
elif opt == '-L': rlon = float(arg)
elif opt == '-r': refFile = arg
elif opt == '-t': templateFile = arg
elif opt == '--global-average' : method = 'global_average'
elif opt == '--manual' : method = 'manual'
elif opt == '--max-coherence' : method = 'max_coherence'
elif opt == '--random' : method = 'random'
elif len(sys.argv)==2:
if argv[0]=='-h': Usage(); sys.exit(1)
elif os.path.isfile(argv[0]): File = argv[0]
else: print 'Input file does not existed: '+argv[0]; sys.exit(1)
elif len(sys.argv)<2: Usage(); sys.exit(1)
##### Input File Info
try:
File
atr = readfile.read_attributes(File)
k = atr['FILE_TYPE']
length = int(atr['FILE_LENGTH'])
width = int(atr['WIDTH'])
except: Usage() ; sys.exit(1)
ext = os.path.splitext(File)[1].lower()
try: outFile
except: outFile = 'Seeded_'+File
############################## Reference Point Input ####################
try:
refFile
atr_ref = readfile.read_attributes(refFile)
except: pass
try:
templateFile
templateContents = readfile.read_template(templateFile)
except: pass
### Priority
## lat/lon > y/x
## Direct Input > Reference File > Template File
try:
rlat
rlon
except:
try:
rlat = float(atr_ref['ref_lat'])
rlon = float(atr_ref['ref_lon'])
except:
try: rlat,rlon = [float(i) for i in templateContents['pysar.seed.lalo'].split(',')]
except: pass
try:
ry
rx
except:
try:
ry = int(atr_ref['ref_y'])
rx = int(atr_ref['ref_x'])
except:
try: ry,rx = [int(i) for i in templateContents['pysar.seed.yx'].split(',')]
except: pass
##### Check lalo / YX
print '\n************** Reference Point ******************'
try:
rlat
rlon
y = sub.coord_geo2radar(rlat,atr,'lat')
x = sub.coord_geo2radar(rlon,atr,'lon')
0<= x <= width
0<= y <= length
rx = x
ry = y
print 'Reference point: lat = %.4f, lon = %.4f'%(rlat,rlon)
print ' y = %d, x = %d'%(ry,rx)
except:
print 'Skip input lat/lon reference point.'
print 'Continue with the y/x reference point.'
######################### a. Read Mask File #########################
## Priority: Input mask file > pysar.mask.file
try: maskFile
except:
try: maskFile = templateContents['pysar.mask.file']
except: print 'No mask found!';
try:
M,Matr = readfile.read(maskFile);
print 'mask: '+maskFile
except:
print '---------------------------------------------------------'
print 'WARNING: No mask, use the whole area as mask'
print '---------------------------------------------------------'
M = np.ones((length,width))
## Message
try:
rx
ry
0<= rx <= width
0<= ry <= length
if M[ry,rx] == 0:
print 'Input point has 0 value in mask.'
except: pass
######################### b. Stack ##################################
stackFile = os.path.basename(File).split(ext)[0] + '_stack.h5'
stack_file_exist = 'no'
try:
os.path.isfile(stackFile)
stack,atrStack = readfile.read(stackFile)
if width == int(atrStack['WIDTH']) and length == int(atrStack['FILE_LENGTH']):
stack_file_exist = 'yes'
print 'read stack from file: '+stackFile
except: pass
if stack_file_exist == 'no':
print 'calculating stack of input file ...'
stack = ut.stacking(File)
atrStack = atr.copy()
atrStack['FILE_TYPE'] = 'mask'
writefile.write(stack,atrStack,stackFile)
## Message
try:
rx
ry
if stack[ry,rx] == 0:
print 'Input point has nan value in data.'
except: pass
stack[M==0] = 0
if np.nansum(M) == 0.0:
print '\n*****************************************************'
print 'ERROR:'
print 'There is no pixel that has valid phase value in all datasets.'
print 'Check the file!'
print 'Seeding failed'
sys.exit(1)
######################### Check Method ##############################
try:
not stack[ry,rx] == 0
method = 'input_coord'
except:
try: method
except: method = method_default
print 'Skip input y/x reference point.'
print 'Continue with '+method
#h5file = h5py.File(File)
######################### Seeding ###################################
##### Sub-function
def seed_method(method,File,stack,outFile,corFile=''):
SeedingDone = 'no'
next_method = method_default
M = stack != 0
if method == 'manual':
SeedingDone = seed_manual(File,stack,outFile)
if SeedingDone == 'no':
next_method = method_default
print_warning(next_method)
elif method == 'max_coherence':
try: SeedingDone = seed_max_coherence(File,M,outFile,corFile)
except: SeedingDone = seed_max_coherence(File,M,outFile)
if SeedingDone == 'no':
next_method = 'random'
print_warning(next_method)
elif method == 'random':
y,x = random_selection(stack)
seed_xy(File,x,y,outFile)
SeedingDone = 'yes'
elif method == 'global_average':
print '\n---------------------------------------------------------'
print 'Automatically Seeding using Global Spatial Average Value '
print '---------------------------------------------------------'
print 'Calculating the global spatial average value for each epoch'+\
' of all valid pixels ...'
box = (0,0,width,length)
meanList = ut.spatial_mean(File,M,box)
seed_file(File,outFile,meanList,'','')
SeedingDone = 'yes'
return SeedingDone, next_method
##### Seeding
SeedingDone = 'no'
if method == 'input_coord':
seed_xy(File,rx,ry,outFile)
SeedingDone = 'yes'
else:
i = 0
while SeedingDone == 'no' and i < 5:
try: SeedingDone,method = seed_method(method,File,stack,outFile,corFile)
except: SeedingDone,method = seed_method(method,File,stack,outFile)
i += 1
if i >= 5:
print 'ERROR: Seeding failed after more than '+str(i)+' times try ...'
sys.exit(1)
def main(argv):
inps = cmdLineParse()
print '\n**************** Transect *********************'
print 'number of file: ' + str(len(inps.file))
print inps.file
##### Start / End Point Input
# 1. lonlat file
if inps.lola_file:
inps.start_lalo, inps.end_lalo = read_lonlat_file(inps.lola_file)
# 2. Manually select in window display
if (not inps.start_yx or not inps.end_yx) and (not inps.start_lalo
or not inps.end_lalo):
print 'No input yx/lalo found.'
print 'Continue with manually select start and end point.'
inps.start_yx, inps.end_yx = manual_select_start_end_point(
inps.file[0])
# Message
if inps.start_lalo and inps.end_lalo:
print 'Start point: lat = ' + str(
inps.start_lalo[0]) + ', lon = ' + str(inps.start_lalo[1])
print 'End point: lat = ' + str(
inps.end_lalo[0]) + ', lon = ' + str(inps.end_lalo[1])
else:
print 'Start point: y = ' + str(inps.start_yx[0]) + ', x = ' + str(
inps.start_yx[1])
print 'End point: y = ' + str(inps.end_yx[0]) + ', x = ' + str(
inps.end_yx[1])
##### Get Transection/Profiles Data
print 'extract transect from input files ...'
transectList, atrList = transect_list(inps.file, inps)
if inps.dem:
demTransectList, demAtrList = transect_list([inps.dem], inps)
print 'profile length: ' + str(transectList[0][-1, 0] / 1000.0) + ' km'
##### Plot
# Figure 1 - Profile line in the 1st input file
print 'plot profile line in the 1st input file'
fig0 = plt.figure()
ax0 = fig0.add_axes([0.1, 0.1, 0.8, 0.8])
data0, atr0 = readfile.read(inps.file[0])
ax0.imshow(data0)
if inps.start_lalo and inps.end_lalo:
[y0, y1] = sub.coord_geo2radar([inps.start_lalo[0], inps.end_lalo[0]],
atr0, 'lat')
[x0, x1] = sub.coord_geo2radar([inps.start_lalo[1], inps.end_lalo[1]],
atr0, 'lon')
else:
[y0, y1] = [inps.start_yx[0], inps.end_yx[0]]
[x0, x1] = [inps.start_yx[1], inps.end_yx[1]]
ax0.plot([x0, x1], [y0, y1], 'ro-')
ax0.set_xlim(0, np.shape(data0)[1])
ax0.set_ylim(np.shape(data0)[0], 0)
ax0.set_title('Transect Line in ' + inps.file[0])
# Status bar
def format_coord(x, y):
col = int(x)
row = int(y)
if 0 <= col < data0.shape[1] and 0 <= row < data0.shape[0]:
z = data0[row, col]
if 'X_FIRST' in atr0.keys():
lat = sub.coord_radar2geo(row, atr0, 'row')
lon = sub.coord_radar2geo(col, atr0, 'col')
return 'lon=%.4f, lat=%.4f, x=%.0f, y=%.0f, value=%.4f' % (
lon, lat, x, y, z)
else:
return 'x=%.0f, y=%.0f, value=%.4f' % (x, y, z)
else:
return 'x=%.0f, y=%.0f' % (x, y)
ax0.format_coord = format_coord
# Figure 2 - Transections/Profiles
print 'plot profiles'
fig, ax = plt.subplots(figsize=inps.fig_size)
# Plot 2.1 - Input Files
if not inps.disp_unit:
inps.disp_unit = atrList[0]['UNIT']
inps.disp_scale, inps.disp_unit = get_scale_from_disp_unit(
inps.disp_unit, atrList[0]['UNIT'])
value_min = 0
value_max = 0
for i in range(len(inps.file)):
# Profile Color based on Asc/Desc direction
if atrList[i]['ORBIT_DIRECTION'][0].upper() == 'A':
p_color = 'crimson'
else:
p_color = 'royalblue'
# Plot
distance = transectList[i][:, 0] / 1000.0 # km
value = transectList[i][:, 1] * inps.disp_scale - inps.disp_offset * i
ax.plot(distance,
value,
'.',
color=p_color,
markersize=inps.marker_size)
# Y Stat
value_min = np.nanmin([value_min, np.nanmin(value)])
value_max = np.nanmax([value_max, np.nanmax(value)])
# Y axis
if not inps.disp_min:
inps.disp_min = np.floor(value_min - (value_max - value_min) * 1.2 /
len(inps.file))
if not inps.disp_max:
inps.disp_max = np.ceil(value_max)
ax.set_ylim(inps.disp_min, inps.disp_max)
ax.set_ylabel('Mean LOS Velocity (' + inps.disp_unit + ')',
fontsize=inps.font_size)
# X axis
ax.set_xlabel('Distance (km)', fontsize=inps.font_size)
ax.tick_params(which='both', direction='out', labelsize=inps.font_size)
# Plot 2.2 - DEM
if inps.dem:
ax2 = ax.twinx()
distance = demTransectList[0][:, 0] / 1000.0 # km
value = demTransectList[0][:, 1] / 1000.0 # km
ax2.fill_between(distance, 0, value, facecolor='gray')
# Y axis - display DEM in the bottom
value_min = np.nanmin(value)
value_max = np.nanmax(value)
if not inps.dem_disp_min:
inps.dem_disp_min = np.floor(value_min * 2.0) / 2.0
if not inps.dem_disp_max:
inps.dem_disp_max = np.ceil((value_max + (value_max - value_min) *
(len(inps.file) + 0.0)) * 2.0) / 2.0
ax2.set_ylim(inps.dem_disp_min, inps.dem_disp_max)
## Show lower part of yaxis
#dem_tick = ax2.yaxis.get_majorticklocs()
#dem_tick = dem_tick[:len(dem_tick)/2]
#ax2.set_yticks(dem_tick)
ax2.set_ylabel('Elevation (km)', fontsize=inps.font_size)
ax2.tick_params(which='both',
direction='out',
labelsize=inps.font_size)
## X axis - Shared
distanceMax = np.nanmax(transectList[0][:, 0] / 1000.0) # in km
plt.xlim(0, distanceMax)
plt.tight_layout()
##### Output
if not inps.outfile:
figBase = 'transect_x' + str(x0) + 'y' + str(y0) + '_x' + str(
x1) + 'y' + str(y1)
else:
figBase, inps.outfile_ext = os.path.splitext(inps.outfile)
if not inps.outfile_ext:
inps.outfile_ext = '.png'
if inps.save_fig:
print 'writing >>> ' + figBase + inps.outfile_ext
fig0.savefig(inps.file[-1] + inps.outfile_ext,
bbox_inches='tight',
transparent=True,
dpi=inps.fig_dpi)
fig.savefig(figBase + inps.outfile_ext,
bbox_inches='tight',
transparent=True,
dpi=inps.fig_dpi)
print 'writing >>> ' + figBase + '.mat'
transect_mat = {}
for i in range(len(inps.file)):
project = atrList[i]['PROJECT_NAME']
transect_mat[project] = transectList[i]
if inps.dem:
transect_mat['elevation'] = demTransectList[0]
sio.savemat(figBase + '.mat', {'transection': transect_mat})
# Display
if inps.disp_fig:
print 'showing ...'
plt.show()
return
def transect_lalo(z, atr, start_lalo, end_lalo, interpolation='nearest'):
'''Extract 2D matrix (z) value along the line [start_lalo, end_lalo]'''
[y0, y1] = sub.coord_geo2radar([start_lalo[0], end_lalo[0]], atr, 'lat')
[x0, x1] = sub.coord_geo2radar([start_lalo[1], end_lalo[1]], atr, 'lon')
transect = transect_yx(z, atr, [y0, x0], [y1, x1], interpolation)
return transect