def texture2(humfile, sonpath, win, doplot, numclasses):
'''
Create a texture lengthscale map using the algorithm detailed by Buscombe et al. (2015)
This textural lengthscale is not a direct measure of grain size. Rather, it is a statistical
representation that integrates over many attributes of bed texture, of which grain size is the most important.
The technique is a physically based means to identify regions of texture within a sidescan echogram,
and could provide a basis for objective, automated riverbed sediment classification.
Syntax
----------
[] = PyHum.texture(humfile, sonpath, win, doplot, numclasses)
Parameters
----------
humfile : str
path to the .DAT file
sonpath : str
path where the *.SON files are
win : int, *optional* [Default=10]
pixel in pixels of the moving window
doplot : int, *optional* [Default=1]
if 1, make plots, otherwise do not make plots
numclasses : int, *optional* [Default=4]
number of 'k means' that the texture lengthscale will be segmented into
Returns
-------
sonpath+base+'_data_class.dat': memory-mapped file
contains the texture lengthscale map
sonpath+base+'_data_kclass.dat': memory-mapped file
contains the k-means segmented texture lengthscale map
References
----------
.. [1] Buscombe, D., Grams, P.E., and Smith, S.M.C., 2015, Automated riverbed sediment
classification using low-cost sidescan sonar. Journal of Hydraulic Engineering 10.1061/(ASCE)HY.1943-7900.0001079, 06015019.
'''
# prompt user to supply file if no input file given
if not humfile:
print('An input file is required!!!!!!')
Tk().withdraw(
) # we don't want a full GUI, so keep the root window from appearing
humfile = askopenfilename(filetypes=[("DAT files", "*.DAT")])
# prompt user to supply directory if no input sonpath is given
if not sonpath:
print('A *.SON directory is required!!!!!!')
Tk().withdraw(
) # we don't want a full GUI, so keep the root window from appearing
sonpath = askdirectory()
# print given arguments to screen and convert data type where necessary
if humfile:
print('Input file is %s' % (humfile))
if sonpath:
print('Sonar file path is %s' % (sonpath))
if win:
win = np.asarray(win, int)
print('Window is %s square pixels' % (str(win)))
if numclasses:
numclasses = np.asarray(numclasses, int)
print('Number of sediment classes: %s' % (str(numclasses)))
if doplot:
doplot = int(doplot)
if doplot == 0:
print("Plots will not be made")
print('[Default] Number of processors is %s' % (str(cpu_count())))
########################################################
########################################################
# start timer
if os.name == 'posix': # true if linux/mac or cygwin on windows
start = time.time()
else: # windows
start = time.clock()
# if son path name supplied has no separator at end, put one on
if sonpath[-1] != os.sep:
sonpath = sonpath + os.sep
base = humfile.split('.DAT') # get base of file name for output
base = base[0].split(os.sep)[-1]
# remove underscores, negatives and spaces from basename
base = humutils.strip_base(base)
meta = loadmat(os.path.normpath(os.path.join(sonpath, base + 'meta.mat')))
ft = 1 / loadmat(sonpath + base + 'meta.mat')['pix_m']
#pix_m = np.squeeze(meta['pix_m'])
#dep_m = np.squeeze(meta['dep_m'])
dist_m = np.squeeze(meta['dist_m'])
### port
print("processing port side ...")
# load memory mapped scan ... port
shape_port = np.squeeze(meta['shape_port'])
if shape_port != '':
if os.path.isfile(
os.path.normpath(
os.path.join(sonpath, base + '_data_port_lar.dat'))):
port_fp = io.get_mmap_data(sonpath, base, '_data_port_lar.dat',
'float32', tuple(shape_port))
else:
port_fp = io.get_mmap_data(sonpath, base, '_data_port_la.dat',
'float32', tuple(shape_port))
port_fp2 = io.get_mmap_data(sonpath, base, '_data_port_l.dat',
'float32', tuple(shape_port))
### star
print("processing starboard side ...")
# load memory mapped scan ... port
shape_star = np.squeeze(loadmat(sonpath + base + 'meta.mat')['shape_star'])
if shape_star != '':
if os.path.isfile(
os.path.normpath(
os.path.join(sonpath, base + '_data_star_lar.dat'))):
star_fp = io.get_mmap_data(sonpath, base, '_data_star_lar.dat',
'float32', tuple(shape_star))
else:
star_fp = io.get_mmap_data(sonpath, base, '_data_star_la.dat',
'float32', tuple(shape_star))
star_fp2 = io.get_mmap_data(sonpath, base, '_data_star_l.dat',
'float32', tuple(shape_star))
if len(shape_star) > 2:
shape = shape_port.copy()
shape[1] = shape_port[1] + shape_star[1]
else:
shape = []
shape.append(1)
shape.append(shape_port[0])
shape.append(shape_port[1])
shape[1] = shape_port[0] + shape_star[0]
# create memory mapped file for Sp
#with open(os.path.normpath(os.path.join(sonpath,base+'_data_class.dat')), 'w+') as ff:
# fp = np.memmap(ff, dtype='float32', mode='w+', shape=tuple(shape))
fp = np.zeros(tuple(shape), dtype='float32')
if len(shape_star) > 2:
for p in range(len(port_fp)):
merge = np.vstack((np.flipud(port_fp[p]), star_fp[p]))
merge = denoise_tv_chambolle(merge.copy(),
weight=2,
multichannel=False).astype('float32')
Snn = std_convoluted(merge, win)[1]
del merge
try:
Snn = medfilt2d(Snn, (win + 1, win + 1))
except:
Snn = medfilt2d(Snn, (win, win))
Snn[np.isnan(np.vstack(
(np.flipud(port_fp[p]), star_fp[p])))] = np.nan
Snn[np.isnan(np.vstack(
(np.flipud(port_fp2[p]), star_fp2[p])))] = np.nan
R_fp = io.get_mmap_data(sonpath, base, '_data_range.dat',
'float32', tuple(shape_star))
R = np.vstack((np.flipud(R_fp[0]), R_fp[0]))
R = R / np.max(R)
rn = replace_nans.RN(R.astype('float64'), 1000, 0.01, 2,
'localmean')
R = rn.getdata()
del rn
Sp = (Snn**2) * np.cos(np.deg2rad(R)) / win ##**2
fp[p] = Sp.astype('float32')
del Sp
#del fp # flush data to file
shape = io.set_mmap_data(sonpath, base, '_data_class.dat', 'float32',
np.squeeze(fp))
del fp
class_fp = io.get_mmap_data(sonpath, base, '_data_class.dat',
'float32', tuple(shape))
else:
merge = np.vstack((np.flipud(port_fp), star_fp))
merge = denoise_tv_chambolle(merge.copy(),
weight=2,
multichannel=False).astype('float32')
Snn = std_convoluted(merge, win)[1]
del merge
try:
Snn = medfilt2d(Snn, (win + 1, win + 1))
except:
Snn = medfilt2d(Snn, (win, win))
Snn[np.isnan(np.vstack((np.flipud(port_fp), star_fp)))] = np.nan
Snn[np.isnan(np.vstack((np.flipud(port_fp2), star_fp2)))] = np.nan
R_fp = io.get_mmap_data(sonpath, base, '_data_range.dat', 'float32',
tuple(shape_star))
R = np.vstack((np.flipud(R_fp), R_fp))
R = R / np.max(R)
rn = replace_nans.RN(R.astype('float64'), 1000, 0.01, 2, 'localmean')
R = rn.getdata()
del rn
Sp = (Snn**2) * np.cos(np.deg2rad(R)) / win ##**2
shape = io.set_mmap_data(sonpath, base, '_data_class.dat', 'float32',
np.squeeze(Sp))
#with open(os.path.normpath(os.path.join(sonpath,base+'_data_class.dat')), 'w+') as ff:
# np.save(ff, np.squeeze(Sp).astype('float32'))
#with open(os.path.normpath(os.path.join(sonpath,base+'_data_class.dat')), 'r') as ff:
# class_fp = np.load(ff)
#del Sp
class_fp = io.get_mmap_data(sonpath, base, '_data_class.dat',
'float32', tuple(shape))
dist_m = np.squeeze(loadmat(sonpath + base + 'meta.mat')['dist_m'])
########################################################
if doplot == 1:
if len(shape_star) > 2:
for p in range(len(star_fp)):
plot_class(dist_m, shape_port, port_fp[p], star_fp[p],
class_fp[p], ft, humfile, sonpath, base, p)
else:
plot_class(dist_m, shape_port, port_fp, star_fp, class_fp, ft,
humfile, sonpath, base, 0)
if len(shape_star) > 2:
for p in range(len(star_fp)):
plot_contours(dist_m, shape_port, port_fp[p], star_fp[p],
class_fp[p], ft, humfile, sonpath, base,
numclasses, p)
else:
plot_contours(dist_m, shape_port, port_fp, star_fp, class_fp, ft,
humfile, sonpath, base, numclasses, 0)
#######################################################
# k-means
if len(shape_star) > 2:
with open(
os.path.normpath(
os.path.join(sonpath, base + '_data_kclass.dat')),
'w+') as ff:
fp = np.memmap(ff, dtype='float32', mode='w+', shape=tuple(shape))
for p in range(len(port_fp)):
wc = get_kclass(class_fp[p].copy(), numclasses)
fp[p] = wc.astype('float32')
del wc
del fp
kclass_fp = io.get_mmap_data(sonpath, base, '_data_kclass.dat',
'float32', tuple(shape))
else:
wc = get_kclass(class_fp.copy(), numclasses)
with open(
os.path.normpath(
os.path.join(sonpath, base + '_data_kclass.dat')),
'w+') as ff:
np.save(ff, np.squeeze(wc).astype('float32'))
del wc
with open(
os.path.normpath(
os.path.join(sonpath, base + '_data_kclass.dat')),
'r') as ff:
kclass_fp = np.load(ff)
########################################################
if doplot == 1:
if len(shape_star) > 2:
for p in range(len(star_fp)):
plot_kmeans(dist_m, shape_port, port_fp[p], star_fp[p],
kclass_fp[p], ft, humfile, sonpath, base, p)
else:
plot_kmeans(dist_m, shape_port, port_fp, star_fp, kclass_fp, ft,
humfile, sonpath, base, 0)
if os.name == 'posix': # true if linux/mac
elapsed = (time.time() - start)
else: # windows
elapsed = (time.clock() - start)
print("Processing took " + str(elapsed) + "seconds to analyse")
print("Done!")
print("===================================================")
def sliding_window(a,ws,ss = None,flatten = True):
'''
Return a sliding window over a in any number of dimensions
'''
if None is ss:
# ss was not provided. the windows will not overlap in any direction.
ss = ws
ws = norm_shape(ws)
ss = norm_shape(ss)
# convert ws, ss, and a.shape to numpy arrays
ws = np.array(ws)
ss = np.array(ss)
#import PyHum.io as io
shape_tmp = io.set_mmap_data('', '', 'tmp.dat', 'float32', a)
del a
a = io.get_mmap_data('', '', 'tmp.dat', 'float32', shape_tmp)
shap = np.array(a.shape)
try:
os.remove('tmp.dat')
except:
pass
# ensure that ws, ss, and a.shape all have the same number of dimensions
ls = [len(shap),len(ws),len(ss)]
if 1 != len(set(ls)):
raise ValueError(\
'a.shape, ws and ss must all have the same length. They were %s' % str(ls))
# ensure that ws is smaller than a in every dimension
if np.any(ws > shap):
raise ValueError(\
'ws cannot be larger than a in any dimension.\
a.shape was %s and ws was %s' % (str(a.shape),str(ws)))
# how many slices will there be in each dimension?
newshape = norm_shape(((shap - ws) // ss) + 1)
# the shape of the strided array will be the number of slices in each dimension
# plus the shape of the window (tuple addition)
newshape += norm_shape(ws)
# the strides tuple will be the array's strides multiplied by step size, plus
try:
# the array's strides (tuple addition)
newstrides = norm_shape(np.array(a.strides) * ss) + a.strides
a = ast(a,shape = newshape,strides = newstrides)
if not flatten:
return a
# Collapse strided so that it has one more dimension than the window. I.e.,
# the new array is a flat list of slices.
meat = len(ws) if ws.shape else 0
firstdim = (int(np.product(newshape[:-meat])),) if ws.shape else ()
dim = firstdim + (newshape[-meat:])
# remove any dimensions with size 1
dim = filter(lambda i : i != 1,dim)
return a.reshape(dim), newshape
except:
from itertools import product
print "memory error, windowing using slower method"
# For each dimension, create a list of all valid slices
slices = [[] for i in range(len(ws))]
for i in xrange(len(ws)):
nslices = ((shap[i] - ws[i]) // ss[i]) + 1
for j in xrange(0,nslices):
start = j * ss[i]
stop = start + ws[i]
slices[i].append(slice(start,stop))
# Get an iterator over all valid n-dimensional slices of the input
allslices = product(*slices)
# Allocate memory to hold all valid n-dimensional slices
nslices = np.product([len(s) for s in slices])
#out = np.ndarray((nslices,) + tuple(ws),dtype = a.dtype)
out=[]
for i,s in enumerate(allslices):
#out[i] = a[s]
out.append(a[s])
del a
import dask.bag as db
tmp = db.from_sequence(out, npartitions=1000)
del out
return tmp.compute(), newshape
def read(humfile, sonpath, cs2cs_args="epsg:26949", c=1450.0, draft=0.3, doplot=1, t=0.108, bedpick=1, flip_lr=0, model=998, calc_bearing = 0, filt_bearing = 0, chunk='d100'): #cog = 1,
'''
Read a .DAT and associated set of .SON files recorded by a Humminbird(R)
instrument.
Parse the data into a set of memory mapped files that will
subsequently be used by the other functions of the PyHum module.
Export time-series data and metadata in other formats.
Create a kml file for visualising boat track
Syntax
----------
[] = PyHum.read(humfile, sonpath, cs2cs_args, c, draft, doplot, t, bedpick, flip_lr, chunksize, model, calc_bearing, filt_bearing, chunk)
Parameters
------------
humfile : str
path to the .DAT file
sonpath : str
path where the *.SON files are
cs2cs_args : int, *optional* [Default="epsg:26949"]
arguments to create coordinates in a projected coordinate system
this argument gets given to pyproj to turn wgs84 (lat/lon) coordinates
into any projection supported by the proj.4 libraries
c : float, *optional* [Default=1450.0]
speed of sound in water (m/s). Defaults to a value of freshwater
draft : float, *optional* [Default=0.3]
draft from water surface to transducer face (m)
doplot : float, *optional* [Default=1]
if 1, plots will be made
t : float, *optional* [Default=0.108]
length of transducer array (m).
Default value is that of the 998 series Humminbird(R)
bedpick : int, *optional* [Default=1]
if 1, bedpicking with be carried out automatically
if 0, user will be prompted to pick the bed location on screen
flip_lr : int, *optional* [Default=0]
if 1, port and starboard scans will be flipped
(for situations where the transducer is flipped 180 degrees)
model: int, *optional* [Default=998]
A 3 or 4 number code indicating the model number
Examples: 998, 997, 1198, 1199
calc_bearing : float, *optional* [Default=0]
if 1, bearing will be calculated from coordinates
filt_bearing : float, *optional* [Default=0]
if 1, bearing will be filtered
chunk : str, *optional* [Default='d100' (distance, 100 m)]
letter, followed by a number.
There are the following letter options:
'd' - parse chunks based on distance, then number which is distance in m
'p' - parse chunks based on number of pings, then number which is number of pings
'h' - parse chunks based on change in heading, then number which is the change in heading in degrees
'1' - process just 1 chunk
Returns
---------
sonpath+base+'_data_port.dat': memory-mapped file
contains the raw echogram from the port side
sidescan sonar (where present)
sonpath+base+'_data_port.dat': memory-mapped file
contains the raw echogram from the starboard side
sidescan sonar (where present)
sonpath+base+'_data_dwnhi.dat': memory-mapped file
contains the raw echogram from the high-frequency
echosounder (where present)
sonpath+base+'_data_dwnlow.dat': memory-mapped file
contains the raw echogram from the low-frequency
echosounder (where present)
sonpath+base+"trackline.kml": google-earth kml file
contains the trackline of the vessel during data
acquisition
sonpath+base+'rawdat.csv': comma separated value file
contains time-series data. columns corresponding to
longitude
latitude
easting (m)
northing (m)
depth to bed (m)
alongtrack cumulative distance (m)
vessel heading (deg.)
sonpath+base+'meta.mat': .mat file
matlab format file containing a dictionary object
holding metadata information. Fields are:
e : ndarray, easting (m)
n : ndarray, northing (m)
es : ndarray, low-pass filtered easting (m)
ns : ndarray, low-pass filtered northing (m)
lat : ndarray, latitude
lon : ndarray, longitude
shape_port : tuple, shape of port scans in memory mapped file
shape_star : tuple, shape of starboard scans in memory mapped file
shape_hi : tuple, shape of high-freq. scans in memory mapped file
shape_low : tuple, shape of low-freq. scans in memory mapped file
dep_m : ndarray, depth to bed (m)
dist_m : ndarray, distance along track (m)
heading : ndarray, heading of vessel (deg. N)
pix_m: float, size of 1 pixel in across-track dimension (m)
bed : ndarray, depth to bed (m)
c : float, speed of sound in water (m/s)
t : length of sidescan transducer array (m)
spd : ndarray, vessel speed (m/s)
time_s : ndarray, time elapsed (s)
caltime : ndarray, unix epoch time (s)
'''
# prompt user to supply file if no input file given
if not humfile:
print 'An input file is required!!!!!!'
Tk().withdraw() # we don't want a full GUI, so keep the root window from appearing
humfile = askopenfilename(filetypes=[("DAT files","*.DAT")])
# prompt user to supply directory if no input sonpath is given
if not sonpath:
print 'A *.SON directory is required!!!!!!'
Tk().withdraw() # we don't want a full GUI, so keep the root window from appearing
sonpath = askdirectory()
# print given arguments to screen and convert data type where necessary
if humfile:
print 'Input file is %s' % (humfile)
if sonpath:
print 'Son files are in %s' % (sonpath)
if cs2cs_args:
print 'cs2cs arguments are %s' % (cs2cs_args)
if draft:
draft = float(draft)
print 'Draft: %s' % (str(draft))
if c:
c = float(c)
print 'Celerity of sound: %s m/s' % (str(c))
if doplot:
doplot = int(doplot)
if doplot==0:
print "Plots will not be made"
if flip_lr:
flip_lr = int(flip_lr)
if flip_lr==1:
print "Port and starboard will be flipped"
if t:
t = np.asarray(t,float)
print 'Transducer length is %s m' % (str(t))
if bedpick:
bedpick = np.asarray(bedpick,int)
if bedpick==1:
print 'Bed picking is auto'
elif bedpick==0:
print 'Bed picking is manual'
else:
print 'User will be prompted per chunk about bed picking method'
if chunk:
chunk = str(chunk)
if chunk[0]=='d':
chunkmode=1
chunkval = int(chunk[1:])
print 'Chunks based on distance of %s m' % (str(chunkval))
elif chunk[0]=='p':
chunkmode=2
chunkval = int(chunk[1:])
print 'Chunks based on %s pings' % (str(chunkval))
elif chunk[0]=='h':
chunkmode=3
chunkval = int(chunk[1:])
print 'Chunks based on heading devation of %s degrees' % (str(chunkval))
elif chunk[0]=='1':
chunkmode=4
chunkval = 1
print 'Only 1 chunk will be produced'
else:
print "Chunk mode not understood - should be 'd', 'p', or 'h' - using defaults"
chunkmode=1
chunkval = 100
print 'Chunks based on distance of %s m' % (str(chunkval))
if model:
model = int(model)
print "Data is from the %s series" % (str(model))
# if cog:
# cog = int(cog)
# if cog==1:
# print "Heading based on course-over-ground"
if calc_bearing:
calc_bearing = int(calc_bearing)
if calc_bearing==1:
print "Bearing will be calculated from coordinates"
if filt_bearing:
filt_bearing = int(filt_bearing)
if filt_bearing==1:
print "Bearing will be filtered"
## for debugging
#humfile = r"test.DAT"; sonpath = "test_data"
#cs2cs_args = "epsg:26949"; doplot = 1; draft = 0
#c=1450; bedpick=1; fliplr=1; chunk = 'd100'
#model=998; cog=1; calc_bearing=0; filt_bearing=0
f = 455
try:
print "Checking the epsg code you have chosen for compatibility with Basemap ... "
from mpl_toolkits.basemap import Basemap
m = Basemap(projection='merc', epsg=cs2cs_args.split(':')[1],
resolution = 'i', llcrnrlon=10, llcrnrlat=10, urcrnrlon=30, urcrnrlat=30)
del m
print "... epsg code compatible"
except:
print "Error: the epsg code you have chosen is not compatible with Basemap"
print "please choose a different epsg code (http://spatialreference.org/)"
print "program will now close"
sys.exit()
# start timer
if os.name=='posix': # true if linux/mac or cygwin on windows
start = time.time()
else: # windows
start = time.clock()
# if son path name supplied has no separator at end, put one on
if sonpath[-1]!=os.sep:
sonpath = sonpath + os.sep
# get the SON files from this directory
sonfiles = glob.glob(sonpath+'*.SON')
if not sonfiles:
sonfiles = glob.glob(os.getcwd()+os.sep+sonpath+'*.SON')
base = humfile.split('.DAT') # get base of file name for output
base = base[0].split(os.sep)[-1]
# remove underscores, negatives and spaces from basename
base = humutils.strip_base(base)
print "WARNING: Because files have to be read in byte by byte,"
print "this could take a very long time ..."
#reading each sonfile in parallel should be faster ...
try:
o = Parallel(n_jobs = np.min([len(sonfiles), cpu_count()]), verbose=0)(delayed(getscans)(sonfiles[k], humfile, c, model, cs2cs_args) for k in xrange(len(sonfiles)))
X, Y, A, B = zip(*o)
for k in xrange(len(Y)):
if Y[k] == 'sidescan_port':
dat = A[k] #data.gethumdat()
metadat = B[k] #data.getmetadata()
if flip_lr==0:
data_port = X[k].astype('int16')
else:
data_star = X[k].astype('int16')
elif Y[k] == 'sidescan_starboard':
if flip_lr==0:
data_star = X[k].astype('int16')
else:
data_port = X[k].astype('int16')
elif Y[k] == 'down_lowfreq':
data_dwnlow = X[k].astype('int16')
elif Y[k] == 'down_highfreq':
data_dwnhi = X[k].astype('int16')
del X, Y, A, B, o
old_pyread = 0
if 'data_port' not in locals():
data_port = ''
print "portside scan not available"
if 'data_star' not in locals():
data_star = ''
print "starboardside scan not available"
if 'data_dwnhi' not in locals():
data_dwnlow = ''
print "high-frq. downward scan not available"
if 'data_dwnlow' not in locals():
data_dwnlow = ''
print "low-frq. downward scan not available"
except: # revert back to older version if paralleleised version fails
print "something went wrong with the parallelised version of pyread ..."
import pyread
data = pyread.pyread(sonfiles, humfile, c, model, cs2cs_args)
dat = data.gethumdat()
metadat = data.getmetadata()
old_pyread = 1
nrec = len(metadat['n'])
metadat['instr_heading'] = metadat['heading'][:nrec]
#metadat['heading'] = humutils.get_bearing(calc_bearing, filt_bearing, cog, metadat['lat'], metadat['lon'], metadat['instr_heading'])
try:
es = humutils.runningMeanFast(metadat['e'][:nrec],len(metadat['e'][:nrec])/100)
ns = humutils.runningMeanFast(metadat['n'][:nrec],len(metadat['n'][:nrec])/100)
except:
es = metadat['e'][:nrec]
ns = metadat['n'][:nrec]
metadat['es'] = es
metadat['ns'] = ns
try:
trans = pyproj.Proj(init=cs2cs_args)
except:
trans = pyproj.Proj(cs2cs_args.lstrip(), inverse=True)
lon, lat = trans(es, ns, inverse=True)
metadat['lon'] = lon
metadat['lat'] = lat
metadat['heading'] = humutils.get_bearing(calc_bearing, filt_bearing, metadat['lat'], metadat['lon'], metadat['instr_heading']) #cog
dist_m = humutils.get_dist(lat, lon)
metadat['dist_m'] = dist_m
if calc_bearing==1: # recalculate speed, m/s
ds=np.gradient(np.squeeze(metadat['time_s']))
dx=np.gradient(np.squeeze(metadat['dist_m']))
metadat['spd'] = dx[:nrec]/ds[:nrec]
# theta at 3dB in the horizontal
theta3dB = np.arcsin(c/(t*(f*1000)))
#resolution of 1 sidescan pixel to nadir
ft = (np.pi/2)*(1/theta3dB) #/ (f/455)
dep_m = humutils.get_depth(metadat['dep_m'][:nrec])
if old_pyread == 1: #older pyread version
# port scan
try:
if flip_lr==0:
data_port = data.getportscans().astype('int16')
else:
data_port = data.getstarscans().astype('int16')
except:
data_port = ''
print "portside scan not available"
if data_port!='':
Zt, ind_port = makechunks_scan(chunkmode, chunkval, metadat, data_port, 0)
del data_port
## create memory mapped file for Z
shape_port = io.set_mmap_data(sonpath, base, '_data_port.dat', 'int16', Zt)
##we are only going to access the portion of memory required
port_fp = io.get_mmap_data(sonpath, base, '_data_port.dat', 'int16', shape_port)
if old_pyread == 1: #older pyread version
# starboard scan
try:
if flip_lr==0:
data_star = data.getstarscans().astype('int16')
else:
data_star = data.getportscans().astype('int16')
except:
data_star = ''
print "starboardside scan not available"
if data_star!='':
Zt, ind_star = makechunks_scan(chunkmode, chunkval, metadat, data_star, 1)
del data_star
# create memory mapped file for Z
shape_star = io.set_mmap_data(sonpath, base, '_data_star.dat', 'int16', Zt)
star_fp = io.get_mmap_data(sonpath, base, '_data_star.dat', 'int16', shape_star)
if 'star_fp' in locals() and 'port_fp' in locals():
# check that port and starboard are same size
# and trim if not
if np.shape(star_fp)!=np.shape(port_fp):
print "port and starboard scans are different sizes ... rectifying"
if np.shape(port_fp[0])[1] > np.shape(star_fp[0])[1]:
tmp = port_fp.copy()
tmp2 = np.empty_like(star_fp)
for k in xrange(len(tmp)):
tmp2[k] = tmp[k][:,:np.shape(star_fp[k])[1]]
del tmp
# create memory mapped file for Z
shape_port = io.set_mmap_data(sonpath, base, '_data_port2.dat', 'int16', tmp2)
#shape_star = shape_port.copy()
shape_star = tuple(np.asarray(shape_port).copy())
##we are only going to access the portion of memory required
port_fp = io.get_mmap_data(sonpath, base, '_data_port2.dat', 'int16', shape_port)
ind_port = list(ind_port)
ind_port[-1] = np.shape(star_fp[0])[1]
ind_port = tuple(ind_port)
elif np.shape(port_fp[0])[1] < np.shape(star_fp[0])[1]:
tmp = star_fp.copy()
tmp2 = np.empty_like(port_fp)
for k in xrange(len(tmp)):
tmp2[k] = tmp[k][:,:np.shape(port_fp[k])[1]]
del tmp
# create memory mapped file for Z
shape_port = io.set_mmap_data(sonpath, base, '_data_star2.dat', 'int16', tmp2)
#shape_star = shape_port.copy()
shape_star = tuple(np.asarray(shape_port).copy())
#we are only going to access the portion of memory required
star_fp = io.get_mmap_data(sonpath, base, '_data_star2.dat', 'int16', shape_star)
ind_star = list(ind_star)
ind_star[-1] = np.shape(port_fp[0])[1]
ind_star = tuple(ind_star)
if old_pyread == 1: #older pyread version
# low-freq. sonar
try:
data_dwnlow = data.getlowscans().astype('int16')
except:
data_dwnlow = ''
print "low-freq. scan not available"
if data_dwnlow!='':
Zt, ind_low = makechunks_scan(chunkmode, chunkval, metadat, data_dwnlow, 2)
del data_dwnlow
# create memory mapped file for Z
shape_low = io.set_mmap_data(sonpath, base, '_data_dwnlow.dat', 'int16', Zt)
##we are only going to access the portion of memory required
dwnlow_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow.dat', 'int16', shape_low)
if old_pyread == 1: #older pyread version
# hi-freq. sonar
try:
data_dwnhi = data.gethiscans().astype('int16')
except:
data_dwnhi = ''
print "high-freq. scan not available"
if data_dwnhi!='':
Zt, ind_hi = makechunks_scan(chunkmode, chunkval, metadat, data_dwnhi, 3)
del data_dwnhi
# create memory mapped file for Z
shape_hi = io.set_mmap_data(sonpath, base, '_data_dwnhi.dat', 'int16', Zt)
dwnhi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi.dat', 'int16', shape_hi)
if 'dwnhi_fp' in locals() and 'dwnlow_fp' in locals():
# check that low and high are same size
# and trim if not
if (np.shape(dwnhi_fp)!=np.shape(dwnlow_fp)) and (chunkmode!=4):
print "dwnhi and dwnlow are different sizes ... rectifying"
if np.shape(dwnhi_fp[0])[1] > np.shape(dwnlow_fp[0])[1]:
tmp = dwnhi_fp.copy()
tmp2 = np.empty_like(dwnlow_fp)
for k in xrange(len(tmp)):
tmp2[k] = tmp[k][:,:np.shape(dwnlow_fp[k])[1]]
del tmp
# create memory mapped file for Z
shape_low = io.set_mmap_data(sonpath, base, '_data_dwnhi2.dat', 'int16', tmp2)
#shape_hi = shape_low.copy()
shape_hi = tuple(np.asarray(shape_low).copy())
##we are only going to access the portion of memory required
dwnhi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi2.dat', 'int16', shape_hi)
ind_hi = list(ind_hi)
ind_hi[-1] = np.shape(dwnlow_fp[0])[1]
ind_hi = tuple(ind_hi)
elif np.shape(dwnhi_fp[0])[1] < np.shape(dwnlow_fp[0])[1]:
tmp = dwnlow_fp.copy()
tmp2 = np.empty_like(dwnhi_fp)
for k in xrange(len(tmp)):
tmp2[k] = tmp[k][:,:np.shape(dwnhi_fp[k])[1]]
del tmp
# create memory mapped file for Z
shape_low = io.set_mmap_data(sonpath, base, '_data_dwnlow2.dat', 'int16', tmp2)
#shape_hi = shape_low.copy()
shape_hi = tuple(np.asarray(shape_low).copy())
##we are only going to access the portion of memory required
dwnlow_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow2.dat', 'int16', shape_low)
ind_low = list(ind_low)
ind_low[-1] = np.shape(dwnhi_fp[0])[1]
ind_low = tuple(ind_low)
if old_pyread == 1: #older pyread version
del data
if ('shape_port' in locals()) and (chunkmode!=4):
metadat['shape_port'] = shape_port
nrec = metadat['shape_port'][0] * metadat['shape_port'][2]
elif ('shape_port' in locals()) and (chunkmode==4):
metadat['shape_port'] = shape_port
nrec = metadat['shape_port'][1]
else:
metadat['shape_port'] = ''
if ('shape_star' in locals()) and (chunkmode!=4):
metadat['shape_star'] = shape_star
nrec = metadat['shape_star'][0] * metadat['shape_star'][2]
elif ('shape_star' in locals()) and (chunkmode==4):
metadat['shape_star'] = shape_star
nrec = metadat['shape_star'][1]
else:
metadat['shape_star'] = ''
if ('shape_hi' in locals()) and (chunkmode!=4):
metadat['shape_hi'] = shape_hi
#nrec = metadat['shape_hi'][0] * metadat['shape_hi'][2] * 2
elif ('shape_hi' in locals()) and (chunkmode==4):
metadat['shape_hi'] = shape_hi
else:
metadat['shape_hi'] = ''
if ('shape_low' in locals()) and (chunkmode!=4):
metadat['shape_low'] = shape_low
#nrec = metadat['shape_low'][0] * metadat['shape_low'][2] * 2
elif ('shape_low' in locals()) and (chunkmode==4):
metadat['shape_low'] = shape_low
else:
metadat['shape_low'] = ''
#make kml boat trackline
humutils.make_trackline(lon,lat, sonpath, base)
if 'port_fp' in locals() and 'star_fp' in locals():
#if not os.path.isfile(os.path.normpath(os.path.join(sonpath,base+'meta.mat'))):
if 2>1:
if bedpick == 1: # auto
x, bed = humutils.auto_bedpick(ft, dep_m, chunkmode, port_fp, c)
if len(dist_m)<len(bed):
dist_m = np.append(dist_m,dist_m[-1]*np.ones(len(bed)-len(dist_m)))
if doplot==1:
if chunkmode!=4:
for k in xrange(len(star_fp)):
plot_2bedpicks(port_fp[k], star_fp[k], bed[ind_port[-1]*k:ind_port[-1]*(k+1)], dist_m[ind_port[-1]*k:ind_port[-1]*(k+1)], x[ind_port[-1]*k:ind_port[-1]*(k+1)], ft, shape_port, sonpath, k, chunkmode)
else:
plot_2bedpicks(port_fp, star_fp, bed, dist_m, x, ft, shape_port, sonpath, 0, chunkmode)
# 'real' bed is estimated to be the minimum of the two
bed = np.min(np.vstack((bed[:nrec],np.squeeze(x[:nrec]))),axis=0)
bed = humutils.runningMeanFast(bed, 3)
elif bedpick>1: # user prompt
x, bed = humutils.auto_bedpick(ft, dep_m, chunkmode, port_fp, c)
if len(dist_m)<len(bed):
dist_m = np.append(dist_m,dist_m[-1]*np.ones(len(bed)-len(dist_m)))
# 'real' bed is estimated to be the minimum of the two
bed = np.min(np.vstack((bed[:nrec],np.squeeze(x[:nrec]))),axis=0)
bed = humutils.runningMeanFast(bed, 3)
# manually intervene
fig = plt.figure()
ax = plt.gca()
if chunkmode !=4:
im = ax.imshow(np.hstack(port_fp), cmap = 'gray', origin = 'upper')
else:
im = ax.imshow(port_fp, cmap = 'gray', origin = 'upper')
plt.plot(bed,'r')
plt.axis('normal'); plt.axis('tight')
pts1 = plt.ginput(n=300, timeout=30) # it will wait for 200 clicks or 60 seconds
x1=map(lambda x: x[0],pts1) # map applies the function passed as
y1=map(lambda x: x[1],pts1) # first parameter to each element of pts
plt.close()
del fig
if x1 != []: # if x1 is not empty
tree = KDTree(zip(np.arange(1,len(bed)), bed))
try:
dist, inds = tree.query(zip(x1, y1), k = 100, eps=5, n_jobs=-1)
except:
dist, inds = tree.query(zip(x1, y1), k = 100, eps=5)
b = np.interp(inds,x1,y1)
bed2 = bed.copy()
bed2[inds] = b
bed = bed2
if doplot==1:
if chunkmode!=4:
for k in xrange(len(star_fp)):
plot_2bedpicks(port_fp[k], star_fp[k], bed[ind_port[-1]*k:ind_port[-1]*(k+1)], dist_m[ind_port[-1]*k:ind_port[-1]*(k+1)], x[ind_port[-1]*k:ind_port[-1]*(k+1)], ft, shape_port, sonpath, k, chunkmode)
else:
plot_2bedpicks(port_fp, star_fp, bed, dist_m, x, ft, shape_port, sonpath, 0, chunkmode)
else: #manual
beds=[]
if chunkmode!=4:
for k in xrange(len(port_fp)):
raw_input("Bed picking "+str(k+1)+" of "+str(len(port_fp))+", are you ready? 30 seconds. Press Enter to continue...")
bed={}
fig = plt.figure()
ax = plt.gca()
im = ax.imshow(port_fp[k], cmap = 'gray', origin = 'upper')
pts1 = plt.ginput(n=300, timeout=30) # it will wait for 200 clicks or 60 seconds
x1=map(lambda x: x[0],pts1) # map applies the function passed as
y1=map(lambda x: x[1],pts1) # first parameter to each element of pts
bed = np.interp(np.r_[:ind_port[-1]],x1,y1)
plt.close()
del fig
beds.append(bed)
extent = np.shape(port_fp[k])[0]
bed = np.asarray(np.hstack(beds),'float')
else:
raw_input("Bed picking - are you ready? 30 seconds. Press Enter to continue...")
bed={}
fig = plt.figure()
ax = plt.gca()
im = ax.imshow(port_fp, cmap = 'gray', origin = 'upper')
pts1 = plt.ginput(n=300, timeout=30) # it will wait for 200 clicks or 60 seconds
x1=map(lambda x: x[0],pts1) # map applies the function passed as
y1=map(lambda x: x[1],pts1) # first parameter to each element of pts
bed = np.interp(np.r_[:ind_port[-1]],x1,y1)
plt.close()
del fig
beds.append(bed)
extent = np.shape(port_fp)[1]
bed = np.asarray(np.hstack(beds),'float')
# now revise the depth in metres
dep_m = (1/ft)*bed
if doplot==1:
if chunkmode!=4:
for k in xrange(len(star_fp)):
plot_bedpick(port_fp[k], star_fp[k], (1/ft)*bed[ind_port[-1]*k:ind_port[-1]*(k+1)], dist_m[ind_port[-1]*k:ind_port[-1]*(k+1)], ft, shape_port, sonpath, k, chunkmode)
else:
plot_bedpick(port_fp, star_fp, (1/ft)*bed, dist_m, ft, shape_port, sonpath, 0, chunkmode)
metadat['bed'] = bed[:nrec]
else:
metadat['bed'] = dep_m[:nrec]*ft
metadat['heading'] = metadat['heading'][:nrec]
metadat['lon'] = lon[:nrec]
metadat['lat'] = lat[:nrec]
metadat['dist_m'] = dist_m[:nrec]
metadat['dep_m'] = dep_m[:nrec]
metadat['pix_m'] = 1/ft
metadat['bed'] = metadat['bed'][:nrec]
metadat['c'] = c
metadat['t'] = t
metadat['f'] = f
metadat['spd'] = metadat['spd'][:nrec]
metadat['time_s'] = metadat['time_s'][:nrec]
metadat['e'] = metadat['e'][:nrec]
metadat['n'] = metadat['n'][:nrec]
metadat['es'] = metadat['es'][:nrec]
metadat['ns'] = metadat['ns'][:nrec]
metadat['caltime'] = metadat['caltime'][:nrec]
savemat(os.path.normpath(os.path.join(sonpath,base+'meta.mat')), metadat ,oned_as='row')
f = open(os.path.normpath(os.path.join(sonpath,base+'rawdat.csv')), 'wt')
writer = csv.writer(f)
writer.writerow( ('longitude', 'latitude', 'easting', 'northing', 'depth (m)', 'distance (m)', 'instr. heading (deg)', 'heading (deg.)' ) )
for i in range(0, nrec):
writer.writerow(( float(lon[i]),float(lat[i]),float(es[i]),float(ns[i]),float(dep_m[i]),float(dist_m[i]), float(metadat['instr_heading'][i]), float(metadat['heading'][i]) ))
f.close()
del lat, lon, dep_m #, dist_m
if doplot==1:
plot_pos(sonpath, metadat, es, ns)
if 'dwnlow_fp' in locals():
plot_dwnlow(dwnlow_fp, chunkmode, sonpath)
if 'dwnhi_fp' in locals():
plot_dwnhi(dwnhi_fp, chunkmode, sonpath)
if os.name=='posix': # true if linux/mac
elapsed = (time.time() - start)
else: # windows
elapsed = (time.clock() - start)
print "Processing took ", elapsed , "seconds to analyse"
print "Done!"
def correct(humfile,
sonpath,
maxW=1000,
doplot=1,
dofilt=0,
correct_withwater=0,
ph=7,
temp=10,
salinity=0,
dconcfile=None):
'''
Remove water column and carry out some rudimentary radiometric corrections,
accounting for directivity and attenuation with range
Syntax
----------
[] = PyHum.correct(humfile, sonpath, maxW, doplot, correct_withwater, ph, temp, salinity, dconcfile)
Parameters
----------
humfile : str
path to the .DAT file
sonpath : str
path where the *.SON files are
maxW : int, *optional* [Default=1000]
maximum transducer power
doplot : int, *optional* [Default=1]
1 = make plots, otherwise do not
dofilt : int, *optional* [Default=0]
1 = apply a phase preserving filter to the scans
correct_withwater : int, *optional* [Default=0]
1 = apply radiometric correction but don't remove water column from scans
ph : float, *optional* [Default=7.0]
water acidity in pH
temp : float, *optional* [Default=10.0]
water temperature in degrees Celsius
salinity : float, *optional* [Default=0.0]
salinity of water in parts per thousand
dconcfile : str, *optional* [Default=None]
file path of a text file containing sediment concentration data
this file must contain the following fields separated by spaces:
size (microns) conc (mg/L) dens (kg/m3)
with one row per grain size, for example:
30 1700 2200
100 15 2650
Returns
-------
sonpath+base+'_data_star_l.dat': memory-mapped file
contains the starboard scan with water column removed
sonpath+base+'_data_port_l.dat': memory-mapped file
contains the portside scan with water column removed
sonpath+base+'_data_star_la.dat': memory-mapped file
contains the starboard scan with water column removed and
radiometrically corrected
sonpath+base+'_data_port_la.dat': memory-mapped file
contains the portside scan with water column removed and
radiometrically corrected
sonpath+base+'_data_range.dat': memory-mapped file
contains the cosine of the range which is used to correct
for attenuation with range
sonpath+base+'_data_dwnlow_l.dat': memory-mapped file
contains the low freq. downward scan with water column removed
sonpath+base+'_data_dwnhi_l.dat': memory-mapped file
contains the high freq. downward scan with water column removed
sonpath+base+'_data_dwnlow_la.dat': memory-mapped file
contains the low freq. downward scan with water column removed and
radiometrically corrected
sonpath+base+'_data_dwnhi_la.dat': memory-mapped file
contains the high freq. downward scan with water column removed and
radiometrically corrected
if correct_withwater == 1:
sonpath+base+'_data_star_lw.dat': memory-mapped file
contains the starboard scan with water column retained and
radiometrically corrected
sonpath+base+'_data_port_lw.dat': memory-mapped file
contains the portside scan with water column retained and
radiometrically corrected
'''
# prompt user to supply file if no input file given
if not humfile:
print 'An input file is required!!!!!!'
Tk().withdraw(
) # we don't want a full GUI, so keep the root window from appearing
inputfile = askopenfilename(filetypes=[("DAT files", "*.DAT")])
# prompt user to supply directory if no input sonpath is given
if not sonpath:
print 'A *.SON directory is required!!!!!!'
Tk().withdraw(
) # we don't want a full GUI, so keep the root window from appearing
sonpath = askdirectory()
# print given arguments to screen and convert data type where necessary
if humfile:
print 'Input file is %s' % (humfile)
if sonpath:
print 'Sonar file path is %s' % (sonpath)
if maxW:
maxW = np.asarray(maxW, float)
print 'Max. transducer power is %s W' % (str(maxW))
if doplot:
doplot = int(doplot)
if doplot == 0:
print "Plots will not be made"
if dofilt:
dofilt = int(dofilt)
if dofilt == 0:
print "Phase preserving filter will not be applied"
else:
print "Phase preserving filter will be applied"
if correct_withwater:
correct_withwater = int(correct_withwater)
if correct_withwater == 1:
print "Correction will be applied without removing water column"
if salinity:
salinity = np.asarray(salinity, float)
print 'Salinity is %s ppt' % (str(salinity))
if ph:
ph = np.asarray(ph, float)
print 'pH is %s' % (str(ph))
if temp:
temp = np.asarray(temp, float)
print 'Temperature is %s' % (str(temp))
if dconcfile is not None:
try:
print 'Suspended sediment size/conc. file is %s' % (dconcfile)
dconc = np.genfromtxt(dconcfile).T
conc = dconc[1]
dens = dconc[2]
d = dconc[0]
except:
pass
#================================
# start timer
if os.name == 'posix': # true if linux/mac or cygwin on windows
start = time.time()
else: # windows
start = time.clock()
# if son path name supplied has no separator at end, put one on
if sonpath[-1] != os.sep:
sonpath = sonpath + os.sep
base = humfile.split('.DAT') # get base of file name for output
base = base[0].split(os.sep)[-1]
# remove underscores, negatives and spaces from basename
base = humutils.strip_base(base)
# add wattage to metadata dict
meta = loadmat(os.path.normpath(os.path.join(sonpath, base + 'meta.mat')))
dep_m = meta['dep_m'][0]
pix_m = meta['pix_m'][0]
meta['maxW'] = maxW
savemat(os.path.normpath(os.path.join(sonpath, base + 'meta.mat')),
meta,
oned_as='row')
bed = np.squeeze(meta['bed'])
ft = 1 / (meta['pix_m'])
dist_m = np.squeeze(meta['dist_m'])
try:
if dconcfile is not None:
# sediment attenuation
alpha = sed_atten(meta['f'], conc, dens, d, meta['c'])
else:
alpha = 0
except:
alpha = 0
# load memory mapped scans
shape_port = np.squeeze(meta['shape_port'])
if shape_port != '':
if os.path.isfile(
os.path.normpath(
os.path.join(sonpath, base + '_data_port2.dat'))):
port_fp = io.get_mmap_data(sonpath, base, '_data_port2.dat',
'int16', tuple(shape_port))
else:
port_fp = io.get_mmap_data(sonpath, base, '_data_port.dat',
'int16', tuple(shape_port))
shape_star = np.squeeze(meta['shape_star'])
if shape_star != '':
if os.path.isfile(
os.path.normpath(
os.path.join(sonpath, base + '_data_star2.dat'))):
star_fp = io.get_mmap_data(sonpath, base, '_data_star2.dat',
'int16', tuple(shape_star))
else:
star_fp = io.get_mmap_data(sonpath, base, '_data_star.dat',
'int16', tuple(shape_star))
if len(shape_star) == 2:
extent = shape_star[0]
else:
extent = shape_star[1] #np.shape(data_port)[0]
bed = np.asarray(bed, 'int') + int(0.25 * ft)
# calculate in dB
######### star
Zt, R, A = remove_water(star_fp, bed, shape_star, dep_m, pix_m, 1, maxW)
Zt = np.squeeze(Zt)
# create memory mapped file for Z)
shape_star = io.set_mmap_data(sonpath, base, '_data_star_l.dat', 'float32',
Zt)
del Zt
A = np.squeeze(A)
# create memory mapped file for A
shape_A = io.set_mmap_data(sonpath, base, '_data_incidentangle.dat',
'float32', A)
del A
R = np.squeeze(R)
R[np.isnan(R)] = 0
try:
alpha_w = water_atten(R, meta['f'], meta['c'], ph, temp, salinity)
except:
alpha_w = 1e-5
# compute transmission losses
TL = (40 * np.log10(R) + alpha_w + (2 * alpha) * R / 1000) / 255
del alpha_w
# create memory mapped file for R
shape_R = io.set_mmap_data(sonpath, base, '_data_range.dat', 'float32', R)
del R
TL[np.isnan(TL)] = 0
TL[TL < 0] = 0
shape_TL = io.set_mmap_data(sonpath, base, '_data_TL.dat', 'float32', TL)
del TL
A_fp = io.get_mmap_data(sonpath, base, '_data_incidentangle.dat',
'float32', shape_star)
TL_fp = io.get_mmap_data(sonpath, base, '_data_TL.dat', 'float32',
shape_star)
R_fp = io.get_mmap_data(sonpath, base, '_data_range.dat', 'float32',
shape_star)
if correct_withwater == 1:
Zt = correct_scans(star_fp, A_fp, TL_fp, dofilt)
# create memory mapped file for Z)
shape_star = io.set_mmap_data(sonpath, base, '_data_star_lw.dat',
'float32', Zt)
#we are only going to access the portion of memory required
star_fp = io.get_mmap_data(sonpath, base, '_data_star_l.dat', 'float32',
shape_star)
##Zt = correct_scans(star_fp, A_fp, TL_fp, dofilt)
#phi=1.69
alpha = 59 # vertical beam width at 3db
theta = 35 #opening angle theta
# lambertian correction
Zt = correct_scans_lambertian(star_fp, A_fp, TL_fp, R_fp, meta['c'],
meta['f'], theta, alpha)
Zt = np.squeeze(Zt)
avg = np.nanmedian(Zt, axis=1)
Zt2 = np.empty(np.shape(Zt))
for kk in xrange(np.shape(Zt)[1]):
Zt2[:, kk] = (Zt[:, kk] - avg) + np.nanmean(avg)
Zt2[Zt <= 0] = np.nan
Zt2[Zt2 <= 0] = np.nan
del Zt
# create memory mapped file for Z
shape_star = io.set_mmap_data(sonpath, base, '_data_star_la.dat',
'float32', Zt2)
del Zt2
#we are only going to access the portion of memory required
star_fp = io.get_mmap_data(sonpath, base, '_data_star_la.dat', 'float32',
shape_star)
######### port
if correct_withwater == 1:
Zt = correct_scans(port_fp, A_fp, TL, dofilt)
# create memory mapped file for Z)
shape_port = io.set_mmap_data(sonpath, base, '_data_port_lw.dat',
'float32', Zt)
Zt = remove_water(port_fp, bed, shape_port, dep_m, pix_m, 0, maxW)
Zt = np.squeeze(Zt)
# create memory mapped file for Z
shape_port = io.set_mmap_data(sonpath, base, '_data_port_l.dat', 'float32',
Zt)
#we are only going to access the portion of memory required
port_fp = io.get_mmap_data(sonpath, base, '_data_port_l.dat', 'float32',
shape_port)
##Zt = correct_scans(port_fp, A_fp, TL_fp, dofilt)
# lambertian correction
Zt = correct_scans_lambertian(port_fp, A_fp, TL_fp, R_fp, meta['c'],
meta['f'], theta, alpha)
Zt = np.squeeze(Zt)
Zt2 = np.empty(np.shape(Zt))
for kk in xrange(np.shape(Zt)[1]):
Zt2[:, kk] = (Zt[:, kk] - avg) + np.nanmean(avg)
Zt2[Zt <= 0] = np.nan
Zt2[Zt2 <= 0] = np.nan
del Zt
# create memory mapped file for Z
shape_port = io.set_mmap_data(sonpath, base, '_data_port_la.dat',
'float32', Zt2)
del Zt2
#we are only going to access the portion of memory required
port_fp = io.get_mmap_data(sonpath, base, '_data_port_la.dat', 'float32',
shape_port)
## do plots of merged scans
if doplot == 1:
if correct_withwater == 1:
port_fpw = io.get_mmap_data(sonpath, base, '_data_port_lw.dat',
'float32', shape_port)
star_fpw = io.get_mmap_data(sonpath, base, '_data_star_lw.dat',
'float32', shape_star)
if len(np.shape(star_fpw)) > 2:
for p in xrange(len(star_fpw)):
plot_merged_scans(port_fpw[p], star_fpw[p], dist_m,
shape_port, ft, sonpath, p)
else:
plot_merged_scans(port_fpw, star_fpw, dist_m, shape_port, ft,
sonpath, 0)
else:
if len(np.shape(star_fp)) > 2:
for p in xrange(len(star_fp)):
plot_merged_scans(port_fp[p], star_fp[p], dist_m,
shape_port, ft, sonpath, p)
else:
plot_merged_scans(port_fp, star_fp, dist_m, shape_port, ft,
sonpath, 0)
# load memory mapped scans
shape_low = np.squeeze(meta['shape_low'])
shape_hi = np.squeeze(meta['shape_hi'])
if shape_low != '':
if os.path.isfile(
os.path.normpath(
os.path.join(sonpath, base + '_data_dwnlow2.dat'))):
try:
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow2.dat',
'int16', tuple(shape_low))
except:
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow.dat',
'int16', tuple(shape_low))
finally:
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow.dat',
'int16', tuple(shape_hi))
#if 'shape_hi' in locals():
# low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow2.dat', 'int16', tuple(shape_hi))
else:
try:
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow.dat',
'int16', tuple(shape_low))
except:
if 'shape_hi' in locals():
low_fp = io.get_mmap_data(sonpath, base,
'_data_dwnlow.dat', 'int16',
tuple(shape_hi))
shape_hi = np.squeeze(meta['shape_hi'])
if shape_hi != '':
if os.path.isfile(
os.path.normpath(
os.path.join(sonpath, base + '_data_dwnhi2.dat'))):
try:
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi2.dat',
'int16', tuple(shape_hi))
except:
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi.dat',
'int16', tuple(shape_hi))
finally:
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi.dat',
'int16', tuple(shape_low))
#if 'shape_low' in locals():
# hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi2.dat', 'int16', tuple(shape_low))
else:
try:
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi.dat',
'int16', tuple(shape_hi))
except:
if 'shape_low' in locals():
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi.dat',
'int16', tuple(shape_low))
if 'low_fp' in locals():
######### low
Zt = remove_water(low_fp, bed, shape_low, dep_m, pix_m, 0, maxW)
Zt = np.squeeze(Zt)
# create memory mapped file for Z
shape_low = io.set_mmap_data(sonpath, base, '_data_dwnlow_l.dat',
'float32', Zt)
del Zt
#we are only going to access the portion of memory required
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow_l.dat',
'float32', shape_low)
Zt = correct_scans2(low_fp, TL_fp)
# create memory mapped file for Z
shape_low = io.set_mmap_data(sonpath, base, '_data_dwnlow_la.dat',
'float32', Zt)
del Zt
#we are only going to access the lowion of memory required
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow_la.dat',
'float32', shape_low)
if doplot == 1:
if len(np.shape(low_fp)) > 2:
for p in xrange(len(low_fp)):
plot_dwnlow_scans(low_fp[p], dist_m, shape_low, ft,
sonpath, p)
else:
plot_dwnlow_scans(low_fp, dist_m, shape_low, ft, sonpath, 0)
if 'hi_fp' in locals():
######### hi
Zt = remove_water(hi_fp, bed, shape_hi, dep_m, pix_m, 0, maxW)
Zt = np.squeeze(Zt)
# create memory mapped file for Z
shape_hi = io.set_mmap_data(sonpath, base, '_data_dwnhi_l.dat',
'float32', Zt)
del Zt
#we are only going to access the portion of memory required
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi_l.dat', 'float32',
shape_hi)
Zt = correct_scans2(hi_fp, TL_fp)
# create memory mapped file for Z
shape_hi = io.set_mmap_data(sonpath, base, '_data_dwnhi_la.dat',
'float32', Zt)
del Zt
#we are only going to access the hiion of memory required
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi_la.dat',
'float32', shape_hi)
if doplot == 1:
if len(np.shape(hi_fp)) > 2:
for p in xrange(len(hi_fp)):
plot_dwnhi_scans(hi_fp[p], dist_m, shape_hi, ft, sonpath,
p)
else:
plot_dwnhi_scans(hi_fp, dist_m, shape_hi, ft, sonpath, 0)
if os.name == 'posix': # true if linux/mac
elapsed = (time.time() - start)
else: # windows
elapsed = (time.clock() - start)
print "Processing took ", elapsed, "seconds to analyse"
print "Done!"
def sliding_window(a,ws,ss = None,flatten = True):
'''
Return a sliding window over a in any number of dimensions
'''
if None is ss:
# ss was not provided. the windows will not overlap in any direction.
ss = ws
ws = norm_shape(ws)
ss = norm_shape(ss)
# convert ws, ss, and a.shape to numpy arrays
ws = np.array(ws)
ss = np.array(ss)
import PyHum.io as io
shape_tmp = io.set_mmap_data('', '', 'tmp.dat', 'float32', a)
del a
a = io.get_mmap_data('', '', 'tmp.dat', 'float32', shape_tmp)
shap = np.array(a.shape)
try:
os.remove('tmp.dat')
except:
pass
# ensure that ws, ss, and a.shape all have the same number of dimensions
ls = [len(shap),len(ws),len(ss)]
if 1 != len(set(ls)):
raise ValueError(\
'a.shape, ws and ss must all have the same length. They were %s' % str(ls))
# ensure that ws is smaller than a in every dimension
if np.any(ws > shap):
raise ValueError(\
'ws cannot be larger than a in any dimension.\
a.shape was %s and ws was %s' % (str(a.shape),str(ws)))
# how many slices will there be in each dimension?
newshape = norm_shape(((shap - ws) // ss) + 1)
# the shape of the strided array will be the number of slices in each dimension
# plus the shape of the window (tuple addition)
newshape += norm_shape(ws)
# the strides tuple will be the array's strides multiplied by step size, plus
try:
# the array's strides (tuple addition)
newstrides = norm_shape(np.array(a.strides) * ss) + a.strides
a = ast(a,shape = newshape,strides = newstrides)
if not flatten:
return a
# Collapse strided so that it has one more dimension than the window. I.e.,
# the new array is a flat list of slices.
meat = len(ws) if ws.shape else 0
firstdim = (int(np.product(newshape[:-meat])),) if ws.shape else ()
dim = firstdim + (newshape[-meat:])
# remove any dimensions with size 1
dim = filter(lambda i : i != 1,dim)
return a.reshape(dim), newshape
except:
from itertools import product
print("memory error, windowing using slower method")
# For each dimension, create a list of all valid slices
slices = [[] for i in range(len(ws))]
for i in range(len(ws)):
nslices = ((shap[i] - ws[i]) // ss[i]) + 1
for j in range(0,nslices):
start = j * ss[i]
stop = start + ws[i]
slices[i].append(slice(start,stop))
# Get an iterator over all valid n-dimensional slices of the input
allslices = product(*slices)
# Allocate memory to hold all valid n-dimensional slices
nslices = np.product([len(s) for s in slices])
#out = np.ndarray((nslices,) + tuple(ws),dtype = a.dtype)
out=[]
for i,s in enumerate(allslices):
#out[i] = a[s]
out.append(a[s])
del a
import dask.bag as db
tmp = db.from_sequence(out, npartitions=1000)
del out
return tmp.compute(), newshape
def correct(humfile, sonpath, maxW, doplot, dofilt, correct_withwater, ph, temp, salinity, dconcfile):
'''
Remove water column and carry out some rudimentary radiometric corrections,
accounting for directivity and attenuation with range
Syntax
----------
[] = PyHum.correct(humfile, sonpath, maxW, doplot, correct_withwater, ph, temp, salinity, dconcfile)
Parameters
----------
humfile : str
path to the .DAT file
sonpath : str
path where the *.SON files are
maxW : int, *optional* [Default=1000]
maximum transducer power
doplot : int, *optional* [Default=1]
1 = make plots, otherwise do not
dofilt : int, *optional* [Default=0]
1 = apply a phase preserving filter to the scans
correct_withwater : int, *optional* [Default=0]
1 = apply radiometric correction but don't remove water column from scans
ph : float, *optional* [Default=7.0]
water acidity in pH
temp : float, *optional* [Default=10.0]
water temperature in degrees Celsius
salinity : float, *optional* [Default=0.0]
salinity of water in parts per thousand
dconcfile : str, *optional* [Default=None]
file path of a text file containing sediment concentration data
this file must contain the following fields separated by spaces:
size (microns) conc (mg/L) dens (kg/m3)
with one row per grain size, for example:
30 1700 2200
100 15 2650
Returns
-------
sonpath+base+'_data_star_l.dat': memory-mapped file
contains the starboard scan with water column removed
sonpath+base+'_data_port_l.dat': memory-mapped file
contains the portside scan with water column removed
sonpath+base+'_data_star_la.dat': memory-mapped file
contains the starboard scan with water column removed and
radiometrically corrected
sonpath+base+'_data_port_la.dat': memory-mapped file
contains the portside scan with water column removed and
radiometrically corrected
sonpath+base+'_data_range.dat': memory-mapped file
contains the cosine of the range which is used to correct
for attenuation with range
sonpath+base+'_data_dwnlow_l.dat': memory-mapped file
contains the low freq. downward scan with water column removed
sonpath+base+'_data_dwnhi_l.dat': memory-mapped file
contains the high freq. downward scan with water column removed
sonpath+base+'_data_dwnlow_la.dat': memory-mapped file
contains the low freq. downward scan with water column removed and
radiometrically corrected
sonpath+base+'_data_dwnhi_la.dat': memory-mapped file
contains the high freq. downward scan with water column removed and
radiometrically corrected
if correct_withwater == 1:
sonpath+base+'_data_star_lw.dat': memory-mapped file
contains the starboard scan with water column retained and
radiometrically corrected
sonpath+base+'_data_port_lw.dat': memory-mapped file
contains the portside scan with water column retained and
radiometrically corrected
'''
# prompt user to supply file if no input file given
if not humfile:
print('An input file is required!!!!!!')
Tk().withdraw() # we don't want a full GUI, so keep the root window from appearing
inputfile = askopenfilename(filetypes=[("DAT files","*.DAT")])
# prompt user to supply directory if no input sonpath is given
if not sonpath:
print('A *.SON directory is required!!!!!!')
Tk().withdraw() # we don't want a full GUI, so keep the root window from appearing
sonpath = askdirectory()
# print given arguments to screen and convert data type where necessary
if humfile:
print('Input file is %s' % (humfile))
if sonpath:
print('Sonar file path is %s' % (sonpath))
if maxW:
maxW = np.asarray(maxW,float)
print('Max. transducer power is %s W' % (str(maxW)))
if doplot:
doplot = int(doplot)
if doplot==0:
print("Plots will not be made")
if dofilt:
dofilt = int(dofilt)
if dofilt==0:
print("Phase preserving filter will not be applied")
else:
print("Phase preserving filter will be applied")
if correct_withwater:
correct_withwater = int(correct_withwater)
if correct_withwater==1:
print("Correction will be applied without removing water column")
if salinity:
salinity = np.asarray(salinity,float)
print('Salinity is %s ppt' % (str(salinity)))
if ph:
ph = np.asarray(ph,float)
print('pH is %s' % (str(ph)))
if temp:
temp = np.asarray(temp,float)
print('Temperature is %s' % (str(temp)))
if dconcfile is not None:
try:
print('Suspended sediment size/conc. file is %s' % (dconcfile))
dconc = np.genfromtxt(dconcfile).T
conc = dconc[1]
dens = dconc[2]
d = dconc[0]
except:
pass
#================================
# start timer
if os.name=='posix': # true if linux/mac or cygwin on windows
start = time.time()
else: # windows
start = time.clock()
# if son path name supplied has no separator at end, put one on
if sonpath[-1]!=os.sep:
sonpath = sonpath + os.sep
base = humfile.split('.DAT') # get base of file name for output
base = base[0].split(os.sep)[-1]
# remove underscores, negatives and spaces from basename
base = humutils.strip_base(base)
# add wattage to metadata dict
meta = loadmat(os.path.normpath(os.path.join(sonpath,base+'meta.mat')))
dep_m = meta['dep_m'][0]
pix_m = meta['pix_m'][0]
meta['maxW'] = maxW
savemat(os.path.normpath(os.path.join(sonpath,base+'meta.mat')), meta ,oned_as='row')
bed = np.squeeze(meta['bed'])
ft = 1/(meta['pix_m'])
dist_m = np.squeeze(meta['dist_m'])
try:
if dconcfile is not None:
# sediment attenuation
alpha = sed_atten(meta['f'],conc,dens,d,meta['c'])
else:
alpha = 0
except:
alpha = 0
# load memory mapped scans
shape_port = np.squeeze(meta['shape_port'])
if shape_port!='':
if os.path.isfile(os.path.normpath(os.path.join(sonpath,base+'_data_port2.dat'))):
port_fp = io.get_mmap_data(sonpath, base, '_data_port2.dat', 'int16', tuple(shape_port))
else:
port_fp = io.get_mmap_data(sonpath, base, '_data_port.dat', 'int16', tuple(shape_port))
shape_star = np.squeeze(meta['shape_star'])
if shape_star!='':
if os.path.isfile(os.path.normpath(os.path.join(sonpath,base+'_data_star2.dat'))):
star_fp = io.get_mmap_data(sonpath, base, '_data_star2.dat', 'int16', tuple(shape_star))
else:
star_fp = io.get_mmap_data(sonpath, base, '_data_star.dat', 'int16', tuple(shape_star))
if len(shape_star)==2:
extent = shape_star[0]
else:
extent = shape_star[1] #np.shape(data_port)[0]
bed = np.asarray(bed,'int')+int(0.25*ft)
# calculate in dB
######### star
Zt, R, A = remove_water(star_fp, bed, shape_star, dep_m, pix_m, 1, maxW)
Zt = np.squeeze(Zt)
# create memory mapped file for Z)
shape_star = io.set_mmap_data(sonpath, base, '_data_star_l.dat', 'float32', Zt)
del Zt
A = np.squeeze(A)
# create memory mapped file for A
shape_A = io.set_mmap_data(sonpath, base, '_data_incidentangle.dat', 'float32', A)
del A
R = np.squeeze(R)
R[np.isnan(R)] = 0
try:
alpha_w = water_atten(R,meta['f'],meta['c'], ph, temp, salinity)
except:
alpha_w = 1e-5
# compute transmission losses
TL = (40 * np.log10(R) + alpha_w + (2*alpha)*R/1000)/255
del alpha_w
# create memory mapped file for R
shape_R = io.set_mmap_data(sonpath, base, '_data_range.dat', 'float32', R)
del R
TL[np.isnan(TL)] = 0
TL[TL<0] = 0
shape_TL = io.set_mmap_data(sonpath, base, '_data_TL.dat', 'float32', TL)
del TL
A_fp = io.get_mmap_data(sonpath, base, '_data_incidentangle.dat', 'float32', shape_star)
TL_fp = io.get_mmap_data(sonpath, base, '_data_TL.dat', 'float32', shape_star)
R_fp = io.get_mmap_data(sonpath, base, '_data_range.dat', 'float32', shape_star)
if correct_withwater == 1:
Zt = correct_scans(star_fp, A_fp, TL_fp, dofilt)
# create memory mapped file for Z)
shape_star = io.set_mmap_data(sonpath, base, '_data_star_lw.dat', 'float32', Zt)
#we are only going to access the portion of memory required
star_fp = io.get_mmap_data(sonpath, base, '_data_star_l.dat', 'float32', shape_star)
##Zt = correct_scans(star_fp, A_fp, TL_fp, dofilt)
#phi=1.69
alpha=59 # vertical beam width at 3db
theta=35 #opening angle theta
# lambertian correction
Zt = correct_scans_lambertian(star_fp, A_fp, TL_fp, R_fp, meta['c'], meta['f'], theta, alpha)
Zt = np.squeeze(Zt)
avg = np.nanmedian(Zt,axis=0)
##avg = median_filter(avg,int(len(avg)/10))
Zt2 = Zt-avg + np.nanmean(avg)
Zt2 = Zt2 + np.abs(np.nanmin(Zt2))
try:
Zt2 = median_filter(Zt2, (3,3))
except:
pass
##Zt2 = np.empty(np.shape(Zt))
##for kk in range(np.shape(Zt)[1]):
## Zt2[:,kk] = (Zt[:,kk] - avg) + np.nanmean(avg)
##Zt2[Zt<=0] = np.nan
##Zt2[Zt2<=0] = np.nan
del Zt
# create memory mapped file for Z
shape_star = io.set_mmap_data(sonpath, base, '_data_star_la.dat', 'float32', Zt2)
del Zt2
#we are only going to access the portion of memory required
star_fp = io.get_mmap_data(sonpath, base, '_data_star_la.dat', 'float32', shape_star)
######### port
if correct_withwater == 1:
Zt = correct_scans(port_fp, A_fp, TL, dofilt)
# create memory mapped file for Z)
shape_port = io.set_mmap_data(sonpath, base, '_data_port_lw.dat', 'float32', Zt)
Zt = remove_water(port_fp, bed, shape_port, dep_m, pix_m, 0, maxW)
Zt = np.squeeze(Zt)
# create memory mapped file for Z
shape_port = io.set_mmap_data(sonpath, base, '_data_port_l.dat', 'float32', Zt)
#we are only going to access the portion of memory required
port_fp = io.get_mmap_data(sonpath, base, '_data_port_l.dat', 'float32', shape_port)
##Zt = correct_scans(port_fp, A_fp, TL_fp, dofilt)
# lambertian correction
Zt = correct_scans_lambertian(port_fp, A_fp, TL_fp, R_fp, meta['c'], meta['f'], theta, alpha)
Zt = np.squeeze(Zt)
Zt2 = Zt-avg + np.nanmean(avg)
Zt2 = Zt2 + np.abs(np.nanmin(Zt2))
##Zt2 = np.empty(np.shape(Zt))
##for kk in range(np.shape(Zt)[1]):
## Zt2[:,kk] = (Zt[:,kk] - avg) + np.nanmean(avg)
##Zt2[Zt<=0] = np.nan
##Zt2[Zt2<=0] = np.nan
del Zt
# create memory mapped file for Z
shape_port = io.set_mmap_data(sonpath, base, '_data_port_la.dat', 'float32', Zt2)
del Zt2
#we are only going to access the portion of memory required
port_fp = io.get_mmap_data(sonpath, base, '_data_port_la.dat', 'float32', shape_port)
## do plots of merged scans
if doplot==1:
if correct_withwater == 1:
port_fpw = io.get_mmap_data(sonpath, base, '_data_port_lw.dat', 'float32', shape_port)
star_fpw = io.get_mmap_data(sonpath, base, '_data_star_lw.dat', 'float32', shape_star)
if len(np.shape(star_fpw))>2:
for p in range(len(star_fpw)):
plot_merged_scans(port_fpw[p], star_fpw[p], dist_m, shape_port, ft, sonpath, p)
else:
plot_merged_scans(port_fpw, star_fpw, dist_m, shape_port, ft, sonpath, 0)
else:
if len(np.shape(star_fp))>2:
for p in range(len(star_fp)):
plot_merged_scans(port_fp[p], star_fp[p], dist_m, shape_port, ft, sonpath, p)
else:
plot_merged_scans(port_fp, star_fp, dist_m, shape_port, ft, sonpath, 0)
# load memory mapped scans
shape_low = np.squeeze(meta['shape_low'])
shape_hi = np.squeeze(meta['shape_hi'])
if shape_low!='':
if os.path.isfile(os.path.normpath(os.path.join(sonpath,base+'_data_dwnlow2.dat'))):
try:
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow2.dat', 'int16', tuple(shape_low))
except:
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow.dat', 'int16', tuple(shape_low))
finally:
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow.dat', 'int16', tuple(shape_hi))
#if 'shape_hi' in locals():
# low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow2.dat', 'int16', tuple(shape_hi))
else:
try:
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow.dat', 'int16', tuple(shape_low))
except:
if 'shape_hi' in locals():
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow.dat', 'int16', tuple(shape_hi))
shape_hi = np.squeeze(meta['shape_hi'])
if shape_hi!='':
if os.path.isfile(os.path.normpath(os.path.join(sonpath,base+'_data_dwnhi2.dat'))):
try:
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi2.dat', 'int16', tuple(shape_hi))
except:
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi.dat', 'int16', tuple(shape_hi))
finally:
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi.dat', 'int16', tuple(shape_low))
#if 'shape_low' in locals():
# hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi2.dat', 'int16', tuple(shape_low))
else:
try:
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi.dat', 'int16', tuple(shape_hi))
except:
if 'shape_low' in locals():
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi.dat', 'int16', tuple(shape_low))
if 'low_fp' in locals():
######### low
Zt = remove_water(low_fp, bed, shape_low, dep_m, pix_m, 0, maxW)
Zt = np.squeeze(Zt)
# create memory mapped file for Z
shape_low = io.set_mmap_data(sonpath, base, '_data_dwnlow_l.dat', 'float32', Zt)
del Zt
#we are only going to access the portion of memory required
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow_l.dat', 'float32', shape_low)
Zt = correct_scans2(low_fp, TL_fp)
# create memory mapped file for Z
shape_low = io.set_mmap_data(sonpath, base, '_data_dwnlow_la.dat', 'float32', Zt)
del Zt
#we are only going to access the lowion of memory required
low_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow_la.dat', 'float32', shape_low)
if doplot==1:
if len(np.shape(low_fp))>2:
for p in range(len(low_fp)):
plot_dwnlow_scans(low_fp[p], dist_m, shape_low, ft, sonpath, p)
else:
plot_dwnlow_scans(low_fp, dist_m, shape_low, ft, sonpath, 0)
if 'hi_fp' in locals():
######### hi
Zt = remove_water(hi_fp, bed, shape_hi, dep_m, pix_m, 0, maxW)
Zt = np.squeeze(Zt)
# create memory mapped file for Z
shape_hi = io.set_mmap_data(sonpath, base, '_data_dwnhi_l.dat', 'float32', Zt)
del Zt
#we are only going to access the portion of memory required
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi_l.dat', 'float32', shape_hi)
Zt = correct_scans2(hi_fp, TL_fp)
# create memory mapped file for Z
shape_hi = io.set_mmap_data(sonpath, base, '_data_dwnhi_la.dat', 'float32', Zt)
del Zt
#we are only going to access the hiion of memory required
hi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi_la.dat', 'float32', shape_hi)
if doplot==1:
if len(np.shape(hi_fp))>2:
for p in range(len(hi_fp)):
plot_dwnhi_scans(hi_fp[p], dist_m, shape_hi, ft, sonpath, p)
else:
plot_dwnhi_scans(hi_fp, dist_m, shape_hi, ft, sonpath, 0)
if os.name=='posix': # true if linux/mac
elapsed = (time.time() - start)
else: # windows
elapsed = (time.clock() - start)
print("Processing took "+ str(elapsed) + "seconds to analyse")
print("Done!")
print("===================================================")
def read(humfile, sonpath, cs2cs_args, c, draft, doplot, t, bedpick, flip_lr, model, calc_bearing, filt_bearing, chunk): #cog = 1,
'''
Read a .DAT and associated set of .SON files recorded by a Humminbird(R)
instrument.
Parse the data into a set of memory mapped files that will
subsequently be used by the other functions of the PyHum module.
Export time-series data and metadata in other formats.
Create a kml file for visualising boat track
Syntax
----------
[] = PyHum.read(humfile, sonpath, cs2cs_args, c, draft, doplot, t, bedpick, flip_lr, chunksize, model, calc_bearing, filt_bearing, chunk)
Parameters
------------
humfile : str
path to the .DAT file
sonpath : str
path where the *.SON files are
cs2cs_args : int, *optional* [Default="epsg:26949"]
arguments to create coordinates in a projected coordinate system
this argument gets given to pyproj to turn wgs84 (lat/lon) coordinates
into any projection supported by the proj.4 libraries
c : float, *optional* [Default=1450.0]
speed of sound in water (m/s). Defaults to a value of freshwater
draft : float, *optional* [Default=0.3]
draft from water surface to transducer face (m)
doplot : float, *optional* [Default=1]
if 1, plots will be made
t : float, *optional* [Default=0.108]
length of transducer array (m).
Default value is that of the 998 series Humminbird(R)
bedpick : int, *optional* [Default=1]
if 1, bedpicking with be carried out automatically
if 0, user will be prompted to pick the bed location on screen
flip_lr : int, *optional* [Default=0]
if 1, port and starboard scans will be flipped
(for situations where the transducer is flipped 180 degrees)
model: int, *optional* [Default=998]
A 3 or 4 number code indicating the model number
Examples: 998, 997, 1198, 1199
calc_bearing : float, *optional* [Default=0]
if 1, bearing will be calculated from coordinates
filt_bearing : float, *optional* [Default=0]
if 1, bearing will be filtered
chunk : str, *optional* [Default='d100' (distance, 100 m)]
letter, followed by a number.
There are the following letter options:
'd' - parse chunks based on distance, then number which is distance in m
'p' - parse chunks based on number of pings, then number which is number of pings
'h' - parse chunks based on change in heading, then number which is the change in heading in degrees
'1' - process just 1 chunk
Returns
---------
sonpath+base+'_data_port.dat': memory-mapped file
contains the raw echogram from the port side
sidescan sonar (where present)
sonpath+base+'_data_port.dat': memory-mapped file
contains the raw echogram from the starboard side
sidescan sonar (where present)
sonpath+base+'_data_dwnhi.dat': memory-mapped file
contains the raw echogram from the high-frequency
echosounder (where present)
sonpath+base+'_data_dwnlow.dat': memory-mapped file
contains the raw echogram from the low-frequency
echosounder (where present)
sonpath+base+"trackline.kml": google-earth kml file
contains the trackline of the vessel during data
acquisition
sonpath+base+'rawdat.csv': comma separated value file
contains time-series data. columns corresponding to
longitude
latitude
easting (m)
northing (m)
depth to bed (m)
alongtrack cumulative distance (m)
vessel heading (deg.)
sonpath+base+'meta.mat': .mat file
matlab format file containing a dictionary object
holding metadata information. Fields are:
e : ndarray, easting (m)
n : ndarray, northing (m)
es : ndarray, low-pass filtered easting (m)
ns : ndarray, low-pass filtered northing (m)
lat : ndarray, latitude
lon : ndarray, longitude
shape_port : tuple, shape of port scans in memory mapped file
shape_star : tuple, shape of starboard scans in memory mapped file
shape_hi : tuple, shape of high-freq. scans in memory mapped file
shape_low : tuple, shape of low-freq. scans in memory mapped file
dep_m : ndarray, depth to bed (m)
dist_m : ndarray, distance along track (m)
heading : ndarray, heading of vessel (deg. N)
pix_m: float, size of 1 pixel in across-track dimension (m)
bed : ndarray, depth to bed (m)
c : float, speed of sound in water (m/s)
t : length of sidescan transducer array (m)
spd : ndarray, vessel speed (m/s)
time_s : ndarray, time elapsed (s)
caltime : ndarray, unix epoch time (s)
'''
# prompt user to supply file if no input file given
if not humfile:
print('An input file is required!!!!!!')
Tk().withdraw() # we don't want a full GUI, so keep the root window from appearing
humfile = askopenfilename(filetypes=[("DAT files","*.DAT")])
# prompt user to supply directory if no input sonpath is given
if not sonpath:
print('A *.SON directory is required!!!!!!')
Tk().withdraw() # we don't want a full GUI, so keep the root window from appearing
sonpath = askdirectory()
# print given arguments to screen and convert data type where necessary
if humfile:
print('Input file is %s' % (humfile))
if sonpath:
print('Son files are in %s' % (sonpath))
if cs2cs_args:
print('cs2cs arguments are %s' % (cs2cs_args))
if draft:
draft = float(draft)
print('Draft: %s' % (str(draft)))
if c:
c = float(c)
print('Celerity of sound: %s m/s' % (str(c)))
if doplot:
doplot = int(doplot)
if doplot==0:
print("Plots will not be made")
if flip_lr:
flip_lr = int(flip_lr)
if flip_lr==1:
print("Port and starboard will be flipped")
if t:
t = np.asarray(t,float)
print('Transducer length is %s m' % (str(t)))
if bedpick:
bedpick = np.asarray(bedpick,int)
if bedpick==1:
print('Bed picking is auto')
elif bedpick==0:
print('Bed picking is manual')
else:
print('User will be prompted per chunk about bed picking method')
if chunk:
chunk = str(chunk)
if chunk[0]=='d':
chunkmode=1
chunkval = int(chunk[1:])
print('Chunks based on distance of %s m' % (str(chunkval)))
elif chunk[0]=='p':
chunkmode=2
chunkval = int(chunk[1:])
print('Chunks based on %s pings' % (str(chunkval)))
elif chunk[0]=='h':
chunkmode=3
chunkval = int(chunk[1:])
print('Chunks based on heading devation of %s degrees' % (str(chunkval)))
elif chunk[0]=='1':
chunkmode=4
chunkval = 1
print('Only 1 chunk will be produced')
else:
print("Chunk mode not understood - should be 'd', 'p', or 'h' - using defaults")
chunkmode=1
chunkval = 100
print('Chunks based on distance of %s m' % (str(chunkval)))
if model:
try:
model = int(model)
print("Data is from the %s series" % (str(model)))
except:
if model=='onix':
model=0
print("Data is from the ONIX series")
elif model=='helix':
model=1
print("Data is from the HELIX series")
elif model=='mega':
model=2
print("Data is from the MEGA series")
# if cog:
# cog = int(cog)
# if cog==1:
# print "Heading based on course-over-ground"
if calc_bearing:
calc_bearing = int(calc_bearing)
if calc_bearing==1:
print("Bearing will be calculated from coordinates")
if filt_bearing:
filt_bearing = int(filt_bearing)
if filt_bearing==1:
print("Bearing will be filtered")
## for debugging
#humfile = r"test.DAT"; sonpath = "test_data"
#cs2cs_args = "epsg:26949"; doplot = 1; draft = 0
#c=1450; bedpick=1; fliplr=1; chunk = 'd100'
#model=998; cog=1; calc_bearing=0; filt_bearing=0
#if model==2:
# f = 1000
#else:
f = 455
try:
print("Checking the epsg code you have chosen for compatibility with Basemap ... ")
from mpl_toolkits.basemap import Basemap
m = Basemap(projection='merc', epsg=cs2cs_args.split(':')[1],
resolution = 'i', llcrnrlon=10, llcrnrlat=10, urcrnrlon=30, urcrnrlat=30)
del m
print("... epsg code compatible")
except (ValueError):
print("Error: the epsg code you have chosen is not compatible with Basemap")
print("please choose a different epsg code (http://spatialreference.org/)")
print("program will now close")
sys.exit()
# start timer
if os.name=='posix': # true if linux/mac or cygwin on windows
start = time.time()
else: # windows
start = time.clock()
# if son path name supplied has no separator at end, put one on
if sonpath[-1]!=os.sep:
sonpath = sonpath + os.sep
# get the SON files from this directory
sonfiles = glob.glob(sonpath+'*.SON')
if not sonfiles:
sonfiles = glob.glob(os.getcwd()+os.sep+sonpath+'*.SON')
base = humfile.split('.DAT') # get base of file name for output
base = base[0].split(os.sep)[-1]
# remove underscores, negatives and spaces from basename
base = humutils.strip_base(base)
print("WARNING: Because files have to be read in byte by byte,")
print("this could take a very long time ...")
#reading each sonfile in parallel should be faster ...
try:
o = Parallel(n_jobs = np.min([len(sonfiles), cpu_count()]), verbose=0)(delayed(getscans)(sonfiles[k], humfile, c, model, cs2cs_args) for k in range(len(sonfiles)))
X, Y, A, B = zip(*o)
for k in range(len(Y)):
if Y[k] == 'sidescan_port':
dat = A[k] #data.gethumdat()
metadat = B[k] #data.getmetadata()
if flip_lr==0:
data_port = X[k].astype('int16')
else:
data_star = X[k].astype('int16')
elif Y[k] == 'sidescan_starboard':
if flip_lr==0:
data_star = X[k].astype('int16')
else:
data_port = X[k].astype('int16')
elif Y[k] == 'down_lowfreq':
data_dwnlow = X[k].astype('int16')
elif Y[k] == 'down_highfreq':
data_dwnhi = X[k].astype('int16')
elif Y[k] == 'down_vhighfreq': #hopefully this only applies to mega systems
data_dwnhi = X[k].astype('int16')
del X, Y, A, B, o
old_pyread = 0
if 'data_port' not in locals():
data_port = ''
print("portside scan not available")
if 'data_star' not in locals():
data_star = ''
print("starboardside scan not available")
if 'data_dwnhi' not in locals():
data_dwnlow = ''
print("high-frq. downward scan not available")
if 'data_dwnlow' not in locals():
data_dwnlow = ''
print("low-frq. downward scan not available")
except: # revert back to older version if paralleleised version fails
print("something went wrong with the parallelised version of pyread ...")
try:
import pyread
except:
from . import pyread
data = pyread.pyread(sonfiles, humfile, c, model, cs2cs_args)
dat = data.gethumdat()
metadat = data.getmetadata()
old_pyread = 1
nrec = len(metadat['n'])
metadat['instr_heading'] = metadat['heading'][:nrec]
#metadat['heading'] = humutils.get_bearing(calc_bearing, filt_bearing, cog, metadat['lat'], metadat['lon'], metadat['instr_heading'])
try:
es = humutils.runningMeanFast(metadat['e'][:nrec],len(metadat['e'][:nrec])/100)
ns = humutils.runningMeanFast(metadat['n'][:nrec],len(metadat['n'][:nrec])/100)
except:
es = metadat['e'][:nrec]
ns = metadat['n'][:nrec]
metadat['es'] = es
metadat['ns'] = ns
try:
trans = pyproj.Proj(init=cs2cs_args)
except:
trans = pyproj.Proj(cs2cs_args.lstrip(), inverse=True)
lon, lat = trans(es, ns, inverse=True)
metadat['lon'] = lon
metadat['lat'] = lat
metadat['heading'] = humutils.get_bearing(calc_bearing, filt_bearing, metadat['lat'], metadat['lon'], metadat['instr_heading']) #cog
dist_m = humutils.get_dist(lat, lon)
metadat['dist_m'] = dist_m
if calc_bearing==1: # recalculate speed, m/s
ds=np.gradient(np.squeeze(metadat['time_s']))
dx=np.gradient(np.squeeze(metadat['dist_m']))
metadat['spd'] = dx[:nrec]/ds[:nrec]
# theta at 3dB in the horizontal
theta3dB = np.arcsin(c/(t*(f*1000)))
#resolution of 1 sidescan pixel to nadir
ft = (np.pi/2)*(1/theta3dB) #/ (f/455)
dep_m = humutils.get_depth(metadat['dep_m'][:nrec])
if old_pyread == 1: #older pyread version
# port scan
try:
if flip_lr==0:
data_port = data.getportscans().astype('int16')
else:
data_port = data.getstarscans().astype('int16')
except:
data_port = ''
print("portside scan not available")
if data_port!='':
Zt, ind_port = makechunks_scan(chunkmode, chunkval, metadat, data_port, 0)
del data_port
## create memory mapped file for Z
shape_port = io.set_mmap_data(sonpath, base, '_data_port.dat', 'int16', Zt)
##we are only going to access the portion of memory required
port_fp = io.get_mmap_data(sonpath, base, '_data_port.dat', 'int16', shape_port)
if old_pyread == 1: #older pyread version
# starboard scan
try:
if flip_lr==0:
data_star = data.getstarscans().astype('int16')
else:
data_star = data.getportscans().astype('int16')
except:
data_star = ''
print("starboardside scan not available")
if data_star!='':
Zt, ind_star = makechunks_scan(chunkmode, chunkval, metadat, data_star, 1)
del data_star
# create memory mapped file for Z
shape_star = io.set_mmap_data(sonpath, base, '_data_star.dat', 'int16', Zt)
star_fp = io.get_mmap_data(sonpath, base, '_data_star.dat', 'int16', shape_star)
if 'star_fp' in locals() and 'port_fp' in locals():
# check that port and starboard are same size
# and trim if not
if np.shape(star_fp)!=np.shape(port_fp):
print("port and starboard scans are different sizes ... rectifying")
if np.shape(port_fp[0])[1] > np.shape(star_fp[0])[1]:
tmp = port_fp.copy()
tmp2 = np.empty_like(star_fp)
for k in range(len(tmp)):
tmp2[k] = tmp[k][:,:np.shape(star_fp[k])[1]]
del tmp
# create memory mapped file for Z
shape_port = io.set_mmap_data(sonpath, base, '_data_port2.dat', 'int16', tmp2)
#shape_star = shape_port.copy()
shape_star = tuple(np.asarray(shape_port).copy())
##we are only going to access the portion of memory required
port_fp = io.get_mmap_data(sonpath, base, '_data_port2.dat', 'int16', shape_port)
ind_port = list(ind_port)
ind_port[-1] = np.shape(star_fp[0])[1]
ind_port = tuple(ind_port)
elif np.shape(port_fp[0])[1] < np.shape(star_fp[0])[1]:
tmp = star_fp.copy()
tmp2 = np.empty_like(port_fp)
for k in range(len(tmp)):
tmp2[k] = tmp[k][:,:np.shape(port_fp[k])[1]]
del tmp
# create memory mapped file for Z
shape_port = io.set_mmap_data(sonpath, base, '_data_star2.dat', 'int16', tmp2)
#shape_star = shape_port.copy()
shape_star = tuple(np.asarray(shape_port).copy())
#we are only going to access the portion of memory required
star_fp = io.get_mmap_data(sonpath, base, '_data_star2.dat', 'int16', shape_star)
ind_star = list(ind_star)
ind_star[-1] = np.shape(port_fp[0])[1]
ind_star = tuple(ind_star)
if old_pyread == 1: #older pyread version
# low-freq. sonar
try:
data_dwnlow = data.getlowscans().astype('int16')
except:
data_dwnlow = ''
print("low-freq. scan not available")
if data_dwnlow!='':
Zt, ind_low = makechunks_scan(chunkmode, chunkval, metadat, data_dwnlow, 2)
del data_dwnlow
# create memory mapped file for Z
shape_low = io.set_mmap_data(sonpath, base, '_data_dwnlow.dat', 'int16', Zt)
##we are only going to access the portion of memory required
dwnlow_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow.dat', 'int16', shape_low)
if old_pyread == 1: #older pyread version
# hi-freq. sonar
try:
data_dwnhi = data.gethiscans().astype('int16')
except:
data_dwnhi = ''
print("high-freq. scan not available")
if data_dwnhi!='':
Zt, ind_hi = makechunks_scan(chunkmode, chunkval, metadat, data_dwnhi, 3)
del data_dwnhi
# create memory mapped file for Z
shape_hi = io.set_mmap_data(sonpath, base, '_data_dwnhi.dat', 'int16', Zt)
dwnhi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi.dat', 'int16', shape_hi)
if 'dwnhi_fp' in locals() and 'dwnlow_fp' in locals():
# check that low and high are same size
# and trim if not
if (np.shape(dwnhi_fp)!=np.shape(dwnlow_fp)) and (chunkmode!=4):
print("dwnhi and dwnlow are different sizes ... rectifying")
if np.shape(dwnhi_fp[0])[1] > np.shape(dwnlow_fp[0])[1]:
tmp = dwnhi_fp.copy()
tmp2 = np.empty_like(dwnlow_fp)
for k in range(len(tmp)):
tmp2[k] = tmp[k][:,:np.shape(dwnlow_fp[k])[1]]
del tmp
# create memory mapped file for Z
shape_low = io.set_mmap_data(sonpath, base, '_data_dwnhi2.dat', 'int16', tmp2)
#shape_hi = shape_low.copy()
shape_hi = tuple(np.asarray(shape_low).copy())
##we are only going to access the portion of memory required
dwnhi_fp = io.get_mmap_data(sonpath, base, '_data_dwnhi2.dat', 'int16', shape_hi)
ind_hi = list(ind_hi)
ind_hi[-1] = np.shape(dwnlow_fp[0])[1]
ind_hi = tuple(ind_hi)
elif np.shape(dwnhi_fp[0])[1] < np.shape(dwnlow_fp[0])[1]:
tmp = dwnlow_fp.copy()
tmp2 = np.empty_like(dwnhi_fp)
for k in range(len(tmp)):
tmp2[k] = tmp[k][:,:np.shape(dwnhi_fp[k])[1]]
del tmp
# create memory mapped file for Z
shape_low = io.set_mmap_data(sonpath, base, '_data_dwnlow2.dat', 'int16', tmp2)
#shape_hi = shape_low.copy()
shape_hi = tuple(np.asarray(shape_low).copy())
##we are only going to access the portion of memory required
dwnlow_fp = io.get_mmap_data(sonpath, base, '_data_dwnlow2.dat', 'int16', shape_low)
ind_low = list(ind_low)
ind_low[-1] = np.shape(dwnhi_fp[0])[1]
ind_low = tuple(ind_low)
if old_pyread == 1: #older pyread version
del data
if ('shape_port' in locals()) and (chunkmode!=4):
metadat['shape_port'] = shape_port
nrec = metadat['shape_port'][0] * metadat['shape_port'][2]
elif ('shape_port' in locals()) and (chunkmode==4):
metadat['shape_port'] = shape_port
nrec = metadat['shape_port'][1]
else:
metadat['shape_port'] = ''
if ('shape_star' in locals()) and (chunkmode!=4):
metadat['shape_star'] = shape_star
nrec = metadat['shape_star'][0] * metadat['shape_star'][2]
elif ('shape_star' in locals()) and (chunkmode==4):
metadat['shape_star'] = shape_star
nrec = metadat['shape_star'][1]
else:
metadat['shape_star'] = ''
if ('shape_hi' in locals()) and (chunkmode!=4):
metadat['shape_hi'] = shape_hi
#nrec = metadat['shape_hi'][0] * metadat['shape_hi'][2] * 2
elif ('shape_hi' in locals()) and (chunkmode==4):
metadat['shape_hi'] = shape_hi
else:
metadat['shape_hi'] = ''
if ('shape_low' in locals()) and (chunkmode!=4):
metadat['shape_low'] = shape_low
#nrec = metadat['shape_low'][0] * metadat['shape_low'][2] * 2
elif ('shape_low' in locals()) and (chunkmode==4):
metadat['shape_low'] = shape_low
else:
metadat['shape_low'] = ''
#make kml boat trackline
humutils.make_trackline(lon,lat, sonpath, base)
if 'port_fp' in locals() and 'star_fp' in locals():
#if not os.path.isfile(os.path.normpath(os.path.join(sonpath,base+'meta.mat'))):
if 2>1:
if bedpick == 1: # auto
x, bed = humutils.auto_bedpick(ft, dep_m, chunkmode, port_fp, c)
if len(dist_m)<len(bed):
dist_m = np.append(dist_m,dist_m[-1]*np.ones(len(bed)-len(dist_m)))
if doplot==1:
if chunkmode!=4:
for k in range(len(star_fp)):
plot_2bedpicks(port_fp[k], star_fp[k], bed[ind_port[-1]*k:ind_port[-1]*(k+1)], dist_m[ind_port[-1]*k:ind_port[-1]*(k+1)], x[ind_port[-1]*k:ind_port[-1]*(k+1)], ft, shape_port, sonpath, k, chunkmode)
else:
plot_2bedpicks(port_fp, star_fp, bed, dist_m, x, ft, shape_port, sonpath, 0, chunkmode)
# 'real' bed is estimated to be the minimum of the two
bed = np.min(np.vstack((bed[:nrec],np.squeeze(x[:nrec]))),axis=0)
bed = humutils.runningMeanFast(bed, 3)
elif bedpick>1: # user prompt
x, bed = humutils.auto_bedpick(ft, dep_m, chunkmode, port_fp, c)
if len(dist_m)<len(bed):
dist_m = np.append(dist_m,dist_m[-1]*np.ones(len(bed)-len(dist_m)))
# 'real' bed is estimated to be the minimum of the two
bed = np.min(np.vstack((bed[:nrec],np.squeeze(x[:nrec]))),axis=0)
bed = humutils.runningMeanFast(bed, 3)
# manually intervene
fig = plt.figure()
ax = plt.gca()
if chunkmode !=4:
im = ax.imshow(np.hstack(port_fp), cmap = 'gray', origin = 'upper')
else:
im = ax.imshow(port_fp, cmap = 'gray', origin = 'upper')
plt.plot(bed,'r')
plt.axis('normal'); plt.axis('tight')
pts1 = plt.ginput(n=300, timeout=30) # it will wait for 200 clicks or 60 seconds
x1=map(lambda x: x[0],pts1) # map applies the function passed as
y1=map(lambda x: x[1],pts1) # first parameter to each element of pts
plt.close()
del fig
if x1 != []: # if x1 is not empty
tree = KDTree(zip(np.arange(1,len(bed)), bed))
try:
dist, inds = tree.query(zip(x1, y1), k = 100, eps=5, n_jobs=-1)
except:
dist, inds = tree.query(zip(x1, y1), k = 100, eps=5)
b = np.interp(inds,x1,y1)
bed2 = bed.copy()
bed2[inds] = b
bed = bed2
if doplot==1:
if chunkmode!=4:
for k in range(len(star_fp)):
plot_2bedpicks(port_fp[k], star_fp[k], bed[ind_port[-1]*k:ind_port[-1]*(k+1)], dist_m[ind_port[-1]*k:ind_port[-1]*(k+1)], x[ind_port[-1]*k:ind_port[-1]*(k+1)], ft, shape_port, sonpath, k, chunkmode)
else:
plot_2bedpicks(port_fp, star_fp, bed, dist_m, x, ft, shape_port, sonpath, 0, chunkmode)
else: #manual
beds=[]
if chunkmode!=4:
for k in range(len(port_fp)):
raw_input("Bed picking "+str(k+1)+" of "+str(len(port_fp))+", are you ready? 30 seconds. Press Enter to continue...")
bed={}
fig = plt.figure()
ax = plt.gca()
im = ax.imshow(port_fp[k], cmap = 'gray', origin = 'upper')
pts1 = plt.ginput(n=300, timeout=30) # it will wait for 200 clicks or 60 seconds
x1=map(lambda x: x[0],pts1) # map applies the function passed as
y1=map(lambda x: x[1],pts1) # first parameter to each element of pts
bed = np.interp(np.r_[:ind_port[-1]],x1,y1)
plt.close()
del fig
beds.append(bed)
extent = np.shape(port_fp[k])[0]
bed = np.asarray(np.hstack(beds),'float')
else:
raw_input("Bed picking - are you ready? 30 seconds. Press Enter to continue...")
bed={}
fig = plt.figure()
ax = plt.gca()
im = ax.imshow(port_fp, cmap = 'gray', origin = 'upper')
pts1 = plt.ginput(n=300, timeout=30) # it will wait for 200 clicks or 60 seconds
x1=map(lambda x: x[0],pts1) # map applies the function passed as
y1=map(lambda x: x[1],pts1) # first parameter to each element of pts
bed = np.interp(np.r_[:ind_port[-1]],x1,y1)
plt.close()
del fig
beds.append(bed)
extent = np.shape(port_fp)[1]
bed = np.asarray(np.hstack(beds),'float')
# now revise the depth in metres
dep_m = (1/ft)*bed
if doplot==1:
if chunkmode!=4:
for k in range(len(star_fp)):
plot_bedpick(port_fp[k], star_fp[k], (1/ft)*bed[ind_port[-1]*k:ind_port[-1]*(k+1)], dist_m[ind_port[-1]*k:ind_port[-1]*(k+1)], ft, shape_port, sonpath, k, chunkmode)
else:
plot_bedpick(port_fp, star_fp, (1/ft)*bed, dist_m, ft, shape_port, sonpath, 0, chunkmode)
metadat['bed'] = bed[:nrec]
else:
metadat['bed'] = dep_m[:nrec]*ft
metadat['heading'] = metadat['heading'][:nrec]
metadat['lon'] = lon[:nrec]
metadat['lat'] = lat[:nrec]
metadat['dist_m'] = dist_m[:nrec]
metadat['dep_m'] = dep_m[:nrec]
metadat['pix_m'] = 1/ft
metadat['bed'] = metadat['bed'][:nrec]
metadat['c'] = c
metadat['t'] = t
if model==2:
metadat['f'] = f*2
else:
metadat['f'] = f
metadat['spd'] = metadat['spd'][:nrec]
metadat['time_s'] = metadat['time_s'][:nrec]
metadat['e'] = metadat['e'][:nrec]
metadat['n'] = metadat['n'][:nrec]
metadat['es'] = metadat['es'][:nrec]
metadat['ns'] = metadat['ns'][:nrec]
try:
metadat['caltime'] = metadat['caltime'][:nrec]
except:
metadat['caltime'] = metadat['caltime']
savemat(os.path.normpath(os.path.join(sonpath,base+'meta.mat')), metadat ,oned_as='row')
f = open(os.path.normpath(os.path.join(sonpath,base+'rawdat.csv')), 'wt')
writer = csv.writer(f)
writer.writerow( ('longitude', 'latitude', 'easting', 'northing', 'depth (m)', 'distance (m)', 'instr. heading (deg)', 'heading (deg.)' ) )
for i in range(0, nrec):
writer.writerow(( float(lon[i]),float(lat[i]),float(es[i]),float(ns[i]),float(dep_m[i]),float(dist_m[i]), float(metadat['instr_heading'][i]), float(metadat['heading'][i]) ))
f.close()
del lat, lon, dep_m #, dist_m
if doplot==1:
plot_pos(sonpath, metadat, es, ns)
if 'dwnlow_fp' in locals():
plot_dwnlow(dwnlow_fp, chunkmode, sonpath)
if 'dwnhi_fp' in locals():
plot_dwnhi(dwnhi_fp, chunkmode, sonpath)
if os.name=='posix': # true if linux/mac
elapsed = (time.time() - start)
else: # windows
elapsed = (time.clock() - start)
print("Processing took "+ str(elapsed) + "seconds to analyse")
print("Done!")
print("===================================================")
def texture2(humfile, sonpath, win, doplot, numclasses):
'''
Create a texture lengthscale map using the algorithm detailed by Buscombe et al. (2015)
This textural lengthscale is not a direct measure of grain size. Rather, it is a statistical
representation that integrates over many attributes of bed texture, of which grain size is the most important.
The technique is a physically based means to identify regions of texture within a sidescan echogram,
and could provide a basis for objective, automated riverbed sediment classification.
Syntax
----------
[] = PyHum.texture(humfile, sonpath, win, doplot, numclasses)
Parameters
----------
humfile : str
path to the .DAT file
sonpath : str
path where the *.SON files are
win : int, *optional* [Default=10]
pixel in pixels of the moving window
doplot : int, *optional* [Default=1]
if 1, make plots, otherwise do not make plots
numclasses : int, *optional* [Default=4]
number of 'k means' that the texture lengthscale will be segmented into
Returns
-------
sonpath+base+'_data_class.dat': memory-mapped file
contains the texture lengthscale map
sonpath+base+'_data_kclass.dat': memory-mapped file
contains the k-means segmented texture lengthscale map
References
----------
.. [1] Buscombe, D., Grams, P.E., and Smith, S.M.C., 2015, Automated riverbed sediment
classification using low-cost sidescan sonar. Journal of Hydraulic Engineering 10.1061/(ASCE)HY.1943-7900.0001079, 06015019.
'''
# prompt user to supply file if no input file given
if not humfile:
print('An input file is required!!!!!!')
Tk().withdraw() # we don't want a full GUI, so keep the root window from appearing
humfile = askopenfilename(filetypes=[("DAT files","*.DAT")])
# prompt user to supply directory if no input sonpath is given
if not sonpath:
print('A *.SON directory is required!!!!!!')
Tk().withdraw() # we don't want a full GUI, so keep the root window from appearing
sonpath = askdirectory()
# print given arguments to screen and convert data type where necessary
if humfile:
print('Input file is %s' % (humfile))
if sonpath:
print('Sonar file path is %s' % (sonpath))
if win:
win = np.asarray(win,int)
print('Window is %s square pixels' % (str(win)))
if numclasses:
numclasses = np.asarray(numclasses,int)
print('Number of sediment classes: %s' % (str(numclasses)))
if doplot:
doplot = int(doplot)
if doplot==0:
print("Plots will not be made")
print('[Default] Number of processors is %s' % (str(cpu_count())))
########################################################
########################################################
# start timer
if os.name=='posix': # true if linux/mac or cygwin on windows
start = time.time()
else: # windows
start = time.clock()
# if son path name supplied has no separator at end, put one on
if sonpath[-1]!=os.sep:
sonpath = sonpath + os.sep
base = humfile.split('.DAT') # get base of file name for output
base = base[0].split(os.sep)[-1]
# remove underscores, negatives and spaces from basename
base = humutils.strip_base(base)
meta = loadmat(os.path.normpath(os.path.join(sonpath,base+'meta.mat')))
ft = 1/loadmat(sonpath+base+'meta.mat')['pix_m']
#pix_m = np.squeeze(meta['pix_m'])
#dep_m = np.squeeze(meta['dep_m'])
dist_m = np.squeeze(meta['dist_m'])
### port
print("processing port side ...")
# load memory mapped scan ... port
shape_port = np.squeeze(meta['shape_port'])
if shape_port!='':
if os.path.isfile(os.path.normpath(os.path.join(sonpath,base+'_data_port_lar.dat'))):
port_fp = io.get_mmap_data(sonpath, base, '_data_port_lar.dat', 'float32', tuple(shape_port))
else:
port_fp = io.get_mmap_data(sonpath, base, '_data_port_la.dat', 'float32', tuple(shape_port))
port_fp2 = io.get_mmap_data(sonpath, base, '_data_port_l.dat', 'float32', tuple(shape_port))
### star
print("processing starboard side ...")
# load memory mapped scan ... port
shape_star = np.squeeze(loadmat(sonpath+base+'meta.mat')['shape_star'])
if shape_star!='':
if os.path.isfile(os.path.normpath(os.path.join(sonpath,base+'_data_star_lar.dat'))):
star_fp = io.get_mmap_data(sonpath, base, '_data_star_lar.dat', 'float32', tuple(shape_star))
else:
star_fp = io.get_mmap_data(sonpath, base, '_data_star_la.dat', 'float32', tuple(shape_star))
star_fp2 = io.get_mmap_data(sonpath, base, '_data_star_l.dat', 'float32', tuple(shape_star))
if len(shape_star)>2:
shape = shape_port.copy()
shape[1] = shape_port[1] + shape_star[1]
else:
shape = []
shape.append(1)
shape.append(shape_port[0])
shape.append(shape_port[1])
shape[1] = shape_port[0] + shape_star[0]
# create memory mapped file for Sp
#with open(os.path.normpath(os.path.join(sonpath,base+'_data_class.dat')), 'w+') as ff:
# fp = np.memmap(ff, dtype='float32', mode='w+', shape=tuple(shape))
fp = np.zeros(tuple(shape), dtype='float32')
if len(shape_star)>2:
for p in range(len(port_fp)):
merge = np.vstack((np.flipud(port_fp[p]), star_fp[p]))
merge = denoise_tv_chambolle(merge.copy(), weight=2, multichannel=False).astype('float32')
Snn = std_convoluted(merge, win)[1]
del merge
try:
Snn = medfilt2d(Snn, (win+1,win+1))
except:
Snn = medfilt2d(Snn, (win,win))
Snn[np.isnan(np.vstack((np.flipud(port_fp[p]), star_fp[p])))] = np.nan
Snn[np.isnan(np.vstack((np.flipud(port_fp2[p]), star_fp2[p])))] = np.nan
R_fp = io.get_mmap_data(sonpath, base, '_data_range.dat', 'float32', tuple(shape_star))
R = np.vstack((np.flipud(R_fp[0]),R_fp[0]))
R = R/np.max(R)
rn = replace_nans.RN(R.astype('float64'),1000,0.01,2,'localmean')
R = rn.getdata()
del rn
Sp = (Snn**2) * np.cos(np.deg2rad(R)) /win ##**2
fp[p] = Sp.astype('float32')
del Sp
#del fp # flush data to file
shape = io.set_mmap_data(sonpath, base, '_data_class.dat', 'float32', np.squeeze(fp))
del fp
class_fp = io.get_mmap_data(sonpath, base, '_data_class.dat', 'float32', tuple(shape))
else:
merge = np.vstack((np.flipud(port_fp), star_fp))
merge = denoise_tv_chambolle(merge.copy(), weight=2, multichannel=False).astype('float32')
Snn = std_convoluted(merge, win)[1]
del merge
try:
Snn = medfilt2d(Snn, (win+1,win+1))
except:
Snn = medfilt2d(Snn, (win,win))
Snn[np.isnan(np.vstack((np.flipud(port_fp), star_fp)))] = np.nan
Snn[np.isnan(np.vstack((np.flipud(port_fp2), star_fp2)))] = np.nan
R_fp = io.get_mmap_data(sonpath, base, '_data_range.dat', 'float32', tuple(shape_star))
R = np.vstack((np.flipud(R_fp),R_fp))
R = R/np.max(R)
rn = replace_nans.RN(R.astype('float64'),1000,0.01,2,'localmean')
R = rn.getdata()
del rn
Sp = (Snn**2) * np.cos(np.deg2rad(R)) / win ##**2
shape = io.set_mmap_data(sonpath, base, '_data_class.dat', 'float32', np.squeeze(Sp))
#with open(os.path.normpath(os.path.join(sonpath,base+'_data_class.dat')), 'w+') as ff:
# np.save(ff, np.squeeze(Sp).astype('float32'))
#with open(os.path.normpath(os.path.join(sonpath,base+'_data_class.dat')), 'r') as ff:
# class_fp = np.load(ff)
#del Sp
class_fp = io.get_mmap_data(sonpath, base, '_data_class.dat', 'float32', tuple(shape))
dist_m = np.squeeze(loadmat(sonpath+base+'meta.mat')['dist_m'])
########################################################
if doplot==1:
if len(shape_star)>2:
for p in range(len(star_fp)):
plot_class(dist_m, shape_port, port_fp[p], star_fp[p], class_fp[p], ft, humfile, sonpath, base, p)
else:
plot_class(dist_m, shape_port, port_fp, star_fp, class_fp, ft, humfile, sonpath, base, 0)
if len(shape_star)>2:
for p in range(len(star_fp)):
plot_contours(dist_m, shape_port, class_fp[p], ft, humfile, sonpath, base, numclasses, p)
else:
plot_contours(dist_m, shape_port, port_fp, star_fp,class_fp, ft, humfile, sonpath, base, numclasses, 0)
#######################################################
# k-means
if len(shape_star)>2:
with open(os.path.normpath(os.path.join(sonpath,base+'_data_kclass.dat')), 'w+') as ff:
fp = np.memmap(ff, dtype='float32', mode='w+', shape=tuple(shape))
for p in range(len(port_fp)):
wc = get_kclass(class_fp[p].copy(), numclasses)
fp[p] = wc.astype('float32')
del wc
del fp
kclass_fp = io.get_mmap_data(sonpath, base, '_data_kclass.dat', 'float32', tuple(shape))
else:
wc = get_kclass(class_fp.copy(), numclasses)
with open(os.path.normpath(os.path.join(sonpath,base+'_data_kclass.dat')), 'w+') as ff:
np.save(ff, np.squeeze(wc).astype('float32'))
del wc
with open(os.path.normpath(os.path.join(sonpath,base+'_data_kclass.dat')), 'r') as ff:
kclass_fp = np.load(ff)
########################################################
if doplot==1:
if len(shape_star)>2:
for p in range(len(star_fp)):
plot_kmeans(dist_m, shape_port, port_fp[p], star_fp[p], kclass_fp[p], ft, humfile, sonpath, base, p)
else:
plot_kmeans(dist_m, shape_port, port_fp, star_fp, kclass_fp, ft, humfile, sonpath, base, 0)
if os.name=='posix': # true if linux/mac
elapsed = (time.time() - start)
else: # windows
elapsed = (time.clock() - start)
print("Processing took " +str(elapsed)+ "seconds to analyse")
print("Done!")
print("===================================================")
