def __init__(self, **kwargs):
Notice.title()
Notice.hr_header("Initializing")
params = kwargs.get('params')
layers = kwargs.get('layers')
potfields = kwargs.get('potfields')
data = kwargs.get('data')
velocity = kwargs.get('velocity')
super(TransectContainer, self).__init__(params)
print "Starting {}, id {}, file {}".format(self.title,
self.id,
self.config_file)
# Set up 'data' — the transect line — from shapefile.
self.data = None
with fiona.open(data['transect_file']) as c:
for line in c:
if line['properties']['id'] == self.id:
self.data = shape(line['geometry'])
if not self.data:
Notice.fail("No transect with ID "+self.id)
# self.data.length holds the length of the transect in metres
# But often we want ints, and sometimes the number of samples.
# This will give us a nice linspace. Put them in params.
params['length'] = self.length = int(np.floor(self.data.length))
params['nsamples'] = self.nsamples = self.length + 1
params['linspace'] = self.linspace = np.linspace(0, self.length,
self.nsamples)
self.time = time.strftime("%Y/%m/%d %H:%M", time.localtime())
self.tops_file = data['tops_file']
self.log = LogContainer(data['well_dir'], params)
self.velocity = self.__velocity_factory(velocity, params)
self.seismic = SeismicContainer(data['seismic_dir'],
self.velocity,
params)
self.horizons = HorizonContainer(data['horizon_dir'],
self.velocity,
params)
self.elevation = ElevationContainer(data['elevation_file'], params)
self.bedrock = BedrockContainer(data['bedrock_dir'], params)
self.potfield = PotfieldContainer(potfields, params)
self.locmap = LocmapContainer(layers, params)
def __init__(self, **kwargs):
Notice.title()
Notice.hr_header("Initializing")
params = kwargs.get('params')
layers = kwargs.get('layers')
potfields = kwargs.get('potfields')
data = kwargs.get('data')
velocity = kwargs.get('velocity')
super(TransectContainer, self).__init__(params)
print "Starting {}, id {}, file {}".format(self.title, self.id,
self.config_file)
# Set up 'data' — the transect line — from shapefile.
self.data = None
with fiona.open(data['transect_file']) as c:
for line in c:
if line['properties']['id'] == self.id:
self.data = shape(line['geometry'])
if not self.data:
Notice.fail("No transect with ID " + self.id)
# self.data.length holds the length of the transect in metres
# But often we want ints, and sometimes the number of samples.
# This will give us a nice linspace. Put them in params.
params['length'] = self.length = int(np.floor(self.data.length))
params['nsamples'] = self.nsamples = self.length + 1
params['linspace'] = self.linspace = np.linspace(
0, self.length, self.nsamples)
self.time = time.strftime("%Y/%m/%d %H:%M", time.localtime())
self.tops_file = data['tops_file']
self.log = LogContainer(data['well_dir'], params)
self.velocity = self.__velocity_factory(velocity, params)
self.seismic = SeismicContainer(data['seismic_dir'], self.velocity,
params)
self.horizons = HorizonContainer(data['horizon_dir'], self.velocity,
params)
self.elevation = ElevationContainer(data['elevation_file'], params)
self.bedrock = BedrockContainer(data['bedrock_dir'], params)
self.potfield = PotfieldContainer(potfields, params)
self.locmap = LocmapContainer(layers, params)
def plot(self):
"""
Generates plot for the transect.
"""
# Set the extent to the length? Or keep them all the same?
self.extents[0] = 0
self.extents[1] = self.data.length
Notice.hr_header("Updating")
# update the containers
self.velocity.update(self.data)
self.log.update(self.data)
self.seismic.update(self.data)
self.horizons.update(self.data)
self.elevation.update(self.data)
self.bedrock.update(self.data)
self.potfield.update(self.data)
self.locmap.update(self.data)
Notice.hr_header("Plotting")
plot(self)
plt.show()
def plot(self):
"""
Generates plot for the transect.
"""
# Set the extent to the length? Or keep them all the same?
self.extents[0] = 0
self.extents[1] = self.data.length
Notice.hr_header("Updating")
# update the containers
self.velocity.update(self.data)
self.log.update(self.data)
self.seismic.update(self.data)
self.horizons.update(self.data)
self.elevation.update(self.data)
self.bedrock.update(self.data)
self.potfield.update(self.data)
self.locmap.update(self.data)
Notice.hr_header("Plotting")
plot(self)
plt.show()
def main(target, cfg):
"""
Puts everything together.
"""
t0 = time.time()
#####################################################################
#
# READ SEGY
#
#####################################################################
if cfg['segy_library'].lower() == 'obspy':
s = Seismic.from_segy_with_obspy(target, params={'ndim': cfg['ndim']})
else:
s = Seismic.from_segy(target, params={'ndim': cfg['ndim']})
# Set the line and/or xline number.
try:
n, xl = cfg['number']
except:
n, xl = cfg['number'], 0.5
# Set the direction.
if (s.ndim) == 2:
direction = ['inline']
elif cfg['direction'].lower()[0] == 'i':
direction = ['inline']
elif cfg['direction'].lower()[0] in ['x', 'c']: # Allow 'crossline' too.
direction = ['xline']
elif cfg['direction'].lower()[0] == 't':
direction = ['tslice']
else:
direction = ['xline', 'inline']
# Get the data.
try:
ss = [
Seismic.from_seismic(s, n=n, direction=d)
for n, d in zip((n, xl), direction)
]
except IndexError:
# Perhaps misinterpreted 2D as 3D
s = Seismic.from_segy(target, params={'ndim': 2})
direction = ['inline']
ss = [
Seismic.from_seismic(s, n=n, direction=d)
for n, d in zip((n, xl), direction)
]
clip_val = np.percentile(s.data, cfg['percentile'])
if clip_val < 10:
fstr = '{:.3f}'
elif clip_val < 100:
fstr = '{:.2f}'
elif clip_val < 1000:
fstr = '{:.1f}'
else:
fstr = '{:.0f}'
# Notify user of parameters.
Notice.info("n_traces {}".format(s.ntraces))
Notice.info("n_samples {}".format(s.nsamples))
Notice.info("dt {}".format(s.dt))
Notice.info("t_start {}".format(s.tstart))
Notice.info("t_end {}".format(s.tend))
Notice.info("max_val " + fstr.format(np.amax(s.data)))
Notice.info("min_val " + fstr.format(np.amin(s.data)))
Notice.info("clip_val " + fstr.format(clip_val))
t1 = time.time()
Notice.ok("Read data in {:.1f} s".format(t1 - t0))
#####################################################################
#
# MAKE PLOT
#
#####################################################################
Notice.hr_header("Plotting")
# Plot size parameters.
wsl = 6 # Width of sidelabel, inches
mih = 11 # Minimum plot height, inches
fhh = 5 # File header box height, inches
m = 0.75 # basic unit of margins, inches
# Margins, CSS like: top, right, bottom, left.
mt, mr, mb, ml = m, 1.5 * m, m, 1.5 * m
mm = 2 * m # padded margin between seismic and label
# Determine plot dimensions. Kind of laborious and repetitive (see below).
if cfg['plot_width']:
seismic_width = cfg['plot_width'] - wsl - mm - ml - mr
tpi = max([s.ntraces for s in ss]) / seismic_width
else:
tpi = cfg['tpi']
if cfg['plot_height']:
seismic_height = max(
mih, cfg['plot_height']) - mb - 0.75 * (len(ss) - 1) - mt
seismic_height_raw = seismic_height / len(ss)
ips = seismic_height_raw / (s.tbasis[-1] - s.tbasis[0])
else:
ips = cfg['ips']
# Width is determined by seismic width, plus sidelabel, plus margins.
# Height is given by ips, but with a minimum of mih inches.
if 'tslice' in direction:
seismic_width = [s.ntraces / tpi for s in ss]
seismic_height_raw = max([s.nxlines for s in ss]) / tpi
else:
seismic_width = [s.ntraces / tpi for s in ss]
seismic_height_raw = ips * (s.tbasis[-1] - s.tbasis[0])
w = ml + max(seismic_width) + mm + wsl + mr # inches
seismic_height = len(ss) * seismic_height_raw
h_reqd = mb + seismic_height + 0.75 * (len(ss) - 1) + mt # inches
h = max(mih, h_reqd)
# Calculate where to start sidelabel and seismic data.
# Depends on whether sidelabel is on the left or right.
if cfg['sidelabel'] == 'right':
ssl = (ml + max(seismic_width) + mm) / w # Start of side label (ratio)
seismic_left = ml / w
else:
ssl = ml / w
seismic_left = (ml + wsl + mm) / w
adj = max(0, h - h_reqd) / 2
seismic_bottom = (mb / h) + adj / h
seismic_width_fraction = [sw / w for sw in seismic_width]
seismic_height_fraction = seismic_height_raw / h
# Publish some notices so user knows plot size.
Notice.info("plot width {:.2f} in".format(w))
Notice.info("plot height {:.2f} in".format(h))
# Make the figure.
fig = plt.figure(figsize=(w, h), facecolor='w')
# Set the tickformat.
tickfmt = mtick.FormatStrFormatter('%.0f')
# Could definitely do better for default fontsize than 10.
# Ideally would be adaptive to plot size.
cfg['fontsize'] = cfg['fontsize'] or 10
# Plot title.
if cfg['title']:
# Deal with Windows paths: \1 gets interpreted as a group by regex.
newt = re.sub(r'\\', '@@@@@', target)
temp = re.sub(r'_filename', newt, cfg['title'])
title = re.sub(r'@@@', r'\\', temp)
title_ax = fig.add_axes([ssl, 1 - mt / h, wsl / w, mt / h])
title_ax = plotter.plot_title(title_ax,
title,
fs=1.4 * cfg['fontsize'],
cfg=cfg)
# Plot title.
if cfg['subtitle']:
date = str(datetime.date.today())
subtitle = re.sub(r'_date', date, cfg['subtitle'])
subtitle_ax = fig.add_axes([ssl, 1 - mt / h, wsl / w, mt / h],
label='subtitle')
title_ax = plotter.plot_subtitle(subtitle_ax,
subtitle,
fs=0.75 * cfg['fontsize'],
cfg=cfg)
# Plot text header.
start = (h - 1.5 * mt - fhh) / h
head_ax = fig.add_axes([ssl, start, wsl / w, fhh / h])
head_ax = plotter.plot_header(head_ax,
s.header,
fs=9,
cfg=cfg,
version=__version__)
# Plot histogram.
# Params for histogram plot.
pady = 0.75 / h # 0.75 inch
padx = 0.75 / w # 0.75 inch
cstrip = 0.3 / h # color_strip height = 0.3 in
charth = 1.25 / h # height of charts = 1.25 in
chartw = wsl / w - mr / w - padx # or ml/w for left-hand sidelabel; same thing
chartx = (ssl + padx)
histy = 1.5 * mb / h + charth + pady
# Plot colourbar under histogram.
clrbar_ax = fig.add_axes([chartx, histy - cstrip, chartw, cstrip])
clrbar_ax = plotter.plot_colourbar(clrbar_ax, cmap=cfg['cmap'])
# Plot histogram itself.
hist_ax = fig.add_axes([chartx, histy, chartw, charth])
hist_ax = plotter.plot_histogram(hist_ax, s.data, tickfmt, cfg)
# Plot spectrum.
specy = 1.5 * mb / h
spec_ax = fig.add_axes([chartx, specy, chartw, charth])
try:
colour = utils.rgb_to_hex(cfg['highlight_colour'])
spec_ax = s.plot_spectrum(
ax=spec_ax,
tickfmt=tickfmt,
ntraces=20,
fontsize=cfg['fontsize'],
colour=colour,
)
except:
pass # No spectrum, oh well.
for i, line in enumerate(ss):
# Add the seismic axis.
ax = fig.add_axes([
seismic_left,
seismic_bottom + i * seismic_height_fraction + i * pady,
seismic_width_fraction[i], seismic_height_fraction
])
# Plot seismic data.
if cfg['display'].lower() in ['vd', 'varden', 'variable', 'both']:
im = ax.imshow(line.data.T,
cmap=cfg['cmap'],
clim=[-clip_val, clip_val],
extent=[
line.olineidx[0], line.olineidx[-1],
1000 * line.tbasis[-1], line.tbasis[0]
],
aspect='auto',
interpolation=cfg['interpolation'])
if np.argmin(seismic_width) == i:
cax = utils.add_subplot_axes(ax, [1.01, 0.02, 0.01, 0.2])
_ = plt.colorbar(im, cax=cax)
if cfg['display'].lower() in ['wiggle', 'both']:
ax = line.wiggle_plot(
cfg['number'],
direction,
ax=ax,
skip=cfg['skip'],
gain=cfg['gain'],
rgb=cfg['colour'],
alpha=cfg['opacity'],
lw=cfg['lineweight'],
)
valid = ['vd', 'varden', 'variable', 'wiggle', 'both']
if cfg['display'].lower() not in valid:
Notice.fail("You must specify the display: wiggle, vd, both.")
return
# Seismic axis annotations.
ax.set_ylabel(utils.LABELS[line.ylabel], fontsize=cfg['fontsize'])
ax.set_xlabel(utils.LABELS[line.xlabel],
fontsize=cfg['fontsize'],
ha='center')
ax.tick_params(axis='both', labelsize=cfg['fontsize'] - 2)
ax.xaxis.set_major_formatter(tickfmt)
ax.yaxis.set_major_formatter(tickfmt)
if ('tslice' not in direction):
ax.set_ylim(1000 * cfg['trange'][1] or 1000 * line.tbasis[-1],
1000 * cfg['trange'][0])
# Crossing point. Will only work for non-arb lines.
try:
ax.axvline(ss[i - 1].slineidx[0],
c=utils.rgb_to_hex(cfg['highlight_colour']),
alpha=0.5)
except IndexError:
pass # Nevermind.
# Grid, optional.
if cfg['grid_time'] or cfg['grid_traces']:
ax.grid()
for l in ax.get_xgridlines():
l.set_color(utils.rgb_to_hex(cfg['grid_colour']))
l.set_linestyle('-')
if cfg['grid_traces']:
l.set_linewidth(1)
else:
l.set_linewidth(0)
l.set_alpha(min(1, cfg['grid_alpha']))
for l in ax.get_ygridlines():
l.set_color(utils.rgb_to_hex(cfg['grid_colour']))
l.set_linestyle('-')
if cfg['grid_time']:
if 'tslice' in direction:
l.set_linewidth(1)
else:
l.set_linewidth(1.4)
else:
l.set_linewidth(0)
l.set_alpha(min(1, 2 * cfg['grid_alpha']))
# Watermark.
if cfg['watermark_text']:
ax = plotter.watermark_seismic(ax, cfg)
# Make parasitic (top) axis for labeling CDP number.
if (s.data.ndim > 2) and ('tslice' not in direction):
ylim = ax.get_ylim()
par1 = ax.twiny()
par1.spines["top"].set_position(("axes", 1.0))
par1.plot(line.slineidx, np.zeros_like(line.slineidx), alpha=0)
par1.set_xlabel(utils.LABELS[line.slabel],
fontsize=cfg['fontsize'])
par1.set_ylim(ylim)
# Adjust ticks
tx = par1.get_xticks()
newtx = [
line.slineidx[len(line.slineidx) * (i // len(tx))]
for i, _ in enumerate(tx)
]
par1.set_xticklabels(newtx, fontsize=cfg['fontsize'] - 2)
t2 = time.time()
Notice.ok("Built plot in {:.1f} s".format(t2 - t1))
#####################################################################
#
# SAVE FILE
#
#####################################################################
Notice.hr_header("Saving")
dname, fname, ext = utils.path_bits(target)
outfile = cfg['outfile'] or ''
if not os.path.splitext(outfile)[1]:
outfile = os.path.join(cfg['outfile'] or dname, fname + '.png')
fig.savefig(outfile)
t3 = time.time()
Notice.info("output file {}".format(outfile))
Notice.ok("Saved output in {:.1f} s".format(t3 - t2))
if cfg['stain_paper'] or cfg['coffee_rings'] or cfg['distort'] or cfg[
'scribble']:
fname = os.path.splitext(outfile)[0] + ".stupid.png"
fig.savefig(fname)
else:
return
#####################################################################
#
# SAVE STUPID FILE
#
#####################################################################
Notice.hr_header("Applying the stupidity")
stupid_image = Image.open(fname)
if cfg['stain_paper']:
utils.stain_paper(stupid_image)
utils.add_rings(stupid_image, cfg['coffee_rings'])
if cfg['scribble']:
utils.add_scribble(stupid_image)
# Trick to remove remaining semi-transparent pixels.
result = Image.new("RGB", stupid_image.size, (255, 255, 255))
result.paste(stupid_image)
result.save(fname)
t4 = time.time()
Notice.info("output file {}".format(fname))
Notice.ok("Saved stupidity in {:.1f} s".format(t4 - t3))
return
'--demo',
action='store_true',
help='Run with the demo file, data/31_81_PR.png.')
parser.add_argument('-v',
'--version',
action='store_true',
help='Get the version number.')
args = parser.parse_args()
if args.version:
Notice.info(__version__)
sys.exit()
Notice.title()
target = args.filename
with args.config as f:
cfg = yaml.safe_load(f)
Notice.hr_header("Initializing")
Notice.info("config {}".format(args.config.name))
# Fill in 'missing' fields in cfg.
cfg = {k: cfg.get(k, v) for k, v in utils.DEFAULTS.items()}
cfg['outfile'] = args.out
cfg['ndim'] = args.ndim or cfg['ndim']
if args.demo:
target = './data/31_81_PR.sgy'
# Go do it!
try:
globule = glob.iglob(target, recursive=True) # Python 3.5+
except:
globule = glob.iglob(target) # Python < 3.5
def main(target, cfg):
"""
Puts everything together.
"""
t0 = time.time()
# Read the file.
section = readSEGY(target, unpack_headers=True)
# Calculate some things.
# NB Getting nsamples and dt from the first trace assumes that all
# traces are the same length, which is not a safe assumption in SEGY v2.
ninlines = section.traces[-1].header.trace_sequence_number_within_line
last_tr = section.traces[-1].header.trace_sequence_number_within_segy_file
nxlines = last_tr / ninlines
nsamples = section.traces[0].header.number_of_samples_in_this_trace
dt = section.traces[0].header.sample_interval_in_ms_for_this_trace
ntraces = len(section.traces)
tbase = 0.001 * np.arange(0, nsamples * dt, dt)
tstart = 0
tend = np.amax(tbase)
# Make the data array.
data = np.vstack([t.data for t in section.traces]).T
threed = False
if nxlines > 1: # Then it's a 3D and `data` is an ensemble.
threed = True
cube = np.reshape(data.T, (ninlines, nxlines, nsamples))
l = cfg['number']
if cfg['direction'].lower()[0] == 'i':
direction = 'inline'
ntraces = nxlines
l *= ninlines if (l < 1) else 1
data = cube[l, :, :].T
else:
direction = 'xline'
ntraces = ninlines
l *= nxlines if (l < 1) else 1
data = cube[:, l, :].T
# Collect some other data. Use a for loop because there are several.
elev, esp, ens, tsq = [], [], [], []
for i, trace in enumerate(section.traces):
elev.append(trace.header.receiver_group_elevation)
esp.append(trace.header.energy_source_point_number)
tsq.append(trace.header.trace_sequence_number_within_line)
if threed:
trs = []
if direction == 'inline':
cdp_label_text = 'Crossline number'
trace_label_text = 'Trace number'
ens.append(trace.header.for_3d_poststack_data_this_field_is_for_cross_line_number)
trs.append(trace.header.for_3d_poststack_data_this_field_is_for_in_line_number)
else:
cdp_label_text = 'Inline number'
trace_label_text = 'Trace number'
ens.append(trace.header.for_3d_poststack_data_this_field_is_for_in_line_number)
trs.append(trace.header.for_3d_poststack_data_this_field_is_for_cross_line_number)
line_no = min(trs)
else:
cdp_label_text = 'CDP number'
trace_label_text = 'Trace number'
ens.append(trace.header.ensemble_number)
min_tr, max_tr = 0, ntraces
traces = (min_tr, max_tr)
clip_val = np.percentile(data, cfg['percentile'])
# Notify user of parameters
Notice.info("n_traces {}".format(ntraces))
Notice.info("n_samples {}".format(nsamples))
Notice.info("dt {}".format(dt))
Notice.info("t_start {}".format(tstart))
Notice.info("t_end {}".format(tend))
Notice.info("max_val {}".format(np.amax(data)))
Notice.info("min_val {}".format(np.amin(data)))
Notice.info("clip_val {}".format(clip_val))
t1 = time.time()
Notice.ok("Read data in {:.1f} s".format(t1-t0))
#####################################################################
#
# MAKE PLOT
#
#####################################################################
Notice.hr_header("Plotting")
##################################
# Plot size parameters
# Some constants
fs = cfg['fontsize']
wsl = 6 # Width of sidelabel, inches
mih = 12 # Minimum plot height, inches
fhh = 5 # File header box height, inches
m = 0.5 # basic unit of margins, inches
# Margins, CSS like: top, right, bottom, left.
mt, mr, mb, ml = m, 2 * m, m, 2 * m
mm = m # padded margin between seismic and label
# Width is determined by seismic width, plus sidelabel, plus margins.
seismic_width = ntraces / cfg['tpi']
w = ml + seismic_width + mm + wsl + mr # inches
# Height is given by ips, but with a minimum of mih inches
seismic_height = cfg['ips'] * (tbase[-1] - tbase[0]) / 1000
h_reqd = mb + seismic_height + mt # inches
h = max(mih, h_reqd)
# Calculate where to start sidelabel and seismic data.
# Depends on whether sidelabel is on the left or right.
if cfg['sidelabel'] == 'right':
ssl = (ml + seismic_width + mm) / w # Start of side label (ratio)
seismic_left = ml / w
else:
ssl = ml / w
seismic_left = (ml + wsl + mm) / w
adj = max(0, h - h_reqd) / 2
seismic_bottom = (mb / h) + adj / h
seismic_width_fraction = seismic_width / w
seismic_height_fraction = seismic_height / h
# Publish some notices so user knows plot size.
Notice.info("Width of plot {} in".format(w))
Notice.info("Height of plot {} in".format(h))
##################################
# Make the figure.
fig = plt.figure(figsize=(w, h), facecolor='w')
# Add the main seismic axis.
ax = fig.add_axes([seismic_left,
seismic_bottom,
seismic_width_fraction,
seismic_height_fraction
])
# make parasitic axes for labeling CDP number
par1 = ax.twiny()
par1.spines["top"].set_position(("axes", 1.0))
tickfmt = mtick.FormatStrFormatter('%.0f')
par1.plot(ens, np.zeros_like(ens))
par1.set_xlabel(cdp_label_text, fontsize=fs-2)
par1.set_xticklabels(par1.get_xticks(), fontsize=fs-2)
par1.xaxis.set_major_formatter(tickfmt)
# Plot title
title_ax = fig.add_axes([ssl, 1-mt/h, wsl/w, mt/(h)])
title_ax = plotter.plot_title(title_ax, target, fs=1.5*fs, cfg=cfg)
if threed:
title_ax.text(0.0, 0.0, '{} {}'.format(direction.title(), line_no))
# Plot text header.
s = section.textual_file_header.decode()
start = (h - 1.5*mt - fhh) / h
head_ax = fig.add_axes([ssl, start, wsl/w, fhh/h])
head_ax = plotter.plot_header(head_ax, s, fs=fs-1, cfg=cfg)
# Plot histogram.
# Params for histogram plot
pady = 0.75 / h # 0.75 inch
padx = 0.75 / w # 0.75 inch
cstrip = 0.3/h # color_strip height = 0.3 in
charth = 1.5/h # height of charts = 1.5 in
chartw = wsl/w - mr/w - padx # or ml/w for left-hand sidelabel; same thing
chartx = (ssl + padx)
histy = 1.5 * mb/h + charth + pady
# Plot colourbar under histogram
clrbar_ax = fig.add_axes([chartx, histy - cstrip, chartw, cstrip])
clrbar_ax = plotter.plot_colourbar(clrbar_ax, cmap=cfg['cmap'])
# Plot histogram itself
hist_ax = fig.add_axes([chartx, histy, chartw, charth])
hist_ax = plotter.plot_histogram(hist_ax,
data,
tickfmt,
percentile=cfg['percentile'],
fs=fs)
# Plot spectrum.
specy = 1.5 * mb/h
spec_ax = fig.add_axes([chartx, specy, chartw, charth])
try:
spec_ax = plotter.plot_spectrum(spec_ax,
data,
dt,
tickfmt,
ntraces=20,
fontsize=fs)
except:
pass
# Plot seismic data.
if cfg['display'].lower() in ['vd', 'varden', 'variable']:
_ = ax.imshow(data,
cmap=cfg['cmap'],
clim=[-clip_val, clip_val],
extent=[0, ntraces, tbase[-1], tbase[0]],
aspect='auto'
)
elif cfg['display'].lower() == 'wiggle':
ax = plotter.wiggle_plot(ax,
data,
tbase,
ntraces,
skip=cfg['skip'],
gain=cfg['gain'],
rgb=cfg['colour'],
alpha=cfg['opacity'],
lw=cfg['lineweight']
)
ax.set_ylim(ax.get_ylim()[::-1])
elif cfg['display'].lower() == 'both':
# variable density goes on first
_ = ax.imshow(data,
cmap=cfg['cmap'],
clim=[-clip_val, clip_val],
extent=[0, ntraces, tbase[-1], tbase[0]],
aspect='auto'
)
# wiggle plots go on top
ax = plotter.wiggle_plot(ax,
data,
tbase,
ntraces,
skip=cfg['skip'],
gain=cfg['gain'],
rgb=cfg['colour'],
alpha=cfg['opacity'],
lw=cfg['lineweight']
)
# ax.set_ylim(ax.get_ylim()[::-1])
else:
Notice.fail("You need to specify the type of display: wiggle or vd")
# Seismic axis annotations.
ax = plotter.decorate_seismic(ax, traces, trace_label_text, tickfmt, cfg)
# Watermark.
if cfg['watermark_text']:
Notice.info("Adding watermark")
ax = plotter.watermark_seismic(ax, cfg)
t2 = time.time()
Notice.ok("Built plot in {:.1f} s".format(t2-t1))
#####################################################################
#
# SAVE FILE
#
#####################################################################
Notice.hr_header("Saving")
if cfg['stain_paper'] or cfg['coffee_rings'] or cfg['distort'] or cfg['scribble']:
stupid = True
else:
stupid = False
s = "Saved image file {} in {:.1f} s"
if cfg['outfile']:
if os.path.isfile(cfg['outfile']):
outfile = cfg['outfile']
else: # is directory
stem, ext = os.path.splitext(os.path.split(target)[1])
outfile = os.path.join(cfg['outfile'], stem + '.png')
stem, _ = os.path.splitext(outfile) # Needed for stupidity.
fig.savefig(outfile)
t3 = time.time()
Notice.ok(s.format(outfile, t3-t2))
else: # Do the default: save a PNG in the same dir as the target.
stem, _ = os.path.splitext(target)
fig.savefig(stem)
t3 = time.time()
Notice.ok(s.format(stem+'.png', t3-t2))
if stupid:
fig.savefig(stem + ".stupid.png")
else:
return
#####################################################################
#
# SAVE STUPID FILE
#
#####################################################################
Notice.hr_header("Applying the stupidity")
stupid_image = Image.open(stem + ".stupid.png")
if cfg['stain_paper']:
utils.stain_paper(stupid_image)
utils.add_rings(stupid_image, cfg['coffee_rings'])
if cfg['scribble']:
utils.add_scribble(stupid_image)
stupid_image.save(stem + ".stupid.png")
s = "Saved stupid file stupid.png in {:.1f} s"
t4 = time.time()
Notice.ok(s.format(t4-t3))
return
nargs='?',
help='The path to a SEGY file.')
parser.add_argument('-o', '--out',
metavar='Output file',
type=str,
nargs='?',
default='',
help='The path to an output file.')
parser.add_argument('-R', '--recursive',
action='store_true',
help='Descend into subdirectories.')
args = parser.parse_args()
target = args.filename
with args.config as f:
cfg = yaml.load(f)
Notice.hr_header("Initializing")
Notice.info("Config {}".format(args.config.name))
# Fill in 'missing' fields in cfg.
defaults = {'line': 'inline',
'number': 0.5,
'sidelabel': 'right',
'tpi': 10,
'ips': 1,
'skip': 2,
'display': 'vd',
'gain': 1.0,
'percentile': 99.0,
'colour': [0, 0, 0],
'opacity': 1.0,
'lineweight': 0.2,
def main(target, cfg):
"""
Puts everything together.
"""
t0 = time.time()
# Read the file.
section = readSEGY(target, unpack_headers=True)
# Calculate some things
nsamples = section.traces[0].header.number_of_samples_in_this_trace
dt = section.traces[0].header.sample_interval_in_ms_for_this_trace
ntraces = len(section.traces)
tbase = 0.001 * np.arange(0, nsamples * dt, dt)
tstart = 0
tend = np.amax(tbase)
wsd = ntraces / cfg['tpi']
# Build the data container
elev, esp, ens, tsq = [], [], [], [] # energy source point number
data = np.zeros((nsamples, ntraces))
for i, trace in enumerate(section.traces):
data[:, i] = trace.data
elev.append(trace.header.receiver_group_elevation)
esp.append(trace.header.energy_source_point_number)
ens.append(trace.header.ensemble_number)
tsq.append(trace.header.trace_sequence_number_within_line)
clip_val = np.percentile(data, 99.0)
# Notify user of parameters
Notice.info("n_traces {}".format(ntraces))
Notice.info("n_samples {}".format(nsamples))
Notice.info("dt {}".format(dt))
Notice.info("t_start {}".format(tstart))
Notice.info("t_end {}".format(tend))
Notice.info("max_val {}".format(np.amax(data)))
Notice.info("min_val {}".format(np.amin(data)))
Notice.info("clip_val {}".format(clip_val))
t1 = time.time()
Notice.ok("Read data successfully in {:.1f} s".format(t1-t0))
#####################################################################
#
# MAKE PLOT
#
#####################################################################
Notice.hr_header("Plotting")
##################################
# Plot size parameters
# Some constants
wsl = 6 # Width of sidelabel
mih = 10 # Minimum plot height
fhh = 5 # File header height
m = 0.5 # margin in inches
# Margins, CSS like
mt, mb, ml, mr = m, m, 2 * m, 2 * m
mm = mr / 2 # padded margin between seismic and label
# Width is determined by tpi, plus a constant for the sidelabel, plus 1 in
w = ml + wsd + wsl + mr + mm
# Height is given by ips, but with a minimum of 8 inches, plus 1 in
h = max(mih, cfg['ips'] * (np.amax(tbase) - np.amin(tbase)) / 1000 + mt + mb)
# More settings
ssl = (ml + wsd + mm) / w # Start of side label (ratio)
fs = cfg['fontsize']
Notice.info("Width of plot {} in".format(w))
Notice.info("Height of plot {} in".format(h))
##################################
# Make the figure.
fig = plt.figure(figsize=(w, h), facecolor='w')
ax = fig.add_axes([ml / w, mb / h, wsd / w, (h - mb - mt) / h])
# make parasitic axes for labeling CDP number
par1 = ax.twiny()
par1.spines["top"].set_position(("axes", 1.0))
tickfmt = mtick.FormatStrFormatter('%.0f')
par1.plot(ens, np.zeros_like(ens))
par1.set_xlabel("CDP number", fontsize=fs-2)
par1.set_xticklabels(par1.get_xticks(), fontsize=fs-2)
par1.xaxis.set_major_formatter(tickfmt)
ax = wiggle_plot(ax,
data,
tbase,
ntraces,
skip=cfg['skip'],
gain=cfg['gain'],
rgb=cfg['colour'],
alpha=cfg['opacity'],
lw=cfg['lineweight']
)
ax = decorate_seismic(ax, ntraces, tickfmt, fs)
# Plot title
title_ax = fig.add_axes([ssl, 1-mt/h, wsl/w, mt/(2*h)])
title_ax = plot_title(title_ax, target, fs=fs)
# Plot text header.
s = str(section.textual_file_header)[2:-1]
start = (h - mt - fhh) / h
head_ax = fig.add_axes([ssl, start, wsl/w, fhh/h])
head_ax = plot_header(head_ax, s, fs)
# Plot histogram.
pad = 0.05
charty = 0.125 # height of chart
xhist = (ssl + pad)
whist = (1 - ssl - (ml/w)) - 2 * pad
hist_ax = fig.add_axes([xhist, 1.5 * mb/h + charty + pad, whist, charty])
hist_ax = plot_histogram(hist_ax, data, fs)
# Plot spectrum.
spec_ax = fig.add_axes([xhist, 1.5 * mb/h, whist, charty])
spec_ax = plot_spectrum(spec_ax, data, dt, fs)
t2 = time.time()
Notice.ok("Built plot in {:.1f} s".format(t2-t1))
#####################################################################
#
# SAVE FILE
#
#####################################################################
Notice.hr_header("Saving")
s = "Saved image file {} in {:.1f} s"
if cfg['outfile']:
fig.savefig(cfg['outfile'])
t3 = time.time()
Notice.ok(s.format(cfg['outfile'], t3-t2))
else:
stem, _ = os.path.splitext(target)
fig.savefig(stem)
t3 = time.time()
Notice.ok(s.format(stem+'.png', t3-t2))
return
Notice.title()
parser = argparse.ArgumentParser(description='Plot a SEGY file.')
parser.add_argument("-c", "--config",
metavar="config file",
type=argparse.FileType('r'),
default="config.yaml",
nargs="?",
help="The name of a YAML config file.")
parser.add_argument('filename',
metavar='SEGY file',
type=str,
nargs='?',
help='The path to a SEGY file.')
parser.add_argument('-o', '--out',
metavar='Output file',
type=str,
nargs='?',
default='',
help='The path to an output file.')
args = parser.parse_args()
target = args.filename
with args.config as f:
cfg = yaml.load(f)
Notice.hr_header("Initializing")
Notice.info("Filename {}".format(target))
Notice.info("Config {}".format(args.config.name))
cfg['outfile'] = args.out
main(target, cfg)
Notice.hr_header("Done")
def main(target, cfg):
"""
Puts everything together.
"""
t0 = time.time()
#####################################################################
#
# READ SEGY
#
#####################################################################
s = Seismic.from_segy(target, params={'ndim': cfg['ndim']})
# Set the line and/or xline number.
try:
n, xl = cfg['number']
except:
n, xl = cfg['number'], 0.5
# Set the direction.
if (s.ndim) == 2:
direction = ['inline']
elif cfg['direction'].lower()[0] == 'i':
direction = ['inline']
elif cfg['direction'].lower()[0] == 'x':
direction = ['xline']
elif cfg['direction'].lower()[0] == 't':
direction = ['tslice']
else:
direction = ['inline', 'xline']
# Get the data.
ss = [Seismic.from_seismic(s, n=n, direction=d) for n, d in zip((n, xl), direction)]
data = [s.data for s in ss]
clip_val = np.percentile(s.data, cfg['percentile'])
# Notify user of parameters.
Notice.info("n_traces {}".format(s.ntraces))
Notice.info("n_samples {}".format(s.nsamples))
Notice.info("dt {}".format(s.dt))
Notice.info("t_start {}".format(s.tstart))
Notice.info("t_end {}".format(s.tend))
Notice.info("max_val {:.3f}".format(np.amax(s.data)))
Notice.info("min_val {:.3f}".format(np.amin(s.data)))
Notice.info("clip_val {:.3f}".format(clip_val))
t1 = time.time()
Notice.ok("Read data in {:.1f} s".format(t1-t0))
#####################################################################
#
# MAKE PLOT
#
#####################################################################
Notice.hr_header("Plotting")
# Plot size parameters.
fs = cfg['fontsize']
wsl = 6 # Width of sidelabel, inches
mih = 12 # Minimum plot height, inches
fhh = 5 # File header box height, inches
m = 0.5 # basic unit of margins, inches
# Margins, CSS like: top, right, bottom, left.
mt, mr, mb, ml = m, 2 * m, m, 2 * m
mm = m # padded margin between seismic and label
# Width is determined by seismic width, plus sidelabel, plus margins.
# Height is given by ips, but with a minimum of mih inches.
if 'tslice' in direction:
print('doing tslice')
seismic_width = max([s.ninlines for s in ss]) / cfg['tpi']
seismic_height_raw = max([s.nxlines for s in ss]) / cfg['tpi']
print(seismic_width, seismic_height_raw)
else:
seismic_width = max([s.ntraces for s in ss]) / cfg['tpi']
seismic_height_raw = cfg['ips'] * (s.tbasis[-1] - s.tbasis[0])
w = ml + seismic_width + mm + wsl + mr # inches
seismic_height = len(ss) * seismic_height_raw
h_reqd = mb + seismic_height + 0.75*(len(ss)-1) + mt # inches
h = max(mih, h_reqd)
# Calculate where to start sidelabel and seismic data.
# Depends on whether sidelabel is on the left or right.
if cfg['sidelabel'] == 'right':
ssl = (ml + seismic_width + mm) / w # Start of side label (ratio)
seismic_left = ml / w
else:
ssl = ml / w
seismic_left = (ml + wsl + mm) / w
adj = max(0, h - h_reqd) / 2
seismic_bottom = (mb / h) + adj / h
seismic_width_fraction = seismic_width / w
seismic_height_fraction = seismic_height_raw / h
# Publish some notices so user knows plot size.
Notice.info("Width of plot {} in".format(w))
Notice.info("Height of plot {} in".format(h))
# Make the figure.
fig = plt.figure(figsize=(w, h), facecolor='w')
# Set the tickformat.
tickfmt = mtick.FormatStrFormatter('%.0f')
# Plot title.
if cfg['filename']:
title_ax = fig.add_axes([ssl, 1-mt/h, wsl/w, mt/h])
title_ax = plotter.plot_title(title_ax, target, fs=1.5*fs, cfg=cfg)
# Plot text header.
start = (h - 1.5*mt - fhh) / h
head_ax = fig.add_axes([ssl, start, wsl/w, fhh/h])
head_ax = plotter.plot_header(head_ax, s.header, fs=fs-1, cfg=cfg)
# Plot histogram.
# Params for histogram plot.
pady = 0.75 / h # 0.75 inch
padx = 0.75 / w # 0.75 inch
cstrip = 0.3/h # color_strip height = 0.3 in
charth = 1.5/h # height of charts = 1.5 in
chartw = wsl/w - mr/w - padx # or ml/w for left-hand sidelabel; same thing
chartx = (ssl + padx)
histy = 1.5 * mb/h + charth + pady
# Plot colourbar under histogram.
clrbar_ax = fig.add_axes([chartx, histy - cstrip, chartw, cstrip])
clrbar_ax = plotter.plot_colourbar(clrbar_ax, cmap=cfg['cmap'])
# Plot histogram itself.
hist_ax = fig.add_axes([chartx, histy, chartw, charth])
hist_ax = plotter.plot_histogram(hist_ax,
s.data,
tickfmt,
percentile=cfg['percentile'],
fs=fs)
# Plot spectrum.
specy = 1.5 * mb/h
spec_ax = fig.add_axes([chartx, specy, chartw, charth])
try:
spec_ax = s.plot_spectrum(ax=spec_ax,
tickfmt=tickfmt,
ntraces=20,
fontsize=fs)
except:
pass
for i, line in enumerate(ss):
# Add the seismic axis.
ax = fig.add_axes([seismic_left,
seismic_bottom + i*seismic_height_fraction + i*pady,
seismic_width_fraction,
seismic_height_fraction
])
# Plot seismic data.
if cfg['display'].lower() in ['vd', 'varden', 'variable', 'both']:
_ = ax.imshow(line.data.T,
cmap=cfg['cmap'],
clim=[-clip_val, clip_val],
extent=[0,
line.ntraces,
1000*line.tbasis[-1],
line.tbasis[0]],
aspect='auto'
)
# This does not work: should cut off line at cfg['tmax']
# ax.set_ylim(1000*cfg['tmax'] or 1000*line.tbasis[-1], line.tbasis[0])
if cfg['display'].lower() in ['wiggle', 'both']:
ax = line.wiggle_plot(cfg['number'], direction,
ax=ax,
skip=cfg['skip'],
gain=cfg['gain'],
rgb=cfg['colour'],
alpha=cfg['opacity'],
lw=cfg['lineweight'],
tmax=cfg['tmax'],
)
if cfg['display'].lower() not in ['vd', 'varden', 'variable', 'wiggle', 'both']:
Notice.fail("You must specify the type of display: wiggle, vd, both.")
return
# Seismic axis annotations.
fs = cfg['fontsize'] - 2
ax.set_xlim([0, line.data.shape[0]])
ax.set_ylabel(line.ylabel, fontsize=fs)
ax.set_xlabel(line.xlabel, fontsize=fs, horizontalalignment='center')
ax.set_xticklabels(ax.get_xticks(), fontsize=fs)
ax.set_yticklabels(ax.get_yticks(), fontsize=fs)
ax.xaxis.set_major_formatter(tickfmt)
ax.yaxis.set_major_formatter(tickfmt)
# Watermark.
if cfg['watermark_text']:
ax = plotter.watermark_seismic(ax, cfg)
# Make parasitic axes for labeling CDP number.
par1 = ax.twiny()
par1.spines["top"].set_position(("axes", 1.0))
par1.plot(s.xlines, np.zeros_like(s.xlines))
par1.set_xlabel(line.xlabel, fontsize=fs)
par1.set_xticklabels(par1.get_xticks(), fontsize=fs)
par1.xaxis.set_major_formatter(tickfmt)
t2 = time.time()
Notice.ok("Built plot in {:.1f} s".format(t2-t1))
#####################################################################
#
# SAVE FILE
#
#####################################################################
Notice.hr_header("Saving")
dname, fname, ext = utils.path_bits(target)
outfile = cfg['outfile'] or ''
if not os.path.splitext(outfile)[1]:
outfile = os.path.join(cfg['outfile'] or dname, fname + '.png')
fig.savefig(outfile)
t3 = time.time()
Notice.ok("Saved image file {} in {:.1f} s".format(outfile, t3-t2))
if cfg['stain_paper'] or cfg['coffee_rings'] or cfg['distort'] or cfg['scribble']:
fname = os.path.splitext(outfile)[0] + ".stupid.png"
fig.savefig(fname)
else:
return
#####################################################################
#
# SAVE STUPID FILE
#
#####################################################################
Notice.hr_header("Applying the stupidity")
stupid_image = Image.open(fname)
if cfg['stain_paper']: utils.stain_paper(stupid_image)
utils.add_rings(stupid_image, cfg['coffee_rings'])
if cfg['scribble']: utils.add_scribble(stupid_image)
stupid_image.save(fname)
t4 = time.time()
Notice.ok("Saved stupid file {} in {:.1f} s".format(fname, t4-t3))
return