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Merge 238c17a into e9edc36
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@amoodie
amoodie committed Jun 10, 2020
2 parents e9edc36 + 238c17a commit 1d38685
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Showing 6 changed files with 488 additions and 93 deletions.
5 changes: 4 additions & 1 deletion pyDeltaRCM/default.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -75,10 +75,13 @@ save_depth_figs:
default: False
save_discharge_figs:
type: 'bool'
default: True
default: False
save_velocity_figs:
type: 'bool'
default: False
save_figs_sequential:
type: 'bool'
default: True
save_eta_grids:
type: 'bool'
default: False
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181 changes: 99 additions & 82 deletions pyDeltaRCM/deltaRCM_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -242,82 +242,74 @@ def output_data(self):
"""

timestep = self._time

if timestep % self.save_dt == 0:
_timestep = self._time
if _timestep % self.save_dt == 0:

if (self.save_eta_grids or
self.save_depth_grids or
self.save_stage_grids or
self.save_discharge_grids or
self.save_velocity_grids or
self.save_strata):

timestep = self._time
shape = self.output_netcdf.variables['time'].shape
self.output_netcdf.variables['time'][shape[0]] = timestep
_timestep = int(self._time)

# ------------------ Figures ------------------
if self.save_eta_figs:

plt.pcolor(self.eta)
plt.clim(self.clim_eta[0], self.clim_eta[1])
plt.colorbar()
plt.axis('equal')
self.save_figure(os.path.join(self.prefix, 'eta_' + str(timestep)))
if self._save_any_figs:

if self.save_stage_figs:

plt.pcolor(self.stage)
plt.colorbar()
plt.axis('equal')
self.save_figure(os.path.join(self.prefix, 'stage_' + str(timestep)))

if self.save_depth_figs:

plt.pcolor(self.depth)
plt.colorbar()
plt.axis('equal')
self.save_figure(os.path.join(self.prefix, 'depth_' + str(timestep)))
_msg = 'Saving figures'
self.logger.info(_msg)
if self.verbose >= 2:
print(_msg)

if self.save_discharge_figs:
if self.save_eta_figs:
_fe = self.make_figure('eta', _timestep)
self.save_figure(_fe, directory=self.prefix,
filename_root='eta_',
timestep=_timestep)

if self.save_stage_figs:
_fs = self.make_figure('stage', _timestep)
self.save_figure(_fs, directory=self.prefix,
filename_root='stage_',
timestep=_timestep)

if self.save_depth_figs:
_fh = self.make_figure('depth', _timestep)
self.save_figure(_fh, directory=self.prefix,
filename_root='depth_',
timestep=_timestep)

if self.save_discharge_figs:
_fq = self.make_figure('qw', _timestep)
self.save_figure(_fq, directory=self.prefix,
filename_root='discharge_',
timestep=_timestep)

if self.save_velocity_figs:
_fu = self.make_figure('uw', _timestep)
self.save_figure(_fu, directory=self.prefix,
filename_root='velocity_',
timestep=_timestep)

plt.pcolor(self.qw)
plt.colorbar()
plt.axis('equal')
self.save_figure(os.path.join(self.prefix, 'discharge_' + str(timestep)))
# ------------------ grids ------------------
if self._save_any_grids:

if self.save_velocity_figs:
plt.pcolor(self.uw)
plt.colorbar()
plt.axis('equal')
self.save_figure(os.path.join(self.prefix, 'velocity_' + str(timestep)))
shape = self.output_netcdf.variables['time'].shape
self.output_netcdf.variables['time'][shape[0]] = _timestep

# ------------------ grids ------------------
if self.save_eta_grids:
_msg = 'Saving grids'
self.logger.info(_msg)
if self.verbose >= 2:
self.logger.info('Saving grid: eta')
self.save_grids('eta', self.eta, shape[0])
print(_msg)

if self.save_depth_grids:
if self.verbose >= 2:
self.logger.info('Saving grid: depth')
self.save_grids('depth', self.depth, shape[0])
if self.save_eta_grids:
self.save_grids('eta', self.eta, shape[0])

if self.save_stage_grids:
if self.verbose >= 2:
self.logger.info('Saving grid: stage')
self.save_grids('stage', self.stage, shape[0])
if self.save_depth_grids:
self.save_grids('depth', self.depth, shape[0])

if self.save_discharge_grids:
if self.verbose >= 2:
self.logger.info('Saving grid: discharge')
self.save_grids('discharge', self.qw, shape[0])
if self.save_stage_grids:
self.save_grids('stage', self.stage, shape[0])

if self.save_velocity_grids:
if self.verbose >= 2:
self.logger.info('Saving grid: velocity')
self.save_grids('velocity', self.uw, shape[0])
if self.save_discharge_grids:
self.save_grids('discharge', self.qw, shape[0])

if self.save_velocity_grids:
self.save_grids('velocity', self.uw, shape[0])

def output_strata(self):
"""Save stratigraphy as sparse matrix to file.
Expand Down Expand Up @@ -381,10 +373,38 @@ def output_strata(self):

self.output_netcdf.variables['strata_depth'][i, :, :] = sz

_msg = 'Stratigraphy data saved.'
self.logger.info(_msg)
if self.verbose >= 2:
self.logger.info('Stratigraphy data saved.')
print(_msg)

def make_figure(self, var, timestep):
"""Create a figure.
Parameters
----------
var : :obj:`str`
Which variable to plot into the figure. Specified as a string and
looked up via `getattr`.
def save_figure(self, path, ext='png', close=True):
Returns
-------
fig : :obj:`matplotlib.figure`
The created figure object.
"""

_data = getattr(self, var)

fig, ax = plt.subplots()
pc = ax.pcolor(_data)
fig.colorbar(pc)
ax.set_title(var + ' --- ' + 'time = ' + str(timestep))
ax.axis('equal')

return fig

def save_figure(self, fig, directory, filename_root,
timestep, ext='.png', close=True):
"""Save a figure.
Parameters
Expand All @@ -393,9 +413,10 @@ def save_figure(self, path, ext='png', close=True):
The path (and filename without extension) to save the figure to.
ext : :obj:`str`, optional
The file extension (default='png'). This must be supported by the
The file extension (default='.png'). This must be supported by the
active matplotlib backend (see matplotlib.backends module). Most
backends support 'png', 'pdf', 'ps', 'eps', and 'svg'.
backends support '.png', '.pdf', '.ps', '.eps', and '.svg'. Be
sure to include the '.' before the extension.
close : :obj:`bool`, optional
Whether to close the file after saving.
Expand All @@ -404,20 +425,16 @@ def save_figure(self, path, ext='png', close=True):
-------
"""

directory = os.path.split(path)[0]
filename = "%s.%s" % (os.path.split(path)[1], ext)
if directory == '':
directory = '.'

if not os.path.exists(directory):
if self.verbose >= 2:
self.logger.info('Creating output directory')
os.makedirs(directory)

savepath = os.path.join(directory, filename)
plt.savefig(savepath)

if self._save_figs_sequential:
# save as a padded number with the timestep
savepath = os.path.join(directory,
filename_root + str(timestep).zfill(5) + ext)
else:
# save as "latest"
savepath = os.path.join(directory,
filename_root + 'latest' + ext)

fig.savefig(savepath)
if close:
plt.close()

Expand Down Expand Up @@ -446,5 +463,5 @@ def save_grids(self, var_name, var, ts):
try:
self.output_netcdf.variables[var_name][ts, :, :] = var
except:
self.logger.info('Error: Cannot save grid to netCDF file.')
self.logger.error('Cannot save grid to netCDF file.')
warnings.warn(UserWarning('Cannot save grid to netCDF file.'))
7 changes: 7 additions & 0 deletions pyDeltaRCM/init_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -252,6 +252,13 @@ def create_other_variables(self):
self.diffusion_multiplier = (self.dt / self.N_crossdiff * self.alpha
* 0.5 / self.dx**2)

self._save_any_grids = (self.save_eta_grids or self.save_depth_grids or
self.save_stage_grids or self.save_discharge_grids or
self.save_velocity_grids)
self._save_any_figs = (self.save_eta_figs or self.save_depth_figs or
self.save_stage_figs or self.save_discharge_figs or
self.save_velocity_figs)
self._save_figs_sequential = self.save_figs_sequential # copy as private
self._is_finalized = False

def create_domain(self):
Expand Down
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