"""Package initialization file for pynoddy"""
import os.path
import subprocess
# save this module path for relative paths
package_directory = os.path.dirname(os.path.abspath(__file__))
# paths to noddy & topology executables
# noddyPath = os.path.join(package_directory,'../noddy/noddy')
# topologyPath = os.path.join(package_directory,'../topology/topology')
noddyPath = os.path.join(package_directory, 'noddy/noddy')
topologyPath = os.path.join(package_directory, 'topology/topology')
# global variables
ensure_discrete_volumes = True # if True, spatially separated but otherwise
# identical volumes are given separate codes.
null_volume_threshold = 20 # volumes smaller than this are ignored
# completely (as they represent pixelation artefacts).
# ensure correct noddy & topology builds are present
if not os.path.exists(noddyPath) and not os.path.exists(noddyPath + ".exe"):
print("Error: could not find a compiled version of noddy at %s. \
Please ensure the source has been compiled (using GCC and compile.bat \
(windows) or compile.sh (unix))." % noddyPath)
if not os.path.exists(topologyPath) and not os.path.exists(topologyPath + ".exe"):
print("Warning: could not find a compiled version of topology at %s. \
Please ensure the source has been compiled (using GCC and compile.bat\
(windows) or compile.sh (unix))." % topologyPath)
# Some helper functions are defined directly here:
[docs]def compute_model(history, output_name, **kwds):
"""Call Noddy and compute the history file
**Arguments**:
- *history* = string : filename of history file
- *output_name* = string : basename for output files
**Optional Keywords**:
- *sim_type* = 'BLOCK', 'GEOPHYSICS', 'SURFACES', 'BLOCK_GEOPHYS',
'TOPOLOGY', 'BLOCK_SURFACES', 'ALL':
type of Noddy simulation (default: 'BLOCK')
- *program_name* = string : name of program
(default: noddy.exe or noddy, both checked)
- *verbose* = bool: verbose mode, print out information for debugging (default = False)
**Returns**:
-Returns any text outputted by the noddy executable.
"""
sim_type = kwds.get("sim_type", 'BLOCK')
if kwds.has_key("verbose") and kwds['verbose']:
out = "Running noddy exectuable at %s(.exe)\n" % noddyPath
else:
out = ""
try: # try running .exe file (windows only)
out += subprocess.Popen([noddyPath + ".exe", history, output_name, sim_type],
shell=False, stderr=subprocess.PIPE,
stdout=subprocess.PIPE).stdout.read()
except OSError: # obviously not running windows - try just the binary
out += subprocess.Popen([noddyPath, history, output_name, sim_type],
shell=False, stderr=subprocess.PIPE,
stdout=subprocess.PIPE).stdout.read()
# Thought: Is there any reason compute_topology should not be called here if sim_type == "TOPOLOGY"???
# It could simplify things a lot....
return out
[docs]def compute_topology(rootname, **kwds):
"""Call the topology executable to compute a models topology.
**Arguments**:
- *rootname* = string : rootname of the noddy model to calculate topology for
**Optional Keywords**:
- *ensure_discrete_volumes* = True if topological units are broken down into
separate, spatially continuous volumes. Otherwise
some topological units may represent two separate
rock volumes (eg. if a folded unit has been truncated
by an unconformity). Default is True, though this is
a global variable (pynoddy.ensure_discrete_volumes)
so it can be changed during runtime.
- *null_volume_threshold* = The smallest non-null volume. volumes smaller than this are
ignored by the topology algorithm (as they represent pixelation artefacts).
The default is 20 voxels, though this is a global variable and can be changed
with pynoddy.null_volume_threshold.
**Returns**
-Returns any text outputted by the topology executable, including errors.
"""
dvol = kwds.get('ensure_discrete_volumes', ensure_discrete_volumes)
nvt = kwds.get('null_volume_threshold', null_volume_threshold)
# convert to string
if dvol:
dvol = "1"
else:
dvol = "0"
out = "Running topology exectuable at %s(.exe)\n" % topologyPath
try: # try running .exe file (windows only)
out = subprocess.Popen([topologyPath + ".exe", rootname, dvol, str(nvt)],
shell=False, stderr=subprocess.PIPE,
stdout=subprocess.PIPE).stdout.read()
except OSError: # obviously not running windows - try just the binary
out = subprocess.Popen([topologyPath, rootname, dvol, str(nvt)],
shell=False, stderr=subprocess.PIPE,
stdout=subprocess.PIPE).stdout.read()
return out