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Fix/add parameter separator #243

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Merged
lachlangrose merged 4 commits into from
Jun 5, 2025
Merged

Fix/add parameter separator #243

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9178d1e
adding n_elements to surfe
Jun 4, 2025
3be6cf1
fix: add parameter separator to clean up api
Jun 4, 2025
47be99a
fix: add option to pass a dataframe directly to the create and add me…
Jun 4, 2025
a8bd694
updating calls to regular_grid
Jun 5, 2025
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4 changes: 2 additions & 2 deletions LoopStructural/export/exporters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -423,7 +423,7 @@ def _write_vol_evtk(model, file_name, data_label, nsteps, real_coords=True):

"""
# Define grid spacing
xyz = model.bounding_box.regular_grid(nsteps)
xyz = model.bounding_box.regular_grid(nsteps=nsteps)
vals = model.evaluate_model(xyz, scale=False)
if real_coords:
model.rescale(xyz)
Expand Down Expand Up @@ -465,7 +465,7 @@ def _write_vol_gocad(model, file_name, data_label, nsteps, real_coords=True):

"""
# Define grid spacing in model scale coords
xyz = model.bounding_box.regular_grid(nsteps)
xyz = model.bounding_box.regular_grid(nsteps=nsteps)

vals = model.evaluate_model(xyz, scale=False)
# Use FORTRAN style indexing for GOCAD VOXET
Expand Down
3 changes: 3 additions & 0 deletions LoopStructural/interpolators/_surfe_wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -205,3 +205,6 @@ def evaluate_gradient(self, evaluation_points):
@property
def nx(self):
return self.get_data_locations().shape[0]
@property
def n_elements(self)->int:
return self.get_data_locations().shape[0]
147 changes: 103 additions & 44 deletions LoopStructural/modelling/core/geological_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

import numpy as np
import pandas as pd
from typing import List
from typing import List, Optional
import pathlib
from ...modelling.features.fault import FaultSegment

Expand Down Expand Up @@ -654,7 +654,9 @@ def set_stratigraphic_column(self, stratigraphic_column, cmap="tab20"):

def create_and_add_foliation(
self,
series_surface_data: str,
series_surface_name: str,
*,
series_surface_data: pd.DataFrame = None,
interpolatortype: str = "FDI",
nelements: int = 1000,
tol=None,
Expand All @@ -664,8 +666,18 @@ def create_and_add_foliation(
"""
Parameters
----------
series_surface_data : string
series_surface_name : string
corresponding to the feature_name in the data
series_surface_data : pd.DataFrame, optional
data frame containing the surface data
interpolatortype : str
the type of interpolator to use, default is 'FDI'
nelements : int
the number of elements to use in the series surface
tol : float, optional
tolerance for the solver, if not specified uses the model default
faults : list, optional
list of faults to be used in the series surface, if not specified uses the model faults
kwargs

Returns
Expand Down Expand Up @@ -696,16 +708,18 @@ def create_and_add_foliation(
bounding_box=self.bounding_box,
interpolatortype=interpolatortype,
nelements=nelements,
name=series_surface_data,
name=series_surface_name,
model=self,
**kwargs,
)
# add data
series_data = self.data[self.data["feature_name"] == series_surface_data]
if series_data.shape[0] == 0:
if series_surface_data is None:
series_surface_data = self.data.loc[self.data["feature_name"] == series_surface_name]

if series_surface_data.shape[0] == 0:
logger.warning("No data for {series_surface_data}, skipping")
return
series_builder.add_data_from_data_frame(series_data)
series_builder.add_data_from_data_frame(series_surface_data)
self._add_faults(series_builder, features=faults)

# build feature
Expand All @@ -721,7 +735,9 @@ def create_and_add_foliation(

def create_and_add_fold_frame(
self,
foldframe_data,
fold_frame_name:str,
*,
fold_frame_data=None,
interpolatortype="FDI",
nelements=1000,
tol=None,
Expand All @@ -731,10 +747,24 @@ def create_and_add_fold_frame(
"""
Parameters
----------
foldframe_data : string
fold_frame_name : string
unique string in feature_name column

kwargs
fold_frame_data : pandas data frame
if not specified uses the model data
interpolatortype : str
the type of interpolator to use, default is 'FDI'
nelements : int
the number of elements to use in the fold frame
tol : float, optional
tolerance for the solver
buffer : float
buffer to add to the bounding box of the fold frame
**kwargs : dict
additional parameters to be passed to the
:class:`LoopStructural.modelling.features.builders.StructuralFrameBuilder`
and :meth:`LoopStructural.modelling.features.builders.StructuralFrameBuilder.setup`
and the interpolator, such as `domain` or `tol`


Returns
-------
Expand All @@ -751,14 +781,18 @@ def create_and_add_fold_frame(
fold_frame_builder = StructuralFrameBuilder(
interpolatortype=interpolatortype,
bounding_box=self.bounding_box.with_buffer(buffer),
name=foldframe_data,
name=fold_frame_name,
frame=FoldFrame,
nelements=nelements,
model=self,
**kwargs,
)
# add data
fold_frame_data = self.data[self.data["feature_name"] == foldframe_data]
if fold_frame_data is None:
fold_frame_data = self.data.loc[self.data["feature_name"] == fold_frame_name]
if fold_frame_data.shape[0] == 0:
logger.warning(f"No data for {fold_frame_name}, skipping")
return
fold_frame_builder.add_data_from_data_frame(fold_frame_data)
self._add_faults(fold_frame_builder[0])
self._add_faults(fold_frame_builder[1])
Expand All @@ -775,7 +809,9 @@ def create_and_add_fold_frame(

def create_and_add_folded_foliation(
self,
foliation_data,
foliation_name,
*,
foliation_data=None,
interpolatortype="DFI",
nelements=10000,
buffer=0.1,
Expand Down Expand Up @@ -832,15 +868,18 @@ def create_and_add_folded_foliation(
bounding_box=self.bounding_box.with_buffer(buffer),
nelements=nelements,
fold=fold,
name=foliation_data,
name=foliation_name,
svario=svario,
model=self,
**kwargs,
)

if foliation_data is None:
foliation_data = self.data.loc[self.data["feature_name"] == foliation_name]
if foliation_data.shape[0] == 0:
logger.warning(f"No data for {foliation_name}, skipping")
return
series_builder.add_data_from_data_frame(
self.data[self.data["feature_name"] == foliation_data]
)
foliation_data )
self._add_faults(series_builder)
# series_builder.add_data_to_interpolator(True)
# build feature
Expand All @@ -858,7 +897,9 @@ def create_and_add_folded_foliation(

def create_and_add_folded_fold_frame(
self,
fold_frame_data,
fold_frame_name: str,
*,
fold_frame_data: Optional[pd.DataFrame] = None,
interpolatortype="FDI",
nelements=10000,
fold_frame=None,
Expand All @@ -869,14 +910,22 @@ def create_and_add_folded_fold_frame(

Parameters
----------
fold_frame_data : string
fold_frame_name : string
name of the feature to be added

fold_frame_data : pandas data frame, optional
data frame containing the fold frame data, if not specified uses the model data
interpolatortype : str
the type of interpolator to use, default is 'FDI' (unused) 5/6/2025
fold_frame : StructuralFrame, optional
the fold frame for the fold if not specified uses last feature added

kwargs : dict
parameters passed to child functions
nelements : int
the number of elements to use in the fold frame
tol : float, optional
tolerance for the solver, if not specified uses the model default
**kwargs : dict
additional parameters to be passed to the
:class:`LoopStructural.modelling.features.builders.StructuralFrameBuilder`
and :meth:`LoopStructural.modelling.features.builders.StructuralFrameBuilder.setup`

Returns
-------
Expand Down Expand Up @@ -917,15 +966,15 @@ def create_and_add_folded_fold_frame(
interpolatortype=interpolatortypes,
bounding_box=self.bounding_box.with_buffer(kwargs.get("buffer", 0.1)),
nelements=[nelements, nelements, nelements],
name=fold_frame_data,
name=fold_frame_name,
fold=fold,
frame=FoldFrame,
model=self,
**kwargs,
)
fold_frame_builder.add_data_from_data_frame(
self.data[self.data["feature_name"] == fold_frame_data]
)
if fold_frame_data is None:
fold_frame_data = self.data[self.data["feature_name"] == fold_frame_name]
fold_frame_builder.add_data_from_data_frame(fold_frame_data)

for i in range(3):
self._add_faults(fold_frame_builder[i])
Expand All @@ -947,6 +996,7 @@ def create_and_add_intrusion(
self,
intrusion_name,
intrusion_frame_name,
*,
intrusion_frame_parameters={},
intrusion_lateral_extent_model=None,
intrusion_vertical_extent_model=None,
Expand Down Expand Up @@ -1224,7 +1274,7 @@ def add_onlap_unconformity(self, feature: GeologicalFeature, value: float) -> Ge
return uc_feature

def create_and_add_domain_fault(
self, fault_surface_data, nelements=10000, interpolatortype="FDI", **kwargs
self, fault_surface_data,*, nelements=10000, interpolatortype="FDI", **kwargs
):
"""
Parameters
Expand Down Expand Up @@ -1252,7 +1302,7 @@ def create_and_add_domain_fault(
)

# add data
unconformity_data = self.data[self.data["feature_name"] == fault_surface_data]
unconformity_data = self.data.loc[self.data["feature_name"] == fault_surface_data]

domain_fault_feature_builder.add_data_from_data_frame(unconformity_data)
# look through existing features if there is a fault before an
Expand All @@ -1275,8 +1325,10 @@ def create_and_add_domain_fault(

def create_and_add_fault(
self,
fault_surface_data,
displacement,
fault_name: str,
displacement: float,
*,
fault_data:Optional[pd.DataFrame] = None,
interpolatortype="FDI",
tol=None,
fault_slip_vector=None,
Expand All @@ -1299,9 +1351,12 @@ def create_and_add_fault(
"""
Parameters
----------
fault_surface_data : string
fault_name : string
name of the fault surface data in the dataframe
displacement : displacement magnitude
displacement magnitude of the fault, in model units
fault_data : pd.DataFrame, optional
data frame containing the fault data, if not specified uses the model data
major_axis : [type], optional
[description], by default None
minor_axis : [type], optional
Expand All @@ -1328,7 +1383,7 @@ def create_and_add_fault(
if "fault_vectical_radius" in kwargs and intermediate_axis is None:
intermediate_axis = kwargs["fault_vectical_radius"]

logger.info(f'Creating fault "{fault_surface_data}"')
logger.info(f'Creating fault "{fault_name}"')
logger.info(f"Displacement: {displacement}")
logger.info(f"Tolerance: {tol}")
logger.info(f"Fault function: {faultfunction}")
Expand All @@ -1353,7 +1408,7 @@ def create_and_add_fault(
# tol *= 0.1*minor_axis

if displacement == 0:
logger.warning(f"{fault_surface_data} displacement is 0")
logger.warning(f"{fault_name} displacement is 0")

if "data_region" in kwargs:
kwargs.pop("data_region")
Expand All @@ -1363,14 +1418,18 @@ def create_and_add_fault(
interpolatortype,
bounding_box=self.bounding_box,
nelements=kwargs.pop("nelements", 1e4),
name=fault_surface_data,
name=fault_name,
model=self,
**kwargs,
)
fault_frame_data = self.data.loc[self.data["feature_name"] == fault_surface_data].copy()
if fault_data is None:
fault_data = self.data.loc[self.data["feature_name"] == fault_name]
if fault_data.shape[0] == 0:
logger.warning(f"No data for {fault_name}, skipping")
return

self._add_faults(fault_frame_builder, features=faults)
# add data
fault_frame_data = self.data.loc[self.data["feature_name"] == fault_surface_data].copy()

if fault_center is not None and ~np.isnan(fault_center).any():
fault_center = self.scale(fault_center, inplace=False)
Expand All @@ -1381,7 +1440,7 @@ def create_and_add_fault(
if intermediate_axis:
intermediate_axis = intermediate_axis / self.scale_factor
fault_frame_builder.create_data_from_geometry(
fault_frame_data=fault_frame_data,
fault_frame_data=fault_data,
fault_center=fault_center,
fault_normal_vector=fault_normal_vector,
fault_slip_vector=fault_slip_vector,
Expand Down Expand Up @@ -1418,7 +1477,7 @@ def create_and_add_fault(
return fault

# TODO move rescale to bounding box/transformer
def rescale(self, points: np.ndarray, inplace: bool = False) -> np.ndarray:
def rescale(self, points: np.ndarray, *, inplace: bool = False) -> np.ndarray:
"""
Convert from model scale to real world scale - in the future this
should also do transformations?
Expand All @@ -1441,7 +1500,7 @@ def rescale(self, points: np.ndarray, inplace: bool = False) -> np.ndarray:
return points

# TODO move scale to bounding box/transformer
def scale(self, points: np.ndarray, inplace: bool = False) -> np.ndarray:
def scale(self, points: np.ndarray, *, inplace: bool = False) -> np.ndarray:
"""Take points in UTM coordinates and reproject
into scaled model space

Expand All @@ -1467,7 +1526,7 @@ def scale(self, points: np.ndarray, inplace: bool = False) -> np.ndarray:
points /= self.scale_factor
return points

def regular_grid(self, nsteps=None, shuffle=True, rescale=False, order="C"):
def regular_grid(self, *, nsteps=None, shuffle=True, rescale=False, order="C"):
"""
Return a regular grid within the model bounding box

Expand All @@ -1483,7 +1542,7 @@ def regular_grid(self, nsteps=None, shuffle=True, rescale=False, order="C"):
"""
return self.bounding_box.regular_grid(nsteps=nsteps, shuffle=shuffle, order=order)

def evaluate_model(self, xyz: np.ndarray, scale: bool = True) -> np.ndarray:
def evaluate_model(self, xyz: np.ndarray, *, scale: bool = True) -> np.ndarray:
"""Evaluate the stratigraphic id at each location

Parameters
Expand Down Expand Up @@ -1559,7 +1618,7 @@ def evaluate_model(self, xyz: np.ndarray, scale: bool = True) -> np.ndarray:
logger.error(f"Model does not contain {group}")
return strat_id

def evaluate_model_gradient(self, points: np.ndarray, scale: bool = True) -> np.ndarray:
def evaluate_model_gradient(self, points: np.ndarray, *, scale: bool = True) -> np.ndarray:
"""Evaluate the gradient of the stratigraphic column at each location

Parameters
Expand Down
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