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fix: allow data to be specified in create and add function. #248

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merged 2 commits into from
Jul 1, 2025
Merged

fix: allow data to be specified in create and add function. #248

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c837d6c
fix: allow data to be specified in create and add function.
Jun 16, 2025
5e51e7c
Merge branch 'master' into fix/model-data
lachlangrose Jun 23, 2025
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92 changes: 46 additions & 46 deletions LoopStructural/modelling/core/geological_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -125,9 +125,7 @@ def __init__(
self.features = []
self.feature_name_index = {}
self._data = pd.DataFrame() # None



self.stratigraphic_column = None

self.tol = 1e-10 * np.max(self.bounding_box.maximum - self.bounding_box.origin)
Expand Down Expand Up @@ -179,8 +177,40 @@ def __str__(self):
def _ipython_key_completions_(self):
return self.feature_name_index.keys()


def prepare_data(self, data: pd.DataFrame) -> pd.DataFrame:
data = data.copy()
data[['X', 'Y', 'Z']] = self.bounding_box.project(data[['X', 'Y', 'Z']].to_numpy())

if "type" in data:
logger.warning("'type' is deprecated replace with 'feature_name' \n")
data.rename(columns={"type": "feature_name"}, inplace=True)
if "feature_name" not in data:
logger.error("Data does not contain 'feature_name' column")
raise BaseException("Cannot load data")
for h in all_heading():
if h not in data:
data[h] = np.nan
if h == "w":
data[h] = 1.0
if h == "coord":
data[h] = 0
if h == "polarity":
data[h] = 1.0
# LS wants polarity as -1 or 1, change 0 to -1
data.loc[data["polarity"] == 0, "polarity"] = -1.0
data.loc[np.isnan(data["w"]), "w"] = 1.0
if "strike" in data and "dip" in data:
logger.info("Converting strike and dip to vectors")
mask = np.all(~np.isnan(data.loc[:, ["strike", "dip"]]), axis=1)
data.loc[mask, gradient_vec_names()] = (
strikedip2vector(data.loc[mask, "strike"], data.loc[mask, "dip"])
* data.loc[mask, "polarity"].to_numpy()[:, None]
)
data.drop(["strike", "dip"], axis=1, inplace=True)
data[['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']] = data[
['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']
].astype(float)
return data
@classmethod
def from_processor(cls, processor):
"""Builds a model from a :class:`LoopStructural.modelling.input.ProcessInputData` object
Expand Down Expand Up @@ -473,40 +503,9 @@ def data(self, data: pd.DataFrame):
raise BaseException("Cannot load data")
logger.info(f"Adding data to GeologicalModel with {len(data)} data points")
self._data = data.copy()
self._data[['X','Y','Z']] = self.bounding_box.project(self._data[['X','Y','Z']].to_numpy())


if "type" in self._data:
logger.warning("'type' is deprecated replace with 'feature_name' \n")
self._data.rename(columns={"type": "feature_name"}, inplace=True)
if "feature_name" not in self._data:
logger.error("Data does not contain 'feature_name' column")
raise BaseException("Cannot load data")
for h in all_heading():
if h not in self._data:
self._data[h] = np.nan
if h == "w":
self._data[h] = 1.0
if h == "coord":
self._data[h] = 0
if h == "polarity":
self._data[h] = 1.0
# LS wants polarity as -1 or 1, change 0 to -1
self._data.loc[self._data["polarity"] == 0, "polarity"] = -1.0
self._data.loc[np.isnan(self._data["w"]), "w"] = 1.0
if "strike" in self._data and "dip" in self._data:
logger.info("Converting strike and dip to vectors")
mask = np.all(~np.isnan(self._data.loc[:, ["strike", "dip"]]), axis=1)
self._data.loc[mask, gradient_vec_names()] = (
strikedip2vector(self._data.loc[mask, "strike"], self._data.loc[mask, "dip"])
* self._data.loc[mask, "polarity"].to_numpy()[:, None]
)
self._data.drop(["strike", "dip"], axis=1, inplace=True)
self._data[['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']] = (
self._data[
['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']
].astype(float)
)
# self._data[['X','Y','Z']] = self.bounding_box.project(self._data[['X','Y','Z']].to_numpy())



def set_model_data(self, data):
logger.warning("deprecated method. Model data can now be set using the data attribute")
Expand Down Expand Up @@ -623,7 +622,7 @@ def create_and_add_foliation(
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_surface_data)
series_builder.add_data_from_data_frame(self.prepare_data(series_surface_data))
self._add_faults(series_builder, features=faults)

# build feature
Expand Down Expand Up @@ -697,7 +696,7 @@ def create_and_add_fold_frame(
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)
fold_frame_builder.add_data_from_data_frame(self.prepare_data(fold_frame_data))
self._add_faults(fold_frame_builder[0])
self._add_faults(fold_frame_builder[1])
self._add_faults(fold_frame_builder[2])
Expand Down Expand Up @@ -783,7 +782,10 @@ def create_and_add_folded_foliation(
logger.warning(f"No data for {foliation_name}, skipping")
return
series_builder.add_data_from_data_frame(
foliation_data )
self.prepare_data(
foliation_data
)
)
self._add_faults(series_builder)
# series_builder.add_data_to_interpolator(True)
# build feature
Expand Down Expand Up @@ -878,7 +880,7 @@ def create_and_add_folded_fold_frame(
)
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)
fold_frame_builder.add_data_from_data_frame(self.prepare_data(fold_frame_data))

for i in range(3):
self._add_faults(fold_frame_builder[i])
Expand Down Expand Up @@ -1331,7 +1333,7 @@ def create_and_add_fault(
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

Expand All @@ -1344,7 +1346,7 @@ def create_and_add_fault(
if intermediate_axis:
intermediate_axis = intermediate_axis
fault_frame_builder.create_data_from_geometry(
fault_frame_data=fault_data,
fault_frame_data=self.prepare_data(fault_data),
fault_center=fault_center,
fault_normal_vector=fault_normal_vector,
fault_slip_vector=fault_slip_vector,
Expand Down Expand Up @@ -1397,9 +1399,8 @@ def rescale(self, points: np.ndarray, *, inplace: bool = False) -> np.ndarray:
points : np.array((N,3),dtype=double)

"""

return self.bounding_box.reproject(points,inplace=inplace)


# TODO move scale to bounding box/transformer
def scale(self, points: np.ndarray, *, inplace: bool = False) -> np.ndarray:
Expand All @@ -1418,7 +1419,6 @@ def scale(self, points: np.ndarray, *, inplace: bool = False) -> np.ndarray:

"""
return self.bounding_box.project(np.array(points).astype(float),inplace=inplace)


def regular_grid(self, *, nsteps=None, shuffle=True, rescale=False, order="C"):
"""
Expand Down
6 changes: 3 additions & 3 deletions tests/unit/modelling/intrusions/test_intrusions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,9 +65,9 @@ def test_intrusion_builder():
model.data = data
model.nsteps = [10, 10, 10]

intrusion_data = data[data["feature_name"] == "tabular_intrusion"]
intrusion_frame_data = model.data[model.data["feature_name"] == "tabular_intrusion_frame"]

intrusion_data = model.prepare_data(data[data["feature_name"] == "tabular_intrusion"])
intrusion_frame_data = model.prepare_data(model.data[model.data["feature_name"] == "tabular_intrusion_frame"])
conformable_feature = model.create_and_add_foliation("stratigraphy")

intrusion_frame_parameters = {
Expand Down
2 changes: 1 addition & 1 deletion tests/unit/modelling/test_geological_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ def test_rescale_model_data():
model.set_model_data(data)
# Check that the model data is rescaled to local coordinates
expected = data[['X', 'Y', 'Z']].values - bb[None, 0, :]
actual = model.data[['X', 'Y', 'Z']].values
actual = model.prepare_data(model.data)[['X', 'Y', 'Z']].values
assert np.allclose(actual, expected, atol=1e-6)
def test_access_feature_model():
data, bb = load_claudius()
Expand Down
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