def test_outside_box_normal(): for interpolator in ['PLI', 'FDI']: print(f'Running test for {interpolator} with normal constraints') model = GeologicalModel(np.zeros(3), np.ones(3)) data = pd.DataFrame( [[0.5, 0.5, 0.5, 0, 1., 0., 'strati'], [1.5, 0.5, 0.5, 0, 1., 0., 'strati'], [0.5, 1.5, 1.5, 0, 1., 0., 'strati']], columns=['X', 'Y', 'Z', 'nx', 'ny', 'nz', 'feature_name']) model.data = data model.create_and_add_foliation('strati', interpolatortype=interpolator) model.update()
def test_remove_constraints_PLI(): data, bb = load_claudius() model = GeologicalModel(bb[0, :], bb[1, :]) model.set_model_data(data) s0 = model.create_and_add_foliation("s0", interpolatortype="FDI", nelements=1000, solver="cg", damp=False)
def test_create_stratigraphy_PLI_pyamg(): data, bb = load_claudius() model = GeologicalModel(bb[0, :], bb[1, :]) model.set_model_data(data) s0 = model.create_and_add_foliation("s0", interpolatortype="PLI", nelements=1000, solver="pyamg", damp=True)
def test_create_stratigraphy_PLI_lu(): data, bb = load_claudius() model = GeologicalModel(bb[0, :], bb[1, :]) model.set_model_data(data) s0 = model.create_and_add_foliation('s0', interpolatortype='PLI', nelements=1000, solver='lu', damp=True)
def test_access_feature_model(): data, bb = load_claudius() model = GeologicalModel(bb[0, :], bb[1, :]) model.set_model_data(data) s0 = model.create_and_add_foliation("s0", interpolatortype="FDI", nelements=1000, solver="fake", damp=False) assert s0 == model["s0"]
def test_intrusion_builder(): model = GeologicalModel(boundary_points[0, :], boundary_points[1, :]) model.data = data model.nsteps = [10, 10, 10] intrusion_data = data[data['feature_name'] == 'tabular_intrusion'] frame_data = model.data[model.data["feature_name"] == 'tabular_intrusion_frame'].copy() conformable_feature = model.create_and_add_foliation('stratigraphy') intrusion_network_parameters = {'type': 'interpolated', 'contact': 'roof'} interpolator = model.get_interpolator(interpolatortype='FDI') intrusion_frame_builder = IntrusionFrameBuilder( interpolator, name='tabular_intrusion_frame', model=model) # -- create intrusion network intrusion_frame_builder.set_intrusion_network_parameters( intrusion_data, intrusion_network_parameters) intrusion_network_geometry = intrusion_frame_builder.create_intrusion_network( ) # -- create intrusion frame using intrusion network points and flow/inflation measurements intrusion_frame_builder.set_intrusion_frame_data( frame_data, intrusion_network_geometry) ## -- create intrusion frame intrusion_frame_builder.setup() intrusion_frame = intrusion_frame_builder.frame # -- create intrusion builder to simulate distance thresholds along frame coordinates intrusion_builder = IntrusionBuilder(intrusion_frame, model=model, name="tabular intrusion") intrusion_builder.lateral_extent_model = rectangle_function #intrusion_lateral_extent_model intrusion_builder.vertical_extent_model = parallelepiped_function #intrusion_vertical_extent_model intrusion_builder.set_data_for_extent_simulation(intrusion_data) intrusion_builder.build_arguments = { "lateral_extent_sgs_parameters": {}, "vertical_extent_sgs_parameters": {} } intrusion_feature = intrusion_builder.feature intrusion_builder.update() assert len(intrusion_feature._lateral_simulated_thresholds) > 0 assert len(intrusion_feature._growth_simulated_thresholds) > 0
data, bb = load_claudius() data = data.reset_index() data.loc[:, 'val'] *= -1 data.loc[:, ['nx', 'ny', 'nz']] *= -1 data.loc[792, 'feature_name'] = 'strati2' data.loc[792, ['nx', 'ny', 'nz']] = [0, 0, 1] data.loc[792, 'val'] = 0 model = GeologicalModel(bb[0, :], bb[1, :]) model.set_model_data(data) strati2 = model.create_and_add_foliation('strati2', interpolatortype='PLI', nelements=1e4, solver='pyamg') uc = model.add_unconformity(strati2, 1) strati = model.create_and_add_foliation('strati', interpolatortype='PLI', nelements=1e4, solver='pyamg') ######################################################################## # Stratigraphic columns # ~~~~~~~~~~~~~~~~~~~~~~~ # We define the stratigraphic column using a nested dictionary stratigraphic_column = {} stratigraphic_column['strati2'] = {}
# ~~~~~~~~~~~~~~~~~~~~ # # - Use the toggle bar to change the amount of data used by the # interpolation algorithm. # - How does the shape of the fold change as we remove data points? # - Now what happens if we only consider data from the map view? # # **HINT** you can view the strike and dip data by unchecking the scalar # field box. # # **The black arrows are the normal vector to the folded surface** # npoints = 20 model = GeologicalModel(boundary_points[0,:],boundary_points[1,:]) model.set_model_data(data[:npoints]) stratigraphy = model.create_and_add_foliation("s0",interpolatortype="PLI",nelements=5000,buffer=0.3,cgw=0.1)#.2) viewer = LavaVuModelViewer(model,background="white") # viewer.add_scalar_field(model.bounding_box,(38,55,30), # 'box', # paint_with=stratigraphy, # cmap='prism') viewer.add_data(stratigraphy) viewer.add_isosurface(stratigraphy, ) viewer.rotate([-85.18760681152344, 42.93233871459961, 0.8641873002052307]) viewer.display() ###################################################################### # Modelling folds using structural geology # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# To create a GeologicalModel we need to define the extent of the model with an origin vector and a maximum vector. # The pandas dataframe that contains the model data need to be linked to the geological model. # from LoopStructural import GeologicalModel model = GeologicalModel(extent[:,0],extent[:,1]) model.set_model_data(data) ############################################################################################### # Adding a conformable foliation # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # We can create a geological feature using the create_and_add_foliation method. # This returns a To build a scalar field representing the conformable_feature = model.create_and_add_foliation('conformable') ############################################################################################### # Visualising a 2-D section # ~~~~~~~~~~~~~~~~~~~~~~~~~ # Geological feature can be evaluated: # * for the scalar field value at a location # * for the gradient of the scalar field at a location # To evaluate a model feature (scalar value or gradient) use the: # :code:`model.evaluate_feature_value(feature_name, locations)` or # :code:`model.evaluate_feature_gradient(feature_name, locations)` # Where the feature_name is the string naming the feature and locations is a numpy array of # xyz coordinates. # # In the following example we will use matplotlib to visualise these results however, the # next tutorial will show how to use the lavavu visualisation model.
origin=origin, maximum=maximum, ) ############################## # The process input data can be used to directly build a geological model model = GeologicalModel.from_processor(processor) model.update() ############################## # Or build directly from the dataframe and processor attributes. model2 = GeologicalModel(processor.origin, processor.maximum) model2.data = processor.data model2.create_and_add_foliation("supergroup_0") model2.update() ############################## # Visualising model # ~~~~~~~~~~~~~~~~~ view = LavaVuModelViewer(model) view.add_model_surfaces() view.rotation = [-37.965614318847656, 13.706363677978516, 3.110347032546997] view.display() ############################## # Adding faults # ~~~~~~~~~~~~~
def build_model(m2l_data, evaluate=True, skip_faults=False, unconformities=False, fault_params=None, foliation_params=None, rescale=True, skip_features=[], **kwargs): """[summary] [extended_summary] Parameters ---------- m2l_data : dict [description] skip_faults : bool, optional [description], by default False fault_params : dict, optional [description], by default None foliation_params : dict, optional [description], by default None Returns ------- [type] [description] """ from LoopStructural import GeologicalModel boundary_points = np.zeros((2, 3)) boundary_points[0, 0] = m2l_data["bounding_box"]["minx"] boundary_points[0, 1] = m2l_data["bounding_box"]["miny"] boundary_points[0, 2] = m2l_data["bounding_box"]["lower"] boundary_points[1, 0] = m2l_data["bounding_box"]["maxx"] boundary_points[1, 1] = m2l_data["bounding_box"]["maxy"] boundary_points[1, 2] = m2l_data["bounding_box"]["upper"] model = GeologicalModel(boundary_points[0, :], boundary_points[1, :], rescale=rescale) # m2l_data['data']['val'] /= model.scale_factor model.set_model_data(m2l_data["data"]) if not skip_faults: faults = [] for f in m2l_data["max_displacement"].keys(): if model.data[model.data["feature_name"] == f].shape[0] == 0: continue if f in skip_features: continue fault_id = f overprints = [] try: overprint_id = m2l_data["fault_fault"][ m2l_data["fault_fault"][fault_id] == 1]["fault_id"].to_numpy() for i in overprint_id: overprints.append(i) logger.info("Adding fault overprints {}".format(f)) except: logger.info("No entry for %s in fault_fault_relations" % f) # continue fault_center = m2l_data["stratigraphic_column"]["faults"][f][ "FaultCenter"] fault_influence = m2l_data["stratigraphic_column"]["faults"][f][ "InfluenceDistance"] fault_extent = m2l_data["stratigraphic_column"]["faults"][f][ "HorizontalRadius"] fault_vertical_radius = m2l_data["stratigraphic_column"]["faults"][ f]["VerticalRadius"] fault_slip_vector = m2l_data["stratigraphic_column"]["faults"][f][ "FaultSlip"] faults.append( model.create_and_add_fault( f, -m2l_data["max_displacement"][f], faultfunction="BaseFault", fault_slip_vector=fault_slip_vector, fault_center=fault_center, fault_extent=fault_extent, fault_influence=fault_influence, fault_vectical_radius=fault_vertical_radius, # overprints=overprints, **fault_params, )) # for f in m2l_data['fault_intersection_angles']: # if f in m2l_data['max_displacement'].keys(): # f1_norm = m2l_data['stratigraphic_column']['faults'][f]['FaultNorm'] # for intersection in m2l_data['fault_intersection_angles'][f]: # if intersection[0] in m2l_data['max_displacement'].keys(): # f2_norm = m2l_data['stratigraphic_column']['faults'][intersection[0]]['FaultNorm'] # if intersection[2] < 30 and np.dot(f1_norm,f2_norm)>0: # logger.info('Adding splay {} to {}'.format(intersection[0],f)) # if model[f] is None: # logger.error('Fault {} does not exist, cannot be added as splay') # elif model[intersection[0]] is None: # logger.error('Fault {} does not exist') # else: # model[intersection[0]].builder.add_splay(model[f]) # else: # logger.info('Adding abut {} to {}'.format(intersection[0],f)) # model[intersection[0]].add_abutting_fault(model[f]) faults = m2l_data.get("fault_graph", None) if faults: for f in faults.nodes: f1_norm = m2l_data["stratigraphic_column"]["faults"][f][ "FaultNorm"] for e in faults.edges(f): data = faults.get_edge_data(*e) f2_norm = m2l_data["stratigraphic_column"]["faults"][ e[1]]["FaultNorm"] if float(data["angle"]) < 30 and np.dot(f1_norm, f2_norm) > 0: if model[f] is None or model[e[1]] is None: logger.error( "Fault {} does not exist, cannot be added as splay" ) elif model[e[1]] is None: logger.error("Fault {} does not exist") else: region = model[e[1]].builder.add_splay(model[f]) model[e[1]].splay[model[f].name] = region else: if model[f] is None or model[e[1]] is None: continue logger.info("Adding abut {} to {}".format(e[1], f)) model[e[1]].add_abutting_fault(model[f]) ## loop through all of the groups and add them to the model in youngest to oldest. group_features = [] for i in np.sort(m2l_data["groups"]["group number"].unique()): g = (m2l_data["groups"].loc[m2l_data["groups"]["group number"] == i, "group"].unique()[0]) group_features.append( model.create_and_add_foliation(g, **foliation_params)) # if the group was successfully added (not null) then lets add the base (0 to be unconformity) if group_features[-1] and unconformities: model.add_unconformity(group_features[-1], 0) model.set_stratigraphic_column(m2l_data["stratigraphic_column"]) if evaluate: model.update(verbose=True) return model
def build_model(m2l_data, skip_faults=False, unconformities=False, fault_params=None, foliation_params=None, rescale=True, **kwargs): """[summary] [extended_summary] Parameters ---------- m2l_data : dict [description] skip_faults : bool, optional [description], by default False fault_params : dict, optional [description], by default None foliation_params : dict, optional [description], by default None Returns ------- [type] [description] """ from LoopStructural import GeologicalModel boundary_points = np.zeros((2, 3)) boundary_points[0, 0] = m2l_data['bounding_box']['minx'] boundary_points[0, 1] = m2l_data['bounding_box']['miny'] boundary_points[0, 2] = m2l_data['bounding_box']['lower'] boundary_points[1, 0] = m2l_data['bounding_box']['maxx'] boundary_points[1, 1] = m2l_data['bounding_box']['maxy'] boundary_points[1, 2] = m2l_data['bounding_box']['upper'] model = GeologicalModel(boundary_points[0, :], boundary_points[1, :], rescale=rescale) # m2l_data['data']['val'] /= model.scale_factor model.set_model_data(m2l_data['data']) if not skip_faults: faults = [] for f in m2l_data['max_displacement'].keys(): if model.data[model.data['feature_name'] == f].shape[0] == 0: continue fault_id = f overprints = [] try: overprint_id = m2l_data['fault_fault'][ m2l_data['fault_fault'][fault_id] == 1]['fault_id'].to_numpy() for i in overprint_id: overprints.append(i) logger.info('Adding fault overprints {}'.format(f)) except: logger.info('No entry for %s in fault_fault_relations' % f) # continue faults.append( model.create_and_add_fault( f, -m2l_data['max_displacement'][f], faultfunction='BaseFault', overprints=overprints, **fault_params, )) ## loop through all of the groups and add them to the model in youngest to oldest. group_features = [] for i in np.sort(m2l_data['groups']['group number'].unique()): g = m2l_data['groups'].loc[m2l_data['groups']['group number'] == i, 'group'].unique()[0] group_features.append( model.create_and_add_foliation(g, **foliation_params)) # if the group was successfully added (not null) then lets add the base (0 to be unconformity) if group_features[-1] and unconformities: model.add_unconformity(group_features[-1], 0) model.set_stratigraphic_column(m2l_data['stratigraphic_column']) return model
from LoopStructural import GeologicalModel from LoopStructural.visualisation import LavaVuModelViewer from LoopStructural.datasets import load_claudius #demo data import pandas as pd import numpy as np ##################### # Build the model # ~~~~~~~~~~~~~~~~~ data, bb = load_claudius() model = GeologicalModel(bb[0,:],bb[1,:]) model.set_model_data(data) strati = model.create_and_add_foliation("strati") strat_column = {'strati':{}} vals = [0,60,250,330,600] for i in range(len(vals)-1): strat_column['strati']['unit_{}'.format(i)] = {'min':vals[i],'max':vals[i+1],'id':i} model.set_stratigraphic_column(strat_column) ###################################################################### # Visualising results # ~~~~~~~~~~~~~~~~~~~ # # The LavaVuModelViewer is an LoopStructural class that provides easy 3D # plotting options for plotting data points and resulting implicit # functions. # # The implicit function can be visualised by looking at isosurfaces of the
import logging logging.getLogger().setLevel(logging.INFO) data, bb = load_claudius()#claudius.get_data() bb[1,0]+=200 bb[0,0]-=200 bb[1,1]+=200 bb[0,1]-=200 bb[1,2]+=200 bb[0,2]-=200 model = GeologicalModel(bb[0,:],bb[1,:]) data['random'] = np.random.random(data.shape[0]) model.set_model_data(data[data['random'] < 0.01])#[np.isnan(data['val'])]) strati = model.create_and_add_foliation("strati", interpolatortype="surfe", method='single_surface' ) print(strati.evaluate_value(model.regular_grid((10,10,10)))) viewer = LavaVuModelViewer(model,background="white") # determine the number of unique surfaces in the model from # the input data and then calculate isosurfaces for this unique = np.unique(strati.interpolator.get_value_constraints()[:,3]) viewer.add_isosurface(model.features[0], slices=unique, cmap='prism', paint_with=model.features[0]) # # # viewer.add_section(model.features[0], # # axis='x', # # value=0,
def loop2LoopStructural(thickness_file,orientation_file,contacts_file,bbox): from LoopStructural import GeologicalModel from LoopStructural.visualisation import LavaVuModelViewer import lavavu df = pd.read_csv(thickness_file) thickness = {} for f in df['formation'].unique(): thickness[f] = np.mean(df[df['formation']==f]['thickness']) #display(thickness) order = ['P__TKa_xs_k','P__TKo_stq','P__TKk_sf','P__TK_s', 'A_HAu_xsl_ci', 'A_HAd_kd', 'A_HAm_cib', 'A_FOj_xs_b', 'A_FO_xo_a', 'A_FO_od', 'A_FOu_bbo', 'A_FOp_bs', 'A_FOo_bbo', 'A_FOh_xs_f', 'A_FOr_b'] strat_val = {} val = 0 for o in order: if o in thickness: strat_val[o] = val val+=thickness[o] #display(strat_val) orientations = pd.read_csv(orientation_file) contacts = pd.read_csv(contacts_file) contacts['val'] = np.nan for o in strat_val: contacts.loc[contacts['formation']==o,'val'] = strat_val[o] data = pd.concat([orientations,contacts],sort=False) data['type'] = np.nan for o in order: data.loc[data['formation']==o,'type'] = 's0' data boundary_points = np.zeros((2,3)) boundary_points[0,0] = bbox[0] boundary_points[0,1] = bbox[1] boundary_points[0,2] = -20000 boundary_points[1,0] = bbox[2] boundary_points[1,1] = bbox[3] boundary_points[1,2] = 1200 model = GeologicalModel(boundary_points[0,:],boundary_points[1,:]) model.set_model_data(data) strati = model.create_and_add_foliation('s0', #identifier in data frame interpolatortype="FDI", #which interpolator to use nelements=400000, # how many tetras/voxels buffer=0.1, # how much to extend nterpolation around box solver='external', external=solve_pyamg ) #viewer = LavaVuModelViewer() viewer = LavaVuModelViewer(model) viewer.add_data(strati['feature']) viewer.add_isosurface(strati['feature'], # nslices=10, slices= strat_val.values(), # voxet={'bounding_box':boundary_points,'nsteps':(100,100,50)}, paint_with=strati['feature'], cmap='tab20' ) #viewer.add_scalar_field(model.bounding_box,(100,100,100), # 'scalar', ## norm=True, # paint_with=strati['feature'], # cmap='tab20') viewer.add_scalar_field(strati['feature']) viewer.set_viewer_rotation([-53.8190803527832, -17.1993350982666, -2.1576387882232666]) #viewer.save("fdi_surfaces.png") viewer.interactive()
################################################################################################## # Create model # ~~~~~~~~~~~~~~~~~~~~ data, bb = load_claudius() model = GeologicalModel(bb[0,:],bb[1,:]) model.set_model_data(data) vals = [0,60,250,330,600] strat_column = {'strati':{}} for i in range(len(vals)-1): strat_column['strati']['unit_{}'.format(i)] = {'min':vals[i],'max':vals[i+1],'id':i} model.set_stratigraphic_column(strat_column) strati = model.create_and_add_foliation("strati", interpolatortype="FDI", # try changing this to 'PLI' nelements=1e4, # try changing between 1e3 and 5e4 buffer=0.3, solver='pyamg', damp=True ) viewer = LavaVuModelViewer(model,background="white") viewer.add_model_surfaces() viewer.rotate([-85.18760681152344, 42.93233871459961, 0.8641873002052307]) viewer.display() ################################################################################################# # Looking at the log file # ~~~~~~~~~~~~~~~~~~~~~~~ # Here are the first 10 lines of the log file. # Most operations in loopstructural are recorded and this will allow you to identify whether # an operation is not occuring as you would expect. from itertools import islice
name='prefault') viewer.rotation = [-73.24819946289062, -86.82220458984375, -13.912878036499023] viewer.display() displacement = 400 #INSERT YOUR DISPLACEMENT NUMBER HERE BEFORE # model = GeologicalModel(bb[0, :], bb[1, :]) model.set_model_data(data) fault = model.create_and_add_fault('fault', displacement, nelements=2000, steps=4, interpolatortype='PLI', buffer=2) strati = model.create_and_add_foliation('strati', nelements=30000, interpolatortype='PLI', cgw=0.03) model.update() viewer = LavaVuModelViewer(model) viewer.add_isosurface(strati, isovalue=0) # viewer.add_data(model.features[0][0]) viewer.add_data(strati) viewer.add_isosurface(fault, isovalue=0 # slices=[0,1]#nslices=10 ) viewer.add_points( model.data[model.data['feature_name'] == 'strati'][['X', 'Y', 'Z']], name='prefault') viewer.rotation = [-73.24819946289062, -86.82220458984375, -13.912878036499023] viewer.display()
for v in [1, 5, 1 / 5]: v_data = np.zeros((1, 4)) v_data[0, :3] += 0.1 data = pd.DataFrame(v_data, columns=["X", "Y", "Z", "val"]) data["feature_name"] = "test" data["feature_name"] = "test" data["nx"] = np.nan data["ny"] = np.nan data["nz"] = np.nan data.loc[3, :] = [0, 0, 0, np.nan, "test", v, 0, 0] # data.loc[3,['nx','ny','nz']]/=np.linalg.norm(data.loc[3,['nx','ny','nz']]) # data.loc[4,:] = [0,0,1,np.nan,'test',1,0,0] model = GeologicalModel(np.zeros(3), np.ones(3) * 10) model.data = data model.create_and_add_foliation("test", nelements=1e4, interpolatortype="FDI") view = LavaVuModelViewer(model) view.add_isosurface(model["test"], slices=[0, 1], name="test") view.add_data(model["test"]) view.rotate([-92.68915557861328, 2.879497528076172, 1.5840799808502197]) view.xmin = 0 view.ymin = 0 view.zmin = 0 view.xmax = 10 view.ymax = 10 view.zmax = 10 images[v] = view.image_array() fig, ax = plt.subplots(1, 3, figsize=(30, 10)) ax[0].imshow(images[1]) ax[1].imshow(images[5])
def test_intrusion_freame_builder(): model = GeologicalModel(boundary_points[0, :], boundary_points[1, :]) model.data = data model.nsteps = [10, 10, 10] intrusion_data = data[data['feature_name'] == 'tabular_intrusion'] frame_data = model.data[model.data["feature_name"] == 'tabular_intrusion_frame'].copy() conformable_feature = model.create_and_add_foliation('stratigraphy') intrusion_network_parameters = { 'type': 'shortest path', 'contact': 'roof', 'delta_c': [2], 'contact_anisotropies': [conformable_feature], 'shortest_path_sequence': [conformable_feature], 'shortest_path_axis': 'X' } delta_c = intrusion_network_parameters.get('delta_c')[0] # -- get variables for intrusion frame interpolation interpolatortype = "FDI" nelements = 1e2 weights = [0, 0, 0] interpolator = model.get_interpolator(interpolatortype=interpolatortype) intrusion_frame_builder = IntrusionFrameBuilder( interpolator, name='tabular_intrusion_frame', model=model) # -- create intrusion network intrusion_frame_builder.set_intrusion_network_parameters( intrusion_data, intrusion_network_parameters) intrusion_network_geometry = intrusion_frame_builder.create_intrusion_network( ) keys = list(intrusion_frame_builder.anisotropies_series_parameters.keys()) # #test if points lie in the contact of interest mean = intrusion_frame_builder.anisotropies_series_parameters[keys[0]][1] # mean = -10 stdv = intrusion_frame_builder.anisotropies_series_parameters[keys[0]][2] evaluated_inet_points = conformable_feature.evaluate_value( model.scale(intrusion_network_geometry[:, :3])) assert np.all( np.logical_and((mean - stdv * delta_c) <= evaluated_inet_points, (mean + stdv * delta_c) >= evaluated_inet_points)) # -- create intrusion frame using intrusion network points and flow/inflation measurements intrusion_frame_builder.set_intrusion_frame_data( frame_data, intrusion_network_geometry) ## -- create intrusion frame intrusion_frame_builder.setup( nelements=nelements, w2=weights[0], w1=weights[1], gxygz=weights[2], ) intrusion_frame = intrusion_frame_builder.frame assert isinstance(intrusion_frame, StructuralFrame)