LoopStructural 1.0.9__cp38-cp38-win32.whl

LoopStructural/utils/map2loop.py

@@ -0,0 +1,353 @@
+import pandas as pd
+import numpy as np
+import os
+import logging
+import networkx
+
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
+
+def process_map2loop(m2l_directory, flags={}):
+    """
+    Extracts relevant information from map2loop outputs
+
+    Parameters
+    ----------
+    m2l_directory : string
+        absolute path to a directory containing map2loop outputs
+    Returns
+    -------
+    m2l_data : dict
+        a dictionary containing the extracted and collated data
+    """
+    gradient = flags.get('gradient',False)
+    vector_scale = flags.get('vector_scale',None)
+    tangents = pd.read_csv(m2l_directory + '/tmp/raw_contacts.csv')
+    groups = pd.read_csv(m2l_directory + '/tmp/all_sorts_clean.csv', index_col=0)
+    contact_orientations = pd.read_csv(m2l_directory + '/output/orientations_clean.csv')
+    # formation_thickness = pd.read_csv)
+    contacts = pd.read_csv(m2l_directory + '/output/contacts_clean.csv')
+    displacements = pd.read_csv(m2l_directory + '/output/fault_displacements3.csv')
+    fault_orientations = pd.read_csv(m2l_directory + '/output/fault_orientations.csv')
+    fault_locations = pd.read_csv(m2l_directory + '/output/faults.csv')
+    fault_fault_relations = pd.read_csv(m2l_directory + '/output/fault-fault-relationships.csv')
+    fault_strat_relations = pd.read_csv(m2l_directory + '/output/group-fault-relationships.csv')
+    fault_dimensions = pd.read_csv(m2l_directory + '/output/fault_dimensions.csv')
+    fault_graph = networkx.read_gml(m2l_directory + '/tmp/fault_network.gml')
+
+    supergroups = {}
+    sgi = 0
+    try:
+        with open(m2l_directory + '/tmp/super_groups.csv') as    f:
+            for l in f:
+                for g in l.split(','):
+                    g = g.replace('-','_').replace(' ','_')
+                    if g.find('\n') > 0:
+                        g = g[:g.find('\n')]
+                    supergroups[g] = 'supergroup_{}'.format(sgi)
+                    if g == '\n':
+                        sgi += 1
+                        break
+    except:
+        for g in groups['group'].unique():
+            supergroups[g] = g
+    try:
+        supergroups.pop('\n')
+    except KeyError:
+        pass
+    
+
+    bb = pd.read_csv(m2l_directory+'/tmp/bbox.csv')
+
+    # process tangent data to be tx, ty, tz
+    tangents['tz'] = 0
+    tangents['tx'] = tangents['lsx']
+    tangents['ty'] = tangents['lsy']
+    tangents.drop(['angle', 'lsx', 'lsy'], inplace=True, axis=1)
+
+    # convert azimuth and dip to gx, gy, gz
+    
+
+    # calculate scalar field values
+    i = 0
+    thickness = {}
+    max_thickness = 0
+    thickness_file = flags.get('thickness',m2l_directory + '/output/formation_summary_thicknesses.csv')
+    with open(thickness_file) as file:
+        for l in file:
+            if i>=1:
+                linesplit = l.split(',')
+                thickness[linesplit[0]] = float(linesplit[1])
+                # normalise the thicknesses
+                if float(linesplit[1]) > max_thickness:
+                    max_thickness=float(linesplit[1])
+    #             print(l.split(',')[1])
+            i+=1
+    # for k in thickness.keys():
+    #     thickness[k] /= max_thickness
+    if vector_scale is None:
+        vector_scale = max_thickness
+
+    if gradient:
+        from LoopStructural.utils.helper import strike_dip_vector
+        contact_orientations['strike'] = contact_orientations['azimuth'] - 90
+        contact_orientations['gx'] = np.nan
+        contact_orientations['gy'] = np.nan
+        contact_orientations['gz'] = np.nan
+        contact_orientations[['gx', 'gy', 'gz']] = strike_dip_vector(contact_orientations['strike'],
+                                                                    contact_orientations['dip'])*max_thickness   
+    if np.sum(contact_orientations['polarity']==0) >0 and np.sum(contact_orientations['polarity']==-1)==0:
+        # contact_orientations['polarity']+=1
+        contact_orientations.loc[contact_orientations['polarity']==0]=-1
+    if not gradient:
+        from LoopStructural.utils.helper import strike_dip_vector
+        contact_orientations['strike'] = contact_orientations['azimuth'] - 90
+        contact_orientations['nx'] = np.nan
+        contact_orientations['ny'] = np.nan
+        contact_orientations['nz'] = np.nan
+        contact_orientations[['nx', 'ny', 'nz']] = strike_dip_vector(contact_orientations['strike'],
+                                                                    contact_orientations['dip'])*vector_scale *contact_orientations['polarity'].to_numpy()[:,None]
+    contact_orientations.drop(['strike', 'dip', 'azimuth'], inplace=True, axis=1)
+    # with open(m2l_directory + '/output/formation_summary_thicknesses.csv') as file:
+
+    # thickness = {}
+    # for f in formation_thickness['formation'].unique():
+    #     thickness[f] = formation_thickness[formation_thickness['formation'] == f]['thickness'])
+
+    strat_val = {}
+    stratigraphic_column = {}
+    unit_id = 0
+    val = {}
+    for i in groups['group number'].unique():
+        g = supergroups[groups.loc[groups['group number'] == i, 'group'].iloc[0]]
+        if g not in stratigraphic_column:
+            stratigraphic_column[g] = {}
+            val[g] = 0
+
+        for c, colour in zip(groups.loc[groups['group number'] == i, 'code'],groups.loc[groups['group number'] == i, 'colour']):
+            strat_val[c] = np.nan
+            if c in thickness:
+                stratigraphic_column[g][c] = {'max': val[g], 'min': val[g] - thickness[c], 'id': unit_id, 'colour':colour}
+                unit_id += 1
+                strat_val[c] = val[g] - thickness[c]
+                val[g] -= thickness[c]
+    group_name = None
+    for g, i in stratigraphic_column.items():
+        if len(i) ==0:
+            for gr, sg in supergroups.items():
+                if sg == g:
+                    group_name = gr
+                    break
+            try:
+                if group_name is None:
+                    continue
+                c=groups.loc[groups['group']==group_name,'code'].to_numpy()[0]
+                strat_val[c] = 0
+                stratigraphic_column[g] = {c:{'min':0,'max':9999,'id':unit_id}}
+                unit_id+=1
+                group_name = None
+            except:
+                print('Couldnt process {}'.format(g))
+    #whether to use thickness or interface
+    use_thickness = flags.get('use_thickness',True)
+    if use_thickness:
+        contacts['val'] = np.nan
+        for o in strat_val:
+            contacts.loc[contacts['formation'] == o, 'val'] = strat_val[o]
+    if use_thickness == False:
+        contacts['interface'] = np.nan
+        interface_val = 0
+        for u in contacts['formation'].unique():
+            contacts.loc[contacts['formation'] == u,'interface'] = interface_val
+            interface_val+=1
+    tangents['feature_name'] = tangents['group']
+    contact_orientations['feature_name'] = None
+    contacts['feature_name'] = None
+    for g in groups['group'].unique():
+        val = 0
+        for c in groups.loc[groups['group'] == g, 'code']:
+            contact_orientations.loc[contact_orientations['formation'] == c, 'feature_name'] = supergroups[g]
+            contacts.loc[contacts['formation'] == c, 'feature_name'] = supergroups[g]
+    displacements['dip_dir'] = np.nan
+    for fname in fault_orientations['formation'].unique():
+        displacements.loc[displacements['fname'] == fname, 'dip_dir'] = np.mean(
+            fault_orientations.loc[fault_orientations['formation'] == fname, 'DipDirection'])
+    max_displacement = {}
+    downthrow_dir = {}
+    fault_locations['val'] = 0
+    fault_locations['coord'] = 0
+    fault_orientations['coord'] = 0
+    fault_orientations['gx'] = np.nan
+    fault_orientations['gy'] = np.nan
+    fault_orientations['gz'] = np.nan
+
+    stratigraphic_column['faults'] = {}
+    for f in displacements['fname'].unique():
+        fault_centers = np.zeros(6)
+        normal_vector = np.zeros(3)
+        strike_vector = np.zeros(3)
+        slip_vector = np.zeros(3)
+
+        fault_edges = np.zeros((2,3))
+        fault_tips = np.zeros((2,3))
+        fault_depth = np.zeros((2,3))
+        displacements_numpy = displacements.loc[
+            displacements['fname'] == f, ['vertical_displacement', 'downthrow_dir', 'dip_dir','X','Y']].to_numpy()
+        # index = np.argmax(np.abs(displacements_numpy[:, 0]), )
+        index = np.argsort(np.abs(displacements_numpy[:, 0]))[len(np.abs(displacements_numpy[:, 0]))//2]
+        
+        max_displacement[f] = displacements_numpy[
+            index, 0]
+        downthrow_dir[f] = displacements_numpy[index,[1,3,4]]
+        if np.abs(displacements_numpy[index, 1] - displacements_numpy[index, 2]) > 90:
+            # fault_orientations.loc[fault_orientations['formation'] == f, ['gx','gy','gy']]=-fault_orientations.loc[fault_orientations['formation'] == f, ['gx','gy','gy']]
+            fault_orientations.loc[fault_orientations['formation'] == f, 'DipDirection'] -= 180#displacements_numpy[
+                # index, 1]
+        # find the middle of the fault as the mean of the line, average dip direction and the influence distance
+        fault_centers[:3] = np.mean(fault_locations.loc[fault_locations['formation']==f,['X','Y','Z']],axis=0)
+        fault_centers[3] = np.mean(fault_orientations.loc[fault_orientations['formation']==f,['DipDirection']])
+        fault_centers[4] = fault_dimensions.loc[fault_dimensions['Fault']==f,'InfluenceDistance']
+        fault_centers[5] = fault_dimensions.loc[fault_dimensions['Fault']==f,'HorizontalRadius']
+        stratigraphic_column['faults'][f] = {'FaultCenter':fault_centers[:3],
+                                            'FaultDipDirection':fault_centers[3],
+                                            'InfluenceDistance':fault_dimensions.loc[fault_dimensions['Fault']==f,'InfluenceDistance'].to_numpy(),
+                                            'HorizontalRadius':fault_dimensions.loc[fault_dimensions['Fault']==f,'HorizontalRadius'].to_numpy(),
+                                            'VerticalRadius':fault_dimensions.loc[fault_dimensions['Fault']==f,'VerticalRadius'].to_numpy(),
+                                            'FaultSlip':np.array([0.,0.,-1.]),
+                                            'FaultNorm':normal_vector}
+
+        if 'colour' in fault_dimensions.columns:
+            stratigraphic_column['faults'][f]['colour'] = fault_dimensions.loc[fault_dimensions['Fault']==f,'colour'].to_numpy()
+        normal_vector[0] = np.sin(np.deg2rad(fault_centers[3]))
+        normal_vector[1] = np.cos(np.deg2rad(fault_centers[3]))
+        strike_vector[0] = normal_vector[1]
+        strike_vector[1] = -normal_vector[0]
+        slip_vector[2]=1
+        fault_edges[0,:] = fault_centers[:3]+normal_vector*fault_centers[4]
+        fault_edges[1,:] = fault_centers[:3]-normal_vector*fault_centers[4]
+        fault_tips[0,:] = fault_centers[:3]+strike_vector*fault_centers[5]
+        fault_tips[1,:] = fault_centers[:3]-strike_vector*fault_centers[5]
+        # fault_depth[0,:] = fault_centers[:3]+slip_vector*fault_centers[5]
+        # fault_depth[1,:] = fault_centers[:3]-slip_vector*fault_centers[5]
+        # fault_locations.loc[len(fault_locations),['X','Y','Z','formation','val','coord']] = [fault_edges[0,0],fault_edges[0,1],fault_edges[0,2],f,1,0]
+        # fault_locations.loc[len(fault_locations),['X','Y','Z','formation','val','coord']] = [fault_edges[1,0],fault_edges[1,1],fault_edges[1,2],f,-1,0]
+        # fault_locations.loc[len(fault_locations),['X','Y','Z','formation','val','coord']] = [fault_tips[0,0],fault_tips[0,1],fault_tips[0,2],f,1,2]
+        # fault_locations.loc[len(fault_locations),['X','Y','Z','formation','val','coord']] = [fault_tips[1,0],fault_tips[1,1],fault_tips[1,2],f,-1,2]
+        # # add strike vector to constraint fault extent
+        # fault_orientations.loc[len(fault_orientations),['X','Y','Z','formation','DipDirection','coord']] = [fault_centers[0],fault_centers[1],fault_centers[2],f, fault_centers[3]-90,2]
+        # fault_orientations.loc[len(fault_orientations),['X','Y','Z','formation','dip','coord']] = [fault_centers[0],fault_centers[1],fault_centers[2],f, 0,2]
+
+        # print('downthro',displacements_numpy[index, 1])
+        
+    fault_orientations['strike'] = fault_orientations['DipDirection'] - 90
+    fault_orientations[['gx', 'gy', 'gz']] = strike_dip_vector(fault_orientations['strike'], fault_orientations['dip'])
+    for g in groups['group'].unique():
+        groups.loc[groups['group']==g,'group'] = supergroups[g]
+    # fault_orientations['strike'] = fault_orientations['DipDirection'] - 90
+    # fault_orientations['gx'] = np.nan
+    # fault_orientations['gy'] = np.nan
+    # fault_orientations['gz'] = np.nan
+
+    fault_orientations.drop(['strike', 'DipDirection', 'dip', 'DipPolarity'], inplace=True, axis=1)
+    fault_orientations['feature_name'] = fault_orientations['formation']
+    fault_locations['feature_name'] = fault_locations['formation']
+
+    data = pd.concat([tangents, contact_orientations, contacts, fault_orientations, fault_locations])
+    data.reset_index(inplace=True)
+    
+    return {'data': data,
+            'groups': groups,
+            'max_displacement': max_displacement,
+            'fault_fault': fault_fault_relations,
+            'stratigraphic_column': stratigraphic_column,
+            'bounding_box':bb,
+            'strat_va':strat_val,
+            'downthrow_dir':downthrow_dir,
+            'fault_graph':fault_graph}
+
+def build_model(m2l_data, evaluate=True, 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
+            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 e in networkx.edge_bfs(m2l_data['fault_graph']):
+    #     model[e[1]].builder.add_fault(model[e[0]])
+    #     model[e[1]][0].interpolator.reset()
+    #     model[e[1]][1].interpolator.reset()
+    #     model[e[1]][2].interpolator.reset()
+
+    ## 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

LoopStructural/utils/regions.py

@@ -0,0 +1,11 @@
+import numpy as np
+
+class RegionEverywhere:
+    def __call__(self,xyz):
+        return np.ones(xyz.shape[0],dtype='bool')
+
+class RegionFunction:
+    def __init__(self,function):
+        self.function = function
+    def __call__(self,xyz):
+        return self.function(xyz)

LoopStructural/utils/utils.py

@@ -0,0 +1,69 @@
+import logging
+
+import numpy as np
+import re
+from LoopStructural.utils import getLogger
+logger = getLogger(__name__)
+
+
+def strike_symbol(strike):
+    R = np.zeros((2, 2))
+    R[0, 0] = np.cos(np.deg2rad(-strike))
+    R[0, 1] = -np.sin(np.deg2rad(-strike))
+    R[1, 0] = np.sin(np.deg2rad(-strike))
+    R[1, 1] = np.cos(np.deg2rad(-strike))
+    R = np.zeros((2, 2))
+    R[0, 0] = np.cos(np.deg2rad(-strike))
+    R[0, 1] = -np.sin(np.deg2rad(-strike))
+    R[1, 0] = np.sin(np.deg2rad(-strike))
+    R[1, 1] = np.cos(np.deg2rad(-strike))
+
+    vec = np.array([0, 1])
+    rotated = R @ vec
+    vec2 = np.array([-0.5, 0])
+    r2 = R @ vec2
+    return rotated, r2
+
+
+def read_voxet(voxetname,propertyfile):
+    """
+    Read a gocad property file and the geometry information from the .vo file
+    voxetname - is the path to the voxet file
+    propertyfile is the path to the binary file
+    Returns
+    origin numpy array
+    voxet_extent - is the length of each axis of the voxet
+    N is the number of steps in the voxet
+    array is the property values
+    steps is the size of the step vector for the voxet 
+    """
+    array = np.fromfile(propertyfile,dtype='float32')
+    array = array.astype('<f4') # little endian
+    with open(voxetname,'r') as file:
+        for l in file:
+            if 'AXIS_O ' in l:
+                origin = np.array(re.findall(r"[-+]?\d*\.?\d+|[-+]?\d+",l)).astype(float)
+            if 'AXIS_U ' in l:
+                U = float(re.findall(r'[\d\.\d]+',l)[0])
+            if 'AXIS_V ' in l:
+                V = float(re.findall(r'[\d\.\d]+',l)[1])
+            if 'AXIS_W ' in l:
+                W = float(re.findall(r'[\d\.\d]+',l)[2])
+            if 'AXIS_N ' in l:
+                N = np.array(re.findall(r'[\d\.\d]+',l)).astype(int) 
+    voxet_extent = np.array([U,V,W])
+    steps = (voxet_extent ) / (N-1)
+    return origin, voxet_extent, N, array, steps
+
+def write_property_to_gocad_voxet(propertyfilename, propertyvalues):
+    """
+    This function writes a numpy array into the right format for a gocad
+    voxet property file. This assumet there is a property already added to the .vo file,
+    and is just updating the file.
+    propertyfile - string giving the path to the file to write
+    propertyvalues - numpy array nz,ny,nx ordering and in float format
+    """
+    propertyvalues = propertyvalues.astype('>f4') #big endian
+#     array = propertyvalues.newbyteorder()
+    propertyvalues.tofile(propertyfilename)
+    

LoopStructural/visualisation/__init__.py

@@ -0,0 +1,31 @@
+"""
+This is the base visualistion module for loop structural
+
+Submodules
+==========
+
+.. autosummary::
+    :toctree: _autosummary
+
+    map_viewer
+    model_visualisation
+    rotation_angle_plotter
+
+"""
+from ..utils import getLogger
+logger = getLogger(__name__)
+try:
+    import matplotlib
+    from .map_viewer import MapView
+    from .rotation_angle_plotter import RotationAnglePlotter
+except ImportError:
+    logger.warning('Cannot use MapView or RotationAnglePlotter as matplotlib is not installed. \n'\
+                   'Install matplotlib and try again. ')
+try:
+    from .sphinx_scraper import _get_loop_visualisation_scraper
+except:
+    logger.error('Cannot use sphinx scraper, pip install -r docs/requirements.txt')
+try:
+    from .model_visualisation import LavaVuModelViewer
+except:
+    logger.error("Missing lavavu, can't import LavaVuModelViewer")