Merge pull request #61 from softwareunderground/pr_pyv

change _arrays to _data

requirements_opt.txt

@@ -1,6 +1,6 @@
 openpyxl
 
-welly == 0.4.8
+welly
 
 # There is an open PR for striplog
 git+https://github.com/Leguark/striplog.git

subsurface/geological_formats/seismic.py

@@ -92,7 +92,7 @@ def create_pyvista_grid(self) -> pv.grid.UniformGrid:
         grid = pv.UniformGrid()
         grid.spacing = (1, 1, 1)  # TODO: cell sizes? vertical exaggeration etc
         grid.dimensions = np.array(self.data.shape) + 1
-        grid.cell_arrays["values"] = self.data.flatten(order="F")
+        grid.cell_data["values"] = self.data.flatten(order="F")
         # TODO: correct orientation of cube
         return grid
 

subsurface/reader/readers_data.py

@@ -36,7 +36,7 @@ class ReaderFilesHelper:
     file_or_buffer_type: Any = field(init=False)
 
     index_col: Union[int, str] = False
-    header: Union[None, int, List[int]] = "infer"
+    header: Union[None, int, List[int]] = 0
 
     def __post_init__(self):
         if self.format is None: self.format = get_extension(self.file_or_buffer)

subsurface/reader/wells/pandas_to_welly.py

@@ -4,14 +4,14 @@
 import pandas as pd
 
 try:
+    import welly
     from welly import Well, Location, Project, Curve
     from striplog import Striplog, Component
 
     welly_imported = True
 except ImportError:
     welly_imported = False
 
-
 __all__ = ['WellyToSubsurfaceHelper', ]
 
 
@@ -61,16 +61,16 @@ def __init__(self,
 
     def __repr__(self):
         return self.p.__repr__()
-    
+
     @property
     def p(self):
         """Project Alias"""
         return self.welly_project
-    
+
     @p.setter
     def p(self, p):
         self.welly_project = p
-    
+
     @property
     def lith_component_table(self):
         return [Component({'lith': l}) for l in self._unique_formations]
@@ -85,8 +85,13 @@ def add_wells(self, well_names: Iterable):
         self._well_names = self._well_names.union(well_names)
         for b in new_boreholes:
             # TODO: Name and uwi should be different
-            w = Well(params={'header': {'name': b, 'uwi': b}})
-            w.location = Location(params={'kb': 100})
+            if welly.__version__ < '0.5':
+                w = Well(params={'header': {'name': b, 'uwi': b}})
+            else:
+                w = Well()
+                w.uwi = b
+                w.name = b
+            # w.location = Location(params={'kb': 100})
             self.p += w
         return self.p
 
@@ -116,8 +121,8 @@ def add_striplog(self, data: pd.DataFrame):
             w = self.p.get_well(b)
             data_dict = data.loc[[b]].to_dict('list')
             data_csv = data.loc[[b]].to_csv()
-            #s = Striplog.from_dict_advanced(data_dict, points=True)
-            #s = Striplog.from_dict(data_dict)
+            # s = Striplog.from_dict_advanced(data_dict, points=True)
+            # s = Striplog.from_dict(data_dict)
             s = Striplog.from_csv(text=data_csv)
 
             try:

subsurface/reader/wells/welly_reader.py

@@ -43,7 +43,7 @@ def welly_to_subsurface(wts: WellyToSubsurfaceHelper,
 
     """
     vertex = np.zeros((0, 3))
-    cells = np.zeros((0, 2), dtype=np.int_)
+    cells = np.zeros((0, 2), dtype=int)
 
     last_index = 0
     missed_wells = []
@@ -62,7 +62,7 @@ def welly_to_subsurface(wts: WellyToSubsurfaceHelper,
                 if table is None: table = wts.lith_component_table
                 w.data['lith_log'] = striplog_to_curve_log(n_vertex_per_well, table, w, wts)
             else:
-                w.data["lith_log"] = Curve(-1 * np.ones(n_vertex_per_well - 1, dtype=int))
+                w.data["lith_log"] = Curve(-1 * np.ones(n_vertex_per_well - 1, dtype=int), mnemonic='lith_log')
 
             if w.data["lith_log"].shape[0] != n_vertex_per_well - 1:
                 raise ValueError("Cell_attr does not match cells")
@@ -84,7 +84,7 @@ def welly_to_subsurface(wts: WellyToSubsurfaceHelper,
 def striplog_to_curve_log(n_vertex_per_well, table, w: Well, wts: WellyToSubsurfaceHelper) -> Curve:
     start, stop, step_size = wts._calculate_basis_parameters(w, n_vertex_per_well - 1)
     s_log, basis, _table = w.data['lith'].to_log(step_size, start, stop, table=table, return_meta=True)
-    return Curve(s_log, basis)
+    return Curve(s_log, basis, mnemonic='lith_log')
 
 
 def change_curve_basis_to_n_vertex_per_well_inplace(n_points, w, wts):

subsurface/visualization/to_pyvista.py

@@ -89,7 +89,7 @@ def to_pyvista_points(point_set: PointSet):
         pv.PolyData
     """
     poly = pv.PolyData(point_set.data.vertex)
-    poly.point_arrays.update(point_set.data.attributes_to_dict)
+    poly.point_data.update(point_set.data.attributes_to_dict)
 
     return poly
 
@@ -106,8 +106,8 @@ def to_pyvista_mesh(unstructured_element: Union[TriSurf],
     cells = np.c_[np.full(unstructured_element.mesh.n_elements, nve),
                   unstructured_element.mesh.cells]
     mesh = pv.PolyData(vertices, cells)
-    mesh.cell_arrays.update(unstructured_element.mesh.attributes_to_dict)
-    mesh.point_arrays.update(unstructured_element.mesh.points_attributes)
+    mesh.cell_data.update(unstructured_element.mesh.attributes_to_dict)
+    mesh.point_data.update(unstructured_element.mesh.points_attributes)
 
     return mesh
 
@@ -162,7 +162,7 @@ def to_pyvista_line(line_set: LineSet, as_tube=True, radius=None,
     else:
         raise NotImplementedError
         # mesh = pv.Spline(ver)
-    mesh.cell_arrays.update(line_set.data.attributes_to_dict)
+    mesh.cell_data.update(line_set.data.attributes_to_dict)
     if as_tube is True:
         return mesh.tube(radius=radius)
     else:
@@ -177,7 +177,7 @@ def to_pyvista_tetra(tetra_mesh: TetraMesh):
     import vtk
     ctypes = np.array([vtk.VTK_TETRA, ], np.int32)
     mesh = pv.UnstructuredGrid(cells, ctypes, vertices)
-    mesh.cell_arrays.update(tetra_mesh.data.attributes_to_dict)
+    mesh.cell_data.update(tetra_mesh.data.attributes_to_dict)
     return mesh
 
 
@@ -236,7 +236,7 @@ def update_grid_attribute(mesh, structured_grid,
     if data_set_name is None:
         data_set_name = structured_grid.ds.data_array_name
 
-    mesh.point_arrays.update(
+    mesh.point_data.update(
         {data_set_name: structured_grid.ds.data[data_set_name].sel(
             **attribute_slice
         ).values.ravel(data_order)})