resqpy 4.14.2__py3-none-any.whl → 5.1.6__py3-none-any.whl

resqpy/rq_import/_import_nexus.py

@@ -67,55 +67,78 @@ def import_nexus(
         ensemble_size_limit = None,
         grid_title = 'ROOT',
         mode = 'w',
-        progress_fn = None):
-    """Read a simulation grid geometry and optionally grid properties.
-
-    Input may be from nexus ascii input files, or nexus vdb output.
-
-    Arguments:
-        resqml_file_root (str): output path and file name without .epc or .h5 extension
-        extent_ijk (triple float, optional): ijk extents (fortran ordering)
-        vdb_file (str, optional): vdb input file, either this or corp_file should be not None. Required if importing from a vdb
-        vdb_case (str, optional): required if the vdb contains more than one case. If None, first case in vdb is used
-        corp_file (str, optional): required if importing from corp ascii file. corp ascii input file: nexus corp data without keyword
-        corp_bin_file (str, optional): required if importing from corp binary file
-        corp_xy_units (str, default 'm'): xy length units
-        corp_z_units (str, default 'm'): z length units
-        corp_z_inc_down (bool, default True): if True z values increase with depth
-        ijk_handedness (str, default 'right'): 'right' or 'left'
-        corp_eight_mode (bool, default False): if True the ordering of corner point data is in nexus EIGHT mode
-        geometry_defined_everywhere (bool, default True): if False then inactive cells are marked as not having geometry
-        treat_as_nan (float, default None): if a value is provided corner points with this value will be assigned nan
-        active_mask_file (str, default None): ascii property file holding values 0 or 1, with 1 indicating active cells
-        use_binary (bool, default False): if True a cached binary version of ascii files will be used (pure binary, not corp bin format)
-        resqml_xy_units (str, default 'm'): output xy units for resqml file
-        resqml_z_units (str, default 'm'): output z units for resqml file
-        resqml_z_inc_down (bool, default True): if True z values increase with depth for output resqml file
-        shift_to_local (bool, default False): if True then a local origin will be used in the CRS
-        local_origin_place (str, default 'centre'): 'centre' or 'minimum'. If 'centre' the local origin is placed at the centre of the grid; ignored if shift_to_local is False
-        max_z_void (float, default 0.1): maximum z gap between vertically neighbouring corner points. Vertical gaps greater than this will introduce k gaps into resqml grid. Units are corp z units
-        split_pillars (bool, default True): if False an unfaulted grid will be generated
-        split_tolerance (float, default 0.01): maximum distance between neighbouring corner points before a pillar is considered 'split'. Applies to each of x, y, z differences
-        property_array_files (list, default None): list of (filename, keyword, uom, time_index, null_value, discrete)
-        summary_file (str, default None): nexus output summary file, used to extract timestep dates when loading recurrent data from vdb
-        vdb_static_properties (bool, default True): if True, static vdb properties are imported (only relevant if vdb_file is not None)
-        vdb_recurrent_properties (bool, default False): # if True, recurrent vdb properties are imported (only relevant if vdb_file is not None)
-        timestep_selection (str, default 'all): 'first', 'last', 'first and last', 'all', or list of ints being reporting timestep numbers. Ignored if vdb_recurrent_properties is False
-        use_compressed_time_series (bool, default True): generates reduced time series containing timesteps with recurrent properties from vdb, rather than full nexus summary time series
-        decoarsen (bool, default True): where ICOARSE is present, redistribute data to uncoarse cells
-        ab_property_list (list, default None):  list of (file_name, keyword, property_kind, facet_type, facet, uom, time_index, null_value, discrete)
-        create_property_set (bool, default False): if True a resqml PropertySet is created
-        ensemble_case_dirs_root (str, default None): path up to but excluding realisation number
-        ensemble_property_dictionary (str, default None): dictionary mapping title (or keyword) to (filename, property_kind, facet_type, facet, uom, time_index, null_value, discrete)
-        ensemble_size_limit (int, default None): if present processing of ensemble will terminate after this number of cases is reached
-        grid_title (str, default 'ROOT'): grid citation title
-        mode (str, default 'w'): 'w' or 'a', mode to write or append to hdf5
-        progress_fn (function, default None): if present function must have one floating argument with value increasing from 0 to 1, and is called at intervals to indicate progress
-
-    Returns:
-        resqml model in memory & written to disc
+        progress_fn = None,
+        vdb_property_list = None):
+    """Read a Nexus grid geometry (from ascii input or vdb) and optionally grid properties.
+
+    arguments:
+        - resqml_file_root (str): output path and file name without .epc or .h5 extension
+        - extent_ijk (triple float, optional): ijk extents (fortran ordering)
+        - vdb_file (str, optional): vdb input file, either this or corp_file should be not None;
+          required if importing from a vdb
+        - vdb_case (str, optional): required if the vdb contains more than one case;
+          if None, first case in vdb is used
+        - corp_file (str, optional): required if importing from corp ascii file;
+          corp ascii input file containing nexus corp data without keyword
+        - corp_bin_file (str, optional): required if importing from corp binary file
+        - corp_xy_units (str, default 'm'): xy length units
+        - corp_z_units (str, default 'm'): z length units
+        - corp_z_inc_down (bool, default True): if True z values increase with depth
+        - ijk_handedness (str, default 'right'): 'right' or 'left'
+        - corp_eight_mode (bool, default False): if True the ordering of corner point data
+          is in nexus EIGHT mode
+        - geometry_defined_everywhere (bool, default True): if False then inactive cells are
+          marked as not having geometry
+        - treat_as_nan (float, default None): if a value is provided corner points with
+          this value will be assigned not-a-number
+        - active_mask_file (str, default None): ascii property file holding values 0 or 1,
+          with 1 indicating active cells
+        - use_binary (bool, default False): if True a cached binary version of ascii files
+          will be used (pure binary, not corp bin format)
+        - resqml_xy_units (str, default 'm'): output xy units for resqml file
+        - resqml_z_units (str, default 'm'): output z units for resqml file
+        - resqml_z_inc_down (bool, default True): if True z values increase with depth for
+          output resqml file
+        - shift_to_local (bool, default False): if True then a local origin will be used in the CRS
+        - local_origin_place (str, default 'centre'): 'centre' or 'minimum'; if 'centre' the
+          local origin is placed at the centre of the grid; ignored if shift_to_local is False
+        - max_z_void (float, default 0.1): maximum z gap between vertically neighbouring corner points;
+          vertical gaps greater than this will introduce k gaps into resqml grid; units are corp z units
+        - split_pillars (bool, default True): if False an unfaulted grid will be generated
+        - split_tolerance (float, default 0.01): maximum distance between neighbouring corner points
+          before a pillar is considered 'split'; applies to each of x, y, z differences
+        - property_array_files (list, default None): list of (filename, keyword, uom, time_index, null_value, discrete)
+        - summary_file (str, default None): nexus output summary file, used to extract timestep dates
+          when loading recurrent data from vdb
+        - vdb_static_properties (bool, default True): if True, static vdb properties are imported;
+          only relevant if vdb_file is not None; see also vdb_property_list
+        - vdb_recurrent_properties (bool, default False): if True, recurrent vdb properties are imported;
+          only relevant if vdb_file is not None; see also vdb_property_list
+        - timestep_selection (str, default 'all): 'first', 'last', 'first and last', 'all',
+          or list of ints being reporting timestep numbers; ignored if vdb_recurrent_properties is False
+        - use_compressed_time_series (bool, default True): generates reduced time series containing
+          timesteps with recurrent properties from vdb, rather than full nexus summary time series
+        - decoarsen (bool, default True): where ICOARSE is present, redistribute data to uncoarse cells
+        - ab_property_list (list, optional):  list of
+          (file_name, keyword, property_kind, facet_type, facet, uom, time_index, null_value, discrete)
+        - create_property_set (bool, default False): if True a resqml PropertySet is created
+        - ensemble_case_dirs_root (str, optional): path up to but excluding realisation number
+        - ensemble_property_dictionary (str, optional): dictionary mapping title (or keyword) to
+          (filename, property_kind, facet_type, facet, uom, time_index, null_value, discrete)
+        - ensemble_size_limit (int, optional): if present processing of ensemble will terminate
+          after this number of cases is reached
+        - grid_title (str, default 'ROOT'): grid citation title
+        - mode (str, default 'w'): 'w' or 'a', mode to write or append to hdf5
+        - progress_fn (function, default None): if present function must have one floating argument
+          with value increasing from 0.0 to 1.0, and is called at intervals to indicate progress
+        - vdb_property_list (list of str, optional): list of vdb static and/or recurrent properties to
+          include in the import; if None, all properties are imported; vdb_static_properties and
+          vdb_recurrent_properties boolean arguments must also be set True for respective properties
+          to be included; ignored if not importing from vdb
+
+    returns:
+        - resqml model in memory & written to disc
     """
-
     if resqml_file_root.endswith('.epc'):
         resqml_file_root = resqml_file_root[:-4]
     assert mode in ['w', 'a']
@@ -333,6 +356,8 @@ def import_nexus(
                 prop_import_collection = rp.GridPropertyCollection()
                 prop_import_collection.set_grid(grid)
                 for keyword in props:
+                    if vdb_property_list is not None and keyword not in vdb_property_list:
+                        continue
                     prop_import_collection.import_vdb_static_property_to_cache(vdbase, keyword, grid_name = grid_title)
     #      if active_mask is not None:
     #         prop_import_collection.add_cached_array_to_imported_list(active_mask, active_mask_file, 'ACTIVE', property_kind = 'active',
@@ -520,6 +545,8 @@ def import_nexus(
                     for keyword in recur_prop_list:
                         if vdb.bad_keyword(keyword):
                             continue
+                        if vdb_property_list is not None and keyword not in vdb_property_list:
+                            continue
                         prop_kind, facet_type, facet = rp.property_kind_and_facet_from_keyword(keyword)
                         step_import_collection.import_vdb_recurrent_property_to_cache(
                             vdbase,

resqpy/rq_import/_import_vdb_all_grids.py

@@ -10,60 +10,71 @@ import resqpy.olio.vdb as vdb
 import resqpy.rq_import as rqi
 
 
-def import_vdb_all_grids(
-    resqml_file_root,  # output path and file name without .epc or .h5 extension
-    extent_ijk = None,  # 3 element numpy vector applicable to ROOT
-    vdb_file = None,
-    vdb_case = None,  # if None, first case in vdb is used (usually a vdb only holds one case)
-    corp_xy_units = 'm',
-    corp_z_units = 'm',
-    corp_z_inc_down = True,
-    ijk_handedness = 'right',
-    geometry_defined_everywhere = True,
-    treat_as_nan = None,
-    resqml_xy_units = 'm',
-    resqml_z_units = 'm',
-    resqml_z_inc_down = True,
-    shift_to_local = False,
-    local_origin_place = 'centre',  # 'centre' or 'minimum'
-    max_z_void = 0.1,  # vertical gaps greater than this will introduce k gaps intp resqml grid
-    split_pillars = True,
-    split_tolerance = 0.01,  # applies to each of x, y, z differences
-    vdb_static_properties = True,
-    # if True, static vdb properties are imported (only relevant if vdb_file is not None)
-    vdb_recurrent_properties = False,
-    decoarsen = True,
-    timestep_selection = 'all',
-    # 'first', 'last', 'first and last', 'all', or list of ints being reporting timestep numbers
-    create_property_set = False):
+def import_vdb_all_grids(resqml_file_root,
+                         extent_ijk = None,
+                         vdb_file = None,
+                         vdb_case = None,
+                         corp_xy_units = 'm',
+                         corp_z_units = 'm',
+                         corp_z_inc_down = True,
+                         ijk_handedness = 'right',
+                         geometry_defined_everywhere = True,
+                         treat_as_nan = None,
+                         resqml_xy_units = 'm',
+                         resqml_z_units = 'm',
+                         resqml_z_inc_down = True,
+                         shift_to_local = False,
+                         local_origin_place = 'centre',
+                         max_z_void = 0.1,
+                         split_pillars = True,
+                         split_tolerance = 0.01,
+                         vdb_static_properties = True,
+                         vdb_recurrent_properties = False,
+                         decoarsen = True,
+                         timestep_selection = 'all',
+                         create_property_set = False,
+                         vdb_property_list = None):
     """Creates a RESQML dataset containing grids and grid properties, including LGRs, for a single realisation.
 
-    Arguments:
-        resqml_file_root (str): output path and file name without .epc or .h5 extension
-        extent_ijk (triple float, optional): ijk extents (fortran ordering)
-        vdb_file (str, optional): vdb input file, either this or corp_file should be not None. Required if importing from a vdb
-        vdb_case (str, optional): required if the vdb contains more than one case. If None, first case in vdb is used
-        corp_xy_units (str, default 'm'): xy length units
-        corp_z_units (str, default 'm'): z length units
-        corp_z_inc_down (bool, default True): if True z values increase with depth
-        ijk_handedness (str, default 'right'): 'right' or 'left'
-        geometry_defined_everywhere (bool, default True): if False then inactive cells are marked as not having geometry
-        treat_as_nan (float, default None): if a value is provided corner points with this value will be assigned nan
-        resqml_xy_units (str, default 'm'): output xy units for resqml file
-        resqml_z_units (str, default 'm'): output z units for resqml file
-        resqml_z_inc_down (bool, default True): if True z values increase with depth for output resqml file
-        shift_to_local (bool, default False): if True then a local origin will be used in the CRS
-        local_origin_place (str, default 'centre'): 'centre' or 'minimum'. If 'centre' the local origin is placed at the centre of the grid; ignored if shift_to_local is False
-        max_z_void (float, default 0.1): maximum z gap between vertically neighbouring corner points. Vertical gaps greater than this will introduce k gaps into resqml grid. Units are corp z units
-        split_pillars (bool, default True): if False an unfaulted grid will be generated
-        split_tolerance (float, default 0.01): maximum distance between neighbouring corner points before a pillar is considered 'split'. Applies to each of x, y, z differences
-        vdb_static_properties (bool, default True): if True, static vdb properties are imported (only relevant if vdb_file is not None)
-        vdb_recurrent_properties (bool, default False): # if True, recurrent vdb properties are imported (only relevant if vdb_file is not None)
-        decoarsen (bool, default True): where ICOARSE is present, redistribute data to uncoarse cells
-        timestep_selection (str, default 'all): 'first', 'last', 'first and last', 'all', or list of ints being reporting timestep numbers. Ignored if vdb_recurrent_properties is False
-        create_property_set (bool, default False): if True a resqml PropertySet is created
+    arguments:
+        - resqml_file_root (str): output path and file name without .epc or .h5 extension
+        - extent_ijk (triple float, optional): ijk extents (fortran ordering)
+        - vdb_file (str, optional): vdb input file, either this or corp_file should be not None;
+          required if importing from a vdb
+        - vdb_case (str, optional): required if the vdb contains more than one case;
+          if None, first case in vdb is used
+        - corp_xy_units (str, default 'm'): xy length units
+        - corp_z_units (str, default 'm'): z length units
+        - corp_z_inc_down (bool, default True): if True z values increase with depth
+        - ijk_handedness (str, default 'right'): 'right' or 'left'
+        - geometry_defined_everywhere (bool, default True): if False then inactive cells are marked
+          as not having geometry
+        - treat_as_nan (float, default None): if a value is provided corner points with this value
+          will be assigned nan (not-a-number)
+        - resqml_xy_units (str, default 'm'): output xy units for resqml file
+        - resqml_z_units (str, default 'm'): output z units for resqml file
+        - resqml_z_inc_down (bool, default True): if True z values increase with depth in output resqml file
+        - shift_to_local (bool, default False): if True then a local origin will be used in the CRS
+        - local_origin_place (str, default 'centre'): 'centre' or 'minimum'; if 'centre' the local origin
+          is placed at the centre of the grid; ignored if shift_to_local is False
+        - max_z_void (float, default 0.1): maximum z gap between vertically neighbouring corner points;
+          vertical gaps greater than this will introduce k gaps into resqml grid; units are corp z units
+        - split_pillars (bool, default True): if False an unfaulted grid will be generated
+        - split_tolerance (float, default 0.01): maximum distance between neighbouring corner points
+          before a pillar is considered 'split'; applies to each of x, y, z differences
+        - vdb_static_properties (bool, default True): if True, static vdb properties are imported;
+          only relevant if vdb_file is not None; see also vdb_property_list
+        - vdb_recurrent_properties (bool, default False): if True, recurrent vdb properties are imported;
+          only relevant if vdb_file is not None; see also vdb_property_list
+        - decoarsen (bool, default True): where ICOARSE is present, redistribute data to uncoarse cells
+        - timestep_selection (str, default 'all): 'first', 'last', 'first and last', 'all', or list of ints
+          being reporting timestep numbers to include; ignored if vdb_recurrent_properties is False
+        - create_property_set (bool, default False): if True a resqml PropertySet is created
+        - vdb_property_list (list of str, optional): list of vdb static and/or recurrent properties to
+          include in the import; if None, all properties are imported; vdb_static_properties and
+          vdb_recurrent_properties boolean arguments must also be set True for respective properties
+          to be included; ignored if not importing from vdb
     """
-
     vdbase = vdb.VDB(vdb_file)
     case_list = vdbase.cases()
     assert len(case_list) > 0, 'no cases found in vdb'
@@ -104,5 +115,6 @@ def import_vdb_all_grids(
             timestep_selection = timestep_selection,
             create_property_set = create_property_set,
             grid_title = grid_name,
-            mode = 'w' if index == 0 else 'a')
+            mode = 'w' if index == 0 else 'a',
+            vdb_property_list = vdb_property_list)
         index += 1

resqpy/rq_import/_import_vdb_ensemble.py

@@ -225,11 +225,11 @@ def import_vdb_ensemble(
         vdb_file = ensemble_list[realisation]
         log.info('processing realisation ' + str(realisation) + ' from: ' + str(vdb_file))
         vdbase = vdb.VDB(vdb_file)
-        #      case_list = vdbase.cases()
-        #      assert len(case_list) > 0, 'no cases found in vdb: ' + str(vdb_file)
-        #      if len(case_list) > 1: log.warning('more than one case found in vdb (using first): ' + str(vdb_file))
-        #      vdb_case = case_list[0]
-        #      vdbase.set_use_case(vdb_case)
+        # case_list = vdbase.cases()
+        # assert len(case_list) > 0, 'no cases found in vdb: ' + str(vdb_file)
+        # if len(case_list) > 1: log.warning('more than one case found in vdb (using first): ' + str(vdb_file))
+        # vdb_case = case_list[0]
+        # vdbase.set_use_case(vdb_case)
         vdbase.set_extent_kji(grid.extent_kji)
 
         prop_import_collection = rp.GridPropertyCollection(realization = realisation)
@@ -243,9 +243,8 @@ def import_vdb_ensemble(
                     if keyword_list is not None and keyword not in keyword_list:
                         continue
                     prop_kind, facet_type, facet = rp.property_kind_and_facet_from_keyword(keyword)
-                    if property_kind_list is not None and prop_kind not in property_kind_list and prop_kind not in [
-                            'active', 'region initialization'
-                    ]:
+                    if property_kind_list is not None and prop_kind not in property_kind_list and  \
+                        prop_kind not in ['active', 'region initialization']:
                         continue
                     prop_import_collection.import_vdb_static_property_to_cache(vdbase,
                                                                                keyword,
@@ -312,9 +311,9 @@ def import_vdb_ensemble(
                     if decoarsen_array is not None:
                         step_import_collection.decoarsen_imported_list(decoarsen_array = decoarsen_array)
                     # extend hdf5 with cached arrays for this timestep
-                    #         log.info('number of recurrent grid property arrays for timestep: ' + str(timestep_number) +
-                    #                  ' is: ' + str(step_import_collection.number_of_imports()))
-                    #         log.info('extending hdf5 file with recurrent properties for timestep: ' + str(timestep_number))
+                    # log.info('number of recurrent grid property arrays for timestep: ' + str(timestep_number) +
+                    #          ' is: ' + str(step_import_collection.number_of_imports()))
+                    # log.info('extending hdf5 file with recurrent properties for timestep: ' + str(timestep_number))
                     grid.write_hdf5_from_caches(hdf5_file,
                                                 mode = 'a',
                                                 geometry = False,
@@ -322,8 +321,8 @@ def import_vdb_ensemble(
                                                 write_active = False)
                     # add imported list for this timestep to full imported list
                     prop_import_collection.inherit_imported_list_from_other_collection(step_import_collection)
-                    #         log.debug('total number of property arrays after timestep: ' + str(timestep_number) +
-                    #                   ' is: ' + str(prop_import_collection.number_of_imports()))
+                    # log.debug('total number of property arrays after timestep: ' + str(timestep_number) +
+                    #           ' is: ' + str(prop_import_collection.number_of_imports()))
                     # remove cached copies of arrays
                     step_import_collection.remove_all_cached_arrays()
 

resqpy/surface/_mesh.py

@@ -207,6 +207,10 @@ class Mesh(rqsb.BaseSurface):
                    extra_metadata = em)
         return mesh
 
+    def is_big(self):
+        """Returns True if the number of nodes exceeds 2^31 - 1, False otherwise."""
+        return (self.ni * self.nj >= 2_147_483_648)
+
     def set_represented_interpretation_root(self, interp_root):
         """Makes a note of the xml root of the represented interpretation."""