import inspect
import math
import os
import sys
import numpy as np
from ...datbase import DataListInterface, DataType
from ...mbase import ModelInterface
from ...utils import datautil
from ..data import mfdata, mfstructure
from ..mfbase import ExtFileAction, MFDataException, VerbosityLevel
from ..utils.mfenums import DiscretizationType
from .mfdatastorage import DataStorage, DataStorageType, DataStructureType
from .mfdatautil import to_string
from .mffileaccess import MFFileAccessList
from .mfstructure import DatumType
[docs]class MFList(mfdata.MFMultiDimVar, DataListInterface):
"""
Provides an interface for the user to access and update MODFLOW
list data. MFList objects are not designed to be directly constructed by
the end user. When a flopy for MODFLOW 6 package object is constructed, the
appropriate MFList objects are automatically built.
Parameters
----------
sim_data : MFSimulationData
data contained in the simulation
structure : MFDataStructure
describes the structure of the data
data : list or ndarray
actual data
enable : bool
enable/disable the array
path : tuple
path in the data dictionary to this MFArray
dimensions : MFDataDimensions
dimension information related to the model, package, and array
"""
def __init__(
self,
sim_data,
model_or_sim,
structure,
data=None,
enable=True,
path=None,
dimensions=None,
package=None,
block=None,
):
super().__init__(
sim_data, model_or_sim, structure, enable, path, dimensions
)
try:
self._data_storage = self._new_storage()
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
structure.get_model(),
structure.get_package(),
path,
"creating storage",
structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
sim_data.debug,
ex,
)
self._package = package
self._block = block
self._last_line_info = []
self._data_line = None
self._temp_dict = {}
self._crnt_line_num = 1
if data is not None:
try:
self.set_data(data, True)
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
structure.get_model(),
structure.get_package(),
path,
"setting data",
structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
sim_data.debug,
ex,
)
@property
def data_type(self):
"""Type of data (DataType) stored in the list"""
return DataType.list
@property
def package(self):
"""Package object that this data belongs to."""
return self._package
@property
def dtype(self):
"""Type of data (numpy.dtype) stored in the list"""
return self.get_data().dtype
@property
def plottable(self):
"""If this list data is plottable"""
if self.model is None:
return False
else:
return True
[docs] def to_array(self, kper=0, mask=False):
"""Convert stress period boundary condition (MFDataList) data for a
specified stress period to a 3-D numpy array.
Parameters
----------
kper : int
MODFLOW zero-based stress period number to return. (default is
zero)
mask : bool
return array with np.NaN instead of zero
Returns
----------
out : dict of numpy.ndarrays
Dictionary of 3-D numpy arrays containing the stress period data
for a selected stress period. The dictionary keys are the
MFDataList dtype names for the stress period data."""
i0 = 1
sarr = self.get_data(key=kper)
if not isinstance(sarr, list):
sarr = [sarr]
if len(sarr) == 0 or sarr[0] is None:
return None
if "inode" in sarr[0].dtype.names:
raise NotImplementedError()
arrays = {}
model_grid = self._data_dimensions.get_model_grid()
if model_grid._grid_type.value == 1:
shape = (
model_grid.num_layers(),
model_grid.num_rows(),
model_grid.num_columns(),
)
elif model_grid._grid_type.value == 2:
shape = (
model_grid.num_layers(),
model_grid.num_cells_per_layer(),
)
else:
shape = (model_grid.num_cells_per_layer(),)
for name in sarr[0].dtype.names[i0:]:
if not sarr[0].dtype.fields[name][0] == object:
arr = np.zeros(shape)
arrays[name] = arr.copy()
if np.isscalar(sarr[0]):
# if there are no entries for this kper
if sarr[0] == 0:
if mask:
for name, arr in arrays.items():
arrays[name][:] = np.NaN
return arrays
else:
raise Exception("MfList: something bad happened")
for name, arr in arrays.items():
cnt = np.zeros(shape, dtype=np.float64)
for sp_rec in sarr:
if sp_rec is not None:
for rec in sp_rec:
arr[rec["cellid"]] += rec[name]
cnt[rec["cellid"]] += 1.0
# average keys that should not be added
if name != "cond" and name != "flux":
idx = cnt > 0.0
arr[idx] /= cnt[idx]
if mask:
arr = np.ma.masked_where(cnt == 0.0, arr)
arr[cnt == 0.0] = np.NaN
arrays[name] = arr.copy()
# elif mask:
# for name, arr in arrays.items():
# arrays[name][:] = np.NaN
return arrays
[docs] def new_simulation(self, sim_data):
"""Initialize MFList object for a new simulation.
Parameters
----------
sim_data : MFSimulationData
Simulation data object for the simulation containing this
data.
"""
try:
super().new_simulation(sim_data)
self._data_storage = self._new_storage()
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"reinitializing",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
self._data_line = None
[docs] def store_as_external_file(
self,
external_file_path,
binary=False,
replace_existing_external=True,
check_data=True,
):
"""Store all data externally in file external_file_path. the binary
allows storage in a binary file. If replace_existing_external is set
to False, this method will not do anything if the data is already in
an external file.
Parameters
----------
external_file_path : str
Path to external file
binary : bool
Store data in a binary file
replace_existing_external : bool
Whether to replace an existing external file.
check_data : bool
Verify data prior to storing
"""
# only store data externally (do not subpackage info)
if self.structure.construct_package is None:
storage = self._get_storage_obj()
# check if data is already stored external
if (
replace_existing_external
or storage is None
or storage.layer_storage.first_item().data_storage_type
== DataStorageType.internal_array
or storage.layer_storage.first_item().data_storage_type
== DataStorageType.internal_constant
):
data = self._get_data()
# if not empty dataset
if data is not None:
if (
self._simulation_data.verbosity_level.value
>= VerbosityLevel.verbose.value
):
print(
"Storing {} to external file {}.."
".".format(self.structure.name, external_file_path)
)
external_data = {
"filename": external_file_path,
"data": data,
"binary": binary,
}
self._set_data(external_data, check_data=check_data)
[docs] def store_internal(
self,
check_data=True,
):
"""Store all data internally.
Parameters
----------
check_data : bool
Verify data prior to storing
"""
storage = self._get_storage_obj()
# check if data is already stored external
if (
storage is None
or storage.layer_storage.first_item().data_storage_type
== DataStorageType.external_file
):
data = self._get_data()
# if not empty dataset
if data is not None:
if (
self._simulation_data.verbosity_level.value
>= VerbosityLevel.verbose.value
):
print(f"Storing {self.structure.name} internally...")
internal_data = {
"data": data,
}
self._set_data(internal_data, check_data=check_data)
[docs] def has_data(self, key=None):
"""Returns whether this MFList has any data associated with it."""
try:
if self._get_storage_obj() is None:
return False
return self._get_storage_obj().has_data()
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"checking for data",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
def _get_data(self, apply_mult=False, **kwargs):
try:
if self._get_storage_obj() is None:
return None
block_exists = self._block.header_exists(
self._current_key, self.path
)
return self._get_storage_obj().get_data(block_exists=block_exists)
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"getting data",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
[docs] def get_data(self, apply_mult=False, **kwargs):
"""Returns the list's data.
Parameters
----------
apply_mult : bool
Whether to apply a multiplier.
Returns
-------
data : recarray
"""
return self._get_data(apply_mult, **kwargs)
def _get_min_record_entries(self, data=None):
try:
if isinstance(data, dict) and "data" in data:
data = data["data"]
type_list = self._get_storage_obj().build_type_list(
data=data,
min_size=True,
overwrite_existing_type_list=False,
)
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"getting min record entries",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
return len(type_list)
def _set_data(self, data, autofill=False, check_data=True):
# set data
self._resync()
try:
if self._get_storage_obj() is None:
self._data_storage = self._new_storage()
# store data
self._get_storage_obj().set_data(
data, autofill=autofill, check_data=check_data
)
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"setting data",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
if check_data and self._simulation_data.verify_data:
# verify cellids
self._check_valid_cellids()
def _check_valid_cellids(self):
# only check packages that are a part of a model
if isinstance(self._model_or_sim, ModelInterface) and hasattr(
self._model_or_sim, "modelgrid"
):
# get model grid info
mg = self._get_model_grid()
if not mg.is_complete:
return
idomain = mg.idomain
model_shape = idomain.shape
# check to see if there are any cellids
storage_obj = self._get_storage_obj()
if True in storage_obj.recarray_cellid_list:
# get data
data = storage_obj.get_data()
# check data for invalid cellids
for index, is_cellid in enumerate(
storage_obj.resolve_cellidlist(data)
):
if is_cellid:
for record in data:
if not isinstance(record[index], tuple):
# cellids are not always a tuple of integers,
# like sfr. nothing to check in this case
break
idomain_val = idomain
# cellid should be within the model grid
for idx, cellid_part in enumerate(record[index]):
if (
model_shape[idx] <= cellid_part
or cellid_part < 0
):
message = (
"Cellid {} is outside of the "
"model grid "
"{}".format(record[index], model_shape)
)
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self.structure.path,
"storing data",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
message,
self._simulation_data.debug,
)
idomain_val = idomain_val[cellid_part]
# cellid should be at an active cell
if idomain_val < 1:
message = (
"Cellid {} is outside of the "
"active model grid"
".".format(record[index])
)
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self.structure.path,
"storing data",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
message,
self._simulation_data.debug,
)
def _check_line_size(self, data_line, min_line_size):
if 0 < len(data_line) < min_line_size:
message = (
"Data line {} only has {} entries, "
"minimum number of entries is "
"{}.".format(data_line, len(data_line), min_line_size)
)
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self.structure.path,
"storing data",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
message,
self._simulation_data.debug,
)
[docs] def set_data(self, data, autofill=False, check_data=True):
"""Sets the contents of the data to "data" with. Data can have the
following formats:
1) recarray - recarray containing the datalist
2) [(line_one), (line_two), ...] - list where each line of the
datalist is a tuple within the list
3) {'filename':filename, factor=fct, iprn=print_code, data=data}
- dictionary defining the external file containing the datalist.
If the data is transient, a dictionary can be used to specify each
stress period where the dictionary key is <stress period> - 1 and
the dictionary value is the datalist data defined above:
{0:ndarray, 1:[(line_one), (line_two), ...], 2:{'filename':filename})
Parameters
----------
data : ndarray/list/dict
Data to set
autofill : bool
Automatically correct data
check_data : bool
Whether to verify the data
"""
self._set_data(data, autofill, check_data=check_data)
[docs] def append_data(self, data):
"""Appends "data" to the end of this list. Assumes data is in a format
that can be appended directly to a numpy recarray.
Parameters
----------
data : list(tuple)
Data to append.
"""
try:
self._resync()
if self._get_storage_obj() is None:
self._data_storage = self._new_storage()
# store data
self._get_storage_obj().append_data(data)
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"appending data",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
[docs] def append_list_as_record(self, record):
"""Appends the list `record` as a single record in this list's
recarray. Assumes "data" has the correct dimensions.
Parameters
----------
record : list
List to be appended as a single record to the data's existing
recarray.
"""
self._resync()
try:
# convert to tuple
tuple_record = ()
for item in record:
tuple_record += (item,)
# store
self._get_storage_obj().append_data([tuple_record])
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"appending data",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
[docs] def update_record(self, record, key_index):
"""Updates a record at index "key_index" with the contents of "record".
If the index does not exist update_record appends the contents of
"record" to this list's recarray.
Parameters
----------
record : list
New record to update data with
key_index : int
Stress period key of record to update. Only used in transient
data types.
"""
self.append_list_as_record(record)
[docs] def search_data(self, search_term, col=None):
"""Searches the list data at column "col" for "search_term". If col is
None search_data searches the entire list.
Parameters
----------
search_term : str
String to search for
col : int
Column number to search
"""
try:
data = self._get_storage_obj().get_data()
if data is not None:
search_term = search_term.lower()
for row in data:
col_num = 0
for val in row:
if (
val is not None
and val.lower() == search_term
and (col == None or col == col_num)
):
return (row, col)
col_num += 1
return None
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
if col is None:
col = ""
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"searching for data",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
f"search_term={search_term}\ncol={col}",
self._simulation_data.debug,
ex,
)
[docs] def get_file_entry(
self,
ext_file_action=ExtFileAction.copy_relative_paths,
):
"""Returns a string containing the data formatted for a MODFLOW 6
file.
Parameters
----------
ext_file_action : ExtFileAction
How to handle external paths.
Returns
-------
file entry : str
"""
return self._get_file_entry(ext_file_action)
def _get_file_entry(
self,
ext_file_action=ExtFileAction.copy_relative_paths,
):
try:
# freeze model grid to boost performance
self._data_dimensions.lock()
# init
indent = self._simulation_data.indent_string
file_entry = []
storage = self._get_storage_obj()
if storage is None or not storage.has_data():
return ""
# write out initial comments
if storage.pre_data_comments:
file_entry.append(storage.pre_data_comments.get_file_entry())
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"get file entry initialization",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
if (
storage.layer_storage.first_item().data_storage_type
== DataStorageType.external_file
):
try:
ext_string = self._get_external_formatting_string(
0, ext_file_action
)
file_entry.append(f"{indent}{indent}{ext_string}")
# write file
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"formatting external file string",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
else:
try:
data_complete = storage.get_data()
if (
storage.layer_storage.first_item().data_storage_type
== DataStorageType.internal_constant
):
data_lines = 1
else:
data_lines = len(data_complete)
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"getting data from storage",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
# loop through list line by line - assumes first data_item size
# is representative
self._crnt_line_num = 1
for mflist_line in range(0, data_lines):
text_line = []
# data
index = 0
self._get_file_entry_record(
data_complete,
mflist_line,
text_line,
index,
self.structure,
storage,
indent,
)
# comments
if (
mflist_line + 1 in storage.comments
and storage.comments[mflist_line + 1].text
):
text_line.append(storage.comments[mflist_line + 1].text)
file_entry.append(f"{indent}{indent.join(text_line)}\n")
self._crnt_line_num += 1
# unfreeze model grid
self._data_dimensions.unlock()
return "".join(file_entry)
def _get_file_entry_record(
self,
data_complete,
mflist_line,
text_line,
index,
data_set,
storage,
indent,
):
if (
storage.layer_storage.first_item().data_storage_type
== DataStorageType.internal_constant
):
try:
# constant data
data_type = self.structure.data_item_structures[1].type
const_str = self._get_constant_formatting_string(
storage.get_const_val(0), 0, data_type, ""
)
text_line.append(f"{indent}{indent}{const_str.upper()}")
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"getting constant data",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
else:
data_dim = self._data_dimensions
data_line = data_complete[mflist_line]
for data_item in data_set.data_item_structures:
if data_item.is_aux:
try:
aux_var_names = (
data_dim.package_dim.get_aux_variables()
)
if aux_var_names is not None:
for aux_var_name in aux_var_names[0]:
if aux_var_name.lower() != "auxiliary":
data_val = data_line[index]
if data_val is not None:
text_line.append(
to_string(
data_val,
data_item.type,
self._simulation_data,
self._data_dimensions,
data_item.is_cellid,
data_item.possible_cellid,
data_item,
self._simulation_data.verify_data,
)
)
index += 1
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"processing auxiliary variables",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
None,
self._simulation_data.debug,
ex,
)
elif data_item.type == DatumType.record:
# record within a record, recurse
self._get_file_entry_record(
data_complete,
mflist_line,
text_line,
index,
data_item,
storage,
indent,
)
elif (
not data_item.is_boundname
or data_dim.package_dim.boundnames()
) and (
not data_item.optional
or data_item.name_length < 5
or not data_item.is_mname
or not storage.in_model
):
data_complete_len = len(data_line)
if data_complete_len <= index:
if data_item.optional == False:
message = (
"Not enough data provided "
"for {}. Data for required data "
'item "{}" not '
"found (data path: {})"
".".format(
self.structure.name,
data_item.name,
self._path,
)
)
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"building file entry record",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
message,
self._simulation_data.debug,
)
else:
break
try:
# resolve size of data
resolved_shape, shape_rule = data_dim.get_data_shape(
data_item,
self.structure,
[data_line],
repeating_key=self._current_key,
)
data_val = data_line[index]
if data_item.is_cellid or (
data_item.possible_cellid
and storage._validate_cellid([data_val], 0)
):
if (
data_item.shape is not None
and len(data_item.shape) > 0
and data_item.shape[0] == "ncelldim"
):
model_grid = data_dim.get_model_grid()
cellid_size = (
model_grid.get_num_spatial_coordinates()
)
data_item.remove_cellid(
resolved_shape, cellid_size
)
data_size = 1
if len(
resolved_shape
) == 1 and datautil.DatumUtil.is_int(
resolved_shape[0]
):
data_size = int(resolved_shape[0])
if data_size < 0:
# unable to resolve data size based on shape, use
# the data heading names to resolve data size
data_size = storage.resolve_data_size(index)
except Exception as ex:
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"resolving data shape",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
"Verify that your data is the correct shape",
self._simulation_data.debug,
ex,
)
for data_index in range(0, data_size):
if data_complete_len > index:
data_val = data_line[index]
if data_item.type == DatumType.keyword:
if data_val is not None:
text_line.append(data_item.display_name)
if self.structure.block_variable:
# block variables behave differently for
# now. this needs to be resolved
# more consistently at some point
index += 1
elif data_item.type == DatumType.keystring:
if data_val is not None:
text_line.append(data_val)
index += 1
# keystring must be at the end of the line so
# everything else is part of the keystring data
data_key = data_val.lower()
if data_key not in data_item.keystring_dict:
keystr_struct = data_item.keystring_dict[
f"{data_key}record"
]
else:
keystr_struct = data_item.keystring_dict[
data_key
]
if isinstance(
keystr_struct, mfstructure.MFDataStructure
):
# data items following keystring
ks_structs = (
keystr_struct.data_item_structures[1:]
)
else:
# key string stands alone
ks_structs = [keystr_struct]
ks_struct_index = 0
max_index = len(ks_structs) - 1
data_index = index
while data_index != data_complete_len:
if data_line[data_index] is not None:
try:
k_data_item = ks_structs[
ks_struct_index
]
if (
k_data_item.type
== DatumType.keyword
):
if (
data_line[data_index]
is not None
):
text_line.append(
k_data_item.display_name
)
else:
text_line.append(
to_string(
data_line[data_index],
k_data_item.type,
self._simulation_data,
self._data_dimensions,
k_data_item.is_cellid,
k_data_item.possible_cellid,
k_data_item,
self._simulation_data.verify_data,
)
)
data_index += 1
except Exception as ex:
message = (
"An error occurred "
"while converting data "
"to a string. This "
"error occurred while "
'processing "{}" line '
'{} data item "{}".'
"(data path: {})"
".".format(
self.structure.name,
data_item.name,
self._crnt_line_num,
self._path,
)
)
(
type_,
value_,
traceback_,
) = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"converting data "
"to a string",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
message,
self._simulation_data.debug,
ex,
)
if ks_struct_index < max_index:
# increment until last record
# entry then repeat last entry
ks_struct_index += 1
else:
data_index += 1
index = data_index
elif data_val is not None and (
not isinstance(data_val, float)
or not math.isnan(data_val)
):
try:
if data_item.tagged and data_index == 0:
# data item tagged, include data item name
# as a keyword
text_line.append(
to_string(
data_val,
DatumType.string,
self._simulation_data,
self._data_dimensions,
False,
data_item=data_item,
verify_data=self._simulation_data.verify_data,
)
)
index += 1
data_val = data_line[index]
text_line.append(
to_string(
data_val,
data_item.type,
self._simulation_data,
self._data_dimensions,
data_item.is_cellid,
data_item.possible_cellid,
data_item,
self._simulation_data.verify_data,
)
)
except Exception as ex:
message = (
"An error occurred while "
"converting data to a "
"string. "
"This error occurred while "
'processing "{}" line {} data '
'item "{}".(data path: {})'
".".format(
self.structure.name,
data_item.name,
self._crnt_line_num,
self._path,
)
)
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"converting data to a string",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
message,
self._simulation_data.debug,
ex,
)
index += 1
elif not data_item.optional and shape_rule is None:
message = (
"Not enough data provided "
"for {}. Data for required data "
'item "{}" not '
"found (data path: {})"
".".format(
self.structure.name,
data_item.name,
self._path,
)
)
type_, value_, traceback_ = sys.exc_info()
raise MFDataException(
self.structure.get_model(),
self.structure.get_package(),
self._path,
"building data line",
self.structure.name,
inspect.stack()[0][3],
type_,
value_,
traceback_,
message,
self._simulation_data.debug,
)
[docs] def load(
self,
first_line,
file_handle,
block_header,
pre_data_comments=None,
external_file_info=None,
):
"""Loads data from first_line (the first line of data) and open file
file_handle which is pointing to the second line of data. Returns a
tuple with the first item indicating whether all data was read
and the second item being the last line of text read from the file.
This method was only designed for internal FloPy use and is not
recommended for end users.
Parameters
----------
first_line : str
A string containing the first line of data in this list.
file_handle : file descriptor
A file handle for the data file which points to the second
line of data for this list
block_header : MFBlockHeader
Block header object that contains block header information
for the block containing this data
pre_data_comments : MFComment
Comments immediately prior to the data
external_file_info : list
Contains information about storing files externally
Returns
-------
more data : bool,
next data line : str
"""
super().load(
first_line, file_handle, block_header, pre_data_comments=None
)
self._resync()
file_access = MFFileAccessList(
self.structure,
self._data_dimensions,
self._simulation_data,
self._path,
self._current_key,
)
storage = self._get_storage_obj()
result = file_access.load_from_package(
first_line, file_handle, storage, pre_data_comments
)
if external_file_info is not None:
storage.point_to_existing_external_file(external_file_info, 0)
return result
def _new_storage(self, stress_period=0):
return DataStorage(
self._simulation_data,
self._model_or_sim,
self._data_dimensions,
self._get_file_entry,
DataStorageType.internal_array,
DataStructureType.recarray,
stress_period=stress_period,
data_path=self._path,
)
def _get_storage_obj(self):
return self._data_storage
[docs] def plot(
self,
key=None,
names=None,
filename_base=None,
file_extension=None,
mflay=None,
**kwargs,
):
"""
Plot boundary condition (MfList) data
Parameters
----------
key : str
MfList dictionary key. (default is None)
names : list
List of names for figure titles. (default is None)
filename_base : str
Base file name that will be used to automatically generate file
names for output image files. Plots will be exported as image
files if file_name_base is not None. (default is None)
file_extension : str
Valid matplotlib.pyplot file extension for savefig(). Only used
if filename_base is not None. (default is 'png')
mflay : int
MODFLOW zero-based layer number to return. If None, then all
all layers will be included. (default is None)
**kwargs : dict
axes : list of matplotlib.pyplot.axis
List of matplotlib.pyplot.axis that will be used to plot
data for each layer. If axes=None axes will be generated.
(default is None)
pcolor : bool
Boolean used to determine if matplotlib.pyplot.pcolormesh
plot will be plotted. (default is True)
colorbar : bool
Boolean used to determine if a color bar will be added to
the matplotlib.pyplot.pcolormesh. Only used if pcolor=True.
(default is False)
inactive : bool
Boolean used to determine if a black overlay in inactive
cells in a layer will be displayed. (default is True)
contour : bool
Boolean used to determine if matplotlib.pyplot.contour
plot will be plotted. (default is False)
clabel : bool
Boolean used to determine if matplotlib.pyplot.clabel
will be plotted. Only used if contour=True. (default is False)
grid : bool
Boolean used to determine if the model grid will be plotted
on the figure. (default is False)
masked_values : list
List of unique values to be excluded from the plot.
Returns
----------
out : list
Empty list is returned if filename_base is not None. Otherwise
a list of matplotlib.pyplot.axis is returned.
"""
from ...plot import PlotUtilities
if not self.plottable:
raise TypeError("Simulation level packages are not plottable")
if "cellid" not in self.dtype.names:
return
PlotUtilities._plot_mflist_helper(
mflist=self,
key=key,
kper=None,
names=names,
filename_base=None,
file_extension=None,
mflay=None,
**kwargs,
)
[docs]class MFTransientList(MFList, mfdata.MFTransient, DataListInterface):
"""
Provides an interface for the user to access and update MODFLOW transient
list data.
Parameters
----------
sim_data : MFSimulationData
data contained in the simulation
structure : MFDataStructure
describes the structure of the data
data : list or ndarray
actual data
enable : bool
enable/disable the array
path : tuple
path in the data dictionary to this MFArray
dimensions : MFDataDimensions
dimension information related to the model, package, and array
"""
def __init__(
self,
sim_data,
model_or_sim,
structure,
enable=True,
path=None,
dimensions=None,
package=None,
block=None,
):
super().__init__(
sim_data=sim_data,
model_or_sim=model_or_sim,
structure=structure,
data=None,
enable=enable,
path=path,
dimensions=dimensions,
package=package,
block=block,
)
self._transient_setup(self._data_storage)
self.repeating = True
self.empty_keys = {}
@property
def data_type(self):
return DataType.transientlist
@property
def dtype(self):
data = self.get_data()
if len(data) > 0:
if 0 in data:
return data[0].dtype
else:
return next(iter(data.values())).dtype
else:
return None
@property
def data(self):
"""Returns list data. Calls get_data with default parameters."""
return self.get_data()
@property
def masked_4D_arrays(self):
"""Returns list data as a masked 4D array."""
model_grid = self._data_dimensions.get_model_grid()
nper = self._data_dimensions.package_dim.model_dim[
0
].simulation_time.get_num_stress_periods()
# get the first kper
arrays = self.to_array(kper=0, mask=True)
if arrays is not None:
# initialize these big arrays
if model_grid.grid_type() == DiscretizationType.DIS:
m4ds = {}
for name, array in arrays.items():
m4d = np.zeros(
(
nper,
model_grid.num_layers,
model_grid.num_rows,
model_grid.num_columns,
)
)
m4d[0, :, :, :] = array
m4ds[name] = m4d
for kper in range(1, nper):
arrays = self.to_array(kper=kper, mask=True)
for name, array in arrays.items():
m4ds[name][kper, :, :, :] = array
return m4ds
else:
m3ds = {}
for name, array in arrays.items():
m3d = np.zeros(
(
nper,
model_grid.num_layers,
model_grid.num_cells_per_layer(),
)
)
m3d[0, :, :] = array
m3ds[name] = m3d
for kper in range(1, nper):
arrays = self.to_array(kper=kper, mask=True)
for name, array in arrays.items():
m3ds[name][kper, :, :] = array
return m3ds
[docs] def masked_4D_arrays_itr(self):
"""Returns list data as an iterator of a masked 4D array."""
model_grid = self._data_dimensions.get_model_grid()
nper = self._data_dimensions.package_dim.model_dim[
0
].simulation_time.get_num_stress_periods()
# get the first kper
arrays = self.to_array(kper=0, mask=True)
if arrays is not None:
# initialize these big arrays
for name, array in arrays.items():
if model_grid.grid_type() == DiscretizationType.DIS:
m4d = np.zeros(
(
nper,
model_grid.num_layers(),
model_grid.num_rows(),
model_grid.num_columns(),
)
)
m4d[0, :, :, :] = array
for kper in range(1, nper):
arrays = self.to_array(kper=kper, mask=True)
for tname, array in arrays.items():
if tname == name:
m4d[kper, :, :, :] = array
yield name, m4d
else:
m3d = np.zeros(
(
nper,
model_grid.num_layers(),
model_grid.num_cells_per_layer(),
)
)
m3d[0, :, :] = array
for kper in range(1, nper):
arrays = self.to_array(kper=kper, mask=True)
for tname, array in arrays.items():
if tname == name:
m3d[kper, :, :] = array
yield name, m3d
[docs] def to_array(self, kper=0, mask=False):
"""Returns list data as an array."""
return super().to_array(kper, mask)
[docs] def remove_transient_key(self, transient_key):
"""Remove transient stress period key. Method is used
internally by FloPy and is not intended to the end user.
"""
if transient_key in self._data_storage:
del self._data_storage[transient_key]
[docs] def add_transient_key(self, transient_key):
"""Adds a new transient time allowing data for that time to be stored
and retrieved using the key `transient_key`. Method is used
internally by FloPy and is not intended to the end user.
Parameters
----------
transient_key : int
Zero-based stress period to add
"""
super().add_transient_key(transient_key)
if isinstance(transient_key, int):
stress_period = transient_key
else:
stress_period = 1
self._data_storage[transient_key] = super()._new_storage(stress_period)
[docs] def store_as_external_file(
self,
external_file_path,
binary=False,
replace_existing_external=True,
check_data=True,
):
"""Store all data externally in file external_file_path. the binary
allows storage in a binary file. If replace_existing_external is set
to False, this method will not do anything if the data is already in
an external file.
Parameters
----------
external_file_path : str
Path to external file
binary : bool
Store data in a binary file
replace_existing_external : bool
Whether to replace an existing external file.
check_data : bool
Verify data prior to storing
"""
self._cache_model_grid = True
for sp in self._data_storage.keys():
self._current_key = sp
layer_storage = self._get_storage_obj().layer_storage
if (
layer_storage.get_total_size() > 0
and self._get_storage_obj().layer_storage[0].data_storage_type
!= DataStorageType.external_file
):
fname, ext = os.path.splitext(external_file_path)
if datautil.DatumUtil.is_int(sp):
full_name = f"{fname}_{sp + 1}{ext}"
else:
full_name = f"{fname}_{sp}{ext}"
super().store_as_external_file(
full_name,
binary,
replace_existing_external,
check_data,
)
self._cache_model_grid = False
[docs] def store_internal(
self,
check_data=True,
):
"""Store all data internally.
Parameters
----------
check_data : bool
Verify data prior to storing
"""
self._cache_model_grid = True
for sp in self._data_storage.keys():
self._current_key = sp
if (
self._get_storage_obj().layer_storage[0].data_storage_type
== DataStorageType.external_file
):
super().store_internal(
check_data,
)
self._cache_model_grid = False
[docs] def has_data(self, key=None):
"""Returns whether this MFList has any data associated with it in key
"key"."""
if key is None:
for sto_key in self._data_storage.keys():
self.get_data_prep(sto_key)
if super().has_data():
return True
return False
else:
self.get_data_prep(key)
return super().has_data()
[docs] def get_data(self, key=None, apply_mult=False, **kwargs):
"""Returns the data for stress period `key`.
Parameters
----------
key : int
Zero-based stress period to return data from.
apply_mult : bool
Apply multiplier
Returns
-------
data : recarray
"""
if self._data_storage is not None and len(self._data_storage) > 0:
if key is None:
if "array" in kwargs:
output = []
sim_time = self._data_dimensions.package_dim.model_dim[
0
].simulation_time
num_sp = sim_time.get_num_stress_periods()
data = None
for sp in range(0, num_sp):
if sp in self._data_storage:
self.get_data_prep(sp)
data = super().get_data(apply_mult=apply_mult)
elif self._block.header_exists(sp):
data = None
output.append(data)
return output
else:
output = {}
for key in self._data_storage.keys():
self.get_data_prep(key)
output[key] = super().get_data(apply_mult=apply_mult)
return output
self.get_data_prep(key)
return super().get_data(apply_mult=apply_mult)
else:
return None
[docs] def set_data(self, data, key=None, autofill=False):
"""Sets the contents of the data at time `key` to `data`.
Parameters
----------
data : dict, recarray, list
Data being set. Data can be a dictionary with keys as
zero-based stress periods and values as the data. If data is
an recarray or list of tuples, it will be assigned to the the
stress period specified in `key`. If any is set to None, that
stress period of data will be removed.
key : int
Zero based stress period to assign data too. Does not apply
if `data` is a dictionary.
autofill : bool
Automatically correct data.
"""
self._cache_model_grid = True
if isinstance(data, dict):
if "filename" not in data:
# each item in the dictionary is a list for one stress period
# the dictionary key is the stress period the list is for
del_keys = []
for key, list_item in data.items():
if list_item is None:
self.remove_transient_key(key)
del_keys.append(key)
self.empty_keys[key] = False
elif isinstance(list_item, list) and len(list_item) == 0:
self.empty_keys[key] = True
else:
self.empty_keys[key] = False
if (
isinstance(list_item, dict)
and "check" in list_item
):
check = list_item["check"]
else:
check = True
self._set_data_prep(list_item, key)
super().set_data(
list_item, autofill=autofill, check_data=check
)
for key in del_keys:
del data[key]
else:
self.empty_keys[key] = False
self._set_data_prep(data["data"], key)
super().set_data(data, autofill)
else:
if key is None:
# search for a key
new_key_index = self.structure.first_non_keyword_index()
if new_key_index is not None and len(data) > new_key_index:
key = data[new_key_index]
else:
key = 0
if isinstance(data, list) and len(data) == 0:
self.empty_keys[key] = True
else:
check = True
if (
isinstance(data, list)
and len(data) > 0
and data[0] == "no_check"
):
# not checking data
check = False
data = data[1:]
self.empty_keys[key] = False
if data is None:
self.remove_transient_key(key)
else:
self._set_data_prep(data, key)
super().set_data(data, autofill, check_data=check)
self._cache_model_grid = False
[docs] def get_file_entry(
self, key=0, ext_file_action=ExtFileAction.copy_relative_paths
):
"""Returns a string containing the data at time `key` formatted for a
MODFLOW 6 file.
Parameters
----------
key : int
Zero based stress period to return data from.
ext_file_action : ExtFileAction
How to handle external paths.
Returns
-------
file entry : str
"""
if key in self.empty_keys and self.empty_keys[key]:
return ""
else:
self._get_file_entry_prep(key)
return super().get_file_entry(ext_file_action=ext_file_action)
[docs] def load(
self,
first_line,
file_handle,
block_header,
pre_data_comments=None,
external_file_info=None,
):
"""Loads data from first_line (the first line of data) and open file
file_handle which is pointing to the second line of data. Returns a
tuple with the first item indicating whether all data was read
and the second item being the last line of text read from the file.
Parameters
----------
first_line : str
A string containing the first line of data in this list.
file_handle : file descriptor
A file handle for the data file which points to the second
line of data for this array
block_header : MFBlockHeader
Block header object that contains block header information
for the block containing this data
pre_data_comments : MFComment
Comments immediately prior to the data
external_file_info : list
Contains information about storing files externally
"""
self._load_prep(block_header)
return super().load(
first_line,
file_handle,
block_header,
pre_data_comments,
external_file_info,
)
[docs] def append_list_as_record(self, record, key=0):
"""Appends the list `data` as a single record in this list's recarray
at time `key`. Assumes `data` has the correct dimensions.
Parameters
----------
data : list
Data to append
key : int
Zero based stress period to append data too.
"""
self._append_list_as_record_prep(record, key)
super().append_list_as_record(record)
[docs] def update_record(self, record, key_index, key=0):
"""Updates a record at index `key_index` and time `key` with the
contents of `record`. If the index does not exist update_record
appends the contents of `record` to this list's recarray.
Parameters
----------
record : list
Record to append
key_index : int
Index to update
key : int
Zero based stress period to append data too
"""
self._update_record_prep(key)
super().update_record(record, key_index)
def _new_storage(self, stress_period=0):
return {}
def _get_storage_obj(self):
if (
self._current_key is None
or self._current_key not in self._data_storage
):
return None
return self._data_storage[self._current_key]
[docs] def plot(
self,
key=None,
names=None,
kper=0,
filename_base=None,
file_extension=None,
mflay=None,
**kwargs,
):
"""
Plot stress period boundary condition (MfList) data for a specified
stress period
Parameters
----------
key : str
MfList dictionary key. (default is None)
names : list
List of names for figure titles. (default is None)
kper : int
MODFLOW zero-based stress period number to return. (default is zero)
filename_base : str
Base file name that will be used to automatically generate file
names for output image files. Plots will be exported as image
files if file_name_base is not None. (default is None)
file_extension : str
Valid matplotlib.pyplot file extension for savefig(). Only used
if filename_base is not None. (default is 'png')
mflay : int
MODFLOW zero-based layer number to return. If None, then all
all layers will be included. (default is None)
**kwargs : dict
axes : list of matplotlib.pyplot.axis
List of matplotlib.pyplot.axis that will be used to plot
data for each layer. If axes=None axes will be generated.
(default is None)
pcolor : bool
Boolean used to determine if matplotlib.pyplot.pcolormesh
plot will be plotted. (default is True)
colorbar : bool
Boolean used to determine if a color bar will be added to
the matplotlib.pyplot.pcolormesh. Only used if pcolor=True.
(default is False)
inactive : bool
Boolean used to determine if a black overlay in inactive
cells in a layer will be displayed. (default is True)
contour : bool
Boolean used to determine if matplotlib.pyplot.contour
plot will be plotted. (default is False)
clabel : bool
Boolean used to determine if matplotlib.pyplot.clabel
will be plotted. Only used if contour=True. (default is False)
grid : bool
Boolean used to determine if the model grid will be plotted
on the figure. (default is False)
masked_values : list
List of unique values to be excluded from the plot.
Returns
----------
out : list
Empty list is returned if filename_base is not None. Otherwise
a list of matplotlib.pyplot.axis is returned.
"""
from ...plot import PlotUtilities
if not self.plottable:
raise TypeError("Simulation level packages are not plottable")
# model.plot() will not work for a mf6 model oc package unless
# this check is here
if self.get_data() is None:
return
if "cellid" not in self.dtype.names:
return
axes = PlotUtilities._plot_mflist_helper(
self,
key=key,
names=names,
kper=kper,
filename_base=filename_base,
file_extension=file_extension,
mflay=mflay,
**kwargs,
)
return axes
[docs]class MFMultipleList(MFTransientList):
"""
Provides an interface for the user to access and update MODFLOW multiple
list data. This is list data that is in the same format as the
MFTransientList, but is not time based.
Parameters
----------
sim_data : MFSimulationData
data contained in the simulation
structure : MFDataStructure
describes the structure of the data
data : list or ndarray
actual data
enable : bool
enable/disable the array
path : tuple
path in the data dictionary to this MFArray
dimensions : MFDataDimensions
dimension information related to the model, package, and array
"""
def __init__(
self,
sim_data,
model_or_sim,
structure,
enable=True,
path=None,
dimensions=None,
package=None,
block=None,
):
super().__init__(
sim_data=sim_data,
model_or_sim=model_or_sim,
structure=structure,
enable=enable,
path=path,
dimensions=dimensions,
package=package,
block=block,
)
[docs] def get_data(self, key=None, apply_mult=False, **kwargs):
"""Returns the data for stress period `key`.
Parameters
----------
key : int
Zero-based stress period to return data from.
apply_mult : bool
Apply multiplier
Returns
-------
data : ndarray
"""
return super().get_data(key=key, apply_mult=apply_mult, **kwargs)