ladim 2.0.9__tar.gz → 2.1.5__tar.gz

{ladim-2.0.9 → ladim-2.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: ladim
-Version: 2.0.9
+Version: 2.1.5
 Summary: Lagrangian Advection and Diffusion Model
 Home-page: https://github.com/pnsaevik/ladim
 Author: Bjørn Ådlandsvik
@@ -25,6 +25,7 @@ Requires-Dist: pyproj
 Requires-Dist: pyyaml
 Requires-Dist: scipy
 Requires-Dist: xarray
+Dynamic: license-file
 
 LADiM – the Lagrangian Advection and Diffusion Model
 ====================================================

{ladim-2.0.9 → ladim-2.1.5}/ladim/__init__.py

@@ -1,3 +1,3 @@
-__version__ = '2.0.9'
+__version__ = '2.1.5'
 
 from .main import main, run

{ladim-2.0.9 → ladim-2.1.5}/ladim/config.py

@@ -82,7 +82,6 @@ def convert_1_to_2(c):
     out['solver']['stop'] = dict_get(c, 'time_control.stop_time')
     out['solver']['step'] = dt_sec
     out['solver']['seed'] = dict_get(c, 'numerics.seed')
-    out['solver']['order'] = ['release', 'forcing', 'output', 'tracker', 'ibm', 'state']
 
     out['grid'] = {}
     out['grid']['file'] = dict_get(c, [
@@ -93,7 +92,7 @@ def convert_1_to_2(c):
     out['grid']['start_time'] = np.datetime64(dict_get(c, 'time_control.start_time', '1970'), 's')
     out['grid']['subgrid'] = dict_get(c, 'gridforce.subgrid', None)
 
-    out['forcing'] = {}
+    out['forcing'] = {k: v for k, v in c.get('gridforce', {}).items() if k not in ('input_file', 'module')}
     out['forcing']['file'] = dict_get(c, ['gridforce.input_file', 'files.input_file'])
     out['forcing']['first_file'] = dict_get(c, 'gridforce.first_file', "")
     out['forcing']['last_file'] = dict_get(c, 'gridforce.last_file', "")
@@ -142,7 +141,6 @@ def convert_1_to_2(c):
 
     out['ibm'] = {}
     if 'ibm' in c:
-        out['ibm']['module'] = 'ladim.ibms.LegacyIBM'
         out['ibm']['legacy_module'] = dict_get(c, ['ibm.ibm_module', 'ibm.module'])
         if out['ibm']['legacy_module'] == 'ladim.ibms.ibm_salmon_lice':
             out['ibm']['legacy_module'] = 'ladim_plugins.salmon_lice'

{ladim-2.0.9 → ladim-2.1.5}/ladim/forcing.py

@@ -1,10 +1,19 @@
-from .model import Model, Module
+import typing
+if typing.TYPE_CHECKING:
+    from ladim.model import Model
 
 
-class Forcing(Module):
+class Forcing:
+    @staticmethod
+    def from_roms(**conf):
+        return RomsForcing(**conf)
+
     def velocity(self, X, Y, Z, tstep=0.0):
         raise NotImplementedError
 
+    def update(self, model: "Model"):
+        raise NotImplementedError
+
 
 class RomsForcing(Forcing):
     def __init__(self, file, variables=None, **conf):
@@ -37,11 +46,7 @@ class RomsForcing(Forcing):
 
         grid_ref = GridReference()
         legacy_conf = dict(
-            gridforce=dict(
-                input_file=file,
-                first_file=conf.get('first_file', ""),
-                last_file=conf.get('last_file', ""),
-            ),
+            gridforce=dict(input_file=file, **conf),
             ibm_forcing=conf.get('ibm_forcing', []),
             start_time=conf.get('start_time', None),
             stop_time=conf.get('stop_time', None),
@@ -50,7 +55,7 @@ class RomsForcing(Forcing):
         if conf.get('subgrid', None) is not None:
             legacy_conf['gridforce']['subgrid'] = conf['subgrid']
 
-        from .model import load_class
+        from .utilities import load_class
         LegacyForcing = load_class(conf.get('legacy_module', 'ladim.gridforce.ROMS.Forcing'))
 
         # Allow gridforce module in current directory
@@ -63,7 +68,7 @@ class RomsForcing(Forcing):
         # self.U = self.forcing.U
         # self.V = self.forcing.V
 
-    def update(self, model: Model):
+    def update(self, model: "Model"):
         elapsed = model.solver.time - model.solver.start
         t = elapsed // model.solver.step
 

{ladim-2.0.9 → ladim-2.1.5}/ladim/grid.py

@@ -1,16 +1,19 @@
-from .model import Module
 import numpy as np
 from typing import Sequence
 from scipy.ndimage import map_coordinates
 
 
-class Grid(Module):
+class Grid:
     """
     The grid class represents the coordinate system used for particle tracking.
     It contains methods for converting between global coordinates (latitude,
     longitude, depth and posix time) and internal coordinates.
     """
 
+    @staticmethod
+    def from_roms(**conf):
+        return RomsGrid(**conf)
+
     def ingrid(self, X, Y):
         raise NotImplementedError
 
@@ -188,7 +191,7 @@ class RomsGrid(Grid):
         if subgrid is not None:
             legacy_conf['gridforce']['subgrid'] = subgrid
 
-        from .model import load_class
+        from .utilities import load_class
         LegacyGrid = load_class(legacy_module)
 
         # Allow gridforce module in current directory

{ladim-2.0.9 → ladim-2.1.5}/ladim/gridforce/ROMS.py

@@ -62,7 +62,7 @@ class Grid:
         # Here, imax, jmax refers to whole grid
         jmax, imax = ncid.variables["h"].shape
         whole_grid = [1, imax - 1, 1, jmax - 1]
-        if "subgrid" in config["gridforce"]:
+        if config["gridforce"].get('subgrid', None):
             limits = list(config["gridforce"]["subgrid"])
         else:
             limits = whole_grid

ladim-2.1.5/ladim/ibms/__init__.py

@@ -0,0 +1,38 @@
+import numpy as np
+import typing
+
+if typing.TYPE_CHECKING:
+    from ..model import Model
+
+
+class IBM:
+    def __init__(self, legacy_module=None, conf: dict = None):
+        from ..utilities import load_class
+
+        if legacy_module is None:
+            UserIbmClass = EmptyIBM
+        else:
+            UserIbmClass = load_class(legacy_module + '.IBM')
+
+        self.user_ibm = UserIbmClass(conf or {})
+
+    def update(self, model: "Model"):
+        grid = model.grid
+        state = model.state
+
+        state.dt = model.solver.step
+        state.timestamp = np.int64(model.solver.time).astype('datetime64[s]')
+        state.timestep = (
+                (model.solver.time - model.solver.start) // model.solver.step
+        )
+
+        forcing = model.forcing
+        self.user_ibm.update_ibm(grid, state, forcing)
+
+
+class EmptyIBM:
+    def __init__(self, _):
+        pass
+
+    def update_ibm(self, grid, state, forcing):
+        return

ladim-2.1.5/ladim/model.py

@@ -0,0 +1,79 @@
+from ladim.ibms import IBM
+from ladim.solver import Solver
+from ladim.release import Releaser
+from ladim.grid import Grid
+from ladim.forcing import Forcing
+from ladim.state import State
+from ladim.tracker import Tracker
+from ladim.output import Output
+
+
+class Model:
+    """
+    The Model class represents the entire simulation model. The different
+    submodules control the simulation behaviour. In particular, the solver
+    submodule controls the execution flow while the other submodules are
+    called once every time step within the main simulation loop.
+    """
+
+    def __init__(
+            self, grid: "Grid", forcing: "Forcing", release: "Releaser",
+            state: "State", output: "Output", ibm: "IBM", tracker: "Tracker",
+            solver: "Solver",
+    ):
+        self.grid = grid
+        self.forcing = forcing
+        self.release = release
+        self.state = state
+        self.output = output
+        self.ibm = ibm
+        self.tracker = tracker
+        self.solver = solver
+
+    @staticmethod
+    def from_config(config: dict) -> "Model":
+        """
+        Initialize a model class by supplying the configuration parameters
+        of each submodule.
+
+        :param config: Configuration parameters for each submodule
+        :return: An initialized Model class
+        """
+
+        grid = Grid.from_roms(**config['grid'])
+        forcing = Forcing.from_roms(**config['forcing'])
+
+        release = Releaser.from_textfile(
+            lonlat_converter=grid.ll2xy, **config['release']
+        )
+        tracker = Tracker.from_config(**config['tracker'])
+
+        output = Output(**config['output'])
+        ibm = IBM(**config['ibm'])
+        solver = Solver(**config['solver'])
+
+        state = State()
+
+        # noinspection PyTypeChecker
+        return Model(grid, forcing, release, state, output, ibm, tracker, solver)
+
+    @property
+    def modules(self) -> dict:
+        return dict(
+            grid=self.grid,
+            forcing=self.forcing,
+            release=self.release,
+            state=self.state,
+            output=self.output,
+            ibm=self.ibm,
+            tracker=self.tracker,
+            solver=self.solver,
+        )
+
+    def run(self):
+        self.solver.run(self)
+
+    def close(self):
+        for m in self.modules.values():
+            if hasattr(m, 'close') and callable(m.close):
+                m.close()

{ladim-2.0.9 → ladim-2.1.5}/ladim/output.py

@@ -1,13 +1,11 @@
-from .model import Model, Module
 import netCDF4 as nc
 import numpy as np
+import typing
+if typing.TYPE_CHECKING:
+    from .model import Model
 
 
-class Output(Module):
-    pass
-
-
-class RaggedOutput(Output):
+class Output:
     def __init__(self, variables: dict, file: str, frequency):
         """
         Writes simulation output to netCDF file in ragged array format
@@ -52,7 +50,7 @@ class RaggedOutput(Output):
         """Returns a handle to the netCDF dataset currently being written to"""
         return self._dset
 
-    def update(self, model: Model):
+    def update(self, model: "Model"):
         if self._dset is None:
             self._create_dset()
 

ladim-2.1.5/ladim/release.py

@@ -0,0 +1,376 @@
+import contextlib
+import numpy as np
+import pandas as pd
+from .utilities import read_timedelta
+import logging
+import typing
+
+if typing.TYPE_CHECKING:
+    from ladim.model import Model
+
+
+logger = logging.getLogger(__name__)
+
+
+class Releaser:
+    def __init__(self, particle_generator: typing.Callable[[float, float], pd.DataFrame]):
+        self.particle_generator = particle_generator
+
+    @staticmethod
+    def from_textfile(
+            file, colnames: list = None, formats: dict = None,
+            frequency=(0, 's'), defaults=None, lonlat_converter=None,
+    ):
+        """
+        Release module which reads from a text file
+
+        The text file must be a whitespace-separated csv file
+
+        :param lonlat_converter: Function that converts lon, lat coordinates to
+            x, y coordinates
+
+        :param file: Release file
+
+        :param colnames: Column names, if the release file does not contain any
+
+        :param formats: Data column formats, one dict entry per column. If any column
+            is missing, the default format is used. Keys should correspond to column names.
+            Values should be either ``"float"``, ``"int"`` or ``"time"``. Default value
+            is ``"float"`` for all columns except ``release_time``, which has default
+            value ``"time"``.
+
+        :param frequency: A two-element list with entries ``[value, unit]``, where
+            ``unit`` can be any numpy-compatible timedelta unit (such as "s", "m", "h", "D").
+
+        :param defaults: A dict of variables to be added to each particle. The keys
+            are the variable names, the values are the initial values at particle
+            release.
+        """
+
+        release_table = ReleaseTable.from_filename_or_stream(
+            file=file,
+            column_names=colnames,
+            column_formats=formats or dict(),
+            interval=read_timedelta(frequency) / np.timedelta64(1, 's'),
+            defaults=defaults or dict(),
+            lonlat_converter=lonlat_converter,
+        )
+        return Releaser(particle_generator=release_table.subset)
+
+    def update(self, model: "Model"):
+        self._add_new(model)
+        self._kill_old(model)
+
+    # noinspection PyMethodMayBeStatic
+    def _kill_old(self, model: "Model"):
+        state = model.state
+        if 'alive' in state:
+            alive = state['alive']
+            alive &= model.grid.ingrid(state['X'], state['Y'])
+            state.remove(~alive)
+
+    def _add_new(self, model: "Model"):
+        # Get the portion of the release dataset that corresponds to
+        # current simulation time
+        df = self.particle_generator(
+            model.solver.time,
+            model.solver.time + model.solver.step,
+        )
+
+        # If there are no new particles, but the state is empty, we should
+        # still initialize the state by adding the appropriate columns
+        if (len(df) == 0) and ('X' not in model.state):
+            model.state.append(df.to_dict(orient='list'))
+
+        # If there are no new particles, we are done.
+        if len(df) == 0:
+            return
+
+        # If we are at the final time step, we should not release any more particles
+        if model.solver.time >= model.solver.stop:
+            return
+
+        # Add new particles
+        new_particles = df.to_dict(orient='list')
+        state = model.state
+        state.append(new_particles)
+
+
+def release_data_subset(dataframe, start_time, stop_time, interval: typing.Any = 0):
+    events = resolve_schedule(
+        times=dataframe['release_time'].values,
+        interval=interval,
+        start_time=start_time,
+        stop_time=stop_time,
+    )
+
+    return dataframe.iloc[events]
+
+
+def load_release_file(stream, names: list, formats: dict) -> pd.DataFrame:
+    if names is None:
+        import re
+        first_line = stream.readline()
+        names = re.split(pattern=r'\s+', string=first_line.strip())
+
+    converters = get_converters(varnames=names, conf=formats)
+
+    df = pd.read_csv(
+        stream,
+        names=names,
+        converters=converters,
+        sep='\\s+',
+    )
+    df = df.sort_values(by='release_time')
+    return df
+
+
+def get_converters(varnames: list, conf: dict) -> dict:
+    """
+    Given a list of varnames and config keywords, return a dict of converters
+
+    Returns a dict where the keys are ``varnames`` and the values are
+    callables.
+
+    :param varnames: For instance, ['release_time', 'X', 'Y']
+    :param conf: For instance, {'release_time': 'time', 'X': 'float'}
+    :return: A mapping of varnames to converters
+    """
+    dtype_funcs = dict(
+        time=lambda item: np.datetime64(item, 's').astype('int64'),
+        int=int,
+        float=float,
+    )
+
+    dtype_defaults = dict(
+        release_time='time',
+    )
+
+    converters = {}
+    for varname in varnames:
+        dtype_default = dtype_defaults.get(varname, 'float')
+        dtype_str = conf.get(varname, dtype_default)
+        dtype_func = dtype_funcs[dtype_str]
+        converters[varname] = dtype_func
+
+    return converters
+
+
+class ReleaseTable:
+    def __init__(
+            self,
+            dataframe: pd.DataFrame,
+            interval: float,
+            defaults: dict[str, typing.Any],
+            lonlat_converter: typing.Callable[[np.ndarray, np.ndarray], tuple[np.ndarray, np.ndarray]],
+    ):
+        self.dataframe = dataframe
+        self.interval = interval
+        self.defaults = defaults
+        self.lonlat_converter = lonlat_converter
+
+    def subset(self, start_time, stop_time):
+        events = resolve_schedule(
+            times=self.dataframe['release_time'].values,
+            interval=self.interval,
+            start_time=start_time,
+            stop_time=stop_time,
+        )
+
+        df = self.dataframe.iloc[events].copy(deep=True)
+        df = replace_lonlat_in_release_table(df, self.lonlat_converter)
+        df = add_default_variables_in_release_table(df, self.defaults)
+        df = expand_multiplicity_in_release_table(df)
+
+        return df
+
+    @staticmethod
+    def from_filename_or_stream(file, column_names, column_formats, interval, defaults, lonlat_converter):
+        with open_or_relay(file, 'r', encoding='utf-8') as fp:
+            return ReleaseTable.from_stream(
+                fp, column_names, column_formats, interval, defaults, lonlat_converter)
+
+    @staticmethod
+    def from_stream(fp, column_names, column_formats, interval, defaults, lonlat_converter):
+        df = load_release_file(stream=fp, names=column_names, formats=column_formats)
+        return ReleaseTable(df, interval, defaults, lonlat_converter)
+
+
+def replace_lonlat_in_release_table(df, lonlat_converter):
+    if "lon" not in df.columns or "lat" not in df.columns:
+        return df
+
+    X, Y = lonlat_converter(df["lon"].values, df["lat"].values)
+    df_new = df.drop(columns=['X', 'Y', 'lat', 'lon'], errors='ignore')
+    df_new["X"] = X
+    df_new["Y"] = Y
+    return df_new
+
+
+def add_default_variables_in_release_table(df, defaults):
+    df_new = df.copy()
+    for k, v in defaults.items():
+        if k not in df:
+            df_new[k] = v
+    return df_new
+
+
+def expand_multiplicity_in_release_table(df):
+    if 'mult' not in df:
+        return df
+    df = df.loc[np.repeat(df.index, df['mult'].values.astype('i4'))]
+    df = df.reset_index(drop=True).drop(columns='mult')
+    return df
+
+
+def resolve_schedule(times, interval, start_time, stop_time):
+    """
+    Convert decriptions of repeated events to actual event indices
+
+    The variable `times` specifies start time of scheduled events. Each event occurs
+    repeatedly (specified by `interval`) until there is a new scheduling time.
+    The function returns the index of all events occuring within the time span.
+
+    Example 1: times = [0, 0], interval = 2. These are 2 events (index [0, 1]),
+    occuring at times [0, 2, 4, 6, ...], starting at time = 0. The time interval
+    start_time = 0, stop_time = 6 will contain the event times 0, 2, 4. The
+    returned event indices are [0, 1, 0, 1, 0, 1].
+
+    Example 2: times = [0, 0, 3, 3, 3], interval = 2. The schedule starts with
+    2 events (index [0, 1]) occuring at time = 0. At time = 2, there are no new
+    scheduled events, and the previous events are repeated. At time = 3 there
+    are 3 new events scheduled (index [2, 3, 4]), which cancel the previous
+    events. The new events are repeated at times [3, 5, 7, ...]. The time
+    interval start_time = 0, stop_time = 7 contain the event times [0, 2, 3, 5].
+    The returned event indices are [0, 1, 0, 1, 2, 3, 4, 2, 3, 4].
+
+    :param times: Nondecreasing list of event times
+    :param interval: Maximum interval between scheduled times
+    :param start_time: Start time of schedule
+    :param stop_time: Stop time of schedule (not inclusive)
+    :return: Index of events in resolved schedule
+    """
+
+    sched = Schedule(times=np.asarray(times), events=np.arange(len(times)))
+    sched2 = sched.resolve(start_time, stop_time, interval)
+    return sched2.events
+
+
+class Schedule:
+    def __init__(self, times: np.ndarray, events: np.ndarray):
+        self.times = times.view()
+        self.events = events.view()
+        self.times.flags.writeable = False
+        self.events.flags.writeable = False
+
+    def valid(self):
+        return np.all(np.diff(self.times) >= 0)
+
+    def copy(self):
+        return Schedule(times=self.times.copy(), events=self.events.copy())
+
+    def append(self, other: "Schedule"):
+        return Schedule(
+            times=np.concatenate((self.times, other.times)),
+            events=np.concatenate((self.events, other.events)),
+        )
+
+    def extend_backwards_using_interval(self, time, interval):
+        min_time = self.times[0]
+        if min_time <= time:
+            return self
+
+        num_extensions = int(np.ceil((min_time - time) / interval))
+        new_time = min_time - num_extensions * interval
+        return self.extend_backwards(new_time)
+
+    def extend_backwards(self, new_minimum_time):
+        idx_to_be_copied = (self.times == self.times[0])
+        num_to_be_copied = np.count_nonzero(idx_to_be_copied)
+        extension = Schedule(
+            times=np.repeat(new_minimum_time, num_to_be_copied),
+            events=self.events[idx_to_be_copied],
+        )
+        return extension.append(self)
+
+    def trim_tail(self, stop_time):
+        num = np.sum(self.times < stop_time)
+        return Schedule(
+            times=self.times[:num],
+            events=self.events[:num],
+        )
+
+    def trim_head(self, start_time):
+        num = np.sum(self.times < start_time)
+        return Schedule(
+            times=self.times[num:],
+            events=self.events[num:],
+        )
+
+    def rightshift_closest_time_value(self, time, interval):
+        # If interval=0 is specified, this means there is nothing to right-shift
+        if interval <= 0:
+            return self
+
+        # Find largest value that is smaller than or equal to time
+        idx_target_time = sum(self.times <= time) - 1
+
+        # If no tabulated time values are smaller than the given time, there
+        # is nothing to right-shift
+        if idx_target_time == -1:
+            return self
+
+        # Compute new value to write
+        target_time = self.times[idx_target_time]
+        num_offsets = np.ceil((time - target_time) / interval)
+        new_target_time = target_time + num_offsets * interval
+
+        # Check if the new value is larger than the next value
+        if idx_target_time + 1 < len(self.times):  # If not, then there is no next value
+            next_time = self.times[idx_target_time + 1]
+            if new_target_time > next_time:
+                return self
+
+        # Change times
+        new_times = self.times.copy()
+        new_times[self.times == target_time] = new_target_time
+        return Schedule(times=new_times, events=self.events)
+
+    def expand(self, interval, stop):
+        # If there are no times, there should be no expansion
+        # Also, interval = 0 means no expansion
+        if (len(self.times) == 0) or (interval <= 0):
+            return self
+
+        t_unq, t_inv, t_cnt = np.unique(self.times, return_inverse=True, return_counts=True)
+        stop2 = np.maximum(stop, t_unq[-1])
+        diff = np.diff(np.concatenate((t_unq, [stop2])))
+        unq_repeats = np.ceil(diff / interval).astype(int)
+        repeats = np.repeat(unq_repeats, t_cnt)
+
+        base_times = np.repeat(self.times, repeats)
+        offsets = [i * interval for n in repeats for i in range(n)]
+        times = base_times + offsets
+        events = np.repeat(self.events, repeats)
+
+        idx = np.lexsort((events, times))
+
+        return Schedule(times=times[idx], events=events[idx])
+
+    def resolve(self, start, stop, interval):
+        s = self
+        if interval:
+            s = s.rightshift_closest_time_value(start, interval)
+        s = s.trim_head(start)
+        s = s.trim_tail(stop)
+        s = s.expand(interval, stop)
+        return s
+
+
+@contextlib.contextmanager
+def open_or_relay(file_or_buf, *args, **kwargs):
+    if hasattr(file_or_buf, 'read'):
+        yield file_or_buf
+    else:
+        with open(file_or_buf, *args, **kwargs) as f:
+            yield f