Source code for satpy.multiscene

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2019 Satpy developers
#
# This file is part of satpy.
#
# satpy is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
#
# satpy is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with
# satpy.  If not, see <http://www.gnu.org/licenses/>.
"""MultiScene object to work with multiple timesteps of satellite data."""

import copy
import logging
from queue import Queue
from threading import Thread

import dask.array as da
import numpy as np
import pandas as pd
import xarray as xr

from satpy.dataset import DataID, combine_metadata
from satpy.scene import Scene
from satpy.writers import get_enhanced_image

try:
    import imageio
except ImportError:
    imageio = None

try:
    from dask.distributed import get_client
except ImportError:
    get_client = None

log = logging.getLogger(__name__)


[docs]def stack(datasets): """Overlay series of datasets on top of each other.""" base = datasets[0].copy() for dataset in datasets[1:]: base = base.where(dataset.isnull(), dataset) return base
[docs]def timeseries(datasets): """Expand dataset with and concatenate by time dimension.""" expanded_ds = [] for ds in datasets: if 'time' not in ds.dims: tmp = ds.expand_dims("time") tmp.coords["time"] = pd.DatetimeIndex([ds.attrs["start_time"]]) else: tmp = ds expanded_ds.append(tmp) res = xr.concat(expanded_ds, dim="time") res.attrs = combine_metadata(*[x.attrs for x in expanded_ds]) return res
[docs]def add_group_aliases(scenes, groups): """Add aliases for the groups datasets belong to.""" for scene in scenes: scene = scene.copy() for group_id, member_names in groups.items(): # Find out whether one of the datasets in this scene belongs # to this group member_ids = [scene[name].attrs['_satpy_id'] for name in member_names if name in scene] # Add an alias for the group it belongs to if len(member_ids) == 1: member_id = member_ids[0] new_ds = scene[member_id].copy() new_ds.attrs.update(group_id.to_dict()) scene[group_id] = new_ds elif len(member_ids) > 1: raise ValueError('Cannot add multiple datasets from the same ' 'scene to a group') else: # Datasets in this scene don't belong to any group pass yield scene
class _SceneGenerator(object): """Fancy way of caching Scenes from a generator.""" def __init__(self, scene_gen): self._scene_gen = scene_gen self._scene_cache = [] self._dataset_idx = {} # this class itself is not an iterator, make one self._self_iter = self._create_cached_iter() @property def first(self): """First element in the generator.""" return next(iter(self)) def _create_cached_iter(self): """Iterate over the provided scenes, caching them for later.""" for scn in self._scene_gen: self._scene_cache.append(scn) yield scn def __iter__(self): """Iterate over the provided scenes, caching them for later.""" idx = 0 while True: if idx >= len(self._scene_cache): try: scn = next(self._self_iter) except StopIteration: return else: scn = self._scene_cache[idx] yield scn idx += 1 def __getitem__(self, ds_id): """Get a specific dataset from the scenes.""" for scn in self: yield scn.get(ds_id)
[docs]class MultiScene(object): """Container for multiple `Scene` objects.""" def __init__(self, scenes=None): """Initialize MultiScene and validate sub-scenes. Args: scenes (iterable): `Scene` objects to operate on (optional) .. note:: If the `scenes` passed to this object are a generator then certain operations performed will try to preserve that generator state. This may limit what properties or methods are available to the user. To avoid this behavior compute the passed generator by converting the passed scenes to a list first: ``MultiScene(list(scenes))``. """ self._scenes = scenes or [] scenes = iter(self._scenes) self._scene_gen = _SceneGenerator(iter(scenes)) # if we were originally given a generator-like object then we want to # coordinate the loading between _SceneGenerator and _scenes # otherwise it doesn't really matter and other operations may prefer # a list if not isinstance(scenes, (list, tuple)): self._scenes = iter(self._scene_gen) @property def first_scene(self): """First Scene of this MultiScene object.""" return self._scene_gen.first
[docs] @classmethod def from_files(cls, files_to_sort, reader=None, ensure_all_readers=False, scene_kwargs=None, **kwargs): """Create multiple Scene objects from multiple files. Args: files_to_sort (Collection[str]): files to read reader (str or Collection[str]): reader or readers to use ensure_all_readers (bool): If True, limit to scenes where all readers have at least one file. If False (default), include all scenes where at least one reader has at least one file. scene_kwargs (Mapping): additional arguments to pass on to :func:`Scene.__init__` for each created scene. This uses the :func:`satpy.readers.group_files` function to group files. See this function for more details on additional possible keyword arguments. In particular, it is strongly recommended to pass `"group_keys"` when using multiple instruments. .. versionadded:: 0.12 """ from satpy.readers import group_files if scene_kwargs is None: scene_kwargs = {} file_groups = group_files(files_to_sort, reader=reader, **kwargs) if ensure_all_readers: file_groups = [fg for fg in file_groups if all(fg.values())] scenes = (Scene(filenames=fg, **scene_kwargs) for fg in file_groups) return cls(scenes)
def __iter__(self): """Iterate over the provided Scenes once.""" for scn in self._scenes: yield scn @property def scenes(self): """Get list of Scene objects contained in this MultiScene. .. note:: If the Scenes contained in this object are stored in a generator (not list or tuple) then accessing this property will load/iterate through the generator possibly """ if self.is_generator: log.debug("Forcing iteration of generator-like object of Scenes") self._scenes = list(self._scenes) return self._scenes @property def is_generator(self): """Contained Scenes are stored as a generator.""" return not isinstance(self._scenes, (list, tuple)) @property def loaded_dataset_ids(self): """Union of all Dataset IDs loaded by all children.""" return set(ds_id for scene in self.scenes for ds_id in scene.keys()) @property def shared_dataset_ids(self): """Dataset IDs shared by all children.""" shared_ids = set(self.scenes[0].keys()) for scene in self.scenes[1:]: shared_ids &= set(scene.keys()) return shared_ids def _all_same_area(self, dataset_ids): """Return True if all areas for the provided IDs are equal.""" all_areas = [] for ds_id in dataset_ids: for scn in self.scenes: ds = scn.get(ds_id) if ds is None: continue all_areas.append(ds.attrs.get('area')) all_areas = [area for area in all_areas if area is not None] return all(all_areas[0] == area for area in all_areas[1:]) @property def all_same_area(self): """Determine if all contained Scenes have the same 'area'.""" return self._all_same_area(self.loaded_dataset_ids) @staticmethod def _call_scene_func(gen, func_name, create_new_scene, *args, **kwargs): """Abstract method for running a Scene method on each Scene.""" for scn in gen: new_scn = getattr(scn, func_name)(*args, **kwargs) if create_new_scene: yield new_scn else: yield scn def _generate_scene_func(self, gen, func_name, create_new_scene, *args, **kwargs): """Abstract method for running a Scene method on each Scene. Additionally, modifies current MultiScene or creates a new one if needed. """ new_gen = self._call_scene_func(gen, func_name, create_new_scene, *args, **kwargs) new_gen = new_gen if self.is_generator else list(new_gen) if create_new_scene: return self.__class__(new_gen) self._scene_gen = _SceneGenerator(new_gen) self._scenes = iter(self._scene_gen)
[docs] def load(self, *args, **kwargs): """Load the required datasets from the multiple scenes.""" self._generate_scene_func(self._scenes, 'load', False, *args, **kwargs)
[docs] def crop(self, *args, **kwargs): """Crop the multiscene and return a new cropped multiscene.""" return self._generate_scene_func(self._scenes, 'crop', True, *args, **kwargs)
[docs] def resample(self, destination=None, **kwargs): """Resample the multiscene.""" return self._generate_scene_func(self._scenes, 'resample', True, destination=destination, **kwargs)
[docs] def blend(self, blend_function=stack): """Blend the datasets into one scene. .. note:: Blending is not currently optimized for generator-based MultiScene. """ new_scn = Scene() common_datasets = self.shared_dataset_ids for ds_id in common_datasets: datasets = [scn[ds_id] for scn in self.scenes if ds_id in scn] new_scn[ds_id] = blend_function(datasets) return new_scn
[docs] def group(self, groups): """Group datasets from the multiple scenes. By default, `MultiScene` only operates on dataset IDs shared by all scenes. Using this method you can specify groups of datasets that shall be treated equally by `MultiScene`. Even if their dataset IDs differ (for example because the names or wavelengths are slightly different). Groups can be specified as a dictionary `{group_id: dataset_names}` where the keys must be of type `DataQuery`, for example:: groups={ DataQuery('my_group', wavelength=(10, 11, 12)): ['IR_108', 'B13', 'C13'] } """ self._scenes = add_group_aliases(self._scenes, groups)
def _distribute_save_datasets(self, scenes_iter, client, batch_size=1, **kwargs): """Distribute save_datasets across a cluster.""" def load_data(q): idx = 0 while True: future_list = q.get() if future_list is None: break # save_datasets shouldn't be returning anything for future in future_list: future.result() log.info("Finished saving %d scenes", idx) idx += 1 q.task_done() input_q = Queue(batch_size if batch_size is not None else 1) load_thread = Thread(target=load_data, args=(input_q,)) load_thread.start() for scene in scenes_iter: delayed = scene.save_datasets(compute=False, **kwargs) if isinstance(delayed, (list, tuple)) and len(delayed) == 2: # TODO Make this work for (source, target) datasets # given a target, source combination raise NotImplementedError("Distributed save_datasets does not support writers " "that return (source, target) combinations at this time. Use " "the non-distributed save_datasets instead.") future = client.compute(delayed) input_q.put(future) input_q.put(None) log.debug("Waiting for child thread to get saved results...") load_thread.join() log.debug("Child thread died successfully") def _simple_save_datasets(self, scenes_iter, **kwargs): """Run save_datasets on each Scene.""" for scn in scenes_iter: scn.save_datasets(**kwargs)
[docs] def save_datasets(self, client=True, batch_size=1, **kwargs): """Run save_datasets on each Scene. Note that some writers may not be multi-process friendly and may produce unexpected results or fail by raising an exception. In these cases ``client`` should be set to ``False``. This is currently a known issue for basic 'geotiff' writer work loads. Args: batch_size (int): Number of scenes to compute at the same time. This only has effect if the `dask.distributed` package is installed. This will default to 1. Setting this to 0 or less will attempt to process all scenes at once. This option should be used with care to avoid memory issues when trying to improve performance. client (bool or dask.distributed.Client): Dask distributed client to use for computation. If this is ``True`` (default) then any existing clients will be used. If this is ``False`` or ``None`` then a client will not be created and ``dask.distributed`` will not be used. If this is a dask ``Client`` object then it will be used for distributed computation. kwargs: Additional keyword arguments to pass to :meth:`~satpy.scene.Scene.save_datasets`. Note ``compute`` can not be provided. """ if 'compute' in kwargs: raise ValueError("The 'compute' keyword argument can not be provided.") client = self._get_client(client=client) scenes = iter(self._scenes) if client is not None: self._distribute_save_datasets(scenes, client, batch_size=batch_size, **kwargs) else: self._simple_save_datasets(scenes, **kwargs)
def _get_animation_info(self, all_datasets, filename, fill_value=None): """Determine filename and shape of animation to be created.""" valid_datasets = [ds for ds in all_datasets if ds is not None] first_dataset = valid_datasets[0] last_dataset = valid_datasets[-1] first_img = get_enhanced_image(first_dataset) first_img_data = first_img.finalize(fill_value=fill_value)[0] shape = tuple(first_img_data.sizes.get(dim_name) for dim_name in ('y', 'x', 'bands')) if fill_value is None and filename.endswith('gif'): log.warning("Forcing fill value to '0' for GIF Luminance images") fill_value = 0 shape = shape[:2] attrs = first_dataset.attrs.copy() if 'end_time' in last_dataset.attrs: attrs['end_time'] = last_dataset.attrs['end_time'] this_fn = filename.format(**attrs) return this_fn, shape, fill_value @staticmethod def _format_decoration(ds, decorate): """Maybe format decoration. If the nested dictionary in decorate (argument to ``save_animation``) contains a text to be added, format those based on dataset parameters. """ if decorate is None or "decorate" not in decorate: return decorate deco_local = copy.deepcopy(decorate) for deco in deco_local["decorate"]: if "text" in deco and "txt" in deco["text"]: deco["text"]["txt"] = deco["text"]["txt"].format(**ds.attrs) return deco_local def _get_single_frame(self, ds, enh_args, fill_value): """Get single frame from dataset. Yet a single image frame from a dataset. """ enh_args = enh_args.copy() # don't change caller's dict! if "decorate" in enh_args: enh_args["decorate"] = self._format_decoration( ds, enh_args["decorate"]) img = get_enhanced_image(ds, **enh_args) data, mode = img.finalize(fill_value=fill_value) if data.ndim == 3: # assume all other shapes are (y, x) # we need arrays grouped by pixel so # transpose if needed data = data.transpose('y', 'x', 'bands') return data def _get_animation_frames(self, all_datasets, shape, fill_value=None, ignore_missing=False, enh_args=None): """Create enhanced image frames to save to a file.""" if enh_args is None: enh_args = {} for idx, ds in enumerate(all_datasets): if ds is None and ignore_missing: continue elif ds is None: log.debug("Missing frame: %d", idx) data = da.zeros(shape, dtype=np.uint8, chunks=shape) data = xr.DataArray(data) else: data = self._get_single_frame(ds, enh_args, fill_value) yield data.data def _get_client(self, client=True): """Determine what dask distributed client to use.""" client = client or None # convert False/None to None if client is True and get_client is None: log.debug("'dask.distributed' library was not found, will " "use simple serial processing.") client = None elif client is True: try: # get existing client client = get_client() except ValueError: log.warning("No dask distributed client was provided or found, " "but distributed features were requested. Will use simple serial processing.") client = None return client def _distribute_frame_compute(self, writers, frame_keys, frames_to_write, client, batch_size=1): """Use ``dask.distributed`` to compute multiple frames at a time.""" def load_data(frame_gen, q): for frame_arrays in frame_gen: future_list = client.compute(frame_arrays) for frame_key, arr_future in zip(frame_keys, future_list): q.put({frame_key: arr_future}) q.put(None) input_q = Queue(batch_size if batch_size is not None else 1) load_thread = Thread(target=load_data, args=(frames_to_write, input_q,)) load_thread.start() while True: input_future = input_q.get() future_dict = client.gather(input_future) if future_dict is None: break # write the current frame # this should only be one element in the dictionary, but this is # also the easiest way to get access to the data for frame_key, result in future_dict.items(): # frame_key = rev_future_dict[future] w = writers[frame_key] w.append_data(result) input_q.task_done() log.debug("Waiting for child thread...") load_thread.join(10) if load_thread.is_alive(): import warnings warnings.warn("Background thread still alive after failing to die gracefully") else: log.debug("Child thread died successfully") @staticmethod def _simple_frame_compute(writers, frame_keys, frames_to_write): """Compute frames the plain dask way.""" for frame_arrays in frames_to_write: for frame_key, product_frame in zip(frame_keys, frame_arrays): w = writers[frame_key] w.append_data(product_frame.compute()) def _get_writers_and_frames( self, filename, datasets, fill_value, ignore_missing, enh_args, imio_args): """Get writers and frames. Helper function for save_animation. """ scene_gen = self._scene_gen first_scene = self.first_scene scenes = iter(self._scene_gen) info_scenes = [first_scene] if 'end_time' in filename: # if we need the last scene to generate the filename # then compute all the scenes so we can figure it out log.debug("Generating scenes to compute end_time for filename") scenes = list(scenes) info_scenes.append(scenes[-1]) available_ds = [first_scene.get(ds) for ds in first_scene.wishlist] available_ds = [DataID.from_dataarray(ds) for ds in available_ds if ds is not None] dataset_ids = datasets or available_ds if not dataset_ids: raise RuntimeError("No datasets found for saving (resampling may be needed to generate composites)") writers = {} frames = {} for dataset_id in dataset_ids: if not self.is_generator and not self._all_same_area([dataset_id]): raise ValueError("Sub-scene datasets must all be on the same " "area (see the 'resample' method).") all_datasets = scene_gen[dataset_id] info_datasets = [scn.get(dataset_id) for scn in info_scenes] this_fn, shape, this_fill = self._get_animation_info(info_datasets, filename, fill_value=fill_value) data_to_write = self._get_animation_frames( all_datasets, shape, this_fill, ignore_missing, enh_args) writer = imageio.get_writer(this_fn, **imio_args) frames[dataset_id] = data_to_write writers[dataset_id] = writer return (writers, frames)
[docs] def save_animation(self, filename, datasets=None, fps=10, fill_value=None, batch_size=1, ignore_missing=False, client=True, enh_args=None, **kwargs): """Save series of Scenes to movie (MP4) or GIF formats. Supported formats are dependent on the `imageio` library and are determined by filename extension by default. .. note:: Starting with ``imageio`` 2.5.0, the use of FFMPEG depends on a separate ``imageio-ffmpeg`` package. By default all datasets available will be saved to individual files using the first Scene's datasets metadata to format the filename provided. If a dataset is not available from a Scene then a black array is used instead (np.zeros(shape)). This function can use the ``dask.distributed`` library for improved performance by computing multiple frames at a time (see `batch_size` option below). If the distributed library is not available then frames will be generated one at a time, one product at a time. Args: filename (str): Filename to save to. Can include python string formatting keys from dataset ``.attrs`` (ex. "{name}_{start_time:%Y%m%d_%H%M%S.gif") datasets (list): DataIDs to save (default: all datasets) fps (int): Frames per second for produced animation fill_value (int): Value to use instead creating an alpha band. batch_size (int): Number of frames to compute at the same time. This only has effect if the `dask.distributed` package is installed. This will default to 1. Setting this to 0 or less will attempt to process all frames at once. This option should be used with care to avoid memory issues when trying to improve performance. Note that this is the total number of frames for all datasets, so when saving 2 datasets this will compute ``(batch_size / 2)`` frames for the first dataset and ``(batch_size / 2)`` frames for the second dataset. ignore_missing (bool): Don't include a black frame when a dataset is missing from a child scene. client (bool or dask.distributed.Client): Dask distributed client to use for computation. If this is ``True`` (default) then any existing clients will be used. If this is ``False`` or ``None`` then a client will not be created and ``dask.distributed`` will not be used. If this is a dask ``Client`` object then it will be used for distributed computation. enh_args (Mapping): Optional, arguments passed to :func:`satpy.writers.get_enhanced_image`. If this includes a keyword "decorate", in any text added to the image, string formatting will be applied based on dataset attributes. For example, passing ``enh_args={"decorate": {"decorate": [{"text": {"txt": "{start_time:%H:%M}"}}]}`` will replace the decorated text accordingly. kwargs: Additional keyword arguments to pass to `imageio.get_writer`. """ if imageio is None: raise ImportError("Missing required 'imageio' library") (writers, frames) = self._get_writers_and_frames( filename, datasets, fill_value, ignore_missing, enh_args, imio_args={"fps": fps, **kwargs}) client = self._get_client(client=client) # get an ordered list of frames frame_keys, frames_to_write = list(zip(*frames.items())) frames_to_write = zip(*frames_to_write) if client is not None: self._distribute_frame_compute(writers, frame_keys, frames_to_write, client, batch_size=batch_size) else: self._simple_frame_compute(writers, frame_keys, frames_to_write) for writer in writers.values(): writer.close()