sdf-xarray 0.3.2__cp311-cp311-win_amd64.whl → 0.4.0__cp311-cp311-win_amd64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
lib/SDFC_14.4.7/sdfc.lib CHANGED
Binary file
sdf_xarray/__init__.py CHANGED
@@ -22,6 +22,7 @@ from xarray.core.variable import Variable
22
22
  # NOTE: Do not delete these lines, otherwise the "epoch" dataset and dataarray
23
23
  # accessors will not be imported when the user imports sdf_xarray
24
24
  import sdf_xarray.dataset_accessor
25
+ import sdf_xarray.download
25
26
  import sdf_xarray.plotting # noqa: F401
26
27
 
27
28
  # NOTE: This attempts to initialise with the "pint" accessor if the user
sdf_xarray/_version.py CHANGED
@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
28
28
  commit_id: COMMIT_ID
29
29
  __commit_id__: COMMIT_ID
30
30
 
31
- __version__ = version = '0.3.2'
32
- __version_tuple__ = version_tuple = (0, 3, 2)
31
+ __version__ = version = '0.4.0'
32
+ __version_tuple__ = version_tuple = (0, 4, 0)
33
33
 
34
- __commit_id__ = commit_id = 'g331520e50'
34
+ __commit_id__ = commit_id = 'gc5cdb3bf9'
@@ -1,5 +1,3 @@
1
- from typing import Union
2
-
3
1
  import xarray as xr
4
2
 
5
3
 
@@ -13,7 +11,7 @@ class EpochAccessor:
13
11
  self,
14
12
  multiplier: float,
15
13
  unit_label: str,
16
- coord_names: Union[str, list[str]],
14
+ coord_names: str | list[str],
17
15
  ) -> xr.Dataset:
18
16
  """
19
17
  Rescales specified X and Y coordinates in the Dataset by a given multiplier
sdf_xarray/download.py ADDED
@@ -0,0 +1,87 @@
1
+ from pathlib import Path
2
+ from shutil import move
3
+ from typing import TYPE_CHECKING, Literal, TypeAlias
4
+
5
+ if TYPE_CHECKING:
6
+ import pooch # noqa: F401
7
+
8
+ DatasetName: TypeAlias = Literal[
9
+ "test_array_no_grids",
10
+ "test_dist_fn",
11
+ "test_files_1D",
12
+ "test_files_2D_moving_window",
13
+ "test_files_3D",
14
+ "test_mismatched_files",
15
+ "test_two_probes_2D",
16
+ "tutorial_dataset_1d",
17
+ "tutorial_dataset_2d",
18
+ "tutorial_dataset_2d_moving_window",
19
+ "tutorial_dataset_3d",
20
+ ]
21
+
22
+
23
+ def fetch_dataset(
24
+ dataset_name: DatasetName, save_path: Path | str | None = None
25
+ ) -> Path:
26
+ """
27
+ Downloads the specified dataset from its Zenodo URL. If it is already
28
+ downloaded, then the path to the cached, unzipped directory is returned.
29
+
30
+ Parameters
31
+ ---------
32
+ dataset_name
33
+ The name of the dataset to download
34
+ save_path
35
+ The directory to save the dataset to (defaults to the cache folder ``"sdf_datasets"``.
36
+ See `pooch.os_cache` for details on how the cache works)
37
+
38
+ Returns
39
+ -------
40
+ Path
41
+ The path to the directory containing the unzipped dataset files
42
+
43
+ Examples
44
+ --------
45
+ >>> # Assuming the dataset has not been downloaded yet
46
+ >>> path = fetch_dataset("tutorial_dataset_1d")
47
+ Downloading file 'tutorial_dataset_1d.zip' ...
48
+ Unzipping contents of '.../sdf_datasets/tutorial_dataset_1d.zip' to '.../sdf_datasets/tutorial_dataset_1d'
49
+ >>> path
50
+ '.../sdf_datasets/tutorial_dataset_1d'
51
+ """
52
+ import pooch # noqa: PLC0415
53
+
54
+ logger = pooch.get_logger()
55
+ datasets = pooch.create(
56
+ path=pooch.os_cache("sdf_datasets"),
57
+ base_url="doi:10.5281/zenodo.17618510",
58
+ registry={
59
+ "test_array_no_grids.zip": "md5:583c85ed8c31d0e34e7766b6d9f2d6da",
60
+ "test_dist_fn.zip": "md5:a582ff5e8c59bad62fe4897f65fc7a11",
61
+ "test_files_1D.zip": "md5:42e53b229556c174c538c5481c4d596a",
62
+ "test_files_2D_moving_window.zip": "md5:3744483bbf416936ad6df8847c54dad1",
63
+ "test_files_3D.zip": "md5:a679e71281bab1d373dc4980e6da1a7c",
64
+ "test_mismatched_files.zip": "md5:710fdc94666edf7777523e8fc9dd1bd4",
65
+ "test_two_probes_2D.zip": "md5:0f2a4fefe84a15292d066b3320d4d533",
66
+ "tutorial_dataset_1d.zip": "md5:7fad744d8b8b2b84bba5c0e705fdef7b",
67
+ "tutorial_dataset_2d.zip": "md5:1945ecdbc1ac1798164f83ea2b3d1b31",
68
+ "tutorial_dataset_2d_moving_window.zip": "md5:a795f40d18df69263842055de4559501",
69
+ "tutorial_dataset_3d.zip": "md5:d9254648867016292440fdb028f717f7",
70
+ },
71
+ )
72
+
73
+ datasets.fetch(
74
+ f"{dataset_name}.zip", processor=pooch.Unzip(extract_dir="."), progressbar=True
75
+ )
76
+ cache_path = Path(datasets.path) / dataset_name
77
+
78
+ if save_path is not None:
79
+ save_path = Path(save_path)
80
+ logger.info(
81
+ "Moving contents of '%s' to '%s'",
82
+ cache_path,
83
+ save_path / dataset_name,
84
+ )
85
+ return move(cache_path, save_path / dataset_name)
86
+
87
+ return cache_path
sdf_xarray/plotting.py CHANGED
@@ -9,37 +9,69 @@ if TYPE_CHECKING:
9
9
  import matplotlib.pyplot as plt
10
10
  from matplotlib.animation import FuncAnimation
11
11
 
12
+ from types import MethodType
13
+
12
14
 
13
15
  def get_frame_title(
14
16
  data: xr.DataArray,
15
17
  frame: int,
16
18
  display_sdf_name: bool = False,
17
19
  title_custom: str | None = None,
20
+ t: str = "time",
18
21
  ) -> str:
19
- """Generate the title for a frame"""
22
+ """Generate the title for a frame
23
+
24
+ Parameters
25
+ ----------
26
+ data
27
+ DataArray containing the target data
28
+ frame
29
+ Frame number
30
+ display_sdf_name
31
+ Display the sdf file name in the animation title
32
+ title_custom
33
+ Custom title to add to the plot
34
+ t
35
+ Time coordinate
36
+ """
37
+
20
38
  # Adds custom text to the start of the title, if specified
21
39
  title_custom = "" if title_custom is None else f"{title_custom}, "
22
- # Adds the time and associated units to the title
23
- time = data["time"][frame].to_numpy()
40
+ # Adds the time axis and associated units to the title
41
+ t_axis_value = data[t][frame].values
24
42
 
25
- time_units = data["time"].attrs.get("units", False)
26
- time_units_formatted = f" [{time_units}]" if time_units else ""
27
- title_time = f"time = {time:.2e}{time_units_formatted}"
43
+ t_axis_units = data[t].attrs.get("units", False)
44
+ t_axis_units_formatted = f" [{t_axis_units}]" if t_axis_units else ""
45
+ title_t_axis = f"{data[t].long_name} = {t_axis_value:.2e}{t_axis_units_formatted}"
28
46
 
29
47
  # Adds sdf name to the title, if specifed
30
48
  title_sdf = f", {frame:04d}.sdf" if display_sdf_name else ""
31
- return f"{title_custom}{title_time}{title_sdf}"
49
+ return f"{title_custom}{title_t_axis}{title_sdf}"
32
50
 
33
51
 
34
52
  def calculate_window_boundaries(
35
- data: xr.DataArray, xlim: tuple[float, float] | False = False
53
+ data: xr.DataArray,
54
+ xlim: tuple[float, float] | None = None,
55
+ x_axis_name: str = "X_Grid_mid",
56
+ t: str = "time",
36
57
  ) -> np.ndarray:
37
58
  """Calculate the bounderies a moving window frame. If the user specifies xlim, this will
38
59
  be used as the initial bounderies and the window will move along acordingly.
60
+
61
+ Parameters
62
+ ----------
63
+ data
64
+ DataArray containing the target data
65
+ xlim
66
+ x limits
67
+ x_axis_name
68
+ Name of coordinate to assign to the x-axis
69
+ t
70
+ Time coordinate
39
71
  """
40
- x_grid = data["X_Grid_mid"].values
72
+ x_grid = data[x_axis_name].values
41
73
  x_half_cell = (x_grid[1] - x_grid[0]) / 2
42
- N_frames = data["time"].size
74
+ N_frames = data[t].size
43
75
 
44
76
  # Find the window bounderies by finding the first and last non-NaN values in the 0th lineout
45
77
  # along the x-axis.
@@ -56,7 +88,7 @@ def calculate_window_boundaries(
56
88
  window_boundaries[i, 1] = x_grid_non_nan[-1] + x_half_cell
57
89
 
58
90
  # User's choice for initial window edge supercides the one calculated
59
- if xlim:
91
+ if xlim is not None:
60
92
  window_boundaries = window_boundaries + xlim - window_boundaries[0]
61
93
  return window_boundaries
62
94
 
@@ -68,6 +100,15 @@ def compute_global_limits(
68
100
  ) -> tuple[float, float]:
69
101
  """Remove all NaN values from the target data to calculate the global minimum and maximum of the data.
70
102
  User defined percentiles can remove extreme outliers.
103
+
104
+ Parameters
105
+ ----------
106
+ data
107
+ DataArray containing the target data
108
+ min_percentile
109
+ Minimum percentile of the data
110
+ max_percentile
111
+ Maximum percentile of the data
71
112
  """
72
113
 
73
114
  # Removes NaN values, needed for moving windows
@@ -86,74 +127,103 @@ def animate(
86
127
  max_percentile: float = 100,
87
128
  title: str | None = None,
88
129
  display_sdf_name: bool = False,
130
+ t: str | None = None,
89
131
  ax: plt.Axes | None = None,
90
132
  **kwargs,
91
133
  ) -> FuncAnimation:
92
- """Generate an animation
134
+ """Generate an animation using an xarray.DataArray
93
135
 
94
136
  Parameters
95
137
  ---------
96
138
  data
97
- The dataarray containing the target data
139
+ DataArray containing the target data
98
140
  fps
99
- Frames per second for the animation (default: 10)
141
+ Frames per second for the animation
100
142
  min_percentile
101
- Minimum percentile of the data (default: 0)
143
+ Minimum percentile of the data
102
144
  max_percentile
103
- Maximum percentile of the data (default: 100)
145
+ Maximum percentile of the data
104
146
  title
105
- Custom title to add to the plot.
147
+ Custom title to add to the plot
106
148
  display_sdf_name
107
149
  Display the sdf file name in the animation title
150
+ t
151
+ Coordinate for t axis (the coordinate which will be animated over). If `None`, use data.dims[0]
108
152
  ax
109
- Matplotlib axes on which to plot.
153
+ Matplotlib axes on which to plot
110
154
  kwargs
111
- Keyword arguments to be passed to matplotlib.
155
+ Keyword arguments to be passed to matplotlib
112
156
 
113
157
  Examples
114
158
  --------
115
- >>> dataset["Derived_Number_Density_Electron"].epoch.animate()
159
+ >>> ds["Derived_Number_Density_Electron"].epoch.animate()
116
160
  """
117
161
  import matplotlib.pyplot as plt # noqa: PLC0415
118
162
  from matplotlib.animation import FuncAnimation # noqa: PLC0415
119
163
 
120
164
  kwargs_original = kwargs.copy()
121
165
 
166
+ # Create plot if no ax is provided
122
167
  if ax is None:
123
- _, ax = plt.subplots()
124
-
125
- N_frames = data["time"].size
126
- global_min, global_max = compute_global_limits(data, min_percentile, max_percentile)
168
+ fig, ax = plt.subplots()
169
+ # Prevents figure from prematurely displaying in Jupyter notebook
170
+ plt.close(fig)
171
+
172
+ # Sets the animation coordinate (t) for iteration. If time is in the coords
173
+ # then it will set time to be t. If it is not it will fallback to the last
174
+ # coordinate passed in. By default coordinates are passed in from xarray in
175
+ # the form x, y, z so in order to preserve the x and y being on their
176
+ # respective axes we animate over the final coordinate that is passed in
177
+ # which in this example is z
178
+ coord_names = list(data.dims)
179
+ if t is None:
180
+ t = "time" if "time" in coord_names else coord_names[-1]
181
+ coord_names.remove(t)
182
+
183
+ N_frames = data[t].size
127
184
 
128
- # Initialise plot and set y-limits for 1D data
129
185
  if data.ndim == 2:
130
- kwargs.setdefault("x", "X_Grid_mid")
131
- plot = data.isel(time=0).plot(ax=ax, **kwargs)
132
- ax.set_title(get_frame_title(data, 0, display_sdf_name, title))
186
+ kwargs.setdefault("x", coord_names[0])
187
+ plot = data.isel({t: 0}).plot(ax=ax, **kwargs)
188
+ ax.set_title(get_frame_title(data, 0, display_sdf_name, title, t))
189
+ global_min, global_max = compute_global_limits(
190
+ data, min_percentile, max_percentile
191
+ )
133
192
  ax.set_ylim(global_min, global_max)
134
193
 
135
- # Initilise plot and set colour bar for 2D data
136
194
  if data.ndim == 3:
137
- kwargs["norm"] = plt.Normalize(vmin=global_min, vmax=global_max)
195
+ if "norm" not in kwargs:
196
+ global_min, global_max = compute_global_limits(
197
+ data, min_percentile, max_percentile
198
+ )
199
+ kwargs["norm"] = plt.Normalize(vmin=global_min, vmax=global_max)
138
200
  kwargs["add_colorbar"] = False
139
- # Set default x and y coordinates for 2D data if not provided
140
- kwargs.setdefault("x", "X_Grid_mid")
141
- kwargs.setdefault("y", "Y_Grid_mid")
201
+ # Set default x and y coordinates for 3D data if not provided
202
+ kwargs.setdefault("x", coord_names[0])
203
+ kwargs.setdefault("y", coord_names[1])
142
204
 
143
- # Initialize the plot with the first timestep
144
- plot = data.isel(time=0).plot(ax=ax, **kwargs)
145
- ax.set_title(get_frame_title(data, 0, display_sdf_name, title))
205
+ # Finds the time step with the minimum data value
206
+ # This is needed so that the animation can use the correct colour bar
207
+ argmin_time = np.unravel_index(data.argmin(), data.shape)[0]
208
+
209
+ # Initialize the plot, the final output will still start at the first time step
210
+ plot = data.isel({t: argmin_time}).plot(ax=ax, **kwargs)
211
+ ax.set_title(get_frame_title(data, 0, display_sdf_name, title, t))
212
+ kwargs["cmap"] = plot.cmap
146
213
 
147
214
  # Add colorbar
148
215
  if kwargs_original.get("add_colorbar", True):
149
216
  long_name = data.attrs.get("long_name")
150
217
  units = data.attrs.get("units")
151
- plt.colorbar(plot, ax=ax, label=f"{long_name} [${units}$]")
218
+ fig = plot.get_figure()
219
+ fig.colorbar(plot, ax=ax, label=f"{long_name} [{units}]")
152
220
 
153
221
  # check if there is a moving window by finding NaNs in the data
154
222
  move_window = np.isnan(np.sum(data.values))
155
223
  if move_window:
156
- window_boundaries = calculate_window_boundaries(data, kwargs.get("xlim", False))
224
+ window_boundaries = calculate_window_boundaries(
225
+ data, kwargs.get("xlim"), kwargs["x"]
226
+ )
157
227
 
158
228
  def update(frame):
159
229
  # Set the xlim for each frame in the case of a moving window
@@ -163,12 +233,12 @@ def animate(
163
233
  # Update plot for the new frame
164
234
  ax.clear()
165
235
 
166
- data.isel(time=frame).plot(ax=ax, **kwargs)
167
- ax.set_title(get_frame_title(data, frame, display_sdf_name, title))
236
+ plot = data.isel({t: frame}).plot(ax=ax, **kwargs)
237
+ ax.set_title(get_frame_title(data, frame, display_sdf_name, title, t))
168
238
 
169
- # Update y-limits for 1D data
170
239
  if data.ndim == 2:
171
240
  ax.set_ylim(global_min, global_max)
241
+ return plot
172
242
 
173
243
  return FuncAnimation(
174
244
  ax.get_figure(),
@@ -179,6 +249,19 @@ def animate(
179
249
  )
180
250
 
181
251
 
252
+ def show(anim):
253
+ """Shows the FuncAnimation in a Jupyter notebook.
254
+
255
+ Parameters
256
+ ----------
257
+ anim
258
+ `matplotlib.animation.FuncAnimation`
259
+ """
260
+ from IPython.display import HTML # noqa: PLC0415
261
+
262
+ return HTML(anim.to_jshtml())
263
+
264
+
182
265
  @xr.register_dataarray_accessor("epoch")
183
266
  class EpochAccessor:
184
267
  def __init__(self, xarray_obj):
@@ -190,16 +273,21 @@ class EpochAccessor:
190
273
  Parameters
191
274
  ----------
192
275
  args
193
- Positional arguments passed to :func:`generate_animation`.
276
+ Positional arguments passed to :func:`animation`.
194
277
  kwargs
195
- Keyword arguments passed to :func:`generate_animation`.
278
+ Keyword arguments passed to :func:`animation`.
196
279
 
197
280
  Examples
198
281
  --------
199
- >>> import xarray as xr
200
- >>> from sdf_xarray import SDFPreprocess
201
- >>> ds = xr.open_mfdataset("*.sdf", preprocess=SDFPreprocess())
202
- >>> ani = ds["Electric_Field_Ey"].epoch.animate()
203
- >>> ani.save("myfile.mp4")
282
+ >>> anim = ds["Electric_Field_Ey"].epoch.animate()
283
+ >>> anim.save("myfile.mp4")
284
+ >>> # Or in a jupyter notebook:
285
+ >>> anim.show()
204
286
  """
205
- return animate(self._obj, *args, **kwargs)
287
+
288
+ # Add anim.show() functionality
289
+ # anim.show() will display the animation in a jupyter notebook
290
+ anim = animate(self._obj, *args, **kwargs)
291
+ anim.show = MethodType(show, anim)
292
+
293
+ return anim
@@ -110,12 +110,12 @@ _CONSTANT_UNITS_RE = re.compile(r"(?P<name>.*) \((?P<units>.*)\)$")
110
110
  cdef class Constant:
111
111
  _id: str
112
112
  name: str
113
- data: int | str | float
113
+ data: int | str | float | bool
114
114
  units: str | None
115
115
 
116
116
  @staticmethod
117
117
  cdef Constant from_block(str name, csdf.sdf_block_t* block):
118
- data: int | str | float | double
118
+ data: int | str | float | double | bool
119
119
 
120
120
  if block.datatype == csdf.SDF_DATATYPE_REAL4:
121
121
  data = (<float*>block.const_value)[0]
@@ -125,6 +125,8 @@ cdef class Constant:
125
125
  data = (<csdf.int32_t*>block.const_value)[0]
126
126
  if block.datatype == csdf.SDF_DATATYPE_INTEGER8:
127
127
  data = (<csdf.int64_t*>block.const_value)[0]
128
+ if block.datatype == csdf.SDF_DATATYPE_LOGICAL:
129
+ data = (<bint*>block.const_value)[0]
128
130
 
129
131
  # There's no metadata with e.g. units, but there's a
130
132
  # convention to put one in brackets at the end of the name,
@@ -1,8 +1,8 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: sdf-xarray
3
- Version: 0.3.2
3
+ Version: 0.4.0
4
4
  Summary: Provides a backend for xarray to read SDF files as created by the EPOCH plasma PIC code.
5
- Author-Email: Peter Hill <peter.hill@york.ac.uk>, Joel Adams <joel.adams@york.ac.uk>, Shaun Doherty <shaun.doherty@york.ac.uk>, Chris Herdman <chris.herdman@york.ac.uk>
5
+ Author-Email: Peter Hill <peter.hill@york.ac.uk>, Joel Adams <joel.adams@york.ac.uk>, Shaun Doherty <shaun.doherty@york.ac.uk>, Chris Herdman <chris.herdman@york.ac.uk>, Liam Pattinson <liam.pattinson@york.ac.uk>
6
6
  License-Expression: BSD-3-Clause
7
7
  Classifier: Development Status :: 5 - Production/Stable
8
8
  Classifier: Intended Audience :: Science/Research
@@ -14,30 +14,11 @@ Classifier: Programming Language :: Python :: 3.10
14
14
  Classifier: Programming Language :: Python :: 3.11
15
15
  Classifier: Programming Language :: Python :: 3.12
16
16
  Classifier: Programming Language :: Python :: 3.13
17
- Requires-Python: <3.14,>=3.10
17
+ Classifier: Programming Language :: Python :: 3.14
18
+ Requires-Python: <3.15,>=3.10
18
19
  Requires-Dist: numpy>=2.0.0
19
20
  Requires-Dist: xarray>=2024.1.0
20
21
  Requires-Dist: dask>=2024.7.1
21
- Provides-Extra: docs
22
- Requires-Dist: sphinx>=5.3; extra == "docs"
23
- Requires-Dist: sphinx_autodoc_typehints>=1.19; extra == "docs"
24
- Requires-Dist: sphinx-book-theme>=0.4.0rc1; extra == "docs"
25
- Requires-Dist: sphinx-argparse-cli>=1.10.0; extra == "docs"
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- Requires-Dist: sphinx-inline-tabs; extra == "docs"
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- Requires-Dist: pickleshare; extra == "docs"
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- Requires-Dist: ipython; extra == "docs"
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- Requires-Dist: matplotlib; extra == "docs"
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- Requires-Dist: pint; extra == "docs"
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- Requires-Dist: pint-xarray; extra == "docs"
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- Requires-Dist: myst-parser; extra == "docs"
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- Provides-Extra: test
34
- Requires-Dist: pytest>=3.3.0; extra == "test"
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- Requires-Dist: dask[complete]; extra == "test"
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- Requires-Dist: matplotlib; extra == "test"
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- Provides-Extra: lint
38
- Requires-Dist: ruff; extra == "lint"
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- Provides-Extra: build
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- Requires-Dist: cibuildwheel[uv]; extra == "build"
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22
  Provides-Extra: jupyter
42
23
  Requires-Dist: dask[diagnostics]; extra == "jupyter"
43
24
  Requires-Dist: ipykernel>=6.29.5; extra == "jupyter"
@@ -61,28 +42,21 @@ sdf-xarray provides a backend for [xarray](https://xarray.dev) to read SDF files
61
42
  [EPOCH](https://epochpic.github.io) using the [SDF-C](https://github.com/epochpic/SDF_C) library.
62
43
  Part of [BEAM](#broad-epoch-analysis-modules-beam) (Broad EPOCH Analysis Modules).
63
44
 
45
+ ## Installation
46
+
64
47
  > [!IMPORTANT]
65
48
  > To install this package make sure you are using one of the Python versions listed above.
66
49
 
67
- ## Installation
68
-
69
50
  Install from PyPI with:
70
51
 
71
52
  ```bash
72
53
  pip install sdf-xarray
73
54
  ```
74
55
 
75
- > [!NOTE]
76
- > For use within jupyter notebooks, run this additional command after installation:
77
- >
78
- > ```bash
79
- > pip install "sdf-xarray[jupyter]"
80
- > ```
81
-
82
- or from a local checkout:
56
+ or download this code locally:
83
57
 
84
58
  ```bash
85
- git clone https://github.com/epochpic/sdf-xarray.git
59
+ git clone --recursive https://github.com/epochpic/sdf-xarray.git
86
60
  cd sdf-xarray
87
61
  pip install .
88
62
  ```
@@ -91,6 +65,9 @@ We recommend switching to [uv](https://docs.astral.sh/uv/) to manage packages.
91
65
 
92
66
  ## Usage
93
67
 
68
+ Below are some simple examples to get you started. Please read the full
69
+ documentation here <https://sdf-xarray.readthedocs.io>.
70
+
94
71
  ### Single file loading
95
72
 
96
73
  ```python
@@ -111,15 +88,22 @@ print(df["Electric_Field_Ex"])
111
88
 
112
89
  ### Multi-file loading
113
90
 
114
- To open a whole simulation at once, pass `preprocess=sdf_xarray.SDFPreprocess()`
115
- to `xarray.open_mfdataset`:
91
+ You can open all the SDF files for a given simulation by calling the `open_mfdataset`
92
+ function from `sdf_xarray`. This will additionally add a time dimension using the `"time"`
93
+ value stored in each files attributes.
94
+
95
+ > [!IMPORTANT]
96
+ > If your simulation has multiple `output` blocks so that not all variables are
97
+ > output at every time step, then at the timesteps where those variables are not
98
+ > present they will have have a value of nan. To clean your dataset by removing
99
+ > these nan values we suggest using the `xarray.DataArray.dropna` function or
100
+ > loading sparse data along separate time dimensions using `separate_times=True`.
116
101
 
117
102
  ```python
118
- import xarray as xr
119
- from sdf_xarray import SDFPreprocess
103
+ from sdf_xarray import open_mfdataset
120
104
 
121
- with xr.open_mfdataset("*.sdf", preprocess=SDFPreprocess()) as ds:
122
- print(ds)
105
+ ds = open_mfdataset("*.sdf")
106
+ print(ds)
123
107
 
124
108
  # Dimensions:
125
109
  # time: 301, X_Grid_mid: 128, ...
@@ -129,15 +113,6 @@ with xr.open_mfdataset("*.sdf", preprocess=SDFPreprocess()) as ds:
129
113
  # Attributes: (22) ...
130
114
  ```
131
115
 
132
- `SDFPreprocess` checks that all the files are from the same simulation, as
133
- ensures there's a `time` dimension so the files are correctly concatenated.
134
-
135
- If your simulation has multiple `output` blocks so that not all variables are
136
- output at every time step, then those variables will have `NaN` values at the
137
- corresponding time points.
138
-
139
- For more in depth documentation please visit: <https://sdf-xarray.readthedocs.io/>
140
-
141
116
  ## Citing
142
117
 
143
118
  If sdf-xarray contributes to a project that leads to publication, please acknowledge this by citing sdf-xarray. This can be done by clicking the "cite this repository" button located near the top right of this page.
@@ -6,20 +6,21 @@ include/SDFC_14.4.7/sdf_list_type.h,sha256=Quu8v0-SEsQuJpGtEZnm09tAyXqWNitx0sXl5
6
6
  include/SDFC_14.4.7/sdf_vector_type.h,sha256=dbKjhzRRsvhzrnTwVjtVlvnuisEnRMKY-vvdm94ok_Q,1595
7
7
  include/SDFC_14.4.7/stack_allocator.h,sha256=L7U9vmGiVSw3VQLIv9EzTaVq7JbFxs9aNonKStTkUSg,1335
8
8
  include/SDFC_14.4.7/uthash.h,sha256=rIyy_-ylY6S_7WaZCCC3VtvXaC9q37rFyA0f1U9xc4w,63030
9
- lib/SDFC_14.4.7/sdfc.lib,sha256=2X2DUE3jjnJGQOI2wQFQLidt_6vFdzEizuQHMEFoMqc,350158
9
+ lib/SDFC_14.4.7/sdfc.lib,sha256=ZhhC5S7yHBXQwkey_wOemw7Cw-iik423_0nVcmM_P7c,350158
10
10
  lib/SDFC_14.4.7/SDFCConfig.cmake,sha256=IOA1eusC-KvUK4LNTEiOAmEdaPH1ZvNvbYPgiG1oZio,802
11
11
  lib/SDFC_14.4.7/SDFCConfigVersion.cmake,sha256=pN7Qqyf04s3izw7PYQ0XK6imvmhaVegSdR_nEl3Ok_o,2830
12
12
  lib/SDFC_14.4.7/SDFCTargets-release.cmake,sha256=G4zdx5PyjePigeD_a6rmZAxbk7L8Nf0klUnV78Lm2fI,828
13
13
  lib/SDFC_14.4.7/SDFCTargets.cmake,sha256=OVt1Gm8n7Ew4fiTmA9yHoef3vIIGwsXUZfqeG9p9Bys,4152
14
- sdf_xarray/__init__.py,sha256=obgAD4Aecvvpd8GkxLIAiIagSaY0bFVP2Q397N48_5g,24201
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- sdf_xarray/_version.py,sha256=bmLiJYnZTISDv_NDGANk6QDMSY0XTk0CwXXKhbOvW3Y,746
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+ sdf_xarray/__init__.py,sha256=OAihj1CQVqoVvf-eEmwIttedjyplcoiTOfXpDafNqT8,24229
15
+ sdf_xarray/_version.py,sha256=q0PPvfDga48CLepNF0cz12bk-1nMuF8tgn-8a0yG_w4,746
16
16
  sdf_xarray/csdf.pxd,sha256=ADPjAuHsodAvdOz96Z_XlFF7VL3KmVaXcTifWDP3rK0,4205
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- sdf_xarray/dataset_accessor.py,sha256=TvnVMBefnT1d94Bkllhd-__O3ittzpaVjZKfze-3WQ4,2484
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- sdf_xarray-0.3.2.dist-info/RECORD,,
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+ sdf_xarray/dataset_accessor.py,sha256=IhROgmqgdD5SvuMbpZz-G6WoTre06-SOYgXVQSb7VAY,2450
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