Note: The default ITS GitLab runner is a shared resource and is subject to slowdowns during heavy usage.
You can run your own GitLab runner that is dedicated just to your group if you need to avoid processing delays.

tecplottools.py 18.8 KB
Newer Older
1
#!/usr/bin/env python
2
3
4
5
6
7
8
9
10
"""Tools for working with the Tecplot visualization software.

Requires an active Tecplot license and the pytecplot python package.
pytecplot ships with Tecplot 360 2017 R1 and later versions
but it is recommended that you install the latest version with
`pip install pytecplot`.
See the pytecplot documentation for more details about
[installation](https://www.tecplot.com/docs/pytecplot/install.html).
See also [TECPLOT](TECPLOT.markdown) for tips targeted to SWMF users.
11
12

Some useful references:
13
14
15
- [Tecplot User's Manual](download.tecplot.com/360/current/360_users_manual.pdf)
- [Tecplot Scripting Guide](download.tecplot.com/360/current/360_scripting_guide.pdf)
- [Pytecplot documentation](www.tecplot.com/docs/pytecplot/index.html)
16
17
"""
__all__ = [
18
    'apply_equations',
19
    'bracketify',
20
21
    'write_zone',
    'interpolate_zone_to_geometry'
22
23
]
__author__ = 'Camilla D. K. Harris'
24
__email__ = 'cdha@umich.edu'
25

26
import h5py
27
import numpy as np
28
29
import tecplot

30

31
def _shell_geometry(geometry_params: dict) -> dict:
32
33
    """Returns a dict containing points for the described shell geometry.
    """
34
35
    nlon = geometry_params['npoints'][0] # 360
    nlat = geometry_params['npoints'][1] # 179
36
37
    lons = np.linspace(0, 360, nlon, endpoint=False)
    dlat = 180/(nlat + 1)
38
    lats = np.linspace(-90.0+dlat, 90.0-dlat, nlat)
39
40
41
    print(f'lons: {lons}')
    print(f'lats: {lats}')

42
43
44
45
46
47
48
49
    latvals, lonvals = np.meshgrid(lats, lons)
    phvals = np.deg2rad(-1*lonvals + 90)
    thvals = np.deg2rad(90 - latvals)
    rhovals = geometry_params['radius'] * np.sin(thvals)
    xvals = rhovals * np.cos(phvals) + geometry_params['center'][0]
    yvals = rhovals * np.sin(phvals) + geometry_params['center'][1]
    zvals = (geometry_params['radius'] * np.cos(thvals)
             + geometry_params['center'][2])
50

51
    geometry_points = {
52
53
54
55
56
57
        'npoints': nlon * nlat,
        'latitude': latvals.flatten(),
        'longitude': lonvals.flatten(),
        'X': xvals.flatten(),
        'Y': yvals.flatten(),
        'Z': zvals.flatten()
58
59
    }
    return geometry_points
60
61


62
def _line_geometry(geometry_params: dict) -> dict:
63
64
    """Returns a dict containing points for the described line geometry.
    """
65
    geometry_points = {
66
67
68
69
70
71
72
73
74
75
76
77
78
        'npoints': geometry_params['npoints'],
        'X': np.linspace(
            geometry_params['r1'][0],
            geometry_params['r2'][0],
            geometry_params['npoints']),
        'Y': np.linspace(
            geometry_params['r1'][1],
            geometry_params['r2'][1],
            geometry_params['npoints']),
        'Z': np.linspace(
            geometry_params['r1'][2],
            geometry_params['r2'][2],
            geometry_params['npoints'])
79
80
    }
    return geometry_points
81
82


83
def _rectprism_geometry(geometry_params: dict) -> dict:
84
85
    """Returns a dict containing points for the described rectprism geometry.
    """
86
87
88
    npoints = (geometry_params['npoints'][0]
               * geometry_params['npoints'][1]
               * geometry_params['npoints'][2])
89
90
91
92
93
94
95
96
97
98
99
100
    vals = []
    for dim in range(3):
        minval = (geometry_params['center'][dim]
                  - geometry_params['halfwidths'][dim])
        maxval = (geometry_params['center'][dim]
                  + geometry_params['halfwidths'][dim])
        vals.append(np.linspace(
            minval,
            maxval,
            geometry_params['npoints'][dim]
        ))
    xvals, yvals, zvals = np.meshgrid(vals[0], vals[1], vals[2])
101
    geometry_points = {
102
103
104
105
        'npoints': npoints,
        'X': xvals.flatten(),
        'Y': yvals.flatten(),
        'Z': zvals.flatten(),
106
107
    }
    return geometry_points
108
109


110
def _trajectory_geometry(geometry_params: dict) -> dict:
111
    """Returns a dict containing points for the described trajectory geometry.
112
113

    Assumes format of trajectory file after SWMF SATELLITE command.
114
    """
115
116
    do_read = False
    trajectory_data = []
117
    with open(geometry_params['trajectory_data'], 'r') as trajectory_file:
118
119
120
121
122
123
124
125
        for line in trajectory_file:
            if do_read:
                if len(line.split()) == 10:
                    trajectory_data.append(line.split())
                else:
                    do_read = False
            elif '#START' in line:
                do_read = True
126
127
128
129
130
131
132
    try:
        assert len(trajectory_data) >= 1
    except:
        raise ValueError(
            'No points could be read from the trajectory file. Consult the '
            'SWMF documentation for advice on trajectory format.'
        )
133
    geometry_points = {
134
135
136
137
138
139
140
        'npoints': len(trajectory_data),
        'X': [float(trajectory_point[7])
              for trajectory_point in trajectory_data],
        'Y': [float(trajectory_point[8])
              for trajectory_point in trajectory_data],
        'Z': [float(trajectory_point[9])
              for trajectory_point in trajectory_data],
141
        'time': [((np.datetime64(
142
143
144
145
146
147
148
            f'{trajectory_point[0]}'
            f'-{trajectory_point[1]}'
            f'-{trajectory_point[2]}'
            f'T{trajectory_point[3]}'
            f':{trajectory_point[4]}'
            f':{trajectory_point[5]}'
            f'.{trajectory_point[6]}')
149
150
                   - np.datetime64('1970-01-01T00:00:00Z'))
                  / np.timedelta64(1, 's'))
151
                 for trajectory_point in trajectory_data]
152
    }
153
    return geometry_points
154
155


156
def _save_hdf5(filename, geometry_params, new_zone, variables) -> None:
157
158
    """Save the aux data and a subset of the variables in hdf5 format.
    """
159
160
161
162
163
164
165
166
167
    column_names = [var.name for var in variables]
    tp_data = []
    for var in variables:
        tp_data.append(new_zone.values(var)[:])
    tp_data_np = np.array(tp_data).transpose()
    with h5py.File(filename, 'w-') as h5_file:
        h5_file['data'] = tp_data_np
        h5_file['data'].attrs.update(geometry_params)
        h5_file['data'].attrs['names'] = column_names
168
169


170
def _save_csv(filename, geometry_params, new_zone, variables) -> None:
171
172
    """Save the aux data and a subset of the variables in plain-text format.
    """
173
174
175
    aux_data = geometry_params.__repr__() + '\n'
    column_names = variables[0].name.__repr__()
    for var in variables[1:]:
176
        column_names += ',' + var.name.__repr__()
177
178
179
180
181
182
183
    tp_data = []
    for var in variables:
        tp_data.append(new_zone.values(var)[:])
    tp_data_np = np.array(tp_data).transpose()
    np.savetxt(
        filename,
        tp_data_np,
184
        delimiter=',',
185
186
187
        header=aux_data + column_names,
        comments=''
    )
188
189


190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
def _add_variable_value(dataset, variable_name: str, zone, values):
    """Adds and populates a new variable to a zone in a dataset."""
    dataset.add_variable(variable_name)
    zone.values(bracketify(variable_name))[:] = values


def apply_equations(eqn_path: str, verbose: bool = False) -> None:
    """Apply an equations file in the Tecplot macro format to the active dataset

    Please reference the Tecplot User's Manual for more details on
    equation files and syntax. It is recommended to use this function with eqn
    files generated with the Tecplot GUI.
    See [TECPLOT](TECPLOT.markdown) for tips on using pytecplot.

    Args:
        eqn_file_path (str): The path to the equation macro file (typically with
            extension `.eqn`).
        verbose (bool): (Optional) Whether or not to print the equations as they
            are applied. Default behavior is silent.

    Examples:
        ```python
        import tecplot
        import swmfpy.tecplottools as tpt

        ## Uncomment this line if you are connecting to a running tecplot
        ## session. Be sure that the port number matches the port the GUI is
        ## listening to. See TECPLOT.markdown for tips on connecting to a
        ## running session or running your script seperately.
        # tecplot.session.connect(port=7600)

        ## load a dataset
        dataset = tecplot.data.load_tecplot('./z=0_mhd_1_n00000000.plt')

        ## apply an equations file
        tpt.apply_equations('./gse_to_ephio.eqn', verbose= True)

        ## apply a frame style
        frame = tecplot.active_frame()
        frame.load_stylesheet('./density.sty')

        ## annotate with the zone name
        frame.add_text('&(ZONENAME[ACTIVEOFFSET=1])', position= (5, 95))

        ## save the image
        tecplot.export.save_png('./density.png', width= 1200, supersample= 8)
        ```
    """
    if verbose:
        print('Executing:')
    with open(eqn_path, 'r') as eqn_file:
        for line in eqn_file:
            if '$!alterdata' in line.lower():
                eqn_line = eqn_file.readline()
                try:
                    eqn_str = eqn_line.split("'")[1]
                except IndexError:
                    try:
                        eqn_str = eqn_line.split("\"")[1]
                    except:
                        raise ValueError(f'Unable to read equation: {eqn_line}')
                tecplot.data.operate.execute_equation(eqn_str)
                if verbose:
                    print(eqn_str)
    if verbose:
        print('Successfully applied equations.')


def bracketify(variable_name: str) -> str:
    """Surrounds square brackets with more brackets.

    This is helpful for accessing Tecplot variables.

    Examples:
        In a dataset which contains the variable 'X [R]',
        ```print(dataset.variable_names)
        >>> ['X [R]', ... ]```
        The following will fail:
        ```print(dataset.variable('X [R]').name)
        >>> TecplotPatternMatchWarning: no variables found matching: "X [R]" For
        a literal match, the meta-characters: * ? [ ] must be wrapped in square-
        brackets. For example, "[?]" matches the character "?"...```
        However,
        ```print(dataset.variable(tpt.bracketify('X [R]')).name)```
        will succeed.
    """
    return variable_name.translate(str.maketrans({'[':'[[]', ']':'[]]'}))


279
def write_zone(
280
281
        tecplot_dataset
        , tecplot_zone
282
283
284
285
286
287
288
289
        , write_as: str
        , filename: str
        , variables=None
        , verbose: bool = False
) -> None:
    """Writes a tecplot zone to various formats.

    Args:
290
        tecplot_dataset (): The dataset to save.
291
292
293
294
295
296
297
298
299
        tecplot_zone (): The zone to save.
        write_as (str): Type of file to write to. Supported options are 'hdf5',
            'csv', 'tecplot_ascii', and 'tecplot_plt'.
        filename (str): Name of the file to write to.
        variables (): (Optional) Specify a subset of the dataset variables to
            save. This option may decrease the size of the output. Default
            behavior is to save all variables.
        verbose: (Optional) Print diagnostic information. Defaults to False.
    """
300
    if verbose and variables:
301
302
303
304
305
306
        print('Saving variables:')
        for var in variables:
            print(var.name)
    aux_data = tecplot_zone.aux_data.as_dict()
    if verbose:
        print('Attaching auxiliary data:')
307
        print(aux_data.__repr__())
308
309
310
311
312
313
    ## save zone
    if verbose:
        print('Saving as:')
    if 'hdf5' in write_as:
        if verbose:
            print('hdf5')
314
315
        if not variables:
            variables = list(tecplot_dataset.variables())
316
317
318
319
320
321
322
        _save_hdf5(
            filename,
            aux_data,
            tecplot_zone,
            variables
        )
    elif 'csv' in write_as:
323
324
        if not variables:
            variables = list(tecplot_dataset.variables())
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
        _save_csv(
            filename,
            aux_data,
            tecplot_zone,
            variables
        )
    elif 'tecplot_ascii' in write_as:
        tecplot.data.save_tecplot_ascii(
            filename
            , zones=tecplot_zone
            , variables=variables
            , use_point_format=True
        )
    elif 'tecplot_plt' in write_as:
        tecplot.data.save_tecplot_plt(
            filename
            , zones=tecplot_zone
            , variables=variables
        )
344
345
    else:
        raise ValueError(f'File type {write_as} not supported!')
346
347
348
349
    if verbose:
        print(f'Wrote {filename}')


350
351
352
def interpolate_zone_to_geometry(
        dataset
        , source_zone
353
        , geometry: str
354
        , variables: list = None
355
356
        , verbose: bool = False
        , **kwargs
357
):
358
359
360
    """Interpolates Tecplot binary data onto various geometries.

    Args:
361
362
        dataset: The loaded Tecplot dataset.
        source_zone: The Tecplot zone to interpolate onto the geometry.
363
        geometry (str): Type of geometry for interpolation. Supported geometries
364
365
366
367
            are 'shell', 'line', 'rectprism', or 'trajectory'. See below for the
            required keyword arguments for each geometry.
        variables (list): (Optional) Subset of variables to interpolate. Default
            behavior is to interpolate all variables.
368
369
370
371
372
373
374
375
        verbose: (Optional) Print diagnostic information. Defaults to False.

    Keyword Args:
        center (array-like): Argument for the 'shell' geometry. Contains the X,
            Y, and Z positions of the shell. Defaults to (0,0,0).
        radius (float): Argument for the 'shell' geometry. Required.
        npoints (array-like): Argument for the 'shell' geometry. Contains the
            number of points in the azimuthal and polar directions to
376
377
            interpolate onto, excluding the north and south polar points.
            Defaults to (360,179).
378
379
380
381
382
383
384
385
386
        r1 (array-like): Argument for the 'line' geometry. Contains the X, Y,
            and Z positions of the point where the line starts. Required.
        r2 (array-like): Argument for the 'line' geometry. Contains the X, Y,
            and Z positions of the point where the line ends. Required.
        npoints (int): Argument for the 'line' geometry. The number of points
            along the line to interpolate onto. Required.
        center (array-like): Argument for the 'rectprism' geometry. Contains the
            X, Y, and Z positions of the center of the rectangular prism.
            Defaults to (0,0,0).
387
        halfwidths (array-like): Argument for the 'rectprism' geometry. Contains
388
389
390
391
392
393
394
395
396
397
398
399
400
            the half widths of the rectangular prism in the X, Y, and Z
            directions. Required.
        npoints (array-like): Argument for the 'rectprism' geometry. Contains
            the number of points in the X, Y, and Z directions to interpolate
            onto. Required.
        trajectory_data (str): Argument for the 'trajectory' geometry. The path
            to the ASCII trajectory data file. Required.
        trajectory_format (str): Argument for the 'trajectory' geometry. The
            format of the trajectory data file. Supported formats are 'tecplot'
            (data is a tecplot zone with 3D positional variables and 'time') and
            'batsrus' (data is formatted as described for the #SATELLITE
            command, see SWMF documentation). Required.
    """
401
402
403
404
405
    if verbose:
        print('Collecting parameters')

    ## collect the geometry parameters
    geometry_params = {
406
        'geometry':geometry
407
408
409
410
411
    }
    geometry_params.update(kwargs)

    if verbose:
        print('Adding defaults')
412
413
    ## assign defaults for shell and rectprism
    if 'shell' in geometry_params['geometry']:
414
415
416
417
418
419
420
421
        geometry_params['center'] = geometry_params.get(
            'center'
            , (0.0, 0.0, 0.0)
        )
        geometry_params['npoints'] = geometry_params.get(
            'npoints'
            , (359, 181)
        )
422
    elif 'rectprism' in geometry_params['geometry']:
423
424
425
426
        geometry_params['center'] = geometry_params.get(
            'center'
            , (0.0, 0.0, 0.0)
        )
427
428
429

    ## check that we support the geometry
    geometry_param_names = {
430
431
432
433
        'shell': ('radius',),
        'line': ('r1', 'r2', 'npoints'),
        'rectprism': ('halfwidths', 'npoints'),
        'trajectory': ('trajectory_data', 'trajectory_format')
434
    }
435
436
437
    if geometry_params['geometry'] not in geometry_param_names:
        raise ValueError(f'Geometry {geometry_params["geometry"]} '
                         'not supported!')
438
    ## check that we've gotten the right /required/ geometry arguments
439
    for param in geometry_param_names[geometry_params['geometry']]:
440
441
        if param not in geometry_params:
            raise TypeError(
442
                f'Geometry {geometry_params["geometry"]} '
443
444
445
446
447
                f'requires argument {param}!')

    ## describe the interpolation we're about to do on the data
    if verbose:
        print('Geometry to be interpolated:')
448
        for key, value in geometry_params.items():
449
450
451
452
453
            print(f'\t{key}: {value.__repr__()}')

    ## describe the loaded tecplot data
    if verbose:
        print('Loaded tecplot data with variables:')
454
        print(dataset.variable_names)
455
456

    ## create geometry zone
457
    if 'shell' in geometry_params['geometry']:
458
        geometry_points = _shell_geometry(geometry_params)
459
    elif 'line' in geometry_params['geometry']:
460
        geometry_points = _line_geometry(geometry_params)
461
    elif 'rectprism' in geometry_params['geometry']:
462
        geometry_points = _rectprism_geometry(geometry_params)
463
    elif 'trajectory' in geometry_params['geometry']:
464
465
        if 'batsrus' in geometry_params['trajectory_format']:
            geometry_points = _trajectory_geometry(geometry_params)
466

467
    if ('trajectory' in geometry_params['geometry']
468
            and 'tecplot' in geometry_params['trajectory_format']):
469
        dataset = tecplot.data.load_tecplot(
470
            filenames=geometry_params['trajectory_data']
471
            , read_data_option=tecplot.constant.ReadDataOption.Append
472
        )
473
        dataset.zone(-1).name = 'geometry'
474
    else:
475
        dataset.add_ordered_zone(
476
477
478
            'geometry'
            , geometry_points['npoints']
        )
479
        for i, direction in zip((0, 1, 2), ('X', 'Y', 'Z')):
480
481
            dataset.zone('geometry').values(i)[:] = \
                geometry_points[direction][:]
482

483
    ## interpolate variables on to the geometry
484
    if verbose and variables:
485
486
487
        print('Interpolating variables:')
        for var in variables:
            print(var.name)
488
489
490
    ## dataset.variables('...') will return a generator of variables.
    ## This call will break if `variables` is not recast as a list before
    ## passing it to the function. Why?????
491
    tecplot.data.operate.interpolate_linear(
492
493
494
        destination_zone=dataset.zone('geometry'),
        source_zones=source_zone,
        variables=variables
495
    )
496

497
498
499
500
501
502
503
    ## add variables for shell and trajectory cases
    if 'shell' in  geometry_params['geometry']:
        _add_variable_value(
            dataset,
            'latitude [deg]',
            dataset.zone('geometry'),
            geometry_points['latitude']
504
        )
505
506
507
508
509
        _add_variable_value(
            dataset,
            'longitude [deg]',
            dataset.zone('geometry'),
            geometry_points['longitude']
510
        )
511
512
513
514
515
516
517
    if ('trajectory' in geometry_params['geometry']
            and 'batsrus' in geometry_params['trajectory_format']):
        _add_variable_value(
            dataset,
            'time',
            dataset.zone('geometry'),
            geometry_points['time']
518
        )
519
520
521
522
523

        ## add auxiliary data
    dataset.zone('geometry').aux_data.update(geometry_params)

    return dataset.zone('geometry')