GrisFitsFile.py 17.1 KB
Newer Older
Carl Schaffer's avatar
Carl Schaffer committed
1
2
3
4
5
6
"""
Created on 2018-04-09
@author Carl Schaffer
@mail   carl.schaffer@leibniz-kis.de
"""

Carl Schaffer's avatar
Carl Schaffer committed
7
import datetime  # date handling
8
import logging
9
10
import os  # path and file manipulations
import sys  # error handling
11
from glob import glob
12
from os.path import basename, exists, join, dirname
13

Carl Schaffer's avatar
linting    
Carl Schaffer committed
14
import astropy.io.fits as fitsio  # fits reading and writing
15
import astropy.units as u
16
import matplotlib.pyplot as plt
Carl Schaffer's avatar
Carl Schaffer committed
17
import numpy as np
18
from astropy.coordinates import SkyCoord, Angle
19
from astropy.wcs import WCS
Carl Schaffer's avatar
Carl Schaffer committed
20

Carl Schaffer's avatar
Carl Schaffer committed
21
from kis_tools.generic.fits import FitsFile
22
23
24
from kis_tools.gris.coord_correction_ml import get_coords_ml
from kis_tools.gris.util import gregor_parallactic_angle, telescope_to_hpc
from kis_tools.util.calculations import estimate_telescope_drift
Carl Schaffer's avatar
Carl Schaffer committed
25
from kis_tools.util.util import date_from_fn, gris_obs_mode
Carl Schaffer's avatar
Carl Schaffer committed
26

27
28
logger = logging.getLogger(__name__)

Carl Schaffer's avatar
Carl Schaffer committed
29

30
class GrisFitsFile(FitsFile):
Carl Schaffer's avatar
Carl Schaffer committed
31
32
33
34
35
    """Class for handling fits files for GRIS db
    When the constructor is called, the filename is stored and basic
    metadata parameters such as date and runnumber are extracted from
    the filename. Once the class function GrisFitsFile.parse() is
    called, metadata from the fits file is available as a dictionary
Carl Schaffer's avatar
typo    
Carl Schaffer committed
36
    stored at GrisFitsFile.properties. Any errors occurring during
Carl Schaffer's avatar
Carl Schaffer committed
37
38
    opening and parsing of the file are stored as strings in
    GrisFitsFile.errors
Carl Schaffer's avatar
Carl Schaffer committed
39

40
41
42
43
44
    Args:
      filename: filename of target fits file

    Returns:

Carl Schaffer's avatar
Carl Schaffer committed
45
    """
Carl Schaffer's avatar
Carl Schaffer committed
46

Carl Schaffer's avatar
Carl Schaffer committed
47
48
    def __init__(self, filename):
        """Constructor"""
49
        super().__init__(filename)
Carl Schaffer's avatar
Carl Schaffer committed
50
        assert exists(filename)
Carl Schaffer's avatar
Carl Schaffer committed
51
52
53
54
        self.properties = {}
        self.errors = []

        self.filename = filename
55
        self.name = basename(filename)
56
        self.path = self.filename
57

58
        self.dirname = dirname(self.path)
Carl Schaffer's avatar
Carl Schaffer committed
59
60
61
62
        self.parse_filename()
        self.is_parsed = False

    def parse_filename(self):
63
        """Extract metadata from filename"""
Carl Schaffer's avatar
Carl Schaffer committed
64
        # Extract time from Filename
65
        name = os.path.splitext(basename(self.filename))[0].split("_")
Carl Schaffer's avatar
linting    
Carl Schaffer committed
66
67
68
        year = int(name[1][:4])
        month = int(name[1][4:6])
        day = int(name[1][6:])
Carl Schaffer's avatar
Carl Schaffer committed
69
70

        # Get time
Carl Schaffer's avatar
linting    
Carl Schaffer committed
71
72
73
        # hh = int(name[2][:2])
        # mm = int(name[2][2:4])
        # outstring = int(name[2][4:6])
Carl Schaffer's avatar
Carl Schaffer committed
74

Carl Schaffer's avatar
linting    
Carl Schaffer committed
75
        # self.date = datetime.datetime(year,month,day,hh,mm,outstring)
Carl Schaffer's avatar
Carl Schaffer committed
76
        self.date = datetime.datetime(year, month, day, 0, 0, 0)
Carl Schaffer's avatar
Carl Schaffer committed
77

78
        # Extract Run-, Map-, and Stepnumber, as well as mode string
79
        self.runnumber = int(name[4])
80
        self.mapnumber = int(name[5])
Carl Schaffer's avatar
linting    
Carl Schaffer committed
81
        self.slitposnumber = name[6]
82
83
        self.modestring = name[3]

84
    @property
Carl Schaffer's avatar
Carl Schaffer committed
85
    def verbose_runname(self):
86
87
88
89
90
91
        """
        Get verbose run name such as 24apr14.002

        Returns:
            outstring: verbose run name
        """
92
93
94
95
        outstring = self.date.strftime("%d%b%y").lower()
        outstring += f".{int(self.runnumber):03d}"
        return outstring

96
97
98
99
100
101
102
103
104
105
106
107
108
    @property
    def telescope_centering(self):
        """
        Determine state of telescope centering at the time of observation, queries GDBS
        for centering data

        Returns:
            outstring: x_offset, y_offset, x_uncertainty, y_uncertainty all in arcseconds
        """
        # Query centering from GDBS
        try:
            from kis_tools.gdbs.query_gdbs import query_gdbs
            gdbs_usable = True
109
110
            x_telcenter, x_valid, x_age = query_gdbs('xsuncenter', self.obs_time)
            y_telcenter, y_valid, y_age = query_gdbs('ysuncenter', self.obs_time)
111
112
113
114
115
116
117
118
119
120
            # Determine uncertainties for centering values
            centering_age = max(x_age, y_age)
            drift = estimate_telescope_drift(centering_age.seconds / 3600)
            x_std, y_std = drift, drift

            # if the centering is older than 24 hours, discard
            if centering_age > datetime.timedelta(hours=24):
                gdbs_usable = False
        except IOError:
            gdbs_usable = False
121
122
        except ValueError:
            gdbs_usable = False
123
124
125
126
127
128
129
130

        if not gdbs_usable:
            # Determined from offset between uncentered and cross_correlated data
            # STD-DEV of distances in X and Y again see gris coord study for details
            uncertainty_no_center_x = 117.1
            uncertainty_no_center_y = 182.4
            x_telcenter, y_telcenter, x_std, y_std = 0, 0, uncertainty_no_center_x, uncertainty_no_center_y

131
        return float(x_telcenter), float(y_telcenter), x_std, y_std
132

Carl Schaffer's avatar
Carl Schaffer committed
133
    @property
134
    def _coords_from_simple_header(self):
135
136
137
138
139
140
141
142
143
144
145
146
147
        """coordinates for slit, the Keywords 'SLITPOSX' and 'SLITPOSY' are assumed to be the center of the slit
         while the keyword 'SLITORIE' describes the rotation of the slit w.r.t. the helioprojective axes. The
         algorithm further assumes that each pixel represents a square area with side length of 'STEPSIZE'.
         These assumptions are used to calculate the coordinates for the center of each pixel within the data array.

        Returns:
            (X,Y):ndarray(float) x and y coordinates for each pixel of the slit


        WARNING! The code below is not checked for correctness! We do not know what direction SLITORIE references
        off and coordinates provided by GREGOR are very error-prone.
        """

Carl Schaffer's avatar
Carl Schaffer committed
148
        h = self.header
149
        slit_length_pixels = h["NAXIS2"] if self.old_header else h['NAXIS1']
Carl Schaffer's avatar
Carl Schaffer committed
150
151
        center_pixel = slit_length_pixels // 2

152
        # Slit center in telescope coordinates
153
154
        x_slitcenter = h["SLITPOSX"] if h["SLITPOSX"] != "" else 0
        y_slitcenter = h["SLITPOSY"] if h["SLITPOSY"] != "" else 0
Carl Schaffer's avatar
Carl Schaffer committed
155

156
157
158
159
160
        # Transform to HPC (shift by telescope centering, rotate by p0 angle)
        delta_x, delta_y, std_delta_x, std_delta_y = self.telescope_centering

        # If uncertainties are too large, use ML model to correct the coordinates
        from kis_tools.gris.coord_correction_ml import coord_model_stdx, coord_model_stdy
161

162
        if std_delta_x > coord_model_stdx or std_delta_y > coord_model_stdy:
163
164
165
166
167
168
            try:
                x_hpc, y_hpc, std_delta_x, std_delta_y = get_coords_ml(self)
            except ValueError as e:
                logger.warning(f"Error in finding ML coords for {self.__repr__()}:{e}")
                # Point to slitpos with 1 solar disk uncertainty if coord retrieval didn't work
                x_hpc, y_hpc, std_delta_x, std_delta_y = x_slitcenter, y_slitcenter, 1000, 1000
169
170
        else:
            x_hpc, y_hpc = telescope_to_hpc(x_slitcenter, y_slitcenter, self.p0_angle, delta_x, delta_y)
Carl Schaffer's avatar
Carl Schaffer committed
171

172
        # Setup grid of pixels
Carl Schaffer's avatar
Carl Schaffer committed
173
174
        delta_pix = [i - center_pixel for i in range(slit_length_pixels)]
        delta_pix = np.array(delta_pix)
175
        arcsec_per_pixel_x = h["STEPSIZE"]  # assuming square pixels
Carl Schaffer's avatar
Carl Schaffer committed
176
177
178
        arcsec_per_pixel_y = (
            h["STEPSIZE"] if h["STEPSIZE"] else 0.135
        )  # assuming square pixels
Carl Schaffer's avatar
Carl Schaffer committed
179

180
181
182
183
184
        try:
            angle = self.slit_orientation
        except ValueError as e:
            logger.warning(f"Could not determine Slit orientation! \n {e}")
            angle = 0
Carl Schaffer's avatar
Carl Schaffer committed
185

186
187
188
        # generate coordinates for full grid of slit pixels
        X = x_hpc - np.sin(angle) * delta_pix * arcsec_per_pixel_x
        Y = y_hpc - np.cos(angle) * delta_pix * arcsec_per_pixel_y
189
190
191
192
193

        coord_array = np.array([X, Y]) * u.arcsec
        # reorder axes for consistency with other coordinate retrieval methods
        coord_array = np.swapaxes(coord_array, 0, 1)

194
195
        # track coordinate uncertainty within class
        self.coord_uncertainty = (std_delta_x, std_delta_y)
196
        return coord_array
197

198
199
200
201
202
203
204
205
    @property
    def coords(self):
        try:
            coords = self._coords_from_wcs
        except AssertionError:
            coords = self._coords_from_simple_header
        return coords

206
207
208
209
    @property
    def old_header(self):
        """Check if the header of this file has already been processed"""
        old_header = True
Carl Schaffer's avatar
Carl Schaffer committed
210
        if any([k in self.header for k in ["SOLARNET"]]):
211
212
            old_header = False
        return old_header
Carl Schaffer's avatar
Carl Schaffer committed
213

214
215
216
217
218
    @property
    def zenit(self):
        """
        Get Zenit angle (90° - elevation)
        Returns: zenit float in degrees
219
        Raises Value error if elevation is not contained in the header
220
221

        """
222
223
224
225
        elev = self._get_value(['ELEV_ANG', 'ELEVATIO'])
        if elev == '':
            raise ValueError(f'No elevation tracked for {self.__repr__()}')
        zenit = 90 - elev
226
227
        return zenit

Carl Schaffer's avatar
Carl Schaffer committed
228
229
    @property
    def slit_orientation(self):
230
231
        """Get slitorie:
         clockwise angle from the western section of the solar equator
232

233
        Attempts to correct for derotator and image rotation, usually correct within a couple 10s of degrees.
234
        Returns:
235
            slitorie: float (degrees)
236
        """
237

238
239
240
241
242
243
244
        p0_angle = self.p0_angle
        azimut = self._get_value(['AZIMUT'])
        zenit = self.zenit
        slitorie = self.SLITORIE
        const_term = -130  # determined by trial and error to match results from cross correlation with HMI
        alpha = -1 * gregor_parallactic_angle(self.obs_time) + azimut - zenit - p0_angle + const_term
        if self.derotator_in:
245
            rotangle = self.ROTANGLE
246
247
248
249
            alpha = -2 * rotangle + (const_term / 2)
        angle = slitorie - alpha

        return angle
Carl Schaffer's avatar
Carl Schaffer committed
250
251

    @property
252
253
    def number_of_maps(self):
        """
254
255

        Returns:
256
            nmaps: int number of maps in associated observation
257
        """
Carl Schaffer's avatar
Carl Schaffer committed
258
        return self._get_value(["NMAPS", "SERIES"])
Carl Schaffer's avatar
Carl Schaffer committed
259
260
261

    @property
    def map_index(self):
262
263
264
265
266
        """

        Returns:
            i_map: int map index within observation
        """
Carl Schaffer's avatar
Carl Schaffer committed
267
        return self._get_value(["IMAP", "ISERIE"])
Carl Schaffer's avatar
Carl Schaffer committed
268
269
270

    @property
    def n_steps(self):
271
272
273
274
275
276
277
278
279
280
281
282
283
        """
        Determine the number of slit scanning steps in the associated map.

        Returns:
            nsteps: number of steps in the associated map

        """
        # get initial guess from header
        nsteps = self._get_value(["STEPS", "NSTEPS"])

        # check if other files matching the same run are present. If so, check the running step number
        # for the same map to determine the actual number of steps. It is assumed, that all files belonging to the
        # same map are stored in the same directory
Carl Schaffer's avatar
Carl Schaffer committed
284
        pattern = f"gris_*_*_*_{self.runnumber:03d}_{self.mapnumber:03d}_*.fits"
285
286
        matching_files = glob(join(self.dirname, pattern))
        max_steps = int(
Carl Schaffer's avatar
Carl Schaffer committed
287
            max([basename(m).split(".")[0].split("_")[-1] for m in matching_files])
288
289
290
291
292
293
        )

        if max_steps < nsteps:
            nsteps = max_steps

        return nsteps
Carl Schaffer's avatar
Carl Schaffer committed
294

295
296
    @property
    def obs_time(self):
297
298
299
300
301
        """

        Returns:
            obs_time: observation time given in filename
        """
Carl Schaffer's avatar
Carl Schaffer committed
302
        return date_from_fn(self.filename)
303

Carl Schaffer's avatar
Carl Schaffer committed
304
305
    @property
    def step_index(self):
306
307
308
309
310
        """

        Returns:
            step_index: index of scanning step within current map
        """
Carl Schaffer's avatar
Carl Schaffer committed
311
        return self._get_value(["ISTEP"])
Carl Schaffer's avatar
Carl Schaffer committed
312

313
314
315
316
317
318
319
320
321
    @property
    def p0_angle(self):
        """

        Returns:
            p0_angle: angle between telescope and solar north
        """
        return self._get_value(["P0ANGLE", 'SOLAR_P0'])

322
323
    @property
    def step_angle(self):
324
325
326
327
328
329
        """

        Returns:
            step_angle: scanning angle
        """

Carl Schaffer's avatar
Carl Schaffer committed
330
        return self._get_value(["STEPANGL"])
331
332
333
334

    @property
    def wavelength_step_size(self):
        """Get step length along wavelength axis. We use the values from the continuum correction fitting"""
Carl Schaffer's avatar
Carl Schaffer committed
335
        return self._kw_mean(["FF1WLDSP", "FF2WLDSP"])
336
337
338
339
340

    @property
    def wavelength_region(self):
        """Get wavelength region covered by file. Returns tuple of (upper, lower)"""
        step_size = self.wavelength_step_size
341
        n_steps_wl = self.data.shape[-1] if self.old_header else self.NAXIS3
342
343

        # average for lower border:
Carl Schaffer's avatar
Carl Schaffer committed
344
345
        lower = self._kw_mean(["FF1WLOFF", "FF2WLOFF"])
        # add wl steps to calculate upper border
346
347
348
349
        upper = lower + step_size * n_steps_wl

        return lower, upper

350
351
352
353
354
355
356
357
358
    @property
    def derotator_in(self):
        """
        Determine whether the derotator is inserted

        Returns:
            bool: derotator in

        """
359
360
361
362
363
364
        try:
            rotval = self._get_value(["ROTCODE"])
        except KeyError:
            # if no derotator keywords are scontained, assume it doesn't exist yet
            return False

365
366
367
368
369
        if rotval == 0:
            return True
        else:
            return False

Carl Schaffer's avatar
Carl Schaffer committed
370
371
372
373
374
375
376
377
378
379
380
381
    @property
    def states(self):
        """
        Determine number of polarimetric states

        Returns:
            n_states int: number of states
        """

        # Number of polarimetric states is stored in the last axis. Determine
        # number of axes from NAXIS keyword and query value for last axis.
        naxes = self.query("NAXIS")
382
        keyword = f"NAXIS{naxes}"
Carl Schaffer's avatar
Carl Schaffer committed
383
384
385
386
        states = self.query(keyword)

        return states

387
388
    @property
    def obs_mode(self):
389
        """Get observation mode"""
390
        self.parse()
391
392
393
394
        # extract obs mode keywords
        states = self.states
        n_maps = self.number_of_maps
        n_steps = self.n_steps
395

396
        mode = gris_obs_mode(states, n_maps, n_steps)
397
        return mode
Carl Schaffer's avatar
Carl Schaffer committed
398

Carl Schaffer's avatar
Carl Schaffer committed
399
400
401
    def parse(self):
        """extract data and metadata from file"""
        if self.is_parsed:
Carl Schaffer's avatar
Carl Schaffer committed
402
            return
403
404
405
406
407
408
409
410
411

        def is_valid(value):
            valid = True
            if isinstance(value, fitsio.card.Undefined):
                valid = False
            elif value == "-NAN":
                valid = False

            return valid
Carl Schaffer's avatar
Carl Schaffer committed
412
413

        # Read file
Carl Schaffer's avatar
Carl Schaffer committed
414
        try:
Carl Schaffer's avatar
Carl Schaffer committed
415
            header = self.header
416

Carl Schaffer's avatar
Carl Schaffer committed
417
            # Add header to self.properties, cast strange data types where
418
419
            # necessary, fill invalid values with empty strings

Carl Schaffer's avatar
Carl Schaffer committed
420
            for key in header.keys():
421
422
423
                value = header[key]
                # check validity:
                value = value if is_valid(value) else ""
Carl Schaffer's avatar
Carl Schaffer committed
424
                if key in ["COMMENT", "HISTORY"]:
425
                    self.properties[key] = str(value)
Carl Schaffer's avatar
Carl Schaffer committed
426
                else:
427
428
                    self.properties[key] = value

Carl Schaffer's avatar
Carl Schaffer committed
429
            self.is_parsed = True
Carl Schaffer's avatar
Carl Schaffer committed
430
        except:
Carl Schaffer's avatar
linting    
Carl Schaffer committed
431
            exception = sys.exc_info()[0]
Carl Schaffer's avatar
Carl Schaffer committed
432
            self.errors.append("File %s" % self.filename + str(exception))
Carl Schaffer's avatar
Carl Schaffer committed
433
434

    def make_bson(self):
Carl Schaffer's avatar
Carl Schaffer committed
435
436
        """construct BSON document for mongodb storage"""
        return self.properties
Carl Schaffer's avatar
Carl Schaffer committed
437

438
    @property
439
    def _coords_from_wcs(self):
440
441
442
443
444
445
        """
        Retrieve spatial coordinates for each pixel in for slices projected into the spatial dimensions.
        Returns a data cube shaped s the spatial dimensions
        Returns: arcsec, cube of (NAXIS1, NAXIS2, 2) Values are Helioprojective X and Y in arcseconds
        """

Carl Schaffer's avatar
Carl Schaffer committed
446
447
448
        assert (
            not self.old_header
        ), f"Can't get coordinates from {self.path} ! Run header conversion first!"
449

450
451
452
        wcs = WCS(self.header)
        pixel_shape = wcs.pixel_shape
        n_y = pixel_shape[1]
453
        slit_list = np.zeros((n_y, self["NAXIS"]))
454
455
        slit_list[:, 1] = np.arange(n_y)
        slit_list[:, 0] = 0
456
        converted = np.array(wcs.pixel_to_world_values(slit_list))
457
        degrees = Angle(u.degree * converted[:, :2]).wrap_at(180 * u.degree)
458
        arcsec = degrees.to(u.arcsec)
459

460
461
462
        # Track coord uncertainty within instance
        self.coord_uncertainty = (self.CSYER1, self.CSYER2)

463
464
        return arcsec

465
    def plot_slit(self):
466
        m = self.full_disk_map
467

468
        # retrieve different data sources
469
        coordinates = self.coords
470
471
472
473

        X, Y = coordinates[:, 0], coordinates[:, 1]

        # determine fov limits for plotting
474

475
        plotting_padding = 300 * u.arcsec
476
477
478
479
        x_min = min(X) - plotting_padding
        x_max = max(X) + plotting_padding
        y_min = min(Y) - plotting_padding
        y_max = max(Y) + plotting_padding
480
481

        # Create submap of FOV and plot
Carl Schaffer's avatar
Carl Schaffer committed
482
483
484
485
        submap = m.submap(
            SkyCoord(x_min, y_min, frame=m.coordinate_frame),
            SkyCoord(x_max, y_max, frame=m.coordinate_frame),
        )
486
487
488
489
490
491
        fig = plt.figure()  # noqa F841
        ax = plt.subplot(projection=submap)
        im = submap.plot()  # noqa:F841

        # create SkyCoord objects and overplot
        slit_wcs = SkyCoord(X, Y, frame=submap.coordinate_frame)
Carl Schaffer's avatar
Carl Schaffer committed
492
        ax.plot_coord(slit_wcs, "g-", label="WCS Coordinates")
493
494
495

        # Create Legend and annotations
        title = "Gris Slit {0}_{1:03d}_{2:03d}_{3:03d}"
Carl Schaffer's avatar
Carl Schaffer committed
496
497
498
499
500
501
        title = title.format(
            self.obs_time.strftime("%Y%m%d"),
            self.runnumber,
            self.mapnumber,
            self.step_index,
        )
502
503
        plt.title(title)

Carl Schaffer's avatar
Carl Schaffer committed
504
505
506
507
508
509
510
511
512
        annotation = (
            f"Spectrum taken at \n{self.obs_time.strftime('%Y-%m-%d %H:%M:%S')}"
        )
        annotation += (
            f"\nHMI Reference taken at \n{submap.date.strftime('%Y-%m-%d %H:%M:%S')}"
        )
        plt.text(
            0.05, 0.8, annotation, horizontalalignment="left", transform=ax.transAxes
        )
513
514
        plt.tight_layout(pad=3.5)
        _ = plt.legend()
515
516
517

        return fig, ax

Carl Schaffer's avatar
Carl Schaffer committed
518
    def __str__(self):
Carl Schaffer's avatar
Carl Schaffer committed
519
520
521
        outstring = (
            "GrisFitsFile %s from %s:\n\tRun: %s\n\tMap: %s\n\tSlitposition: %s\n"
        )
Carl Schaffer's avatar
linting    
Carl Schaffer committed
522
        outstring = outstring % (
Carl Schaffer's avatar
Carl Schaffer committed
523
            os.path.basename(self.filename),
Carl Schaffer's avatar
Carl Schaffer committed
524
525
            self.date,
            self.runnumber,
526
            self.map_index,
Carl Schaffer's avatar
Carl Schaffer committed
527
            self.slitposnumber,
Carl Schaffer's avatar
Carl Schaffer committed
528
        )
Carl Schaffer's avatar
linting    
Carl Schaffer committed
529
        return outstring
530
531


Carl Schaffer's avatar
Carl Schaffer committed
532
if __name__ == "__main__":
533
534
535
    gf = GrisFitsFile(sys.argv[1])
    gf.parse()
    print(gf)