Coverage for python/lsst/sims/maf/slicers/orbits.py : 5%

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1import warnings
2import numpy as np
3import pandas as pd
5__all__ = ['Orbits']
8class Orbits(object):
9 """Orbits reads, checks for required values, and stores orbit parameters for moving objects.
11 Instantiate the class and then use readOrbits or setOrbits to set the orbit values.
13 self.orbits stores the orbital parameters, as a pandas dataframe.
14 self.dataCols defines the columns required, although objId, H, g, and sed_filename are optional.
15 """
16 def __init__(self):
17 self.orbits = None
18 self.orb_format = None
20 # Specify the required columns/values in the self.orbits dataframe.
21 # Which columns are required depends on self.orb_format.
22 self.dataCols = {}
23 self.dataCols['COM'] = ['objId', 'q', 'e', 'inc', 'Omega', 'argPeri',
24 'tPeri', 'epoch', 'H', 'g', 'sed_filename']
25 self.dataCols['KEP'] = ['objId', 'a', 'e', 'inc', 'Omega', 'argPeri',
26 'meanAnomaly', 'epoch', 'H', 'g', 'sed_filename']
27 self.dataCols['CAR'] = ['objId', 'x', 'y', 'z', 'xdot', 'ydot', 'zdot',
28 'epoch', 'H', 'g', 'sed_filename']
30 def __len__(self):
31 return len(self.orbits)
33 def __getitem__(self, i):
34 orb = Orbits()
35 orb.setOrbits(self.orbits.iloc[i])
36 return orb
38 def __iter__(self):
39 for i, orbit in self.orbits.iterrows():
40 orb = Orbits()
41 orb.setOrbits(orbit)
42 yield orb
44 def __eq__(self, otherOrbits):
45 if isinstance(otherOrbits, Orbits):
46 if self.orb_format != otherOrbits.orb_format:
47 return False
48 for col in self.dataCols[self.orb_format]:
49 if not np.all(self.orbits[col].values == otherOrbits.orbits[col].values):
50 return False
51 else:
52 return True
53 else:
54 return False
56 def __neq__(self, otherOrbits):
57 if self == otherOrbits:
58 return False
59 else:
60 return True
62 def setOrbits(self, orbits):
63 """Set and validate orbital parameters contain all required values.
65 Sets self.orbits and self.orb_format.
66 If objid is not present in orbits, a sequential series of integers will be used.
67 If H is not present in orbits, a default value of 20 will be used.
68 If g is not present in orbits, a default value of 0.15 will be used.
69 If sed_filename is not present in orbits, either C or S type will be assigned,
70 according to the semi-major axis value.
72 Parameters
73 ----------
74 orbits : pandas.DataFrame, pandas.Series or numpy.ndarray
75 Array-like object containing orbital parameter information.
76 """
77 # Do we have a single item or multiples?
78 if isinstance(orbits, pd.Series):
79 # Passed a single SSO in Series, convert to a DataFrame.
80 orbits = pd.DataFrame([orbits])
81 elif isinstance(orbits, np.ndarray):
82 # Passed a numpy array, convert to DataFrame.
83 orbits = pd.DataFrame.from_records(orbits)
84 elif isinstance(orbits, np.record):
85 # This was a single object in a numpy array and we should be a bit fancy.
86 orbits = pd.DataFrame.from_records([orbits], columns=orbits.dtype.names)
87 elif isinstance(orbits, pd.DataFrame):
88 # This was a pandas dataframe .. but we probably want to drop the index and recount.
89 orbits.reset_index(drop=True, inplace=True)
91 if 'index' in orbits:
92 del orbits['index']
94 nSso = len(orbits)
96 # Error if orbits is empty (this avoids hard-to-interpret error messages from pyoorb).
97 if nSso == 0:
98 raise ValueError('Length of the orbits dataframe was 0.')
100 # Discover which type of orbital parameters we have on disk.
101 self.orb_format = None
102 if 'FORMAT' in orbits:
103 if ~(orbits['FORMAT'] == orbits['FORMAT'].iloc[0]).all():
104 raise ValueError('All orbital elements in the set should have the same FORMAT.')
105 self.orb_format = orbits['FORMAT'].iloc[0]
106 # Backwards compatibility .. a bit. CART is deprecated, so swap it to CAR.
107 if self.orb_format == 'CART':
108 self.orb_format = 'CAR'
109 del orbits['FORMAT']
110 # Check that the orbit format is approximately right.
111 if self.orb_format == 'COM':
112 if 'q' not in orbits:
113 raise ValueError('The stated format was COM, but "q" not present in orbital elements?')
114 if self.orb_format == 'KEP':
115 if 'a' not in orbits:
116 raise ValueError('The stated format was KEP, but "a" not present in orbital elements?')
117 if self.orb_format == 'CAR':
118 if 'x' not in orbits:
119 raise ValueError('The stated format was CAR but "x" not present in orbital elements?')
120 if self.orb_format is None:
121 # Try to figure out the format, if it wasn't provided.
122 if 'q' in orbits:
123 self.orb_format = 'COM'
124 elif 'a' in orbits:
125 self.orb_format = 'KEP'
126 elif 'x' in orbits:
127 self.orb_format = 'CAR'
128 else:
129 raise ValueError("Can't determine orbital type, as neither q, a or x in input orbital elements.\n"
130 "Was attempting to base orbital element quantities on header row, "
131 "with columns: \n%s" % orbits.columns)
133 # Check that the orbit epoch is within a 'reasonable' range, to detect possible column mismatches.
134 general_epoch = orbits['epoch'].head(1).values[0]
135 # Look for epochs between 1800 and 2200 - this is primarily to check if people used MJD (and not JD).
136 expect_min_epoch = -21503.
137 expect_max_epoch = 124594.
138 if general_epoch < expect_min_epoch or general_epoch > expect_max_epoch:
139 raise ValueError("The epoch detected for this orbit is odd - %f. "
140 "Expecting a value between %.1f and %.1f (MJD!)" % (general_epoch,
141 expect_min_epoch,
142 expect_max_epoch))
144 # If these columns are not available in the input data, auto-generate them.
145 if 'objId' not in orbits:
146 objId = np.arange(0, nSso, 1)
147 orbits = orbits.assign(objId = objId)
148 if 'H' not in orbits:
149 orbits = orbits.assign(H = 20.0)
150 if 'g' not in orbits:
151 orbits = orbits.assign(g = 0.15)
152 if 'sed_filename' not in orbits:
153 orbits = orbits.assign(sed_filename = self.assignSed(orbits))
155 # Make sure we gave all the columns we need.
156 for col in self.dataCols[self.orb_format]:
157 if col not in orbits:
158 raise ValueError('Missing required orbital element %s for orbital format type %s'
159 % (col, self.orb_format))
161 # Check to see if we have duplicates.
162 if len(orbits['objId'].unique()) != nSso:
163 warnings.warn('There are duplicates in the orbit objId values' +
164 ' - was this intended? (continuing).')
165 # All is good.
166 self.orbits = orbits
168 def assignSed(self, orbits, randomSeed=None):
169 """Assign either a C or S type SED, depending on the semi-major axis of the object.
170 P(C type) = 0 (a<2); 0.5*a - 1 (2<a<4); 1 (a > 4),
171 based on figure 23 from Ivezic et al 2001 (AJ, 122, 2749).
173 Parameters
174 ----------
175 orbits : pandas.DataFrame, pandas.Series or numpy.ndarray
176 Array-like object containing orbital parameter information.
178 Returns
179 -------
180 numpy.ndarray
181 Array containing the SED type for each object in 'orbits'.
182 """
183 # using fig. 23 from Ivezic et al. 2001 (AJ, 122, 2749),
184 # we can approximate the sed types with a simple linear form:
185 # p(C) = 0 for a<2
186 # p(C) = 0.5*a-1 for 2<a<4
187 # p(C) = 1 for a>4
188 # where a is semi-major axis, and p(C) is the probability that
189 # an asteroid is C type, with p(S)=1-p(C) for S types.
190 if 'a' in orbits:
191 a = orbits['a']
192 elif 'q' in orbits:
193 a = orbits['q'] / (1 - orbits['e'])
194 elif 'x' in orbits:
195 # This definitely isn't right, but it's a placeholder to make it work for now.
196 a = np.sqrt(orbits['x']**2 + orbits['y']**2 + orbits['z']**2)
197 else:
198 raise ValueError('Need either a or q (plus e) in orbit data frame.')
200 if not hasattr(self, "_rng"):
201 if randomSeed is not None:
202 self._rng = np.random.RandomState(randomSeed)
203 else:
204 self._rng = np.random.RandomState(42)
206 chance = self._rng.random_sample(len(orbits))
207 prob_c = 0.5 * a - 1.0
208 # if chance <= prob_c:
209 sedvals = np.where(chance <= prob_c, 'C.dat', 'S.dat')
210 return sedvals
212 def readOrbits(self, orbitfile, delim=None, skiprows=None):
213 """Read orbits from a file, generating a pandas dataframe containing columns matching dataCols,
214 for the appropriate orbital parameter format (currently accepts COM, KEP or CAR formats).
216 After reading and standardizing the column names, calls self.setOrbits to validate the
217 orbital parameters. Expects angles in orbital element formats to be in degrees.
219 Note that readOrbits uses pandas.read_csv to read the data file with the orbital parameters.
220 Thus, it should have column headers specifying the column names ..
221 unless skiprows = -1 or there is just no header line at all.
222 in which case it is assumed to be a standard DES format file, with no header line.
224 Parameters
225 ----------
226 orbitfile : str
227 The name of the input file containing orbital parameter information.
228 delim : str, optional
229 The delimiter for the input orbit file. Default is None, will use delim_whitespace=True.
230 skiprows : int, optional
231 The number of rows to skip before reading the header information for pandas.
232 Default is None, which will trigger a check of the file to look for the header columns.
233 """
234 names = None
236 # If skiprows is set, then we will assume the user has handled this so that the
237 # first line read has the header information.
238 # But, if skiprows is not set, then we have to do some checking to see if there is
239 # header information and which row it might start in.
240 if skiprows is None:
241 skiprows = -1
242 # Figure out whether the header is in the first line, or if there are rows to skip.
243 # We need to do a bit of juggling to do this before pandas reads the whole orbit file though.
244 with open(orbitfile, 'r') as fp:
245 headervalues = None
246 for line in fp:
247 values = line.split()
248 try:
249 # If it is a valid orbit line, we expect column 3 to be a number.
250 float(values[3])
251 # And if it worked, we're done here (it's an orbit) - go on to parsing header values.
252 break
253 except (ValueError, IndexError):
254 # This wasn't a valid number or there wasn't anything in the third value.
255 # So this is either the header line or it's a comment line before the header columns.
256 skiprows += 1
257 headervalues = values
260 if headervalues is not None: # (and skiprows > -1)
261 # There is a header, but we also need to check if there is a comment key at the start
262 # of the proper header line.
263 # ... Because this varies as well, and is sometimes separated from header columns.
264 linestart = headervalues[0]
265 if linestart == '#' or linestart == '!!' or linestart == '##':
266 names = headervalues[1:]
267 else:
268 names = headervalues
269 # Add 1 to skiprows, so that we skip the header column line.
270 skiprows += 1
272 # So now skiprows is a value. If it is -1, then there is no header information.
273 if skiprows == -1:
274 # No header; assume it's a typical DES file -
275 # we'll assign the column names based on the FORMAT.
276 names_COM = ('objId', 'FORMAT', 'q', 'e', 'i', 'node', 'argperi', 't_p',
277 'H', 'epoch', 'INDEX', 'N_PAR', 'MOID', 'COMPCODE')
278 names_KEP = ('objId', 'FORMAT', 'a', 'e', 'i', 'node', 'argperi', 'meanAnomaly',
279 'H', 'epoch', 'INDEX', 'N_PAR', 'MOID', 'COMPCODE')
280 names_CAR = ('objId', 'FORMAT', 'x', 'y', 'z', 'xdot', 'ydot', 'zdot',
281 'H', 'epoch', 'INDEX', 'N_PAR', 'MOID', 'COMPCODE')
282 # First use names_COM, and then change if required.
283 orbits = pd.read_csv(orbitfile, delim_whitespace=True, header=None, names=names_COM)
285 if orbits['FORMAT'][0] == 'KEP':
286 orbits.columns = names_KEP
287 elif orbits['FORMAT'][0] == 'CAR':
288 orbits.columns = names_CAR
290 else:
291 if delim is None:
292 orbits = pd.read_csv(orbitfile, delim_whitespace=True, skiprows=skiprows,
293 names=names)
294 else:
295 orbits = pd.read_csv(orbitfile, sep=delim, skiprows=skiprows, names=names)
297 # Drop some columns that are typically present in DES files but that we don't need.
298 if 'INDEX' in orbits:
299 del orbits['INDEX']
300 if 'N_PAR' in orbits:
301 del orbits['N_PAR']
302 if 'MOID' in orbits:
303 del orbits['MOID']
304 if 'COMPCODE' in orbits:
305 del orbits['COMPCODE']
306 if 'tmp' in orbits:
307 del orbits['tmp']
309 # Normalize the column names to standard values and identify the orbital element types.
310 ssoCols = orbits.columns.values.tolist()
312 # These are the alternative possibilities for various column headers
313 # (depending on file version, origin, etc.)
314 # that might need remapping from the on-file values to our standardized values.
315 altNames = {}
316 altNames['objId'] = ['objId', 'objid', '!!ObjID', '!!OID', '!!S3MID', 'OID', 'S3MID'
317 'objid(int)', 'full_name', '#name']
318 altNames['q'] = ['q']
319 altNames['a'] = ['a']
320 altNames['e'] = ['e', 'ecc']
321 altNames['inc'] = ['inc', 'i', 'i(deg)', 'incl']
322 altNames['Omega'] = ['Omega', 'omega', 'node', 'om', 'node(deg)',
323 'BigOmega', 'Omega/node', 'longNode']
324 altNames['argPeri'] = ['argPeri', 'argperi', 'omega/argperi', 'w', 'argperi(deg)', 'peri']
325 altNames['tPeri'] = ['tPeri', 't_p', 'timeperi', 't_peri', 'T_peri']
326 altNames['epoch'] = ['epoch', 't_0', 'Epoch', 'epoch_mjd']
327 altNames['H'] = ['H', 'magH', 'magHv', 'Hv', 'H_v']
328 altNames['g'] = ['g', 'phaseV', 'phase', 'gV', 'phase_g', 'G']
329 altNames['meanAnomaly'] = ['meanAnomaly', 'meanAnom', 'M', 'ma']
330 altNames['sed_filename'] = ['sed_filename', 'sed']
331 altNames['xdot'] = ['xdot', 'xDot']
332 altNames['ydot'] = ['ydot', 'yDot']
333 altNames['zdot'] = ['zdot', 'zDot']
335 # Update column names that match any of the alternatives above.
336 for name, alternatives in altNames.items():
337 intersection = list(set(alternatives) & set(ssoCols))
338 if len(intersection) > 1:
339 raise ValueError('Received too many possible matches to %s in orbit file %s'
340 % (name, orbitfile))
341 if len(intersection) == 1:
342 idx = ssoCols.index(intersection[0])
343 ssoCols[idx] = name
344 # Assign the new column names back to the orbits dataframe.
345 orbits.columns = ssoCols
346 # Validate and assign orbits to self.
347 self.setOrbits(orbits)
349 def updateOrbits(self, neworb):
350 """Update existing orbits with new values, leaving OrbitIds, H, g, and sed_filenames in place.
352 Example use: transform orbital parameters (using PyOrbEphemerides) and then replace original values.
353 Example use: propagate orbital parameters (using PyOrbEphemerides) and then replace original values.
355 Parameters
356 ----------
357 neworb: pandas.DataFrame
358 """
359 col_orig = ['objId', 'sed_filename']
360 new_order = ['objId'] + [n for n in neworb.columns] + ['sed_filename']
361 updated_orbits = neworb.join(self.orbits[col_orig])[new_order]
362 self.setOrbits(updated_orbits)