Coverage for python/lsst/obs/base/formatters/fitsExposure.py : 17%

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1# This file is part of obs_base.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (http://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <http://www.gnu.org/licenses/>.
22__all__ = ("FitsExposureFormatter", "FitsImageFormatter", "FitsMaskFormatter",
23 "FitsMaskedImageFormatter")
25from astro_metadata_translator import fix_header
26from lsst.daf.base import PropertySet
27from lsst.daf.butler import Formatter
28# Do not use ExposureFitsReader.readMetadata because that strips
29# out lots of headers and there is no way to recover them
30from lsst.afw.fits import readMetadata
31from lsst.afw.image import ExposureFitsReader, ImageFitsReader, MaskFitsReader, MaskedImageFitsReader
32# Needed for ApCorrMap to resolve properly
33from lsst.afw.math import BoundedField # noqa: F401
36class FitsExposureFormatter(Formatter):
37 """Interface for reading and writing Exposures to and from FITS files.
39 This Formatter supports write recipes.
41 Each ``FitsExposureFormatter`` recipe for FITS compression should
42 define ``image``, ``mask`` and ``variance`` entries, each of which may
43 contain ``compression`` and ``scaling`` entries. Defaults will be
44 provided for any missing elements under ``compression`` and
45 ``scaling``.
47 The allowed entries under ``compression`` are:
49 * ``algorithm`` (`str`): compression algorithm to use
50 * ``rows`` (`int`): number of rows per tile (0 = entire dimension)
51 * ``columns`` (`int`): number of columns per tile (0 = entire dimension)
52 * ``quantizeLevel`` (`float`): cfitsio quantization level
54 The allowed entries under ``scaling`` are:
56 * ``algorithm`` (`str`): scaling algorithm to use
57 * ``bitpix`` (`int`): bits per pixel (0,8,16,32,64,-32,-64)
58 * ``fuzz`` (`bool`): fuzz the values when quantising floating-point values?
59 * ``seed`` (`int`): seed for random number generator when fuzzing
60 * ``maskPlanes`` (`list` of `str`): mask planes to ignore when doing
61 statistics
62 * ``quantizeLevel`` (`float`): divisor of the standard deviation for
63 ``STDEV_*`` scaling
64 * ``quantizePad`` (`float`): number of stdev to allow on the low side (for
65 ``STDEV_POSITIVE``/``NEGATIVE``)
66 * ``bscale`` (`float`): manually specified ``BSCALE``
67 (for ``MANUAL`` scaling)
68 * ``bzero`` (`float`): manually specified ``BSCALE``
69 (for ``MANUAL`` scaling)
71 A very simple example YAML recipe:
73 .. code-block:: yaml
75 lsst.obs.base.fitsExposureFormatter.FitsExposureFormatter:
76 default:
77 image: &default
78 compression:
79 algorithm: GZIP_SHUFFLE
80 mask: *default
81 variance: *default
83 """
84 supportedExtensions = frozenset({".fits", ".fits.gz", ".fits.fz", ".fz", ".fit"})
85 extension = ".fits"
86 _metadata = None
87 supportedWriteParameters = frozenset({"recipe"})
88 _readerClass = ExposureFitsReader
90 unsupportedParameters = {}
91 """Support all parameters."""
93 @property
94 def metadata(self):
95 """The metadata read from this file. It will be stripped as
96 components are extracted from it
97 (`lsst.daf.base.PropertyList`).
98 """
99 if self._metadata is None:
100 self._metadata = self.readMetadata()
101 return self._metadata
103 def readMetadata(self):
104 """Read all header metadata directly into a PropertyList.
106 Returns
107 -------
108 metadata : `~lsst.daf.base.PropertyList`
109 Header metadata.
110 """
111 md = readMetadata(self.fileDescriptor.location.path)
112 fix_header(md)
113 return md
115 def stripMetadata(self):
116 """Remove metadata entries that are parsed into components.
118 This is only called when just the metadata is requested; stripping
119 entries there forces code that wants other components to ask for those
120 components directly rather than trying to extract them from the
121 metadata manually, which is fragile. This behavior is an intentional
122 change from Gen2.
124 Parameters
125 ----------
126 metadata : `~lsst.daf.base.PropertyList`
127 Header metadata, to be modified in-place.
128 """
129 # TODO: make sure this covers everything, by delegating to something
130 # that doesn't yet exist in afw.image.ExposureInfo.
131 from lsst.afw.image import bboxFromMetadata
132 from lsst.afw.geom import makeSkyWcs
134 # Protect against the metadata being missing
135 try:
136 bboxFromMetadata(self.metadata) # always strips
137 except LookupError:
138 pass
139 try:
140 makeSkyWcs(self.metadata, strip=True)
141 except Exception:
142 pass
144 def readComponent(self, component, parameters=None):
145 """Read a component held by the Exposure.
147 Parameters
148 ----------
149 component : `str`, optional
150 Component to read from the file.
151 parameters : `dict`, optional
152 If specified, a dictionary of slicing parameters that
153 overrides those in ``fileDescriptor``.
155 Returns
156 -------
157 obj : component-dependent
158 In-memory component object.
160 Raises
161 ------
162 KeyError
163 Raised if the requested component cannot be handled.
164 """
166 # Metadata is handled explicitly elsewhere
167 componentMap = {'wcs': ('readWcs', False),
168 'coaddInputs': ('readCoaddInputs', False),
169 'psf': ('readPsf', False),
170 'image': ('readImage', True),
171 'mask': ('readMask', True),
172 'variance': ('readVariance', True),
173 'photoCalib': ('readPhotoCalib', False),
174 'bbox': ('readBBox', True),
175 'dimensions': ('readBBox', True),
176 'xy0': ('readXY0', True),
177 # TODO: deprecate in DM-27170, remove in DM-27177
178 'filter': ('readFilter', False),
179 # TODO: deprecate in DM-27177, remove in DM-27811
180 'filterLabel': ('readFilterLabel', False),
181 'validPolygon': ('readValidPolygon', False),
182 'apCorrMap': ('readApCorrMap', False),
183 'visitInfo': ('readVisitInfo', False),
184 'transmissionCurve': ('readTransmissionCurve', False),
185 'detector': ('readDetector', False),
186 'extras': ('readExtraComponents', False),
187 'exposureInfo': ('readExposureInfo', False),
188 }
189 method, hasParams = componentMap.get(component, (None, False))
191 if method:
192 # This reader can read standalone Image/Mask files as well
193 # when dealing with components.
194 reader = self._readerClass(self.fileDescriptor.location.path)
195 caller = getattr(reader, method, None)
197 if caller:
198 if parameters is None:
199 parameters = self.fileDescriptor.parameters
200 if parameters is None:
201 parameters = {}
202 self.fileDescriptor.storageClass.validateParameters(parameters)
204 if hasParams and parameters:
205 thisComponent = caller(**parameters)
206 else:
207 thisComponent = caller()
208 if component == "dimensions" and thisComponent is not None:
209 thisComponent = thisComponent.getDimensions()
210 return thisComponent
211 else:
212 raise KeyError(f"Unknown component requested: {component}")
214 def readFull(self, parameters=None):
215 """Read the full Exposure object.
217 Parameters
218 ----------
219 parameters : `dict`, optional
220 If specified a dictionary of slicing parameters that overrides
221 those in ``fileDescriptor``.
223 Returns
224 -------
225 exposure : `~lsst.afw.image.Exposure`
226 Complete in-memory exposure.
227 """
228 fileDescriptor = self.fileDescriptor
229 if parameters is None:
230 parameters = fileDescriptor.parameters
231 if parameters is None:
232 parameters = {}
233 fileDescriptor.storageClass.validateParameters(parameters)
234 reader = self._readerClass(fileDescriptor.location.path)
235 return reader.read(**parameters)
237 def read(self, component=None):
238 """Read data from a file.
240 Parameters
241 ----------
242 component : `str`, optional
243 Component to read from the file. Only used if the `StorageClass`
244 for reading differed from the `StorageClass` used to write the
245 file.
247 Returns
248 -------
249 inMemoryDataset : `object`
250 The requested data as a Python object. The type of object
251 is controlled by the specific formatter.
253 Raises
254 ------
255 ValueError
256 Component requested but this file does not seem to be a concrete
257 composite.
258 KeyError
259 Raised when parameters passed with fileDescriptor are not
260 supported.
261 """
262 fileDescriptor = self.fileDescriptor
263 if fileDescriptor.readStorageClass != fileDescriptor.storageClass:
264 if component == "metadata":
265 self.stripMetadata()
266 return self.metadata
267 elif component is not None:
268 return self.readComponent(component)
269 else:
270 raise ValueError("Storage class inconsistency ({} vs {}) but no"
271 " component requested".format(fileDescriptor.readStorageClass.name,
272 fileDescriptor.storageClass.name))
273 return self.readFull()
275 def write(self, inMemoryDataset):
276 """Write a Python object to a file.
278 Parameters
279 ----------
280 inMemoryDataset : `object`
281 The Python object to store.
282 """
283 # Update the location with the formatter-preferred file extension
284 self.fileDescriptor.location.updateExtension(self.extension)
285 outputPath = self.fileDescriptor.location.path
287 # check to see if we have a recipe requested
288 recipeName = self.writeParameters.get("recipe")
289 recipe = self.getImageCompressionSettings(recipeName)
290 if recipe:
291 # Can not construct a PropertySet from a hierarchical
292 # dict but can update one.
293 ps = PropertySet()
294 ps.update(recipe)
295 inMemoryDataset.writeFitsWithOptions(outputPath, options=ps)
296 else:
297 inMemoryDataset.writeFits(outputPath)
299 def getImageCompressionSettings(self, recipeName):
300 """Retrieve the relevant compression settings for this recipe.
302 Parameters
303 ----------
304 recipeName : `str`
305 Label associated with the collection of compression parameters
306 to select.
308 Returns
309 -------
310 settings : `dict`
311 The selected settings.
312 """
313 # if no recipe has been provided and there is no default
314 # return immediately
315 if not recipeName:
316 if "default" not in self.writeRecipes:
317 return {}
318 recipeName = "default"
320 if recipeName not in self.writeRecipes:
321 raise RuntimeError(f"Unrecognized recipe option given for compression: {recipeName}")
323 recipe = self.writeRecipes[recipeName]
325 # Set the seed based on dataId
326 seed = hash(tuple(self.dataId.items())) % 2**31
327 for plane in ("image", "mask", "variance"):
328 if plane in recipe and "scaling" in recipe[plane]:
329 scaling = recipe[plane]["scaling"]
330 if "seed" in scaling and scaling["seed"] == 0:
331 scaling["seed"] = seed
333 return recipe
335 @classmethod
336 def validateWriteRecipes(cls, recipes):
337 """Validate supplied recipes for this formatter.
339 The recipes are supplemented with default values where appropriate.
341 TODO: replace this custom validation code with Cerberus (DM-11846)
343 Parameters
344 ----------
345 recipes : `dict`
346 Recipes to validate. Can be empty dict or `None`.
348 Returns
349 -------
350 validated : `dict`
351 Validated recipes. Returns what was given if there are no
352 recipes listed.
354 Raises
355 ------
356 RuntimeError
357 Raised if validation fails.
358 """
359 # Schemas define what should be there, and the default values (and by
360 # the default value, the expected type).
361 compressionSchema = {
362 "algorithm": "NONE",
363 "rows": 1,
364 "columns": 0,
365 "quantizeLevel": 0.0,
366 }
367 scalingSchema = {
368 "algorithm": "NONE",
369 "bitpix": 0,
370 "maskPlanes": ["NO_DATA"],
371 "seed": 0,
372 "quantizeLevel": 4.0,
373 "quantizePad": 5.0,
374 "fuzz": True,
375 "bscale": 1.0,
376 "bzero": 0.0,
377 }
379 if not recipes:
380 # We can not insist on recipes being specified
381 return recipes
383 def checkUnrecognized(entry, allowed, description):
384 """Check to see if the entry contains unrecognised keywords"""
385 unrecognized = set(entry) - set(allowed)
386 if unrecognized:
387 raise RuntimeError(
388 f"Unrecognized entries when parsing image compression recipe {description}: "
389 f"{unrecognized}")
391 validated = {}
392 for name in recipes:
393 checkUnrecognized(recipes[name], ["image", "mask", "variance"], name)
394 validated[name] = {}
395 for plane in ("image", "mask", "variance"):
396 checkUnrecognized(recipes[name][plane], ["compression", "scaling"],
397 f"{name}->{plane}")
399 np = {}
400 validated[name][plane] = np
401 for settings, schema in (("compression", compressionSchema),
402 ("scaling", scalingSchema)):
403 np[settings] = {}
404 if settings not in recipes[name][plane]:
405 for key in schema:
406 np[settings][key] = schema[key]
407 continue
408 entry = recipes[name][plane][settings]
409 checkUnrecognized(entry, schema.keys(), f"{name}->{plane}->{settings}")
410 for key in schema:
411 value = type(schema[key])(entry[key]) if key in entry else schema[key]
412 np[settings][key] = value
413 return validated
416class FitsImageFormatter(FitsExposureFormatter):
417 """Specialisation for `~lsst.afw.image.Image` reading.
418 """
420 _readerClass = ImageFitsReader
423class FitsMaskFormatter(FitsExposureFormatter):
424 """Specialisation for `~lsst.afw.image.Mask` reading.
425 """
427 _readerClass = MaskFitsReader
430class FitsMaskedImageFormatter(FitsExposureFormatter):
431 """Specialisation for `~lsst.afw.image.MaskedImage` reading.
432 """
434 _readerClass = MaskedImageFitsReader