Classes | |
| class | AbstractStamp |
| class | Stamp |
| class | Stamps |
| class | StampsBase |
Functions | |
| writeFits (filename, stamps, metadata, type_name, write_mask, write_variance, write_archive=False) | |
| readFitsWithOptions (filename, stamp_factory, options) | |
| _default_position () | |
Detailed Description
Collection of small images (stamps).
Function Documentation
◆ _default_position()
|
protected |
◆ readFitsWithOptions()
| lsst.meas.algorithms.stamps.readFitsWithOptions | ( | filename, | |
| stamp_factory, | |||
| options ) |
Read stamps from FITS file, allowing for only a subregion of the stamps
to be read.
Parameters
----------
filename : `str`
A string indicating the file to read
stamp_factory : classmethod
A factory function defined on a dataclass for constructing
stamp objects a la `~lsst.meas.algorithm.Stamp`
options : `PropertyList` or `dict`
A collection of parameters. If it contains a bounding box
(``bbox`` key), or if certain other keys (``llcX``, ``llcY``,
``width``, ``height``) are available for one to be constructed,
the bounding box is passed to the ``FitsReader`` in order to
return a sub-image.
Returns
-------
stamps : `list` of dataclass objects like `Stamp`, PropertyList
A tuple of a list of `Stamp`-like objects
metadata : `PropertyList`
The metadata
Notes
-----
The data are read using the data type expected by the
`~lsst.afw.image.MaskedImage` class attached to the `AbstractStamp`
dataclass associated with the factory method.
Definition at line 100 of file stamps.py.
100def readFitsWithOptions(filename, stamp_factory, options):
101 """Read stamps from FITS file, allowing for only a subregion of the stamps
102 to be read.
103
104 Parameters
105 ----------
106 filename : `str`
107 A string indicating the file to read
108 stamp_factory : classmethod
109 A factory function defined on a dataclass for constructing
110 stamp objects a la `~lsst.meas.algorithm.Stamp`
111 options : `PropertyList` or `dict`
112 A collection of parameters. If it contains a bounding box
113 (``bbox`` key), or if certain other keys (``llcX``, ``llcY``,
114 ``width``, ``height``) are available for one to be constructed,
115 the bounding box is passed to the ``FitsReader`` in order to
116 return a sub-image.
117
118 Returns
119 -------
120 stamps : `list` of dataclass objects like `Stamp`, PropertyList
121 A tuple of a list of `Stamp`-like objects
122 metadata : `PropertyList`
123 The metadata
124
125 Notes
126 -----
127 The data are read using the data type expected by the
128 `~lsst.afw.image.MaskedImage` class attached to the `AbstractStamp`
129 dataclass associated with the factory method.
130 """
131 # extract necessary info from metadata
132 metadata = readMetadata(filename, hdu=0)
133 nStamps = metadata["N_STAMPS"]
134 has_archive = metadata["HAS_ARCHIVE"]
135 if has_archive:
136 archive_ids = metadata.getArray("ARCHIVE_IDS")
137 with Fits(filename, "r") as f:
138 nExtensions = f.countHdus()
139 # check if a bbox was provided
140 kwargs = {}
141 if options:
142 # gen3 API
143 if "bbox" in options.keys():
144 kwargs["bbox"] = options["bbox"]
145 # gen2 API
146 elif "llcX" in options.keys():
147 llcX = options["llcX"]
148 llcY = options["llcY"]
149 width = options["width"]
150 height = options["height"]
151 bbox = Box2I(Point2I(llcX, llcY), Extent2I(width, height))
152 kwargs["bbox"] = bbox
153 stamp_parts = {}
154
155 # Determine the dtype from the factory. This allows a Stamp class
156 # to be defined in terms of MaskedImageD or MaskedImageI without
157 # forcing everything to floats.
158 masked_image_cls = None
159 for stamp_field in fields(stamp_factory.__self__):
160 if issubclass(stamp_field.type, MaskedImage):
161 masked_image_cls = stamp_field.type
162 break
163 else:
164 raise RuntimeError("Stamp factory does not use MaskedImage.")
165 default_dtype = np.dtype(masked_image_cls.dtype)
166 variance_dtype = np.dtype(np.float32) # Variance is always the same type.
167
168 # We need to be careful because nExtensions includes the primary HDU.
169 stamp_metadata = []
170 for idx in range(nExtensions - 1):
171 dtype = None
172 _metadata = copy.copy(metadata)
173 md = readMetadata(filename, hdu=idx + 1)
174 _metadata.update(md)
175 stamp_metadata.append(_metadata)
176 # Skip binary tables that aren't images or archives.
177 if md["XTENSION"] == "BINTABLE" and not ("ZIMAGE" in md and md["ZIMAGE"]):
178 if md["EXTNAME"] != "ARCHIVE_INDEX":
179 continue
180 if md["EXTNAME"] in ("IMAGE", "VARIANCE"):
181 reader = ImageFitsReader(filename, hdu=idx + 1)
182 if md["EXTNAME"] == "VARIANCE":
183 dtype = variance_dtype
184 else:
185 dtype = default_dtype
186 elif md["EXTNAME"] == "MASK":
187 reader = MaskFitsReader(filename, hdu=idx + 1)
188 elif md["EXTNAME"] == "ARCHIVE_INDEX":
189 f.setHdu(idx + 1)
190 archive = InputArchive.readFits(f)
191 continue
192 elif md["EXTTYPE"] == "ARCHIVE_DATA":
193 continue
194 else:
195 raise ValueError(f"Unknown extension type: {md['EXTNAME']}")
196 stamp_parts.setdefault(md["EXTVER"], {})[md["EXTNAME"].lower()] = reader.read(dtype=dtype,
197 **kwargs)
198 if len(stamp_parts) != nStamps:
199 raise ValueError(
200 f"Number of stamps read ({len(stamp_parts)}) does not agree with the "
201 f"number of stamps recorded in the metadata ({nStamps})."
202 )
203 # construct stamps themselves
204 stamps = []
205 for k in range(nStamps):
206 # Need to increment by one since EXTVER starts at 1
207 maskedImage = masked_image_cls(**stamp_parts[k + 1])
208 archive_element = archive.get(archive_ids[k]) if has_archive else None
209 stamps.append(stamp_factory(maskedImage, stamp_metadata[k], k, archive_element))
210
211 return stamps, metadata
212
213
214@dataclass
◆ writeFits()
| lsst.meas.algorithms.stamps.writeFits | ( | filename, | |
| stamps, | |||
| metadata, | |||
| type_name, | |||
| write_mask, | |||
| write_variance, | |||
| write_archive = False ) |
Write a single FITS file containing all stamps.
Parameters
----------
filename : `str`
A string indicating the output filename
stamps : iterable of `BaseStamp`
An iterable of Stamp objects
metadata : `PropertyList`
A collection of key, value metadata pairs to be
written to the primary header
type_name : `str`
Python type name of the StampsBase subclass to use
write_mask : `bool`
Write the mask data to the output file?
write_variance : `bool`
Write the variance data to the output file?
write_archive : `bool`, optional
Write an archive to store Persistables along with each stamp?
Default: ``False``.
Definition at line 41 of file stamps.py.
41def writeFits(filename, stamps, metadata, type_name, write_mask, write_variance, write_archive=False):
42 """Write a single FITS file containing all stamps.
43
44 Parameters
45 ----------
46 filename : `str`
47 A string indicating the output filename
48 stamps : iterable of `BaseStamp`
49 An iterable of Stamp objects
50 metadata : `PropertyList`
51 A collection of key, value metadata pairs to be
52 written to the primary header
53 type_name : `str`
54 Python type name of the StampsBase subclass to use
55 write_mask : `bool`
56 Write the mask data to the output file?
57 write_variance : `bool`
58 Write the variance data to the output file?
59 write_archive : `bool`, optional
60 Write an archive to store Persistables along with each stamp?
61 Default: ``False``.
62 """
63 metadata["HAS_MASK"] = write_mask
64 metadata["HAS_VARIANCE"] = write_variance
65 metadata["HAS_ARCHIVE"] = write_archive
66 metadata["N_STAMPS"] = len(stamps)
67 metadata["STAMPCLS"] = type_name
68 # Record version number in case of future code changes
69 metadata["VERSION"] = 1
70 # create primary HDU with global metadata
71 fitsFile = Fits(filename, "w")
72 fitsFile.createEmpty()
73 # Store Persistables in an OutputArchive and write it
74 if write_archive:
75 oa = OutputArchive()
76 archive_ids = [oa.put(stamp.archive_element) for stamp in stamps]
77 metadata["ARCHIVE_IDS"] = archive_ids
78 fitsFile.writeMetadata(metadata)
79 oa.writeFits(fitsFile)
80 else:
81 fitsFile.writeMetadata(metadata)
82 fitsFile.closeFile()
83 # add all pixel data optionally writing mask and variance information
84 for i, stamp in enumerate(stamps):
85 metadata = PropertyList()
86 # EXTVER should be 1-based, the index from enumerate is 0-based
87 metadata.update({"EXTVER": i + 1, "EXTNAME": "IMAGE"})
88 stamp.stamp_im.getImage().writeFits(filename, metadata=metadata, mode="a")
89 if write_mask:
90 metadata = PropertyList()
91 metadata.update({"EXTVER": i + 1, "EXTNAME": "MASK"})
92 stamp.stamp_im.getMask().writeFits(filename, metadata=metadata, mode="a")
93 if write_variance:
94 metadata = PropertyList()
95 metadata.update({"EXTVER": i + 1, "EXTNAME": "VARIANCE"})
96 stamp.stamp_im.getVariance().writeFits(filename, metadata=metadata, mode="a")
97 return None
98
99
Generated on Mon Sep 22 2025 07:01:54 for LSST Applications by
1.13.2