lsst.pipe.tasks g4a6547c0d5+de68eba77a
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read_curated_calibs.py
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2from lsst.ip.isr import (Linearizer, CrosstalkCalib, Defects, BrighterFatterKernel)
3
4import os
5import glob
6import dateutil.parser
7
8
9def read_one_chip(root, chip_name, chip_id):
10 """Read data for a particular sensor from the standard format at a particular root.
11
12 Parameters
13 ----------
14 root : `str`
15 Path to the top level of the data tree. This is expected to hold directories
16 named after the sensor names. They are expected to be lower case.
17 chip_name : `str`
18 The name of the sensor for which to read data.
19 chip_id : `int`
20 The identifier for the sensor in question.
21
22 Returns
23 -------
24 `dict`
25 A dictionary of objects constructed from the appropriate factory class.
26 The key is the validity start time as a `datetime` object.
27 """
28 factory_map = {'qe_curve': Curve, 'defects': Defects, 'linearizer': Linearizer,
29 'crosstalk': CrosstalkCalib, 'bfk': BrighterFatterKernel}
30 files = []
31 extensions = (".ecsv", ".yaml")
32 for ext in extensions:
33 files.extend(glob.glob(os.path.join(root, chip_name, f"*{ext}")))
34 parts = os.path.split(root)
35 instrument = os.path.split(parts[0])[1] # convention is that these reside at <instrument>/<data_name>
36 data_name = parts[1]
37 if data_name not in factory_map:
38 raise ValueError(f"Unknown calibration data type, '{data_name}' found. "
39 f"Only understand {','.join(k for k in factory_map)}")
40 factory = factory_map[data_name]
41 data_dict = {}
42 for f in files:
43 date_str = os.path.splitext(os.path.basename(f))[0]
44 valid_start = dateutil.parser.parse(date_str)
45 data_dict[valid_start] = factory.readText(f)
46 check_metadata(data_dict[valid_start], valid_start, instrument, chip_id, f, data_name)
47 return data_dict, data_name
48
49
50def check_metadata(obj, valid_start, instrument, chip_id, filepath, data_name):
51 """Check that the metadata is complete and self consistent
52
53 Parameters
54 ----------
55 obj : object of same type as the factory
56 Object to retrieve metadata from in order to compare with
57 metadata inferred from the path.
58 valid_start : `datetime`
59 Start of the validity range for data
60 instrument : `str`
61 Name of the instrument in question
62 chip_id : `int`
63 Identifier of the sensor in question
64 filepath : `str`
65 Path of the file read to construct the data
66 data_name : `str`
67 Name of the type of data being read
68
69 Returns
70 -------
71 None
72
73 Raises
74 ------
75 ValueError
76 If the metadata from the path and the metadata encoded
77 in the path do not match for any reason.
78 """
79 md = obj.getMetadata()
80 finst = md['INSTRUME']
81 fchip_id = md['DETECTOR']
82 fdata_name = md['OBSTYPE']
83 if not ((finst.lower(), int(fchip_id), fdata_name.lower())
84 == (instrument.lower(), chip_id, data_name.lower())):
85 raise ValueError(f"Path and file metadata do not agree:\n"
86 f"Path metadata: {instrument} {chip_id} {data_name}\n"
87 f"File metadata: {finst} {fchip_id} {fdata_name}\n"
88 f"File read from : %s\n"%(filepath)
89 )
90
91
92def read_all(root, camera):
93 """Read all data from the standard format at a particular root.
94
95 Parameters
96 ----------
97 root : `str`
98 Path to the top level of the data tree. This is expected to hold directories
99 named after the sensor names. They are expected to be lower case.
101 The camera that goes with the data being read.
102
103 Returns
104 -------
105 dict
106 A dictionary of dictionaries of objects constructed with the appropriate factory class.
107 The first key is the sensor name lowered, and the second is the validity
108 start time as a `datetime` object.
109
110 Notes
111 -----
112 Each leaf object in the constructed dictionary has metadata associated with it.
113 The detector ID may be retrieved from the DETECTOR entry of that metadata.
114 """
115 root = os.path.normpath(root)
116 dirs = os.listdir(root) # assumes all directories contain data
117 dirs = [d for d in dirs if os.path.isdir(os.path.join(root, d))]
118 data_by_chip = {}
119 name_map = {det.getName().lower(): det.getName() for
120 det in camera} # we assume the directories have been lowered
121
122 if not dirs:
123 raise RuntimeError(f"No data found on path {root}")
124
125 calib_types = set()
126 for d in dirs:
127 chip_name = os.path.basename(d)
128 # Give informative error message if the detector name is not known
129 # rather than a simple KeyError
130 if chip_name not in name_map:
131 detectors = [det for det in camera.getNameIter()]
132 max_detectors = 10
133 note_str = "knows"
134 if len(detectors) > max_detectors:
135 # report example subset
136 note_str = "examples"
137 detectors = detectors[:max_detectors]
138 raise RuntimeError(f"Detector {chip_name} not known to supplied camera "
139 f"{camera.getName()} ({note_str}: {','.join(detectors)})")
140 chip_id = camera[name_map[chip_name]].getId()
141 data_by_chip[chip_name], calib_type = read_one_chip(root, chip_name, chip_id)
142 calib_types.add(calib_type)
143 if len(calib_types) != 1: # set.add(None) has length 1 so None is OK here.
144 raise ValueError(f'Error mixing calib types: {calib_types}')
145
146 no_data = all([v == {} for v in data_by_chip.values()])
147 if no_data:
148 raise RuntimeError("No data to ingest")
149
150 return data_by_chip, calib_type
def check_metadata(obj, valid_start, instrument, chip_id, filepath, data_name)
def read_one_chip(root, chip_name, chip_id)