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# 

# LSST Data Management System 

# 

# Copyright 2008-2016 AURA/LSST. 

# 

# This product includes software developed by the 

# LSST Project (http://www.lsst.org/). 

# 

# This program is free software: you can redistribute it and/or modify 

# it under the terms of the GNU General Public License as published by 

# the Free Software Foundation, either version 3 of the License, or 

# (at your option) any later version. 

# 

# This program is distributed in the hope that it will be useful, 

# but WITHOUT ANY WARRANTY; without even the implied warranty of 

# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 

# GNU General Public License for more details. 

# 

# You should have received a copy of the LSST License Statement and 

# the GNU General Public License along with this program. If not, 

# see <https://www.lsstcorp.org/LegalNotices/>. 

# 

 

import math 

import os 

import tempfile 

import shutil 

import unittest 

import string 

from collections import Counter 

 

import astropy.time 

import numpy as np 

 

import lsst.geom 

import lsst.afw.table as afwTable 

import lsst.afw.geom as afwGeom 

import lsst.daf.persistence as dafPersist 

from lsst.meas.algorithms import (IngestIndexedReferenceTask, LoadIndexedReferenceObjectsTask, 

LoadIndexedReferenceObjectsConfig, getRefFluxField) 

from lsst.meas.algorithms import IndexerRegistry 

import lsst.utils 

 

OBS_TEST_DIR = lsst.utils.getPackageDir('obs_test') 

INPUT_DIR = os.path.join(OBS_TEST_DIR, "data", "input") 

 

REGENERATE_COMPARISON = False # Regenerate comparison data? 

 

 

def make_coord(ra, dec): 

"""Make an ICRS coord given its RA, Dec in degrees.""" 

return lsst.geom.SpherePoint(ra, dec, lsst.geom.degrees) 

 

 

class HtmIndexTestCase(lsst.utils.tests.TestCase): 

@classmethod 

def make_skyCatalog(cls, outPath, size=1000): 

np.random.seed(123) 

ident = np.arange(1, size+1, dtype=int) 

ra = np.random.random(size)*360. 

dec = np.degrees(np.arccos(2.*np.random.random(size) - 1.)) 

dec -= 90. 

ra_err = np.ones(size)*0.1 # arcsec 

dec_err = np.ones(size)*0.1 # arcsec 

a_mag = 16. + np.random.random(size)*4. 

a_mag_err = 0.01 + np.random.random(size)*0.2 

b_mag = 17. + np.random.random(size)*5. 

b_mag_err = 0.02 + np.random.random(size)*0.3 

is_photometric = np.random.randint(2, size=size) 

is_resolved = np.random.randint(2, size=size) 

is_variable = np.random.randint(2, size=size) 

extra_col1 = np.random.normal(size=size) 

extra_col2 = np.random.normal(1000., 100., size=size) 

# compute proper motion and PM error in arcseconds/year 

# and let the ingest task scale them to radians 

pm_amt_arcsec = cls.properMotionAmt.asArcseconds() 

pm_dir_rad = cls.properMotionDir.asRadians() 

pm_ra = np.ones(size)*pm_amt_arcsec*math.cos(pm_dir_rad) 

pm_dec = np.ones(size)*pm_amt_arcsec*math.sin(pm_dir_rad) 

pm_ra_err = np.ones(size)*cls.properMotionErr.asArcseconds()*abs(math.cos(pm_dir_rad)) 

pm_dec_err = np.ones(size)*cls.properMotionErr.asArcseconds()*abs(math.sin(pm_dir_rad)) 

unixtime = np.ones(size)*cls.epoch.unix 

 

def get_word(word_len): 

return "".join(np.random.choice([s for s in string.ascii_letters], word_len)) 

extra_col3 = np.array([get_word(num) for num in np.random.randint(11, size=size)]) 

 

dtype = np.dtype([('id', float), ('ra_icrs', float), ('dec_icrs', float), 

('ra_err', float), ('dec_err', float), ('a', float), 

('a_err', float), ('b', float), ('b_err', float), ('is_phot', int), 

('is_res', int), ('is_var', int), ('val1', float), ('val2', float), 

('val3', '|S11'), ('pm_ra', float), ('pm_dec', float), ('pm_ra_err', float), 

('pm_dec_err', float), ('unixtime', float)]) 

 

arr = np.array(list(zip(ident, ra, dec, ra_err, dec_err, a_mag, a_mag_err, b_mag, b_mag_err, 

is_photometric, is_resolved, is_variable, extra_col1, extra_col2, extra_col3, 

pm_ra, pm_dec, pm_ra_err, pm_dec_err, unixtime)), dtype=dtype) 

# write the data with full precision; this is not realistic for 

# real catalogs, but simplifies tests based on round tripped data 

saveKwargs = dict( 

header="id,ra_icrs,dec_icrs,ra_err,dec_err," 

"a,a_err,b,b_err,is_phot,is_res,is_var,val1,val2,val3," 

"pm_ra,pm_dec,pm_ra_err,pm_dec_err,unixtime", 

fmt=["%i", "%.15g", "%.15g", "%.15g", "%.15g", 

"%.15g", "%.15g", "%.15g", "%.15g", "%i", "%i", "%i", "%.15g", "%.15g", "%s", 

"%.15g", "%.15g", "%.15g", "%.15g", "%.15g"] 

) 

 

np.savetxt(outPath+"/ref.txt", arr, delimiter=",", **saveKwargs) 

np.savetxt(outPath+"/ref_test_delim.txt", arr, delimiter="|", **saveKwargs) 

return outPath+"/ref.txt", outPath+"/ref_test_delim.txt", arr 

 

@classmethod 

def setUpClass(cls): 

cls.outPath = tempfile.mkdtemp() 

cls.testCatPath = os.path.join(os.path.dirname(os.path.realpath(__file__)), "data", 

"testHtmIndex.fits") 

# arbitrary, but reasonable, amount of proper motion (angle/year) 

# and direction of proper motion 

cls.properMotionAmt = 3.0*lsst.geom.arcseconds 

cls.properMotionDir = 45*lsst.geom.degrees 

cls.properMotionErr = 1e-3*lsst.geom.arcseconds 

cls.epoch = astropy.time.Time(58206.861330339219, scale="tai", format="mjd") 

ret = cls.make_skyCatalog(cls.outPath) 

cls.skyCatalogFile, cls.skyCatalogFileDelim, cls.skyCatalog = ret 

cls.testRas = [210., 14.5, 93., 180., 286., 0.] 

cls.testDecs = [-90., -51., -30.1, 0., 27.3, 62., 90.] 

cls.searchRadius = 3. * lsst.geom.degrees 

cls.compCats = {} # dict of center coord: list of IDs of stars within cls.searchRadius of center 

cls.depth = 4 # gives a mean area of 20 deg^2 per pixel, roughly matching a 3 deg search radius 

 

config = IndexerRegistry['HTM'].ConfigClass() 

# Match on disk comparison file 

config.depth = cls.depth 

cls.indexer = IndexerRegistry['HTM'](config) 

for ra in cls.testRas: 

for dec in cls.testDecs: 

tupl = (ra, dec) 

cent = make_coord(*tupl) 

cls.compCats[tupl] = [] 

for rec in cls.skyCatalog: 

if make_coord(rec['ra_icrs'], rec['dec_icrs']).separation(cent) < cls.searchRadius: 

cls.compCats[tupl].append(rec['id']) 

 

cls.testRepoPath = cls.outPath+"/test_repo" 

config = cls.makeConfig(withMagErr=True, withRaDecErr=True, withPm=True, withPmErr=True) 

# To match on disk test data 

config.dataset_config.indexer.active.depth = cls.depth 

config.id_name = 'id' 

config.pm_scale = 1000.0 # arcsec/yr --> mas/yr 

IngestIndexedReferenceTask.parseAndRun(args=[INPUT_DIR, "--output", cls.testRepoPath, 

cls.skyCatalogFile], config=config) 

cls.defaultDatasetName = config.dataset_config.ref_dataset_name 

cls.testDatasetName = 'diff_ref_name' 

cls.testButler = dafPersist.Butler(cls.testRepoPath) 

os.symlink(os.path.join(cls.testRepoPath, 'ref_cats', cls.defaultDatasetName), 

os.path.join(cls.testRepoPath, 'ref_cats', cls.testDatasetName)) 

 

@classmethod 

def tearDownClass(cls): 

try: 

shutil.rmtree(cls.outPath) 

except Exception: 

print("WARNING: failed to remove temporary dir %r" % (cls.outPath,)) 

del cls.outPath 

del cls.skyCatalogFile 

del cls.skyCatalogFileDelim 

del cls.skyCatalog 

del cls.testRas 

del cls.testDecs 

del cls.searchRadius 

del cls.compCats 

del cls.testButler 

 

def testSanity(self): 

"""Sanity-check that compCats contains some entries with sources.""" 

numWithSources = 0 

for idList in self.compCats.values(): 

if len(idList) > 0: 

numWithSources += 1 

self.assertGreater(numWithSources, 0) 

 

def testAgainstPersisted(self): 

shardId = 2222 

dataset_name = IngestIndexedReferenceTask.ConfigClass().dataset_config.ref_dataset_name 

dataId = self.indexer.makeDataId(shardId, dataset_name) 

self.assertTrue(self.testButler.datasetExists('ref_cat', dataId)) 

refCat = self.testButler.get('ref_cat', dataId) 

189 ↛ 190line 189 didn't jump to line 190, because the condition on line 189 was never true if REGENERATE_COMPARISON: 

if os.path.exists(self.testCatPath): 

os.unlink(self.testCatPath) 

refCat.writeFits(self.testCatPath) 

self.fail("New comparison data written; unset REGENERATE_COMPARISON in order to proceed") 

 

ex1 = refCat.extract('*') 

testCat = afwTable.SimpleCatalog.readFits(self.testCatPath) 

 

ex2 = testCat.extract('*') 

self.assertEqual(set(ex1.keys()), set(ex2.keys())) 

for kk in ex1: 

np.testing.assert_array_equal(ex1[kk], ex2[kk]) 

 

@staticmethod 

def makeConfig(withMagErr=False, withRaDecErr=False, withPm=False, withPmErr=False, 

withParallax=False, withParallaxErr=False): 

"""Make a config for IngestIndexedReferenceTask 

 

This is primarily intended to simplify tests of config validation, 

so fields that are not validated are not set. 

However, it can calso be used to reduce boilerplate in other tests. 

""" 

config = IngestIndexedReferenceTask.ConfigClass() 

config.pm_scale = 1000.0 

config.ra_name = 'ra_icrs' 

config.dec_name = 'dec_icrs' 

config.mag_column_list = ['a', 'b'] 

 

if withMagErr: 

config.mag_err_column_map = {'a': 'a_err', 'b': 'b_err'} 

 

if withRaDecErr: 

config.ra_err_name = "ra_err" 

config.dec_err_name = "dec_err" 

 

if withPm: 

config.pm_ra_name = "pm_ra" 

config.pm_dec_name = "pm_dec" 

 

if withPmErr: 

config.pm_ra_err_name = "pm_ra_err" 

config.pm_dec_err_name = "pm_dec_err" 

 

if withParallax: 

config.parallax_name = "parallax" 

 

if withParallaxErr: 

config.parallax_err_name = "parallax_err" 

 

if withPm or withParallax: 

config.epoch_name = "unixtime" 

config.epoch_format = "unix" 

config.epoch_scale = "utc" 

 

return config 

 

def testValidateRaDecMag(self): 

config = self.makeConfig() 

config.validate() 

 

for name in ("ra_name", "dec_name", "mag_column_list"): 

with self.subTest(name=name): 

config = self.makeConfig() 

setattr(config, name, None) 

with self.assertRaises(ValueError): 

config.validate() 

 

def testValidateRaDecErr(self): 

config = self.makeConfig(withRaDecErr=True) 

config.validate() 

 

for name in ("ra_err_name", "dec_err_name"): 

with self.subTest(name=name): 

config = self.makeConfig(withRaDecErr=True) 

setattr(config, name, None) 

with self.assertRaises(ValueError): 

config.validate() 

 

def testValidateMagErr(self): 

config = self.makeConfig(withMagErr=True) 

config.validate() 

 

# test for missing names 

for name in config.mag_column_list: 

with self.subTest(name=name): 

config = self.makeConfig(withMagErr=True) 

del config.mag_err_column_map[name] 

with self.assertRaises(ValueError): 

config.validate() 

 

# test for incorrect names 

for name in config.mag_column_list: 

with self.subTest(name=name): 

config = self.makeConfig(withMagErr=True) 

config.mag_err_column_map["badName"] = config.mag_err_column_map[name] 

del config.mag_err_column_map[name] 

with self.assertRaises(ValueError): 

config.validate() 

 

def testValidatePm(self): 

basicNames = ["pm_ra_name", "pm_dec_name", "epoch_name", "epoch_format", "epoch_scale"] 

 

for withPmErr in (False, True): 

config = self.makeConfig(withPm=True, withPmErr=withPmErr) 

config.validate() 

del config 

 

if withPmErr: 

names = basicNames + ["pm_ra_err_name", "pm_dec_err_name"] 

else: 

names = basicNames 

for name in names: 

with self.subTest(name=name, withPmErr=withPmErr): 

config = self.makeConfig(withPm=True, withPmErr=withPmErr) 

setattr(config, name, None) 

with self.assertRaises(ValueError): 

config.validate() 

 

def testValidateParallax(self): 

basicNames = ["parallax_name", "epoch_name", "epoch_format", "epoch_scale"] 

 

for withParallaxErr in (False, True): 

config = self.makeConfig(withParallax=True, withParallaxErr=withParallaxErr) 

config.validate() 

del config 

 

if withParallaxErr: 

names = basicNames + ["parallax_err_name"] 

else: 

names = basicNames 

for name in names: 

with self.subTest(name=name, withParallaxErr=withParallaxErr): 

config = self.makeConfig(withParallax=True, withParallaxErr=withParallaxErr) 

setattr(config, name, None) 

if name == "parallax_name" and not withParallaxErr: 

# it is OK to omit parallax_name if no parallax_err_name 

config.validate() 

else: 

with self.assertRaises(ValueError): 

config.validate() 

 

def testIngest(self): 

"""Test IngestIndexedReferenceTask.""" 

# Test with multiple files and standard config 

config = self.makeConfig(withRaDecErr=True, withMagErr=True, withPm=True, withPmErr=True) 

IngestIndexedReferenceTask.parseAndRun( 

args=[INPUT_DIR, "--output", self.outPath+"/output_multifile", 

self.skyCatalogFile, self.skyCatalogFile], 

config=config) 

 

# Test with config overrides 

config2 = self.makeConfig(withRaDecErr=True, withMagErr=True, withPm=True, withPmErr=True) 

config2.ra_name = "ra" 

config2.dec_name = "dec" 

config2.dataset_config.ref_dataset_name = 'myrefcat' 

# Change the indexing depth to prove we can. 

# Smaller is better than larger because it makes fewer files. 

config2.dataset_config.indexer.active.depth = self.depth - 1 

config2.is_photometric_name = 'is_phot' 

config2.is_resolved_name = 'is_res' 

config2.is_variable_name = 'is_var' 

config2.id_name = 'id' 

config2.extra_col_names = ['val1', 'val2', 'val3'] 

config2.file_reader.header_lines = 1 

config2.file_reader.colnames = [ 

'id', 'ra', 'dec', 'ra_err', 'dec_err', 'a', 'a_err', 'b', 'b_err', 'is_phot', 

'is_res', 'is_var', 'val1', 'val2', 'val3', 'pm_ra', 'pm_dec', 'pm_ra_err', 

'pm_dec_err', 'unixtime', 

] 

config2.file_reader.delimiter = '|' 

# this also tests changing the delimiter 

IngestIndexedReferenceTask.parseAndRun( 

args=[INPUT_DIR, "--output", self.outPath+"/output_override", 

self.skyCatalogFileDelim], config=config2) 

 

# This location is known to have objects 

cent = make_coord(93.0, -90.0) 

 

# Test if we can get back the catalog with a non-standard dataset name 

butler = dafPersist.Butler(self.outPath+"/output_override") 

loaderConfig = LoadIndexedReferenceObjectsConfig() 

loaderConfig.ref_dataset_name = "myrefcat" 

loader = LoadIndexedReferenceObjectsTask(butler=butler, config=loaderConfig) 

cat = loader.loadSkyCircle(cent, self.searchRadius, filterName='a').refCat 

self.assertTrue(len(cat) > 0) 

self.assertTrue(cat.isContiguous()) 

 

# test that a catalog can be loaded even with a name not used for ingestion 

butler = dafPersist.Butler(self.testRepoPath) 

loaderConfig2 = LoadIndexedReferenceObjectsConfig() 

loaderConfig2.ref_dataset_name = self.testDatasetName 

loader = LoadIndexedReferenceObjectsTask(butler=butler, config=loaderConfig2) 

cat = loader.loadSkyCircle(cent, self.searchRadius, filterName='a').refCat 

self.assertTrue(len(cat) > 0) 

self.assertTrue(cat.isContiguous()) 

 

def testLoadIndexedReferenceConfig(self): 

"""Make sure LoadIndexedReferenceConfig has needed fields.""" 

""" 

Including at least one from the base class LoadReferenceObjectsConfig 

""" 

config = LoadIndexedReferenceObjectsConfig() 

self.assertEqual(config.ref_dataset_name, "cal_ref_cat") 

self.assertEqual(config.defaultFilter, "") 

 

def testLoadSkyCircle(self): 

"""Test LoadIndexedReferenceObjectsTask.loadSkyCircle with default config.""" 

loader = LoadIndexedReferenceObjectsTask(butler=self.testButler) 

for tupl, idList in self.compCats.items(): 

cent = make_coord(*tupl) 

lcat = loader.loadSkyCircle(cent, self.searchRadius, filterName='a') 

self.assertTrue(lcat.refCat.isContiguous()) 

self.assertFalse("camFlux" in lcat.refCat.schema) 

self.assertEqual(Counter(lcat.refCat['id']), Counter(idList)) 

if len(lcat.refCat) > 0: 

# make sure there are no duplicate ids 

self.assertEqual(len(set(Counter(lcat.refCat['id']).values())), 1) 

self.assertEqual(len(set(Counter(idList).values())), 1) 

for suffix in ("x", "y"): 

self.assertTrue(np.all(np.isnan(lcat.refCat["centroid_%s" % (suffix,)]))) 

self.assertFalse(np.any(lcat.refCat["hasCentroid"])) 

else: 

self.assertEqual(len(idList), 0) 

 

def testLoadPixelBox(self): 

"""Test LoadIndexedReferenceObjectsTask.loadPixelBox with default config.""" 

loader = LoadIndexedReferenceObjectsTask(butler=self.testButler) 

numFound = 0 

for tupl, idList in self.compCats.items(): 

cent = make_coord(*tupl) 

bbox = lsst.geom.Box2I(lsst.geom.Point2I(30, -5), lsst.geom.Extent2I(1000, 1004)) # arbitrary 

ctr_pix = lsst.geom.Box2D(bbox).getCenter() 

# catalog is sparse, so set pixel scale such that bbox encloses region 

# used to generate compCats 

pixel_scale = 2*self.searchRadius/max(bbox.getHeight(), bbox.getWidth()) 

cdMatrix = afwGeom.makeCdMatrix(scale=pixel_scale) 

wcs = afwGeom.makeSkyWcs(crval=cent, crpix=ctr_pix, cdMatrix=cdMatrix) 

result = loader.loadPixelBox(bbox=bbox, wcs=wcs, filterName="a") 

self.assertFalse("camFlux" in result.refCat.schema) 

self.assertGreaterEqual(len(result.refCat), len(idList)) 

numFound += len(result.refCat) 

self.assertGreater(numFound, 0) 

 

def testDefaultFilterAndFilterMap(self): 

"""Test defaultFilter and filterMap parameters of LoadIndexedReferenceObjectsConfig.""" 

config = LoadIndexedReferenceObjectsConfig() 

config.defaultFilter = "b" 

config.filterMap = {"aprime": "a"} 

loader = LoadIndexedReferenceObjectsTask(butler=self.testButler, config=config) 

439 ↛ exitline 439 didn't return from function 'testDefaultFilterAndFilterMap', because the loop on line 439 didn't complete for tupl, idList in self.compCats.items(): 

cent = make_coord(*tupl) 

lcat = loader.loadSkyCircle(cent, self.searchRadius) 

self.assertEqual(lcat.fluxField, "camFlux") 

443 ↛ 439line 443 didn't jump to line 439, because the condition on line 443 was never false if len(idList) > 0: 

defFluxFieldName = getRefFluxField(lcat.refCat.schema, None) 

self.assertTrue(defFluxFieldName in lcat.refCat.schema) 

aprimeFluxFieldName = getRefFluxField(lcat.refCat.schema, "aprime") 

self.assertTrue(aprimeFluxFieldName in lcat.refCat.schema) 

break # just need one test 

 

def testProperMotion(self): 

"""Test proper motion correction""" 

center = make_coord(93.0, -90.0) 

loader = LoadIndexedReferenceObjectsTask(butler=self.testButler) 

references = loader.loadSkyCircle(center, self.searchRadius, filterName='a').refCat 

original = references.copy(True) 

 

# Zero epoch change --> no proper motion correction (except minor numerical effects) 

loader.applyProperMotions(references, self.epoch) 

self.assertFloatsAlmostEqual(references["coord_ra"], original["coord_ra"], rtol=1.0e-14) 

self.assertFloatsAlmostEqual(references["coord_dec"], original["coord_dec"], rtol=1.0e-14) 

self.assertFloatsEqual(references["coord_raErr"], original["coord_raErr"]) 

self.assertFloatsEqual(references["coord_decErr"], original["coord_decErr"]) 

 

# One year difference 

loader.applyProperMotions(references, self.epoch + 1.0*astropy.units.yr) 

self.assertFloatsEqual(references["pm_raErr"], original["pm_raErr"]) 

self.assertFloatsEqual(references["pm_decErr"], original["pm_decErr"]) 

for orig, ref in zip(original, references): 

self.assertAnglesAlmostEqual(orig.getCoord().separation(ref.getCoord()), 

self.properMotionAmt, maxDiff=1.0e-6*lsst.geom.arcseconds) 

self.assertAnglesAlmostEqual(orig.getCoord().bearingTo(ref.getCoord()), 

self.properMotionDir, maxDiff=1.0e-4*lsst.geom.arcseconds) 

predictedRaErr = np.hypot(original["coord_raErr"], original["pm_raErr"]) 

predictedDecErr = np.hypot(original["coord_decErr"], original["pm_decErr"]) 

self.assertFloatsAlmostEqual(references["coord_raErr"], predictedRaErr) 

self.assertFloatsAlmostEqual(references["coord_decErr"], predictedDecErr) 

 

 

class TestMemory(lsst.utils.tests.MemoryTestCase): 

pass 

 

 

def setup_module(module): 

lsst.utils.tests.init() 

 

 

487 ↛ 488line 487 didn't jump to line 488, because the condition on line 487 was never trueif __name__ == "__main__": 

lsst.utils.tests.init() 

unittest.main()