def test_download_data(self, logger, datacoveragepath):
"""
To run this test --runrest it needed when calling pytest
"""
testOutputDir = Path(__file__).absolute().parent.joinpath("test_out")
if testOutputDir.exists():
rmtree(str(testOutputDir))
testOutputDir.mkdir(exist_ok=True, parents=True)
queryEVTPath = testOutputDir.joinpath("EVT.qfile")
queryLOGPath = testOutputDir.joinpath("LOG.qfile")
with open(queryEVTPath, "w") as inf:
inf.write(
"""2020-01-15T00:00:00 2020-01-31T00:00:00\n2020-03-15T00:00:00 2020-03-31T00:00:00"""
)
with open(queryLOGPath, "w") as infLOG:
infLOG.write(
"""2020-01-15T00:00:00 2020-01-31T00:00:00\n2020-03-15T00:00:00 2020-03-31T00:00:00"""
)
os.environ["TEST_LOGS_DIR"] = str(testOutputDir)
configPath = Path(__file__).absolute().parent.joinpath(
"test_data", "test_download_data_config.yaml")
config = AgilepyConfig()
config.loadBaseConfigurations(configPath)
config.loadConfigurationsForClass("AGAnalysis")
datacoveragepath = Path(__file__).absolute().parent.joinpath(
"test_data", "AGILE_test_datacoverage")
agdataset = AGDataset(logger, datacoveragepath)
#test download data
tmin = 57083 # 2015-02-28T00:00:00
tmax = 57090 # 2015-03-15T00:00:00
downloaded = agdataset.downloadData(tmin, tmax,
config.getOptionValue("datapath"),
config.getOptionValue("evtfile"),
config.getOptionValue("logfile"))
assert downloaded == True
sleep(3) # this sleep is to avoid too many requests ban
#test tmax outside data coverage
tmin = 58051
tmax = 59582
with pytest.raises(NoCoverageDataError):
downloaded = agdataset.downloadData(
tmin, tmax, config.getOptionValue("datapath"),
config.getOptionValue("evtfile"),
config.getOptionValue("logfile"))
class AGBaseAnalysis:
def __init__(self, configurationFilePath):
self.config = AgilepyConfig()
# load only "input" and "output" sections
self.config.loadBaseConfigurations(
Utils._expandEnvVar(configurationFilePath))
# Creating output directory
self.outdir = self.config.getConf("output", "outdir")
Path(self.outdir).mkdir(parents=True, exist_ok=True)
self.logger = AgilepyLogger()
self.logger.initialize(
self.outdir, self.config.getConf("output", "logfilenameprefix"),
self.config.getConf("output", "verboselvl"))
self.plottingUtils = PlottingUtils(self.config, self.logger)
if "AGILE" not in os.environ:
raise AGILENotFoundError("$AGILE is not set.")
if "PFILES" not in os.environ:
raise PFILESNotFoundError("$PFILES is not set.")
def getAnalysisDir(self):
"""It returns the path of the output directory
Returns:
path (str) : the path of the output directory
"""
if self.outdir.exists() and self.outdir.is_dir():
return str(self.outdir)
else:
self.logger.warning(self, "OutputDirectory not found")
def deleteAnalysisDir(self):
"""It deletes the output directory where all the products of the analysis are written.
Args:
Returns:
True if the directory is succesfully deleted, False otherwise.
"""
outDir = Path(self.config.getConf("output", "outdir"))
if outDir.exists() and outDir.is_dir():
self.logger.info(self, "Removing directory %s", str(outDir))
self.logger.reset()
rmtree(outDir)
else:
self.logger.warning(self,
"Output directory %s exists? %r is dir? %r",
str(outDir), outDir.exists(), outDir.is_dir())
return False
return True
def setOptions(self, **kwargs):
"""It updates configuration options specifying one or more key=value pairs at once.
Args:
kwargs: key-values pairs, separated by a comma.
Returns:
None
Raises:
ConfigFileOptionTypeError: if the type of the option value is not wrong.
ConfigurationsNotValidError: if the values are not coherent with the configuration.
CannotSetHiddenOptionError: if the option is hidden.
OptionNotFoundInConfigFileError: if the option is not found.
Note:
The ``config`` attribute is initialized by reading the corresponding
yaml configuration file, loading its contents in memory. Updating the values
held by this object will not affect the original values written on disk.
Example:
>>> aganalysis.setOptions(mapsize=60, binsize=0.5)
True
"""
return self.config.setOptions(**kwargs)
def getOption(self, optionName):
"""It reads an option value from the configuration.
Args:
optionName (str): the name of the option.
Returns:
The option value
Raises:
OptionNotFoundInConfigFileError: if the optionName is not found in the configuration.
"""
return self.config.getOptionValue(optionName)
def printOptions(self, section=None):
"""It prints the configuration options in the console.
Args:
section (str): you can specify a configuration file section to be printed out.
Returns:
None
"""
return self.config.printOptions(section)
class AgilepyUtilsUT(unittest.TestCase):
def setUp(self):
self.currentDirPath = Path(__file__).parent.absolute()
self.agilepyconfPath = os.path.join(self.currentDirPath,
"conf/agilepyconf.yaml")
self.config = AgilepyConfig()
self.config.loadBaseConfigurations(self.agilepyconfPath)
self.agilepyLogger = AgilepyLogger()
self.agilepyLogger.initialize(
self.config.getConf("output", "outdir"),
self.config.getConf("output", "logfilenameprefix"),
self.config.getConf("output", "verboselvl"))
self.datadir = os.path.join(self.currentDirPath, "data")
self.outDir = Path(self.config.getOptionValue("outdir"))
if self.outDir.exists() and self.outDir.is_dir():
self.agilepyLogger.reset()
shutil.rmtree(self.outDir)
self.tmpDir = Path("./tmp")
self.tmpDir.mkdir(exist_ok=True)
def tearDown(self):
self.agilepyLogger.reset()
if self.tmpDir.exists() and self.tmpDir.is_dir():
shutil.rmtree(self.tmpDir)
def test_display_sky_map(self):
pu = PlottingUtils(self.config, self.agilepyLogger)
smooth = 4
fileFormat = ".png"
title = "testcase"
cmap = "CMRmap"
regFiles = [
Utils._expandEnvVar("$AGILE/catalogs/2AGL_2.reg"),
Utils._expandEnvVar("$AGILE/catalogs/2AGL_2.reg")
]
regFileColors = ["yellow", "blue"]
file = pu.displaySkyMap(
self.datadir+"/testcase_EMIN00100_EMAX00300_01.cts.gz", \
smooth = smooth,
fileFormat = fileFormat,
title = title,
cmap = cmap,
regFiles = regFiles,
regFileColors=regFileColors,
catalogRegions = "2AGL",
catalogRegionsColor = "red",
saveImage=True,
normType="linear")
assert True == os.path.isfile(file)
def test_display_sky_map_single_mode_3_imgs(self):
pu = PlottingUtils(self.config, self.agilepyLogger)
smooth = 4
fileFormat = ".png"
title = "testcase"
cmap = "CMRmap"
regFiles = [
Utils._expandEnvVar("$AGILE/catalogs/2AGL_2.reg"),
Utils._expandEnvVar("$AGILE/catalogs/2AGL_2.reg")
]
regFileColors = ["yellow", "blue"]
img = self.datadir + "/testcase_EMIN00100_EMAX00300_01.cts.gz"
file = pu.displaySkyMapsSingleMode(
[img, img, img], \
smooth = smooth,
fileFormat = fileFormat,
titles = [title+"_1", title+"_2", title+"_3"],
cmap = cmap,
regFiles = regFiles,
regFileColors=regFileColors,
catalogRegions = "2AGL",
catalogRegionsColor = "red",
saveImage=True,
normType="linear")
assert True == os.path.isfile(file)
def test_display_sky_map_single_mode_2_imgs(self):
pu = PlottingUtils(self.config, self.agilepyLogger)
smooth = 4
fileFormat = ".png"
title = "testcase"
cmap = "CMRmap"
regFiles = [
Utils._expandEnvVar("$AGILE/catalogs/2AGL_2.reg"),
Utils._expandEnvVar("$AGILE/catalogs/2AGL_2.reg")
]
regFileColors = ["yellow", "blue"]
img = self.datadir + "/testcase_EMIN00100_EMAX00300_01.cts.gz"
file = pu.displaySkyMapsSingleMode(
[img, img], \
smooth = smooth,
fileFormat = fileFormat,
titles = [title+"_1", title+"_2", title+"_3"],
cmap = cmap,
regFiles = regFiles,
regFileColors=regFileColors,
catalogRegions = "2AGL",
catalogRegionsColor = "red",
saveImage=True,
normType="linear")
assert True == os.path.isfile(file)
def test_plot_data_availability(self):
outputDir = self.currentDirPath.joinpath(
"output", "test_plot_data_availability")
outputDir.mkdir(parents=True, exist_ok=True)
os.environ["TEST_LOGS_DIR"] = str(outputDir)
config = AgilepyConfig()
config.loadBaseConfigurations(
self.currentDirPath.joinpath("conf",
"test_plot_data_availability.yaml"))
pu = PlottingUtils(config, self.agilepyLogger)
dataDir = Path(self.datadir).joinpath("test_plot_data_availability")
pu.plotDataAvailability(dataDir.joinpath("EVT.qfile"),
dataDir.joinpath("EVT.index"),
saveImage=True)
#pu.plotDataAvailability(dataDir.joinpath("LOG.qfile"), dataDir.joinpath("LOG.index"), saveImage=True)
def test_initialize_logger_verboselvl_2(self):
sleep(1.0)
self.agilepyLogger.reset()
self.config.loadBaseConfigurations(
os.path.join(self.currentDirPath,
"conf/agilepyconf_verbose_2.yaml"))
logfilePath = self.agilepyLogger.initialize(
self.config.getOptionValue("outdir"),
self.config.getOptionValue("logfilenameprefix"),
self.config.getOptionValue("verboselvl"))
assert True == logfilePath.is_file()
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
assert 1 == linesNumber
self.agilepyLogger.debug(self, "%s %s", "Debug", "message")
self.agilepyLogger.info(self, "%s %s", "Info", "message")
self.agilepyLogger.warning(self, "%s %s", "Warning", "message")
self.agilepyLogger.critical(self, "%s %s", "Critical", "message")
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
assert 5 == linesNumber
def test_initialize_logger_verboselvl_1(self):
sleep(1.0)
self.agilepyLogger.reset()
self.config.loadBaseConfigurations(
os.path.join(self.currentDirPath,
"conf/agilepyconf_verbose_1.yaml"))
logfilePath = self.agilepyLogger.initialize(
self.config.getOptionValue("outdir"),
self.config.getOptionValue("logfilenameprefix"),
self.config.getOptionValue("verboselvl"))
assert True == logfilePath.is_file()
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
assert 1 == linesNumber
self.agilepyLogger.debug(self, "%s %s", "Debug", "message")
self.agilepyLogger.info(self, "%s %s", "Info", "message")
self.agilepyLogger.warning(self, "%s %s", "Warning", "message")
self.agilepyLogger.critical(self, "%s %s", "Critical", "message")
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
assert 5 == linesNumber
def test_initialize_logger_verboselvl_0(self):
sleep(1.0)
self.agilepyLogger.reset()
self.config.loadBaseConfigurations(
os.path.join(self.currentDirPath,
"conf/agilepyconf_verbose_0.yaml"))
logfilePath = self.agilepyLogger.initialize(
self.config.getOptionValue("outdir"),
self.config.getOptionValue("logfilenameprefix"),
self.config.getOptionValue("verboselvl"))
assert True == logfilePath.is_file()
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
assert 1 == linesNumber
self.agilepyLogger.debug(self, "%s %s", "Debug", "message")
self.agilepyLogger.info(self, "%s %s", "Info", "message")
self.agilepyLogger.warning(self, "%s %s", "Warning", "message")
self.agilepyLogger.critical(self, "%s %s", "Critical", "message")
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
assert 5 == linesNumber
def test_filterAP(self):
print(self.datadir + "/E1q1_604800s_emin100_emax10000_r2.ap")
print(self.currentDirPath)
product = AstroUtils.AP_filter(
self.datadir + "/E1q1_604800s_emin100_emax10000_r2.ap", 1,
174142800, 447490800, self.currentDirPath)
with open(product, "r") as f:
linesNumber = len(f.readlines())
assert 4 == linesNumber
os.remove(os.path.join(self.currentDirPath, "result.txt"))
os.remove(os.path.join(self.currentDirPath, product))
"""
Time conversions
# https://tools.ssdc.asi.it/conversionTools
# https://heasarc.gsfc.nasa.gov/cgi-bin/Tools/xTime/xTime.pl?time_in_i=&time_in_c=&time_in_d=&time_in_j=&time_in_m=58871.45616898&time_in_sf=&time_in_wf=&time_in_sl=&time_in_sni=&time_in_snu=&time_in_s=&time_in_h=&time_in_sz=&time_in_ss=&time_in_sn=×ys_in=u×ys_out=u&apply_clock_offset=yes
"""
def test_astro_utils_time_mjd_to_agile_seconds(self):
sec_tolerance = 0.001
tt = AstroUtils.time_mjd_to_agile_seconds(
58871.45616898) # 506861812.99987227
assert abs(506861813 - tt) <= sec_tolerance
def test_astro_utils_time_agile_seconds_to_mjd(self):
sec_tolerance = 0.0000001
mjd = AstroUtils.time_agile_seconds_to_mjd(507391426.9447)
assert abs(58877.58595999 - mjd) <= sec_tolerance
def test_astro_utils_time_utc_to_jd(self):
tol = 0.00000001
dt = "2020-01-23T10:56:53.000"
jd = AstroUtils.time_fits_to_jd(dt)
assert abs(2458871.95616898 - jd) <= tol
def test_astro_utils_time_utc_to_mjd(self):
tol = 0.00000001
dt = "2020-01-23T10:56:53.000"
mjd = AstroUtils.time_fits_to_mjd(dt)
assert abs(58871.45616898 - mjd) <= tol
def test_astro_utils_time_utc_to_tt(self):
tol = 0.0001
agileseconds = AstroUtils.time_fits_to_agile_seconds(
"2020-01-23T10:56:53.000")
assert abs(506861813 - agileseconds) <= tol
def test_astro_utils_time_agile_seconds_to_jd(self):
jd = AstroUtils.time_agile_seconds_to_jd(449582332)
assert jd == pytest.approx(2458208.99921296, 0.00001)
def test_astro_utils_time_agile_seconds_to_utc(self):
sec_tol = 1
"""
utc = AstroUtils.time_tt_to_utc(506861813)
dt = datetime.strptime(utc, '%Y-%m-%dT%H:%M:%S.%f')
assert dt.year == 2020
assert dt.month == 1
assert dt.day == 23
assert dt.hour == 10
assert dt.minute == 56
assert abs(53 - dt.second) <= sec_tol
"""
# This date would result in "0 days"
sec_tolerance = 0.0000001
fitstime = AstroUtils.time_agile_seconds_to_fits(449582332)
dt = datetime.strptime(fitstime, '%Y-%m-%dT%H:%M:%S.%f')
assert dt.year == 2018
assert dt.month == 3
assert dt.day == 31
assert dt.hour == 11
assert dt.minute == 58
assert abs(52 - dt.second) <= sec_tol
def test_astro_utils_time_mjd_to_fits(self):
sec_tol = 1
fitstime = AstroUtils.time_mjd_to_fits(58871.45616898)
dt = datetime.strptime(fitstime, '%Y-%m-%dT%H:%M:%S.%f')
assert dt.year == 2020
assert dt.month == 1
assert dt.day == 23
assert dt.hour == 10
assert dt.minute == 56
assert abs(53 - dt.second) <= sec_tol
def test_astro_utils_time_fits_to_mjd_2(self):
sec_tol = 0.00000001
mjd = AstroUtils.time_fits_to_mjd("2020-01-23T10:56:53.000")
assert abs(58871.45616898 - mjd) <= sec_tol
def test_get_first_and_last_line_in_file(self):
line1 = '/ASDC_PROC2/FM3.119_2/EVT/agql2004151750_2004151850.EVT__FM.gz 514057762.000000 514061362.000000 EVT\n'
line2 = '/ASDC_PROC2/FM3.119_2/EVT/agql2004152249_2004160008.EVT__FM.gz 514075704.000000 514080437.000000 EVT\n'
line3 = '/ASDC_PROC2/FM3.119_2/EVT/agql2004160008_2004160045.EVT__FM.gz 514080437.000000 514082644.000000 EVT\n'
# I test: 1 line
test_file = self.tmpDir.joinpath("test_file1.txt")
with open(test_file, "w") as f:
f.write(line1)
(first, last) = Utils._getFirstAndLastLineInFile(test_file)
assert first == line1
assert last == line1
# II test: 2 lines
test_file = self.tmpDir.joinpath("test_file2.txt")
with open(test_file, "w") as f:
f.write(line1)
f.write(line2)
(first, last) = Utils._getFirstAndLastLineInFile(test_file)
assert first == line1
assert last == line2
# III test: 3 lines
test_file = self.tmpDir.joinpath("test_file3.txt")
with open(test_file, "w") as f:
f.write(line1)
f.write(line2)
f.write(line3)
(first, last) = Utils._getFirstAndLastLineInFile(test_file)
assert first == line1
assert last == line3
"""
class AgilepyConfigUT(unittest.TestCase):
def setUp(self):
self.currentDirPath = Path(__file__).parent.absolute()
self.agilepyconfPath = os.path.join(self.currentDirPath,
"conf/agilepyconf.yaml")
outDir = Path(
os.path.join(os.environ["AGILE"],
"agilepy-test-data/unittesting-output/config"))
if outDir.exists() and outDir.is_dir():
shutil.rmtree(outDir)
##### TEST NOT SUPPORTED AFTER REST FEATURE
"""
def test_validation_tmin_not_in_index(self):
self.config = AgilepyConfig()
self.config.loadBaseConfigurations(self.agilepyconfPath)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertRaises(ConfigurationsNotValidError, self.config.setOptions, tmin=40000000, tmax=433957532, timetype="TT")
def test_validation_tmax_not_in_index(self):
self.config = AgilepyConfig()
self.config.loadBaseConfigurations(self.agilepyconfPath)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertRaises(ConfigurationsNotValidError, self.config.setOptions,
tmin=433900000, tmax=456537946, timetype="TT")
"""
def test_validation_min_max(self):
self.config = AgilepyConfig()
self.config.loadBaseConfigurations(self.agilepyconfPath)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
dq=0,
fovradmin=10,
fovradmax=0)
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
emin=10,
emax=0)
def test_set_options(self):
self.config = AgilepyConfig()
self.config.loadBaseConfigurations(self.agilepyconfPath)
self.config.loadConfigurationsForClass("AGAnalysis")
# float instead of int is ok.
self.assertEqual(
None,
self.config.setOptions(tmin=433857532.,
tmax=435153532.,
timetype="TT"))
self.assertEqual("TT", self.config.getOptionValue("timetype"))
self.assertEqual(
None,
self.config.setOptions(tmin=58026.5, tmax=58027.5, timetype="MJD"))
self.assertEqual("MJD", self.config.getOptionValue("timetype"))
self.assertRaises(CannotSetNotUpdatableOptionError,
self.config.setOptions,
tmin=58026.5) # we must pass also timetype
self.assertRaises(CannotSetNotUpdatableOptionError,
self.config.setOptions,
verboselvl=2)
self.assertRaises(CannotSetNotUpdatableOptionError,
self.config.setOptions,
logfilenameprefix="pippo")
self.assertRaises(OptionNotFoundInConfigFileError,
self.config.setOptions(),
pdor="kmer")
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions(),
minimizertype=666)
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions(),
energybins=[1, 2, 3])
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions(),
energybins=666)
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions(),
energybins="100, 300")
self.assertRaises(CannotSetHiddenOptionError,
self.config.setOptions(),
lonpole=100)
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
galcoeff=0.617196)
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
isocoeff=0.617196)
# len(energybins) = 2
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
galcoeff=[0.617196])
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
isocoeff=[0.617196])
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
fluxcorrection=3.14)
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
fluxcorrection=25)
def test_energybins(self):
self.config = AgilepyConfig()
# galcoeff and isocoeff are None
conf1Path = os.path.join(self.currentDirPath, "conf/conf1.yaml")
self.config.loadBaseConfigurations(conf1Path)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertEqual(100, self.config.getOptionValue("energybins")[0][0])
self.assertEqual(300, self.config.getOptionValue("energybins")[0][1])
self.assertEqual(300, self.config.getOptionValue("energybins")[1][0])
self.assertEqual(1000, self.config.getOptionValue("energybins")[1][1])
self.config.setOptions(energybins=[[200, 400], [400, 1000]])
self.assertEqual(200, self.config.getOptionValue("energybins")[0][0])
self.assertEqual(400, self.config.getOptionValue("energybins")[0][1])
self.assertEqual(400, self.config.getOptionValue("energybins")[1][0])
self.assertEqual(1000, self.config.getOptionValue("energybins")[1][1])
# wrong type
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
energybins=["[200, 400]", "[400, 1000]"])
# wrong length
# self.assertRaises(ConfigurationsNotValidError, self.config.setOptions, energybins=[[200, 400]])
# galcoeff and isocoeff are None and len(energybins) = 1
conf3Path = os.path.join(self.currentDirPath, "conf/conf3.yaml")
self.config.loadBaseConfigurations(conf3Path)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertEqual(100, self.config.getOptionValue("energybins")[0][0])
self.assertEqual(300, self.config.getOptionValue("energybins")[0][1])
self.config.setOptions(energybins=[[200, 400], [400, 1000]])
def test_bkg_coeff(self):
self.config = AgilepyConfig()
# galcoeff and isocoeff are None
conf1Path = os.path.join(self.currentDirPath, "conf/conf1.yaml")
self.config.loadBaseConfigurations(conf1Path)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertEqual(4, len(self.config.getOptionValue("isocoeff")))
self.assertEqual(4, len(self.config.getOptionValue("galcoeff")))
for i in range(4):
self.assertEqual(-1, self.config.getOptionValue("isocoeff")[i])
self.assertEqual(-1, self.config.getOptionValue("galcoeff")[i])
# galcoeff isocoeff are lists
conf1Path = os.path.join(self.currentDirPath, "conf/conf2.yaml")
self.config.loadBaseConfigurations(conf1Path)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertEqual(4, len(self.config.getOptionValue("isocoeff")))
self.assertEqual(4, len(self.config.getOptionValue("galcoeff")))
self.assertEqual(10, self.config.getOptionValue("isocoeff")[0])
self.assertEqual(15, self.config.getOptionValue("isocoeff")[1])
self.assertEqual(0.6, self.config.getOptionValue("galcoeff")[0])
self.assertEqual(0.8, self.config.getOptionValue("galcoeff")[1])
# galcoeff and isocoeff are changed at runtime
self.config.setOptions(isocoeff=[10, 15, 10, 15],
galcoeff=[0.6, 0.8, 0.6, 0.8])
self.assertEqual(10, self.config.getOptionValue("isocoeff")[0])
self.assertEqual(15, self.config.getOptionValue("isocoeff")[1])
self.assertEqual(10, self.config.getOptionValue("isocoeff")[2])
self.assertEqual(15, self.config.getOptionValue("isocoeff")[3])
self.assertEqual(0.6, self.config.getOptionValue("galcoeff")[0])
self.assertEqual(0.8, self.config.getOptionValue("galcoeff")[1])
self.assertEqual(0.6, self.config.getOptionValue("galcoeff")[2])
self.assertEqual(0.8, self.config.getOptionValue("galcoeff")[3])
# this should cause an error because len(energybins) == 2
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
isocoeff=[10])
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
galcoeff=[0.6])
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
isocoeff=None,
galcoeff=None)
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
isocoeff="Pluto",
galcoeff="Pippo")
# this should create an error!!
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
isocoeff=["Pluto"],
galcoeff=["Pippo"])
def test_complete_configuration(self):
self.config = AgilepyConfig()
conf1Path = os.path.join(self.currentDirPath, "conf/conf1.yaml")
self.config.loadBaseConfigurations(conf1Path)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertEqual(5.99147, self.config.getOptionValue("loccl"))
self.config.setOptions(loccl=99)
self.assertEqual(9.21034, self.config.getOptionValue("loccl"))
self.assertEqual(4, len(self.config.getOptionValue("isocoeff")))
self.assertEqual(4, len(self.config.getOptionValue("galcoeff")))
conf2Path = os.path.join(self.currentDirPath, "conf/conf2.yaml")
self.config.loadBaseConfigurations(conf2Path)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertEqual(9.21034, self.config.getOptionValue("loccl"))
def test_evt_log_files_env_vars(self):
self.config = AgilepyConfig()
conf1Path = os.path.join(self.currentDirPath, "conf/conf1.yaml")
self.config.loadBaseConfigurations(conf1Path)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertEqual(True, "$"
not in self.config.getOptionValue("evtfile"))
self.assertEqual(True, "$"
not in self.config.getOptionValue("logfile"))
self.config.setOptions(
evtfile="$AGILE/agilepy-test-data/test_dataset_6.0/EVT/EVT.index",
logfile="$AGILE/agilepy-test-data/test_dataset_6.0/LOG/LOG.index")
self.assertEqual(True, "$"
not in self.config.getOptionValue("evtfile"))
self.assertEqual(True, "$"
not in self.config.getOptionValue("logfile"))
def test_datapath_restapi(self):
self.config = AgilepyConfig()
conf1Path = os.path.join(self.currentDirPath, "conf/conf1.yaml")
self.config.loadBaseConfigurations(conf1Path)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertRaises(CannotSetNotUpdatableOptionError,
self.config.setOptions,
datapath="/foo/bar")
self.assertRaises(CannotSetNotUpdatableOptionError,
self.config.setOptions,
userestapi=True)
def test_set_evtlog_ifdatapath(self):
self.config = AgilepyConfig()
conf1Path = os.path.join(self.currentDirPath, "conf/conf4.yaml")
dirpath = Path("/tmp/foo/bar")
dirpath.mkdir(parents=True, exist_ok=True)
self.config.loadBaseConfigurations(conf1Path)
self.config.loadConfigurationsForClass("AGAnalysis")
self.assertEqual(
self.config.getOptionValue("evtfile"),
Path(self.config.getOptionValue("datapath")).joinpath("EVT.index"))
self.assertEqual(
self.config.getOptionValue("logfile"),
Path(self.config.getOptionValue("datapath")).joinpath("LOG.index"))
dirpath.rmdir()
##### TEST NOT SUPPORTED AFTER REST FEATURE
"""
class AgilepyConfigUT(unittest.TestCase):
def setUp(self):
self.currentDirPath = Path(__file__).parent.absolute()
self.agilepyconfPath = os.path.join(self.currentDirPath,
"conf/agilepyconf.yaml")
outDir = Path(
os.path.join(os.environ["AGILE"],
"agilepy-test-data/unittesting-output/config"))
if outDir.exists() and outDir.is_dir():
shutil.rmtree(outDir)
def test_validation_tmin_not_in_index(self):
self.config = AgilepyConfig()
self.config.loadConfigurations(self.agilepyconfPath, validate=False)
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
tmin=456361777,
timetype="TT")
def test_validation_tmax_not_in_index(self):
self.config = AgilepyConfig()
self.config.loadConfigurations(self.agilepyconfPath, validate=False)
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
tmax=456537946,
timetype="TT")
def test_validation_min_max(self):
self.config = AgilepyConfig()
self.config.loadConfigurations(self.agilepyconfPath, validate=False)
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
fovradmin=10,
fovradmax=0)
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
emin=10,
emax=0)
def test_set_options(self):
self.config = AgilepyConfig()
self.config.loadConfigurations(self.agilepyconfPath, validate=False)
# float instead of int is ok.
self.assertEqual(None,
self.config.setOptions(tmin=456361779, timetype="TT"))
self.assertRaises(CannotSetNotUpdatableOptionError,
self.config.setOptions,
verboselvl=2)
self.assertRaises(CannotSetNotUpdatableOptionError,
self.config.setOptions,
logfilenameprefix="pippo")
self.assertRaises(OptionNotFoundInConfigFileError,
self.config.setOptions(),
pdor="kmer")
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions(),
minimizertype=666)
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions(),
energybins=[1, 2, 3])
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions(),
energybins=666)
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions(),
energybins="100, 300")
self.assertRaises(CannotSetHiddenOptionError,
self.config.setOptions(),
lonpole=100)
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
galcoeff=0.617196)
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
isocoeff=0.617196)
# len(energybins) = 2
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
galcoeff=[0.617196])
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
isocoeff=[0.617196])
def test_energybins(self):
self.config = AgilepyConfig()
# galcoeff and isocoeff are None
conf1Path = os.path.join(self.currentDirPath, "conf/conf1.yaml")
self.config.loadConfigurations(conf1Path)
self.assertEqual(100, self.config.getOptionValue("energybins")[0][0])
self.assertEqual(300, self.config.getOptionValue("energybins")[0][1])
self.assertEqual(300, self.config.getOptionValue("energybins")[1][0])
self.assertEqual(1000, self.config.getOptionValue("energybins")[1][1])
self.config.setOptions(energybins=[[200, 400], [400, 1000]])
self.assertEqual(200, self.config.getOptionValue("energybins")[0][0])
self.assertEqual(400, self.config.getOptionValue("energybins")[0][1])
self.assertEqual(400, self.config.getOptionValue("energybins")[1][0])
self.assertEqual(1000, self.config.getOptionValue("energybins")[1][1])
# wrong type
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
energybins=["[200, 400]", "[400, 1000]"])
# wrong length
# self.assertRaises(ConfigurationsNotValidError, self.config.setOptions, energybins=[[200, 400]])
def test_bkg_coeff(self):
self.config = AgilepyConfig()
# galcoeff and isocoeff are None
conf1Path = os.path.join(self.currentDirPath, "conf/conf1.yaml")
self.config.loadConfigurations(conf1Path, validate=False)
self.assertEqual(4, len(self.config.getOptionValue("isocoeff")))
self.assertEqual(4, len(self.config.getOptionValue("galcoeff")))
for i in range(4):
self.assertEqual(-1, self.config.getOptionValue("isocoeff")[i])
self.assertEqual(-1, self.config.getOptionValue("galcoeff")[i])
# galcoeff isocoeff are lists
conf1Path = os.path.join(self.currentDirPath, "conf/conf2.yaml")
self.config.loadConfigurations(conf1Path, validate=False)
self.assertEqual(4, len(self.config.getOptionValue("isocoeff")))
self.assertEqual(4, len(self.config.getOptionValue("galcoeff")))
self.assertEqual(10, self.config.getOptionValue("isocoeff")[0])
self.assertEqual(15, self.config.getOptionValue("isocoeff")[1])
self.assertEqual(0.6, self.config.getOptionValue("galcoeff")[0])
self.assertEqual(0.8, self.config.getOptionValue("galcoeff")[1])
# galcoeff and isocoeff are changed at runtime
self.config.setOptions(isocoeff=[10, 15, 10, 15],
galcoeff=[0.6, 0.8, 0.6, 0.8])
self.assertEqual(10, self.config.getOptionValue("isocoeff")[0])
self.assertEqual(15, self.config.getOptionValue("isocoeff")[1])
self.assertEqual(10, self.config.getOptionValue("isocoeff")[2])
self.assertEqual(15, self.config.getOptionValue("isocoeff")[3])
self.assertEqual(0.6, self.config.getOptionValue("galcoeff")[0])
self.assertEqual(0.8, self.config.getOptionValue("galcoeff")[1])
self.assertEqual(0.6, self.config.getOptionValue("galcoeff")[2])
self.assertEqual(0.8, self.config.getOptionValue("galcoeff")[3])
# this should cause an error because len(energybins) == 2
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
isocoeff=[10])
self.assertRaises(ConfigurationsNotValidError,
self.config.setOptions,
galcoeff=[0.6])
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
isocoeff=None,
galcoeff=None)
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
isocoeff="Pluto",
galcoeff="Pippo")
# this should create an error!!
self.assertRaises(ConfigFileOptionTypeError,
self.config.setOptions,
isocoeff=["Pluto"],
galcoeff=["Pippo"])
def test_complete_configuration(self):
self.config = AgilepyConfig()
conf1Path = os.path.join(self.currentDirPath, "conf/conf1.yaml")
self.config.loadConfigurations(conf1Path, validate=False)
self.assertEqual(5.99147, self.config.getOptionValue("loccl"))
self.config.setOptions(loccl=99)
self.assertEqual(9.21034, self.config.getOptionValue("loccl"))
self.assertEqual(4, len(self.config.getOptionValue("isocoeff")))
self.assertEqual(4, len(self.config.getOptionValue("galcoeff")))
conf2Path = os.path.join(self.currentDirPath, "conf/conf2.yaml")
self.config.loadConfigurations(conf2Path, validate=False)
self.assertEqual(9.21034, self.config.getOptionValue("loccl"))
class AgilepyUtilsUT(unittest.TestCase):
def setUp(self):
self.currentDirPath = Path(__file__).parent.absolute()
self.agilepyconfPath = os.path.join(self.currentDirPath,
"conf/agilepyconf.yaml")
self.config = AgilepyConfig()
self.config.loadConfigurations(self.agilepyconfPath, validate=False)
self.agilepyLogger = AgilepyLogger()
self.agilepyLogger.initialize(
self.config.getConf("output", "outdir"),
self.config.getConf("output", "logfilenameprefix"),
self.config.getConf("output", "verboselvl"))
self.datadir = os.path.join(self.currentDirPath, "data")
self.outDir = Path(self.config.getOptionValue("outdir"))
if self.outDir.exists() and self.outDir.is_dir():
shutil.rmtree(self.outDir)
def tearDown(self):
self.agilepyLogger.reset()
def test_display_sky_map(self):
pu = PlottingUtils(self.config, self.agilepyLogger)
smooth = 4
fileFormat = ".png"
title = "testcase"
cmap = "CMRmap"
regFilePath = self.config._expandEnvVar("$AGILE/catalogs/2AGL_2.reg")
file = pu.displaySkyMap(
self.datadir+"/testcase_EMIN00100_EMAX00300_01.cts.gz", \
smooth = smooth,
fileFormat = fileFormat,
title = title,
cmap = cmap,
regFilePath = regFilePath,
catalogRegions = None,
catalogRegionsColor = "red",
saveImage=True)
self.assertEqual(True, os.path.isfile(file))
def test_display_sky_map_single_mode(self):
pu = PlottingUtils(self.config, self.agilepyLogger)
smooth = 4
fileFormat = ".png"
title = "testcase"
cmap = "CMRmap"
regFilePath = self.config._expandEnvVar("$AGILE/catalogs/2AGL_2.reg")
img = self.datadir + "/testcase_EMIN00100_EMAX00300_01.cts.gz"
file = pu.displaySkyMapsSingleMode(
[img, img, img], \
smooth = smooth,
fileFormat = fileFormat,
titles = [title+"_1", title+"_2", title+"_3"],
cmap = cmap,
regFilePath = regFilePath,
catalogRegions = None,
catalogRegionsColor = "red",
saveImage=True)
self.assertEqual(True, os.path.isfile(file))
def test_display_light_curve(self):
pu = PlottingUtils(self.config, self.agilepyLogger)
file_lc = self.datadir + "/lc-4.txt"
self.assertRaises(ValueError, pu.plotLc, file_lc, 1500, 1000, True)
#with self.assertRaises(ValueError, pu.plotLc, file_lc, 1500, 1000, True) as cm:
# input("..")
# print(cm)
# self.assertEqual(True, os.path.isfile(file))
def test_initialize_logger_verboselvl_2(self):
sleep(1.0)
self.agilepyLogger.reset()
self.config.setOptions(force=True, verboselvl=2)
logfilePath = self.agilepyLogger.initialize(
self.config.getOptionValue("outdir"),
self.config.getOptionValue("logfilenameprefix"),
self.config.getOptionValue("verboselvl"))
self.assertEqual(True, logfilePath.is_file())
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
self.assertEqual(1, linesNumber)
self.agilepyLogger.debug(self, "%s %s", "Debug", "message")
self.agilepyLogger.info(self, "%s %s", "Info", "message")
self.agilepyLogger.warning(self, "%s %s", "Warning", "message")
self.agilepyLogger.critical(self, "%s %s", "Critical", "message")
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
self.assertEqual(5, linesNumber)
def test_initialize_logger_verboselvl_1(self):
sleep(1.0)
self.agilepyLogger.reset()
self.config.setOptions(force=True, verboselvl=1)
logfilePath = self.agilepyLogger.initialize(
self.config.getOptionValue("outdir"),
self.config.getOptionValue("logfilenameprefix"),
self.config.getOptionValue("verboselvl"))
self.assertEqual(True, logfilePath.is_file())
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
self.assertEqual(1, linesNumber)
self.agilepyLogger.debug(self, "%s %s", "Debug", "message")
self.agilepyLogger.info(self, "%s %s", "Info", "message")
self.agilepyLogger.warning(self, "%s %s", "Warning", "message")
self.agilepyLogger.critical(self, "%s %s", "Critical", "message")
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
self.assertEqual(5, linesNumber)
def test_initialize_logger_verboselvl_0(self):
sleep(1.0)
self.agilepyLogger.reset()
self.config.setOptions(force=True, verboselvl=0)
logfilePath = self.agilepyLogger.initialize(
self.config.getOptionValue("outdir"),
self.config.getOptionValue("logfilenameprefix"),
self.config.getOptionValue("verboselvl"))
self.assertEqual(True, logfilePath.is_file())
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
self.assertEqual(1, linesNumber)
self.agilepyLogger.debug(self, "%s %s", "Debug", "message")
self.agilepyLogger.info(self, "%s %s", "Info", "message")
self.agilepyLogger.warning(self, "%s %s", "Warning", "message")
self.agilepyLogger.critical(self, "%s %s", "Critical", "message")
with open(logfilePath, "r") as f:
linesNumber = len(f.readlines())
self.assertEqual(5, linesNumber)
"""
Time conversions
# https://tools.ssdc.asi.it/conversionTools
# https://heasarc.gsfc.nasa.gov/cgi-bin/Tools/xTime/xTime.pl?time_in_i=&time_in_c=&time_in_d=&time_in_j=&time_in_m=58871.45616898&time_in_sf=&time_in_wf=&time_in_sl=&time_in_sni=&time_in_snu=&time_in_s=&time_in_h=&time_in_sz=&time_in_ss=&time_in_sn=×ys_in=u×ys_out=u&apply_clock_offset=yes
"""
def test_astro_utils_time_mjd_to_tt(self):
sec_tolerance = 0.001
tt = AstroUtils.time_mjd_to_tt(58871.45616898) # 506861812.99987227
self.assertEqual(True, abs(506861813 - tt) <= sec_tolerance)
def test_astro_utils_time_tt_to_mjd(self):
sec_tolerance = 0.0000001
mjd = AstroUtils.time_tt_to_mjd(507391426.9447)
self.assertEqual(True, abs(58877.58595999 - mjd) <= sec_tolerance)
def test_astro_utils_time_jd_to_civil(self):
tol = 0.044
civ = AstroUtils.jd_to_civil(2458871.95616898)
self.assertEqual(civ[0], 2020)
self.assertEqual(civ[1], 1)
self.assertEqual(True, abs(23 - civ[2]) <= tol)
# it should be 2020, 1, 23)........
def test_astro_utils_time_utc_to_jd(self):
tol = 0.00000001
dt = datetime.strptime("2020-01-23T10:56:53", '%Y-%m-%dT%H:%M:%S')
jd = AstroUtils.to_jd(dt)
self.assertEqual(True, abs(2458871.95616898 - jd) <= tol)
def test_astro_utils_time_utc_to_mjd(self):
tol = 0.00000001
dt = datetime.strptime("2020-01-23T10:56:53", '%Y-%m-%dT%H:%M:%S')
mjd = AstroUtils.to_jd(dt, fmt="mjd")
self.assertEqual(True, abs(58871.45616898 - mjd) <= tol)
def test_astro_utils_time_utc_to_tt(self):
tol = 0.0001
tt = AstroUtils.time_utc_to_tt("2020-01-23T10:56:53")
self.assertEqual(True, abs(506861813 - tt) <= tol)
def test_astro_utils_time_tt_to_utc(self):
sec_tol = 1
utc = AstroUtils.time_tt_to_utc(506861813)
dt = datetime.strptime(utc, '%Y-%m-%dT%H:%M:%S')
self.assertEqual(dt.year, 2020)
self.assertEqual(dt.month, 1)
self.assertEqual(dt.day, 23)
self.assertEqual(dt.hour, 10)
self.assertEqual(dt.minute, 56)
self.assertEqual(True, abs(53 - dt.second) <= sec_tol)
def test_astro_utils_time_mjd_to_utc(self):
sec_tol = 1
utc = AstroUtils.time_mjd_to_utc(58871.45616898)
dt = datetime.strptime(utc, '%Y-%m-%dT%H:%M:%S')
self.assertEqual(dt.year, 2020)
self.assertEqual(dt.month, 1)
self.assertEqual(dt.day, 23)
self.assertEqual(dt.hour, 10)
self.assertEqual(dt.minute, 56)
self.assertEqual(True, abs(53 - dt.second) <= sec_tol)
def test_astro_utils_time_utc_to_mjd(self):
sec_tol = 0.00000001
mjd = AstroUtils.time_utc_to_mjd("2020-01-23T10:56:53")
self.assertEqual(True, abs(58871.45616898 - mjd) <= sec_tol)
class AGAnalysis:
"""This class contains the high-level API methods you can use to run scientific analysis.
This class is a wrapper around the ``SourcesLibrary``, ``ScienceTools`` and ``AgilepyConfig`` classes and implements
high level functionality.
This class requires you to setup a ``yaml configuration file`` to specify the software's behaviour
and a ``xml descriptor file`` that contains a list of all the sources you want to consider.
Class attributes:
Attributes:
config (:obj:`AgilepyConfig`): it is used to read/update configuration values.
logger (:obj:`AgilepyLogger`): it is used to log messages with different importance levels.
sourcesLibrary (:obj:`SourcesLibrary`): it contains the list of the sources and several useful methods.
"""
def __init__(self, configurationFilePath, sourcesFilePath):
"""AGAnalysis constructor.
Args:
configurationFilePath (str): the relative or absolute path to the yaml configuration file.
sourcesFilePath (str): the relative or absolute path to the xml sources descriptor file.
Raises:
FileExistsError: if the output directory already exists.
AGILENotFoundError: if the AGILE environment variable is not set.
PFILESNotFoundError: if the PFILES environment variable is not set.
Example:
>>> from agilepy.api import AGAnalysis
>>> aganalysis = AGAnalysis('agconfig.yaml', 'sources.xml')
"""
self.config = AgilepyConfig()
self.config.loadConfigurations(configurationFilePath, validate=True)
self.config.printOptions("output")
self.outdir = self.config.getConf("output", "outdir")
if exists(self.outdir):
raise FileExistsError(
"The output directory %s already exists! Please, delete it or specify another output directory!"
% (self.outdir))
self.logger = agilepyLogger
self.logger.initialize(self.outdir,
self.config.getConf("output", "logfilename"),
self.config.getConf("output", "debuglvl"))
self.sourcesLibrary = SourcesLibrary()
self.sourcesLibrary.loadSources(sourcesFilePath)
if "AGILE" not in os.environ:
raise AGILENotFoundError("$AGILE is not set.")
if "PFILES" not in os.environ:
raise PFILESNotFoundError("$PFILES is not set.")
def setOptions(self, **kwargs):
"""It updates configuration options specifying one or more key=value pairs at once.
Args:
\*\*kwargs: key-values pairs, separated by a comma.
Returns:
None
Raises:
ConfigFileOptionTypeError: if the type of the option value is not wrong.
CannotSetHiddenOptionError: if the option is hidden.
OptionNotFoundInConfigFileError: if the option is not found.
Note:
The ``config`` attribute is initialized by reading the corresponding
yaml configuration file, loading its contents in memory. Updating the values
held by this object will not affect the original values written on disk.
Example:
>>> aganalysis.setOptions(mapsize=60, binsize=0.5)
True
"""
return self.config.setOptions(**kwargs)
def resetOptions(self):
"""It resets the configuration options to their original values.
Returns:
None.
"""
return self.config.reset()
def printOptions(self, section=None):
"""It prints the configuration options in the console.
Args:
section (str): you can specify a configuration file section to be printed out.
Returns:
None
"""
return self.config.printOptions(section)
def generateMaps(self):
"""It generates (one or more) counts, exposure, gas and int maps and a ``maplist file``.
The method's behaviour varies according to several configuration options (see docs here).
Note:
It resets the configuration options to their original values before exiting.
Returns:
The absolute path to the generated ``maplist file``.
Raises:
ScienceToolInputArgMissing: if not all the required configuration options have been set.
Example:
>>> aganalysis.generateMaps()
/home/rt/agilepy/output/testcase.maplist4
"""
fovbinnumber = self.config.getOptionValue("fovbinnumber")
energybins = self.config.getOptionValue("energybins")
initialFovmin = self.config.getOptionValue("fovradmin")
initialFovmax = self.config.getOptionValue("fovradmax")
initialFileNamePrefix = self.config.getOptionValue("filenameprefix")
outdir = self.config.getOptionValue("outdir")
mapListFileContent = []
maplistFilePath = join(outdir, initialFileNamePrefix + ".maplist4")
for stepi in range(0, fovbinnumber):
if fovbinnumber == 1:
bincenter = 30
fovmin = initialFovmin
fovmax = initialFovmax
else:
bincenter, fovmin, fovmax = AGAnalysis._updateFovMinMaxValues(
fovbinnumber, initialFovmin, initialFovmax, stepi + 1)
for bgCoeffIdx, stepe in enumerate(energybins):
if Parameters.checkEnergyBin(stepe):
emin = stepe[0]
emax = stepe[1]
skymapL = Parameters.getSkyMap(emin, emax)
skymapH = Parameters.getSkyMap(emin, emax)
fileNamePrefix = Parameters.getMapNamePrefix(
emin, emax, stepi + 1)
self.logger.info(
self,
"Map generation => fovradmin %s fovradmax %s bincenter %s emin %s emax %s fileNamePrefix %s \
skymapL %s skymapH %s", [
fovmin, fovmax, bincenter, emin, emax,
fileNamePrefix, skymapL, skymapH
])
self.config.setOptions(
filenameprefix=initialFileNamePrefix + "_" +
fileNamePrefix)
self.config.setOptions(fovradmin=fovmin, fovradmax=fovmax)
self.config.addOptions("selection", emin=emin, emax=emax)
self.config.addOptions("maps",
skymapL=skymapL,
skymapH=skymapH)
ctsMapGenerator.configure(self.config)
expMapGenerator.configure(self.config)
gasMapGenerator.configure(self.config)
intMapGenerator.configure(self.config)
self.config.addOptions("maps",
expmap=expMapGenerator.outfilePath,
ctsmap=ctsMapGenerator.outfilePath)
if not ctsMapGenerator.allRequiredOptionsSet(self.config) or \
not expMapGenerator.allRequiredOptionsSet(self.config) or \
not gasMapGenerator.allRequiredOptionsSet(self.config) or \
not intMapGenerator.allRequiredOptionsSet(self.config):
raise ScienceToolInputArgMissing(
"Some options have not been set.")
f1 = ctsMapGenerator.call()
self.logger.info(
self, "Science tool ctsMapGenerator produced %s", [f1])
f2 = expMapGenerator.call()
self.logger.info(
self, "Science tool expMapGenerator produced %s", [f2])
f3 = gasMapGenerator.call()
self.logger.info(
self, "Science tool gasMapGenerator produced %s", [f3])
f4 = intMapGenerator.call()
self.logger.info(
self, "Science tool intMapGenerator produced %s", [f4])
mapListFileContent.append( ctsMapGenerator.outfilePath + " " + \
expMapGenerator.outfilePath + " " + \
gasMapGenerator.outfilePath + " " + \
str(bincenter) + " " + \
str(self.config.getOptionValue("galcoeff")[bgCoeffIdx]) + " " + \
str(self.config.getOptionValue("isocoeff")[bgCoeffIdx]) )
else:
self.logger.warning(
self,
"Energy bin [%s, %s] is not supported. Map generation skipped.",
[stepe[0], stepe[1]])
with open(maplistFilePath, "a") as mlf:
for line in mapListFileContent:
mlf.write(line + "\n")
self.logger.info(self, "Maplist file created in %s", [maplistFilePath])
self.config.reset()
return maplistFilePath
def mle(self, maplistFilePath):
"""It performs a maximum likelihood estimation analysis on every source withing the ``sourceLibrary``, producing one output file per source.
The outputfiles have the ``.source`` extension.
The method's behaviour varies according to several configuration options (see docs here).
Note:
It resets the configuration options to their original values before exiting.
Args:
maplistFilePath (str): the absolute path to the ``maplist file`` generated by ``generateMaps()``.
Returns:
A list of absolute paths to the output ``.source`` files.
Raises:
MaplistIsNone: is the input argument is None.
Example:
>>> maplistFilePath = aganalysis.generateMaps()
>>> aganalysis.mle(maplistFilePath)
[/home/rt/agilepy/output/testcase0001_2AGLJ2021+4029.source /home/rt/agilepy/output/testcase0001_2AGLJ2021+3654.source]
"""
if not maplistFilePath:
raise MaplistIsNone(
"The 'maplistFilePath' input argument is None. Please, pass a valid path to a maplist \
file as argument (perhaps you want to call generateMaps() first). "
)
sourceListFilename = "sourceLibrary" + (str(
multi.callCounter).zfill(5))
sourceListAgileFormatFilePath = self.sourcesLibrary.writeToFile(
outfileNamePrefix=join(self.outdir, sourceListFilename),
fileformat="AG")
self.config.addOptions("selection",
maplist=maplistFilePath,
sourcelist=sourceListAgileFormatFilePath)
multisources = self.sourcesLibrary.getSourcesNames()
self.config.addOptions("selection", multisources=multisources)
multi.configure(self.config)
sourceFiles = multi.call()
if len(sourceFiles) == 0:
self.logger.warning(self, "The number of .source files is 0.", [])
self.logger.info(self, "AG_multi produced: %s",
[" ".join(sourceFiles)])
for sourceFile in sourceFiles:
multiOutputData = SourcesLibrary.parseSourceFile(sourceFile)
mapCenterL = float(self.config.getOptionValue("glon"))
mapCenterB = float(self.config.getOptionValue("glat"))
self.sourcesLibrary.updateMulti(multiOutputData, mapCenterL,
mapCenterB)
self.config.reset()
return sourceFiles
def freeSources(self, selection, parameterName, free):
"""It can set to True or False a parameter's ``free`` attribute of one or more source.
Example of source model:
::
<source name="2AGLJ2021+4029" type="PointSource">
<spectrum type="PLExpCutoff">
<parameter name="Flux" free="1" value="119.3e-08"/>
<parameter name="Index" free="0" scale="-1.0" value="1.75" min="0.5" max="5"/>
<parameter name="CutoffEnergy" free="0" value="3307.63" min="20" max="10000"/>
</spectrum>
<spatialModel type="PointSource" location_limit="0" free="0">
<parameter name="GLON" value="78.2375" />
<parameter name="GLAT" value="2.12298" />
</spatialModel>
</source>
The sources can be selected with the ``selection`` argument, supporting either ``lambda functions`` and
``boolean expression strings``.
The selection criteria can be expressed using the following ``Source`` class's parameters:
- Name: the unique code identifying the source.
- Dist: the distance of the source from the center of the maps (generated with ``generateMaps()``)
- Flux: the flux value.
- SqrtTS: the radix square of the ts.
Warning:
The Dist, Flux and SqrtTS parameters are available only after the maximum likelihood estimation analysis.
The supported ``parameterName`` are:
- Flux
- Index
- Index1
- Index2
- CutoffEnergy
- PivotEnergy
- Curvature
- Index2
- Loc
Args:
selection (lambda or str): a lambda function or a boolean expression string specifying the selection criteria.
parameterName (str): the ``free`` attribute of this parameter will be updated.
free (bool): the boolean value used.
Returns:
The list of the sources matching the selection criteria.
Note:
The ``sourcesLibrary`` attribute is initialized by reading the corresponding
xml descriptor file, loading its contents in memory. Updating the values
held by this object will not affect the original values written on disk.
Example:
The following calls are equivalent and they set to True the ``free`` attribute of the "Flux" parameter for all the sources
named "2AGLJ2021+4029" which distance from the map center is greater than zero and which flux value
is greater than zero.
>>> aganalysis.freeSources(lambda Name, Dist, Flux : Name == "2AGLJ2021+4029" and Dist > 0 and Flux > 0, "Flux", True)
[..]
>>> aganalysis.freeSources('Name == "2AGLJ2021+4029" AND Dist > 0 AND Flux > 0', "Flux", True)
[..]
"""
return self.sourcesLibrary.freeSources(selection, parameterName, free)
def selectSources(self, selection):
"""It returns the sources matching the selection criteria from the ``sourcesLibrary``.
Args:
selection (lambda or str): a lambda function or a boolean expression string specifying the selection criteria.
Returns:
List of sources.
"""
return self.sourcesLibrary.selectSources(selection)
def deleteSources(self, selection):
"""It deletes the sources matching the selection criteria from the ``sourcesLibrary``.
Args:
selection (lambda or str): a lambda function or a boolean expression string specifying the selection criteria.
Returns:
The list containing the deleted sources.
"""
return self.sourcesLibrary.deleteSources(selection)
@staticmethod
def _updateFovMinMaxValues(fovbinnumber, fovradmin, fovradmax, stepi):
# print("\nfovbinnumber {}, fovradmin {}, fovradmax {}, stepi {}".format(fovbinnumber, fovradmin, fovradmax, stepi))
A = float(fovradmax) - float(fovradmin)
B = float(fovbinnumber)
C = stepi
binleft = ((A / B) * C)
binright = (A / B)
bincenter = binleft - binright / 2.0
fovmin = bincenter - (A / B) / 2.0
fovmax = bincenter + (A / B) / 2.0
# print("bincenter {}, fovmin {}, fovmax {}".format(bincenter, fovmin, fovmax))
return bincenter, fovmin, fovmax
