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"))
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)
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 SourcesLibraryUT(unittest.TestCase):
def setUp(self):
self.currentDirPath = Path(__file__).parent.absolute()
self.test_logs_dir = Path(self.currentDirPath).joinpath(
"test_logs", "SourcesLibraryUT")
self.test_logs_dir.mkdir(parents=True, exist_ok=True)
os.environ["TEST_LOGS_DIR"] = str(self.test_logs_dir)
self.agilepyConf = os.path.join(self.currentDirPath,
"conf/agilepyconf.yaml")
self.config = AgilepyConfig()
self.config.loadBaseConfigurations(self.agilepyConf)
self.config.loadConfigurationsForClass("AGAnalysis")
self.logger = AgilepyLogger()
self.logger.initialize(
self.config.getConf("output", "outdir"),
self.config.getConf("output", "logfilenameprefix"),
self.config.getConf("output", "verboselvl"))
outDir = Path(
os.path.join(os.environ["AGILE"],
"agilepy-test-data/unittesting-output/core"))
if outDir.exists() and outDir.is_dir():
shutil.rmtree(outDir)
self.sl = SourcesLibrary(self.config, self.logger)
@staticmethod
def get_free_params(source):
return {
"curvature": source.spectrum.curvature["free"],
"pivot_energy": source.spectrum.pivotEnergy["free"],
"index": source.spectrum.index["free"],
"pos": source.spatialModel.pos["free"],
"flux": source.spectrum.flux["free"]
}
def test_load_file_with_wrong_extension(self):
xmlsourcesconfPath = os.path.join(self.currentDirPath,
"test_data/sourceconf.wrongext")
self.assertRaises(SourceModelFormatNotSupported,
self.sl.loadSourcesFromFile, xmlsourcesconfPath)
def test_load_wrong_file(self):
xmlsourcesconfPath = os.path.join(self.currentDirPath,
"conf/idontexitst.txt")
self.assertRaises(FileNotFoundError, self.sl.loadSourcesFromFile,
xmlsourcesconfPath)
def test_load_from_catalog(self):
added = self.sl.loadSourcesFromCatalog("2AGL")
self.assertEqual(175, len(added))
self.assertEqual(175, len(self.sl.sources))
self.assertRaises(FileNotFoundError, self.sl.loadSourcesFromCatalog,
"paperino")
def test_load_catalog_from_catalog_filtering_on_distances(self):
added = self.sl.loadSourcesFromCatalog("2AGL", rangeDist=(70, 80))
self.assertEqual(13, len(added))
self.assertEqual(13, len(self.sl.sources))
self.sl.sources = []
added = self.sl.loadSourcesFromCatalog("2AGL", rangeDist=(0, 10))
self.assertEqual(1, len(added))
self.assertEqual(1, len(self.sl.sources))
self.sl.sources = []
added = self.sl.loadSourcesFromCatalog("2AGL", rangeDist=(0, 50))
self.assertEqual(30, len(added))
self.assertEqual(30, len(self.sl.sources))
def test_load_sources_from_xml_file(self):
added = self.sl.loadSourcesFromFile(
os.path.join(self.currentDirPath, "test_data/sources_2.xml"))
self.assertEqual(2, len(added))
self.assertEqual(2, len(self.sl.sources))
sources = self.sl.selectSources('name == "2AGLJ2021+4029"')
self.assertEqual(1, len(sources))
source = sources.pop()
self.assertEqual(119.3e-08, source.spectrum.getVal("flux"))
self.assertEqual(1.75, source.spectrum.getVal("index"))
self.assertEqual(78.2375, source.spatialModel.getVal("pos")[0])
self.assertEqual(True, source.spatialModel.getVal("dist") > 0)
sources = self.sl.selectSources('name == "2AGLJ2021+3654"')
self.assertEqual(1, len(sources))
source = sources.pop()
self.assertEqual(70.89e-08, source.spectrum.getVal("flux"))
self.assertEqual(1.38, source.spectrum.getVal("index"))
self.assertEqual(75.2562, source.spatialModel.getVal("pos")[0])
self.assertEqual(True, source.spatialModel.getVal("dist") > 0)
def test_load_sources_from_txt_file(self):
added = self.sl.loadSourcesFromFile(
os.path.join(self.currentDirPath, "test_data/sources_2.txt"))
self.assertEqual(10, len(added))
self.assertEqual(10, len(self.sl.sources))
sources = self.sl.selectSources('name == "2AGLJ1801-2334"')
self.assertEqual(1, len(sources))
source = sources.pop()
self.assertEqual(3.579e-07, source.spectrum.getVal("flux"))
self.assertEqual(3.37991, source.spectrum.getVal("index"))
self.assertEqual(6.16978, source.spatialModel.getVal("pos")[0])
# testing fixflags
f0 = {
"curvature": 0,
"pivot_energy": 0,
"index": 0,
"pos": 0,
"flux": 0
} # special case
f1 = {
"curvature": 0,
"pivot_energy": 0,
"index": 0,
"pos": 0,
"flux": 1
}
f2 = {
"curvature": 0,
"pivot_energy": 0,
"index": 0,
"pos": 1,
"flux": 0
}
f3 = {
"curvature": 0,
"pivot_energy": 0,
"index": 0,
"pos": 1,
"flux": 1
}
f4 = {
"curvature": 0,
"pivot_energy": 0,
"index": 1,
"pos": 0,
"flux": 0
}
f5 = {
"curvature": 0,
"pivot_energy": 0,
"index": 1,
"pos": 0,
"flux": 1
}
f7 = {
"curvature": 0,
"pivot_energy": 0,
"index": 1,
"pos": 1,
"flux": 1
}
f28 = {
"curvature": 1,
"pivot_energy": 1,
"index": 1,
"pos": 0,
"flux": 0
}
f30 = {
"curvature": 1,
"pivot_energy": 1,
"index": 1,
"pos": 1,
"flux": 0
}
f32 = {
"curvature": 0,
"pivot_energy": 0,
"index": 0,
"pos": 2,
"flux": 0
} # special case
fs = [f0, f1, f2, f3, f4, f5, f7, f28, f30, f32]
for i in range(len(fs)):
ff = i
if ff == 6: ff = 7
elif ff == 7: ff = 28
elif ff == 8: ff = 30
elif ff == 9: ff = 32
self.assertDictEqual(
fs[i], SourcesLibraryUT.get_free_params(self.sl.sources[i]))
def test_source_file_parsing(self):
sourceFile = os.path.join(self.currentDirPath,
"test_data/testcase_2AGLJ0835-4514.source")
res = self.sl.parseSourceFile(sourceFile)
self.assertEqual(True, bool(res))
self.assertEqual(True, isinstance(res.multiFlux["value"], float))
self.assertEqual(9.07364e-06, res.multiFlux["value"])
self.assertEqual(True, isinstance(res.multiSqrtTS["value"], float))
self.assertEqual(2.17268, res.multiSqrtTS["value"])
self.assertEqual(None, res.multiDist["value"])
def test_load_source_from_catalog_without_scaling(self):
sources = self.sl.loadSourcesFromCatalog(catalogName="2AGL")
self.assertEqual(175, len(sources))
self.assertEqual(7.45398e-08, sources[0].spectrum.getVal("flux"))
def test_load_source_from_catalog_with_scaling(self):
self.config.setOptions(emin_sources=10, emax_sources=1000)
sources = self.sl.loadSourcesFromCatalog(catalogName="2AGL")
self.assertEqual(175, len(sources))
self.assertEqual(6.940938928095228e-07,
sources[0].spectrum.getVal("flux"))
def test_select_sources_with_selection_string(self):
self.sl.loadSourcesFromFile(
os.path.join(self.currentDirPath, "test_data/sources_2.xml"))
self.assertEqual(2, len(self.sl.sources))
sources = self.sl.selectSources(
'name == "2AGLJ2021+3654" AND flux > 0')
self.assertEqual(1, len(sources))
sourceFile = os.path.join(self.currentDirPath,
"test_data/testcase_2AGLJ2021+3654.source")
mleAnalysisResults = self.sl.parseSourceFile(sourceFile)
self.sl.updateSourceWithMLEResults(mleAnalysisResults)
sources = self.sl.selectSources(
'name == "2AGLJ2021+3654" AND flux > 0')
self.assertEqual(1, len(sources))
sources = self.sl.selectSources('multisqrtts == 10')
self.assertEqual(1, len(sources))
sources = self.sl.selectSources('sqrtts == 10')
self.assertEqual(1, len(sources))
def test_select_sources_with_selection_lambda(self):
self.sl.loadSourcesFromFile(
os.path.join(self.currentDirPath, "test_data/sources_2.xml"))
sources = self.sl.selectSources(lambda name: name == "2AGLJ2021+3654")
self.assertEqual(1, len(sources))
sourceFile = os.path.join(self.currentDirPath,
"test_data/testcase_2AGLJ2021+3654.source")
mleAnalysisResults = self.sl.parseSourceFile(sourceFile)
self.sl.updateSourceWithMLEResults(mleAnalysisResults)
sources = self.sl.selectSources(
lambda name, flux: name == "2AGLJ2021+3654" and flux > 0)
self.assertEqual(1, len(sources))
def test_free_sources_with_selection_string(self):
self.sl.loadSourcesFromFile(
os.path.join(self.currentDirPath, "test_data/sources_2.xml"))
sourceFile = os.path.join(self.currentDirPath,
"test_data/testcase_2AGLJ2021+3654.source")
mleAnalysisResults = self.sl.parseSourceFile(sourceFile)
self.sl.updateSourceWithMLEResults(mleAnalysisResults)
sources = self.sl.freeSources('name == "2AGLJ2021+3654" AND flux > 0',
"flux", False)
self.assertEqual(1, len(sources))
self.assertEqual(True, "flux" not in sources[0].getFreeParams())
sources = self.sl.freeSources('name == "2AGLJ2021+3654" AND flux > 0',
"flux", True)
self.assertEqual(True, "flux" in sources[0].getFreeParams())
sources = self.sl.freeSources('name == "2AGLJ2021+3654" AND flux > 0',
"index", True)
self.assertEqual(True, "index" in sources[0].getFreeParams())
sources = self.sl.freeSources('name == "2AGLJ2021+3654" AND flux > 0',
"index", False)
self.assertEqual(True, "index" not in sources[0].getFreeParams())
def test_free_sources_with_selection_lambda(self):
self.sl.loadSourcesFromFile(
os.path.join(self.currentDirPath, "test_data/sources_2.xml"))
sourceFile = os.path.join(self.currentDirPath,
"test_data/testcase_2AGLJ2021+3654.source")
mleAnalysisResults = self.sl.parseSourceFile(sourceFile)
self.sl.updateSourceWithMLEResults(mleAnalysisResults)
sources = self.sl.freeSources(
lambda name, flux: name == "2AGLJ2021+3654" and flux > 0, "flux",
False)
self.assertEqual(1, len(sources))
self.assertEqual(True, "flux" not in sources[0].getFreeParams())
sources = self.sl.freeSources(
lambda name, flux: name == "2AGLJ2021+3654" and flux > 0, "flux",
True)
self.assertEqual(True, "flux" in sources[0].getFreeParams())
sources = self.sl.freeSources(
lambda name, flux: name == "2AGLJ2021+3654" and flux > 0, "index",
True)
self.assertEqual(True, "index" in sources[0].getFreeParams())
sources = self.sl.freeSources(
lambda name, flux: name == "2AGLJ2021+3654" and flux > 0, "index",
False)
self.assertEqual(True, "index" not in sources[0].getFreeParams())
def test_write_to_file_xml(self):
self.config = AgilepyConfig()
self.config.loadBaseConfigurations(self.agilepyConf)
self.sl.loadSourcesFromFile(
os.path.join(self.currentDirPath, "test_data/sources_2.xml"))
outfileName = "write_to_file_testcase"
outputFile = Path(self.sl.writeToFile(outfileName, fileformat="xml"))
self.assertEqual(True, outputFile.exists())
sourcesxml = parse(outputFile).getroot()
self.assertEqual(2, len(sourcesxml))
def test_write_to_file_txt(self):
self.config = AgilepyConfig()
self.config.loadBaseConfigurations(self.agilepyConf)
sourcesFile = os.path.join(
self.currentDirPath,
"test_data/sourcesconf_for_write_to_file_txt.txt")
self.sl.loadSourcesFromFile(sourcesFile)
outfileName = "write_to_file_testcase"
outputFile = Path(self.sl.writeToFile(outfileName, fileformat="txt"))
self.assertEqual(True, outputFile.exists())
with open(outputFile) as of:
lines = of.readlines()
self.assertEqual(
"1.57017e-07 80.3286 1.12047 2.16619 0 2 _2AGLJ2032+4135 0 0 0 0 0.5 5.0 20 10000 0 100",
lines[0].strip())
self.assertEqual(
"1.69737e-07 79.9247 0.661449 1.99734 0 2 CYGX3 0 0 0 0 0.5 5.0 20 10000 0 100",
lines[1].strip())
self.assertEqual(
"1.19303e-06 78.2375 2.12298 1.75823 3 2 _2AGLJ2021+4029 0 1 3307.63 0 0.5 5.0 20.0 10000.0 0 100",
lines[2].strip())
def test_add_source(self):
self.config = AgilepyConfig()
self.config.loadBaseConfigurations(self.agilepyConf)
self.sl.loadSourcesFromFile(
os.path.join(self.currentDirPath, "test_data/sources_2.xml"))
newSourceDict = {"a": 10}
self.assertRaises(SourceParamNotFoundError, self.sl.addSource,
"newsource", newSourceDict)
newSourceDict = {
"glon": 250,
"glat": 30,
"spectrumType": "LogPaperone"
}
self.assertRaises(SpectrumTypeNotFoundError, self.sl.addSource,
"newsource", newSourceDict)
newSourceDict = {
"glon": 250,
"glat": 30,
"spectrumType": "LogParabola"
}
self.assertRaises(SourceParamNotFoundError, self.sl.addSource, "",
newSourceDict)
self.assertRaises(SourceParamNotFoundError, self.sl.addSource, None,
newSourceDict)
self.assertRaises(SourceParamNotFoundError, self.sl.addSource,
"newsource", newSourceDict)
newSourceDict = {
"glon": 250,
"glat": 30,
"spectrumType": "LogParabola",
"flux": 40,
"index": 2,
"pivotEnergy": 4,
"curvature": 5
}
newSourceObj = self.sl.addSource("newsource", newSourceDict)
self.assertEqual(True, isinstance(newSourceObj, PointSource))
newSource = self.sl.selectSources('name == "newsource"').pop()
self.assertEqual(40, newSource.spectrum.getVal("flux"))
self.assertEqual(5, newSource.spectrum.getVal("curvature"))
self.assertEqual("newsource", newSource.name)
self.assertEqual(35.2462913047547,
newSource.spatialModel.getVal("dist"))
def test_convert_catalog_to_xml(self):
catalogFile = "$AGILE/catalogs/2AGL.multi"
outfile = self.sl.convertCatalogToXml(catalogFile)
sourcesxml = parse(outfile).getroot()
self.assertEqual(175, len(sourcesxml))
added = self.sl.loadSourcesFromFile(outfile)
self.assertEqual(175, len(added))
self.assertEqual(175, len(self.sl.sources))
def test_backup_restore(self):
self.config = AgilepyConfig()
self.config.loadBaseConfigurations(self.agilepyConf)
self.sl.loadSourcesFromFile(
os.path.join(self.currentDirPath, "test_data/sources_2.xml"))
"""
for s in self.sl.getSources():
print(s)
"""
self.assertEqual(2, len(self.sl.sources))
self.sl.backupSL()
self.sl.deleteSources('name=="2AGLJ2021+4029"')
self.assertEqual(1, len(self.sl.sources))
self.sl.deleteSources('name=="2AGLJ2021+3654"')
self.assertEqual(0, len(self.sl.sources))
self.sl.restoreSL()
self.assertEqual(2, len(self.sl.sources))
class SourceModelUT(unittest.TestCase):
def setUp(self):
self.currentDirPath = Path(__file__).parent.absolute()
self.test_logs_dir = Path(self.currentDirPath).joinpath(
"test_logs", "SourceModelUT")
self.test_logs_dir.mkdir(parents=True, exist_ok=True)
os.environ["TEST_LOGS_DIR"] = str(self.test_logs_dir)
outDir = Path(os.path.join(os.environ["AGILE"])).joinpath(
"agilepy-test-data/unittesting-output/core")
if outDir.exists() and outDir.is_dir():
shutil.rmtree(outDir)
self.sourcesTxt = os.path.join(self.currentDirPath,
"test_data/sources.txt")
self.sourcesXml = os.path.join(self.currentDirPath,
"test_data/sources.xml")
self.agilepyConf = os.path.join(self.currentDirPath,
"conf/agilepyconf.yaml")
self.config = AgilepyConfig()
self.config.loadBaseConfigurations(self.agilepyConf)
self.config.loadConfigurationsForClass("AGAnalysis")
self.logger = AgilepyLogger()
self.logger.initialize(
self.config.getConf("output", "outdir"),
self.config.getConf("output", "logfilenameprefix"),
self.config.getConf("output", "verboselvl"))
self.sl = SourcesLibrary(self.config, self.logger)
def test_parse_source_XML_format(self):
xmlRoot = parse(self.sourcesXml).getroot()
sources = []
for sourceRoot in xmlRoot:
source = Source.parseSourceXMLFormat(sourceRoot)
sources.append(source)
assert sources[0].get("flux")["value"] == 7.45398e-08
assert sources[0].get("pos")["value"] == (92.4102, -10.3946)
assert sources[1].get("flux")["value"] == 41.6072e-08
assert sources[1].get("pos")["value"] == (119.677, 10.544)
assert sources[2].get("flux")["value"] == 969.539e-08
assert sources[2].get("index2")["value"] == 1.3477
assert sources[2].get("index2")["free"] == 1
assert sources[2].get("pos")["value"] == (263.585, -2.84083)
assert sources[3].get("flux")["value"] == 35.79e-08
assert sources[3].get("curvature")["value"] == 0.682363
assert sources[3].get("curvature")["max"] == 3
assert sources[3].get("pos")["value"] == (6.16978, -0.0676943)
def test_parse_source_TXT_format(self):
sources = []
with open(self.sourcesTxt, "r") as txtFile:
for line in txtFile:
if line == "\n":
continue
source = Source.parseSourceTXTFormat(line)
sources.append(source)
assert sources[0].name == "2AGLJ2021+4029"
assert sources[0].get("flux")["value"] == 119.3e-08
assert sources[0].get("pos")["value"] == (78.2375, 2.12298)
assert sources[1].name == "2AGLJ2021+3654"
assert sources[1].get("flux")["value"] == 70.89e-08
assert sources[1].get("pos")["value"] == (75.2562, 0.151831)
def test_init(self):
source = PointSource(name="test-source")
source.spectrum = Spectrum.getSpectrum("PowerLaw")
assert "PointSource" == type(source.spatialModel).__name__
def test_get(self):
source = PointSource(name="test-source")
source.spectrum = Spectrum.getSpectrum("PowerLaw")
assert "PointSource" == type(source.spatialModel).__name__
assert len(source.get("flux").keys()) == 6
assert source.getVal("flux") == None
with pytest.raises(SourceParameterNotFound):
source.get("fluxxx")
with pytest.raises(SourceParameterNotFound):
source.getVal("fluxxx")
def test_set(self):
source = PointSource(name="test-source")
source.spectrum = Spectrum.getSpectrum("PowerLaw")
assert "PointSource" == type(source.spatialModel).__name__
source.set("flux", {"min": 1})
source.setVal("flux", 10)
assert source.spectrum.flux["min"] == 1
assert source.spectrum.flux["value"] == 10
with pytest.raises(SourceParameterNotFound):
source.set("fluxxx", {"value": 10})
with pytest.raises(ValueError):
source.set("fluxxx", 10)
with pytest.raises(SourceParameterNotFound):
source.setVal("fluxxx", 100)
def test_str(self):
source = PointSource(name="test-source")
source.spectrum = Spectrum.getSpectrum("PowerLaw")
source.setVal("flux", 100)
source.setVal("index", 1000)
source.setVal("pos", (30, 15))
print(source)
"""