Skip to content

Commit

Permalink
introduced logger
Browse files Browse the repository at this point in the history
  • Loading branch information
@ferrigno
ferrigno committed Jan 12, 2024
1 parent 56c15ab commit b2f4d8e
Showing 1 changed file with 55 additions and 81 deletions.
136 changes: 55 additions & 81 deletions mosaic/treat.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
sextractor_share = "/usr/local/share/sextractor"

def render(*args):
print(*args)
logger.info('%s', *args)
return

## 2d gaussian
Expand Down Expand Up @@ -207,7 +207,7 @@ def calibrate(self):

rec_thresh = -(bin_centres[symneg > 0].min())

print("recommended threshold for 1 noise source", rec_thresh)
logger.info("recommended threshold for 1 noise source %f", rec_thresh)

np.plot.p.semilogy()

Expand All @@ -218,7 +218,7 @@ def calibrate(self):

import scipy.stats

print(render("{RED}kurtosis:{/}"), scipy.stats.kurtosis(pixels))
logger.info("{RED}kurtosis:{/} %f", scipy.stats.kurtosis(pixels))

def fit_core(self):
pixels = self.pixels
Expand Down Expand Up @@ -252,7 +252,7 @@ def profile(x, *p):
self.core_fit_function = lambda x: profile(x, *coeff)
self.core_fit = bin_centres, hist_fit

print("fit result", coeff)
logger.info("fit result %s", coeff)

np.plot.p.plot(bin_centres, hist_fit)

Expand Down Expand Up @@ -394,19 +394,19 @@ def raw_variance_ext(self):

def inspect_raw(self):
try:
print("exposure", self.raw_exposure_ext().header["EXTNAME"])
print("intensity", self.raw_intensity_ext().header["EXTNAME"])
print("significance", self.raw_significance_ext().header["EXTNAME"])
print("variance", self.raw_variance_ext().header["EXTNAME"])
logger.info("exposure %s", self.raw_exposure_ext().header["EXTNAME"])
logger.info("intensity %s", self.raw_intensity_ext().header["EXTNAME"])
logger.info("significance %s", self.raw_significance_ext().header["EXTNAME"])
logger.info("variance %s", self.raw_variance_ext().header["EXTNAME"])
except:
print("mosaic without extname?")
logger.info("mosaic without extname?")
try:
print("exposure", self.raw_exposure_ext().header["IMATYPE"])
print("intensity", self.raw_intensity_ext().header["IMATYPE"])
print("significance", self.raw_significance_ext().header["IMATYPE"])
print("variance", self.raw_variance_ext().header["IMATYPE"])
logger.info("exposure %s", self.raw_exposure_ext().header["IMATYPE"])
logger.info("intensity %s", self.raw_intensity_ext().header["IMATYPE"])
logger.info("significance %s", self.raw_significance_ext().header["IMATYPE"])
logger.info("variance %s", self.raw_variance_ext().header["IMATYPE"])
except:
print("mosaic without imatype?")
logger.info("mosaic without imatype?")

def get_shortname(self):
return "ImageAnalysis"
Expand All @@ -421,7 +421,7 @@ def variance_ext(self):
return self.raw_variance_ext()

def main(self):
print("About to analyze %s energy bands" % self.get_n_ebands())
logger.info("About to analyze %s energy bands" % self.get_n_ebands())
for self.i_band in range(self.get_n_ebands()):
self.tag = "%.5lg_%.5lg" % self.raw_erange()
#print(self.tag)
Expand All @@ -442,19 +442,19 @@ def pixel_distribution(self):
# D.show_all()

def estimate_sensitivity(self):
print("opening mosaic...")
logger.info("opening mosaic...")
exposure = self.exposure_ext().data
variance = self.variance_ext().data
image = self.sextractor.filtered_ext().data
sigimage = self.sextractor2.filtered_ext().data

print("opening rms...")
logger.info("opening rms...")

rms = self.sextractor.background_rms_ext().data

bkg = self.sextractor.background_ext().data

print(rms)
logger.debug('%s', rms)

def avg_nonan(a):
return np.average(a[np.where(~np.isnan(a))])
Expand All @@ -475,58 +475,32 @@ def avg_nonan(a):
cts2mcrab = lambda x:x
mcrab2ecs = lambda x:x

print(render("{RED}enery band{/}"), e1, e2)
print(
render("{RED}avg_nonan{/} "),
avg_nonan(sensi),
render("{YEL}mcrab{/}"),
mcrab2ecs(avg_nonan(sensi)),
"ecs",
avg_nonan(exposure) / 1e6,
"Ms",
)
logger.info("{RED}enery band{/} %f %f", e1, e2)
logger.info("{RED}avg_nonan{/} %f", avg_nonan(sensi))
logger.info("{YEL}mcrab{/} %f ecs %f Ms", mcrab2ecs(avg_nonan(sensi)), avg_nonan(exposure) / 1e6,)

print(
render("{RED}minimal sensitivity{/} "),
sensi.min(),
render("{YEL}mcrab{/}"),
mcrab2ecs(sensi.min()),
"ecs",
exposure.flatten()[sensi.flatten().argmin()] / 1e6,
"Ms",
)
logger.info("{RED}minimal sensitivity{/} %f', ", sensi.min())
logger.info("{YEL}mcrab{/} %f ecs %f Ms", mcrab2ecs(sensi.min()), exposure.flatten()[sensi.flatten().argmin()] / 1e6)

print(
render("{RED}exposure-corrected avg_nonan{/} "),
avg_nonan(sensi * np.sqrt(exposure / 1e6)),
render("{YEL}mcrab-Ms{/}"),
mcrab2ecs(avg_nonan(sensi * np.sqrt(exposure / 1e6))),
"ecs",
avg_nonan(exposure) / 1e6,
"Ms",
)
logger.info("{RED}exposure-corrected avg_nonan{/} %f", avg_nonan(sensi * np.sqrt(exposure / 1e6)))
logger.info("{YEL}mcrab-Ms{/} %f ecs %f Ms", mcrab2ecs(avg_nonan(sensi * np.sqrt(exposure / 1e6))), avg_nonan(exposure) / 1e6)

print(
render("{RED}exposure-corrected minimal sensitivity{/}"),
sensi.min() * 1e-3 * np.sqrt(exposure.flatten()[sensi.flatten().argmin()]),
render("{YEL}mcrab-Ms{/}"),
logger.info("{RED}exposure-corrected minimal sensitivity{/} %f" ,
sensi.min() * 1e-3 * np.sqrt(exposure.flatten()[sensi.flatten().argmin()]))
logger.info("{YEL}mcrab-Ms{/} %f ecs %f Ms",
mcrab2ecs(
sensi.min() * 1e-3 * np.sqrt(exposure.flatten()[sensi.flatten().argmin()])
),
"ecs",
exposure.flatten()[sensi.flatten().argmin()] / 1e6,
"Ms",
)
)

bmin, bmax = bkg.min(), bkg.max()
print(
render("{RED}smooth background range{/} "),
logger.info("{RED}smooth background range{/} %f %f",
cts2mcrab(bmin),
cts2mcrab(bmax),
render("{YEL}mcrab{/}"),
cts2mcrab(bmax))
logger.info("{YEL}mcrab{/} %f %f ecs",
cts2ecs(bmin),
cts2ecs(bmax),
"ecs",
)

statdict = dict(
Expand Down Expand Up @@ -604,8 +578,8 @@ def extract_sources(self):
self.sextractor = SExtractor("sextractor")
self.sextractor.back_size = self.back_size

print(self.mosaic_fn + "[1]")
print(self.fullpath(self.mosaic_fn) + "[1]")
logger.debug(self.mosaic_fn + "[1]")
logger.debug(self.fullpath(self.mosaic_fn) + "[1]")

self.sextractor.set_mosaic(self.fullpath(self.mosaic_fn + "[1]"))
self.sextractor.threshold = self.threshold
Expand Down Expand Up @@ -668,7 +642,7 @@ def read_sources(self):
zip(*[reversed(re.search(" *(\d+) (.*?) ", c).groups()) for c in cd])
)
except Exception as e:
print("problem with keys: ", e)
logger.warning("problem with keys: %s", e)

# print("Reading " + self.sextractor2.hostdir + "/test.cat")
sources = np.genfromtxt(self.sextractor2.hostdir + "/test.cat", names=keys)
Expand Down Expand Up @@ -786,7 +760,7 @@ def read_sources(self):
plt.savefig("source_%.5lg.png" % peaksig)
fns += "source_%.5lg.png " % peaksig
except Exception as e:
print("problem with fitting: ", e)
logger.warning("problem with fitting: %s", e)
raise RuntimeError(e)


Expand Down Expand Up @@ -883,16 +857,16 @@ def mask_mosaic(self):

good_exposure = exposure[~np.isnan(exposure) & ~np.isinf(exposure) & (exposure != 0)]

print("maximum exposure", good_exposure.max())
print("average exposure", np.average(good_exposure))
logger.info("maximum exposure %f", good_exposure.max())
logger.info("average exposure %f", np.average(good_exposure))

cut = exposure < good_exposure.max() / self.exposure_fraction_cut

print("exposure cut below: ", exposure[~cut].min())
logger.info("exposure cut below: %f", exposure[~cut].min())

hdu_list = []

print("energy range:", self.raw_erange())
logger.info("energy range: %s", self.raw_erange())

sig_image = self.raw_significance_ext().data
flux_image = self.raw_intensity_ext().data
Expand All @@ -902,7 +876,7 @@ def mask_mosaic(self):
flux_image[cut] = np.NaN
var_image[cut] = np.NaN

print("band", self.i_band)
logger.info("band %s", self.i_band)

# if self.i_band==0:
hdu_list.append(fits.PrimaryHDU(sig_image))
Expand All @@ -920,7 +894,7 @@ def mask_mosaic(self):
h.header.extend(wcsh)
h.header["E_MIN"] = e1
h.header["E_MAX"] = e2
print("updating header:", e1, e2)
logger.info("updating header: %f %f", e1, e2)

fn = self.hostdir+self.out_prefix+"masked_mosaic_%s.fits" % (self.tag)

Expand Down Expand Up @@ -978,19 +952,19 @@ def fullpath(self, x):

def inspect_raw(self):
try:
print("exposure", self.raw_exposure_ext().header["EXTNAME"])
print("intensity", self.raw_intensity_ext().header["EXTNAME"])
print("significance", self.raw_significance_ext().header["EXTNAME"])
print("variance", self.raw_variance_ext().header["EXTNAME"])
logger.info("exposure %s", self.raw_exposure_ext().header["EXTNAME"])
logger.info("intensity %s", self.raw_intensity_ext().header["EXTNAME"])
logger.info("significance %s", self.raw_significance_ext().header["EXTNAME"])
logger.info("variance %s", self.raw_variance_ext().header["EXTNAME"])
except:
print("mosaic without extname?")
logger.info("mosaic without extname?")
try:
print("exposure", self.raw_exposure_ext().header["IMATYPE"])
print("intensity", self.raw_intensity_ext().header["IMATYPE"])
print("significance", self.raw_significance_ext().header["IMATYPE"])
print("variance", self.raw_variance_ext().header["IMATYPE"])
logger.info("exposure %s", self.raw_exposure_ext().header["IMATYPE"])
logger.info("intensity %s", self.raw_intensity_ext().header["IMATYPE"])
logger.info("significance %s", self.raw_significance_ext().header["IMATYPE"])
logger.info("variance %s", self.raw_variance_ext().header["IMATYPE"])
except:
print("mosaic without imatype?")
logger.info("mosaic without imatype?")

def get_shortname(self):
return "ImageAnalysis"
Expand All @@ -1009,7 +983,7 @@ def main(self):
self.dump_statistics()

def estimate_sensitivity(self):
print("opening mosaic...")
logger.info("opening mosaic...")
exposure = self.raw_exposure_ext().data

variance = self.raw_variance_ext().data
Expand Down Expand Up @@ -1077,8 +1051,8 @@ def get_n_ebands(self):

def get_total_ebands(self):
gt = fits.open(self.get_raw_mosaic_fn())[1].data
print("group:", gt)
print("found bands:", (len(gt)) / 5)
logger.info("group: %s", gt)
logger.info("found bands: %f", (len(gt)) / 5)
return (len(gt)) / 5

def set_raw_mosaic_fn(self, fn):
Expand Down

0 comments on commit b2f4d8e

Please sign in to comment.