Merge pull request #151 from eneights/main

Fix documentation link and only print one log-likelihood warning

cosipy/threeml/COSILike.py

@@ -33,6 +33,8 @@
 import logging
 logger = logging.getLogger(__name__)
 
+import inspect
+
 class COSILike(PluginPrototype):
     """
     COSI 3ML plugin.
@@ -127,6 +129,10 @@ def set_model(self, model):
         model : astromodels.core.model.Model
             Any model supported by astromodels
         """
+
+        # Temporary fix to only print log-likelihood warning once max per fit
+        if inspect.stack()[1][3] == '_assign_model_to_data':
+            self._printed_warning = False
 
         # Get point sources and extended sources from model: 
         point_sources = model.point_sources
@@ -294,7 +300,9 @@ def get_log_like(self):
                 expectation = self._signal + self._bkg.contents
 
         expectation += 1e-12 # to avoid -infinite log-likelihood (occurs when expected counts = 0 but data != 0)
-        logger.warning("Adding 1e-12 to each bin of the expectation to avoid log-likelihood = -inf.")
+        if not self._printed_warning:
+            logger.warning("Adding 1e-12 to each bin of the expectation to avoid log-likelihood = -inf.")
+            self._printed_warning = True
         # This 1e-12 should be defined as a parameter in the near future (HY)
 
         # Convert data into an arrary:

docs/tutorials/index.rst

@@ -32,7 +32,7 @@ List of tutorials and contents, as a link to the corresponding Python notebook i
   - Meaning of the TS map and how to compute confidence contours
   - Computing a TS map, getting the best location and estimating the error
 
-5. Fitting the spectrum of a GRB `(ipynb) <https://github.com/cositools/cosipy/tree/main/docs/tutorials/spectral_fits/continuum_fit/grb/SpectralFit.ipynb>`_
+5. Fitting the spectrum of a GRB `(ipynb) <https://github.com/cositools/cosipy/blob/main/docs/tutorials/spectral_fits/continuum_fit/grb/SpectralFit_GRB.ipynb>`_
 
   - Introduction to 3ML and astromodels
   - Likelihood analysis. 
@@ -69,7 +69,7 @@ List of tutorials and contents, as a link to the corresponding Python notebook i
    Spacecraft orientation and location <Point_source_resonse.ipynb>
    Detector response and signal expectation <DetectorResponse.ipynb>
    TS Map: localizing a GRB <ts_map/Parallel_TS_map_computation_DC2.ipynb>
-   Fitting the spectrum of a GRB <spectral_fits/continuum_fit/grb/SpectralFit.ipynb>
+   Fitting the spectrum of a GRB <spectral_fits/continuum_fit/grb/SpectralFit_GRB.ipynb>
    Fitting the spectrum of the Crab <spectral_fits/continuum_fit/crab/SpectralFit_Crab.ipynb>
    Extended source model fitting <spectral_fits/extended_source_fit/diffuse_511_spectral_fit.ipynb>
    Image deconvolution <image_deconvolution/511keV/ScAttBinning/511keV-DC2-ScAtt-ImageDeconvolution.ipynb>