Merge pull request #178 from krishnatejavedula/feature/logging

Change print() to logging.info() #48
cositools · May 23, 2024 · 16c23c2 · 16c23c2
2 parents 7c660b5 + aa80592
commit 16c23c2
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Showing 5 changed files with 51 additions and 54 deletions.
diff --git a/cosipy/data_io/BinnedData.py b/cosipy/data_io/BinnedData.py
@@ -53,8 +53,8 @@ def get_binned_data(self, unbinned_data=None, output_name=None, \
         but it does not explicitly return it.
         """
 
-        # Make print statement:
-        print("binning data...")
+        # Log message:
+        logger.info("binning data...")
 
         # Option to read in unbinned data file:
         if unbinned_data:
@@ -72,18 +72,14 @@ def get_binned_data(self, unbinned_data=None, output_name=None, \
             num_bins = round(delta_t / self.time_bins)
             new_bin_size = delta_t / num_bins
             if self.time_bins != new_bin_size:
-                print()
-                print("Note: time bins must be equally spaced between min and max time.")
-                print("Using time bin size [s]: " + str(new_bin_size))
-                print()
+                logger.info("Note: time bins must be equally spaced between min and max time.")
+                logger.info("Using time bin size [s]: " + str(new_bin_size))
             time_bin_edges = np.linspace(min_time,max_time,num_bins+1)
 
         if type(self.time_bins).__name__ == 'list':
             # Check that bins correspond to min and max time:
             if (self.time_bins[0] > min_time) | (self.time_bins[-1] < max_time):
-                print()
-                print("ERROR: Time bins do not cover the full selected data range!")
-                print()
+                logger.error("ERROR: Time bins do not cover the full selected data range!")
                 sys.exit()
             time_bin_edges = np.array(self.time_bins)
 
@@ -262,7 +258,7 @@ def plot_psichi_map(self):
         Plot psichi healpix map.
         """
 
-        print("plotting psichi in Galactic coordinates...")
+        logger.info("plotting psichi in Galactic coordinates...")
         plot, ax = self.binned_data.project('PsiChi').plot(ax_kw = {'coord':'G'})
         ax.get_figure().set_figwidth(4)
         ax.get_figure().set_figheight(3)
@@ -339,8 +335,8 @@ def get_raw_spectrum(self, binned_data=None, time_rate=False, output_name=None):
             If True, calculates ct/keV/s. The defualt is ct/keV. 
         """
 
-        # Make print statement:
-        print("getting raw spectrum...")
+        # Log message:
+        logger.info("getting raw spectrum...")
 
         # Option to read in binned data from hdf5 file:
         if binned_data:
@@ -384,8 +380,8 @@ def get_raw_lightcurve(self, binned_data=None, output_name=None):
             Prefix of output files. Writes both pdf and dat file. 
         """
 
-        # Make print statement:
-        print("getting raw lightcurve...")
+        # Log message:
+        logger.info("getting raw lightcurve...")
 
         # Option to read in binned data from hdf5 file:
         if binned_data:

diff --git a/cosipy/data_io/ReadTraTest.py b/cosipy/data_io/ReadTraTest.py
@@ -4,6 +4,8 @@
 import numpy as np
 import sys
 import pandas as pd
+import logging
+logger = logging.getLogger(__name__)
 
 try:
     # Load MEGAlib into ROOT
@@ -61,15 +63,14 @@ def read_tra_old(self,make_plots=True):
         # tra file to use:
         tra_file = self.data_file
 
-        # Make print statement:
-        print()
-        print("Read tra test...")
-        print()
+        # Log message:
+        logger.info("Read tra test...")
+
 
         # Check if file exists:
         Reader = M.MFileEventsTra()
         if Reader.Open(M.MString(tra_file)) == False:
-            print("Unable to open file %s. Aborting!" %self.data_file)
+            logger.error("Unable to open file %s. Aborting!" %self.data_file)
             sys.exit()
 
         # Initialise empty lists:

diff --git a/cosipy/data_io/UnBinnedData.py b/cosipy/data_io/UnBinnedData.py
@@ -23,6 +23,7 @@
 import time
 logger = logging.getLogger(__name__)
 
+
 class UnBinnedData(DataIO):
     """Handles unbinned data."""
 
@@ -128,7 +129,7 @@ def read_tra(self, output_name=None, run_test=False, use_ori=False,
         if run_test == True:
             c_E0 = 510.999
 
-        print("Preparing to read file...")
+        logger.info("Preparing to read file...")
 
         # Open .tra.gz file:
         if self.data_file.endswith(".gz"):
@@ -143,8 +144,8 @@ def read_tra(self, output_name=None, run_test=False, use_ori=False,
 
             # If fast method fails, use long method, which should work in all cases.
             except:
-                print("Initial attempt failed.")
-                print("Using long method...")
+                logger.info("Initial attempt failed.")
+                logger.info("Using long method...")
                 g = gzip.open(self.data_file,"rt")
                 num_lines = sum(1 for line in g)
                 g.close()
@@ -159,21 +160,19 @@ def read_tra(self, output_name=None, run_test=False, use_ori=False,
                 num_lines = float(proc.communicate()[0])
 
             except:
-                print("Initial attempt failed.")
-                print("Using long method...")
+                logger.info("Initial attempt failed.")
+                logger.info("Using long method...")
                 g = open(self.data_file,"rt")
                 num_lines = sum(1 for line in g)
                 g.close()
 
         else: 
-            print()
-            print("ERROR: Input data file must have '.tra' or '.gz' extenstion.")
-            print()
+            logger.error("ERROR: Input data file must have '.tra' or '.gz' extenstion.")
             sys.exit()
 
 
         # Read tra file line by line:
-        print("Reading file...")
+        logger.info("Reading file...")
         N_events = 0 # number of events
         pbar = tqdm(total=num_lines) # start progress bar
         for line in f:
@@ -196,7 +195,7 @@ def read_tra(self, output_name=None, run_test=False, use_ori=False,
             if event_max != None:
                 if N_events >= event_max:
                     pbar.close()
-                    print("Stopping here: only reading a subset of events")
+                    logger.info("Stopping here: only reading a subset of events")
                     break
 
             # Total photon energy and Compton angle: 
@@ -258,14 +257,14 @@ def read_tra(self, output_name=None, run_test=False, use_ori=False,
 
         # Close progress bar:
         pbar.close()
-        print("Making COSI data set...")
-        print("total events to procecss: " + str(len(erg)))
+        logger.info("Making COSI data set...")
+        logger.info("total events to procecss: " + str(len(erg)))
 
         # Clear unused memory:
         gc.collect()
 
         # Initialize arrays:
-        print("Initializing arrays...")
+        logger.info("Initializing arrays...")
         erg = np.array(erg)
         phi = np.array(phi)
         tt = np.array(tt)
@@ -281,8 +280,8 @@ def read_tra(self, output_name=None, run_test=False, use_ori=False,
         # Check if the input data has pointing information, 
         # if not, get it from the spacecraft file:
         if (use_ori == False) & (len(lonZ)==0):
-            print("WARNING: No pointing information in input data.")
-            print("Getting pointing information from spacecraft file.")
+            logger.warning("WARNING: No pointing information in input data.")
+            logger.warning("Getting pointing information from spacecraft file.")
             use_ori = True
 
         # Option to get X and Z pointing information from orientation file:
@@ -346,7 +345,7 @@ def read_tra(self, output_name=None, run_test=False, use_ori=False,
         self.chi_gal_test = chi_gal_rad - np.pi
 
         # Make observation dictionary
-        print("Making dictionary...")
+        logger.info("Making dictionary...")
         cosi_dataset = {'Energies':erg,
                         'TimeTags':tt,
                         'Xpointings (glon,glat)':np.array([lonX,latX]).T,
@@ -362,13 +361,13 @@ def read_tra(self, output_name=None, run_test=False, use_ori=False,
 
         # Option to write unbinned data to file (either fits or hdf5):
         if output_name != None:
-            print("Saving file...")
+            logger.info("Saving file...")
             self.write_unbinned_output(output_name) 
 
         # Get processing time:
         end_time = time.time()
         processing_time = end_time - start_time
-        print("total processing time [s]: " + str(processing_time))
+        logger.info("total processing time [s]: " + str(processing_time))
 
         return 
 
@@ -592,7 +591,7 @@ def select_data(self, output_name=None, unbinned_data=None):
         Only cuts in time are allowed for now. 
         """
 
-        print("Making data selections...")
+        logger.info("Making data selections...")
 
         # Option to read in unbinned data file:
         if unbinned_data:
@@ -612,7 +611,7 @@ def select_data(self, output_name=None, unbinned_data=None):
 
         # Write unbinned data to file (either fits or hdf5):
         if output_name != None:
-            print("Saving file...")
+            logger.info("Saving file...")
             self.write_unbinned_output(output_name)
 
         return
@@ -633,9 +632,7 @@ def combine_unbinned_data(self, input_files, output_name=None):
         counter = 0
         for each in input_files:
 
-            print()
-            print("adding %s..." %each)
-            print()
+            logger.info("adding %s..." % each)
 
             # Read dict from hdf5 or fits:
             if self.unbinned_output == 'hdf5':
@@ -661,4 +658,4 @@ def combine_unbinned_data(self, input_files, output_name=None):
         if output_name != None:
             self.write_unbinned_output(output_name)
 
-        return
+        return
diff --git a/cosipy/spacecraftfile/SpacecraftFile.py b/cosipy/spacecraftfile/SpacecraftFile.py
@@ -14,6 +14,9 @@
 
 from .scatt_map import SpacecraftAttitudeMap
 
+import logging
+logger = logging.getLogger(__name__)
+
 class SpacecraftFile():
 
     def __init__(self, time, x_pointings = None, y_pointings = None, z_pointings = None, attitude = None,
@@ -337,7 +340,7 @@ def get_target_in_sc_frame(self, target_name, target_coord, attitude = None, qui
 
         self.target_name = target_name
         if quiet == False:
-            print("Now converting to the Spacecraft frame...")
+            logger.info("Now converting to the Spacecraft frame...")
         self.src_path_cartesian = SkyCoord(np.dot(self.attitude.rot.inv().as_matrix(), target_coord.cartesian.xyz.value),
                                            representation_type = 'cartesian',
                                            frame = SpacecraftFrame())
@@ -348,7 +351,7 @@ def get_target_in_sc_frame(self, target_name, target_coord, attitude = None, qui
                                                          self.src_path_cartesian.y,
                                                          self.src_path_cartesian.z)
         if quiet == False:
-            print(f"Conversion completed!")
+            logger.info(f"Conversion completed!")
 
         # generate the numpy array of l and b to save to a npy file
         l = np.array(self.src_path_spherical[2].deg)  # note that 0 is Quanty, 1 is latitude and 2 is longitude and they are in rad not deg
@@ -543,12 +546,12 @@ def get_psr_rsp(self, response = None, dwell_map = None, dts = None):
             self.Em_hi = np.float32(self.Em_edges[1:])
 
          # get the effective area and matrix
-        print("Getting the effective area ...")
+        logger.info("Getting the effective area ...")
         self.areas = np.float32(np.array(self.psr.project('Ei').to_dense().contents))/self.dts.to_value(u.second).sum()
         spectral_response = np.float32(np.array(self.psr.project(['Ei','Em']).to_dense().contents))
         self.matrix = np.float32(np.zeros((self.Ei_lo.size,self.Em_lo.size))) # initate the matrix
 
-        print("Getting the energy redistribution matrix ...")
+        logger.info("Getting the energy redistribution matrix ...")
         for i in np.arange(self.Ei_lo.size):
             new_raw = spectral_response[i,:]/spectral_response[i,:].sum()
             self.matrix[i,:] = new_raw

diff --git a/cosipy/threeml/COSILike.py b/cosipy/threeml/COSILike.py
@@ -114,11 +114,11 @@ def __init__(self, name, dr, data, bkg, sc_orientation,
         # consistent way for point srcs and extended srcs. 
         self.precomputed_psr_file = precomputed_psr_file
         if self.precomputed_psr_file != None:
-            print("... loading the pre-computed image response ...")
+            logger.info("... loading the pre-computed image response ...")
             self.image_response = DetectorResponse.open(self.precomputed_psr_file)
             # in the near future, we will implement ExtendedSourceResponse class, which should be used here (HY).
             # probably, it is better to move this loading part outside of this class. Then, we don't have to load the response everytime we start the fitting (HY).
-            print("--> done")
+            logger.info("--> done")
 
     def set_model(self, model):
         """
@@ -195,7 +195,7 @@ def set_model(self, model):
 
             if self._psr is None or len(point_sources) != len(self._psr):
 
-                print("... Calculating point source responses ...")
+                logger.info("... Calculating point source responses ...")
 
                 self._psr = {}
                 self._source_location = {} # Should the poition information be in the point source response? (HY)
@@ -214,15 +214,15 @@ def set_model(self, model):
                     else:
                         raise RuntimeError("Unknown coordinate system")
 
-                    print(f"--> done (source name : {name})")
+                    logger.info(f"--> done (source name : {name})")
 
-                print(f"--> all done")
+                logger.info(f"--> all done")
 
         # check if the source location is updated or not
         for name, source in point_sources.items():
 
             if source.position.sky_coord != self._source_location[name]:
-                print(f"... Re-calculating the point source response of {name} ...")
+                logger.info(f"... Re-calculating the point source response of {name} ...")
                 coord = source.position.sky_coord
 
                 self._source_location[name] = copy.deepcopy(coord) # to avoid same memory issue
@@ -236,7 +236,7 @@ def set_model(self, model):
                 else:
                     raise RuntimeError("Unknown coordinate system")
 
-                print(f"--> done (source name : {name})")
+                logger.info(f"--> done (source name : {name})")
 
         # Get expectation for point sources:
         for name,source in point_sources.items():