Issue 464 logger instead of print

nansat/__init__.py

@@ -15,10 +15,14 @@
 # but WITHOUT ANY WARRANTY without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 from __future__ import absolute_import
+import logging.config
 import os
 import sys
+import os.path
 import warnings
 import importlib
+import yaml
+
 pixfun_module_name = 'nansat._pixfun_py{0}'.format(sys.version_info[0])
 
 # check if pixel functions were compiled using setup_tools
@@ -41,3 +45,18 @@
 __all__ = ['NSR', 'Domain', 'Nansat', 'Figure']
 
 os.environ['LOG_LEVEL'] = '30'
+
+#down below is logging configurations
+DEFAULT_LOGGING_CONF_FILE = os.path.join(os.path.dirname(__file__), 'logging.yml')
+LOGGING_CONF_FILE = os.getenv('NANSAT_LOG_CONF_PATH', DEFAULT_LOGGING_CONF_FILE)
+
+try:
+    with open(LOGGING_CONF_FILE, 'rb') as stream:
+        logging_configuration = yaml.safe_load(stream)  # pylint: disable=invalid-name
+except FileNotFoundError:
+    print(f"'{LOGGING_CONF_FILE}' does not exist, logging can't be configured.", file=sys.stderr)
+    logging_configuration = None  # pylint: disable=invalid-name
+
+if logging_configuration:
+    logging.config.dictConfig(logging_configuration)
+    logging.captureWarnings(True)

nansat/logging.yml

@@ -0,0 +1,16 @@
+---
+version: 1
+formatters:
+  precise:
+    format: '%(asctime)s - %(name)s - %(threadName)s - %(levelname)s - %(message)s'
+handlers:
+  console:
+    class: 'logging.StreamHandler'
+    formatter: 'precise'
+    stream  : 'ext://sys.stdout'
+loggers:
+  Nansat:
+    level: 'INFO'
+    handlers:
+      - 'console'
+...

nansat/mappers/mapper_aapp_l1b.py

@@ -10,11 +10,15 @@
 import sys
 import struct
 import datetime
+import logging
 
 from nansat.exceptions import WrongMapperError
 from nansat.geolocation import Geolocation
 from nansat.vrt import VRT
 
+LOGGER = logging.getLogger("Nansat."+__name__)
+LOGGER.addHandler(logging.NullHandler())
+
 satIDs = {4: 'NOAA-15', 2: 'NOAA-16', 6: 'NOAA-17', 7: 'NOAA-18', 8: 'NOAA-19',
           11: 'Metop-B (Metop-1)', 12: 'Metop-A (Metop-2)',
           13: 'Metop-C (Metop-3)'}
@@ -66,8 +70,7 @@ def __init__(self, filename, gdalDataset, gdalMetadata, **kwargs):
         numCalibratedScanLines = int(struct.unpack('<H', fp.read(2))[0])
         missingScanLines = int(struct.unpack('<H', fp.read(2))[0])
         if missingScanLines != 0:
-            print('WARNING: Missing scanlines: ' + str(missingScanLines))
-
+            LOGGER.warning(f"Missing scanlines: {missingScanLines}")
         ##################
         # Read time
         ##################

nansat/mappers/mapper_aapp_l1c.py

@@ -11,6 +11,7 @@
 import struct
 import datetime
 import warnings
+import logging
 
 from nansat.exceptions import WrongMapperError
 from nansat.geolocation import Geolocation
@@ -22,6 +23,8 @@
 headerLength = recordLength
 imageOffset = headerLength + 1092
 
+LOGGER = logging.getLogger("Nansat."+__name__)
+LOGGER.addHandler(logging.NullHandler())
 
 class Mapper(VRT):
     ''' VRT with mapping of WKV for AVHRR L1C output from AAPP '''
@@ -60,7 +63,7 @@ def __init__(self, filename, gdalDataset, gdalMetadata, **kwargs):
         missingScanLines = int(struct.unpack('<l', fp.read(4))[0])
         numCalibratedScanLines = int(struct.unpack('<l', fp.read(4))[0])
         if missingScanLines != 0:
-            print('WARNING: Missing scanlines: ' + str(missingScanLines))
+            LOGGER.warning(f"Missing scanlines: {missingScanLines}")
 
         fp.seek(88)
         dataFormatNum = int(struct.unpack('<l', fp.read(4))[0])
@@ -84,10 +87,10 @@ def int2bitstring(s):
             endsWith3A = False
 
         if startsWith3A != endsWith3A:
-            print('############################################')
-            print('WARNING: channel 3 switches ')
-            print('between daytime and nighttime (3A <-> 3B)')
-            print('###########################################')
+            LOGGER.warning('############################################')
+            LOGGER.warning('WARNING: channel 3 switches ')
+            LOGGER.warning('between daytime and nighttime (3A <-> 3B)')
+            LOGGER.warning('###########################################')
 
         ###########################
         # Make Geolocation Arrays

nansat/mappers/mapper_geostationary.py

@@ -9,11 +9,14 @@
 from datetime import datetime
 from numpy import array, arange
 import warnings
+import logging
 
 from nansat.exceptions import WrongMapperError
 from nansat.vrt import VRT
 from nansat.node import Node
 
+LOGGER = logging.getLogger("Nansat."+__name__)
+LOGGER.addHandler(logging.NullHandler())
 
 def arrays2LUTString(a, b):
     LUTString = ''
@@ -176,24 +179,24 @@ def __init__(self, filename, gdalDataset, gdalMetadata, **kwargs):
 
         for sat in satDict:
             if sat['name'] == satellite:
-                print('This is ' + satellite)
+                LOGGER.info(f'This is {satellite}')
                 wavelengths = sat['wavelengths']
                 try:
                     scale = sat['scale']
                     offset = sat['offset']
                 except:
-                    print("No scale and offset found")
+                    LOGGER.info("No scale and offset found")
                     scale = None
                     offset = None
                 try:
                     LUT = sat['LUT']
                 except:
-                    print("No LUT found")
+                    LOGGER.info("No LUT found")
                     LUT = [""]*len(wavelengths)
                 try:
                     NODATA = sat['NODATA']
                 except:
-                    print("No NODATA values found")
+                    LOGGER.info("No NODATA values found")
                     NODATA = [""]*len(wavelengths)
 
         if wavelengths is None:
@@ -220,8 +223,7 @@ def __init__(self, filename, gdalDataset, gdalMetadata, **kwargs):
             try:
                 gdal.Open(bandSource)
             except:
-                print('Warning: band missing for wavelength ' +
-                       str(wavelength) + 'nm')
+                LOGGER.warning(f"band missing for wavelength {wavelength} nm")
                 continue
             src = {'SourceFilename': bandSource, 'SourceBand': 1,
                    'LUT': LUT[i], 'NODATA': NODATA[i]}

nansat/mappers/mapper_globcolour_l3b.py

@@ -11,6 +11,7 @@
 import json
 import tempfile
 import shutil
+import logging
 
 import numpy as np
 
@@ -22,6 +23,8 @@
 from nansat.vrt import VRT
 from nansat.mappers.globcolour import Globcolour
 
+LOGGER = logging.getLogger("Nansat."+__name__)
+LOGGER.addHandler(logging.NullHandler())
 
 class Mapper(VRT, Globcolour):
     ''' Create VRT with mapping of WKV for MERIS Level 2 (FR or RR)'''
@@ -73,7 +76,7 @@ def __init__(self, filename, gdalDataset, gdalMetadata, latlonGrid=None,
         self.band_vrts = {'mask': [], 'lonlat': []}
         mask = None
         for simFile in simFiles:
-            print('sim: ', simFile)
+            LOGGER.info(f'sim: {simFile}')
             # copy simFile to a temporary file
             tmpf = tempfile.mkstemp()
             shutil.copyfile(simFile, tmpf[1])

nansat/mappers/mapper_globcolour_l3m.py

@@ -9,6 +9,7 @@
 import datetime
 import os.path
 import glob
+import logging
 
 import numpy as np
 
@@ -17,6 +18,8 @@
 from nansat.utils import gdal, ogr
 from nansat.exceptions import WrongMapperError
 
+LOGGER = logging.getLogger("Nansat."+__name__)
+LOGGER.addHandler(logging.NullHandler())
 
 class Mapper(VRT, Globcolour):
     """Mapper for GLOBCOLOR L3M products"""
@@ -25,7 +28,7 @@ def __init__(self, filename, gdalDataset, gdalMetadata, **kwargs):
         ''' GLOBCOLOR L3M VRT '''
 
         try:
-            print("=>%s<=" % gdalMetadata['NC_GLOBAL#title'])
+            LOGGER.info(f"=>{gdalMetadata['NC_GLOBAL#title']}<=")
         except (TypeError, KeyError):
             raise WrongMapperError
 
@@ -35,15 +38,15 @@ def __init__(self, filename, gdalDataset, gdalMetadata, **kwargs):
         # get list of similar (same date) files in the directory
         iDir, iFile = os.path.split(filename)
         iFileName, iFileExt = os.path.splitext(iFile)
-        print('idir:', iDir, iFile, iFileName[0:30], iFileExt[0:8])
+        LOGGER.info(f'idir: {iDir} {iFile} {iFileName[0:30]} {iFileExt[0:8]}')
 
         simFilesMask = os.path.join(iDir, iFileName[0:30] + '*.nc')
         simFiles = glob.glob(simFilesMask)
-        print('simFilesMask, simFiles', simFilesMask, simFiles)
+        LOGGER.info(f'simFilesMask:{simFilesMask}, simFiles:{simFiles}')
 
         metaDict = []
         for simFile in simFiles:
-            print('simFile', simFile)
+            LOGGER.info(f'simFile:{simFile}')
             # open file, get metadata and get parameter name
             simSupDataset = gdal.Open(simFile)
             simSubDatasets = simSupDataset.GetSubDatasets()
@@ -56,7 +59,7 @@ def __init__(self, filename, gdalDataset, gdalMetadata, **kwargs):
                     simBandMetadata = simBand.GetMetadata()
                     simVarname = simBandMetadata['NETCDF_VARNAME']
                     # get WKV
-                    print('    simVarname', simVarname)
+                    LOGGER.info(f'    simVarname:{simVarname}')
                     if simVarname in self.varname2wkv:
                         simWKV = self.varname2wkv[simVarname]
                         break
@@ -93,17 +96,17 @@ def __init__(self, filename, gdalDataset, gdalMetadata, **kwargs):
                                      (simWavelength, solarIrradiance)
                                      }
 
-            print('        metaEntry', metaEntry)
+            LOGGER.info(f'        metaEntry:{metaEntry}')
             metaDict.append(metaEntry)
             if metaEntry2 is not None:
-                print('        metaEntry2', metaEntry2)
+                LOGGER.info(f'        metaEntry2:{metaEntry2}')
                 metaDict.append(metaEntry2)
 
-        print('simSubDatasets', simValidSupDataset.GetSubDatasets())
+        LOGGER.info(f'simSubDatasets:{simValidSupDataset.GetSubDatasets()}')
         for simSubDataset in simValidSupDataset.GetSubDatasets():
-            print('simSubDataset', simSubDataset)
+            LOGGER.info(f'simSubDataset:{simSubDataset}')
             if '_flags ' in simSubDataset[1]:
-                print('    mask simSubDataset', simSubDataset[1])
+                LOGGER.info(f'    mask simSubDataset:{simSubDataset[1]}')
                 flags = gdal.Open(simSubDataset[0]).ReadAsArray()
                 mask = np.ones(flags.shape) * 64
                 mask[np.bitwise_and(flags, np.power(2, 0)) > 0] = 1

nansat/mappers/mapper_metno_local_hires_seaice.py

@@ -18,12 +18,15 @@
 import sys
 import os
 from datetime import datetime, timedelta
+import logging
 
 from nansat.utils import gdal, ogr
 from nansat.exceptions import WrongMapperError
 from nansat.vrt import VRT
 import nansat.mappers.mapper_generic as mg
 
+LOGGER = logging.getLogger("Nansat."+__name__)
+LOGGER.addHandler(logging.NullHandler())
 
 class Mapper(mg.Mapper):
     """Create VRT with mapping of WKV for Met.no seaice"""
@@ -52,8 +55,7 @@ def __init__(self, filename, gdalDataset, gdalMetadata, **kwargs):
             filename = (ice_folder_name + 'ice_conc_svalbard_' +
                         valid_time.strftime('%Y%m%d1500.nc'))
             if os.path.exists(filename):
-                print('Found file:')
-                print(filename)
+                LOGGER.info(f'Found file:{filename}')
                 gdal_dataset = gdal.Open(filename)
                 gdal_metadata = gdalDataset.GetMetadata()
                 mg.Mapper.__init__(self, filename, gdal_dataset, gdal_metadata)

nansat/mappers/mapper_ncep_wind_online.py

@@ -20,11 +20,15 @@
 import os
 import sys
 from datetime import datetime, timedelta
+import logging
 
 from nansat.vrt import VRT
 from nansat.exceptions import WrongMapperError
 from nansat.nansat import Nansat
 
+LOGGER = logging.getLogger("Nansat."+__name__)
+LOGGER.addHandler(logging.NullHandler())
+
 # Place to store downloads - this can be changed via the "outFolder" argument
 # to Mapper.__init__
 downloads = os.path.join(os.path.expanduser('~'), 'ncep_gfs_downloads')
@@ -49,7 +53,7 @@ def __init__(self, filename, gdalDataset, gdalMetadata,
 
         time_str = filename[len(keyword_base)+1::]
         time = datetime.strptime(time_str, '%Y%m%d%H%M')
-        print(time)
+        LOGGER.info(f'{time}')
 
         ########################################
         # Find and download online grib file
@@ -86,13 +90,13 @@ def __init__(self, filename, gdalDataset, gdalMetadata,
                                     '%.2d' % forecast_hour +
                                     '.10m.uv.grib2'))
         if os.path.exists(out_filename):
-            print('NCEP wind is already downloaded: ' + out_filename)
+            LOGGER.info(f'NCEP wind is already downloaded: {out_filename}')
         else:
             os.system('curl -so ' + out_filename + ' ' + url)
             if os.path.exists(out_filename):
-                print('Downloaded ' + out_filename)
+                LOGGER.info(f'Downloaded {out_filename}')
             else:
-                print('NRT GRIB file not available: ' + url)
+                LOGGER.info(f'NRT GRIB file not available: {url}')
                 #########################################################
                 # If NRT file not available, search in long term archive
                 #########################################################
@@ -103,7 +107,7 @@ def __init__(self, filename, gdalDataset, gdalMetadata,
                             '%.3d' % forecast_hour)
                 filename = basename + '.grb2'
                 out_filename = os.path.join(outFolder, filename)
-                print('Downloading ' + url + filename)
+                LOGGER.info(f'Downloading {url}{filename}')
 
                 # Download subset of grib file
                 mapper_dir = os.path.dirname(os.path.abspath(__file__))
@@ -121,9 +125,9 @@ def __init__(self, filename, gdalDataset, gdalMetadata,
                                get_grib + ' ' + url + filename + ' ' + out_filename)
                     os.system(command)
                     if os.path.isfile(out_filename):
-                        print('Downloaded ' + filename + ' to ' + outFolder)
+                        LOGGER.info(f'Downloaded {filename} to {outFolder}')
                 else:
-                    print('Already downloaded %s' % out_filename)
+                    LOGGER.info(f'Already downloaded {out_filename}')
 
                 if not os.path.isfile(out_filename):
                     sys.exit('No NCEP wind files found for requested time')

nansat/mappers/mapper_obpg_l3.py

@@ -9,6 +9,7 @@
 import datetime
 import os.path
 import glob
+import logging
 
 import numpy as np
 
@@ -18,6 +19,9 @@
 
 from nansat.exceptions import WrongMapperError
 
+LOGGER = logging.getLogger("Nansat."+__name__)
+LOGGER.addHandler(logging.NullHandler())
+
 class Mapper(VRT):
     ''' Mapper for Level-3 Standard Mapped Image from
     http://oceancolor.gsfc.nasa.gov'''
@@ -85,7 +89,7 @@ def __init__(self, filename, gdalDataset, gdalMetadata, **kwargs):
                 tmpGdalMetadata = tmpGdalDataset.GetMetadata()
                 simParameter = tmpGdalMetadata['Parameter']
             except:
-                print('No parameter: %s not a supported SMI file')
+                LOGGER.info(f"No parameter: {tmpGdalMetadata['Parameter']} not a supported SMI file")
                 continue
             else:
                 # set params of the similar file