Fix unintended removal of handlers from the root logger (#245)

* Fix logging and clean up

* Fix text

* Fix text

* Remove install of old pybdsm script

bdsf/cleanup.py

@@ -17,7 +17,7 @@ class Op_cleanup(Op):
     """  """
     def __call__(self, img):
 
-        mylog = mylogger.logging.getLogger("PyBDSM.Cleanup")
+        mylog = mylogger.logging.getLogger("PyBDSF.Cleanup")
 
         ### plotresults for all gaussians together
         if img.opts.plot_allgaus and has_pl:

bdsf/collapse.py

@@ -18,7 +18,7 @@ class Op_collapse(Op):
     """Collapse 3D image"""
 
     def __call__(self, img):
-        mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Collapse")
+        mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Collapse")
         if img.opts.polarisation_do:
             pols = ['I', 'Q', 'U', 'V'] # make sure I is done first
         else:

bdsf/functions.py

@@ -781,7 +781,7 @@ def get_errors(img, p, stdav, bm_pix=None, fixed_to_beam=False):
     from . import mylogger
     import numpy as N
 
-    mylog = mylogger.logging.getLogger("PyBDSM.Compute")
+    mylog = mylogger.logging.getLogger("PyBDSF.Compute")
 
     if len(p) % 7 > 0:
         mylog.error("Gaussian parameters passed have to have 7n numbers")
@@ -1116,7 +1116,7 @@ def read_image_from_file(filename, img, indir, quiet=False):
     except ImportError as err:
         has_casacore = False
 
-    mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Readfile")
+    mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Readfile")
     if indir is None or indir == './':
         prefix = ''
     else:
@@ -1370,7 +1370,7 @@ def write_image_to_file(use, filename, image, img, outdir=None,
     import os
     from . import mylogger
 
-    mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Writefile")
+    mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Writefile")
 
     wcs_obj = img.wcs_obj
     if pad_image and img.opts.trim_box is not None:
@@ -1407,7 +1407,7 @@ def write_image_to_file(use, filename, image, img, outdir=None,
             # The "overwrite" argument was added in astropy v1.3, so fall back to "clobber"
             # if it doesn't work
             temp_im.writeto(tfile.name, clobber=clobber)
-        send_fits_image(img.samp_client, img.samp_key, 'PyBDSM image', tfile.name)
+        send_fits_image(img.samp_client, img.samp_key, 'PyBDSF image', tfile.name)
     else:
         # Write image to FITS file
         if outdir is None:
@@ -2017,7 +2017,7 @@ def start_samp_proxy():
     s = ServerProxy(HUB_PARAMS['samp.hub.xmlrpc.url'])
 
     # Register with Hub
-    metadata = {"samp.name": 'PyBDSM', "samp.description.text": 'PyBDSM: the Python Blob Detection and Source Measurement software'}
+    metadata = {"samp.name": 'PyBDSF', "samp.description.text": 'PyBDSF: the Python Blob Detector and Source Finder software'}
     result = s.samp.hub.register(HUB_PARAMS['samp.secret'])
     private_key = result['samp.private-key']
     s.samp.hub.declareMetadata(private_key, metadata)

bdsf/gaul2srl.py

@@ -32,7 +32,7 @@ class Op_gaul2srl(Op):
     def __call__(self, img):
         #  for each island, get the gaussians into a list and then send them to process
         #  src_index is source number, starting from 0
-        mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Gaul2Srl")
+        mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Gaul2Srl")
         mylogger.userinfo(mylog, 'Grouping Gaussians into sources')
         img.aperture = img.opts.aperture
         if img.aperture is not None and img.aperture <= 0.0:
@@ -325,7 +325,7 @@ def process_Multiple(self, img, g_sublist, mask, src_index, isrc, subim, isl, de
         from scipy import ndimage
         from . import functions as func
 
-        mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Gaul2Srl  ")
+        mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Gaul2Srl  ")
         dum = img.beam[0]*img.beam[1]
         cdeltsq = img.wcs_obj.acdelt[0]*img.wcs_obj.acdelt[1]
         bmar_p = 2.0*pi*dum/(cdeltsq*fwsig*fwsig)

bdsf/gausfit.py

@@ -37,7 +37,7 @@ class Op_gausfit(Op):
     def __call__(self, img):
         from . import functions as func
 
-        mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Gausfit")
+        mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Gausfit")
         if len(img.islands) == 0:
             img.gaussians = []
             img.ngaus = 0
@@ -946,7 +946,7 @@ def __init__(self, img, gaussian, isl_idx, g_idx, flg=0):
         """Initialize Gaussian object from fitting data
 
         Parameters:
-        img: PyBDSM image object
+        img: PyBDSF image object
         gaussian: 6-tuple of fitted numbers
         isl_idx: island serial number
         g_idx: gaussian serial number

bdsf/islands.py

@@ -43,7 +43,7 @@ class Op_islands(Op):
     Prerequisites: module rmsimage should be run first.
     """
     def __call__(self, img):
-        mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Islands")
+        mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Islands")
         opts = img.opts
 
         minsize = opts.minpix_isl

bdsf/make_residimage.py

@@ -27,7 +27,7 @@ def __call__(self, img):
         from copy import deepcopy as cp
         import os
 
-        mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"ResidImage")
+        mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"ResidImage")
         mylog.info("Calculating residual image after subtracting reconstructed gaussians")
         shape = img.ch0_arr.shape
         thresh= img.opts.fittedimage_clip

bdsf/mylogger.py

@@ -17,10 +17,10 @@
 def init_logger(logfilename, quiet=False, debug=False):
     logging.USERINFO = logging.INFO + 1
     logging.addLevelName(logging.USERINFO, 'USERINFO')
-    logger = logging.root
+    logger = logging.getLogger('PyBDSF')
     logger.setLevel(logging.DEBUG)
 
-    # First remove any existing handlers (in case PyBDSM has been run
+    # First remove any existing handlers (in case PyBDSF has been run
     # before in this session but the quiet or debug options have changed
     while len(logger.handlers) > 0:
         logger.removeHandler(logger.handlers[0])

bdsf/opts.py

@@ -875,7 +875,7 @@ class Opts(object):
                              group = "output_opts")
     output_all = Bool(False,
                              doc = "Write out all files automatically to directory "\
-                                 "'outdir/filename_pybdsm'",
+                                 "'outdir/filename_pybdsf'",
                              group = "output_opts")
     opdir_overwrite = Enum('overwrite', 'append',
                              doc = "'overwrite'/'append': If output_all=True, "\

bdsf/output.py

@@ -117,7 +117,7 @@ def write_opts(self, img, dir):
         import inspect
         from . import mylogger
 
-        mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Output")
+        mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Output")
         fname = 'parameters_used'
         f = open(dir+fname, 'w')
         mylog.info('Writing '+dir+fname)
@@ -139,11 +139,11 @@ def write_opts(self, img, dir):
         f.close()
 
     def save_opts(self, img, dir):
-        """ Saves input parameters to a PyBDSM save file."""
+        """ Saves input parameters to a PyBDSF save file."""
         from . import interface
         from . import mylogger
 
-        mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Output")
+        mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Output")
         fname = 'parameters.sav'
         mylog.info('Writing '+dir+fname)
         interface.save_pars(img, dir+fname, quiet=True)
@@ -215,7 +215,7 @@ def write_bbs_gaul(img, filename=None, srcroot=None, patch=None,
     from . import mylogger
     import os
 
-    mylog = mylogger.logging.getLogger("PyBDSM.write_gaul")
+    mylog = mylogger.logging.getLogger("PyBDSF.write_gaul")
     if int(img.equinox) != 2000 and int(img.equinox) != 1950:
         mylog.warning('Equinox of input image is not J2000 or B1950. '
                       'Sky model may not be appropriate for BBS.')
@@ -247,7 +247,7 @@ def write_lsm_gaul(img, filename=None, srcroot=None, patch=None,
     from . import mylogger
     import os
 
-    mylog = mylogger.logging.getLogger("PyBDSM.write_gaul")
+    mylog = mylogger.logging.getLogger("PyBDSF.write_gaul")
     if int(img.equinox) != 2000 and int(img.equinox) != 1950:
         mylog.warning('Equinox of input image is not J2000 or B1950. '
                       'Sky model may not be appropriate for Sagecal.')
@@ -277,7 +277,7 @@ def write_ds9_list(img, filename=None, srcroot=None, deconvolve=False,
     from . import mylogger
     import os
 
-    mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Output")
+    mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Output")
     if objtype == 'gaul':
         outl, outn, patl = list_and_sort_gaussians(img, patch=None)
     elif objtype == 'srl':
@@ -316,7 +316,7 @@ def write_ascii_list(img, filename=None, sort_by='indx', format='ascii',
     from . import mylogger
     import os
 
-    mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Output")
+    mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Output")
     if objtype == 'gaul':
         outl, outn, patl = list_and_sort_gaussians(img, patch=None, sort_by=sort_by)
     elif objtype == 'srl':
@@ -346,7 +346,7 @@ def write_casa_gaul(img, filename=None,  incl_empty=False, clobber=False):
     from . import mylogger
     import os
 
-    mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Output")
+    mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Output")
     outl, outn, patl = list_and_sort_gaussians(img, patch=None)
     outstr_list = make_casa_str(img, outl)
     if filename is None:
@@ -371,7 +371,7 @@ def write_fits_list(img, filename=None, sort_by='index', objtype='gaul',
     from astropy.io import fits as pyfits
     from ._version import __version__
 
-    mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Output")
+    mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Output")
     if objtype == 'gaul':
         outl, outn, patl = list_and_sort_gaussians(img, patch=None, sort_by=sort_by)
     elif objtype == 'srl':
@@ -421,7 +421,7 @@ def write_fits_list(img, filename=None, sort_by='index', objtype='gaul',
         tbhdu.header.add_comment('Source list for '+img.filename)
     elif objtype == 'shap':
         tbhdu.header.add_comment('Shapelet list for '+img.filename)
-    tbhdu.header.add_comment('Generated by PyBDSM version %s'
+    tbhdu.header.add_comment('Generated by PyBDSF version %s'
                              % (__version__, ))
     freq = "%.5e" % img.frequency
     tbhdu.header.add_comment('Reference frequency of the detection ("ch0") image: %s Hz' % freq)
@@ -454,7 +454,7 @@ def write_kvis_ann(img, filename=None, sort_by='indx',
     from . import mylogger
     import os
 
-    mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Output")
+    mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Output")
     if filename is None:
         filename = img.imagename + '.kvis.ann'
     if os.path.exists(filename) and not clobber:
@@ -488,7 +488,7 @@ def write_star(img, filename=None, sort_by='indx',
     from . import mylogger
     import os
 
-    mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Output")
+    mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Output")
     if filename is None:
         filename = img.imagename + '.star'
     if os.path.exists(filename) and not clobber:
@@ -621,7 +621,7 @@ def make_lsm_str(img, glist, gnames, incl_empty=False):
 
     outstr_list = ["# SAGECAL sky model\n"]
     freq = "%.5e" % img.frequency
-    outstr_list.append('# Generated by PyBDSM version %s\n'
+    outstr_list.append('# Generated by PyBDSF version %s\n'
                        % (__version__, ))
     outstr_list.append("# Name  | RA (hr,min,sec) | DEC (deg,min,sec) | I | Q | U | V | SI | RM | eX | eY | eP | freq0\n\n")
     for gindx, g in enumerate(glist[0]):
@@ -686,7 +686,7 @@ def make_ds9_str(img, glist, gnames, deconvolve=False, objtype='gaul', incl_empt
         elif int(img.equinox) == 1950:
             equinox = 'fk4'
         else:
-            mylog = mylogger.logging.getLogger("PyBDSM.write_ds9")
+            mylog = mylogger.logging.getLogger("PyBDSF.write_ds9")
             mylog.warning('Equinox of input image is not J2000 or B1950. '
                           'Regions may not be correct.')
             equinox = 'fk5'
@@ -741,7 +741,7 @@ def make_ascii_str(img, glist, objtype='gaul', format='ascii', incl_empty=False,
         outstr_list.append('# Gaussian list for '+img.filename+'\n')
     elif objtype == 'srl':
         outstr_list.append('# Source list for '+img.filename+'\n')
-    outstr_list.append('# Generated by PyBDSM version %s\n'
+    outstr_list.append('# Generated by PyBDSF version %s\n'
                        % (__version__, ))
     outstr_list.append('# Reference frequency of the detection ("ch0") image: %s Hz\n' % freq)
     outstr_list.append('# Equinox : %s \n\n' % img.equinox)
@@ -971,7 +971,7 @@ def list_and_sort_gaussians(img, patch=None, root=None,
         # mask file.
         if 0 in unique_patch_ids:
             from . import mylogger
-            mylog = mylogger.logging.getLogger("PyBDSM.write_gaul")
+            mylog = mylogger.logging.getLogger("PyBDSF.write_gaul")
             mylog.warning('Some sources fall outside of the regions '
                           'defined in the mask file. These sources are not '
                           'included in the output sky model.')

bdsf/plotresults.py

@@ -247,7 +247,7 @@ def plotresults(img, ch0_image=True, rms_image=True, mean_image=True,
         numx = 1
     numy = int(N.ceil(float(len(images))/float(numx)))
     fig = pl.figure(figsize=(max(15, 10.0*float(numy)/float(numx)), 10.0))
-    fig.canvas.manager.set_window_title('PyBDSM Fit Results for '+ img.filename)
+    fig.canvas.manager.set_window_title('PyBDSF Fit Results for '+ img.filename)
     gray_palette = cm.gray
     gray_palette.set_bad('k')
 

bdsf/polarisation.py

@@ -54,7 +54,7 @@ class Op_polarisation(Op):
     Prerequisites: module gaul2srl should be run first."""
 
     def __call__(self, img):
-        mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Polarisatn")
+        mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Polarisatn")
         if img.opts.polarisation_do:
             mylog.info('Extracting polarisation properties for all sources')
             pols = ['I', 'Q', 'U', 'V']

bdsf/preprocess.py

@@ -1,7 +1,7 @@
 """Module preprocess
 
 Calculates some basic statistics of the image and sets up processing
-parameters for PyBDSM.
+parameters for PyBDSF.
 """
 from __future__ import absolute_import
 
@@ -20,7 +20,7 @@ class Op_preprocess(Op):
     are blanked in QC ? """
 
     def __call__(self, img):
-        mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Preprocess")
+        mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Preprocess")
         bstat = func.bstat
         if img.opts.kappa_clip is None:
             kappa = -img.pixel_beamarea()

bdsf/psf_vary.py

@@ -33,7 +33,7 @@ class Op_psf_vary(Op):
     def __call__(self, img):
 
         if img.opts.psf_vary_do:
-            mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Psf_Vary")
+            mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Psf_Vary")
             mylogger.userinfo(mylog, '\nEstimating PSF variations')
             opts = img.opts
             dir = img.basedir + '/misc/'
@@ -847,7 +847,7 @@ def psf_in_tile(self, image, beam, g_gauls, cdelt, factor, snrcutstack, volrank,
         and pass it to stackpsf with a weight for each gaussian, to calculate the average psf per tile.
 
         Should define weights inside a tile to include closure errors """
-        mylog = mylogger.logging.getLogger("PyBDSM."+img.log+"Psf_Vary")
+        mylog = mylogger.logging.getLogger("PyBDSF."+img.log+"Psf_Vary")
 
         tile_list, tile_coord, tile_snr = tile_prop
         tr_gaul = self.trans_gaul(g_gauls)

bdsf/readimage.py

@@ -30,7 +30,7 @@ class Op_readimage(Op):
     Loads image and configures wcslib machinery for it.
     """
     def __call__(self, img):
-        mylog = mylogger.logging.getLogger("PyBDSM." + img.log + "Readimage")
+        mylog = mylogger.logging.getLogger("PyBDSF." + img.log + "Readimage")
 
         if img.opts.filename == '':
             raise RuntimeError('Image file name not specified.')
@@ -310,7 +310,7 @@ def init_beam(self, img):
         """Initialize beam parameters, and conversion routines
         to convert beam to/from pixel coordinates"""
         from .const import fwsig
-        mylog = mylogger.logging.getLogger("PyBDSM.InitBeam")
+        mylog = mylogger.logging.getLogger("PyBDSF.InitBeam")
 
         hdr = img.header
         cdelt1, cdelt2 = img.wcs_obj.acdelt[0:2]
@@ -402,7 +402,7 @@ def pixel_beamarea():
     def init_freq(self, img):
         """Initialize frequency parameters and store them.
 
-        Basically, PyBDSM uses two frequency parameters:
+        Basically, PyBDSF uses two frequency parameters:
 
             img.frequency - the reference frequency in Hz of the ch0 image
             img.freq_pars - the crval, crpix, and cdelt values for the
@@ -419,7 +419,7 @@ def init_freq(self, img):
                 warnings.filterwarnings("ignore", category=DeprecationWarning)
                 from pywcs import WCS
 
-        mylog = mylogger.logging.getLogger("PyBDSM.InitFreq")
+        mylog = mylogger.logging.getLogger("PyBDSF.InitFreq")
         if img.opts.frequency_sp is not None and img.image_arr.shape[1] > 1:
             # If user specifies multiple frequencies, then let
             # collapse.py do the initialization