initial pass at single logger

AegeanTools/AeRes.py

@@ -13,6 +13,7 @@
 from astropy.io import fits
 
 from AegeanTools import catalogs, fitting, wcs_helpers
+from AegeanTools.logging import logger
 
 __author__ = "Paul Hancock"
 
@@ -46,18 +47,18 @@ def load_sources(filename,
     good = True
     for c in required_cols:
         if c not in table.colnames:
-            logging.error("Column {0} not found".format(c))
+            logger.error("Column {0} not found".format(c))
             good = False
     if not good:
-        logging.error("Some required columns missing or mis-labeled")
+        logger.error("Some required columns missing or mis-labeled")
         return None
     # rename the table columns
     for old, new in zip([ra_col, dec_col, peak_col, a_col, b_col, pa_col],
                         ['ra', 'dec', 'peak_flux', 'a', 'b', 'pa']):
         table.rename_column(old, new)
 
     catalog = catalogs.table_to_source_list(table)
-    logging.info("read {0} sources from {1}".format(len(catalog), filename))
+    logger.info("read {0} sources from {1}".format(len(catalog), filename))
     return catalog
 
 
@@ -105,10 +106,10 @@ def make_model(sources, shape, wcshelper, mask=False, frac=None, sigma=4):
 
         # skip sources that have a center that is outside of the image
         if not 0 < xo < shape[0]:
-            logging.debug("source {0} is not within image".format(src.island))
+            logger.debug("source {0} is not within image".format(src.island))
             continue
         if not 0 < yo < shape[1]:
-            logging.debug("source {0} is not within image".format(src.island))
+            logger.debug("source {0} is not within image".format(src.island))
             continue
 
         # pixels over which this model is calculated
@@ -130,15 +131,15 @@ def make_model(sources, shape, wcshelper, mask=False, frac=None, sigma=4):
         if not np.all(np.isfinite([ymin, ymax, xmin, xmax])):
             continue
 
-        if logging.getLogger().isEnabledFor(logging.DEBUG):  # pragma: no cover
-            logging.debug("Source ({0},{1})".format(src.island, src.source))
-            logging.debug(" xo, yo: {0} {1}".format(xo, yo))
-            logging.debug(" sx, sy: {0} {1}".format(sx, sy))
-            logging.debug(" theta, phi: {0} {1}".format(theta, phi))
-            logging.debug(" xoff, yoff: {0} {1}".format(xoff, yoff))
-            logging.debug(" xmin, xmax, ymin, ymax: {0}:{1} {2}:{3}".format(
+        if logging.getLogger().isEnabledFor(logger.debug):  # pragma: no cover
+            logger.debug("Source ({0},{1})".format(src.island, src.source))
+            logger.debug(" xo, yo: {0} {1}".format(xo, yo))
+            logger.debug(" sx, sy: {0} {1}".format(sx, sy))
+            logger.debug(" theta, phi: {0} {1}".format(theta, phi))
+            logger.debug(" xoff, yoff: {0} {1}".format(xoff, yoff))
+            logger.debug(" xmin, xmax, ymin, ymax: {0}:{1} {2}:{3}".format(
                             xmin, xmax, ymin, ymax))
-            logging.debug(" flux, sx, sy: {0} {1} {2}".format(
+            logger.debug(" flux, sx, sy: {0} {1} {2}".format(
                           src.peak_flux, sx, sy))
 
         # positions for which we want to make the model
@@ -163,7 +164,7 @@ def make_model(sources, shape, wcshelper, mask=False, frac=None, sigma=4):
         else:
             m[x, y] += model
         i_count += 1
-    logging.info("modeled {0} sources".format(i_count))
+    logger.info("modeled {0} sources".format(i_count))
     return m
 
 
@@ -238,9 +239,9 @@ def make_residual(fitsfile, catalog, rfile, mfile=None,
 
     hdulist[0].data = residual
     hdulist.writeto(rfile, overwrite=True)
-    logging.info("wrote residual to {0}".format(rfile))
+    logger.info("wrote residual to {0}".format(rfile))
     if mfile is not None:
         hdulist[0].data = model
         hdulist.writeto(mfile, overwrite=True)
-        logging.info("wrote model to {0}".format(mfile))
+        logger.info("wrote model to {0}".format(mfile))
     return

AegeanTools/BANE.py

@@ -19,6 +19,7 @@
 from scipy.interpolate import RegularGridInterpolator
 
 from .fits_tools import compress
+from AegeanTools.logging import logger
 
 __author__ = 'Paul Hancock'
 __version__ = 'v1.10.0'
@@ -92,7 +93,7 @@ def sigmaclip(arr, lo, hi, reps=10):
         mean = np.mean(clipped)
         prev_valid = curr_valid
     else:
-        logging.debug(
+        logger.debug(
             "No stopping criteria was reached after {0} cycles".format(count))
 
     return mean, std
@@ -157,7 +158,7 @@ def sigma_filter(filename, region, step_size, box_size, shape, domask,
     """
 
     ymin, ymax = region
-    logging.debug('rows {0}-{1} starting at {2}'.format(ymin,
+    logger.debug('rows {0}-{1} starting at {2}'.format(ymin,
                   ymax, strftime("%Y-%m-%d %H:%M:%S", gmtime())))
 
     # cut out the region of interest plus 1/2 the box size
@@ -184,8 +185,8 @@ def sigma_filter(filename, region, step_size, box_size, shape, domask,
                              data_row_min:data_row_max, 0:shape[1]]
             )
         else:
-            logging.error("Too many NAXIS for me {0}".format(NAXIS))
-            logging.error("fix your file to be more sane")
+            logger.error("Too many NAXIS for me {0}".format(NAXIS))
+            logger.error("fix your file to be more sane")
             raise Exception("Too many NAXIS")
 
     # Manually scale the data if BSCALE is not 1.0
@@ -198,8 +199,8 @@ def sigma_filter(filename, region, step_size, box_size, shape, domask,
 
     # row_len = shape[1]
 
-    logging.debug('data size is {0}'.format(data.shape))
-    logging.debug('data format is {0}'.format(data.dtype))
+    logger.debug('data size is {0}'.format(data.shape))
+    logger.debug('data format is {0}'.format(data.dtype))
 
     def box(r, c):
         """
@@ -238,22 +239,22 @@ def box(r, c):
     irms_shm = SharedMemory(name=f'irms_{memory_id}', create=False)
     irms = np.ndarray(shape, dtype=np.float64, buffer=irms_shm.buf)
 
-    logging.debug("Interpolating bkg to sharemem")
+    logger.debug("Interpolating bkg to sharemem")
     ifunc = RegularGridInterpolator((rows, cols), vals)
     interp_bkg = np.array(ifunc((gr, gc)), dtype=np.float64)
     ibkg[ymin:ymax, :] = interp_bkg
     del ifunc, interp_bkg
-    logging.debug(" ... done writing bkg")
+    logger.debug(" ... done writing bkg")
 
     # wait for all to complete
     i = barrier.wait()
     if i == 0:
         barrier.reset()
 
-    logging.debug("background subtraction")
+    logger.debug("background subtraction")
     data[0 + ymin - data_row_min: data.shape[0] -
          (data_row_max - ymax), :] -= ibkg[ymin:ymax, :]
-    logging.debug(".. done ")
+    logger.debug(".. done ")
 
     # reset/recycle the vals array
     vals[:] = 0
@@ -266,27 +267,27 @@ def box(r, c):
             _, rms = sigmaclip(new, 3, 3)
             vals[i, j] = rms
 
-    logging.debug("Interpolating rms to sharemem")
+    logger.debug("Interpolating rms to sharemem")
     ifunc = RegularGridInterpolator((rows, cols), vals)
     interp_rms = np.array(ifunc((gr, gc)), dtype=np.float64)
     irms[ymin:ymax, :] = interp_rms
     del ifunc, interp_rms
-    logging.debug(" .. done writing rms")
+    logger.debug(" .. done writing rms")
 
     if domask:
         # wait for all to complete
         i = barrier.wait()
         if i == 0:
             barrier.reset()
 
-        logging.debug("applying mask")
+        logger.debug("applying mask")
         mask = ~np.isfinite(
             data[0 + ymin - data_row_min: data.shape[0] -
                  (data_row_max - ymax), :])
         ibkg[ymin:ymax, :][mask] = np.nan
         irms[ymin:ymax, :][mask] = np.nan
-        logging.debug("... done applying mask")
-    logging.debug('rows {0}-{1} finished at {2}'.format(ymin,
+        logger.debug("... done applying mask")
+    logger.debug('rows {0}-{1} finished at {2}'.format(ymin,
                   ymax, strftime("%Y-%m-%d %H:%M:%S", gmtime())))
     return
 
@@ -339,8 +340,8 @@ def filter_mc_sharemem(filename, step_size, box_size, cores, shape,
 
     img_y, img_x = shape
 
-    logging.info("using {0} cores".format(cores))
-    logging.info("using {0} stripes".format(nslice))
+    logger.info("using {0} cores".format(cores))
+    logger.info("using {0} stripes".format(nslice))
 
     if nslice > 1:
         # box widths should be multiples of the step_size, and not zero
@@ -354,8 +355,8 @@ def filter_mc_sharemem(filename, step_size, box_size, cores, shape,
         ymins = [0]
         ymaxs = [img_y]
 
-    logging.debug("ymins {0}".format(ymins))
-    logging.debug("ymaxs {0}".format(ymaxs))
+    logger.debug("ymins {0}".format(ymins))
+    logger.debug("ymaxs {0}".format(ymaxs))
 
     args = []
     for region in zip(ymins, ymaxs):
@@ -384,7 +385,7 @@ def filter_mc_sharemem(filename, step_size, box_size, cores, shape,
             # process
             pool.map_async(_sf2, args, chunksize=1).get(timeout=10000000)
         except KeyboardInterrupt:
-            logging.error("Caught keyboard interrupt")
+            logger.error("Caught keyboard interrupt")
             pool.close()
             exit = True
         else:
@@ -465,7 +466,7 @@ def filter_image(im_name, out_base, step_size=None, box_size=None,
     if naxis > 2:
         naxis3 = header['NAXIS3']
         if cube_index >= naxis3:
-            logging.error(
+            logger.error(
                 "3rd dimension has len {0} but index {1} was passed".format(
                     naxis3, cube_index)
             )
@@ -481,19 +482,19 @@ def filter_image(im_name, out_base, step_size=None, box_size=None,
     if compressed:
         if not step_size[0] == step_size[1]:
             step_size = (min(step_size), min(step_size))
-            logging.info(
+            logger.info(
                 "Changing grid to be {0} so we can compress the output".format(
                     step_size)
             )
 
-    logging.info("using grid_size {0}, box_size {1}".format(
+    logger.info("using grid_size {0}, box_size {1}".format(
                  step_size, box_size))
-    logging.info("on data shape {0}".format(shape))
+    logger.info("on data shape {0}".format(shape))
     bkg, rms = filter_mc_sharemem(im_name,
                                   step_size=step_size, box_size=box_size,
                                   cores=cores, shape=shape, nslice=nslice,
                                   domask=mask, cube_index=cube_index)
-    logging.info("done")
+    logger.info("done")
 
     if out_base is not None:
         # add a comment to the fits header
@@ -563,8 +564,8 @@ def get_step_size(header):
         # default to 4x the synthesized beam width
         step_size = int(np.ceil(4*beam_size/pix_scale))
     else:
-        logging.info("BMAJ and/or BMIN not in fits header.")
-        logging.info("Assuming 4 pix/beam, so we have step_size = 16 pixels")
+        logger.info("BMAJ and/or BMIN not in fits header.")
+        logger.info("Assuming 4 pix/beam, so we have step_size = 16 pixels")
         step_size = 16
     step_size = (step_size, step_size)
     return step_size
@@ -593,5 +594,5 @@ def write_fits(data, header, file_name):
     hdu.header = header
     hdulist = fits.HDUList([hdu])
     hdulist.writeto(file_name, overwrite=True)
-    logging.info("Wrote {0}".format(file_name))
+    logger.info("Wrote {0}".format(file_name))
     return

AegeanTools/CLI/AeReg.py

@@ -53,7 +53,7 @@ def main(argv=()):
     invocation_string = " ".join(argv)
 
     # configure logging
-    logging_level = logging.DEBUG if options.debug else logging.INFO
+    logging_level = logger.debug if options.debug else logger.info
     log = logging.getLogger("Aegean")
     logging.basicConfig(level=logging_level,
                         format="%(process)d:%(levelname)s %(message)s")

AegeanTools/CLI/AeRes.py

@@ -65,31 +65,31 @@ def main(argv=()):
 
     options = parser.parse_args(args=argv)
 
-    logging_level = logging.DEBUG if options.debug else logging.INFO
+    logging_level = logger.debug if options.debug else logger.info
     logging.basicConfig(level=logging_level,
                         format="%(process)d:%(levelname)s %(message)s")
-    logging.info("This is AeRes {0}-({1})".format(__version__, __date__))
+    logger.info("This is AeRes {0}-({1})".format(__version__, __date__))
 
     if options.catalog is None:
-        logging.error("input catalog is required")
+        logger.error("input catalog is required")
         parser.print_help()
         return 1
     if options.fitsfile is None:
-        logging.error("input fits file is required")
+        logger.error("input fits file is required")
         parser.print_help()
         return 1
     if options.rfile is None:
-        logging.error("output residual filename is required")
+        logger.error("output residual filename is required")
         parser.print_help()
         return 1
     # convert default value of 0 to be None.
     if options.frac <= 0:
         options.frac = None
 
-    logging.info("Using {0} and {1} to make {2}".format(
+    logger.info("Using {0} and {1} to make {2}".format(
         options.fitsfile, options.catalog, options.rfile))
     if options.mfile is not None:
-        logging.info(" and writing model to {0}".format(options.mfile))
+        logger.info(" and writing model to {0}".format(options.mfile))
 
     colmap = {'ra_col': options.ra_col,
               'dec_col': options.dec_col,

AegeanTools/CLI/BANE.py

@@ -62,14 +62,14 @@ def main(argv=()):
 
     # Get the BANE logger.
     logging = BANE.logging
-    logging_level = logging.DEBUG if options.debug else logging.INFO
+    logging_level = logger.debug if options.debug else logger.info
     logging.basicConfig(level=logging_level,
                         format="%(process)d:%(levelname)s %(message)s")
-    logging.info(
+    logger.info(
         "This is BANE {0}-({1})".format(BANE.__version__, BANE.__date__))
 
     if not os.path.exists(options.image):
-        logging.error("File not found: {0} ".format(options.image))
+        logger.error("File not found: {0} ".format(options.image))
         return 1
 
     if options.out_base is None:
@@ -79,9 +79,9 @@ def main(argv=()):
         bkgout = options.out_base + '_bkg.fits'
         rmsout = options.out_base + '_rms.fits'
         if os.path.exists(bkgout) and os.path.exists(rmsout):
-            logging.error("{0} and {1} exist and you said noclobber"
+            logger.error("{0} and {1} exist and you said noclobber"
                           "".format(bkgout, rmsout))
-            logging.error("Not running")
+            logger.error("Not running")
             return 1
 
     BANE.filter_image(im_name=options.image, out_base=options.out_base,

AegeanTools/CLI/MIMAS.py

@@ -131,14 +131,14 @@ def main(argv=()):
 
     # get the MIMAS logger
     logging = MIMAS.logging
-    logging_level = logging.DEBUG if results.debug else logging.INFO
+    logging_level = logger.debug if results.debug else logger.info
     logging.basicConfig(level=logging_level,
                         format="%(process)d:%(levelname)s %(message)s")
-    logging.info(
+    logger.info(
         "This is MIMAS {0}-({1})".format(MIMAS.__version__, MIMAS.__date__))
 
     if len(results.fits_mask) > 0:
-        logging.info("The --fitsmask option is not yet implemented.")
+        logger.info("The --fitsmask option is not yet implemented.")
         return 1
 
     if len(results.mim2reg) > 0: