Convert logger from old astrohack to new general logger.

src/astrohack/_utils/_algorithms.py

@@ -1,13 +1,13 @@
-import scipy.signal as scisig
 import numpy as np
+import scipy.signal as scisig
 
-from astrohack._utils._logger._astrohack_logger import _get_astrohack_logger
+import skriba.logger
 
 
 def _calculate_suggested_grid_paramater(parameter, quantile=0.01):
     import scipy
 
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
 
     # Determine skew properties and return median
     if np.abs(scipy.stats.skew(parameter)) > 0.5:
@@ -43,7 +43,7 @@ def _apply_mask(data, scaling=0.5):
     Returns:
         numpy.ndarray: cropped aperture grid data
     """
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
 
     x, y = data.shape
 

src/astrohack/_utils/_combine.py

@@ -1,8 +1,8 @@
 import numpy as np
-import os
 import xarray as xr
 
-from astrohack._utils._logger._astrohack_logger import _get_astrohack_logger
+import skriba.logger
+
 from astrohack._utils._dio import _load_image_xds
 from scipy.interpolate import griddata
 from astrohack._utils._constants import clight
@@ -15,12 +15,12 @@ def _combine_chunk(combine_chunk_params):
     Args:
         combine_chunk_params: Param dictionary for combine chunk
     """
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
+
     antenna = combine_chunk_params['this_ant']
     ddi_dict = combine_chunk_params['image_mds'][antenna]
     fname = 'combine'
     ddi_list = _parm_to_list(fname, combine_chunk_params['ddi'], ddi_dict, 'ddi')
-    print("DDI_LIST:", ddi_list)
 
     nddi = len(ddi_list)
     out_xds_name = '/'.join([combine_chunk_params['combine_name'], antenna, ddi_list[0]])

src/astrohack/_utils/_conversion.py

@@ -1,7 +1,5 @@
 import skriba.logger
 
-import numpy as np
-
 from astrohack._utils._constants import *
 
 

src/astrohack/_utils/_dask_graph_tools.py

@@ -1,13 +1,22 @@
 import dask
 import xarray
+import skriba.logger
 
-from astrohack._utils._logger._astrohack_logger import _get_astrohack_logger
 from astrohack._utils._tools import _parm_to_list
 
 
-def _construct_general_graph_recursively(caller, looping_dict, chunk_function, param_dict, delayed_list, key_order,
-                                         parallel=False, oneup=None):
-    logger = _get_astrohack_logger()
+def _construct_general_graph_recursively(
+        caller,
+        looping_dict,
+        chunk_function,
+        param_dict,
+        delayed_list,
+        key_order,
+        parallel=False,
+        oneup=None
+):
+
+    logger = skriba.logger.get_logger(logger_name="astrohack")
     if len(key_order) == 0:
         if isinstance(looping_dict, xarray.Dataset):
             param_dict['xds_data'] = looping_dict
@@ -50,7 +59,7 @@ def _dask_general_compute(caller, looping_dict, chunk_function, param_dict, key_
     Returns: True if processing has occured, False if no data was processed
 
     """
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
     delayed_list = []
     _construct_general_graph_recursively(caller, looping_dict, chunk_function, param_dict, delayed_list=delayed_list,
                                          key_order=key_order, parallel=parallel)

src/astrohack/_utils/_diagnostics.py

@@ -1,9 +1,8 @@
-import numpy as np
 import matplotlib.pyplot as plt
-from astropy.time import Time
-
-from astrohack._utils._constants import figsize, fontsize, markersize
+import numpy as np
+from astrohack._utils._constants import fontsize, markersize
 from astrohack._utils._plot_commons import _create_figure_and_axes, _close_figure
+from astropy.time import Time
 
 
 def _calc_index(n, m):

src/astrohack/_utils/_extract_locit.py

@@ -1,13 +1,15 @@
+import skriba.logger
+
 import numpy as np
+import astropy.units as units
+import xarray as xr
 
 from casacore import tables as ctables
 from astropy.coordinates import SkyCoord, CIRS
 from astropy.time import Time
-import astropy.units as units
-import xarray as xr
+
 from prettytable import PrettyTable
 
-from astrohack._utils._logger._astrohack_logger import _get_astrohack_logger
 from astrohack._utils._tools import _casa_time_to_mjd, _rad_to_deg_str
 from astrohack._utils._conversion import _convert_unit
 from astrohack._utils._constants import figsize, twopi, notavail
@@ -27,7 +29,7 @@ def _extract_antenna_data(fname, extract_locit_parms):
     Returns:
     Antenna dictionary
     """
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
     cal_table = extract_locit_parms['cal_table']
     ant_table = ctables.table(cal_table + '::ANTENNA', readonly=True, lockoptions={'option': 'usernoread'}, ack=False)
     ant_off = ant_table.getcol('OFFSET')
@@ -87,7 +89,7 @@ def _extract_spectral_info(fname, extract_locit_parms):
     Returns:
     DDI dictionary
     """
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
     cal_table = extract_locit_parms['cal_table']
     spw_table = ctables.table(cal_table+'::SPECTRAL_WINDOW', readonly=True, lockoptions={'option': 'usernoread'}, ack=False)
     ref_freq = spw_table.getcol('REF_FREQUENCY')
@@ -179,7 +181,7 @@ def _extract_antenna_phase_gains(fname, extract_locit_parms):
     Returns:
     Reference antenna
     """
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
 
     cal_table = extract_locit_parms['cal_table']
     basename = extract_locit_parms['locit_name']
@@ -299,7 +301,7 @@ def _plot_source_table(filename, src_dict, label=True, precessed=False, obs_midp
         figure_size: plot dimensions in inches
         dpi: Dots per inch (plot resolution)
     """
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
     n_src = len(src_dict)
     radec = np.ndarray((n_src, 2))
     name = []

src/astrohack/_utils/_extract_point.py

@@ -4,6 +4,7 @@
 import numpy as np
 import skriba.logger
 import xarray as xr
+
 from astrohack._utils._conversion import convert_dict_from_numba
 from astrohack._utils._dio import _load_point_file
 from casacore import tables as ctables

src/astrohack/_utils/_holog.py

@@ -31,7 +31,7 @@
 from astrohack._utils._panel_classes.antenna_surface import AntennaSurface
 from astrohack._utils._plot_commons import _create_figure_and_axes, _close_figure, _get_proper_color_map
 
-from astrohack._utils._logger._astrohack_logger import _get_astrohack_logger
+import skriba.logger
 
 CURRENT_FUNCTION=0
 
@@ -43,7 +43,7 @@ def _holog_chunk(holog_chunk_params):
     Args:
         holog_chunk_params (dict): Dictionary containing holography parameters.
     """
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
 
 
     function_name = inspect.stack()[CURRENT_FUNCTION].function
@@ -344,7 +344,7 @@ def _export_to_fits_holog_chunk(parm_dict):
     Args:
         parm_dict: parameter dictionary
     """
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
 
     inputxds = parm_dict['xds_data']
     metadata = parm_dict['metadata']
@@ -532,7 +532,7 @@ def _plot_beam(laxis, maxis, pol_axis, data, basename, label, antenna, ddi, unit
 
     function_name = inspect.stack()[CURRENT_FUNCTION].function
 
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
 
     colormap = _get_proper_color_map(colormap)
 

src/astrohack/_utils/_imaging.py

@@ -5,7 +5,6 @@
 import astropy.coordinates as coord
 from skimage.draw import disk
 from astrohack._utils._algorithms import _calc_coords
-from astrohack._utils._logger._astrohack_logger import _get_astrohack_logger
 
 
 def _parallactic_derotation(data, parallactic_angle_dict):
@@ -27,19 +26,19 @@ def _parallactic_derotation(data, parallactic_angle_dict):
     maps = list(parallactic_angle_dict.keys())
 
     # Get the median index for the first map (this should be the same for every map).
-    median_index = len(parallactic_angle_dict[maps[0]].parallactic_samples)//2
-    
+    median_index = len(parallactic_angle_dict[maps[0]].parallactic_samples) // 2
+
     # This is the angle we will rotated the maps to.
     median_angular_reference = parallactic_angle_dict[maps[0]].parallactic_samples[median_index]
-    
+
     for map, map_value in enumerate(maps):
-        #median_angular_offset = median_angular_reference - parallactic_angle_dict[map_value].parallactic_samples[median_index]
-        #median_angular_offset *= 180/np.pi
-        
-        #parallactic_angle = 360 - parallactic_angle_dict[map_value].parallactic_samples[median_index]*180/np.pi
-        
+        # median_angular_offset = median_angular_reference - parallactic_angle_dict[map_value].parallactic_samples[median_index]
+        # median_angular_offset *= 180/np.pi
+
+        # parallactic_angle = 360 - parallactic_angle_dict[map_value].parallactic_samples[median_index]*180/np.pi
+
         data[map] = scipy.ndimage.rotate(input=data[map, ...], angle=90, axes=(3, 2), reshape=False)
-        
+
     return data
 
 
@@ -58,16 +57,16 @@ def _mask_circular_disk(center, radius, array, mask_value=np.nan):
     shape = np.array(array.shape[-2:])
 
     if center is None:
-        center = shape//2
+        center = shape // 2
 
     r, c = disk(center, radius, shape=shape)
-    mask = np.zeros(shape, dtype=array.dtype)   
+    mask = np.zeros(shape, dtype=array.dtype)
     mask[r, c] = 1
-    
+
     mask = np.tile(mask, reps=(array.shape[:-2] + (1, 1)))
-    
+
     mask[mask == 0] = mask_value
-    
+
     return mask
 
 
@@ -83,10 +82,10 @@ def _calculate_aperture_pattern(grid, delta, padding_factor=50):
     Returns:
         numpy.ndarray, numpy.ndarray, numpy.ndarray: aperture grid, u-coordinate array, v-coordinate array
     """
-    logger = _get_astrohack_logger()
+    logger = skriba.logger.get_logger(logger_name="astrohack")
     logger.info("[holog]: Calculating aperture illumination pattern ...")
 
-    assert grid.shape[-1] == grid.shape[-2] ###To do: why is this expected that l.shape == m.shape
+    assert grid.shape[-1] == grid.shape[-2]  ###To do: why is this expected that l.shape == m.shape
     initial_dimension = grid.shape[-1]
 
     # Calculate padding as the nearest power of 2
@@ -124,11 +123,11 @@ def _calculate_aperture_pattern(grid, delta, padding_factor=50):
 
 
 def _calculate_parallactic_angle_chunk(
-    time_samples,
-    observing_location,
-    direction,
-    dir_frame="FK5",
-    zenith_frame="FK5",
+        time_samples,
+        observing_location,
+        direction,
+        dir_frame="FK5",
+        zenith_frame="FK5",
 ):
     """
     Converts a direction and zenith (frame FK5) to a topocentric Altitude-Azimuth (https://docs.astropy.org/en/stable/api/astropy.coordinates.AltAz.html)

src/astrohack/_utils/_locit.py

@@ -16,7 +16,6 @@
 from astrohack._utils._conversion import _convert_unit
 from astrohack._utils._algorithms import _least_squares_fit
 from astrohack._utils._constants import *
-#from astrohack.client import _get_astrohack_logger
 
 
 def _locit_separated_chunk(locit_parms):

src/astrohack/_utils/_locit_commons.py

@@ -2,7 +2,6 @@
 
 from astrohack._utils._panel_classes.telescope import Telescope
 from astrohack._utils._constants import *
-#from astrohack.client import _get_astrohack_logger
 
 import skriba.logger