astrohack 0.3.2__tar.gz → 0.3.3__tar.gz

{astrohack-0.3.2/src/astrohack.egg-info → astrohack-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: astrohack
-Version: 0.3.2
+Version: 0.3.3
 Summary: Holography Antenna Commissioning Kit
 Author-email: Jan-Willem Steeb <jsteeb@nrao.edu>, Joshua Hoskins <jhoskins@nrao.edu>, Victor de Souza Magalhaes <vdesouza@nrao.edu>
 Requires-Python: <3.12,>=3.8

astrohack-0.3.3/pyproject.toml

@@ -0,0 +1,24 @@
+[project]
+name = "astrohack"
+version = "0.3.3"
+description = "Holography Antenna Commissioning Kit"
+readme = "README.md"
+requires-python = ">= 3.8, < 3.12"
+dependencies = [ "astropy", "dask", "distributed", "gdown", "matplotlib", "memory_profiler", "numba>=0.57.0", "numpy", "prettytable", "pytest", "pytest-cov", "pytest-html", "scikit_image", "scipy", "xarray", "zarr", "bokeh", "jupyterlab", "python_casacore>=3.5.2; sys_platform != \"darwin\" ",]
+[[project.authors]]
+name = "Jan-Willem Steeb"
+email = "jsteeb@nrao.edu"
+
+[[project.authors]]
+name = "Joshua Hoskins"
+email = "jhoskins@nrao.edu"
+
+[[project.authors]]
+name = "Victor de Souza Magalhaes"
+email = "vdesouza@nrao.edu"
+
+[project.license]
+file = "LICENSE.txt"
+
+[project.optional-dependencies]
+docs = [ "ipykernel", "ipympl", "ipython", "jupyter-client", "nbsphinx", "recommonmark", "scanpydoc", "sphinx-autoapi", "sphinx-autosummary-accessors", "sphinx_rtd_theme", "twine", "pandoc",]

{astrohack-0.3.2 → astrohack-0.3.3}/src/astrohack/_utils/_algorithms.py

@@ -1,11 +1,9 @@
-import scipy
 import scipy.signal as scisig
-import numba
-
 import numpy as np
 
 from astrohack._utils._logger._astrohack_logger import _get_astrohack_logger
 
+
 def _calculate_suggested_grid_paramater(parameter, quantile=0.01):
     import scipy
 
@@ -33,6 +31,7 @@ def _calculate_suggested_grid_paramater(parameter, quantile=0.01):
 
         return np.mean(parameter)
 
+
 def _apply_mask(data, scaling=0.5):
     """ Applies a cropping mask to the input data according to the scale factor
 
@@ -59,6 +58,7 @@ def _apply_mask(data, scaling=0.5):
     start = int(x // 2 - mask // 2)
     return data[start : (start + mask), start : (start + mask)]
 
+
 def _calc_coords(image_size, cell_size):
     """Calculate the center pixel of the image given a cell and image size
 
@@ -95,7 +95,7 @@ def _find_nearest(array, value):
     return idx, array[idx]
 
 
-#@njit(cache=False, nogil=True)
+# @njit(cache=False, nogil=True)
 def _chunked_average(data, weight, avg_map, avg_freq):
 
     avg_chan_index = np.arange(avg_freq.shape[0])
@@ -133,6 +133,7 @@ def _chunked_average(data, weight, avg_map, avg_freq):
 
     return data_avg, weight_sum
 
+
 def _calculate_euclidean_distance(x, y, center):
     """ Calculates the euclidean distance between a pair of pair of input points.
 
@@ -175,6 +176,7 @@ def _find_peak_beam_value(data, height=0.5, scaling=0.5):
 
     return masked_data[x[index], y[index]]
 
+
 def _gauss_elimination_numpy(system, vector):
     """
     Gauss elimination solving of a system using numpy
@@ -188,6 +190,7 @@ def _gauss_elimination_numpy(system, vector):
     inverse = np.linalg.inv(system)
     return np.dot(inverse, vector)
 
+
 def _least_squares_fit(system, vector):
     """
     Least squares fitting of a system of linear equations
@@ -204,14 +207,17 @@ def _least_squares_fit(system, vector):
     if system.shape[0] < system.shape[1]:
         raise Exception('System must have at least the same number of rows as it has of columns')
     
-    fit = np.linalg.lstsq(system, vector, rcond=None)
-    
-    result = fit[0]
-    residuals = fit[1]
+    result, residuals, _, _ = np.linalg.lstsq(system, vector, rcond=None)
+    dof = len(vector)-len(result)
+    if dof > 0:
+        errs = (vector - np.dot(system, result))/dof
+    else:
+        errs = (vector - np.dot(system, result))
+    sigma2 = np.sum(errs**2)
     covar = np.linalg.inv(np.dot(system.T, system))
-    variances = np.diagonal(covar)
-    
-    return result, variances, residuals
+    variance = np.diagonal(sigma2*covar)
+    return result, variance, residuals
+
 
 def _least_squares_fit_block(system, vector):
     """
@@ -270,6 +276,7 @@ def _get_grid_parms(vis_map_dict, pnt_map_dict, ant_names):
 
     return grid_parms
 
+
 def _significant_digits(x, digits):
     if np.isscalar(x):
         return _significant_digits_scalar(x, digits)

{astrohack-0.3.2 → astrohack-0.3.3}/src/astrohack/_utils/_locit.py

@@ -1,4 +1,3 @@
-import numpy as np
 from prettytable import PrettyTable
 from astropy.coordinates import EarthLocation
 from astropy.time import Time
@@ -306,29 +305,30 @@ def _create_output_xds(coordinates, lst, delays, fit, variance, chi_squared, mod
     fit_kterm = locit_parms['fit_kterm']
     fit_rate = locit_parms['fit_rate']
     antenna = locit_parms['ant_info'][locit_parms['this_ant']]
+    error = np.sqrt(variance)
 
     output_xds = xr.Dataset()
     output_xds.attrs['polarization'] = locit_parms['polarization']
     output_xds.attrs['frequency'] = frequency
     output_xds.attrs['position_fit'] = fit[1:4]
-    output_xds.attrs['position_error'] = variance[1:4]
+    output_xds.attrs['position_error'] = error[1:4]
     output_xds.attrs['fixed_delay_fit'] = fit[0]
-    output_xds.attrs['fixed_delay_error'] = variance[0]
+    output_xds.attrs['fixed_delay_error'] = error[0]
     output_xds.attrs['antenna_info'] = antenna
     output_xds.attrs['elevation_limit'] = elevation_limit
     output_xds.attrs['chi_squared'] = chi_squared
 
     if fit_kterm and fit_rate:
         output_xds.attrs['koff_fit'] = fit[4]
-        output_xds.attrs['koff_error'] = variance[4]
+        output_xds.attrs['koff_error'] = error[4]
         output_xds.attrs['rate_fit'] = fit[5]
-        output_xds.attrs['rate_error'] = variance[5]
+        output_xds.attrs['rate_error'] = error[5]
     elif fit_kterm and not fit_rate:
         output_xds.attrs['koff_fit'] = fit[4]
-        output_xds.attrs['koff_error'] = variance[4]
+        output_xds.attrs['koff_error'] = error[4]
     elif not fit_kterm and fit_rate:
         output_xds.attrs['rate_fit'] = fit[4]
-        output_xds.attrs['rate_error'] = variance[4]
+        output_xds.attrs['rate_error'] = error[4]
     else:
         pass  # Nothing to be added to the attributes
 

{astrohack-0.3.2 → astrohack-0.3.3}/src/astrohack/_utils/_panel_classes/antenna_surface.py

@@ -495,10 +495,13 @@ class AntennaSurface:
             basename: basename for the plot, the prefix 'ancillary_amplitude' will be added to it
             parm_dict: dictionary with plotting parameters
         """
-        vmin, vmax = np.nanmin(self.amplitude), np.nanmax(self.amplitude)
-        title = "Amplitude, min={0:.5f}, max ={1:.5f} V".format(vmin, vmax)
+        if parm_dict['amplitude_limits'] is None or parm_dict['amplitude_limits'] == "None":
+            parm_dict['z_lim'] = np.nanmin(self.amplitude), np.nanmax(self.amplitude)
+        else:
+            parm_dict['z_lim'] = parm_dict['amplitude_limits']
+
+        title = "Amplitude, min={0:.5f}, max ={1:.5f} V".format(parm_dict['z_lim'][0], parm_dict['z_lim'][1])
         plotname = _add_prefix(basename, 'amplitude')
-        parm_dict['z_lim'] = [vmin, vmax]
         parm_dict['unit'] = self.amp_unit
         self._plot_map(plotname, self.amplitude, title, parm_dict)
 

{astrohack-0.3.2 → astrohack-0.3.3}/src/astrohack/_utils/_plot_commons.py

@@ -1,9 +1,14 @@
 from matplotlib import pyplot as plt
 from mpl_toolkits.axes_grid1 import make_axes_locatable
-from matplotlib import colormaps as cmaps
+from matplotlib import colormaps as matplotlib_cmaps
+from matplotlib.colors import ListedColormap
 from astrohack._utils import figsize, fontsize
 
 
+astrohack_cmaps = list(matplotlib_cmaps.keys())
+astrohack_cmaps.append('AIPS')
+
+
 def _create_figure_and_axes(figure_size, boxes, default_figsize=figsize, sharex=False, sharey=False):
     """
     Create a figures and plotting axes within according to a desired figure size and number of boxes
@@ -110,6 +115,19 @@ def _well_positioned_colorbar(ax, fig, image, label, location='right', size='5%'
 
 def _get_proper_color_map(user_cmap, default_cmap='viridis'):
     if user_cmap is None or user_cmap == 'None':
-        return cmaps[default_cmap]
+        return matplotlib_cmaps[default_cmap]
+    elif user_cmap == 'AIPS':
+        # 8 bit color values picked from AIPS plots using GIMP
+        cmap = ListedColormap([[ 71/255.,  71/255.,  71/255., 1],  # Grey
+                               [104/255.,   0/255., 142/255., 1],  # Purple/ dark blue?
+                               [  0/255.,   0/255., 186/255., 1],  # Blue
+                               [ 71/255., 147/255., 230/255., 1],  # Pink
+                               [  0/255., 130/255.,   0/255., 1],  # Green
+                               [  0/255., 243/255.,   0/255., 1],  # Light Green
+                               [255/255., 255/255.,   0/255., 1],  # Yellow
+                               [255/255., 158/255.,   0/255., 1],  # Orange
+                               [255/255.,   0/255.,   0/255., 1]   # Red
+                               ])
+        return cmap
     else:
-        return cmaps[user_cmap]
+        return matplotlib_cmaps[user_cmap]

{astrohack-0.3.2 → astrohack-0.3.3}/src/astrohack/combine.py

@@ -9,7 +9,7 @@ from astrohack.mds import AstrohackImageFile
 from astrohack._utils._dask_graph_tools import _dask_general_compute
 
 
-def combine(image_name, combine_name=None, ant_id=None, ddi=None, weighted=False, parallel=False, overwrite=False):
+def combine(image_name, combine_name=None, ant=None, ddi=None, weighted=False, parallel=False, overwrite=False):
     """Combine DDIs in a Holography image to increase SNR
 
     :param image_name: Input holography data file name. Accepted data format is the output from ``astrohack.holog.holog``
@@ -17,8 +17,8 @@ def combine(image_name, combine_name=None, ant_id=None, ddi=None, weighted=False
     :param combine_name: Name of output file; File name will be appended with suffix *.combine.zarr*. Defaults to \
     *basename* of input file plus holography panel file suffix.
     :type combine_name: str, optional
-    :param ant_id: List of antennas to be processed. None will use all antennas. Defaults to None, ex. ea25.
-    :type ant_id: list or str, optional
+    :param ant: List of antennas to be processed. None will use all antennas. Defaults to None, ex. ea25.
+    :type ant: list or str, optional
     :param ddi: List of DDIs to be combined. None will use all DDIs. Defaults to None, ex. [0, ..., 8].
     :type ddi: list of int, optional
     :param weighted: Weight phases by the corresponding amplitudes.
@@ -52,7 +52,6 @@ def combine(image_name, combine_name=None, ant_id=None, ddi=None, weighted=False
     """
 
     combine_params = locals()
-    combine_params['ant'] = ant_id
     logger = _get_astrohack_logger()
     fname = 'combine'
     combine_params = _check_combine_parms(fname, combine_params)

{astrohack-0.3.2 → astrohack-0.3.3}/src/astrohack/extract_locit.py

@@ -8,7 +8,7 @@ from astrohack._utils._extract_locit import _extract_source_and_telescope, _extr
 from astrohack.mds import AstrohackLocitFile
 
 
-def extract_locit(cal_table, locit_name=None, ant_id=None, ddi=None, overwrite=False):
+def extract_locit(cal_table, locit_name=None, ant=None, ddi=None, overwrite=False):
     """
     Extract Antenna position determination data from an MS and stores it in a locit output file.
 
@@ -16,8 +16,8 @@ def extract_locit(cal_table, locit_name=None, ant_id=None, ddi=None, overwrite=F
     :type cal_table: str
     :param locit_name: Name of *<locit_name>.locit.zarr* file to create. Defaults to measurement set name with *locit.zarr* extension.
     :type locit_name: str, optional
-    :param ant_id: List of antennas/antenna to be extracted, defaults to "all" when None, ex. ea25
-    :type ant_id: list or str, optional
+    :param ant: List of antennas/antenna to be extracted, defaults to "all" when None, ex. ea25
+    :type ant: list or str, optional
     :param ddi: List of ddis/ddi to be extracted, defaults to "all" when None, ex. 0
     :type ddi: list or int, optional
     :param overwrite: Boolean for whether to overwrite current locit.zarr file, defaults to False.
@@ -35,7 +35,6 @@ def extract_locit(cal_table, locit_name=None, ant_id=None, ddi=None, overwrite=F
 
     """
     extract_locit_parms = locals()
-    extract_locit_parms['ant'] = ant_id
     logger = _get_astrohack_logger()
 
     fname = 'extract_locit'

{astrohack-0.3.2 → astrohack-0.3.3}/src/astrohack/extract_pointing.py

@@ -1,37 +1,13 @@
-import os
-import dask
-import json
-import copy
 import inspect
-import numbers
 
-import numpy as np
-
-from astropy.time import Time
-
-from pprint import pformat
-
-from casacore import tables as ctables
-
-from astrohack._utils._constants import pol_str
-
-from astrohack._utils._conversion import _convert_ant_name_to_id
-from astrohack._utils._extract_holog import _create_holog_meta_data
 from astrohack._utils._extract_point import _extract_pointing
 
 from astrohack._utils._dio import _load_point_file
 from astrohack._utils._dio import _check_if_file_will_be_overwritten, _check_if_file_exists
-from astrohack._utils._dio import _load_holog_file
 from astrohack._utils._dio import _write_meta_data
-
-from astrohack._utils._extract_holog import _extract_holog_chunk
-
 from astrohack._utils._logger._astrohack_logger import _get_astrohack_logger
-
 from astrohack._utils._param_utils._check_parms import _check_parms, _parm_check_passed
-
 from astrohack._utils._tools import _remove_suffix
-from astrohack._utils._tools import _jsonify
 
 from astrohack.mds import AstrohackPointFile
 

{astrohack-0.3.2 → astrohack-0.3.3}/src/astrohack/holog.py

@@ -26,7 +26,7 @@ def holog(
         chan_average=True,
         chan_tolerance_factor=0.005,
         scan_average=True,
-        ant_id=None,
+        ant=None,
         ddi=None,
         to_stokes=True,
         apply_mask=True,
@@ -66,8 +66,8 @@ def holog(
     :type chan_tolerance_factor: float, optional
     :param scan_average: Boolean dicating whether averagin is done over scan., defaults to True
     :type scan_average: bool, optional
-    :param ant_id: List of antennas/antenna to be processed, defaults to "all" when None, ex. ea25
-    :type ant_id: list or str, optional
+    :param ant: List of antennas/antenna to be processed, defaults to "all" when None, ex. ea25
+    :type ant: list or str, optional
     :param ddi: List of ddis/ddi to be processed, defaults to "all" when None, ex. 0
     :type ddi: list or int, optional
     :param to_stokes: Dictates whether polarization is computed according to stokes values., defaults to True
@@ -136,9 +136,6 @@ def holog(
 
     function_name = inspect.stack()[CURRENT_FUNCTION].function
 
-    # Shouldn't have to do this but the name changes ant_id->ant for some reason. Fix later.
-    holog_params['ant'] = ant_id
-
     ######### Parameter Checking #########
     holog_params = _check_holog_params(function_name=function_name, holog_params=holog_params)
     input_parms = holog_params.copy()

{astrohack-0.3.2 → astrohack-0.3.3}/src/astrohack/locit.py

@@ -8,7 +8,7 @@ from astrohack._utils._dask_graph_tools import _dask_general_compute
 
 
 def locit(locit_name, position_name=None, elevation_limit=10.0, polarization='both', fit_engine='linear algebra',
-          fit_kterm=False, fit_delay_rate=True, ant_id=None, ddi=None, combine_ddis='simple', parallel=False,
+          fit_kterm=False, fit_delay_rate=True, ant=None, ddi=None, combine_ddis='simple', parallel=False,
           overwrite=False):
     """
     Extract Antenna position determination data from an MS and stores it in a locit output file.
@@ -27,8 +27,8 @@ def locit(locit_name, position_name=None, elevation_limit=10.0, polarization='bo
     :type fit_delay_rate: bool, optional
     :param fit_engine: What engine to use on fitting, default is linear algebra
     :type fit_engine: str, optional
-    :param ant_id: List of antennas/antenna to be processed, defaults to "all" when None, ex. ea25
-    :type ant_id: list or str, optional
+    :param ant: List of antennas/antenna to be processed, defaults to "all" when None, ex. ea25
+    :type ant: list or str, optional
     :param ddi: List of ddis/ddi to be processed, defaults to "all" when None, ex. 0
     :type ddi: list or int, optional
     :param combine_ddis: Type of DDI combination, if desired, defaults to simple
@@ -104,7 +104,6 @@ def locit(locit_name, position_name=None, elevation_limit=10.0, polarization='bo
                                 delays.
     """
     locit_parms = locals()
-    locit_parms['ant'] = ant_id
     logger = _get_astrohack_logger()
 
     fname = 'locit'

{astrohack-0.3.2 → astrohack-0.3.3}/src/astrohack/mds.py

@@ -6,7 +6,6 @@ import distributed
 import numpy as np
 
 from prettytable import PrettyTable
-from matplotlib import colormaps as cmaps
 
 from astrohack._utils._logger._astrohack_logger import _get_astrohack_logger
 from astrohack._utils._dio import _read_meta_data
@@ -33,6 +32,7 @@ from astrohack._utils._locit import _plot_delays_chunk, _plot_position_correctio
 
 from astrohack._utils._panel_classes.antenna_surface import AntennaSurface
 from astrohack._utils._panel_classes.telescope import Telescope
+from astrohack._utils._plot_commons import astrohack_cmaps as cmaps
 
 CURRENT_FUNCTION = 0
 
@@ -160,13 +160,13 @@ class AstrohackImageFile(dict):
         _print_data_contents(self, ["Antenna", "DDI"])
         _print_method_list([self.summary, self.select, self.export_to_fits, self.plot_beams, self.plot_apertures])
 
-    def select(self, ant_id, ddi, complex_split='cartesian'):
+    def select(self, ant, ddi, complex_split='cartesian'):
         """ Select data on the basis of ddi, scan, ant. This is a convenience function.
 
         :param ddi: Data description ID, ex. 0.
         :type ddi: int
-        :param ant_id: Antenna ID, ex. ea25.
-        :type ant_id: str
+        :param ant: Antenna ID, ex. ea25.
+        :type ant: str
         :param complex_split: Is the data to b left as is (Real + imag: cartesian, default) or split into Amplitude and Phase (polar)
         :type complex_split: str, optional
 
@@ -175,27 +175,27 @@ class AstrohackImageFile(dict):
         """
         logger = _get_astrohack_logger()
 
-        ant_id = 'ant_' + ant_id
+        ant = 'ant_' + ant
         ddi = f'ddi_{ddi}'
 
-        if ant_id is None or ddi is None:
+        if ant is None or ddi is None:
             logger.info("[select]: No selections made ...")
             return self
         else:
             if complex_split == 'polar':
-                return self[ant_id][ddi].apply(np.absolute), self[ant_id][ddi].apply(np.angle, deg=True)
+                return self[ant][ddi].apply(np.absolute), self[ant][ddi].apply(np.angle, deg=True)
             else:
-                return self[ant_id][ddi]
+                return self[ant][ddi]
 
-    def export_to_fits(self, destination, complex_split='cartesian', ant_id=None, ddi=None, parallel=False):
+    def export_to_fits(self, destination, complex_split='cartesian', ant=None, ddi=None, parallel=False):
         """ Export contents of an AstrohackImageFile object to several FITS files in the destination folder
 
         :param destination: Name of the destination folder to contain plots
         :type destination: str
         :param complex_split: How to split complex data, cartesian (real + imag, default) or polar (amplitude + phase)
         :type complex_split: str, optional
-        :param ant_id: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
-        :type ant_id: list or str, optional
+        :param ant: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
+        :type ant: list or str, optional
         :param ddi: List of ddis/ddi to be plotted, defaults to "all" when None, ex. 0
         :type ddi: list or int, optional
         :param parallel: If True will use an existing astrohack client to export FITS in parallel, default is False
@@ -218,7 +218,6 @@ class AstrohackImageFile(dict):
         """
 
         parm_dict = locals()
-        parm_dict['ant'] = ant_id
         function_name = inspect.stack()[CURRENT_FUNCTION].function
         
         parms_passed = _check_parms(function_name, parm_dict, 'complex_split', [str], acceptable_data=possible_splits,
@@ -242,20 +241,22 @@ class AstrohackImageFile(dict):
             parallel=parallel
         )
 
-    def plot_apertures(self, destination, ant_id=None, ddi=None, plot_screws=False, phase_unit='deg', phase_limits=None,
-                       deviation_unit='mm', deviation_limits=None, panel_labels=False, display=False,
-                       colormap='viridis',
-                       figure_size=None, dpi=300, parallel=False):
+    def plot_apertures(self, destination, ant=None, ddi=None, plot_screws=False, amplitude_limits=None,
+                       phase_unit='deg', phase_limits=None, deviation_unit='mm', deviation_limits=None,
+                       panel_labels=False, display=False, colormap='viridis', figure_size=None, dpi=300,
+                       parallel=False):
         """ Aperture amplitude and phase plots from the data in an AstrohackImageFIle object.
 
         :param destination: Name of the destination folder to contain plots
         :type destination: str
-        :param ant_id: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
-        :type ant_id: list or str, optional
+        :param ant: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
+        :type ant: list or str, optional
         :param ddi: List of ddis/ddi to be plotted, defaults to "all" when None, ex. 0
         :type ddi: list or int, optional
         :param plot_screws: Add screw positions to plot, default is False
         :type plot_screws: bool, optional
+        :param amplitude_limits: Lower then Upper limit for amplitude in volts default is None (Guess from data)
+        :type amplitude_limits: numpy.ndarray, list, tuple, optional
         :param phase_unit: Unit for phase plots, defaults is 'deg'
         :type phase_unit: str, optional
         :param phase_limits: Lower then Upper limit for phase, value in phase_unit, default is None (Guess from data)
@@ -282,7 +283,6 @@ class AstrohackImageFile(dict):
         Produce plots from ``astrohack.holog`` results for analysis
         """
         parm_dict = locals()
-        parm_dict['ant'] = ant_id
         function_name = inspect.stack()[CURRENT_FUNCTION].function
         
         parms_passed = _check_parms(function_name, parm_dict, 'ant', [str, list], list_acceptable_data_types=[str],
@@ -290,6 +290,9 @@ class AstrohackImageFile(dict):
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'ddi', [int, list],
                                                      list_acceptable_data_types=[int], default='all')
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'destination', [str], default=None)
+        parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'amplitude_limits', [list, np.ndarray],
+                                                     list_acceptable_data_types=[numbers.Number], list_len=2,
+                                                     default='None', log_default_setting=False)
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'phase_unit', [str], acceptable_data=trigo_units,
                                                      default='deg')
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'phase_limits', [list, np.ndarray],
@@ -315,14 +318,14 @@ class AstrohackImageFile(dict):
         _create_destination_folder(parm_dict['destination'])
         _dask_general_compute(function_name, self, _plot_aperture_chunk, parm_dict, ['ant', 'ddi'], parallel=parallel)
 
-    def plot_beams(self, destination, ant_id=None, ddi=None, complex_split='polar', display=False, colormap='viridis',
+    def plot_beams(self, destination, ant=None, ddi=None, complex_split='polar', display=False, colormap='viridis',
                    figure_size=None, dpi=300, parallel=False):
         """ Beam plots from the data in an AstrohackImageFIle object.
 
         :param destination: Name of the destination folder to contain plots
         :type destination: str
-        :param ant_id: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
-        :type ant_id: list or str, optional
+        :param ant: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
+        :type ant: list or str, optional
         :param ddi: List of ddis/ddi to be plotted, defaults to "all" when None, ex. 0
         :type ddi: list or int, optional
         :param complex_split: How to split complex beam data, cartesian (real + imag) or polar (amplitude + phase, default)
@@ -343,7 +346,6 @@ class AstrohackImageFile(dict):
         Produce plots from ``astrohack.holog`` results for analysis
         """
         parm_dict = locals()
-        parm_dict['ant'] = ant_id
 
         function_name = inspect.stack()[CURRENT_FUNCTION].function
         parms_passed = _check_parms(function_name, parm_dict, 'ant', [str, list], list_acceptable_data_types=[str],
@@ -438,29 +440,29 @@ class AstrohackHologFile(dict):
         _print_data_contents(self, ["DDI", "Map", "Antenna"])
         _print_method_list([self.summary, self.select, self.plot_diagnostics])
 
-    def select(self, ddi=None, map_id=None, ant_id=None):
+    def select(self, ddi=None, map_id=None, ant=None):
         """ Select data on the basis of ddi, scan, ant. This is a convenience function.
 
         :param ddi: Data description ID, ex. 0.
         :type ddi: int
         :param map_id: Mapping ID, ex. 0.
         :type map_id: int
-        :param ant_id: Antenna ID, ex. ea25.
-        :type ant_id: str
+        :param ant: Antenna ID, ex. ea25.
+        :type ant: str
 
         :return: Corresponding xarray dataset, or self if selection is None
         :rtype: xarray.Dataset or AstrohackHologFile
         """
         logger = _get_astrohack_logger()
-        ant_id = 'ant_' + ant_id
+        ant = 'ant_' + ant
         ddi = f'ddi_{ddi}'
         map_id = f'map_{map_id}'
 
-        if ant_id is None or ddi is None or map_id is None:
+        if ant is None or ddi is None or map_id is None:
             logger.info("[select]: No selection made ...")
             return self
         else:
-            return self[ddi][map_id][ant_id]
+            return self[ddi][map_id][ant]
 
     @property
     def meta_data(self):
@@ -472,7 +474,7 @@ class AstrohackHologFile(dict):
 
         return self._meta_data
 
-    def plot_diagnostics(self, destination, delta=0.01, ant_id=None, ddi=None, map_id=None, complex_split='polar',
+    def plot_diagnostics(self, destination, delta=0.01, ant=None, ddi=None, map_id=None, complex_split='polar',
                          display=False, figure_size=None, dpi=300, parallel=False):
         """ Plot diagnostic calibration plots from the holography data file.
 
@@ -480,8 +482,8 @@ class AstrohackHologFile(dict):
         :type destination: str
         :param delta: Defines a fraction of cell_size around which to look for peaks., defaults to 0.01
         :type delta: float, optional
-        :param ant_id: antenna ID to use in subselection, defaults to "all" when None, ex. ea25
-        :type ant_id: list or str, optional
+        :param ant: antenna ID to use in subselection, defaults to "all" when None, ex. ea25
+        :type ant: list or str, optional
         :param ddi: data description ID to use in subselection, defaults to "all" when None, ex. 0
         :type ddi: list or int, optional
         :param map_id: map ID to use in subselection. This relates to which antenna are in the mapping vs. scanning \
@@ -519,7 +521,6 @@ class AstrohackHologFile(dict):
         logger = _get_astrohack_logger()
 
         parm_dict = locals()
-        parm_dict['ant'] = ant_id
         if parallel:
             if not distributed.client._get_global_client():
                 try:
@@ -626,31 +627,31 @@ class AstrohackPanelFile(dict):
         _print_method_list([self.summary, self.get_antenna, self.export_screws, self.export_to_fits,
                             self.plot_antennas])
 
-    def get_antenna(self, ant_id, ddi):
+    def get_antenna(self, ant, ddi):
         """ Retrieve an AntennaSurface object for interaction
 
-        :param ant_id: Antenna to be retrieved, ex. ea25.
-        :type ant_id: str
+        :param ant: Antenna to be retrieved, ex. ea25.
+        :type ant: str
         :param ddi: DDI to be retrieved for ant_id, ex. 0
         :type ddi: int
 
         :return: AntennaSurface object describing for further interaction
         :rtype: AntennaSurface
         """
-        ant_id = 'ant_' + ant_id
+        ant = 'ant_' + ant
         ddi = f'ddi_{ddi}'
-        xds = self[ant_id][ddi]
+        xds = self[ant][ddi]
         telescope = Telescope(xds.attrs['telescope_name'])
         return AntennaSurface(xds, telescope, reread=True)
 
-    def export_screws(self, destination, ant_id=None, ddi=None, unit='mm', threshold=None, panel_labels=True,
+    def export_screws(self, destination, ant=None, ddi=None, unit='mm', threshold=None, panel_labels=True,
                       display=False, colormap='RdBu_r', figure_size=None, dpi=300):
         """ Export screw adjustments to text files and optionally plots.
 
         :param destination: Name of the destination folder to contain exported screw adjustments
         :type destination: str
-        :param ant_id: List of antennas/antenna to be exported, defaults to "all" when None, ex. ea25
-        :type ant_id: list or str, optional
+        :param ant: List of antennas/antenna to be exported, defaults to "all" when None, ex. ea25
+        :type ant: list or str, optional
         :param ddi: List of ddis/ddi to be exported, defaults to "all" when None, ex. 0
         :type ddi: list or int, optional
         :param unit: Unit for screws adjustments, most length units supported, defaults to "mm"
@@ -676,7 +677,6 @@ class AstrohackPanelFile(dict):
 
         """
         parm_dict = locals()
-        parm_dict['ant'] = ant_id
 
         function_name = inspect.stack()[CURRENT_FUNCTION].function
         parms_passed = _check_parms(function_name, parm_dict, 'ant', [str, list], list_acceptable_data_types=[str],
@@ -684,8 +684,8 @@ class AstrohackPanelFile(dict):
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'ddi', [int, list],
                                                      list_acceptable_data_types=[int], default='all')
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'destination', [str], default=None)
-        parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'unit', [str], acceptable_data=length_units,
-                                                     default='mm')
+        parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'unit', [str],
+                                                     acceptable_data=length_units, default='mm')
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'threshold', [int, float], default='None')
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'panel_labels', [bool], default=True)
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'display', [bool], default=True)
@@ -700,21 +700,24 @@ class AstrohackPanelFile(dict):
         _create_destination_folder(parm_dict['destination'])
         _dask_general_compute(function_name, self, _export_screws_chunk, parm_dict, ['ant', 'ddi'], parallel=False)
 
-    def plot_antennas(self, destination, ant_id=None, ddi=None, plot_type='deviation', plot_screws=False,
-                      phase_unit='deg', phase_limits=None, deviation_unit='mm', deviation_limits=None,
-                      panel_labels=False, display=False, colormap='viridis', figure_size=None, dpi=300, parallel=False):
+    def plot_antennas(self, destination, ant=None, ddi=None, plot_type='deviation', plot_screws=False,
+                      amplitude_limits=None, phase_unit='deg', phase_limits=None, deviation_unit='mm',
+                      deviation_limits=None, panel_labels=False, display=False, colormap='viridis', figure_size=None,
+                      dpi=300, parallel=False):
         """ Create diagnostic plots of antenna surfaces from panel data file.
 
         :param destination: Name of the destination folder to contain plots
         :type destination: str
-        :param ant_id: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
-        :type ant_id: list or str, optional
+        :param ant: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
+        :type ant: list or str, optional
         :param ddi: List of ddis/ddi to be plotted, defaults to "all" when None, ex. 0
         :type ddi: list or int, optional
         :param plot_type: type of plot to be produced, deviation, phase, ancillary or all, default is deviation
         :type plot_type: str, optional
         :param plot_screws: Add screw positions to plot
         :type plot_screws: bool, optional
+        :param amplitude_limits: Lower then Upper limit for amplitude in volts default is None (Guess from data)
+        :type amplitude_limits: numpy.ndarray, list, tuple, optional
         :param phase_unit: Unit for phase plots, defaults is 'deg'
         :type phase_unit: str, optional
         :param phase_limits: Lower then Upper limit for phase, value in phase_unit, default is None (Guess from data)
@@ -755,7 +758,6 @@ class AstrohackPanelFile(dict):
         """
         logger = _get_astrohack_logger()
         parm_dict = locals()
-        parm_dict['ant'] = ant_id
 
         function_name = inspect.stack()[CURRENT_FUNCTION].function
         parms_passed = _check_parms(function_name, parm_dict, 'ant', [str, list], list_acceptable_data_types=[str],
@@ -765,6 +767,9 @@ class AstrohackPanelFile(dict):
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'destination', [str], default=None)
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'plot_type', [str], acceptable_data=plot_types,
                                                      default=plot_types[0])
+        parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'amplitude_limits', [list, np.ndarray],
+                                                     list_acceptable_data_types=[numbers.Number], list_len=2,
+                                                     default='None', log_default_setting=False)
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'phase_unit', [str], acceptable_data=trigo_units,
                                                      default='deg')
         parms_passed = parms_passed and _check_parms(function_name, parm_dict, 'phase_limits', [list, np.ndarray],
@@ -790,13 +795,13 @@ class AstrohackPanelFile(dict):
         _create_destination_folder(parm_dict['destination'])
         _dask_general_compute(function_name, self, _plot_antenna_chunk, parm_dict, ['ant', 'ddi'], parallel=parallel)
 
-    def export_to_fits(self, destination, ant_id=None, ddi=None, parallel=False):
+    def export_to_fits(self, destination, ant=None, ddi=None, parallel=False):
         """ Export contents of an Astrohack MDS file to several FITS files in the destination folder
 
         :param destination: Name of the destination folder to contain plots
         :type destination: str
-        :param ant_id: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
-        :type ant_id: list or str, optional
+        :param ant: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
+        :type ant: list or str, optional
         :param ddi: List of ddis/ddi to be plotted, defaults to "all" when None, ex. 0
         :type ddi: list or int, optional
         :param parallel: If True will use an existing astrohack client to export FITS in parallel, default is False
@@ -810,10 +815,7 @@ class AstrohackPanelFile(dict):
         The FITS fils produced by this method have been tested and are known to work with CARTA and DS9
         """
 
-        parm_dict = {'ant': ant_id,
-                     'ddi': ddi,
-                     'destination': destination,
-                     'parallel': parallel}
+        parm_dict = locals()
 
         function_name = inspect.stack()[CURRENT_FUNCTION].function
         parms_passed = _check_parms(function_name, parm_dict, 'ant', [str, list], list_acceptable_data_types=[str],
@@ -825,7 +827,8 @@ class AstrohackPanelFile(dict):
 
         _parm_check_passed(function_name, parms_passed)
         _create_destination_folder(parm_dict['destination'])
-        _dask_general_compute(function_name, self, _export_to_fits_panel_chunk, parm_dict, ['ant', 'ddi'], parallel=parallel)
+        _dask_general_compute(function_name, self, _export_to_fits_panel_chunk, parm_dict, ['ant', 'ddi'],
+                              parallel=parallel)
 
 
 class AstrohackPointFile(dict):
@@ -1162,14 +1165,14 @@ class AstrohackPositionFile(dict):
 
         return self._file_is_open
 
-    def export_fit_results(self, destination, ant_id=None, ddi=None, position_unit='m', time_unit='hour',
+    def export_fit_results(self, destination, ant=None, ddi=None, position_unit='m', time_unit='hour',
                            delay_unit='nsec'):
         """ Export antenna position fit results to a text file.
 
         :param destination: Name of the destination folder to contain exported fit results
         :type destination: str
-        :param ant_id: List of antennas/antenna to be exported, defaults to "all" when None, ex. ea25
-        :type ant_id: list or str, optional
+        :param ant: List of antennas/antenna to be exported, defaults to "all" when None, ex. ea25
+        :type ant: list or str, optional
         :param ddi: List of ddis/ddi to be exported, defaults to "all" when None, ex. 0
         :type ddi: list or int, optional
         :param position_unit: Unit to list position fit results, defaults to 'm'
@@ -1185,7 +1188,6 @@ class AstrohackPositionFile(dict):
         """
 
         parm_dict = locals()
-        parm_dict['ant'] = ant_id
         function_name = inspect.stack()[CURRENT_FUNCTION].function
         parms_passed = _check_parms(function_name, parm_dict, 'ant', [str, list],
                                     list_acceptable_data_types=[str], default='all')
@@ -1204,14 +1206,14 @@ class AstrohackPositionFile(dict):
         parm_dict['combined'] = self.combined
         _export_fit_results(self, parm_dict)
 
-    def plot_sky_coverage(self, destination, ant_id=None, ddi=None, time_unit='hour', angle_unit='deg', display=False,
+    def plot_sky_coverage(self, destination, ant=None, ddi=None, time_unit='hour', angle_unit='deg', display=False,
                           figure_size=None, dpi=300, parallel=False):
         """ Plot the sky coverage of the data used for antenna position fitting
 
         :param destination: Name of the destination folder to contain the plots
         :type destination: str
-        :param ant_id: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
-        :type ant_id: list or str, optional
+        :param ant: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
+        :type ant: list or str, optional
         :param ddi: List of ddis/ddi to be plotted, defaults to "all" when None, ex. 0
         :type ddi: list or int, optional
         :param angle_unit: Unit for angle in plots, defaults to 'deg'
@@ -1240,7 +1242,7 @@ class AstrohackPositionFile(dict):
         """
 
         parm_dict = locals()
-        parm_dict['ant'] = ant_id
+
         function_name = inspect.stack()[CURRENT_FUNCTION].function
         parms_passed = _check_parms(function_name, parm_dict, 'ant', [str, list],
                                     list_acceptable_data_types=[str], default='all')
@@ -1268,14 +1270,14 @@ class AstrohackPositionFile(dict):
         else:
             _dask_general_compute(function_name, self, _plot_sky_coverage_chunk, parm_dict, ['ant', 'ddi'], parallel=parallel)
 
-    def plot_delays(self, destination, ant_id=None, ddi=None, time_unit='hour', angle_unit='deg', delay_unit='nsec',
+    def plot_delays(self, destination, ant=None, ddi=None, time_unit='hour', angle_unit='deg', delay_unit='nsec',
                     plot_model=True, display=False, figure_size=None, dpi=300, parallel=False):
         """ Plot the delays used for antenna position fitting and optionally the resulting fit.
 
         :param destination: Name of the destination folder to contain the plots
         :type destination: str
-        :param ant_id: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
-        :type ant_id: list or str, optional
+        :param ant: List of antennas/antenna to be plotted, defaults to "all" when None, ex. ea25
+        :type ant: list or str, optional
         :param ddi: List of ddis/ddi to be plotted, defaults to "all" when None, ex. 0
         :type ddi: list or int, optional
         :param angle_unit: Unit for angle in plots, defaults to 'deg'
@@ -1309,7 +1311,6 @@ class AstrohackPositionFile(dict):
         """
 
         parm_dict = locals()
-        parm_dict['ant'] = ant_id
 
         function_name = inspect.stack()[CURRENT_FUNCTION].function
         parms_passed = _check_parms(function_name, parm_dict, 'ant', [str, list],
@@ -1343,14 +1344,14 @@ class AstrohackPositionFile(dict):
         else:
             _dask_general_compute(function_name, self, _plot_delays_chunk, parm_dict, ['ant', 'ddi'], parallel=parallel)
 
-    def plot_position_corrections(self, destination, ant_id=None, ddi=None, unit='km', box_size=5, scaling=250,
+    def plot_position_corrections(self, destination, ant=None, ddi=None, unit='km', box_size=5, scaling=250,
                                   display=False, figure_size=None, dpi=300):
         """ Plot Antenna position corrections on an array configuration plot
 
         :param destination: Name of the destination folder to contain plot
         :type destination: str
-        :param ant_id: Select which antennas are to be plotted, defaults to all when None, ex. ea25
-        :type ant_id: list or str, optional
+        :param ant: Select which antennas are to be plotted, defaults to all when None, ex. ea25
+        :type ant: list or str, optional
         :param ddi: List of ddis/ddi to be plotted, defaults to "all" when None, ex. 0
         :type ddi: list or int, optional
         :param unit: Unit for the plot, valid values are length units, default is km
@@ -1377,7 +1378,6 @@ class AstrohackPositionFile(dict):
         """
 
         parm_dict = locals()
-        parm_dict['ant'] = ant_id
 
         function_name = inspect.stack()[CURRENT_FUNCTION].function
         parms_passed = _check_parms(function_name, parm_dict, 'destination', [str], default=None)

{astrohack-0.3.2 → astrohack-0.3.3}/src/astrohack/panel.py

@@ -1,4 +1,3 @@
-import numbers
 import os
 import shutil
 
@@ -13,8 +12,8 @@ from astrohack._utils._dask_graph_tools import _dask_general_compute
 from astrohack.mds import AstrohackPanelFile, AstrohackImageFile
 
 
-def panel(image_name, panel_name=None, clip_type='sigma', clip_level=3, panel_model=None, panel_margins=0.05, ant_id=None, ddi=None,
-          parallel=False, overwrite=False):
+def panel(image_name, panel_name=None, clip_type='sigma', clip_level=3, panel_model=None, panel_margins=0.05, ant=None,
+          ddi=None, parallel=False, overwrite=False):
     """Analyze holography images to derive panel adjustments
 
     :param image_name: Input holography data file name. Accepted data formats are the output from ``astrohack.holog.holog`` and AIPS holography data prepackaged using ``astrohack.panel.aips_holog_to_astrohack``.
@@ -29,8 +28,8 @@ def panel(image_name, panel_name=None, clip_type='sigma', clip_level=3, panel_mo
     :type panel_model: str, optional
     :param panel_margins: Relative margin from the edge of the panel used to decide which points are margin points or internal points of each panel. Defaults to 0.05.
     :type panel_margins: float, optional
-    :param ant_id: List of antennas/antenna to be processed, defaults to "all" when None, ex. ea25
-    :type ant_id: list or str, optional
+    :param ant: List of antennas/antenna to be processed, defaults to "all" when None, ex. ea25
+    :type ant: list or str, optional
     :param ddi: List of ddis/ddi to be processed, defaults to "all" when None, ex. 0
     :type ddi: list or int, optional
     :param parallel: Run in parallel. Defaults to False.
@@ -111,7 +110,7 @@ def panel(image_name, panel_name=None, clip_type='sigma', clip_level=3, panel_mo
     """
 
     panel_params = locals()
-    panel_params['ant'] = ant_id
+    panel_params['ant'] = ant
     logger = _get_astrohack_logger()
     fname = 'panel'
     panel_params = _check_panel_parms(fname, panel_params)

{astrohack-0.3.2 → astrohack-0.3.3/src/astrohack.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: astrohack
-Version: 0.3.2
+Version: 0.3.3
 Summary: Holography Antenna Commissioning Kit
 Author-email: Jan-Willem Steeb <jsteeb@nrao.edu>, Joshua Hoskins <jhoskins@nrao.edu>, Victor de Souza Magalhaes <vdesouza@nrao.edu>
 Requires-Python: <3.12,>=3.8

astrohack-0.3.2/pyproject.toml

@@ -1,51 +0,0 @@
-[project]
-name = "astrohack"
-version = "0.3.2"
-description = "Holography Antenna Commissioning Kit"
-authors = [
-    {name = "Jan-Willem Steeb", email="jsteeb@nrao.edu"},
-    {name = "Joshua Hoskins", email="jhoskins@nrao.edu"}, 
-    {name = "Victor de Souza Magalhaes", email="vdesouza@nrao.edu"}
-]
-license = {file = "LICENSE.txt"}
-readme = "README.md"
-requires-python = ">= 3.8, < 3.12"
-
-dependencies = [
-'astropy',
-'dask',
-'distributed',
-'gdown',
-'matplotlib',
-'memory_profiler',
-'numba>=0.57.0',
-'numpy',
-'prettytable',
-'pytest',
-'pytest-cov',
-'pytest-html',
-'scikit_image',
-'scipy',
-'xarray',
-'zarr',
-'bokeh',
-'jupyterlab',
-'python_casacore>=3.5.2; sys_platform != "darwin" '
-]
-
-
-[project.optional-dependencies]
-docs = [
-    'ipykernel',
-    'ipympl',
-    'ipython',
-    'jupyter-client',
-    'nbsphinx',
-    'recommonmark',
-    'scanpydoc',
-    'sphinx-autoapi',
-    'sphinx-autosummary-accessors',
-    'sphinx_rtd_theme',
-    'twine',
-    'pandoc'
-]