astrohack 1.0.3__tar.gz → 1.1.0__tar.gz

{astrohack-1.0.3/src/astrohack.egg-info → astrohack-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: astrohack
-Version: 1.0.3
+Version: 1.1.0
 Summary: Holography Antenna Commissioning Kit
 Author-email: Joshua Hoskins <jhoskins@nrao.edu>, Victor de Souza Magalhaes <vdesouza@nrao.edu>, Jan-Willem Steeb <jsteeb@nrao.edu>
 Requires-Python: <3.14,>=3.11

{astrohack-1.0.3 → astrohack-1.1.0}/README.rst

@@ -33,16 +33,16 @@ holography and antenna position corrections.
 
 Currently AstroHACK supports:
 
-- `Astronomical holographies from the VLA <https://astrohack.readthedocs.io/en/stable/tutorial_vla.html>`_.
+- `Astronomical holographies from the VLA <https://astrohack.readthedocs.io/en/stable/tutorials/vla_holography_tutorial.html>`_.
 - Astronomical holographies from ALMA.
-- `Antenna position corrections for the VLA <https://astrohack.readthedocs.io/en/stable/locit_tutorial>`_.
-- `Near-field ALMA holographies <./https://astrohack.readthedocs.io/en/stable/AstroHACK-for-NF-ALMA.html>`_ have
+- `Antenna position corrections for the VLA <https://astrohack.readthedocs.io/en/stable/tutorials/locit_tutorial.html>`_.
+- `Near-field ALMA holographies <https://astrohack.readthedocs.io/en/stable/online_pages/AstroHACK-for-NF-ALMA.html>`_ have
   basic support, such as the creation of Aperture images, but the
   correction of near-field effects is not yet supported.
 
 In the near term we are working to support the `ngVLA antenna
 prototype <https://public.nrao.edu/ngvla/>`_ comissioning activities.
-The prototype antenna is currently (March 2025) under construction at
+The prototype antenna is currently (August 2026) under imital testing at
 the VLA site.
 
 The holography tasks in AstroHACK port much of the functionality of

{astrohack-1.0.3 → astrohack-1.1.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "astrohack"
-version = "1.0.3"
+version = "1.1.0"
 description = "Holography Antenna Commissioning Kit"
 readme = "README.md"
 requires-python = ">= 3.11, < 3.14"

astrohack-1.1.0/src/astrohack/__init__.py

@@ -0,0 +1,66 @@
+import os
+from importlib.metadata import version
+
+__version__ = version("astrohack")
+
+from astrohack.io.dio import open_beamcut as open_beamcut
+from astrohack.io.dio import open_position as open_position
+from astrohack.io.dio import open_image as open_image
+from astrohack.io.dio import open_locit as open_locit
+from astrohack.io.dio import open_panel as open_panel
+from astrohack.io.dio import open_pointing as open_pointing
+from astrohack.io.dio import open_holog as open_holog
+
+from astrohack.io.point_mds import AstrohackPointFile as AstrohackPointFile
+from astrohack.io.locit_mds import AstrohackLocitFile as AstrohackLocitFile
+from astrohack.io.holog_mds import AstrohackHologFile as AstrohackHologFile
+from astrohack.io.panel_mds import AstrohackPanelFile as AstrohackPanelFile
+from astrohack.io.beamcut_mds import AstrohackBeamcutFile as AstrohackBeamcutFile
+from astrohack.io.position_mds import AstrohackPositionFile as AstrohackPositionFile
+from astrohack.io.image_mds import AstrohackImageFile as AstrohackImageFile
+
+from .extract_holog import extract_holog as extract_holog
+from .extract_holog import generate_holog_obs_dict as generate_holog_obs_dict
+from .beamcut import beamcut as beamcut
+from .extract_pointing import extract_pointing as extract_pointing
+from .holog import holog as holog
+from .panel import panel as panel
+from .combine import combine as combine
+from .locit import locit as locit
+from .extract_locit import extract_locit as extract_locit
+from .fringefit_locit import fringefit_locit as fringefit_locit
+from .cassegrain_ray_tracing import (
+    cassegrain_ray_tracing_pipeline as cassegrain_ray_tracing_pipeline,
+)
+from .cassegrain_ray_tracing import (
+    create_ray_tracing_telescope_parameter_dict as create_ray_tracing_telescope_parameter_dict,
+)
+from .cassegrain_ray_tracing import plot_2d_maps_from_rt_xds as plot_2d_maps_from_rt_xds
+from .cassegrain_ray_tracing import (
+    plot_radial_projection_from_rt_xds as plot_radial_projection_from_rt_xds,
+)
+from .cassegrain_ray_tracing import (
+    apply_holog_phase_fitting_to_rt_xds as apply_holog_phase_fitting_to_rt_xds,
+)
+
+from .image_comparison_tool import compare_fits_images as compare_fits_images
+from .image_comparison_tool import (
+    rms_table_from_zarr_datatree as rms_table_from_zarr_datatree,
+)
+from .antenna.telescope import get_proper_telescope as get_proper_telescope
+
+# This installs a slick, informational tracebacks logger
+from rich.traceback import install
+from toolviper.utils.logger import setup_logger
+
+install(show_locals=False)
+
+if not os.getenv("LOGGER_NAME"):
+    os.environ["LOGGER_NAME"] = "astrohack"
+    setup_logger(
+        logger_name="astrohack",
+        log_to_term=True,
+        log_to_file=False,
+        log_file="astrohack-logfile",
+        log_level="INFO",
+    )

{astrohack-1.0.3 → astrohack-1.1.0}/src/astrohack/antenna/antenna_surface.py

@@ -1,4 +1,5 @@
 import xarray as xr
+import numpy as np
 
 from matplotlib import patches
 
@@ -9,7 +10,7 @@ from astrohack.utils.algorithms import (
     data_statistics,
     phase_wrapping,
 )
-from astrohack.utils.constants import *
+from astrohack.utils.constants import clight, fourpi
 from astrohack.utils.conversion import to_db
 from astrohack.utils.conversion import convert_unit
 from astrohack.utils.text import (
@@ -139,11 +140,9 @@ class AntennaSurface:
             .values
         )
 
-        self.npoint = np.sqrt(inputxds.sizes["l"] ** 2 + inputxds.sizes["m"] ** 2)
         self.amp_unit = "V"
         self.u_axis = inputxds.u_prime.values
         self.v_axis = inputxds.v_prime.values
-        self.computephase = False
 
     def _read_panel_xds(self, inputxds):
         self.wavelength = inputxds.attrs["wavelength"]
@@ -244,7 +243,7 @@ class AntennaSurface:
         while fraction_in < threshold:
             clip *= multiplier
             data_in = np.where(in_disk_amp > clip, 1.0, 0.0)
-            fraction_in = np.sum(data_in) / n_in_disk
+            fraction_in = float(np.sum(data_in)) / n_in_disk
             multiplier *= step_multiplier
 
         return clip
@@ -271,23 +270,6 @@ class AntennaSurface:
         self.amplitude = np.where(self.base_mask, self.amplitude, np.nan)
         self.deviation = np.where(self.base_mask, self.deviation, np.nan)
 
-    def _fetch_panel_ringed(self, ring, panel):
-        """
-        Fetch a panel object from the panel list using its ring and panel numbers,
-        specific for circular antennas with panels arranged in rings
-        Args:
-            ring: Ring number
-            panel: Panel number
-
-        Returns:
-        Panel object
-        """
-        if ring == 1:
-            ipanel = panel - 1
-        else:
-            ipanel = np.sum(self.telescope.n_panel_per_ring[: ring - 1]) + panel - 1
-        return self.panels[ipanel]
-
     def gains(self):
         """
         Computes antenna gains in decibels before and after panel surface fitting
@@ -518,8 +500,8 @@ class AntennaSurface:
             raise ValueError("Map list and label list must be of the same size")
         nplots = len(maps)
         if parm_dict["z_lim"] is None or parm_dict["z_lim"] == "None":
-            vmax = np.nanmax(
-                np.abs(factor * maps[0])
+            vmax = float(
+                np.nanmax(np.abs(factor * maps[0]))
             )  # Gotten from the original map (displays the biggest variation)
             parm_dict["z_lim"] = [-vmax, vmax]
         for iplot in range(nplots):
@@ -606,7 +588,7 @@ class AntennaSurface:
         fig, ax = create_figure_and_axes(parm_dict["figure_size"], [1, 1])
 
         fac = convert_unit("m", unit, "length")
-        vmax = np.nanmax(np.abs(fac * self.screw_adjustments))
+        vmax = float(np.nanmax(np.abs(fac * self.screw_adjustments)))
         vmin = -vmax
         if threshold is None or threshold == "None":
             threshold = 0.1 * vmax

{astrohack-1.0.3 → astrohack-1.1.0}/src/astrohack/antenna/base_panel.py

@@ -4,8 +4,9 @@ from matplotlib import pyplot as plt
 from matplotlib.colors import Normalize
 
 from astrohack.antenna.panel_fitting import PANEL_MODEL_DICT, PanelPoint, PanelModel
-from astrohack.utils.constants import *
+from astrohack.utils.constants import pi, fontsize, markersize
 from astrohack.utils.conversion import convert_unit
+import numpy as np
 
 
 class BasePanel:

{astrohack-1.0.3 → astrohack-1.1.0}/src/astrohack/antenna/panel_fitting.py

@@ -694,6 +694,3 @@ class PanelPoint:
 
     def __repr__(self):
         return f"{self.xc}, {self.yc}, {self.ix}, {self.iy}, {self.value}"
-
-    def get_array(self):
-        return np.array([self.xc, self.yc, self.ix, self.iy, self.value])

{astrohack-1.0.3 → astrohack-1.1.0}/src/astrohack/antenna/telescope.py

@@ -1,14 +1,14 @@
 from shapely.geometry.point import Point
 from shapely.geometry.polygon import Polygon
 from shapely.strtree import STRtree
-
+import numpy as np
 import pathlib
 
 import xarray as xr
 import toolviper.utils.logger as logger
 
 from astrohack.antenna.polygon_panel import PolygonPanel
-from astrohack.utils.constants import *
+from astrohack.utils.constants import twopi, fourpi
 from astrohack.antenna.ring_panel import RingPanel
 from astrohack.utils.algorithms import create_coordinate_images, arm_shadow_masking
 from astrohack.utils.ray_tracing_general import GlobalQPS

{astrohack-1.0.3 → astrohack-1.1.0}/src/astrohack/cassegrain_ray_tracing.py

@@ -1,15 +1,30 @@
 import toolviper
-import xarray as xr
+import toolviper.utils.logger as logger
+import numpy as np
 
 from astrohack.utils.validation import custom_unit_checker, custom_plots_checker
-from astrohack.core.cassegrain_ray_tracing import *
-from astrohack.utils.conversion import convert_unit, clight
+from astrohack.core.cassegrain_ray_tracing import (
+    make_gridded_cassegrain_primary,
+    reflect_off_primary,
+    reflect_off_analytical_secondary,
+    detect_light,
+    compute_phase,
+    write_rt_xds_to_zarr,
+    open_rt_zarr,
+    title_from_input_parameters,
+    plot_2d_map,
+    add_rz_ray_to_plot,
+    compare_ray_tracing_to_phase_fit_results,
+)
+from astrohack.utils.constants import clight
+from astrohack.utils.conversion import convert_unit
 from astrohack.utils.algorithms import regrid_data_onto_2d_grid
 from astrohack.utils.file import add_caller_and_version_to_dict
 from astrohack.utils.phase_fitting import aips_like_phase_fitting
 from astrohack.visualization.plot_tools import create_figure_and_axes, close_figure
 from typing import Union
 from astrohack.utils.text import spc, undscr
+from astrohack.antenna.telescope import get_proper_telescope
 
 
 @toolviper.utils.parameter.validate(custom_checker=custom_unit_checker)

astrohack-1.1.0/src/astrohack/config/fringefit_locit.param.json

@@ -0,0 +1,51 @@
+{
+    "fringefit_locit":{
+        "fringefit_caltable":{
+            "type":["str"],
+            "required": true
+        },
+        "position_name":{
+            "type":["str"],
+            "required": false,
+            "nullable": true
+        },
+        "elevation_limit":{
+            "type":["float"],
+            "required": false
+        },
+        "polarization": {
+            "type": ["str"],
+            "nullable": false,
+            "allowed": ["R", "L", "X", "Y", "both", "RL", "LR", "XY", "YX"]
+        },
+        "fit_engine": {
+            "type": ["str"],
+            "nullable": false,
+            "allowed": ["linear algebra", "scipy"]
+        },
+        "fit_kterm":{
+            "type":["boolean"],
+            "nullable": false
+        },
+        "fit_delay_rate":{
+            "type":["boolean"],
+            "nullable": false
+        },
+        "ant":{
+            "type":["list", "str"],
+            "struct type": ["str"],
+            "nullable": false
+        },
+        "ddi":{
+            "type":["ndarray", "int", "list", "str"],
+            "struct type": ["int", "str"],
+            "nullable": false
+        },
+        "parallel":{
+            "type":["boolean"]
+        },
+        "overwrite":{
+            "type":["boolean"]
+        }
+    }
+}

astrohack-1.1.0/src/astrohack/config/locit_mds.param.json

@@ -0,0 +1,212 @@
+{
+    "AstrohackLocitFile.print_source_table": {
+        "save_to": {
+            "nullable": true,
+            "required": false,
+            "type": ["string"]
+        }
+    },
+    "AstrohackLocitFile.print_array_configuration":{
+        "relative":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "save_to": {
+            "nullable": true,
+            "required": false,
+            "type": ["string"]
+        }
+    },
+    "AstrohackLocitFile.plot_source_positions":{
+        "destination":{
+            "nullable": false,
+            "required": true,
+            "type": ["string"]
+        },
+        "labels":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "precessed":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "display":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "figure_size":{
+            "nullable": true,
+            "required": false,
+            "struct_type": ["float"],
+            "minlength": 2,
+            "maxlength": 2,
+            "type": ["list", "tuple", "ndarray"]
+        },
+        "dpi":{
+            "nullable": false,
+            "required": false,
+            "type": ["int"],
+            "min": 1,
+            "max": 1200
+        }
+        },
+    "AstrohackLocitFile.plot_array_configuration":{
+        "destination":{
+            "nullable": false,
+            "required": true,
+            "type": ["string"]
+        },
+        "stations":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "zoff":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "unit":{
+            "nullable": false,
+            "required": false,
+            "type": ["string"],
+            "check allowed with": "units.length"
+        },
+        "box_size":{
+            "nullable": true,
+            "required": false,
+            "type": ["int", "float"],
+            "min": 0
+        },
+        "display":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "figure_size":{
+            "nullable": true,
+            "required": false,
+            "struct_type": ["float"],
+            "minlength": 2,
+            "maxlength": 2,
+            "type": ["list", "tuple", "ndarray"]
+        },
+        "dpi": {
+            "nullable": false,
+            "required": false,
+            "type": ["int"],
+            "min": 1,
+            "max": 1200
+        }
+    },
+    "AstrohackPositionFile.print_source_table": {
+        "save_to": {
+            "nullable": true,
+            "required": false,
+            "type": ["string"]
+        }
+    },
+    "AstrohackPositionFile.print_array_configuration":{
+        "relative":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "save_to": {
+            "nullable": true,
+            "required": false,
+            "type": ["string"]
+        }
+    },
+    "AstrohackPositionFile.plot_source_positions":{
+        "destination":{
+            "nullable": false,
+            "required": true,
+            "type": ["string"]
+        },
+        "labels":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "precessed":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "display":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "figure_size":{
+            "nullable": true,
+            "required": false,
+            "struct_type": ["float"],
+            "minlength": 2,
+            "maxlength": 2,
+            "type": ["list", "tuple", "ndarray"]
+        },
+        "dpi":{
+            "nullable": false,
+            "required": false,
+            "type": ["int"],
+            "min": 1,
+            "max": 1200
+        }
+        },
+    "AstrohackPositionFile.plot_array_configuration":{
+        "destination":{
+            "nullable": false,
+            "required": true,
+            "type": ["string"]
+        },
+        "stations":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "zoff":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "unit":{
+            "nullable": false,
+            "required": false,
+            "type": ["string"],
+            "check allowed with": "units.length"
+        },
+        "box_size":{
+            "nullable": true,
+            "required": false,
+            "type": ["int", "float"],
+            "min": 0
+        },
+        "display":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
+        },
+        "figure_size":{
+            "nullable": true,
+            "required": false,
+            "struct_type": ["float"],
+            "minlength": 2,
+            "maxlength": 2,
+            "type": ["list", "tuple", "ndarray"]
+        },
+        "dpi": {
+            "nullable": false,
+            "required": false,
+            "type": ["int"],
+            "min": 1,
+            "max": 1200
+        }
+    }
+}

{astrohack-1.0.3 → astrohack-1.1.0}/src/astrohack/core/beamcut.py

@@ -1,6 +1,5 @@
 from copy import deepcopy
 
-import numpy
 import toolviper.utils.logger as logger
 import numpy as np
 from scipy.optimize import curve_fit
@@ -18,8 +17,6 @@ from astrohack.utils.text import (
 )
 from astrohack.utils.constants import sig_2_fwhm
 
-quack_chans = 4
-
 
 ###########################################################
 ### Working Chunks
@@ -40,11 +37,15 @@ def process_beamcut_chunk(beamcut_chunk_params: dict, output_mds: AstrohackBeamc
     ddi_key = beamcut_chunk_params["this_ddi"]
     ant_key = beamcut_chunk_params["this_ant"]
     xdt_data = beamcut_chunk_params["xdt_data"]
+    datalabel = create_dataset_label(ant_key, ddi_key)
 
     # This assumes that there will be no more than one mapping
-    input_xds = xdt_data["map_0"]
+    try:
+        input_xds = xdt_data["map_0"]
+    except KeyError:
+        logger.warning(f"No beamcut data for {datalabel}")
+        return
 
-    datalabel = create_dataset_label(ant_key, ddi_key)
     logger.info(f"processing {datalabel}")
 
     cut_xdtree = _extract_cuts_from_visibilities(input_xds, ant_key, ddi_key)
@@ -378,7 +379,7 @@ def _multi_gaussian(xdata, *args):
     """
     nargs = len(args)
     if nargs % 3 != 0:
-        raise ValueError("Number of arguments should be multiple of 3")
+        raise ValueError(f"Number of arguments should be multiple of 3, (got {nargs})")
     y_values = np.zeros_like(xdata)
     for iarg in range(0, nargs, 3):
         y_values += _fwhm_gaussian(xdata, args[iarg], args[iarg + 1], args[iarg + 2])
@@ -516,6 +517,38 @@ def _identify_pb_and_sidelobes_in_fit(
     return n_peaks, fit_pars, pb_center, pb_fwhm, first_side_lobe_ratio
 
 
+def estimate_pb_center_and_fwhm_from_data(x_data, y_data, datalabel):
+    """
+    Estimate primary beam parameters forcefully from data
+    :param x_data: Cut X data
+    :param y_data: Cut Y data
+    :param datalabel: Data label
+    :return: estimated primary beam center, fwhm and amplitude.
+    """
+    logger.info(
+        f"Estimating primary beam center and fwhm from maximum amplitude for {datalabel}"
+    )
+    i_max = np.argmax(y_data.values)
+    amp_max = y_data.values[i_max]
+    pb_center = x_data[i_max]
+    n_pnt = x_data.shape[0]
+
+    hw_plus = np.nan
+    for i_pnt in range(i_max, n_pnt):
+        if y_data[i_pnt] <= amp_max / 2:
+            hw_plus = x_data[i_pnt]
+            break
+    hw_minus = np.nan
+    for i_pnt in range(i_max, 0, -1):
+        if y_data[i_pnt] <= amp_max / 2:
+            hw_minus = x_data[i_pnt]
+            break
+    pb_fwhm = hw_plus - hw_minus
+    fslr = np.nan
+
+    return pb_center, pb_fwhm, fslr, amp_max
+
+
 def _beamcut_multi_lobes_gaussian_fit(cut_xdtree, datalabel):
     """
     Execute multi gaussian fit to beam cut data.
@@ -573,8 +606,16 @@ def _beamcut_multi_lobes_gaussian_fit(cut_xdtree, datalabel):
                     )
                 )
             else:
-                pb_center, pb_fwhm, first_side_lobe_ratio = np.nan, np.nan, np.nan
-                fit = np.full_like(y_data, np.nan)
+                pb_center, pb_fwhm, first_side_lobe_ratio, amp_max = (
+                    estimate_pb_center_and_fwhm_from_data(
+                        x_data, y_data, this_corr_data_label
+                    )
+                )
+                fit = _multi_gaussian(x_data, pb_center, amp_max, pb_fwhm)
+                n_peaks = 1
+                fit_pars = [pb_center, amp_max, pb_fwhm]
+                if np.all(np.isfinite(fit_pars)):
+                    fit_succeeded = True
 
             cut_xds.attrs[f"{parallel_hand}_amp_fit_pars"] = fit_pars
             cut_xds.attrs[f"{parallel_hand}_n_peaks"] = n_peaks

{astrohack-1.0.3 → astrohack-1.1.0}/src/astrohack/core/cassegrain_ray_tracing.py

@@ -637,7 +637,7 @@ def compare_ray_tracing_to_phase_fit_results(
         ax[1],
         fig,
         fac * correction,
-        f"Fitted correction",
+        "Fitted correction",
         extent,
         f"Phase [{phase_unit}]",
         colormap,

{astrohack-1.0.3 → astrohack-1.1.0}/src/astrohack/core/combine.py

@@ -67,13 +67,13 @@ def process_combine_chunk(combine_chunk_params: dict, output_mds: AstrohackImage
         out_xds = deepcopy(ant_xdt[ddi_ref_key].dataset)
         shape = list(out_xds["CORRECTED_PHASE"].values.shape)
         if out_xds.sizes["chan"] != 1:
-            msg = f"Only single channel holographies supported"
+            msg = "Only single channel holographies supported"
             logger.error(msg)
             raise RuntimeError(msg)
 
         nmap = shape[0]
         if nmap != 1:
-            msg = f"Only single mapping holographies supported"
+            msg = "Only single mapping holographies supported"
             logger.error(msg)
             raise RuntimeError(msg)