astrohack 1.0.2__tar.gz → 1.0.3__tar.gz

{astrohack-1.0.2/src/astrohack.egg-info → astrohack-1.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: astrohack
-Version: 1.0.2
+Version: 1.0.3
 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
@@ -29,18 +29,13 @@ Requires-Dist: zarr<3.0.0
 Requires-Dist: bokeh
 Requires-Dist: pillow
 Requires-Dist: jupyterlab
-Requires-Dist: python_casacore>=3.6.1; sys_platform != "darwin"
+Requires-Dist: casacoretables>=0.0.3
 Provides-Extra: docs
-Requires-Dist: ipykernel; extra == "docs"
-Requires-Dist: ipympl; extra == "docs"
-Requires-Dist: ipython; extra == "docs"
-Requires-Dist: jupyter-client; extra == "docs"
+Requires-Dist: pandoc; extra == "docs"
+Requires-Dist: sphinx-autosummary-accessors; extra == "docs"
 Requires-Dist: nbsphinx; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
 Requires-Dist: recommonmark; extra == "docs"
-Requires-Dist: scanpydoc; extra == "docs"
 Requires-Dist: sphinx-autoapi; extra == "docs"
-Requires-Dist: sphinx-autosummary-accessors; extra == "docs"
-Requires-Dist: sphinx_rtd_theme; extra == "docs"
-Requires-Dist: twine; extra == "docs"
-Requires-Dist: pandoc; extra == "docs"
+Requires-Dist: ipython; extra == "docs"
 Dynamic: license-file

{astrohack-1.0.2 → astrohack-1.0.3}/pyproject.toml

@@ -1,10 +1,10 @@
 [project]
 name = "astrohack"
-version = "1.0.2"
+version = "1.0.3"
 description = "Holography Antenna Commissioning Kit"
 readme = "README.md"
 requires-python = ">= 3.11, < 3.14"
-dependencies = [ "astropy", "dask", "shapely", "distributed", "toolviper", "ipywidgets", "matplotlib", "numba>=0.57.0", "numpy<=2.2", "prettytable", "pycryptodome", "pytest", "pytest-cov", "pytest-html", "scikit_image", "scikit-learn", "scipy", "rich", "xarray", "zarr<3.0.0", "bokeh", "pillow", "jupyterlab", "python_casacore>=3.6.1; sys_platform != \"darwin\" ",]
+dependencies = [ "astropy", "dask", "shapely", "distributed", "toolviper", "ipywidgets", "matplotlib", "numba>=0.57.0", "numpy<=2.2", "prettytable", "pycryptodome", "pytest", "pytest-cov", "pytest-html", "scikit_image", "scikit-learn", "scipy", "rich", "xarray", "zarr<3.0.0", "bokeh", "pillow", "jupyterlab", "casacoretables>=0.0.3",]
 [[project.authors]]
 name = "Joshua Hoskins"
 email = "jhoskins@nrao.edu"
@@ -21,4 +21,8 @@ email = "jsteeb@nrao.edu"
 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",]
+docs = [ "pandoc", "sphinx-autosummary-accessors", "nbsphinx", "sphinx_rtd_theme", "recommonmark", "sphinx-autoapi", "ipython",]
+
+[project.scripts]
+beamcut-reduction-pipeline = "astrohack.scripts.beamcuts.beamcut_reduction_pipeline:main"
+baseline-reduction-pipeline = "astrohack.scripts.baseline.baseline_reduction_pipeline:main"

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/__init__.py

@@ -3,12 +3,27 @@ from importlib.metadata import version
 
 __version__ = version("astrohack")
 
+
+from astrohack.io.dio import (
+    open_beamcut,
+    open_pointing,
+    open_holog,
+    open_image,
+    open_locit,
+    open_panel,
+    open_position,
+)
+from astrohack.io.point_mds import AstrohackPointFile
+from astrohack.io.locit_mds import AstrohackLocitFile
+from astrohack.io.holog_mds import AstrohackHologFile
+from astrohack.io.panel_mds import AstrohackPanelFile
+from astrohack.io.beamcut_mds import AstrohackBeamcutFile
+from astrohack.io.position_mds import AstrohackPositionFile
+from astrohack.io.image_mds import AstrohackImageFile
 from .extract_holog import (
     extract_holog,
     generate_holog_obs_dict,
 )
-from .io import *
-
 from .beamcut import beamcut
 from .extract_pointing import extract_pointing
 from .holog import holog
@@ -24,7 +39,7 @@ from .cassegrain_ray_tracing import (
     apply_holog_phase_fitting_to_rt_xds,
 )
 from .image_comparison_tool import compare_fits_images, rms_table_from_zarr_datatree
-from .antenna import get_proper_telescope
+from .antenna.telescope import get_proper_telescope
 
 # This installs a slick, informational tracebacks logger
 from rich.traceback import install

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/antenna/antenna_surface.py

@@ -5,11 +5,8 @@ from matplotlib import patches
 import toolviper.utils.logger as logger
 
 from astrohack.antenna.telescope import get_proper_telescope
-from astrohack.utils import (
-    string_to_ascii_file,
-    create_dataset_label,
+from astrohack.utils.algorithms import (
     data_statistics,
-    statistics_to_text,
     phase_wrapping,
 )
 from astrohack.utils.constants import *
@@ -20,6 +17,12 @@ from astrohack.utils.text import (
     bool_to_str,
     format_frequency,
     format_value_unit,
+    string_to_ascii_file,
+    create_dataset_label,
+    statistics_to_text,
+    lnbr,
+    spc,
+    create_informative_label_from_summary,
 )
 from astrohack.visualization.plot_tools import (
     create_figure_and_axes,
@@ -36,7 +39,6 @@ from astrohack.utils.fits import (
     put_axis_in_fits_header,
 )
 
-lnbr = "\n"
 SUPPORTED_POL_STATES = ["I", "RR", "LL", "XX", "YY"]
 
 
@@ -414,7 +416,7 @@ class AntennaSurface:
         plotmask = np.where(self.mask, 1, np.nan)
         plotname = add_prefix(basename, f"{caller}_mask")
         parm_dict["z_lim"] = [0, 1]
-        parm_dict["unit"] = " "
+        parm_dict["unit"] = spc
         self._plot_map(plotname, plotmask, "Mask", parm_dict)
 
     def plot_amplitude(self, basename, caller, parm_dict):
@@ -551,7 +553,8 @@ class AntennaSurface:
                 ax, screws=parm_dict["plot_screws"], label=parm_dict["panel_labels"]
             )
 
-        suptitle = f"{self.label}, Pol. state: {self.pol_state}"
+        suptitle = create_informative_label_from_summary(self.summary, "deg")
+        suptitle += f", Pol. state: {self.pol_state}"
         close_figure(fig, suptitle, filename, parm_dict["dpi"], parm_dict["display"])
 
     def _add_resolution_to_plot(self, ax, xpos=0.9, ypos=0.1):
@@ -610,7 +613,7 @@ class AntennaSurface:
         else:
             threshold = np.abs(threshold)
 
-        ax.set_title(f"\nThreshold = {threshold:.2f} {unit}", fontsize="small")
+        ax.set_title(f"{lnbr}Threshold = {threshold:.2f} {unit}", fontsize="small")
         # set the limits of the plot to the limits of the data
         extent = compute_extent(self.u_axis, self.v_axis)
         im = ax.imshow(
@@ -643,7 +646,8 @@ class AntennaSurface:
                 ax, cmap, fac * self.screw_adjustments[ipanel], threshold, vmin, vmax
             )
 
-        suptitle = f"{self.label}, Pol. state: {self.pol_state}"
+        suptitle = create_informative_label_from_summary(self.summary, "deg")
+        suptitle += f", Pol. state: {self.pol_state}"
         close_figure(fig, suptitle, filename, parm_dict["dpi"], parm_dict["display"])
 
     def _build_panel_data_arrays(self):
@@ -685,22 +689,26 @@ class AntennaSurface:
             unit: unit for panel screw adjustments ['mm','miliinches']
             comment_char: Character used for comments
         """
-        outfile = f"# Screw adjustments for {self.telescope.name}'s {self.label}, pol. state {self.pol_state}\n"
+        date_str = create_informative_label_from_summary(self.summary, "deg").split(
+            ","
+        )[-1]
+        outfile = f"# Screw adjustments for {self.telescope.name}'s {self.label}, pol. state {self.pol_state}{lnbr}"
+        outfile += f"# Observation date:{date_str}{lnbr}"
         freq = clight / self.wavelength
         rmses = self.get_rms(unit)
         outfile += f"# Frequency = {format_frequency(freq)}{lnbr}"
         if unit == "mm":
-            outfile += f"# Antenna surface RMS before adjustment: {format_value_unit(rmses[0], unit)}\n"
-            outfile += f"# Antenna surface RMS after adjustment: {format_value_unit(rmses[1], unit)}\n"
+            outfile += f"# Antenna surface RMS before adjustment: {format_value_unit(rmses[0], unit)}{lnbr}"
+            outfile += f"# Antenna surface RMS after adjustment: {format_value_unit(rmses[1], unit)}{lnbr}"
         else:
             mmrms = self.get_rms("mm")
             outfile += (
                 f"# Antenna surface RMS before adjustment: {format_value_unit(rmses[0], unit)} or "
-                f'{format_value_unit(mmrms[0], "mm")}\n'
+                f'{format_value_unit(mmrms[0], "mm")}{lnbr}'
             )
             outfile += (
                 f"# Antenna surface RMS after adjustment: {format_value_unit(rmses[1], unit)} or "
-                f'{format_value_unit(mmrms[1], "mm")}\n'
+                f'{format_value_unit(mmrms[1], "mm")}{lnbr}'
             )
         outfile += "# Lower means away from subreflector" + lnbr
         outfile += "# Raise means toward the subreflector" + lnbr
@@ -708,7 +716,6 @@ class AntennaSurface:
         outfile += "# RAISE the panel if the number is NEGATIVE" + lnbr
         outfile += "# Adjustments are in " + unit + lnbr
         outfile += lnbr
-        spc = " "
         outfile += f"{comment_char} Panel{2*spc}"
         nscrews = len(self.telescope.screw_description)
         for screw in self.telescope.screw_description:

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/antenna/base_panel.py

@@ -5,7 +5,7 @@ from matplotlib.colors import Normalize
 
 from astrohack.antenna.panel_fitting import PANEL_MODEL_DICT, PanelPoint, PanelModel
 from astrohack.utils.constants import *
-from astrohack.utils import convert_unit
+from astrohack.utils.conversion import convert_unit
 
 
 class BasePanel:

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/antenna/panel_fitting.py

@@ -3,7 +3,7 @@ import scipy.optimize as opt
 
 import toolviper.utils.logger as logger
 
-from astrohack.utils import gauss_elimination, least_squares_jit
+from astrohack.utils.algorithms import gauss_elimination, least_squares_jit
 
 ###################################
 #  General purpose                #

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/antenna/polygon_panel.py

@@ -1,11 +1,13 @@
 from shapely import Polygon, Point
 from shapely.plotting import plot_polygon
 
-from astrohack.utils import markersize
+from astrohack.utils.constants import markersize
 from astrohack.antenna.base_panel import BasePanel
 from astrohack.antenna.panel_fitting import PanelPoint
 import numpy as np
 
+from astrohack.utils.text import spc
+
 
 class PolygonPanel(BasePanel):
 
@@ -89,7 +91,7 @@ class PolygonPanel(BasePanel):
         """
         print("########################################")
         print("{0:20s}={1:8d}".format("label", self.label))
-        print("{0:20s}={1:8s}".format("model", " " + self.model_name))
+        print("{0:20s}={1:8s}".format("model", spc + self.model_name))
         print("{0:20s}={1:8d}".format("nsamp", len(self.samples)))
         if verbose:
             for sample in self.samples:

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/antenna/ring_panel.py

@@ -2,6 +2,7 @@ import numpy as np
 from matplotlib import pyplot as plt
 from astrohack.antenna.base_panel import BasePanel, markersize
 from astrohack.antenna.panel_fitting import PanelPoint
+from astrohack.utils.text import spc
 
 
 class RingPanel(BasePanel):
@@ -139,7 +140,7 @@ class RingPanel(BasePanel):
         """
         print("########################################")
         print("{0:20s}={1:8s}".format("ipanel", self.label))
-        print("{0:20s}={1:8s}".format("model", " " + self.model_name))
+        print("{0:20s}={1:8s}".format("model", spc + self.model_name))
         print("{0:20s}={1:8.5f}".format("inrad", self.inrad))
         print("{0:20s}={1:8.5f}".format("ourad", self.ourad))
         print("{0:20s}={1:8.5f}".format("theta1", self.theta1))

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/antenna/telescope.py

@@ -2,18 +2,18 @@ from shapely.geometry.point import Point
 from shapely.geometry.polygon import Polygon
 from shapely.strtree import STRtree
 
-import astrohack
 import pathlib
 
 import xarray as xr
 import toolviper.utils.logger as logger
 
-import astrohack.utils.tools
 from astrohack.antenna.polygon_panel import PolygonPanel
 from astrohack.utils.constants import *
 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
+from astrohack.utils.package_info import get_astrohack_path
+from astrohack.utils.text import spc, lnbr, undscr
 
 
 class Telescope:
@@ -76,9 +76,7 @@ class Telescope:
         Returns:
             None
         """
-        dest_path = "/".join(
-            [astrohack.__path__[0], f"data/telescopes/{name.lower()}.zarr"]
-        )
+        dest_path = get_astrohack_path() / f"data/telescopes/{name.lower()}.zarr"
         self.read(dest_path)
 
     def write(self, filename):
@@ -105,11 +103,9 @@ class Telescope:
         return
 
     def write_to_distro(self):
-        dest_path = "/".join(
-            [
-                astrohack.__path__[0],
-                f'data/telescopes/{self.name.lower().replace(" ", "_")}.zarr',
-            ]
+        dest_path = (
+            get_astrohack_path()
+            / f"data/telescopes/{self.name.lower().replace(spc, undscr)}.zarr"
         )
         self.write(dest_path)
 
@@ -124,9 +120,9 @@ class Telescope:
         for key, item in obj_dict.items():
             if isinstance(item, dict):
                 key_list = list(item.keys())
-                outstr += f"{key:20s} = dict({str(key_list)})\n"
+                outstr += f"{key:20s} = dict({str(key_list)}){lnbr}"
             else:
-                outstr += f"{key:20s} = {str(item)}\n"
+                outstr += f"{key:20s} = {str(item)}{lnbr}"
         return outstr
 
 

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/beamcut.py

@@ -5,7 +5,7 @@ from toolviper.utils.parameter import validate
 import toolviper.utils.logger as logger
 
 from astrohack.core.beamcut import process_beamcut_chunk
-from astrohack.utils import get_default_file_name
+from astrohack.utils.text import get_default_file_name
 from astrohack.utils.file import overwrite_file
 from astrohack.utils.graph import create_and_execute_graph_from_dict
 from astrohack.io.beamcut_mds import AstrohackBeamcutFile
@@ -18,15 +18,15 @@ from typing import Union, List, Tuple
 @validate(custom_checker=custom_plots_checker)
 def beamcut(
     holog_name: str,
-    beamcut_name: str = None,
+    beamcut_name: str | None = None,
     ant: Union[str, List[str]] = "all",
     ddi: Union[int, List[int], str] = "all",
-    destination: str = None,
+    destination: str | None = None,
     lm_unit: str = "amin",
     azel_unit: str = "deg",
     phase_unit: str = "deg",
-    phase_scale: Union[List[float], Tuple[float], np.array] = None,
-    y_scale: list[float] = None,
+    phase_scale: Union[List[float | int], Tuple[float | int], np.ndarray, None] = None,
+    y_scale: list[float | int] | None = None,
     dpi: int = 300,
     display: bool = False,
     parallel: bool = False,
@@ -140,12 +140,11 @@ def beamcut(
         param_dict=beamcut_params,
         key_order=["ant", "ddi"],
         output_mds=beamcut_mds,
-        parallel=parallel,
     )
     if executed_graph:
         if destination is not None:
             logger.info("Producing plots...")
-            beamcut_mds.plot_beamcut_in_amplitude(
+            beamcut_mds.plot_in_amplitude(
                 destination,
                 lm_unit=lm_unit,
                 azel_unit=azel_unit,
@@ -154,7 +153,7 @@ def beamcut(
                 dpi=dpi,
                 parallel=parallel,
             )
-            beamcut_mds.plot_beamcut_in_attenuation(
+            beamcut_mds.plot_in_db(
                 destination,
                 lm_unit=lm_unit,
                 azel_unit=azel_unit,
@@ -163,7 +162,7 @@ def beamcut(
                 dpi=dpi,
                 parallel=parallel,
             )
-            beamcut_mds.plot_beamcut_in_phase(
+            beamcut_mds.plot_in_phase(
                 destination,
                 lm_unit=lm_unit,
                 azel_unit=azel_unit,
@@ -173,7 +172,7 @@ def beamcut(
                 dpi=dpi,
                 parallel=parallel,
             )
-            beamcut_mds.plot_beam_cuts_over_sky(
+            beamcut_mds.plot_lm_offsets(
                 destination,
                 lm_unit=lm_unit,
                 azel_unit=azel_unit,
@@ -181,7 +180,7 @@ def beamcut(
                 dpi=dpi,
                 parallel=parallel,
             )
-            beamcut_mds.create_beam_fit_report(
+            beamcut_mds.export_report(
                 destination,
                 lm_unit=lm_unit,
                 azel_unit=azel_unit,

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/cassegrain_ray_tracing.py

@@ -3,15 +3,13 @@ import xarray as xr
 
 from astrohack.utils.validation import custom_unit_checker, custom_plots_checker
 from astrohack.core.cassegrain_ray_tracing import *
-from astrohack.utils import (
-    convert_unit,
-    clight,
-    regrid_data_onto_2d_grid,
-)
+from astrohack.utils.conversion import convert_unit, clight
+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
 
 
 @toolviper.utils.parameter.validate(custom_checker=custom_unit_checker)
@@ -273,13 +271,13 @@ def plot_2d_maps_from_rt_xds(
     if isinstance(keys, str):
         keys = [keys]
 
-    suptitle = "Cassegrain Ray tracing model for:\n" + title_from_input_parameters(
+    suptitle = "Cassegrain Ray tracing model for:{lnbr}" + title_from_input_parameters(
         rt_xds.attrs["input_parameters"]
     )
     for key in keys:
         filename = f"{rootname}_{key}.png"
 
-        zlabel = key.capitalize().replace("_", " ")
+        zlabel = key.capitalize().replace(undscr, spc)
         if key == "phase":
             fac = convert_unit("rad", phase_unit, "trigonometric")
             zlabel += f" [{phase_unit}]"

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/combine.py

@@ -2,7 +2,7 @@ from typing import Union, List
 
 import toolviper.utils.parameter
 
-from astrohack import open_image
+from astrohack.io.dio import open_image
 from astrohack.core.combine import process_combine_chunk
 from astrohack.utils.graph import create_and_execute_graph_from_dict
 from astrohack.utils.file import overwrite_file
@@ -13,7 +13,7 @@ from astrohack.io.image_mds import AstrohackImageFile
 @toolviper.utils.parameter.validate()
 def combine(
     image_name: str,
-    combine_name: str = None,
+    combine_name: str | None = None,
     ant: Union[str, List[str]] = "all",
     ddi: Union[int, List[int], str] = "all",
     weighted: bool = False,

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/config/beamcut_mds.param.json

@@ -74,7 +74,7 @@
             ]
         }
     },
-    "AstrohackBeamcutFile.plot_beamcut_in_amplitude":{
+    "AstrohackBeamcutFile.plot_in_amplitude":{
         "destination":{
             "nullable": false,
             "required": true,
@@ -150,7 +150,7 @@
             "type": ["boolean"]
         }
     },
-    "AstrohackBeamcutFile.plot_beamcut_in_attenuation":{
+    "AstrohackBeamcutFile.plot_in_db":{
         "destination":{
             "nullable": false,
             "required": true,
@@ -226,7 +226,7 @@
             "type": ["boolean"]
         }
     },
-    "AstrohackBeamcutFile.plot_beam_cuts_over_sky":{
+    "AstrohackBeamcutFile.plot_lm_offsets":{
         "destination":{
             "nullable": false,
             "required": true,
@@ -287,7 +287,7 @@
             "type": ["boolean"]
         }
     },
-    "AstrohackBeamcutFile.plot_beamcut_in_phase":{
+    "AstrohackBeamcutFile.plot_in_phase":{
         "destination":{
             "nullable": false,
             "required": true,
@@ -369,7 +369,7 @@
             "type": ["boolean"]
         }
     },
-    "AstrohackBeamcutFile.create_beam_fit_report":{
+    "AstrohackBeamcutFile.export_report":{
         "destination":{
             "nullable": false,
             "required": true,

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/config/extract_holog.param.json

@@ -23,7 +23,7 @@
         },
         "exclude_antennas": {
             "type":["ndarray", "list", "str"],
-            "struct type": ["int"],
+            "struct type": ["str"],
             "nullable": true
         },
         "holog_name":{

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/config/extract_pointing.param.json

@@ -7,11 +7,6 @@
             "type":["str"],
             "nullable": true
         },
-        "exclude":{
-            "type":["list", "str"],
-            "nullable": true,
-            "struct_type": ["str"]
-        },
         "parallel":{
             "type":["boolean"]
         },

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/config/panel_mds.param.json

@@ -73,6 +73,11 @@
             "type": ["int"],
             "min": 1,
             "max": 1200
+        },
+        "parallel":{
+            "nullable": false,
+            "required": false,
+            "type": ["boolean"]
         }
     },
     "AstrohackPanelFile.plot_antennas":{

{astrohack-1.0.2 → astrohack-1.0.3}/src/astrohack/config/position_mds.param.json

@@ -140,6 +140,14 @@
             "type": ["string"],
             "check allowed with": "units.time"
         },
+        "delay_limits": {
+            "nullable": true,
+            "required": false,
+            "struct_type": ["float"],
+            "minlength": 2,
+            "maxlength": 2,
+            "type": ["list", "tuple", "ndarray"]
+        },
         "plot_model":{
             "nullable": false,
             "required": false,
@@ -198,7 +206,7 @@
             "check allowed with": "units.length"
         },
         "box_size":{
-            "nullable": false,
+            "nullable": true,
             "required": false,
             "type": ["int", "float"],
             "min": 0