astrohack 0.10.1__tar.gz → 1.0.1__tar.gz

{astrohack-0.10.1/src/astrohack.egg-info → astrohack-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: astrohack
-Version: 0.10.1
+Version: 1.0.1
 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
@@ -10,7 +10,6 @@ Requires-Dist: astropy
 Requires-Dist: dask
 Requires-Dist: shapely
 Requires-Dist: distributed
-Requires-Dist: dropbox
 Requires-Dist: toolviper
 Requires-Dist: ipywidgets
 Requires-Dist: matplotlib

{astrohack-0.10.1 → astrohack-1.0.1}/pyproject.toml

@@ -1,10 +1,10 @@
 [project]
 name = "astrohack"
-version = "0.10.1"
+version = "1.0.1"
 description = "Holography Antenna Commissioning Kit"
 readme = "README.md"
 requires-python = ">= 3.11, < 3.14"
-dependencies = [ "astropy", "dask", "shapely", "distributed", "dropbox", "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", "python_casacore>=3.6.1; sys_platform != \"darwin\" ",]
 [[project.authors]]
 name = "Joshua Hoskins"
 email = "jhoskins@nrao.edu"

{astrohack-0.10.1 → astrohack-1.0.1}/src/astrohack/__init__.py

@@ -4,36 +4,16 @@ from importlib.metadata import version
 __version__ = version("astrohack")
 
 from .extract_holog import (
-    HologObsDict,
     extract_holog,
     generate_holog_obs_dict,
-    model_memory_usage,
 )
+from .io import *
 
 from .beamcut import beamcut
-from astrohack.io.beamcut_mds import AstrohackBeamcutFile
-
 from .extract_pointing import extract_pointing
 from .holog import holog
-from astrohack.io.dio import (
-    open_holog,
-    open_image,
-    open_pointing,
-    open_panel,
-    open_locit,
-    open_position,
-    open_beamcut,
-)
 from .panel import panel
 from .combine import combine
-from astrohack.io.mds import (
-    AstrohackHologFile,
-    AstrohackPointFile,
-    AstrohackImageFile,
-    AstrohackPanelFile,
-    AstrohackLocitFile,
-    AstrohackPositionFile,
-)
 from .locit import locit
 from .extract_locit import extract_locit
 from .cassegrain_ray_tracing import (

{astrohack-0.10.1 → astrohack-1.0.1}/src/astrohack/antenna/antenna_surface.py

@@ -1,4 +1,3 @@
-import numpy as np
 import xarray as xr
 
 from matplotlib import patches
@@ -115,7 +114,7 @@ class AntennaSurface:
     def _read_holog_xds(self, inputxds):
         if "chan" in inputxds.dims:
             if inputxds.sizes["chan"] != 1:
-                raise Exception("Only single channel holographies supported")
+                raise RuntimeError("Only single channel holographies supported")
             self.wavelength = clight / inputxds.chan.values[0]
         else:
             self.wavelength = inputxds.attrs["wavelength"]
@@ -126,7 +125,7 @@ class AntennaSurface:
                 f'{inputxds.coords["pol"]})'
             )
             logger.error(msg)
-            raise Exception(msg)
+            raise ValueError(msg)
 
         self.amplitude = (
             inputxds["AMPLITUDE"].sel(pol=self.pol_state).isel(time=0, chan=0).values
@@ -224,7 +223,7 @@ class AntennaSurface:
             clip = self._compute_noise_threshold_clip(clip_level)
         else:
             msg = f"Unrecognized clipping type: {clip_type}"
-            raise Exception(msg)
+            raise ValueError(msg)
         return clip
 
     def _compute_noise_threshold_clip(self, threshold, step_multiplier=0.95):
@@ -315,7 +314,7 @@ class AntennaSurface:
                     "Cannot computed gains for corrected dish if panels are not fitted."
                 )
                 logger.error(msg)
-                raise Exception(msg)
+                raise RuntimeError(msg)
         else:
             scaled_phase = wavelength_scaling * self.phase
 
@@ -377,7 +376,7 @@ class AntennaSurface:
         Apply corrections determined by the panel surface fitting methods to the antenna surface
         """
         if not self.fitted:
-            raise Exception("Panels must be fitted before atempting a correction")
+            raise RuntimeError("Panels must be fitted before atempting a correction")
         self.corrections = np.where(self.mask, 0, np.nan)
         for panel in self.panels:
             corrections = panel.get_corrections()
@@ -514,7 +513,7 @@ class AntennaSurface:
 
     def _multi_plot(self, maps, labels, prefix, basename, factor, parm_dict, caller):
         if len(maps) != len(labels):
-            raise Exception("Map list and label list must be of the same size")
+            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(
@@ -663,8 +662,8 @@ class AntennaSurface:
 
         nscrews = self.panels[0].screws.shape[0]
 
-        self.panel_labels = np.ndarray([npanels], dtype=object)
-        self.panel_model_array = np.ndarray([npanels], dtype=object)
+        self.panel_labels = np.ndarray([npanels], dtype="U22")
+        self.panel_model_array = np.ndarray([npanels], dtype="U22")
         self.panel_pars = np.full((npanels, max_par), np.nan, dtype=float)
         self.screw_adjustments = np.ndarray((npanels, nscrews), dtype=float)
         self.panel_fallback = np.ndarray([npanels], dtype=bool)

{astrohack-0.10.1 → astrohack-1.0.1}/src/astrohack/antenna/base_panel.py

@@ -76,7 +76,7 @@ class BasePanel:
         except KeyError:
             msg = f"Unknown model {self.model_name}"
             logger.error(msg)
-            raise Exception(msg)
+            raise ValueError(msg)
 
         self.model = PanelModel(model_dict, self.zeta, self.ref_points, self.center)
 
@@ -130,7 +130,7 @@ class BasePanel:
         if not self.solved:
             msg = "Cannot correct a panel that is not solved"
             logger.error(msg)
-            raise Exception(msg)
+            raise RuntimeError(msg)
         self.corr = self.model.correct(self.samples, self.margins)
         return self.corr
 

{astrohack-0.10.1 → astrohack-1.0.1}/src/astrohack/antenna/panel_fitting.py

@@ -5,7 +5,6 @@ import toolviper.utils.logger as logger
 
 from astrohack.utils import gauss_elimination, least_squares_jit
 
-
 ###################################
 #  General purpose                #
 ###################################
@@ -630,7 +629,7 @@ class PanelModel:
             Array of corrections and the indices linking them to the aperture.
         """
         if not self.fitted:
-            raise Exception("Cannot correct using a panel model that is not fitted")
+            raise RuntimeError("Cannot correct using a panel model that is not fitted")
 
         nsamp = len(samples)
         nmarg = len(margins)

{astrohack-0.10.1 → astrohack-1.0.1}/src/astrohack/antenna/polygon_panel.py

@@ -2,7 +2,6 @@ from shapely import Polygon, Point
 from shapely.plotting import plot_polygon
 
 from astrohack.utils import markersize
-from astrohack.utils.ray_tracing_general import generalized_norm
 from astrohack.antenna.base_panel import BasePanel
 from astrohack.antenna.panel_fitting import PanelPoint
 import numpy as np

{astrohack-0.10.1 → astrohack-1.0.1}/src/astrohack/antenna/ring_panel.py

@@ -147,14 +147,14 @@ class RingPanel(BasePanel):
         print("{0:20s}={1:8.5f}".format("zeta", self.zeta))
         print()
 
-    def plot(self, ax, screws=False, label=False, margins=False, samples=False):
+    def plot(self, ax, screws=False, label=False, _=False, samples=False):
         """
         Plot panel outline to ax
         Args:
             ax: matplotlib axes instance
             screws: Display screws in plot
             label: Add panel labels to plot
-            margins: does nothing (interface compatibility)
+            _: does nothing (interface compatibility)
             samples: plot samples and margins
         """
         x1 = self.inrad * np.sin(self.theta1)

{astrohack-0.10.1 → astrohack-1.0.1}/src/astrohack/antenna/telescope.py

@@ -1,5 +1,3 @@
-import time
-
 from shapely.geometry.point import Point
 from shapely.geometry.polygon import Polygon
 from shapely.strtree import STRtree
@@ -195,7 +193,7 @@ class RingedCassegrain(Telescope):
             error = True
 
         if error:
-            raise Exception("Failed Consistency check")
+            raise RuntimeError("Failed Consistency check")
         else:
             print("Consistency passed")
 
@@ -253,7 +251,9 @@ class RingedCassegrain(Telescope):
         elif "ALMA" in self.name or self.name == "ACA 7m":
             self._panel_label = self._alma_panel_labeling
         else:
-            raise Exception(f"Don't know how to build panel list for {self.name}")
+            raise NotImplementedError(
+                f"Don't know how to build panel list for {self.name}"
+            )
 
         panel_list = []
         for iring in range(self.n_rings_of_panels):
@@ -371,7 +371,7 @@ class RingedCassegrain(Telescope):
                 )
 
         else:
-            raise Exception(
+            raise TypeError(
                 f"Don't know how to handle an arm width of class {type(self.arm_shadow_width)}"
             )
 
@@ -380,13 +380,13 @@ class RingedCassegrain(Telescope):
         else:
             return mask
 
-    def phase_to_deviation(self, u_axis, v_axis, mask, phase, wavelength):
+    def phase_to_deviation(self, u_axis, v_axis, _, phase, wavelength):
         """
         Transform phase image to physical deviation image based on wavelength.
         Args:
             u_axis: Aperture U axis
             v_axis: Aperture V axis
-            mask: dummy argument for interface compatibility
+            _: dummy argument for interface compatibility
             phase: Phase image in Radians
             wavelength: Observation wavelength in meters
 
@@ -400,13 +400,13 @@ class RingedCassegrain(Telescope):
         bcoeff = 4 * self.focus**2
         return acoeff * phase * np.sqrt(radius**2 + bcoeff)
 
-    def deviation_to_phase(self, u_axis, v_axis, mask, deviation, wavelength):
+    def deviation_to_phase(self, u_axis, v_axis, _, deviation, wavelength):
         """ "
         Transform deviation image to physical phase image based on wavelength.
         Args:
             u_axis: Aperture U axis
             v_axis: Aperture V axis
-            mask: dummy argument for interface compatibility
+            _: dummy argument for interface compatibility
             deviation: Deviation image in meters
             wavelength: Observation wavelength in meters
 
@@ -551,14 +551,14 @@ def get_proper_telescope(name: str, antenna_name: str = None):
         elif "na" in antenna_name:
             return NgvlaPrototype.from_name("ngvla_proto_2025")
         else:
-            raise Exception(f"Unsupported antenna type for the VLA: {antenna_name}")
+            raise ValueError(f"Unsupported antenna type for the VLA: {antenna_name}")
 
     elif "vlba" in name:
         return RingedCassegrain.from_name("vlba")
 
     elif "alma" in name:
         if antenna_name is None:
-            raise Exception(
+            raise ValueError(
                 "ALMA is an heterogenious array and hence an antenna name is needed"
             )
         elif "dv" in antenna_name:
@@ -568,7 +568,7 @@ def get_proper_telescope(name: str, antenna_name: str = None):
         elif "tp" in antenna_name:
             return RingedCassegrain.from_name("alma_tp")
         else:
-            raise Exception(f"Unsupported antenna type for ALMA: {antenna_name}")
+            raise ValueError(f"Unsupported antenna type for ALMA: {antenna_name}")
 
     elif "aca" in name:
         return RingedCassegrain.from_name("aca_7m")

{astrohack-0.10.1 → astrohack-1.0.1}/src/astrohack/beamcut.py

@@ -1,19 +1,17 @@
 import pathlib
-import json
-import xarray as xr
-
-import toolviper.utils.logger as logger
+import numpy as np
 
 from toolviper.utils.parameter import validate
 
 from astrohack.core.beamcut import process_beamcut_chunk
-from astrohack.utils import get_default_file_name, add_caller_and_version_to_dict
-from astrohack.utils.file import overwrite_file, check_if_file_can_be_opened
-from astrohack.utils.graph import compute_graph
+from astrohack.utils 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
+from astrohack.io.dio import open_holog
 from astrohack.utils.validation import custom_plots_checker
 
-from typing import Union, List
+from typing import Union, List, Tuple
 
 
 @validate(custom_checker=custom_plots_checker)
@@ -21,13 +19,15 @@ def beamcut(
     holog_name: str,
     beamcut_name: str = None,
     ant: Union[str, List[str]] = "all",
-    ddi: Union[int, List[str]] = "all",
+    ddi: Union[int, List[int], str] = "all",
     destination: str = 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,
     dpi: int = 300,
     display: bool = False,
-    y_scale: list[float] = None,
     parallel: bool = False,
     overwrite: bool = False,
 ):
@@ -55,6 +55,12 @@ def beamcut(
     :param azel_unit: Unit for Az/El information in plots and report, default is "deg".
     :type azel_unit: str, optional
 
+    :param phase_unit: Unit for phase plots, default is "deg".
+    :type phase_unit: str, optional
+
+    :param phase_scale: Scale for the phase plots, in phase_unit, default is None, meaning 1 full cycle.
+    :type phase_scale: Union[List[float], Tuple[float], np.array], optional
+
     :param dpi: Resolution in pixels, defaults to 300.
     :type dpi: int, optional
 
@@ -113,61 +119,73 @@ def beamcut(
         )
     """
 
-    check_if_file_can_be_opened(holog_name, "0.9.5")
+    beamcut_name = get_default_file_name(holog_name, ".beamcut.zarr", beamcut_name)
 
-    if beamcut_name is None:
-        beamcut_name = get_default_file_name(
-            input_file=holog_name, output_type=".beamcut.zarr"
-        )
+    beamcut_params = locals()
 
     if destination is not None:
         pathlib.Path(destination).mkdir(exist_ok=True)
 
-    beamcut_params = locals()
+    overwrite_file(beamcut_name, overwrite)
 
-    input_params = beamcut_params.copy()
-    assert pathlib.Path(beamcut_params["holog_name"]).exists() is True, logger.error(
-        f"File {beamcut_params['holog_name']} does not exists."
+    beamcut_mds = AstrohackBeamcutFile.create_from_input_parameters(
+        beamcut_params["beamcut_name"], beamcut_params
     )
 
-    json_data = "/".join((beamcut_params["holog_name"], ".holog_json"))
-
-    with open(json_data, "r") as json_file:
-        holog_json = json.load(json_file)
-
-    overwrite_file(beamcut_params["beamcut_name"], beamcut_params["overwrite"])
-
-    executed_graph, graph_results = compute_graph(
-        holog_json,
-        process_beamcut_chunk,
-        beamcut_params,
-        ["ant", "ddi"],
+    holog_mds = open_holog(holog_name)
+    executed_graph = create_and_execute_graph_from_dict(
+        looping_dict=holog_mds,
+        chunk_function=process_beamcut_chunk,
+        param_dict=beamcut_params,
+        key_order=["ant", "ddi"],
+        output_mds=beamcut_mds,
         parallel=parallel,
-        fetch_returns=True,
     )
-
     if executed_graph:
-        logger.info("Finished processing")
-        output_attr_file = "{name}/{ext}".format(
-            name=beamcut_params["beamcut_name"], ext=".beamcut_input"
-        )
-        root = xr.DataTree(name="root")
-        root.attrs.update(beamcut_params)
-        add_caller_and_version_to_dict(root.attrs, direct_call=True)
-
-        for xdtree in graph_results:
-            ant, ddi = xdtree.name.split("-")
-            if ant in root.keys():
-                ant = root.children[ant].update({ddi: xdtree})
-            else:
-                ant_tree = xr.DataTree(name=ant, children={ddi: xdtree})
-                root = root.assign({ant: ant_tree})
-
-        root.to_zarr(beamcut_params["beamcut_name"], mode="w", consolidated=True)
-
-        beamcut_mds = AstrohackBeamcutFile(beamcut_params["beamcut_name"])
-        beamcut_mds.open()
+        if destination is not None:
+            beamcut_mds.plot_beamcut_in_amplitude(
+                destination,
+                lm_unit=lm_unit,
+                azel_unit=azel_unit,
+                y_scale=y_scale,
+                display=display,
+                dpi=dpi,
+                parallel=parallel,
+            )
+            beamcut_mds.plot_beamcut_in_attenuation(
+                destination,
+                lm_unit=lm_unit,
+                azel_unit=azel_unit,
+                y_scale=y_scale,
+                display=display,
+                dpi=dpi,
+                parallel=parallel,
+            )
+            beamcut_mds.plot_beamcut_in_phase(
+                destination,
+                lm_unit=lm_unit,
+                azel_unit=azel_unit,
+                phase_unit=phase_unit,
+                phase_scale=phase_scale,
+                display=display,
+                dpi=dpi,
+                parallel=parallel,
+            )
+            beamcut_mds.plot_beam_cuts_over_sky(
+                destination,
+                lm_unit=lm_unit,
+                azel_unit=azel_unit,
+                display=display,
+                dpi=dpi,
+                parallel=parallel,
+            )
+            beamcut_mds.create_beam_fit_report(
+                destination,
+                lm_unit=lm_unit,
+                azel_unit=azel_unit,
+                parallel=parallel,
+            )
+
         return beamcut_mds
     else:
-        logger.warning("No data to process")
         return None

{astrohack-0.10.1 → astrohack-1.0.1}/src/astrohack/cassegrain_ray_tracing.py

@@ -6,9 +6,9 @@ from astrohack.core.cassegrain_ray_tracing import *
 from astrohack.utils import (
     convert_unit,
     clight,
-    add_caller_and_version_to_dict,
     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

{astrohack-0.10.1 → astrohack-1.0.1}/src/astrohack/combine.py

@@ -1,17 +1,13 @@
-import pathlib
-import toolviper.utils.parameter
-import toolviper.utils.logger as logger
-
 from typing import Union, List
 
-from astrohack.core.combine import process_combine_chunk
+import toolviper.utils.parameter
 
-from astrohack.utils.graph import compute_graph
+from astrohack 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
-from astrohack.utils.data import write_meta_data
 from astrohack.utils.text import get_default_file_name
-
-from astrohack.io.mds import AstrohackImageFile
+from astrohack.io.image_mds import AstrohackImageFile
 
 
 @toolviper.utils.parameter.validate()
@@ -52,6 +48,13 @@ def combine(
     :rtype: AstrohackImageFile
 
     .. _Description:
+    **combine**
+
+    Combine combines the amplitude and corrected_phase members of the selected DDIs in the input image file. Currently, \
+    combine only supports the combination of these two quantities to avoid long regridding times. Hence, the output \
+    image file (.combine.zarr file name) contains the combined amplitude and corrected_phase images, but the aperture \
+    and beam images present in this file will be those present in the DDI with the lowest frequency.
+
     **AstrohackImageFile**
 
     Image object allows the user to access image data via compound dictionary keys with values, in order of depth, \
@@ -81,45 +84,28 @@ def combine(
         )
     """
 
-    if combine_name is None:
-        combine_name = get_default_file_name(
-            input_file=image_name, output_type=".image.zarr"
-        )
+    combine_name = get_default_file_name(image_name, ".combine.zarr", combine_name)
 
     combine_params = locals()
 
-    input_params = combine_params.copy()
-
-    assert pathlib.Path(combine_params["image_name"]).exists() is True, logger.error(
-        f'File {combine_params["image_name"]} does not exists.'
-    )
-
     overwrite_file(combine_params["combine_name"], combine_params["overwrite"])
 
-    image_mds = AstrohackImageFile(combine_params["image_name"])
-    image_mds.open()
-
-    combine_params["image_mds"] = image_mds
-    image_attr = image_mds._meta_data
-
-    if compute_graph(
-        image_mds, process_combine_chunk, combine_params, ["ant"], parallel=parallel
-    ):
-        logger.info("Finished processing")
+    image_mds = open_image(image_name)
 
-        output_attr_file = "{name}/{ext}".format(
-            name=combine_params["combine_name"], ext=".image_attr"
-        )
-        write_meta_data(output_attr_file, image_attr)
+    combine_mds = AstrohackImageFile.create_from_input_parameters(
+        combine_name, combine_params
+    )
 
-        output_attr_file = "{name}/{ext}".format(
-            name=combine_params["combine_name"], ext=".image_input"
-        )
-        write_meta_data(output_attr_file, input_params)
+    executed_graph = create_and_execute_graph_from_dict(
+        looping_dict=image_mds,
+        chunk_function=process_combine_chunk,
+        param_dict=combine_params,
+        key_order=["ant"],
+        output_mds=combine_mds,
+    )
 
-        combine_mds = AstrohackImageFile(combine_params["combine_name"])
-        combine_mds.open()
+    if executed_graph:
+        combine_mds.write(mode="a")
         return combine_mds
     else:
-        logger.warning("No data to process")
         return None

{astrohack-0.10.1 → astrohack-1.0.1}/src/astrohack/config/beamcut.param.json

@@ -38,6 +38,12 @@
             "type": ["string"],
             "check allowed with": "units.trig"
         },
+        "phase_unit":{
+            "nullable": false,
+            "required": false,
+            "type": ["string"],
+            "check allowed with": "units.trig"
+        },
         "dpi":{
             "nullable": false,
             "required": false,
@@ -65,6 +71,21 @@
                 "ndarray"
             ]
         },
+        "phase_scale":{
+            "nullable": true,
+            "required": false,
+            "struct_type": [
+                "float",
+                "int"
+            ],
+            "minlength": 2,
+            "maxlength": 2,
+            "type": [
+                "list",
+                "tuple",
+                "ndarray"
+            ]
+        },
         "parallel":{
             "nullable": false,
             "required": false,