tabsim 0.0.2__tar.gz → 0.0.4__tar.gz

{tabsim-0.0.2 → tabsim-0.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tabsim
-Version: 0.0.2
+Version: 0.0.4
 Summary: Trajectory-based Radio Frequency Interference (RFI) simulations for radio interferometeric data.
 Author-email: Chris Finlay <christopher.finlay@epfl.ch>
 Maintainer-email: Chris Finlay <christopher.finlay@epfl.ch>
@@ -680,7 +680,7 @@ License:                     GNU GENERAL PUBLIC LICENSE
         <https://www.gnu.org/licenses/why-not-lgpl.html>.
         
 Project-URL: Repository, https://github.com/chrisfinlay/tab-sim.git
-Requires-Python: <3.13,>=3.10
+Requires-Python: <3.13,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: jax
@@ -704,12 +704,16 @@ Requires-Dist: ipython; extra == "ipy"
 Requires-Dist: ipykernel; extra == "ipy"
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
 Dynamic: license-file
 
 # tab-sim
 
 [![DOI:10.1093/mnras/stad1979](https://zenodo.org/badge/DOI/10.1093/mnras/stad1979.svg)](https://doi.org/10.1093/mnras/stad1979)
 [![DOI:10.48550/arXiv.2502.00106](https://img.shields.io/badge/arXiv-2502.00106-b31b1b.svg)](https://doi.org/10.48550/arXiv.2502.00106)
+[![Documentation Status](https://readthedocs.org/projects/tab-sim/badge/?version=latest)](https://tab-sim.readthedocs.io/en/latest/?badge=latest)
 
 **T**r**A**jectory **B**ased RFI **Sim**ulations of radio interferometry data. 
 A source to visibility model for RFI sources including certain near-field effects. 
@@ -717,6 +721,10 @@ A source to visibility model for RFI sources including certain near-field effect
 `tab-sim` is written in [JAX](https://jax.readthedocs.io/en/latest/notebooks/quickstart.html) 
 and [Dask](https://www.dask.org) and can therefore use GPUs and/or CPUs to perform larger than memory computation.
 
+## Documentation
+
+[https://tab-sim.readthedocs.io/](https://tab-sim.readthedocs.io/)
+
 ## Installation
 
 The following instructions are expected to work on Linux machine. If you are running Windows it is recommended to use WSL. If you are running Mac then it is best to start with a [conda](https://docs.conda.io/en/latest/)/[mamba](https://mamba.readthedocs.io/en/latest/index.html) environment and install `python-casacore` before continuing with the `pip` install method. If all else fails there is the [Docker install](#docker).

{tabsim-0.0.2 → tabsim-0.0.4}/README.md

@@ -2,6 +2,7 @@
 
 [![DOI:10.1093/mnras/stad1979](https://zenodo.org/badge/DOI/10.1093/mnras/stad1979.svg)](https://doi.org/10.1093/mnras/stad1979)
 [![DOI:10.48550/arXiv.2502.00106](https://img.shields.io/badge/arXiv-2502.00106-b31b1b.svg)](https://doi.org/10.48550/arXiv.2502.00106)
+[![Documentation Status](https://readthedocs.org/projects/tab-sim/badge/?version=latest)](https://tab-sim.readthedocs.io/en/latest/?badge=latest)
 
 **T**r**A**jectory **B**ased RFI **Sim**ulations of radio interferometry data. 
 A source to visibility model for RFI sources including certain near-field effects. 
@@ -9,6 +10,10 @@ A source to visibility model for RFI sources including certain near-field effect
 `tab-sim` is written in [JAX](https://jax.readthedocs.io/en/latest/notebooks/quickstart.html) 
 and [Dask](https://www.dask.org) and can therefore use GPUs and/or CPUs to perform larger than memory computation.
 
+## Documentation
+
+[https://tab-sim.readthedocs.io/](https://tab-sim.readthedocs.io/)
+
 ## Installation
 
 The following instructions are expected to work on Linux machine. If you are running Windows it is recommended to use WSL. If you are running Mac then it is best to start with a [conda](https://docs.conda.io/en/latest/)/[mamba](https://mamba.readthedocs.io/en/latest/index.html) environment and install `python-casacore` before continuing with the `pip` install method. If all else fails there is the [Docker install](#docker).

tabsim-0.0.4/docs/conf.py

@@ -0,0 +1,14 @@
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+project = 'tab‑sim'
+author = 'Chris Finlay'
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+]
+templates_path = ['_templates']
+exclude_patterns = []
+html_theme = 'sphinx_rtd_theme'

{tabsim-0.0.2 → tabsim-0.0.4}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tabsim"
-version = "0.0.2"
+version = "0.0.4"
 license = {file = "LICENSE"}
 readme = "README.md"
 # dynamic = ["version", "readme"]
@@ -17,7 +17,7 @@ maintainers = [
 ]
 description = "Trajectory-based Radio Frequency Interference (RFI) simulations for radio interferometeric data."
 
-requires-python = ">=3.10,<3.13"
+requires-python = ">=3.9,<3.13"
 dependencies = [
     "jax", "dask<=2024.10.0", "xarray", "zarr<3.0.0", 
     "dask-ms>=0.2.21", "scipy", "tqdm", "matplotlib", 
@@ -32,6 +32,7 @@ sat = ["regions"]
 # all_cpu = ["regions", "bdsf", "TGEpy @ git+https://github.com/chrisfinlay/TGEpy.git"]
 ipy = ["ipython", "ipykernel"]
 test = ["pytest"]
+docs = ["sphinx", "sphinx-rtd-theme"]
 
 [project.urls]
 Repository = "https://github.com/chrisfinlay/tab-sim.git"

{tabsim-0.0.2 → tabsim-0.0.4}/tabsim/config.py

@@ -5,7 +5,8 @@ import sys
 import shutil
 
 import collections.abc
-from typing import Tuple
+from typing import Tuple, Union, Optional
+
 from datetime import datetime
 
 import dask.array as da
@@ -13,27 +14,23 @@ from dask.array.core import Array
 import xarray as xr
 import numpy as np
 import pandas as pd
+from astropy.time import Time
 
 from tabsim.dask.observation import Observation
 from tabsim.sky import generate_random_sky
 from tabsim.plot import plot_uv, plot_src_alt, plot_angular_seps
 from tabsim.write import write_ms, mk_obs_name, mk_obs_dir
-from tabsim.jax.coordinates import calculate_fringe_frequency
-from tabsim.tle import get_visible_satellite_tles
+from tabsim.jax.coordinates import calculate_fringe_frequency, jd_to_mjd
+from tabsim.tle import get_visible_satellite_tles, id_generator
 
 from daskms import xds_from_ms
 
 from tqdm import tqdm
 from importlib.resources import files
 
-config_dir = files("tabsim.data").joinpath("config_files").__str__()
 
-sim_base_config_path = os.path.join(config_dir, "sim_config_base.yaml")
-tab_base_config_path = os.path.join(config_dir, "tab_config_base.yaml")
-# extract_base_config_path = os.path.join(config_dir, "extract_config_base.yaml")
-# pow_spec_base_config_path = os.path.join(
-#     config_dir, "extract_pow_spec_config_base.yaml"
-# )
+sky_dir = files("tabsim.data").joinpath("sky").__str__()
+
 
 JD0 = 2459997.079914223  # 2023-02-21 13:55:04.589 UTC => GMSA = 0
 MJD0 = JD0 - 2400000.5
@@ -113,24 +110,67 @@ def load_config(path: str, config_type: str = "sim") -> dict:
     dict
         Configuration dictionary.
     """
+    config_dir = files("tabsim.data").joinpath("config").__str__()
+
+    sim_base_config_path = os.path.join(config_dir, "sim_config_base.yaml")
+    tab_base_config_path = os.path.join(config_dir, "tab_config_base.yaml")
+    # extract_base_config_path = os.path.join(config_dir, "extract_config_base.yaml")
+    # pow_spec_base_config_path = os.path.join(
+    #     config_dir, "extract_pow_spec_config_base.yaml"
+    # )
 
     config = yaml_load(path)
     if config_type == "sim":
         base_config = yaml_load(sim_base_config_path)
     elif config_type == "tab":
         base_config = yaml_load(tab_base_config_path)
-    elif config_type == "extract":
-        base_config = yaml_load(extract_base_config_path)
-    elif config_type == "pow_spec":
-        base_config = yaml_load(pow_spec_base_config_path)
+    # elif config_type == "extract":
+    #     base_config = yaml_load(extract_base_config_path)
+    # elif config_type == "pow_spec":
+    #     base_config = yaml_load(pow_spec_base_config_path)
     else:
-        ValueError(
-            "A config type must be specified. Options are {sim, tab, extract, pow_spec}."
-        )
+        raise ValueError("A config type must be specified. Options are {sim, tab}.")
 
     return deep_update(base_config, config)
 
 
+def get_telescope_definitions(tel_name: str):
+
+    tel_dir = files("tabsim.data").joinpath("telescopes").__str__()
+    tel_def = yaml_load(os.path.join(tel_dir, "_telescopes.yaml"))
+
+    tel_name = tel_name.lower()
+    telescope_list = tel_def.keys()
+
+    if tel_name in telescope_list:
+        tel_def = tel_def[tel_name]
+        tel_def["itrf_path"] = os.path.join(tel_dir, tel_def["itrf_path"])
+    else:
+        raise ValueError(
+            f"{tel_name} is not a pre-defined telescope within tab-sim. Choose from {telescope_list}"
+        )
+
+    return tel_def
+
+
+def get_rfi_definitions():
+
+    rfi_dir = files("tabsim.data").joinpath("rfi").__str__()
+
+    rfi_def = {
+        "tle_satellite": {
+            "tle_dir": os.path.join(rfi_dir, "tles"),
+            "norad_spec_model": os.path.join(rfi_dir, "norad_satellite.rfimodel"),
+        },
+        "stationary": {
+            "geo_path": os.path.join(rfi_dir, "stationary.loc"),
+            "spec_path": os.path.join(rfi_dir, "stationary.rfimodel"),
+        },
+    }
+
+    return rfi_def
+
+
 def load_sky_model(file_path: str, freqs: Array, src_type: str) -> tuple:
     """Read in a skymodel file and return parameters to be used in tabascal simulator.
     A skymodel file is a csv file with the following columns:
@@ -188,7 +228,7 @@ def load_sky_model(file_path: str, freqs: Array, src_type: str) -> tuple:
         raise KeyError("'src_type' must be one of {'point', 'gauss', 'exp'}.")
 
 
-def sigma_value(value: str | float | int, obs: Observation):
+def sigma_value(value: Union[str, float, int], obs: Observation):
     try:
         if isinstance(value, str):
             sigma = (np.mean(obs.noise_std) / np.sqrt(obs.n_time * obs.n_bl)).compute()
@@ -212,12 +252,9 @@ def load_obs(obs_spec: dict) -> Observation:
         return x
 
     if obs_["start_time_jd"]:
-        from tabascal.jax.coordinates import jd_to_mjd
 
         start_time_mjd = jd_to_mjd(obs_["start_time_jd"])
     elif obs_["start_time_isot"]:
-        from astropy.time import Time
-        from tabascal.jax.coordinates import jd_to_mjd
 
         start_time_mjd = jd_to_mjd(
             Time(obs_["start_time_isot"], format="isot", scale="ut1").jd
@@ -730,20 +767,7 @@ def save_inputs(obs: Observation, obs_spec: dict, save_path: str) -> None:
         if path is not None:
             shutil.copy(path, save_path)
 
-    key = (
-        2
-        * [
-            "tle_satellite",
-        ]
-        + 2
-        * [
-            "satellite",
-        ]
-        + 2
-        * [
-            "stationary",
-        ]
-    )
+    key = 2 * ["tle_satellite"] + 2 * ["satellite"] + 2 * ["stationary"]
     subkey = [
         "norad_ids_path",
         "norad_spec_model",
@@ -836,8 +860,24 @@ def print_fringe_freq_tle_sat(obs: Observation):
     print(f"Recommended n_int is >=     : {n_int:.0f} ({obs.n_int_samples} used)")
 
 
+def check_telescope_defintion(tel_def: dict):
+
+    dish_d = tel_def["dish_d"]
+
+    if tel_def["itrf_path"] and dish_d:
+        return True
+    elif (
+        tel_def["longitude"] and tel_def["latitude"] and tel_def["enu_path"] and dish_d
+    ):
+        return True
+    else:
+        return False
+
+
 def run_sim_config(
-    obs_spec: dict = None, config_path: str = None, spacetrack_path: str = None
+    obs_spec: Optional[dict] = None,
+    config_path: Optional[str] = None,
+    spacetrack_path: Optional[str] = None,
 ) -> Tuple[Observation, str]:
 
     from tabsim.tle import id_generator
@@ -850,16 +890,22 @@ def run_sim_config(
     start = datetime.now()
     print(datetime.now())
 
-    if config_path is not None:
+    if config_path:
         obs_spec = load_config(config_path, config_type="sim")
     elif obs_spec is None:
-        print("obs_spec or path must be defined.")
-        return None
+        raise ValueError("obs_spec or config_path must be defined.")
+
+    rfi_def = get_rfi_definitions()
+    obs_spec["rfi_sources"] = deep_update(obs_spec["rfi_sources"], rfi_def)
+
+    if not check_telescope_defintion(obs_spec["telescope"]):
+        tel_def = get_telescope_definitions(obs_spec["telescope"]["name"])
+        obs_spec["telescope"] = deep_update(obs_spec["telescope"], tel_def)
 
     obs = load_obs(obs_spec)
     add_astro_sources(obs, obs_spec)
     add_satellite_sources(obs, obs_spec)
-    if obs_spec["rfi_sources"]["tle_satellite"]["max_n_sat"] != 0:
+    if obs_spec["rfi_sources"]["tle_satellite"]["max_n_sat"] != 0 and spacetrack_path:
         add_tle_satellite_sources(obs, obs_spec, spacetrack_path)
     add_stationary_sources(obs, obs_spec)
     add_gains(obs, obs_spec)

{tabsim-0.0.2 → tabsim-0.0.4}/tabsim/dask/observation.py

@@ -1,9 +1,9 @@
-import jax.numpy as jnp
 from jax import config, Array
 
 import dask.array as da
 import numpy as np
 import xarray as xr
+from typing import Optional
 
 from tabsim.dask.coordinates import (
     ENU_to_ITRF,
@@ -75,12 +75,12 @@ class Telescope(object):
         latitude: float,
         longitude: float,
         elevation: float = 0.0,
-        ENU_array: Array = None,
-        ENU_path: str = None,
-        ITRF_array: Array = None,
-        ITRF_path: str = None,
-        tel_name: str = None,
-        n_ant: int = None,
+        ENU_array: Optional[Array] = None,
+        ENU_path: Optional[str] = None,
+        ITRF_array: Optional[Array] = None,
+        ITRF_path: Optional[str] = None,
+        tel_name: Optional[str] = None,
+        n_ant: Optional[int] = None,
     ):
         self.tel_name = tel_name
         self.latitude = da.asarray(latitude)
@@ -132,16 +132,16 @@ Elevation : {elevation}\n"""
         self.ITRF = ENU_to_ITRF(self.ENU, self.latitude, self.longitude, self.elevation)
 
     def createArrayITRF(self, ITRF_array, ITRF_path):
+
         if ITRF_array is not None:
             self.ITRF = ITRF_array
         elif ITRF_path is not None:
             self.ITRF = np.loadtxt(ITRF_path, usecols=(0, 1, 2), max_rows=self.n_ant)
         else:
-            self.ITRF = None
-            msg = """Error : ITRF antenna coordinates are needed either in an 
+            msg = """ITRF antenna coordinates are needed either in an 
                      array or as a csv like file."""
-            print(msg)
-            return
+            raise ValueError(msg)
+
         self.ITRF = da.asarray(self.ITRF)
         self.GEO_ants = da.asarray(itrf_to_geo(self.ITRF.compute()))
 
@@ -205,11 +205,11 @@ class Observation(Telescope):
         times_mjd: Array,
         int_time: float = 2.0,
         chan_width: float = 209e3,
-        ENU_array: Array = None,
-        ENU_path: str = None,
-        ITRF_array: Array = None,
-        ITRF_path: str = None,
-        n_ant: int = None,
+        ENU_array: Optional[Array] = None,
+        ENU_path: Optional[str] = None,
+        ITRF_array: Optional[Array] = None,
+        ITRF_path: Optional[str] = None,
+        n_ant: Optional[int] = None,
         dish_d: float = 13.5,
         random_seed: int = 0,
         auto_corrs: bool = False,
@@ -242,7 +242,7 @@ class Observation(Telescope):
         self.target_name = target_name
         self.auto_corrs = auto_corrs
 
-        a1, a2 = jnp.triu_indices(self.n_ant, 0 if auto_corrs else 1)
+        a1, a2 = np.triu_indices(self.n_ant, 0 if auto_corrs else 1)
         self.n_bl = len(a1)
 
         self.ant_chunk = self.n_ant
@@ -326,17 +326,17 @@ class Observation(Telescope):
         self.vis_rfi = da.zeros(
             shape=(self.n_time, self.n_bl, self.n_freq),
             chunks=(self.time_chunk, self.bl_chunk, self.freq_chunk),
-            dtype=jnp.complex128,
+            dtype=np.complex128,
         )
         self.vis_ast = da.zeros(
             shape=(self.n_time, self.n_bl, self.n_freq),
             chunks=(self.time_chunk, self.bl_chunk, self.freq_chunk),
-            dtype=jnp.complex128,
+            dtype=np.complex128,
         )
         self.gains_ants = da.ones(
             shape=(self.n_time, self.n_ant, self.n_freq),
             chunks=(self.time_chunk, self.ant_chunk, self.freq_chunk),
-            dtype=jnp.complex128,
+            dtype=np.complex128,
         )
         self.random_seed = random_seed
 
@@ -486,7 +486,7 @@ Number of stationary RFI :  {n_stat}"""
 
         self.ast_p_I.append(I)
         self.ast_p_lmn.append(lmn)
-        self.ast_p_radec.append(jnp.array([ra, dec]))
+        self.ast_p_radec.append(np.array([ra, dec]))
         self.n_p_ast += len(I)
         self.n_ast += len(I)
 
@@ -550,7 +550,7 @@ Number of stationary RFI :  {n_stat}"""
         self.ast_g_pos_angle.append(pos_angle)
         self.ast_g_I.append(I)
         self.ast_g_lmn.append(lmn)
-        self.ast_g_radec.append(jnp.array([ra, dec]))
+        self.ast_g_radec.append(np.array([ra, dec]))
         self.n_g_ast += len(I)
         self.n_ast += len(I)
 
@@ -596,7 +596,7 @@ Number of stationary RFI :  {n_stat}"""
         self.ast_e_major.append(shape)
         self.ast_e_I.append(I)
         self.ast_e_lmn.append(lmn)
-        self.ast_e_radec.append(jnp.array([ra, dec]))
+        self.ast_e_radec.append(np.array([ra, dec]))
         self.n_e_ast += len(I)
         self.n_ast += len(I)
 
@@ -959,7 +959,7 @@ Number of stationary RFI :  {n_stat}"""
         self,
         path: str = "Observation.ms",
         overwrite: bool = False,
-        ds: xr.Dataset = None,
+        ds: Optional[xr.Dataset] = None,
     ):
         """
         Write the visibilities to disk using Measurement Set format.

{tabsim-0.0.2/tabsim/data/config_files → tabsim-0.0.4/tabsim/data/config}/sim_config_base.yaml

@@ -2,6 +2,8 @@
 # This is base simulation config that is loaded and then updated with your provided config.
 # Populated parameters here are the default values used if none are specified in your config.
 ###############################################################################################
+# Astronomical Sources
+#######################
 ast_sources:
 ##########################################
 # Exponential shaped astronomical sources
@@ -125,6 +127,9 @@ output:
   path: ./                    # Optional - Path to where the simulation should be saved
   prefix: null                # Optional - Prefix used in the simulation file name
   suffix: null                # Optional - Suffix used in the simulation file name
+##############
+# RFI sources
+##############
 rfi_sources:
 #######################################
 # Circular trajectory based satellites
@@ -164,7 +169,7 @@ rfi_sources:
 telescope:
   latitude: null              # Required - Latitude of the telescope location in decimal degrees. North is +ve
   longitude: null             # Required - Longitude of the telescope in decimal degrees. East from Greenwich meridian
-  elevation: null             # Required - Elevation of the telescope above the WGS84 Earth ellipsoid model in metres.
+  elevation: 0                # Required - Elevation of the telescope above the WGS84 Earth ellipsoid model in metres.
   dish_d: null                # Required - Dish diameter in metres
   enu_path: null              # Required if itrf_path is null - Path to the csv file of the antennas in East, North, Up frame, in metres, relative to the telescope location 
   itrf_path: null             # Required if enu_path is null - Path to the csv file contaning the antenna positions in International Terrestrial Reference Frame in metres.