lisaanalysistools 1.0.2__tar.gz → 1.0.4__tar.gz

{lisaanalysistools-1.0.2 → lisaanalysistools-1.0.4/LISAanalysistools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lisaanalysistools
-Version: 1.0.2
+Version: 1.0.4
 Home-page: https://github.com/mikekatz04/lisa-on-gpu
 Author: Michael Katz
 Author-email: mikekatz04@gmail.com
@@ -18,8 +18,9 @@ License-File: LICENSE
 # LISA Analysis Tools
 
 [![Doc badge](https://img.shields.io/badge/Docs-master-brightgreen)](https://mikekatz04.github.io/LISAanalysistools)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10930980.svg)](https://doi.org/10.5281/zenodo.10930980)
 
-LISA Analysis Tools is a package for performing LISA Data Analysis tasks, including building the LISA Global Fit. 
+LISA Analysis Tools is a package for performing LISA Data Analysis tasks, including building the LISA Global Fit.  
 
 ## 1 - Getting Started
 
@@ -59,16 +60,15 @@ Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduc
 
 We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/BlackHolePerturbationToolkit/FastEMRIWaveforms/tags).
 
-Current Version: 1.0.2
+Current Version: 1.0.4
 
 ## Authors/Developers
 
 * **Michael Katz**
-
-### Contibutors
-
 * Lorenzo Speri
 * Christian Chapman-Bird
+* Natalia Korsakova
+* Nikos Karnesis
 
 ## License
 
@@ -76,5 +76,20 @@ This project is licensed under the Apache License - see the [LICENSE.md](LICENSE
 
 ## Citation
 
-TODO.
+```
+@software{michael_katz_2024_10930980,
+  author       = {Michael Katz and
+                  CChapmanbird and
+                  Lorenzo Speri and
+                  Nikolaos Karnesis and
+                  Korsakova, Natalia},
+  title        = {mikekatz04/LISAanalysistools: First main release.},
+  month        = apr,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {v1.0.3},
+  doi          = {10.5281/zenodo.10930980},
+  url          = {https://doi.org/10.5281/zenodo.10930980}
+}
+```
 

{lisaanalysistools-1.0.2/LISAanalysistools.egg-info → lisaanalysistools-1.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lisaanalysistools
-Version: 1.0.2
+Version: 1.0.4
 Home-page: https://github.com/mikekatz04/lisa-on-gpu
 Author: Michael Katz
 Author-email: mikekatz04@gmail.com
@@ -18,8 +18,9 @@ License-File: LICENSE
 # LISA Analysis Tools
 
 [![Doc badge](https://img.shields.io/badge/Docs-master-brightgreen)](https://mikekatz04.github.io/LISAanalysistools)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10930980.svg)](https://doi.org/10.5281/zenodo.10930980)
 
-LISA Analysis Tools is a package for performing LISA Data Analysis tasks, including building the LISA Global Fit. 
+LISA Analysis Tools is a package for performing LISA Data Analysis tasks, including building the LISA Global Fit.  
 
 ## 1 - Getting Started
 
@@ -59,16 +60,15 @@ Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduc
 
 We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/BlackHolePerturbationToolkit/FastEMRIWaveforms/tags).
 
-Current Version: 1.0.2
+Current Version: 1.0.4
 
 ## Authors/Developers
 
 * **Michael Katz**
-
-### Contibutors
-
 * Lorenzo Speri
 * Christian Chapman-Bird
+* Natalia Korsakova
+* Nikos Karnesis
 
 ## License
 
@@ -76,5 +76,20 @@ This project is licensed under the Apache License - see the [LICENSE.md](LICENSE
 
 ## Citation
 
-TODO.
+```
+@software{michael_katz_2024_10930980,
+  author       = {Michael Katz and
+                  CChapmanbird and
+                  Lorenzo Speri and
+                  Nikolaos Karnesis and
+                  Korsakova, Natalia},
+  title        = {mikekatz04/LISAanalysistools: First main release.},
+  month        = apr,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {v1.0.3},
+  doi          = {10.5281/zenodo.10930980},
+  url          = {https://doi.org/10.5281/zenodo.10930980}
+}
+```
 

{lisaanalysistools-1.0.2 → lisaanalysistools-1.0.4}/README.md

@@ -1,8 +1,9 @@
 # LISA Analysis Tools
 
 [![Doc badge](https://img.shields.io/badge/Docs-master-brightgreen)](https://mikekatz04.github.io/LISAanalysistools)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10930980.svg)](https://doi.org/10.5281/zenodo.10930980)
 
-LISA Analysis Tools is a package for performing LISA Data Analysis tasks, including building the LISA Global Fit. 
+LISA Analysis Tools is a package for performing LISA Data Analysis tasks, including building the LISA Global Fit.  
 
 ## 1 - Getting Started
 
@@ -42,16 +43,15 @@ Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduc
 
 We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/BlackHolePerturbationToolkit/FastEMRIWaveforms/tags).
 
-Current Version: 1.0.2
+Current Version: 1.0.4
 
 ## Authors/Developers
 
 * **Michael Katz**
-
-### Contibutors
-
 * Lorenzo Speri
 * Christian Chapman-Bird
+* Natalia Korsakova
+* Nikos Karnesis
 
 ## License
 
@@ -59,5 +59,20 @@ This project is licensed under the Apache License - see the [LICENSE.md](LICENSE
 
 ## Citation
 
-TODO.
+```
+@software{michael_katz_2024_10930980,
+  author       = {Michael Katz and
+                  CChapmanbird and
+                  Lorenzo Speri and
+                  Nikolaos Karnesis and
+                  Korsakova, Natalia},
+  title        = {mikekatz04/LISAanalysistools: First main release.},
+  month        = apr,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {v1.0.3},
+  doi          = {10.5281/zenodo.10930980},
+  url          = {https://doi.org/10.5281/zenodo.10930980}
+}
+```
 

{lisaanalysistools-1.0.2 → lisaanalysistools-1.0.4}/lisatools/_version.py

@@ -1,4 +1,4 @@
-__version__ = '1.0.2'
+__version__ = '1.0.4'
 __copyright__ = "Michael L. Katz 2024"
 __name__ = "lisaanalysistools"
 __author__ = "Michael L. Katz"

{lisaanalysistools-1.0.2 → lisaanalysistools-1.0.4}/lisatools/analysiscontainer.py

@@ -1,13 +1,17 @@
+from __future__ import annotations
+
+
 import warnings
 from abc import ABC
 from typing import Any, Tuple, Optional, List
 
 import math
 import numpy as np
-from numpy.typing import ArrayLike
+
 from scipy import interpolate
 import matplotlib.pyplot as plt
 
+
 try:
     import cupy as cp
 
@@ -209,7 +213,7 @@ class AnalysisContainer:
         template: DataResidualArray,
         include_psd_info: bool = False,
         phase_maximize: bool = False,
-        **kwargs: dict
+        **kwargs: dict,
     ) -> float:
         """Calculate the Likelihood of a template against the data.
 
@@ -268,7 +272,7 @@ class AnalysisContainer:
             return noise_likelihood_term(self.sens_mat)
         elif source_only:
             return residual_source_likelihood_term(
-                self.data_res_arr, self.sens_mat, **kwargs
+                self.data_res_arr, psd=self.sens_mat, **kwargs
             )
         else:
             return residual_full_source_and_noise_likelihood(
@@ -278,11 +282,11 @@ class AnalysisContainer:
     def _calculate_signal_operation(
         self,
         calc: str,
-        *args: ArrayLike,
+        *args: Any,
         source_only: bool = False,
         waveform_kwargs: Optional[dict] = {},
         data_res_arr_kwargs: Optional[dict] = {},
-        **kwargs: dict
+        **kwargs: dict,
     ) -> float | complex:
         """Return the likelihood of a generated signal with the data.
 
@@ -328,11 +332,11 @@ class AnalysisContainer:
 
     def calculate_signal_likelihood(
         self,
-        *args: ArrayLike,
+        *args: Any,
         source_only: bool = False,
         waveform_kwargs: Optional[dict] = {},
         data_res_arr_kwargs: Optional[dict] = {},
-        **kwargs: dict
+        **kwargs: dict,
     ) -> float | complex:
         """Return the likelihood of a generated signal with the data.
 
@@ -355,16 +359,16 @@ class AnalysisContainer:
             source_only=source_only,
             waveform_kwargs=waveform_kwargs,
             data_res_arr_kwargs=data_res_arr_kwargs,
-            **kwargs
+            **kwargs,
         )
 
     def calculate_signal_inner_product(
         self,
-        *args: ArrayLike,
+        *args: Any,
         source_only: bool = False,
         waveform_kwargs: Optional[dict] = {},
         data_res_arr_kwargs: Optional[dict] = {},
-        **kwargs: dict
+        **kwargs: dict,
     ) -> float | complex:
         """Return the inner product of a generated signal with the data.
 
@@ -387,16 +391,16 @@ class AnalysisContainer:
             source_only=source_only,
             waveform_kwargs=waveform_kwargs,
             data_res_arr_kwargs=data_res_arr_kwargs,
-            **kwargs
+            **kwargs,
         )
 
     def calculate_signal_snr(
         self,
-        *args: ArrayLike,
+        *args: Any,
         source_only: bool = False,
         waveform_kwargs: Optional[dict] = {},
         data_res_arr_kwargs: Optional[dict] = {},
-        **kwargs: dict
+        **kwargs: dict,
     ) -> Tuple[float, float]:
         """Return the SNR of a generated signal with the data.
 
@@ -419,7 +423,7 @@ class AnalysisContainer:
             source_only=source_only,
             waveform_kwargs=waveform_kwargs,
             data_res_arr_kwargs=data_res_arr_kwargs,
-            **kwargs
+            **kwargs,
         )
 
     def eryn_likelihood_function(self, x, *args, **kwargs):

{lisaanalysistools-1.0.2 → lisaanalysistools-1.0.4}/lisatools/datacontainer.py

@@ -4,7 +4,6 @@ from typing import Any, Tuple, Optional, List
 
 import math
 import numpy as np
-from numpy.typing import ArrayLike
 from scipy import interpolate
 import matplotlib.pyplot as plt
 
@@ -36,7 +35,7 @@ class DataResidualArray:
         sens_mat: Input sensitivity list. The shape of the nested lists should represent the shape of the
             desired matrix. Each entry in the list must be an array, :class:`Sensitivity`-derived object,
             or a string corresponding to the :class:`Sensitivity` object.
-        **sens_kwargs: Keyword arguments to pass to :method:`Sensitivity.get_Sn`.
+        **sens_kwargs: Keyword arguments to pass to :func:`Sensitivity.get_Sn`.
 
     """
 

{lisaanalysistools-1.0.2 → lisaanalysistools-1.0.4}/lisatools/detector.py

@@ -22,7 +22,6 @@ class Orbits(ABC):
     Args:
         filename: File name. File should be in the style of LISAOrbits
 
-
     """
 
     def __init__(self, filename: str) -> None:
@@ -51,6 +50,7 @@ class Orbits(ABC):
         return [int(str(link_i)[1]) for link_i in self.LINKS]
 
     def _setup(self) -> None:
+        """Read in orbital data from file and store."""
         with self.open() as f:
             for key in f.attrs.keys():
                 setattr(self, key + "_base", f.attrs[key])
@@ -63,22 +63,33 @@ class Orbits(ABC):
     @filename.setter
     def filename(self, filename: str) -> None:
         """Set file name."""
+
         assert isinstance(filename, str)
+
+        # get path
         path_to_this_file = __file__.split("detector.py")[0]
+
+        # make sure orbit_files directory exists in the right place
         if not os.path.exists(path_to_this_file + "orbit_files/"):
             os.mkdir(path_to_this_file + "orbit_files/")
         path_to_this_file = path_to_this_file + "orbit_files/"
+
         if not os.path.exists(path_to_this_file + filename):
+            # download files from github if they are not there
             github_file = f"https://github.com/mikekatz04/LISAanalysistools/raw/main/lisatools/orbit_files/{filename}"
             r = requests.get(github_file)
+
+            # if not success
             if r.status_code != 200:
                 raise ValueError(
                     f"Cannot find {filename} within default files located at github.com/mikekatz04/LISAanalysistools/lisatools/orbit_files/."
                 )
 
+            # write the contents to a local file
             with open(path_to_this_file + filename, "wb") as f:
                 f.write(r.content)
 
+        # store
         self._filename = path_to_this_file + filename
 
     def open(self) -> h5py.File:
@@ -96,7 +107,7 @@ class Orbits(ABC):
 
     @property
     def t_base(self) -> np.ndarray:
-        """Light travel times along links from file."""
+        """Time array from file."""
         with self.open() as f:
             t_base = np.arange(self.size_base) * self.dt_base
         return t_base
@@ -117,14 +128,14 @@ class Orbits(ABC):
 
     @property
     def x_base(self) -> np.ndarray:
-        """Light travel times along links from file."""
+        """Spacecraft position from file."""
         with self.open() as f:
             x = f["tcb"]["x"][:]
         return x
 
     @property
     def v_base(self) -> np.ndarray:
-        """Light travel times along links from file."""
+        """Spacecraft velocities from file."""
         with self.open() as f:
             v = f["tcb"]["v"][:]
         return v
@@ -154,35 +165,35 @@ class Orbits(ABC):
 
     @property
     def n(self) -> np.ndarray:
-        """Light travel time."""
+        """Normal vectors along links."""
         self._check_configured()
         return self._n
 
     @n.setter
     def n(self, n: np.ndarray) -> np.ndarray:
-        """Set light travel time."""
+        """Set Normal vectors along links."""
         return self._n
 
     @property
     def x(self) -> np.ndarray:
-        """Light travel time."""
+        """Spacecraft positions."""
         self._check_configured()
         return self._x
 
     @x.setter
     def x(self, x: np.ndarray) -> np.ndarray:
-        """Set light travel time."""
+        """Set Spacecraft positions."""
         return self._x
 
     @property
     def v(self) -> np.ndarray:
-        """Light travel time."""
+        """Spacecraft velocities."""
         self._check_configured()
         return self._v
 
     @v.setter
     def v(self, v: np.ndarray) -> np.ndarray:
-        """Set light travel time."""
+        """Set Spacecraft velocities."""
         return self._v
 
     def configure(
@@ -290,6 +301,7 @@ class Orbits(ABC):
 
     @property
     def pycppdetector_args(self) -> tuple:
+        """args for the c++ class."""
         return self._pycppdetector_args
 
     @pycppdetector_args.setter
@@ -311,30 +323,81 @@ class Orbits(ABC):
     def get_light_travel_times(
         self, t: float | np.ndarray, link: int
     ) -> float | np.ndarray:
+        """Compute light travel time as a function of time.
+
+        Computes with the c++ backend.
+
+        Args:
+            t: Time array in seconds.
+            link: which link. Must be ``in self.LINKS``.
+
+        Returns:
+            Light travel times.
+
+        """
         return self.pycppdetector.get_light_travel_time(t, link)
 
     def get_normal_unit_vec(self, t: float | np.ndarray, link: int) -> np.ndarray:
+        """Compute link normal vector as a function of time.
+
+        Computes with the c++ backend.
+
+        Args:
+            t: Time array in seconds.
+            link: which link. Must be ``in self.LINKS``.
+
+        Returns:
+            Link normal vectors.
+
+        """
         return self.pycppdetector.get_normal_unit_vec(t, link)
 
     def get_pos(self, t: float | np.ndarray, sc: int) -> np.ndarray:
+        """Compute spacecraft position as a function of time.
+
+        Computes with the c++ backend.
+
+        Args:
+            t: Time array in seconds.
+            sc: which spacecraft. Must be ``in self.SC``.
+
+        Returns:
+            Spacecraft positions.
+
+        """
         return self.pycppdetector.get_pos(t, sc)
 
     @property
     def ptr(self) -> int:
-        """pointer to c-class"""
+        """pointer to c++ class"""
         return self.pycppdetector.ptr
 
 
 class EqualArmlengthOrbits(Orbits):
-    """Equal Armlength Orbits"""
+    """Equal Armlength Orbits
+
+    Orbit file: equalarmlength-orbits.h5
+
+    """
 
     def __init__(self):
-        # TODO: fix this up
         super().__init__("equalarmlength-orbits.h5")
 
 
+class ESAOrbits(Orbits):
+    """ESA Orbits
+
+    Orbit file: esa-trailing-orbits.h5
+
+    """
+
+    def __init__(self):
+        # TODO: fix this up
+        super().__init__("esa-trailing-orbits.h5")
+
+
 class DefaultOrbits(EqualArmlengthOrbits):
-    """Set default orbit class to Equal Arm Length orbits for now."""
+    """Set default orbit class to Equal Armlength orbits for now."""
 
     pass
 
@@ -343,11 +406,10 @@ class DefaultOrbits(EqualArmlengthOrbits):
 class LISAModelSettings:
     """Required LISA model settings:
 
-    TODO: rename these
-
     Args:
         Soms_d: OMS displacement noise.
         Sa_a: Acceleration noise.
+        orbits: Orbital information.
         name: Name of model.
 
     """
@@ -359,7 +421,16 @@ class LISAModelSettings:
 
 
 class LISAModel(LISAModelSettings, ABC):
-    """Model for the LISA Constellation"""
+    """Model for the LISA Constellation
+
+    This includes sensitivity information computed in
+    :module:`lisatools.sensitivity` and orbital information
+    contained in an :class:`Orbits` class object.
+
+    This class is used to house high-level methods useful
+    to various needed computations.
+
+    """
 
     def __str__(self) -> str:
         out = "LISA Constellation Configurations Settings:\n"
@@ -368,6 +439,7 @@ class LISAModel(LISAModelSettings, ABC):
         return out
 
 
+# defaults
 scirdv1 = LISAModel((15.0e-12) ** 2, (3.0e-15) ** 2, DefaultOrbits(), "scirdv1")
 proposal = LISAModel((10.0e-12) ** 2, (3.0e-15) ** 2, DefaultOrbits(), "proposal")
 mrdv1 = LISAModel((10.0e-12) ** 2, (2.4e-15) ** 2, DefaultOrbits(), "mrdv1")

{lisaanalysistools-1.0.2 → lisaanalysistools-1.0.4}/lisatools/diagnostic.py

@@ -2,7 +2,6 @@ import warnings
 from types import ModuleType, NoneType
 from typing import Optional, Any, Tuple, List
 
-from numpy.typing import ArrayLike
 import matplotlib.pyplot as plt
 
 from eryn.utils import TransformContainer
@@ -387,7 +386,7 @@ def snr(
 def h_var_p_eps(
     step: float,
     waveform_model: callable,
-    params: ArrayLike,
+    params: np.ndarray | list,
     index: int,
     parameter_transforms: Optional[TransformContainer] = None,
     waveform_args: Optional[tuple] = (),
@@ -499,8 +498,8 @@ def dh_dlambda(
 def info_matrix(
     eps: float | np.ndarray,
     waveform_model: callable,
-    params: ArrayLike,
-    deriv_inds: Optional[ArrayLike] = None,
+    params: np.ndarray | list,
+    deriv_inds: Optional[np.ndarray | list] = None,
     inner_product_kwargs: Optional[dict] = {},
     return_derivs: Optional[bool] = False,
     **kwargs: dict,
@@ -793,7 +792,7 @@ def cutler_vallisneri_bias(
     eps: float | np.ndarray,
     input_diagnostics: Optional[dict] = None,
     info_mat: Optional[np.ndarray] = None,
-    deriv_inds: Optional[ArrayLike] = None,
+    deriv_inds: Optional[np.ndarray | list] = None,
     return_derivs: Optional[bool] = False,
     return_cov: Optional[bool] = False,
     parameter_transforms: Optional[TransformContainer] = None,