Compare commits
1 Commits
| Author | SHA1 | Date | |
|---|---|---|---|
1fc1ea66ea
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2
.gitignore
vendored
2
.gitignore
vendored
@ -70,7 +70,7 @@ instance/
|
||||
.scrapy
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||||
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||||
# Sphinx documentation
|
||||
docs/_build/
|
||||
docs/build/
|
||||
|
||||
# PyBuilder
|
||||
.pybuilder/
|
||||
|
||||
20
docs/Makefile
Normal file
20
docs/Makefile
Normal file
@ -0,0 +1,20 @@
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||||
# Minimal makefile for Sphinx documentation
|
||||
#
|
||||
|
||||
# You can set these variables from the command line, and also
|
||||
# from the environment for the first two.
|
||||
SPHINXOPTS ?=
|
||||
SPHINXBUILD ?= sphinx-build
|
||||
SOURCEDIR = source
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||||
BUILDDIR = build
|
||||
|
||||
# Put it first so that "make" without argument is like "make help".
|
||||
help:
|
||||
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
|
||||
|
||||
.PHONY: help Makefile
|
||||
|
||||
# Catch-all target: route all unknown targets to Sphinx using the new
|
||||
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
|
||||
%: Makefile
|
||||
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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||||
35
docs/make.bat
Normal file
35
docs/make.bat
Normal file
@ -0,0 +1,35 @@
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||||
@ECHO OFF
|
||||
|
||||
pushd %~dp0
|
||||
|
||||
REM Command file for Sphinx documentation
|
||||
|
||||
if "%SPHINXBUILD%" == "" (
|
||||
set SPHINXBUILD=sphinx-build
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||||
)
|
||||
set SOURCEDIR=source
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||||
set BUILDDIR=build
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||||
|
||||
if "%1" == "" goto help
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||||
|
||||
%SPHINXBUILD% >NUL 2>NUL
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||||
if errorlevel 9009 (
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||||
echo.
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||||
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
|
||||
echo.installed, then set the SPHINXBUILD environment variable to point
|
||||
echo.to the full path of the 'sphinx-build' executable. Alternatively you
|
||||
echo.may add the Sphinx directory to PATH.
|
||||
echo.
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||||
echo.If you don't have Sphinx installed, grab it from
|
||||
echo.http://sphinx-doc.org/
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||||
exit /b 1
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||||
)
|
||||
|
||||
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
|
||||
|
||||
:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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||||
|
||||
:end
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popd
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55
docs/source/conf.py
Normal file
55
docs/source/conf.py
Normal file
@ -0,0 +1,55 @@
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||||
# Configuration file for the Sphinx documentation builder.
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||||
#
|
||||
# This file only contains a selection of the most common options. For a full
|
||||
# list see the documentation:
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||||
# https://www.sphinx-doc.org/en/master/usage/configuration.html
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||||
|
||||
# -- Path setup --------------------------------------------------------------
|
||||
|
||||
# If extensions (or modules to document with autodoc) are in another directory,
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||||
# add these directories to sys.path here. If the directory is relative to the
|
||||
# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import os
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import sys
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sys.path.insert(0, os.path.abspath('.'))
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# -- Project information -----------------------------------------------------
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project = 'pathfinder'
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copyright = '2021, Deepak Mallubhotla'
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author = 'Deepak Mallubhotla'
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||||
|
||||
|
||||
# -- General configuration ---------------------------------------------------
|
||||
|
||||
# Add any Sphinx extension module names here, as strings. They can be
|
||||
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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||||
# ones.
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||||
extensions = [
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'sphinx.ext.autodoc',
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||||
'sphinx.ext.coverage',
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||||
'sphinx.ext.napoleon'
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||||
]
|
||||
|
||||
# Add any paths that contain templates here, relative to this directory.
|
||||
templates_path = ['_templates']
|
||||
|
||||
# List of patterns, relative to source directory, that match files and
|
||||
# directories to ignore when looking for source files.
|
||||
# This pattern also affects html_static_path and html_extra_path.
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||||
exclude_patterns = []
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||||
|
||||
|
||||
# -- Options for HTML output -------------------------------------------------
|
||||
|
||||
# The theme to use for HTML and HTML Help pages. See the documentation for
|
||||
# a list of builtin themes.
|
||||
#
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||||
html_theme = 'alabaster'
|
||||
|
||||
# Add any paths that contain custom static files (such as style sheets) here,
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||||
# relative to this directory. They are copied after the builtin static files,
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||||
# so a file named "default.css" will overwrite the builtin "default.css".
|
||||
html_static_path = ['_static']
|
||||
15
docs/source/index.rst
Normal file
15
docs/source/index.rst
Normal file
@ -0,0 +1,15 @@
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||||
Welcome to pathfinder's documentation!
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||||
======================================
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||||
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||||
.. toctree::
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||||
:maxdepth: 2
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||||
:caption: Contents:
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||||
|
||||
modules
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||||
|
||||
Indices and tables
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||||
==================
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||||
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||||
* :ref:`genindex`
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||||
* :ref:`modindex`
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||||
* :ref:`search`
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||||
7
docs/source/modules.rst
Normal file
7
docs/source/modules.rst
Normal file
@ -0,0 +1,7 @@
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pathfinder
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||||
==========
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||||
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||||
.. toctree::
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:maxdepth: 4
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||||
pathfinder
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||||
37
docs/source/pathfinder.model.rst
Normal file
37
docs/source/pathfinder.model.rst
Normal file
@ -0,0 +1,37 @@
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||||
pathfinder.model package
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||||
========================
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||||
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Submodules
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----------
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||||
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||||
pathfinder.model.dot module
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||||
---------------------------
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||||
|
||||
.. automodule:: pathfinder.model.dot
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
pathfinder.model.model module
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||||
-----------------------------
|
||||
|
||||
.. automodule:: pathfinder.model.model
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||||
:members:
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||||
:undoc-members:
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||||
:show-inheritance:
|
||||
|
||||
pathfinder.model.staticdipole module
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||||
------------------------------------
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||||
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||||
.. automodule:: pathfinder.model.staticdipole
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Module contents
|
||||
---------------
|
||||
|
||||
.. automodule:: pathfinder.model
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
29
docs/source/pathfinder.rst
Normal file
29
docs/source/pathfinder.rst
Normal file
@ -0,0 +1,29 @@
|
||||
pathfinder package
|
||||
==================
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
pathfinder.model
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
pathfinder.meta module
|
||||
----------------------
|
||||
|
||||
.. automodule:: pathfinder.meta
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Module contents
|
||||
---------------
|
||||
|
||||
.. automodule:: pathfinder
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@ -0,0 +1,5 @@
|
||||
from pathfinder.model.dot import DotMeasurement
|
||||
from pathfinder.model.model import DotDipoleModel
|
||||
from pathfinder.model.staticdipole import StaticDipole
|
||||
|
||||
__all__ = ['DotMeasurement', 'DotDipoleModel', 'StaticDipole']
|
||||
@ -2,6 +2,8 @@ from dataclasses import dataclass
|
||||
import numpy
|
||||
import numpy.typing
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||||
|
||||
from pathfinder.model.staticdipole import StaticDipole
|
||||
|
||||
|
||||
@dataclass
|
||||
class DotMeasurement():
|
||||
@ -31,13 +33,15 @@ class DotMeasurement():
|
||||
|
||||
Returns
|
||||
----------
|
||||
Returns the voltage from that dipole at the point.
|
||||
float
|
||||
The voltage from that dipole at the point.
|
||||
'''
|
||||
p = pt[0:3] # hardcoded here because chances
|
||||
s = pt[3:6] # are we'll only ever work in 3d.
|
||||
|
||||
diff = self.r - s
|
||||
return p.dot(diff) / (numpy.linalg.norm(diff)**3)
|
||||
dipole = StaticDipole(p, s)
|
||||
|
||||
return dipole.v_at_position(self.r)
|
||||
|
||||
def cost(self, pts: numpy.ndarray) -> float:
|
||||
# 6 because dipole in 3d has 6 degrees of freedom.
|
||||
@ -1,7 +1,7 @@
|
||||
from typing import Callable, Sequence
|
||||
import numpy
|
||||
import scipy.optimize
|
||||
from pathfinder.model.static.dot import DotMeasurement
|
||||
|
||||
from pathfinder.model.dot import DotMeasurement
|
||||
|
||||
|
||||
class DotDipoleModel():
|
||||
@ -35,10 +35,3 @@ class DotDipoleModel():
|
||||
return numpy.array([dot.jac(pts) for dot in self.dots])
|
||||
|
||||
return jac_to_return
|
||||
|
||||
def sol(self, initial_dipole=(0.1, 0.1, 0.1), initial_position=(.1, .1, .1), use_root=True):
|
||||
initial = numpy.tile(numpy.append(initial_dipole, initial_position), self.n)
|
||||
if use_root and self.m == 6 * self.n:
|
||||
# We are perfectly specified
|
||||
return scipy.optimize.root(self.costs(), initial, jac=self.jac(), tol=1e-12)
|
||||
return scipy.optimize.least_squares(self.costs(), initial, jac=self.jac(), ftol=1e-15, gtol=3e-16)
|
||||
@ -1,5 +0,0 @@
|
||||
from pathfinder.model.oscillating.oscillating_dipole import OscillatingDipole, OscillatingDipoleArrangement
|
||||
from pathfinder.model.oscillating.dot import DotMeasurement
|
||||
from pathfinder.model.oscillating.model import DotOscillatingDipoleModel
|
||||
|
||||
__all__ = ['DotMeasurement', 'OscillatingDipole', 'OscillatingDipoleArrangement', 'DotOscillatingDipoleModel']
|
||||
@ -1,87 +0,0 @@
|
||||
from dataclasses import dataclass
|
||||
import numpy
|
||||
import numpy.typing
|
||||
|
||||
|
||||
@dataclass
|
||||
class DotMeasurement():
|
||||
'''
|
||||
Representation of a dot measuring oscillating dipoles.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
v : float
|
||||
The voltage measured at the dot.
|
||||
r : numpy.ndarray
|
||||
The position of the dot.
|
||||
f : float
|
||||
The measurement frequency.
|
||||
'''
|
||||
v: float
|
||||
r: numpy.ndarray
|
||||
f: float
|
||||
|
||||
def __post_init__(self) -> None:
|
||||
self.r = numpy.array(self.r)
|
||||
|
||||
def v_for_point(self, pt: numpy.ndarray) -> float:
|
||||
'''
|
||||
Returns the voltage for an oscillating dipole represented as a phase space point.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
pt: A length 7 numpy array representing a dipole, as (px, py, pz, sx, sy, sz, w).
|
||||
|
||||
Returns
|
||||
----------
|
||||
Returns the voltage from that dipole at the point.
|
||||
'''
|
||||
p = pt[0:3] # hardcoded here because chances
|
||||
s = pt[3:6] # are we'll only ever work in 3d.
|
||||
w = pt[6]
|
||||
|
||||
return (self._alpha(p, s))**2 * self._b(w)
|
||||
|
||||
def _alpha(self, p: numpy.ndarray, s: numpy.ndarray) -> float:
|
||||
diff = self.r - s
|
||||
return p.dot(diff) / (numpy.linalg.norm(diff)**3)
|
||||
|
||||
def _b(self, w: float) -> float:
|
||||
return (1 / numpy.pi) * (w / (self.f**2 + w**2))
|
||||
|
||||
def cost(self, pts: numpy.ndarray) -> float:
|
||||
# 7 because dipole in 3d has 7 degrees of freedom.
|
||||
pt_length = 7
|
||||
# creates numpy.ndarrays in groups of pt_length.
|
||||
# Will throw problems for irregular points, but that's okay for now.
|
||||
chunked_pts = [pts[i: i + pt_length] for i in range(0, len(pts), pt_length)]
|
||||
return sum(self.v_for_point(pt) for pt in chunked_pts) - self.v
|
||||
|
||||
def jac_pt(self, pt: numpy.ndarray) -> numpy.ndarray:
|
||||
p = pt[0:3] # hardcoded here because chances
|
||||
s = pt[3:6] # are we'll only ever work in 3d.
|
||||
w = pt[6]
|
||||
|
||||
diff = self.r - s
|
||||
alpha = self._alpha(p, s)
|
||||
b = self._b(w)
|
||||
|
||||
p_divs = 2 * alpha * diff / (numpy.linalg.norm(diff)**3) * b
|
||||
|
||||
r_divs = (-p / (numpy.linalg.norm(diff)**3) + 3 * p.dot(diff) * diff / (numpy.linalg.norm(diff)**5)) * 2 * alpha * b
|
||||
|
||||
f2 = self.f**2
|
||||
w2 = w**2
|
||||
|
||||
w_div = alpha**2 * (1 / numpy.pi) * ((f2 - w2) / ((f2 + w2)**2))
|
||||
|
||||
return numpy.concatenate((p_divs, r_divs, w_div), axis=None)
|
||||
|
||||
def jac(self, pts: numpy.ndarray) -> numpy.ndarray:
|
||||
# 7 because oscillating dipole in 3d has 7 degrees of freedom.
|
||||
pt_length = 7
|
||||
# creates numpy.ndarrays in groups of pt_length.
|
||||
# Will throw problems for irregular points, but that's okay for now.
|
||||
chunked_pts = [pts[i: i + pt_length] for i in range(0, len(pts), pt_length)]
|
||||
|
||||
return numpy.append([], [self.jac_pt(pt) for pt in chunked_pts])
|
||||
@ -1,45 +0,0 @@
|
||||
from typing import Callable, Sequence
|
||||
import numpy
|
||||
import scipy.optimize
|
||||
from pathfinder.model.oscillating.dot import DotMeasurement
|
||||
import pathfinder.model.oscillating.util
|
||||
|
||||
|
||||
class DotOscillatingDipoleModel():
|
||||
'''
|
||||
Model of n static oscillating with a collection of voltage measurements
|
||||
at dots at different positions and frequencies.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
dots : Sequence[DotMeasurement]
|
||||
A collection of dots representing a series of measured noise spectrum values.
|
||||
n: int
|
||||
The number of dipoles to assume.
|
||||
'''
|
||||
def __init__(self, dots: Sequence[DotMeasurement], n: int) -> None:
|
||||
self.dots = dots
|
||||
self.m = len(dots)
|
||||
self.n = n
|
||||
|
||||
def __repr__(self) -> str:
|
||||
return f'DotOscillatingDipoleModel({repr(list(self.dots))}, {self.n})'
|
||||
|
||||
def costs(self) -> Callable[[numpy.ndarray], numpy.ndarray]:
|
||||
def costs_to_return(pt: numpy.ndarray) -> numpy.ndarray:
|
||||
return numpy.array([dot.cost(pt) for dot in self.dots])
|
||||
|
||||
return costs_to_return
|
||||
|
||||
def jac(self) -> Callable[[numpy.ndarray], numpy.ndarray]:
|
||||
def jac_to_return(pts: numpy.ndarray) -> numpy.ndarray:
|
||||
return numpy.array([dot.jac(pts) for dot in self.dots])
|
||||
|
||||
return jac_to_return
|
||||
|
||||
def sol(self, initial_dipole=(0.1, 0.1, 0.1), initial_position=(.1, .1, .1), initial_frequency=1, use_root=True):
|
||||
initial = numpy.tile(numpy.concatenate((initial_dipole, initial_position, initial_frequency), axis=None), self.n)
|
||||
|
||||
result = scipy.optimize.least_squares(self.costs(), initial, jac=self.jac(), ftol=1e-15, gtol=3e-16)
|
||||
result.pathfinder_x = pathfinder.model.oscillating.util.normalize_oscillating_dipole_list(result.x)
|
||||
return result
|
||||
@ -1,77 +0,0 @@
|
||||
from dataclasses import dataclass
|
||||
import numpy
|
||||
import numpy.typing
|
||||
from typing import Sequence, List, Tuple
|
||||
from pathfinder.model.oscillating.dot import DotMeasurement
|
||||
|
||||
|
||||
DotInput = Tuple[numpy.typing.ArrayLike, float]
|
||||
|
||||
|
||||
@dataclass
|
||||
class OscillatingDipole():
|
||||
'''
|
||||
Representation of an oscilltaing dipole, either known or guessed.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
p : numpy.ndarray
|
||||
The oscillating dipole moment, with overall sign arbitrary.
|
||||
s : numpy.ndarray
|
||||
The position of the dipole.
|
||||
w : float
|
||||
The oscillation frequency.
|
||||
'''
|
||||
p: numpy.ndarray
|
||||
s: numpy.ndarray
|
||||
w: float
|
||||
|
||||
def __post_init__(self) -> None:
|
||||
'''
|
||||
Coerce the inputs into numpy arrays.
|
||||
'''
|
||||
self.p = numpy.array(self.p)
|
||||
self.s = numpy.array(self.s)
|
||||
|
||||
def s_at_position(self, r: numpy.ndarray, f: float) -> float:
|
||||
'''
|
||||
Returns the noise potential at a point r, at some frequency f.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
r : numpy.ndarray
|
||||
The position of the dot.
|
||||
f : float
|
||||
The dot frequency to sample.
|
||||
'''
|
||||
return (self._alpha(r))**2 * self._b(f)
|
||||
|
||||
def _alpha(self, r: numpy.ndarray) -> float:
|
||||
diff = r - self.s
|
||||
return self.p.dot(diff) / (numpy.linalg.norm(diff)**3)
|
||||
|
||||
def _b(self, f: float) -> float:
|
||||
return (1 / numpy.pi) * (self.w / (f**2 + self.w**2))
|
||||
|
||||
|
||||
class OscillatingDipoleArrangement():
|
||||
'''
|
||||
A collection of oscillating dipoles, which we are interested in being able to characterise.
|
||||
|
||||
Parameters
|
||||
--------
|
||||
dipoles : Sequence[OscillatingDipole]
|
||||
'''
|
||||
def __init__(self, dipoles: Sequence[OscillatingDipole]):
|
||||
self.dipoles = dipoles
|
||||
|
||||
def get_dot_measurement(self, dot_input: DotInput) -> DotMeasurement:
|
||||
r = numpy.array(dot_input[0])
|
||||
f = dot_input[1]
|
||||
return DotMeasurement(sum([dipole.s_at_position(r, f) for dipole in self.dipoles]), r, f)
|
||||
|
||||
def get_dot_measurements(self, dot_inputs: Sequence[DotInput]) -> List[DotMeasurement]:
|
||||
'''
|
||||
For a series of points, each with three coordinates and a frequency, return a list of the corresponding DotMeasurements.
|
||||
'''
|
||||
return [self.get_dot_measurement(dot_input) for dot_input in dot_inputs]
|
||||
@ -1,19 +0,0 @@
|
||||
import numpy
|
||||
import operator
|
||||
|
||||
|
||||
# flips px, py, pz
|
||||
SIGN_ARRAY = numpy.array((-1, -1, -1, 1, 1, 1, 1))
|
||||
|
||||
|
||||
def flip_chunk_to_positive_px(pt: numpy.ndarray) -> numpy.ndarray:
|
||||
if pt[0] > 0:
|
||||
return pt
|
||||
else:
|
||||
return SIGN_ARRAY * pt
|
||||
|
||||
|
||||
def normalize_oscillating_dipole_list(pts: numpy.ndarray) -> numpy.ndarray:
|
||||
pt_length = 7
|
||||
chunked_pts = [flip_chunk_to_positive_px(pts[i: i + pt_length]) for i in range(0, len(pts), pt_length)]
|
||||
return numpy.concatenate(sorted(chunked_pts, key=lambda x: tuple(round(val, 3) for val in operator.itemgetter(0, 1, 2, 3, 4, 5, 6)(x))), axis=None)
|
||||
@ -1,5 +0,0 @@
|
||||
from pathfinder.model.static.dot import DotMeasurement
|
||||
from pathfinder.model.static.model import DotDipoleModel
|
||||
from pathfinder.model.static.staticdipole import StaticDipoleArrangement, StaticDipole
|
||||
|
||||
__all__ = ['DotMeasurement', 'DotDipoleModel', 'StaticDipoleArrangement', 'StaticDipole']
|
||||
@ -1,58 +0,0 @@
|
||||
from dataclasses import dataclass
|
||||
import numpy
|
||||
import numpy.typing
|
||||
from typing import Sequence, List
|
||||
from pathfinder.model.static.dot import DotMeasurement
|
||||
|
||||
|
||||
@dataclass
|
||||
class StaticDipole():
|
||||
'''
|
||||
Representation of a static dipoles, either known or guessed.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
p : numpy.ndarray
|
||||
The static dipole moment.
|
||||
s : numpy.ndarray
|
||||
The position of the dipole.
|
||||
'''
|
||||
p: numpy.ndarray
|
||||
s: numpy.ndarray
|
||||
|
||||
def __post_init__(self) -> None:
|
||||
'''
|
||||
Coerce the inputs into numpy arrays.
|
||||
'''
|
||||
self.p = numpy.array(self.p)
|
||||
self.s = numpy.array(self.s)
|
||||
|
||||
def v_at_position(self, r: numpy.ndarray) -> float:
|
||||
'''
|
||||
Mirrors the same function in pathfinder.model.dot.
|
||||
'''
|
||||
diff = r - self.s
|
||||
return self.p.dot(diff) / (numpy.linalg.norm(diff)**3)
|
||||
|
||||
|
||||
class StaticDipoleArrangement():
|
||||
'''
|
||||
A collection of static dipoles, which we are interested in being able to characterise.
|
||||
|
||||
Parameters
|
||||
--------
|
||||
dipoles : Sequence[StaticDipole]
|
||||
'''
|
||||
def __init__(self, dipoles):
|
||||
self.dipoles = dipoles
|
||||
|
||||
def get_dot_measurement(self, dot_position: numpy.typing.ArrayLike) -> DotMeasurement:
|
||||
r = numpy.array(dot_position)
|
||||
return DotMeasurement(sum([dipole.v_at_position(r) for dipole in self.dipoles]), r)
|
||||
|
||||
def get_dot_measurements(self, dot_positions: Sequence[numpy.typing.ArrayLike]) -> List[DotMeasurement]:
|
||||
'''
|
||||
For a series of points, each with three coordinates, return
|
||||
'''
|
||||
|
||||
return [self.get_dot_measurement(dot_position) for dot_position in dot_positions]
|
||||
31
pathfinder/model/staticdipole.py
Normal file
31
pathfinder/model/staticdipole.py
Normal file
@ -0,0 +1,31 @@
|
||||
from dataclasses import dataclass
|
||||
import numpy
|
||||
import numpy.typing
|
||||
|
||||
|
||||
@dataclass
|
||||
class StaticDipole():
|
||||
'''
|
||||
Representation of a static dipoles, either known or guessed.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
p : numpy.ndarray
|
||||
The static dipole moment.
|
||||
s : numpy.ndarray
|
||||
The position of the dipole.
|
||||
'''
|
||||
p: numpy.ndarray
|
||||
s: numpy.ndarray
|
||||
|
||||
def __post_init__(self) -> None:
|
||||
'''
|
||||
Coerce the inputs into numpy arrays.
|
||||
'''
|
||||
self.p = numpy.array(self.p)
|
||||
self.s = numpy.array(self.s)
|
||||
|
||||
def v_at_position(self, r: numpy.typing.ArrayLike) -> float:
|
||||
|
||||
diff = r - self.s
|
||||
return self.p.dot(diff) / (numpy.linalg.norm(diff)**3)
|
||||
461
poetry.lock
generated
461
poetry.lock
generated
@ -1,3 +1,11 @@
|
||||
[[package]]
|
||||
name = "alabaster"
|
||||
version = "0.7.12"
|
||||
description = "A configurable sidebar-enabled Sphinx theme"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = "*"
|
||||
|
||||
[[package]]
|
||||
name = "atomicwrites"
|
||||
version = "1.4.0"
|
||||
@ -20,6 +28,36 @@ docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
|
||||
tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
|
||||
tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
|
||||
|
||||
[[package]]
|
||||
name = "babel"
|
||||
version = "2.9.1"
|
||||
description = "Internationalization utilities"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
|
||||
|
||||
[package.dependencies]
|
||||
pytz = ">=2015.7"
|
||||
|
||||
[[package]]
|
||||
name = "certifi"
|
||||
version = "2021.5.30"
|
||||
description = "Python package for providing Mozilla's CA Bundle."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = "*"
|
||||
|
||||
[[package]]
|
||||
name = "charset-normalizer"
|
||||
version = "2.0.4"
|
||||
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.5.0"
|
||||
|
||||
[package.extras]
|
||||
unicode_backport = ["unicodedata2"]
|
||||
|
||||
[[package]]
|
||||
name = "colorama"
|
||||
version = "0.4.4"
|
||||
@ -39,6 +77,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
|
||||
[package.extras]
|
||||
toml = ["toml"]
|
||||
|
||||
[[package]]
|
||||
name = "docutils"
|
||||
version = "0.17.1"
|
||||
description = "Docutils -- Python Documentation Utilities"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
|
||||
|
||||
[[package]]
|
||||
name = "flake8"
|
||||
version = "3.9.2"
|
||||
@ -52,6 +98,22 @@ mccabe = ">=0.6.0,<0.7.0"
|
||||
pycodestyle = ">=2.7.0,<2.8.0"
|
||||
pyflakes = ">=2.3.0,<2.4.0"
|
||||
|
||||
[[package]]
|
||||
name = "idna"
|
||||
version = "3.2"
|
||||
description = "Internationalized Domain Names in Applications (IDNA)"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.5"
|
||||
|
||||
[[package]]
|
||||
name = "imagesize"
|
||||
version = "1.2.0"
|
||||
description = "Getting image size from png/jpeg/jpeg2000/gif file"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
|
||||
|
||||
[[package]]
|
||||
name = "iniconfig"
|
||||
version = "1.1.1"
|
||||
@ -60,6 +122,28 @@ category = "dev"
|
||||
optional = false
|
||||
python-versions = "*"
|
||||
|
||||
[[package]]
|
||||
name = "jinja2"
|
||||
version = "3.0.1"
|
||||
description = "A very fast and expressive template engine."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.6"
|
||||
|
||||
[package.dependencies]
|
||||
MarkupSafe = ">=2.0"
|
||||
|
||||
[package.extras]
|
||||
i18n = ["Babel (>=2.7)"]
|
||||
|
||||
[[package]]
|
||||
name = "markupsafe"
|
||||
version = "2.0.1"
|
||||
description = "Safely add untrusted strings to HTML/XML markup."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.6"
|
||||
|
||||
[[package]]
|
||||
name = "mccabe"
|
||||
version = "0.6.1"
|
||||
@ -78,7 +162,7 @@ python-versions = ">=3.5"
|
||||
|
||||
[[package]]
|
||||
name = "mypy"
|
||||
version = "0.910"
|
||||
version = "0.790"
|
||||
description = "Optional static typing for Python"
|
||||
category = "dev"
|
||||
optional = false
|
||||
@ -86,12 +170,11 @@ python-versions = ">=3.5"
|
||||
|
||||
[package.dependencies]
|
||||
mypy-extensions = ">=0.4.3,<0.5.0"
|
||||
toml = "*"
|
||||
typed-ast = ">=1.4.0,<1.5.0"
|
||||
typing-extensions = ">=3.7.4"
|
||||
|
||||
[package.extras]
|
||||
dmypy = ["psutil (>=4.0)"]
|
||||
python2 = ["typed-ast (>=1.4.0,<1.5.0)"]
|
||||
|
||||
[[package]]
|
||||
name = "mypy-extensions"
|
||||
@ -155,6 +238,14 @@ category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
|
||||
|
||||
[[package]]
|
||||
name = "pygments"
|
||||
version = "2.10.0"
|
||||
description = "Pygments is a syntax highlighting package written in Python."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.5"
|
||||
|
||||
[[package]]
|
||||
name = "pyparsing"
|
||||
version = "2.4.7"
|
||||
@ -200,6 +291,32 @@ toml = "*"
|
||||
[package.extras]
|
||||
testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
|
||||
|
||||
[[package]]
|
||||
name = "pytz"
|
||||
version = "2021.1"
|
||||
description = "World timezone definitions, modern and historical"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = "*"
|
||||
|
||||
[[package]]
|
||||
name = "requests"
|
||||
version = "2.26.0"
|
||||
description = "Python HTTP for Humans."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
|
||||
|
||||
[package.dependencies]
|
||||
certifi = ">=2017.4.17"
|
||||
charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""}
|
||||
idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""}
|
||||
urllib3 = ">=1.21.1,<1.27"
|
||||
|
||||
[package.extras]
|
||||
socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"]
|
||||
use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
|
||||
|
||||
[[package]]
|
||||
name = "scipy"
|
||||
version = "1.5.4"
|
||||
@ -211,6 +328,116 @@ python-versions = ">=3.6"
|
||||
[package.dependencies]
|
||||
numpy = ">=1.14.5"
|
||||
|
||||
[[package]]
|
||||
name = "snowballstemmer"
|
||||
version = "2.1.0"
|
||||
description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = "*"
|
||||
|
||||
[[package]]
|
||||
name = "sphinx"
|
||||
version = "4.1.2"
|
||||
description = "Python documentation generator"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.6"
|
||||
|
||||
[package.dependencies]
|
||||
alabaster = ">=0.7,<0.8"
|
||||
babel = ">=1.3"
|
||||
colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
|
||||
docutils = ">=0.14,<0.18"
|
||||
imagesize = "*"
|
||||
Jinja2 = ">=2.3"
|
||||
packaging = "*"
|
||||
Pygments = ">=2.0"
|
||||
requests = ">=2.5.0"
|
||||
snowballstemmer = ">=1.1"
|
||||
sphinxcontrib-applehelp = "*"
|
||||
sphinxcontrib-devhelp = "*"
|
||||
sphinxcontrib-htmlhelp = ">=2.0.0"
|
||||
sphinxcontrib-jsmath = "*"
|
||||
sphinxcontrib-qthelp = "*"
|
||||
sphinxcontrib-serializinghtml = ">=1.1.5"
|
||||
|
||||
[package.extras]
|
||||
docs = ["sphinxcontrib-websupport"]
|
||||
lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.900)", "docutils-stubs", "types-typed-ast", "types-pkg-resources", "types-requests"]
|
||||
test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"]
|
||||
|
||||
[[package]]
|
||||
name = "sphinxcontrib-applehelp"
|
||||
version = "1.0.2"
|
||||
description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.5"
|
||||
|
||||
[package.extras]
|
||||
lint = ["flake8", "mypy", "docutils-stubs"]
|
||||
test = ["pytest"]
|
||||
|
||||
[[package]]
|
||||
name = "sphinxcontrib-devhelp"
|
||||
version = "1.0.2"
|
||||
description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.5"
|
||||
|
||||
[package.extras]
|
||||
lint = ["flake8", "mypy", "docutils-stubs"]
|
||||
test = ["pytest"]
|
||||
|
||||
[[package]]
|
||||
name = "sphinxcontrib-htmlhelp"
|
||||
version = "2.0.0"
|
||||
description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.6"
|
||||
|
||||
[package.extras]
|
||||
lint = ["flake8", "mypy", "docutils-stubs"]
|
||||
test = ["pytest", "html5lib"]
|
||||
|
||||
[[package]]
|
||||
name = "sphinxcontrib-jsmath"
|
||||
version = "1.0.1"
|
||||
description = "A sphinx extension which renders display math in HTML via JavaScript"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.5"
|
||||
|
||||
[package.extras]
|
||||
test = ["pytest", "flake8", "mypy"]
|
||||
|
||||
[[package]]
|
||||
name = "sphinxcontrib-qthelp"
|
||||
version = "1.0.3"
|
||||
description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.5"
|
||||
|
||||
[package.extras]
|
||||
lint = ["flake8", "mypy", "docutils-stubs"]
|
||||
test = ["pytest"]
|
||||
|
||||
[[package]]
|
||||
name = "sphinxcontrib-serializinghtml"
|
||||
version = "1.1.5"
|
||||
description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=3.5"
|
||||
|
||||
[package.extras]
|
||||
lint = ["flake8", "mypy", "docutils-stubs"]
|
||||
test = ["pytest"]
|
||||
|
||||
[[package]]
|
||||
name = "toml"
|
||||
version = "0.10.2"
|
||||
@ -219,6 +446,14 @@ category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
|
||||
|
||||
[[package]]
|
||||
name = "typed-ast"
|
||||
version = "1.4.3"
|
||||
description = "a fork of Python 2 and 3 ast modules with type comment support"
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = "*"
|
||||
|
||||
[[package]]
|
||||
name = "typing-extensions"
|
||||
version = "3.10.0.0"
|
||||
@ -227,12 +462,29 @@ category = "dev"
|
||||
optional = false
|
||||
python-versions = "*"
|
||||
|
||||
[[package]]
|
||||
name = "urllib3"
|
||||
version = "1.26.6"
|
||||
description = "HTTP library with thread-safe connection pooling, file post, and more."
|
||||
category = "dev"
|
||||
optional = false
|
||||
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
|
||||
|
||||
[package.extras]
|
||||
brotli = ["brotlipy (>=0.6.0)"]
|
||||
secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
|
||||
socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
|
||||
|
||||
[metadata]
|
||||
lock-version = "1.1"
|
||||
python-versions = "^3.8,<3.10"
|
||||
content-hash = "daffa6e91d6921845be603d5c0565d1afb511a57bb9a2f4b9c1084754b7a5314"
|
||||
content-hash = "c24b9a131366246119b2d28776b98d7430e983e25389ad6691928b6e78ab0673"
|
||||
|
||||
[metadata.files]
|
||||
alabaster = [
|
||||
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|
||||
{file = "typed_ast-1.4.3-cp39-cp39-manylinux1_x86_64.whl", hash = "sha256:cae53c389825d3b46fb37538441f75d6aecc4174f615d048321b716df2757fb0"},
|
||||
{file = "typed_ast-1.4.3-cp39-cp39-manylinux2014_aarch64.whl", hash = "sha256:b9574c6f03f685070d859e75c7f9eeca02d6933273b5e69572e5ff9d5e3931c3"},
|
||||
{file = "typed_ast-1.4.3-cp39-cp39-win32.whl", hash = "sha256:209596a4ec71d990d71d5e0d312ac935d86930e6eecff6ccc7007fe54d703808"},
|
||||
{file = "typed_ast-1.4.3-cp39-cp39-win_amd64.whl", hash = "sha256:9c6d1a54552b5330bc657b7ef0eae25d00ba7ffe85d9ea8ae6540d2197a3788c"},
|
||||
{file = "typed_ast-1.4.3.tar.gz", hash = "sha256:fb1bbeac803adea29cedd70781399c99138358c26d05fcbd23c13016b7f5ec65"},
|
||||
]
|
||||
typing-extensions = [
|
||||
{file = "typing_extensions-3.10.0.0-py2-none-any.whl", hash = "sha256:0ac0f89795dd19de6b97debb0c6af1c70987fd80a2d62d1958f7e56fcc31b497"},
|
||||
{file = "typing_extensions-3.10.0.0-py3-none-any.whl", hash = "sha256:779383f6086d90c99ae41cf0ff39aac8a7937a9283ce0a414e5dd782f4c94a84"},
|
||||
{file = "typing_extensions-3.10.0.0.tar.gz", hash = "sha256:50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342"},
|
||||
]
|
||||
urllib3 = [
|
||||
{file = "urllib3-1.26.6-py2.py3-none-any.whl", hash = "sha256:39fb8672126159acb139a7718dd10806104dec1e2f0f6c88aab05d17df10c8d4"},
|
||||
{file = "urllib3-1.26.6.tar.gz", hash = "sha256:f57b4c16c62fa2760b7e3d97c35b255512fb6b59a259730f36ba32ce9f8e342f"},
|
||||
]
|
||||
|
||||
@ -14,7 +14,8 @@ more-itertools = "^8.8.0"
|
||||
pytest = ">=6"
|
||||
flake8 = "^3.8.4"
|
||||
pytest-cov = "^2.10.1"
|
||||
mypy = "^0.910"
|
||||
mypy = "^0.790"
|
||||
Sphinx = "^4.1.2"
|
||||
|
||||
[build-system]
|
||||
requires = ["poetry>=0.12"]
|
||||
@ -22,15 +23,8 @@ build-backend = "poetry.masonry.api"
|
||||
|
||||
[tool.pytest.ini_options]
|
||||
testpaths = ["tests"]
|
||||
addopts = "--junitxml pytest.xml --cov pathfinder --cov-report=xml:coverage.xml --cov-fail-under=90 --cov-report=html"
|
||||
addopts = "--junitxml pytest.xml --cov pathfinder --cov-report=xml:coverage.xml --cov-fail-under=90"
|
||||
junit_family = "xunit1"
|
||||
|
||||
[tool.mypy]
|
||||
plugins = "numpy.typing.mypy_plugin"
|
||||
|
||||
[[tool.mypy.overrides]]
|
||||
module = [
|
||||
"scipy",
|
||||
"scipy.optimize"
|
||||
]
|
||||
ignore_missing_imports = true
|
||||
|
||||
@ -1,109 +0,0 @@
|
||||
import numpy
|
||||
import pathfinder.model.oscillating
|
||||
|
||||
|
||||
def chunk_n_sort(pts):
|
||||
pt_length = 7
|
||||
chunked_pts = [pts[i: i + pt_length] for i in range(0, len(pts), pt_length)]
|
||||
|
||||
return chunked_pts
|
||||
|
||||
|
||||
def print_result(msg, result):
|
||||
print(msg)
|
||||
print(f"\tResult: {result.pathfinder_x}")
|
||||
print(f"\tSuccess: {result.success}. {result.message}")
|
||||
try:
|
||||
print(f"\tFunc evals: {result.nfev}")
|
||||
except AttributeError:
|
||||
pass
|
||||
try:
|
||||
print(f"\tJacb evals: {result.njev}")
|
||||
except AttributeError:
|
||||
pass
|
||||
|
||||
|
||||
def test_one_dipole_six_dot_two_frequencies():
|
||||
# setup
|
||||
dot_inputs = [
|
||||
([0, 0, .01], 5), ([-1, 0, -.01], 5), ([-2, 0, -.01], 5), ([0, -1, .01], 5), ([-1, -1, 0], 5), ([-2, -1, 0], 5),
|
||||
([0, 0, .01], 1), ([-1, 0, -.01], 1), ([-2, 0, -.01], 1), ([0, -1, .01], 1), ([-1, -1, 0], 1), ([-2, -1, 0], 1),
|
||||
]
|
||||
dipole = pathfinder.model.oscillating.OscillatingDipole([1, 2, 3], [0, 4, -1], 7)
|
||||
expected_result = numpy.array([1, 2, 3, 0, 4, -1, 7])
|
||||
dipole_arrangement = pathfinder.model.oscillating.OscillatingDipoleArrangement([dipole])
|
||||
dot_measurements = dipole_arrangement.get_dot_measurements(dot_inputs)
|
||||
|
||||
model = pathfinder.model.oscillating.DotOscillatingDipoleModel(dot_measurements, 1)
|
||||
res = model.sol()
|
||||
|
||||
print_result("one oscillating dipole six dots", res)
|
||||
assert res.success, "The solution for a single dipole and six dots should have succeeded."
|
||||
numpy.testing.assert_allclose(res.pathfinder_x, expected_result, err_msg="Dipole wasn't as expected.", rtol=1e-6, atol=1e-6)
|
||||
|
||||
|
||||
def test_two_dipole_six_dot_two_frequencies():
|
||||
# setup
|
||||
dot_inputs = [
|
||||
([0, 0, .01], 5), ([-1, 0, -.01], 5), ([-2, 0, -.01], 5), ([0, -1, .01], 5), ([-1, -1, 0], 5), ([-2, -1, 0], 5),
|
||||
([0, -2, .01], 5), ([-1, -2, -.01], 5), ([-2, -2, -.01], 5), ([0, -3, .01], 5), ([-1, -3, 0], 5), ([-2, -3, 0], 5),
|
||||
([0, 0, .01], 1), ([-1, 0, -.01], 1), ([-2, 0, -.01], 1), ([0, -1, .01], 1), ([-1, -1, 0], 1), ([-2, -1, 0], 1),
|
||||
([0, -2, .01], 1), ([-1, -2, -.01], 1), ([-2, -2, -.01], 1), ([0, -3, .01], 1), ([-1, -3, 0], 1), ([-2, -3, 0], 1),
|
||||
]
|
||||
dipole = pathfinder.model.oscillating.OscillatingDipole([1, 2, 3], [0, 4, -1], 7)
|
||||
dipole2 = pathfinder.model.oscillating.OscillatingDipole([-1, 2, 0], [2, -1, 1], 4)
|
||||
expected_result = numpy.array([1, -2, 0, 2, -1, 1, 4, 1, 2, 3, 0, 4, -1, 7])
|
||||
dipole_arrangement = pathfinder.model.oscillating.OscillatingDipoleArrangement([dipole, dipole2])
|
||||
dot_measurements = dipole_arrangement.get_dot_measurements(dot_inputs)
|
||||
|
||||
model = pathfinder.model.oscillating.DotOscillatingDipoleModel(dot_measurements, 2)
|
||||
res = model.sol()
|
||||
|
||||
print_result("two oscillating dipole six dots", res)
|
||||
assert res.success, "The solution for two dipole and six dots should have succeeded."
|
||||
numpy.testing.assert_allclose(res.pathfinder_x, expected_result, err_msg="Dipole wasn't as expected.", rtol=1e-6, atol=1e-6)
|
||||
|
||||
|
||||
def test_two_dipole_six_dot_two_frequencies_morerealistic():
|
||||
# setup
|
||||
dot_inputs = [
|
||||
([0, 0, .01], 5), ([-1, 0, -.01], 5), ([-2, 0, -.01], 5), ([-3, 0, 0], 5), ([0, -1, .01], 5), ([-1, -1, 0], 5), ([-2, -1, 0], 5), ([-3, -1, 0], 5),
|
||||
([0, -2, .01], 5), ([-1, -2, -.01], 5), ([-2, -2, -.01], 5), ([-3, -2, 0], 5), ([0, -3, .01], 5), ([-1, -3, 0], 5), ([-2, -3, 0], 5), ([-3, -3, 0], 5),
|
||||
([0, 0, .01], 1), ([-1, 0, -.01], 1), ([-2, 0, -.01], 1), ([-3, 0, 0], 1), ([0, -1, .01], 1), ([-1, -1, 0], 1), ([-2, -1, 0], 1), ([-3, -1, 0], 1),
|
||||
([0, -2, .01], 1), ([-1, -2, -.01], 1), ([-2, -2, -.01], 1), ([-3, -2, 0], 1), ([0, -3, .01], 1), ([-1, -3, 0], 1), ([-2, -3, 0], 1), ([-3, -3, 0], 1),
|
||||
]
|
||||
dipole = pathfinder.model.oscillating.OscillatingDipole([1, 2, 3], [0, 4, -1], 7)
|
||||
dipole2 = pathfinder.model.oscillating.OscillatingDipole([-1, 2, 0], [-1, 2, 1], 4)
|
||||
expected_result = numpy.array([1, -2, 0, -1, 2, 1, 4, 1, 2, 3, 0, 4, -1, 7])
|
||||
dipole_arrangement = pathfinder.model.oscillating.OscillatingDipoleArrangement([dipole, dipole2])
|
||||
dot_measurements = dipole_arrangement.get_dot_measurements(dot_inputs)
|
||||
|
||||
model = pathfinder.model.oscillating.DotOscillatingDipoleModel(dot_measurements, 2)
|
||||
res = model.sol()
|
||||
|
||||
print_result("two oscillating dipole six dots", res)
|
||||
numpy.testing.assert_allclose(res.pathfinder_x, expected_result, err_msg="Dipole wasn't as expected.", rtol=1e-6, atol=1e-6)
|
||||
|
||||
|
||||
def test_two_dipole_eighteen_dot_two_frequencies_morerealistic():
|
||||
# setup
|
||||
dot_inputs = [
|
||||
([0, 0, .01], 5), ([-1, 0, -.01], 5), ([-2, 0, -.01], 5), ([0, -1, .01], 5), ([-1, -1, 0], 5), ([-2, -1, 0], 5),
|
||||
([0, -2, .01], 5), ([-1, -2, -.01], 5), ([-2, -2, -.01], 5), ([0, -3, .01], 5), ([-1, -3, 0], 5), ([-2, -3, 0], 5),
|
||||
([0, -4, .01], 5), ([-1, -4, -.01], 5), ([-2, -4, -.01], 5), ([0, -5, .01], 5), ([-1, -5, 0], 5), ([-2, -5, 0], 5),
|
||||
([0, 0, .01], 1), ([-1, 0, -.01], 1), ([-2, 0, -.01], 1), ([0, -1, .01], 1), ([-1, -1, 0], 1), ([-2, -1, 0], 1),
|
||||
([0, -2, .01], 1), ([-1, -2, -.01], 1), ([-2, -2, -.01], 1), ([0, -3, .01], 1), ([-1, -3, 0], 1), ([-2, -3, 0], 1),
|
||||
([0, -4, .01], 1), ([-1, -4, -.01], 1), ([-2, -4, -.01], 1), ([0, -5, .01], 1), ([-1, -5, 0], 1), ([-2, -5, 0], 1),
|
||||
]
|
||||
dipole = pathfinder.model.oscillating.OscillatingDipole([1, 2, 3], [0, 4, -1], 7)
|
||||
dipole2 = pathfinder.model.oscillating.OscillatingDipole([-1, 2, 0], [-1, 2, 1], 4)
|
||||
expected_result = numpy.array([1, -2, 0, -1, 2, 1, 4, 1, 2, 3, 0, 4, -1, 7])
|
||||
dipole_arrangement = pathfinder.model.oscillating.OscillatingDipoleArrangement([dipole, dipole2])
|
||||
dot_measurements = dipole_arrangement.get_dot_measurements(dot_inputs)
|
||||
|
||||
model = pathfinder.model.oscillating.DotOscillatingDipoleModel(dot_measurements, 2)
|
||||
res = model.sol()
|
||||
|
||||
print_result("two oscillating dipole six dots", res)
|
||||
assert res.success, "The solution for two dipole and six dots should have succeeded."
|
||||
numpy.testing.assert_allclose(res.pathfinder_x, expected_result, err_msg="Dipole wasn't as expected.", rtol=1e-6, atol=1e-6)
|
||||
@ -1,43 +0,0 @@
|
||||
import numpy
|
||||
import numpy.testing
|
||||
|
||||
import pathfinder.model.oscillating as model
|
||||
|
||||
|
||||
def test_dot_v_from_dipole():
|
||||
|
||||
dot_position1 = (-1, -1, -1)
|
||||
dot_frequency1 = 11
|
||||
expected_v1 = 0.00001421963287022476
|
||||
dot = model.DotMeasurement(expected_v1, dot_position1, dot_frequency1)
|
||||
|
||||
# and dipole located at (4, 5, 6) with p=(1, 2, 3) and w = 7
|
||||
pt = numpy.array((1, 2, 3, 4, 5, 6, 7))
|
||||
|
||||
numpy.testing.assert_allclose(dot.v_for_point(pt), dot.v, err_msg="v from dipole at a dot was incorrect!")
|
||||
numpy.testing.assert_allclose(dot.cost(pt), 0, atol=1e-12, err_msg="cost should be zero")
|
||||
|
||||
|
||||
def test_jac():
|
||||
expected_jac = [
|
||||
3.742008650059147e-6, 4.4904103800709765e-6, 5.238812110082806e-6,
|
||||
-3.12967996186765e-6, -3.1568945702317167e-6, -3.184109178595783e-6,
|
||||
8.603475350051953e-7
|
||||
]
|
||||
|
||||
expected_jac2 = [
|
||||
-4.428720903021825e-6, 3.5429767224174605e-6, 4.428720903021825e-6,
|
||||
-6.804125751006259e-6, -4.0261099118380183e-7, 2.3754048479844336e-6,
|
||||
5.181603456535536e-6
|
||||
]
|
||||
|
||||
dot = model.DotMeasurement(50, (-1, -1, -1), 11)
|
||||
|
||||
# dipole located at (4, 5, 6) with p=(1, 2, 3) and w = 7
|
||||
pt = numpy.array((1, 2, 3, 4, 5, 6, 7))
|
||||
pt2 = numpy.array((2, 5, 3, 4, -5, -6, 2))
|
||||
pts = numpy.append(pt, pt2)
|
||||
expected_jac_all = expected_jac + expected_jac2
|
||||
assert len(dot.jac_pt(pt)) == 7
|
||||
numpy.testing.assert_allclose(dot.jac_pt(pt), expected_jac, err_msg="Jac pt doesn't match Mathematica result.")
|
||||
numpy.testing.assert_allclose(dot.jac(pts), expected_jac_all, err_msg="whole row should match")
|
||||
@ -1,22 +0,0 @@
|
||||
import numpy
|
||||
import pathfinder.model.oscillating as model
|
||||
|
||||
|
||||
def test_static_dipole():
|
||||
d1 = model.OscillatingDipole((1, 2, 3), (4, 5, 6), 7)
|
||||
d2 = model.OscillatingDipole((2, 5, 3), (4, -5, -6), 2)
|
||||
dipoles = model.OscillatingDipoleArrangement([d1, d2])
|
||||
|
||||
dot_position1 = (-1, -1, -1)
|
||||
dot_frequency1 = 11
|
||||
expected_v1 = 0.00001421963287022476
|
||||
expected_v2 = 0.00001107180225755457
|
||||
|
||||
numpy.testing.assert_allclose(d1.s_at_position(dot_position1, dot_frequency1), expected_v1, err_msg="Voltage at dot isn't as expected.")
|
||||
|
||||
dot_measurements = dipoles.get_dot_measurements([(dot_position1, dot_frequency1)])
|
||||
assert len(dot_measurements) == 1, "Should have only had one dot measurement."
|
||||
measurement = dot_measurements[0]
|
||||
numpy.testing.assert_allclose(measurement.r, dot_position1, err_msg="Dot position should have been passed over")
|
||||
numpy.testing.assert_allclose(measurement.f, dot_frequency1, err_msg="Dot frequency should have been passed over")
|
||||
numpy.testing.assert_allclose(measurement.v, expected_v1 + expected_v2, err_msg="Voltage at dot isn't as expected.")
|
||||
@ -1,35 +0,0 @@
|
||||
import numpy
|
||||
import pathfinder.model.oscillating as model
|
||||
|
||||
|
||||
def test_dotdipolemodel_repr():
|
||||
mod = model.DotOscillatingDipoleModel((), 1)
|
||||
assert repr(mod) == "DotOscillatingDipoleModel([], 1)"
|
||||
|
||||
|
||||
def test_dotdipolemodel_m():
|
||||
mod = model.DotOscillatingDipoleModel([model.DotMeasurement(1, (-1, -1, -1), 11), model.DotMeasurement(2, (0, 0, 0), 3)], 1)
|
||||
assert mod.m == 2
|
||||
|
||||
|
||||
def test_dotdipolemodel_cost():
|
||||
mod = model.DotOscillatingDipoleModel([model.DotMeasurement(.05, (-1, -1, -1), 11), model.DotMeasurement(.002, (0, 0, 0), 3)], 1)
|
||||
costs = mod.costs()
|
||||
jac = mod.jac()
|
||||
|
||||
pt_to_test = numpy.array((1, 2, 3, 4, 5, 6, 7))
|
||||
expected_cost = [-0.04998578036712978, -0.00191383161468913]
|
||||
expected_jacobian = [
|
||||
[
|
||||
3.742008650059147e-6, 4.4904103800709765e-6, 5.238812110082806e-6,
|
||||
-3.12967996186765e-6, -3.1568945702317167e-6, -3.184109178595783e-6,
|
||||
8.603475350051953e-7
|
||||
], [
|
||||
0.000021542096327717702, 0.000026927620409647127, 0.000032313144491576555,
|
||||
-0.000021472154456523818, -0.0000228010500092077, -0.000024129945561891588,
|
||||
-8.489496089740964e-6
|
||||
]
|
||||
]
|
||||
|
||||
numpy.testing.assert_allclose(costs(pt_to_test), expected_cost, err_msg="Costs aren't as expected.")
|
||||
numpy.testing.assert_allclose(jac(pt_to_test), expected_jacobian, err_msg="Jacobian aren't as expected.")
|
||||
@ -1,20 +0,0 @@
|
||||
import pathfinder.model.oscillating.util as util
|
||||
import numpy
|
||||
|
||||
|
||||
def test_util_flip():
|
||||
pt = numpy.array((1, 2, 3, 4, 5, 6, 7))
|
||||
expected = (1, 2, 3, 4, 5, 6, 7)
|
||||
numpy.testing.assert_allclose(util.flip_chunk_to_positive_px(pt), expected, err_msg="Point should remain unchanged.")
|
||||
|
||||
|
||||
def test_util_flip_negative():
|
||||
pt = numpy.array((-1, -2, 3, 4, 5, 6, 7))
|
||||
expected = (1, 2, -3, 4, 5, 6, 7)
|
||||
numpy.testing.assert_allclose(util.flip_chunk_to_positive_px(pt), expected, err_msg="Point should remain unchanged.")
|
||||
|
||||
|
||||
def test_util_normalise_two():
|
||||
pt = numpy.array((1, 2, 3, 4, 5, 6, 7, -.5, 1, 1.5, 2, 2.5, 3, 3.5))
|
||||
expected = (.5, -1, -1.5, 2, 2.5, 3, 3.5, 1, 2, 3, 4, 5, 6, 7)
|
||||
numpy.testing.assert_allclose(util.normalize_oscillating_dipole_list(pt), expected, err_msg="Sort should have happened.")
|
||||
@ -1,76 +0,0 @@
|
||||
import numpy
|
||||
import pathfinder.model.static as model
|
||||
|
||||
|
||||
def test_dotdipolemodel_repr():
|
||||
mod = model.DotDipoleModel((), 1)
|
||||
assert repr(mod) == "DotDipoleModel([], 1)"
|
||||
|
||||
|
||||
def test_dotdipolemodel_m():
|
||||
mod = model.DotDipoleModel([model.DotMeasurement(1, (0, 0, 0)), model.DotMeasurement(2, (0, 0, 0))], 1)
|
||||
assert mod.m == 2
|
||||
|
||||
|
||||
def test_dotdipolemodel_cost():
|
||||
mod = model.DotDipoleModel([model.DotMeasurement(1, (0, 0, 1)), model.DotMeasurement(2, (1, 0, 0))], 1)
|
||||
costs = mod.costs()
|
||||
jac = mod.jac()
|
||||
|
||||
pt_to_test = numpy.array((1, 2, 3, 4, 5, 6))
|
||||
expected_cost = [-1.05408565512728256, -2.05293155269909457]
|
||||
expected_jacobian = [
|
||||
[
|
||||
-0.007460090362383803, -0.009325112952979752, -0.009325112952979752,
|
||||
0.007968732887091788, 0.00856214916591777, 0.006697126575321822
|
||||
], [
|
||||
-0.00512240832571883, -0.008537347209531383, -0.01024481665143766,
|
||||
0.005098015905120168, 0.007927536694564856, 0.008488562368334061
|
||||
]
|
||||
]
|
||||
|
||||
numpy.testing.assert_allclose(costs(pt_to_test), expected_cost, err_msg="Costs aren't as expected.")
|
||||
numpy.testing.assert_allclose(jac(pt_to_test), expected_jacobian, err_msg="Jacobian aren't as expected.")
|
||||
|
||||
|
||||
def print_result(msg, result):
|
||||
print(msg)
|
||||
print(f"\tResult: {result.x}")
|
||||
print(f"\tSuccess: {result.success}. {result.message}")
|
||||
try:
|
||||
print(f"\tFunc evals: {result.nfev}")
|
||||
except AttributeError:
|
||||
pass
|
||||
try:
|
||||
print(f"\tJacb evals: {result.njev}")
|
||||
except AttributeError:
|
||||
pass
|
||||
|
||||
|
||||
def test_dot_dipole_model_solution():
|
||||
v1 = -0.05547767706400186526225414
|
||||
v2 = -0.06018573388098888319642888
|
||||
v3 = -0.06364032191901859480476888
|
||||
v4 = -0.06488383879243851188402150
|
||||
v5 = -0.06297148063759813929659130
|
||||
v6 = -0.05735489606460216
|
||||
v7 = -0.07237320672886623
|
||||
v8 = -0.1082531754730548
|
||||
v9 = -0.04471694936155558
|
||||
|
||||
c1 = model.DotMeasurement(v1, [0, 0, 1])
|
||||
c2 = model.DotMeasurement(v2, [0, 0, 2])
|
||||
c3 = model.DotMeasurement(v3, [0, 0, 3])
|
||||
c4 = model.DotMeasurement(v4, [0, 0, 4])
|
||||
c5 = model.DotMeasurement(v5, [0, 0, 5])
|
||||
c6 = model.DotMeasurement(v6, [0, 0, 6])
|
||||
c7 = model.DotMeasurement(v7, [1, 1, 7])
|
||||
c8 = model.DotMeasurement(v8, [1, 2, 3])
|
||||
c9 = model.DotMeasurement(v9, [0, -1, 0])
|
||||
|
||||
expected_result = numpy.array([1, 3, 5, 5, 6, 7])
|
||||
|
||||
mod = model.DotDipoleModel([c1, c2, c3, c4, c5, c6, c7, c8, c9], 1)
|
||||
res = mod.sol()
|
||||
assert res.success, "The solution for a single dipole should have succeeded."
|
||||
numpy.testing.assert_allclose(res.x, expected_result, err_msg="Dipole wasn't as expected.")
|
||||
@ -1,120 +0,0 @@
|
||||
import numpy
|
||||
import pathfinder.model.static
|
||||
|
||||
import pytest
|
||||
|
||||
|
||||
def chunk_n_sort(pts):
|
||||
pt_length = 6
|
||||
chunked_pts = [pts[i: i + pt_length] for i in range(0, len(pts), pt_length)]
|
||||
|
||||
return sorted(chunked_pts, key=lambda x: x[0])
|
||||
|
||||
|
||||
def print_result(msg, result):
|
||||
print(msg)
|
||||
print(f"\tResult: {chunk_n_sort(result.x)}")
|
||||
print(f"\tSuccess: {result.success}. {result.message}")
|
||||
try:
|
||||
print(f"\tFunc evals: {result.nfev}")
|
||||
except AttributeError:
|
||||
pass
|
||||
try:
|
||||
print(f"\tJacb evals: {result.njev}")
|
||||
except AttributeError:
|
||||
pass
|
||||
|
||||
|
||||
def test_one_dipole_six_dot():
|
||||
# setup
|
||||
dot_positions = [[0, 0, 0], [-1, 0, 0], [-2, 0, 0], [-1, -1, 0], [-1, -1, 1], [0, -2, 0]]
|
||||
dipole = pathfinder.model.static.StaticDipole([1, 2, 3], [0, 4, 0])
|
||||
expected_result = numpy.array([1, 2, 3, 0, 4, 0])
|
||||
dipole_arrangement = pathfinder.model.static.StaticDipoleArrangement([dipole])
|
||||
dot_measurements = dipole_arrangement.get_dot_measurements(dot_positions)
|
||||
|
||||
model = pathfinder.model.static.DotDipoleModel(dot_measurements, 1)
|
||||
res = model.sol()
|
||||
|
||||
print_result("one dipole six dots", res)
|
||||
assert res.success, "The solution for a single dipole and six dots should have succeeded."
|
||||
numpy.testing.assert_allclose(res.x, expected_result, err_msg="Dipole wasn't as expected.", rtol=1e-6, atol=1e-6)
|
||||
|
||||
|
||||
@pytest.mark.skip(reason="don't care at the moment")
|
||||
def test_two_dipole_thirteen_dot():
|
||||
dot_positions = [[x, y, 0] for x in (-4, -1, 1, 4) for y in (-1, -5, -9)]
|
||||
dot_positions.append((1, -1, 2))
|
||||
# dot_positions.append((-1, -1, -2))
|
||||
dipole = pathfinder.model.static.StaticDipole([0, 8, 0], [0, 5, 0])
|
||||
dipole2 = pathfinder.model.static.StaticDipole([8, 1, 1], [2, 2, -2])
|
||||
expected_result = numpy.array([0, 8, 0, 0, 5, 0, 8, 1, 1, 2, 2, -2])
|
||||
dipole_arrangement = pathfinder.model.static.StaticDipoleArrangement([dipole, dipole2])
|
||||
dot_measurements = dipole_arrangement.get_dot_measurements(dot_positions)
|
||||
|
||||
model = pathfinder.model.static.DotDipoleModel(dot_measurements, 2)
|
||||
res = model.sol(initial_dipole=(2, 2, 0), initial_position=(0, 3, 0))
|
||||
print(model.costs()(res.x))
|
||||
print(res.x)
|
||||
print_result("two dipole 13 dot", res)
|
||||
assert res.success, "The solution for two dipoles and twelve dots should have succeeded."
|
||||
numpy.testing.assert_allclose(chunk_n_sort(res.x), chunk_n_sort(expected_result), err_msg="Dipole wasn't as expected.", rtol=1e-6, atol=1e-4)
|
||||
|
||||
|
||||
@pytest.mark.skip(reason="don't care at the moment")
|
||||
def test_two_dipole_twelve_dot():
|
||||
dot_positions = [[x, y, 0] for x in (-4, -1, 1, 4) for y in (-1, -5, -9)][:-1]
|
||||
dot_positions.append((1, -1, 2))
|
||||
# dot_positions.append((-1, -1, -2))
|
||||
dipole = pathfinder.model.static.StaticDipole([0, 8, 0], [0, 5, 0])
|
||||
dipole2 = pathfinder.model.static.StaticDipole([8, 1, 1], [2, 2, -2])
|
||||
expected_result = numpy.array([0, 8, 0, 0, 5, 0, 8, 1, 1, 2, 2, -2])
|
||||
dipole_arrangement = pathfinder.model.static.StaticDipoleArrangement([dipole, dipole2])
|
||||
dot_measurements = dipole_arrangement.get_dot_measurements(dot_positions)
|
||||
|
||||
model = pathfinder.model.static.DotDipoleModel(dot_measurements, 2)
|
||||
res = model.sol(initial_dipole=(2, 2, 0), initial_position=(0, 3, 0), use_root=False)
|
||||
print(model.costs()(res.x))
|
||||
print(res.x)
|
||||
print_result("two dipole 13 dot", res)
|
||||
assert res.success, "The solution for two dipoles and twelve dots should have succeeded."
|
||||
numpy.testing.assert_allclose(chunk_n_sort(res.x), chunk_n_sort(expected_result), err_msg="Dipole wasn't as expected.", rtol=1e-6, atol=1e-4)
|
||||
|
||||
|
||||
@pytest.mark.skip(reason="don't care at the moment")
|
||||
def test_two_dipole_twelve_dot_smallguy():
|
||||
dot_positions = [[x, y, 0] for x in (-4, -1, 1, 4) for y in (-1, -5, -9)][:-1]
|
||||
dot_positions.append((1, -1, 2))
|
||||
# dot_positions.append((-1, -1, -2))
|
||||
dipole = pathfinder.model.static.StaticDipole([0, 1, 0], [0, 5, 0])
|
||||
dipole2 = pathfinder.model.static.StaticDipole([8, 1, 1], [2, 2, -2])
|
||||
expected_result = numpy.array([0, 1, 0, 0, 5, 0, 8, 1, 1, 2, 2, -2])
|
||||
dipole_arrangement = pathfinder.model.static.StaticDipoleArrangement([dipole, dipole2])
|
||||
dot_measurements = dipole_arrangement.get_dot_measurements(dot_positions)
|
||||
|
||||
model = pathfinder.model.static.DotDipoleModel(dot_measurements, 2)
|
||||
res = model.sol(initial_dipole=(2, 2, 0), initial_position=(0, 3, 0), use_root=False)
|
||||
print(model.costs()(res.x))
|
||||
print(res.x)
|
||||
print_result("two dipole 13 dot", res)
|
||||
assert res.success, "The solution for two dipoles and twelve dots should have succeeded."
|
||||
numpy.testing.assert_allclose(chunk_n_sort(res.x), chunk_n_sort(expected_result), err_msg="Dipole wasn't as expected.", rtol=1e-6, atol=1e-4)
|
||||
|
||||
|
||||
def test_two_dipole_twelve_dot_2():
|
||||
dot_positions = [[x, y, 0] for x in (-4, -1, 1, 4) for y in (-1, -5, -9)]
|
||||
dot_positions.append((1, -1, 2))
|
||||
dot_positions.append((-1, -1, -2))
|
||||
dipole = pathfinder.model.static.StaticDipole([0, 8, 0], [0, 5, 0])
|
||||
dipole2 = pathfinder.model.static.StaticDipole([8, 1, 1], [2, 2, -2])
|
||||
expected_result = numpy.array([0, 8, 0, 0, 5, 0, 8, 1, 1, 2, 2, -2])
|
||||
dipole_arrangement = pathfinder.model.static.StaticDipoleArrangement([dipole, dipole2])
|
||||
dot_measurements = dipole_arrangement.get_dot_measurements(dot_positions)
|
||||
|
||||
model = pathfinder.model.static.DotDipoleModel(dot_measurements, 2)
|
||||
res = model.sol()
|
||||
print(model.costs()(res.x))
|
||||
|
||||
print_result("two dipole twelve dot", res)
|
||||
# assert res.success, "The solution for two dipoles and twelve dots should have succeeded."
|
||||
numpy.testing.assert_allclose(chunk_n_sort(res.x), chunk_n_sort(expected_result), err_msg="Dipole wasn't as expected.", rtol=1e-6, atol=1e-4)
|
||||
@ -1,23 +0,0 @@
|
||||
import numpy
|
||||
import pathfinder.model.static as model
|
||||
|
||||
|
||||
def test_static_dipole():
|
||||
d1 = model.StaticDipole((1, 2, 3), (4, 5, 6))
|
||||
d2 = model.StaticDipole((4, 5, 6), (1, 2, 3))
|
||||
dipoles = model.StaticDipoleArrangement([d1, d2])
|
||||
|
||||
dot_position1 = (-1, -1, -1)
|
||||
expected_v1 = -0.3338923121348659
|
||||
|
||||
numpy.testing.assert_allclose(dipoles.get_dot_measurement(dot_position1).v, expected_v1, err_msg="Voltage at dot isn't as expected.")
|
||||
numpy.testing.assert_allclose(dipoles.get_dot_measurement(dot_position1).r, dot_position1, err_msg="Dot isn't where expected.")
|
||||
|
||||
# test multiple dots
|
||||
dot_position2 = (-1, -1, -5)
|
||||
expected_v2 = -0.1254445237566694
|
||||
|
||||
both_measurements = dipoles.get_dot_measurements([dot_position1, dot_position2])
|
||||
measured_voltages = numpy.sort([m.v for m in both_measurements])
|
||||
expected_measured_voltages = numpy.sort([expected_v1, expected_v2])
|
||||
numpy.testing.assert_allclose(measured_voltages, expected_measured_voltages, err_msg="Didn't get the measured voltages expected")
|
||||
@ -1,7 +1,7 @@
|
||||
import numpy
|
||||
import numpy.testing
|
||||
|
||||
import pathfinder.model.static as model
|
||||
import pathfinder.model as model
|
||||
|
||||
|
||||
def test_dot():
|
||||
107
tests/model/test_model.py
Normal file
107
tests/model/test_model.py
Normal file
@ -0,0 +1,107 @@
|
||||
import numpy
|
||||
import pathfinder.model as model
|
||||
import scipy.optimize
|
||||
import pytest
|
||||
|
||||
|
||||
def test_dotdipolemodel_repr():
|
||||
mod = model.DotDipoleModel((), 1)
|
||||
assert repr(mod) == "DotDipoleModel([], 1)"
|
||||
|
||||
|
||||
def test_dotdipolemodel_m():
|
||||
mod = model.DotDipoleModel([model.DotMeasurement(1, (0, 0, 0)), model.DotMeasurement(2, (0, 0, 0))], 1)
|
||||
assert mod.m == 2
|
||||
|
||||
|
||||
def print_result(msg, result):
|
||||
print(msg)
|
||||
print(f"\tResult: {result.x}")
|
||||
print(f"\tSuccess: {result.success}. {result.message}")
|
||||
try:
|
||||
print(f"\tFunc evals: {result.nfev}")
|
||||
except AttributeError:
|
||||
pass
|
||||
try:
|
||||
print(f"\tJacb evals: {result.njev}")
|
||||
except AttributeError:
|
||||
pass
|
||||
|
||||
|
||||
@pytest.mark.skip(reason="old")
|
||||
def test_dot_dipole_model_jac():
|
||||
v1 = -0.05547767706400186526225414
|
||||
v2 = -0.06018573388098888319642888
|
||||
v3 = -0.06364032191901859480476888
|
||||
v4 = -0.06488383879243851188402150
|
||||
v5 = -0.06297148063759813929659130
|
||||
v6 = -0.05735489606460216
|
||||
v7 = -0.07237320672886623
|
||||
v8 = -0.1082531754730548
|
||||
|
||||
c1 = model.DotMeasurement(v1, [0, 0, 1])
|
||||
c2 = model.DotMeasurement(v2, [0, 0, 2])
|
||||
c3 = model.DotMeasurement(v3, [0, 0, 3])
|
||||
c4 = model.DotMeasurement(v4, [0, 0, 4])
|
||||
c5 = model.DotMeasurement(v5, [0, 0, 5])
|
||||
c6 = model.DotMeasurement(v6, [0, 0, 6])
|
||||
c7 = model.DotMeasurement(v7, [1, 1, 7])
|
||||
c8 = model.DotMeasurement(v8, [1, 2, 3])
|
||||
|
||||
mod = model.DotDipoleModel([c1, c2, c3, c4, c5, c6], 1)
|
||||
res = scipy.optimize.least_squares(mod.costs(), numpy.array([1, 2, 3, 4, 5, 6]), jac=mod.jac(), ftol=1e-12)
|
||||
print_result("6 dots, least sq", res)
|
||||
mod2 = model.DotDipoleModel([c1, c2, c3, c4, c5, c6, c7, c8], 1)
|
||||
res2 = scipy.optimize.least_squares(mod2.costs(), numpy.array([0, 0, 0, 0, 0, 0]), jac=mod2.jac(), ftol=1e-12, gtol=3e-16)
|
||||
print_result("7 dots, least squares", res2)
|
||||
print(mod2.costs()(res2.x))
|
||||
print(mod2.costs()(numpy.array([1, 3, 5, 5, 6, 7])))
|
||||
|
||||
|
||||
@pytest.mark.skip(reason="bad test")
|
||||
def test_dot_2dipoles_model_jac():
|
||||
dots_12andone = [
|
||||
model.DotMeasurement(-0.1978319326584865, [-4, -1, 0]),
|
||||
model.DotMeasurement(-0.1273171638293727, [-4, -5, 0]),
|
||||
model.DotMeasurement(-0.05545025617224288, [-4, -9, 0]),
|
||||
model.DotMeasurement(-0.4960209997369774, [-1, -1, 0]),
|
||||
model.DotMeasurement(-0.1763373289754278, [-1, -5, 0]),
|
||||
model.DotMeasurement(-0.04946346672578462, [-1, -9, 0]),
|
||||
model.DotMeasurement(-0.5633156098386561, [1, -1, 0]),
|
||||
model.DotMeasurement(-0.113765134433174, [1, -5, 0]),
|
||||
model.DotMeasurement(-0.0294893572499722, [1, -9, 0]),
|
||||
model.DotMeasurement(0.7794941616360612, [4, -1, 0]),
|
||||
model.DotMeasurement(0.1110683086477768, [4, -5, 0]),
|
||||
model.DotMeasurement(0.01183272220840589, [4, -9, 0]),
|
||||
model.DotMeasurement(-0.1096485462119833, [1, 1, 1]),
|
||||
model.DotMeasurement(-0.3925851888077783, [1, 1, -1])
|
||||
]
|
||||
# dots = [
|
||||
# model.Dot(-0.1978319326584865, [-4, -1, 0]),
|
||||
# model.Dot(-0.1273171638293727, [-4, -5, 0]),
|
||||
# model.Dot(-0.05545025617224288, [-4, -9, 0]),
|
||||
# model.Dot(-0.4960209997369774, [-1, -1, 0]),
|
||||
# model.Dot(-0.1763373289754278, [-1, -5, 0]),
|
||||
# model.Dot(-0.04946346672578462, [-1, -9, 0]),
|
||||
# model.Dot(-0.5633156098386561, [1, -1, 0]),
|
||||
# model.Dot(-0.113765134433174, [1, -5, 0]),
|
||||
# model.Dot(-0.0294893572499722, [1, -9, 0]),
|
||||
# model.Dot(0.7794941616360612, [4, -1, 0]),
|
||||
# model.Dot(0.1110683086477768, [4, -5, 0]),
|
||||
# model.Dot(0.01183272220840589, [4, -9, 0]),
|
||||
# model.Dot(-0.0261092728062841, [-4, -13, 0]),
|
||||
# model.Dot(-0.02035559593904894, [-1, -13, 0]),
|
||||
# model.Dot(-0.01296894715810522, [1, -13, 0]),
|
||||
# model.Dot(0.0003306001626435171, [4, -13, 0]),
|
||||
# model.Dot(0.2612817068810759, [7, -1, 0]),
|
||||
# model.Dot(0.1203841445911355, [7, -5, 0]),
|
||||
# model.Dot(0.03425933872931543, [7, -9, 0]),
|
||||
# model.Dot(0.01068547688208644, [7, -13, 0]),
|
||||
# ]
|
||||
|
||||
mod = model.DotDipoleModel(dots_12andone, 2)
|
||||
res = scipy.optimize.least_squares(mod.costs(), numpy.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]), jac=mod.jac(), ftol=1e-12)
|
||||
print_result("6 dots, least sq", res)
|
||||
print(mod.costs()(res.x))
|
||||
for val in res.x:
|
||||
print(val)
|
||||
@ -1,7 +1,5 @@
|
||||
from pathfinder import __version__
|
||||
import pathfinder
|
||||
|
||||
|
||||
def test_version():
|
||||
assert __version__ == '0.0.1'
|
||||
assert pathfinder.get_version() == __version__
|
||||
|
||||
Reference in New Issue
Block a user