chore(deps): update dependency scipy to ~1.10

Reviewed-on: #23

CHANGELOG.md

@@ -2,6 +2,19 @@
 
 All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines.
 
+### [0.8.7](https://gitea.deepak.science:2222/physics/pdme/compare/0.8.6...0.8.7) (2022-09-17)
+
+
+### Features
+
+* adds xy model for convenience to pdme ([e894c89](https://gitea.deepak.science:2222/physics/pdme/commit/e894c897029c05a1d4754e7930ae9ba2be7a1cfd))
+* moves xy model up to model package ([2a1ae3b](https://gitea.deepak.science:2222/physics/pdme/commit/2a1ae3b1a7f7e10469b7fd2930fee0b338f0c03f))
+
+
+### Bug Fixes
+
+* Correctly generates monte carlo version of xy model dipoles ([5acf0ac](https://gitea.deepak.science:2222/physics/pdme/commit/5acf0ac347382705674bb596440d27cba3730bac))
+
 ### [0.8.6](https://gitea.deepak.science:2222/physics/pdme/compare/0.8.5...0.8.6) (2022-06-13)
 
 

pdme/model/__init__.py

@@ -11,6 +11,10 @@ from pdme.model.log_spaced_random_choice_model import (
 	LogSpacedRandomCountMultipleDipoleFixedMagnitudeModel,
 )
 
+from pdme.model.log_spaced_random_choice_xy_model import (
+	LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel,
+)
+
 from pdme.model.log_spaced_random_choice_fixed_orientation_model import (
 	LogSpacedRandomCountMultipleDipoleFixedMagnitudeFixedOrientationModel,
 )
@@ -21,5 +25,6 @@ __all__ = [
 	"MultipleDipoleFixedMagnitudeModel",
 	"RandomCountMultipleDipoleFixedMagnitudeModel",
 	"LogSpacedRandomCountMultipleDipoleFixedMagnitudeModel",
+	"LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel",
 	"LogSpacedRandomCountMultipleDipoleFixedMagnitudeFixedOrientationModel",
 ]

pdme/model/log_spaced_random_choice_xy_model.py

@@ -0,0 +1,125 @@
+import numpy
+import numpy.random
+from pdme.model.model import DipoleModel
+from pdme.measurement import (
+	OscillatingDipole,
+	OscillatingDipoleArrangement,
+)
+
+
+class LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(DipoleModel):
+	"""
+	Model of multiple oscillating dipoles with a fixed magnitude, but free rotation in XY plane. Spaced logarithmically.
+
+	Parameters
+	----------
+
+	wexp_min: log-10 lower bound for dipole frequency
+	wexp_min: log-10 upper bound for dipole frequency
+
+	pfixed : float
+	The fixed dipole magnitude.
+
+	n_max : int
+	The maximum number of dipoles.
+
+	prob_occupancy : float
+	The probability of dipole occupancy
+	"""
+
+	def __init__(
+		self,
+		xmin: float,
+		xmax: float,
+		ymin: float,
+		ymax: float,
+		zmin: float,
+		zmax: float,
+		wexp_min: float,
+		wexp_max: float,
+		pfixed: float,
+		n_max: int,
+		prob_occupancy: float,
+	) -> None:
+		self.xmin = xmin
+		self.xmax = xmax
+		self.ymin = ymin
+		self.ymax = ymax
+		self.zmin = zmin
+		self.zmax = zmax
+		self.wexp_min = wexp_min
+		self.wexp_max = wexp_max
+		self.pfixed = pfixed
+		self.rng = numpy.random.default_rng()
+		self.n_max = n_max
+		if prob_occupancy >= 1 or prob_occupancy <= 0:
+			raise ValueError(
+				f"The probability of a dipole site occupancy must be between 0 and 1, got {prob_occupancy}"
+			)
+		self.prob_occupancy = prob_occupancy
+
+	def __repr__(self) -> str:
+		return f"LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel({self.xmin}, {self.xmax}, {self.ymin}, {self.ymax}, {self.zmin}, {self.zmax}, {self.wexp_min}, {self.wexp_max}, {self.pfixed}, {self.n_max}, {self.prob_occupancy})"
+
+	def get_dipoles(
+		self, max_frequency: float, rng_to_use: numpy.random.Generator = None
+	) -> OscillatingDipoleArrangement:
+		rng: numpy.random.Generator
+		if rng_to_use is None:
+			rng = self.rng
+		else:
+			rng = rng_to_use
+
+		dipoles = []
+
+		n = rng.binomial(self.n_max, self.prob_occupancy)
+
+		for i in range(n):
+			phi = rng.uniform(0, 2 * numpy.pi)
+			px = self.pfixed * numpy.cos(phi)
+			py = self.pfixed * numpy.sin(phi)
+			pz = 0
+			s_pts = numpy.array(
+				(
+					rng.uniform(self.xmin, self.xmax),
+					rng.uniform(self.ymin, self.ymax),
+					rng.uniform(self.zmin, self.zmax),
+				)
+			)
+			frequency = 10 ** rng.uniform(self.wexp_min, self.wexp_max)
+
+			dipoles.append(
+				OscillatingDipole(numpy.array([px, py, pz]), s_pts, frequency)
+			)
+		return OscillatingDipoleArrangement(dipoles)
+
+	def get_monte_carlo_dipole_inputs(
+		self,
+		monte_carlo_n: int,
+		_: float,
+		rng_to_use: numpy.random.Generator = None,
+	) -> numpy.ndarray:
+
+		rng: numpy.random.Generator
+		if rng_to_use is None:
+			rng = self.rng
+		else:
+			rng = rng_to_use
+
+		shape = (monte_carlo_n, self.n_max)
+		phi = 2 * numpy.pi * rng.random(shape)
+
+		p_mask = rng.binomial(1, self.prob_occupancy, shape)
+		p_magnitude = self.pfixed * p_mask
+
+		px = p_magnitude * numpy.cos(phi)
+		py = p_magnitude * numpy.sin(phi)
+		pz = p_magnitude * 0
+
+		sx = rng.uniform(self.xmin, self.xmax, shape)
+		sy = rng.uniform(self.ymin, self.ymax, shape)
+		sz = rng.uniform(self.zmin, self.zmax, shape)
+
+		w = 10 ** rng.uniform(self.wexp_min, self.wexp_max, shape)
+
+		return numpy.stack([px, py, pz, sx, sy, sz, w], axis=-1)

poetry.lock

@@ -93,7 +93,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "coverage"
-version = "6.4.2"
+version = "7.0.3"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
@@ -316,8 +316,8 @@ optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-testing = ["pytest-benchmark", "pytest"]
-dev = ["tox", "pre-commit"]
+dev = ["pre-commit", "tox"]
+testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "prompt-toolkit"
@@ -426,18 +426,23 @@ coverage = {version = ">=5.2.1", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
-testing = ["virtualenv", "pytest-xdist", "six", "process-tests", "hunter", "fields"]
+testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
 
 [[package]]
 name = "scipy"
-version = "1.9.0"
-description = "SciPy: Scientific Library for Python"
+version = "1.10.0"
+description = "Fundamental algorithms for scientific computing in Python"
 category = "main"
 optional = false
-python-versions = ">=3.8,<3.12"
+python-versions = "<3.12,>=3.8"
 
 [package.dependencies]
-numpy = ">=1.18.5,<1.25.0"
+numpy = ">=1.19.5,<1.27.0"
+
+[package.extras]
+test = ["pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "asv", "mpmath", "gmpy2", "threadpoolctl", "scikit-umfpack", "pooch"]
+doc = ["sphinx (!=4.1.0)", "pydata-sphinx-theme (==0.9.0)", "sphinx-design (>=0.2.0)", "matplotlib (>2)", "numpydoc"]
+dev = ["mypy", "typing-extensions", "pycodestyle", "flake8", "rich-click", "click", "doit (>=0.36.0)", "pydevtool"]
 
 [[package]]
 name = "six"
@@ -461,7 +466,7 @@ executing = "*"
 pure-eval = "*"
 
 [package.extras]
-tests = ["cython", "littleutils", "pygments", "typeguard", "pytest"]
+tests = ["pytest", "typeguard", "pygments", "littleutils", "cython"]
 
 [[package]]
 name = "toml"
@@ -509,7 +514,7 @@ python-versions = "*"
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8,<3.10"
-content-hash = "ba562365abd9c6b04b231a9f307c8ae109fdb50b99e793a28a33b1438374bfbb"
+content-hash = "f5614947eb2f77e9cd8bd9dc026a924f4cb7394c3fef9cb175ab5afbe201ca73"
 
 [metadata.files]
 appnope = []

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pdme"
-version = "0.8.6"
+version = "0.8.7"
 description = "Python dipole model evaluator"
 authors = ["Deepak <dmallubhotla+github@gmail.com>"]
 license = "GPL-3.0-only"
@@ -9,7 +9,7 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = "^3.8,<3.10"
 numpy = "^1.22.3"
-scipy = "~1.9"
+scipy = "~1.10"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=6"

tests/model/test_log_spaced_random_count_multiple_dipole_fixed_magnitude_xy_model.py

@@ -0,0 +1,206 @@
+from pdme.model import LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel
+import numpy
+import logging
+import pytest
+
+
+_logger = logging.getLogger(__name__)
+
+
+def test_random_count_multiple_dipole_xy_wrong_probability():
+	with pytest.raises(ValueError):
+		LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
+			-10, 10, -5, 5, 2, 3, 1, 2, 10, 5, 2
+		)
+
+
+def test_repr_random_count_multiple_dipole_fixed_mag_xy():
+	model = LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
+		-10, 10, -5, 5, 2, 3, 1, 2, 10, 5, 0.5
+	)
+	assert (
+		repr(model)
+		== "LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(-10, 10, -5, 5, 2, 3, 1, 2, 10, 5, 0.5)"
+	), "Repr should be what I want."
+
+
+def test_random_count_multiple_dipole_fixed_mag_model_get_dipoles_multiple_xy():
+
+	p_fixed = 10
+	dipole_count = 5
+
+	model = LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
+		-10, 10, -5, 5, 2, 3, 0, 5, p_fixed, dipole_count, 0.5
+	)
+
+	dipole_arrangement = model.get_dipoles(20, numpy.random.default_rng(1234))
+	dipoles = dipole_arrangement.dipoles
+
+	assert (
+		len(dipoles) == dipole_count
+	), "Should have had multiple dipole based on count generated."
+
+
+def test_random_count_multiple_dipole_fixed_mag_model_get_dipoles_invariant_xy():
+
+	x_min = -10
+	x_max = 10
+	y_min = -5
+	y_max = 5
+	z_min = 2
+	z_max = 3
+	p_fixed = 10
+	max_frequency = 5
+
+	model = LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
+		x_min, x_max, y_min, y_max, z_min, z_max, 0, max_frequency, p_fixed, 1, 0.5
+	)
+	model.rng = numpy.random.default_rng(1234)
+
+	dipole_arrangement = model.get_dipoles(5)
+	dipoles = dipole_arrangement.dipoles
+
+	assert len(dipoles) == 1, "Should have only had one dipole generated."
+	for i in range(10):
+		dipole_arrangement = model.get_dipoles(max_frequency)
+		dipoles = dipole_arrangement.dipoles
+
+		assert len(dipoles) in (
+			0,
+			1,
+		), "Should have either zero or one dipole generated."
+
+		if len(dipoles) > 0:
+			min_s = numpy.array([x_min, y_min, z_min])
+			max_s = numpy.array([x_max, y_max, z_max])
+
+			numpy.testing.assert_equal(
+				numpy.logical_and(min_s < dipoles[0].s, max_s > dipoles[0].s),
+				True,
+				f"Dipole location [{dipoles[0].s}] should have been between min [{min_s}] and max [{max_s}] bounds.",
+			)
+			assert (
+				dipoles[0].w < 10 ** max_frequency and dipoles[0].w > 10**0
+			), "Dipole frequency should have been between 0 and max."
+
+			numpy.testing.assert_allclose(
+				numpy.linalg.norm(dipoles[0].p),
+				p_fixed,
+				err_msg="Should have had the expected dipole moment magnitude.",
+			)
+
+			_logger.warning(dipoles[0].p)
+			numpy.testing.assert_allclose(
+				dipoles[0].p[2],
+				0,
+				err_msg="Should have had zero z magnitude.",
+			)
+
+
+def test_random_count_multiple_dipole_fixed_mag_model_get_dipoles_invariant_monte_carlo_xy():
+
+	x_min = -10
+	x_max = 10
+	y_min = -5
+	y_max = 5
+	z_min = 2
+	z_max = 3
+	p_fixed = 10
+	max_frequency = 5
+	monte_carlo_n = 20
+
+	model = LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
+		x_min, x_max, y_min, y_max, z_min, z_max, 0, max_frequency, p_fixed, 1, 0.5
+	)
+	model.rng = numpy.random.default_rng(1234)
+
+	dipole_arrangement = model.get_dipoles(5)
+	dipoles = dipole_arrangement.dipoles
+
+	assert len(dipoles) == 1, "Should have only had one dipole generated."
+	for i in range(10):
+		dipoles = model.get_monte_carlo_dipole_inputs(monte_carlo_n, max_frequency)
+
+		min_s = numpy.array([x_min, y_min, z_min])
+		max_s = numpy.array([x_max, y_max, z_max])
+
+		_logger.warning(dipoles)
+		_logger.warning(dipoles[:, 0, 0:3])
+		_logger.warning(dipoles[:, 0, 3:6])
+		_logger.warning(dipoles[:, 0, 6])
+
+		ps = dipoles[:, 0, 0:3]
+		ss = dipoles[:, 0, 3:6]
+		ws = dipoles[:, 0, 6]
+
+		numpy.testing.assert_equal(
+			numpy.logical_and(min_s < ss, max_s > ss).all(),
+			True,
+			f"Dipole location [{ss}] should have been between min [{min_s}] and max [{max_s}] bounds.",
+		)
+		assert (ws < 10**max_frequency).all() and (
+			ws > 10**0
+		).all(), "Dipole frequency should have been between 0 and max."
+
+		norms = numpy.linalg.norm(ps, axis=1)
+		filtered_norms = norms[norms > 0]
+		numpy.testing.assert_allclose(
+			filtered_norms,
+			p_fixed,
+			err_msg="Should have had the expected dipole moment magnitude.",
+		)
+
+		numpy.testing.assert_allclose(
+			ps[:, 2],
+			0,
+			err_msg="Should have had zero z magnitude.",
+		)
+
+
+def test_random_count_multiple_dipole_shape():
+
+	x_min = -10
+	x_max = 10
+	y_min = -5
+	y_max = 5
+	z_min = 2
+	z_max = 3
+	p_fixed = 10
+	max_frequency = 5
+	num_dipoles = 13
+	monte_carlo_n = 11
+
+	model = LogSpacedRandomCountMultipleDipoleFixedMagnitudeXYModel(
+		x_min,
+		x_max,
+		y_min,
+		y_max,
+		z_min,
+		z_max,
+		0,
+		max_frequency,
+		p_fixed,
+		num_dipoles,
+		0.5,
+	)
+	model.rng = numpy.random.default_rng(1234)
+
+	actual_shape = model.get_monte_carlo_dipole_inputs(
+		monte_carlo_n, max_frequency
+	).shape
+
+	numpy.testing.assert_equal(
+		actual_shape,
+		(monte_carlo_n, num_dipoles, 7),
+		err_msg="shape was wrong for monte carlo outputs",
+	)
+
+	actual_shape = model.get_monte_carlo_dipole_inputs(
+		monte_carlo_n, max_frequency, rng_to_use=numpy.random.default_rng(1515)
+	).shape
+
+	numpy.testing.assert_equal(
+		actual_shape,
+		(monte_carlo_n, num_dipoles, 7),
+		err_msg="shape was wrong for monte carlo outputs",
+	)