freealg 0.1.11__py3-none-any.whl → 0.7.12__py3-none-any.whl

freealg/distributions/_wachter.py

@@ -13,8 +13,8 @@
 
 import numpy
 from scipy.interpolate import interp1d
-from .._plot_util import plot_density, plot_hilbert, plot_stieltjes, \
-    plot_stieltjes_on_disk, plot_samples
+from .._free_form._plot_util import plot_density, plot_hilbert, \
+    plot_stieltjes, plot_stieltjes_on_disk, plot_samples
 
 try:
     from scipy.integrate import cumtrapz
@@ -115,7 +115,7 @@ class Wachter(object):
     # density
     # =======
 
-    def density(self, x=None, plot=False, latex=False, save=False):
+    def density(self, x=None, plot=False, latex=False, save=False, eig=None):
         """
         Density of distribution.
 
@@ -142,6 +142,10 @@ class Wachter(object):
             assumed to the save filename (with the file extension). This option
             is relevant only if ``plot=True``.
 
+        eig : numpy.array, default=None
+            A collection of eigenvalues to compare to via histogram. This
+            option is relevant only if ``plot=True``.
+
         Returns
         -------
 
@@ -179,7 +183,11 @@ class Wachter(object):
             numpy.sqrt((self.lam_p - x[mask]) * (x[mask] - self.lam_m))
 
         if plot:
-            plot_density(x, rho, label='', latex=latex, save=save)
+            if eig is not None:
+                label = 'Theoretical'
+            else:
+                label = ''
+            plot_density(x, rho, label=label, latex=latex, save=save, eig=eig)
 
         return rho
 
@@ -282,7 +290,7 @@ class Wachter(object):
         m1 = (-B + sqrtD) / (2 * A)
         m2 = (-B - sqrtD) / (2 * A)
 
-        # pick correct branch only for non‑masked entries
+        # pick correct branch only for non-masked entries
         upper = z.imag >= 0
         branch = numpy.empty_like(m1)
         branch[upper] = numpy.where(sign*m1[upper].imag > 0, m1[upper],
@@ -501,9 +509,6 @@ class Wachter(object):
             :class: custom-dark
         """
 
-        if seed is not None:
-            numpy.random.seed(seed)
-
         if x_min is None:
             x_min = self.lam_m
 
@@ -522,14 +527,23 @@ class Wachter(object):
         inv_cdf = interp1d(cdf, xs, bounds_error=False,
                            fill_value=(x_min, x_max))
 
+        # Random generator
+        rng = numpy.random.default_rng(seed)
+
         # Draw from uniform distribution
         if method == 'mc':
-            u = numpy.random.rand(size)
+            u = rng.random(size)
+
         elif method == 'qmc':
-            engine = qmc.Halton(d=1)
-            u = engine.random(size)
+            try:
+                engine = qmc.Halton(d=1, scramble=True, rng=rng)
+            except TypeError:
+                # Older scipy versions
+                engine = qmc.Halton(d=1, scramble=True, seed=rng)
+            u = engine.random(size).ravel()
+
         else:
-            raise ValueError('"method" is invalid.')
+            raise NotImplementedError('"method" is invalid.')
 
         # Draw from distribution by mapping from inverse CDF
         samples = inv_cdf(u).ravel()
@@ -582,15 +596,13 @@ class Wachter(object):
             >>> A = wa.matrix(2000)
         """
 
-        if seed is not None:
-            numpy.random.seed(seed)
-
         n = size
         m1 = int(self.a * n)
         m2 = int(self.b * n)
 
-        X = numpy.random.randn(n, m1)
-        Y = numpy.random.randn(n, m2)
+        rng = numpy.random.default_rng(seed)
+        X = rng.standard_normal((n, m1))
+        Y = rng.standard_normal((n, m2))
 
         Sx = X @ X.T
         Sy = Y @ Y.T

freealg/distributions/_wigner.py

@@ -13,8 +13,8 @@
 
 import numpy
 from scipy.interpolate import interp1d
-from .._plot_util import plot_density, plot_hilbert, plot_stieltjes, \
-    plot_stieltjes_on_disk, plot_samples
+from .._free_form._plot_util import plot_density, plot_hilbert, \
+    plot_stieltjes, plot_stieltjes_on_disk, plot_samples
 
 try:
     from scipy.integrate import cumtrapz
@@ -96,7 +96,7 @@ class Wigner(object):
     # density
     # =======
 
-    def density(self, x=None, plot=False, latex=False, save=False):
+    def density(self, x=None, plot=False, latex=False, save=False, eig=None):
         """
         Density of distribution.
 
@@ -123,6 +123,10 @@ class Wigner(object):
             assumed to the save filename (with the file extension). This option
             is relevant only if ``plot=True``.
 
+        eig : numpy.array, default=None
+            A collection of eigenvalues to compare to via histogram. This
+            option is relevant only if ``plot=True``.
+
         Returns
         -------
 
@@ -159,7 +163,11 @@ class Wigner(object):
             numpy.sqrt(self.r**2 - x[mask]**2)
 
         if plot:
-            plot_density(x, rho, label='', latex=latex, save=save)
+            if eig is not None:
+                label = 'Theoretical'
+            else:
+                label = ''
+            plot_density(x, rho, label=label, latex=latex, save=save, eig=eig)
 
         return rho
 
@@ -478,9 +486,6 @@ class Wigner(object):
             :class: custom-dark
         """
 
-        if seed is not None:
-            numpy.random.seed(seed)
-
         if x_min is None:
             x_min = self.lam_m
 
@@ -499,14 +504,23 @@ class Wigner(object):
         inv_cdf = interp1d(cdf, xs, bounds_error=False,
                            fill_value=(x_min, x_max))
 
+        # Random generator
+        rng = numpy.random.default_rng(seed)
+
         # Draw from uniform distribution
         if method == 'mc':
-            u = numpy.random.rand(size)
+            u = rng.random(size)
+
         elif method == 'qmc':
-            engine = qmc.Halton(d=1)
-            u = engine.random(size)
+            try:
+                engine = qmc.Halton(d=1, scramble=True, rng=rng)
+            except TypeError:
+                # Older scipy versions
+                engine = qmc.Halton(d=1, scramble=True, seed=rng)
+            u = engine.random(size).ravel()
+
         else:
-            raise ValueError('"method" is invalid.')
+            raise NotImplementedError('"method" is invalid.')
 
         # Draw from distribution by mapping from inverse CDF
         samples = inv_cdf(u).ravel()
@@ -556,12 +570,11 @@ class Wigner(object):
             >>> A = wg.matrix(2000)
         """
 
-        if seed is not None:
-            numpy.random.seed(seed)
+        rng = numpy.random.default_rng(seed)
 
         # Parameters
         n = size
-        X = numpy.random.randn(n, n)
+        X = rng.standard_normal(size=(n, n))
         X = (numpy.triu(X, 0) + numpy.triu(X, 1).T)
 
         return X * (self.r / (2.0 * numpy.sqrt(n)))

freealg/visualization/__init__.py

@@ -0,0 +1,12 @@
+# SPDX-FileCopyrightText: Copyright 2026, Siavash Ameli <sameli@berkeley.edu>
+# SPDX-License-Identifier: BSD-3-Clause
+# SPDX-FileType: SOURCE
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the license found in the LICENSE.txt file in the root
+# directory of this source tree.
+
+from ._rgb_hsv import rgb_hsv
+from ._glue_util import glue_branches
+
+__all__ = ['rgb_hsv', 'glue_branches']

freealg/visualization/_glue_util.py

@@ -0,0 +1,32 @@
+# SPDX-FileCopyrightText: Copyright 2026, Siavash Ameli <sameli@berkeley.edu>
+# SPDX-License-Identifier: BSD-3-Clause
+# SPDX-FileType: SOURCE
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the license found in the LICENSE.txt file in the root
+# directory of this source tree.
+
+
+# =======
+# Imports
+# =======
+
+import numpy
+
+__all__ = ['glue_branches']
+
+
+# =============
+# glue branches
+# =============
+
+def glue_branches(z, m1, m2):
+    """
+    m12 is the mixing of m1 and m2 where it contains m1 on C^+ and m2 on C^-.
+    """
+
+    m12 = numpy.array(m2, copy=True)
+    mask_p = numpy.imag(z) >= 0.0
+    m12[mask_p] = m1[mask_p]
+
+    return m12

freealg/visualization/_rgb_hsv.py

@@ -0,0 +1,125 @@
+# SPDX-FileCopyrightText: Copyright 2026, Siavash Ameli <sameli@berkeley.edu>
+# SPDX-License-Identifier: BSD-3-Clause
+# SPDX-FileType: SOURCE
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the license found in the LICENSE.txt file in the root directory
+# of this source tree.
+
+
+# =======
+# Imports
+# =======
+
+import numpy
+import matplotlib
+
+__all__ = ['rgb_hsv']
+
+
+# =======
+# rgb hsv
+# =======
+
+def rgb_hsv(c, shift=0.0, thresh=numpy.inf, n_mod=12.0, n_ph=12.0, vmin=0.35,
+            vmax=1.0, tile_gamma=1.0, tile_mix=1.0):
+    """
+    Convert complex field c to RGB via HSV domain coloring.
+
+    Parameters
+    ----------
+    c : array_like of complex
+        Complex field.
+
+    shift : float, default 0.0
+        Phase offset in turns (1.0 = full 2*pi rotation). Applied to hue.
+
+    thresh : float, default numpy.inf
+        Optional cap on |c| used for magnitude-related terms. Use to prevent
+        very large magnitudes from dominating the encoding.
+
+    n_mod : float, default 12.0
+        Number of modulus steps per 2*pi in log(|c|). Higher -> more concentric
+        rings. Set to 0.0 to disable modulus stepping.
+
+    n_ph : float, default 12.0
+        Number of phase steps per 2*pi in arg(c). Higher -> more angular
+        sectors. Set to 0.0 to disable phase stepping.
+
+    vmin : float, default 0.35
+        Minimum brightness for the tiling shading (darkest parts of tiles).
+
+    vmax : float, default 1.0
+        Maximum brightness for the tiling shading (brightest parts of tiles).
+        Lowering vmax (e.g. 0.8-0.9) can reduce the "neon" look.
+
+    tile_gamma : float, default 1.0
+        Shapes the within-tile ramp. 1.0 = linear sawtooth. >1.0 makes tiles
+        stay darker longer and brighten sharply near boundaries. <1.0 brightens
+        earlier.
+
+    tile_mix : float in [0, 1], default 1.0
+        Mix between original magnitude brightness and tiling shading:
+          0.0 -> value = 1 - exp(-|c|) (your original, no tiling influence)
+          1.0 -> value = tiling shading only (Wegert-style tiling look)
+        Intermediate values overlay tiling onto the original magnitude shading.
+
+    Notes
+    -----
+
+    The coloring technique is inspired from [1]_.
+
+    References
+    ----------
+
+    [1] Wegert, E. (2015) "Visual Complex Functions: An Introduction +with
+        Phase Portraits", Springer.
+        doi: https://doi.org/10.1007/978-3-0348-0180-5
+    """
+
+    hue = (numpy.angle(c) + numpy.pi) / (2.0 * numpy.pi)
+
+    hue = (hue + shift) % 1.0
+
+    r = numpy.abs(c)
+    if numpy.isfinite(thresh):
+        r = numpy.minimum(r, thresh)
+
+    value0 = 1.0 - numpy.exp(-r)
+
+    eps = 1e-300
+    tau = 2.0 * numpy.pi
+
+    g = numpy.ones_like(hue)
+
+    if n_mod and n_mod > 0.0:
+        x_mod = (n_mod / tau) * numpy.log(r + eps)
+        g_mod = numpy.ceil(x_mod) - x_mod
+        g = g * g_mod
+
+    if n_ph and n_ph > 0.0:
+        theta = (numpy.angle(c) + numpy.pi) % tau
+
+        x_ph = (n_ph / tau) * theta
+        g_ph = numpy.ceil(x_ph) - x_ph
+        g = g * g_ph
+
+    g = numpy.clip(g, 0.0, 1.0)
+    if tile_gamma and tile_gamma != 1.0:
+        g = g ** float(tile_gamma)
+
+    vmin = float(numpy.clip(vmin, 0.0, 1.0))
+    vmax = float(numpy.clip(vmax, 0.0, 1.0))
+    if vmax < vmin:
+        vmin, vmax = vmax, vmin
+
+    value_tile = vmin + (vmax - vmin) * g
+
+    tile_mix = float(numpy.clip(tile_mix, 0.0, 1.0))
+    value = (1.0 - tile_mix) * value0 + tile_mix * value_tile
+
+    saturation = numpy.ones_like(hue)
+    hsv = numpy.stack((hue, saturation, numpy.clip(value, 0.0, 1.0)), axis=-1)
+    rgb = matplotlib.colors.hsv_to_rgb(hsv)
+
+    return rgb

freealg-0.7.12.dist-info/METADATA

@@ -0,0 +1,172 @@
+Metadata-Version: 2.4
+Name: freealg
+Version: 0.7.12
+Summary: Free probability for large matrices
+Home-page: https://github.com/ameli/freealg
+Download-URL: https://github.com/ameli/freealg/archive/main.zip
+Project-URL: Documentation, https://ameli.github.io/freealg
+Project-URL: Source, https://github.com/ameli/freealg
+Project-URL: Tracker, https://github.com/ameli/freealg/issues
+Keywords: linalg,free-probability
+Platform: Linux
+Platform: OSX
+Platform: Windows
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: MacOS
+Classifier: Natural Language :: English
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE.txt
+License-File: AUTHORS.txt
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: texplot
+Requires-Dist: matplotlib
+Requires-Dist: colorcet
+Requires-Dist: statsmodels
+Requires-Dist: numba
+Requires-Dist: tqdm
+Provides-Extra: test
+Provides-Extra: docs
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license-file
+Dynamic: platform
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+.. figure:: https://raw.githubusercontent.com/ameli/freealg/refs/heads/main/docs/source/_static/images/icons/logo-freealg-light.png
+    :align: left
+    :width: 240
+
+`Paper <https://arxiv.org/abs/2506.11994>`__ |
+`Slides <https://www.dropbox.com/scl/fi/03gjuyz17k9yhsqy0isoz/free_decomporession_slides.pdf?rlkey=8f82mhciyl2ju02l7hv1md5li&st=26xmhjga&dl=0>`__ |
+`Docs <https://ameli.github.io/freealg>`__ |
+`Live Demo <https://colab.research.google.com/github/ameli/freealg/blob/main/notebooks/quick_start.ipynb>`__
+
+.. `Slides <https://ameli.github.io/freealg/_static/data/slides.pdf>`__ |
+
+*freealg* is a Python package that employs **free** probability to evaluate the
+spectral densities of large matrix **form**\ s. The fundamental algorithm
+employed by *freealg* is **free decompression**, which extrapolates from the
+empirical spectral densities of small  submatrices to infer the eigenspectrum
+of extremely large matrices. 
+
+Install
+=======
+
+|pypi|
+
+Install with ``pip``:
+
+.. code-block::
+
+    pip install freealg
+
+Alternatively, clone the source code and install with
+
+.. code-block::
+
+    cd source_dir
+    pip install .
+
+Documentation
+=============
+
+|deploy-docs|
+
+Documentation is available at `ameli.github.io/freealg <https://ameli.github.io/freealg>`__.
+
+Quick Usage
+===========
+
+The following code estimates the eigenvalues of a very large Wishart matrix
+using a much smaller Wishart matrix.
+
+.. code-block:: python
+
+    >>> import freealg as fa
+    >>> mp = fa.distributions.MarchenkoPastur(1/50) # Wishart matrices with aspect ratio 1/50
+    >>> A = mp.matrix(1000)                         # Sample a 1000 x 1000 Wishart matrix
+    >>> eigs = fa.eigvalsh(A, 100_000)              # Estimate the eigenvalues of 100000 x 100000
+
+For more details on how to interface with *freealg* check out the 
+`Live Demo <https://colab.research.google.com/github/ameli/freealg/blob/main/notebooks/quick_start.ipynb>`__.
+
+
+Test
+====
+
+|build-linux| 
+
+You may test the package with `tox <https://tox.wiki/>`__:
+
+.. code-block::
+
+    cd source_dir
+    tox
+
+Alternatively, test with `pytest <https://pytest.org>`__:
+
+.. code-block::
+
+    cd source_dir
+    pytest
+
+How to Contribute
+=================
+
+We welcome contributions via GitHub's pull request. Developers should review
+our `Contributing Guidelines <https://github.com/ameli/freealg/blob/main/CONTRIBUTING.rst>`__
+before submitting their code. If you do not feel comfortable modifying the
+code, we also welcome feature requests and bug reports.
+
+How to Cite
+===========
+
+If you use this work, please cite our `paper <https://openreview.net/pdf?id=2CeGVUpOd7>`__.
+
+  .. code::
+
+      @inproceedings{
+            AMELI-2025,
+            title={Spectral Estimation with Free Decompression},
+            author={Siavash Ameli and Chris van der Heide and Liam Hodgkinson and Michael W. Mahoney},
+            booktitle={The Thirty-ninth Annual Conference on Neural Information Processing Systems},
+            year={2025},
+            url={https://openreview.net/forum?id=2CeGVUpOd7}
+      }
+
+
+License
+=======
+
+|license|
+
+.. |build-linux| image:: https://img.shields.io/github/actions/workflow/status/ameli/freealg/build-linux.yml
+   :target: https://github.com/ameli/freealg/actions?query=workflow%3Abuild-linux 
+.. |deploy-docs| image:: https://img.shields.io/github/actions/workflow/status/ameli/freealg/deploy-docs.yml?label=docs
+   :target: https://github.com/ameli/freealg/actions?query=workflow%3Adeploy-docs
+.. |pypi| image:: https://img.shields.io/pypi/v/freealg
+   :target: https://pypi.org/project/freealg/
+.. |license| image:: https://img.shields.io/github/license/ameli/freealg
+   :target: https://opensource.org/licenses/BSD-3-Clause

freealg-0.7.12.dist-info/RECORD

@@ -0,0 +1,53 @@
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+freealg/visualization/__init__.py,sha256=NLq_zwueF7ytZ8sl8zLPqm-AODxxXNvfMozHGmmklcE,435
+freealg/visualization/_glue_util.py,sha256=2oKnEYjUOS4OZfivmciVLauVr53kyHMwi6c2zRKilTQ,693
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+freealg-0.7.12.dist-info/licenses/AUTHORS.txt,sha256=0b67Nz4_JgIzUupHJTAZxu5QdSUM_HRM_X_w4xCb17o,30
+freealg-0.7.12.dist-info/licenses/LICENSE.txt,sha256=J-EEYEtxb3VVf_Bn1TYfWnpY5lMFIM15iLDDcnaDTPA,1443
+freealg-0.7.12.dist-info/METADATA,sha256=vzphSfQr5LulLS_XcKV38zmgb0PFfRPhMhqO0XCrmQg,5537
+freealg-0.7.12.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+freealg-0.7.12.dist-info/top_level.txt,sha256=eR2wrgYwDdnnJ9Zf5PruPqe4kQav0GMvRsqct6y00Q8,8
+freealg-0.7.12.dist-info/RECORD,,

{freealg-0.1.11.dist-info → freealg-0.7.12.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any