acoular 23.11__tar.gz → 24.3__tar.gz

acoular-24.3/.github/workflows/build_docs.yml

@@ -0,0 +1,43 @@
+name: Build docs and deploy
+
+#DEPLOY NOTE: This workflow will only deploy the docs when a workflow is manually triggered from the main branch via github! 
+
+on:
+  pull_request:
+    branches: [ master ] # build docs as additional test on PRs to main
+  workflow_dispatch:
+    branches: [ '*' ] # allow manual trigger for all branches
+  
+permissions:
+  contents: write
+
+jobs:
+  sphinx:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          sudo apt-get install graphviz  
+          sudo apt-get install libportaudio2
+          python -m pip install --upgrade pip
+          pip install ".[dev]"
+      - name: Build docs 
+        run: |
+          cd docs
+          make html
+      - name: Deploy docs
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name =='workflow_dispatch' && github.ref == 'refs/heads/master' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/build/html/
+          cname: www.acoular.org
+          force_orphan: true # This allows you to make your publish branch with only the latest commit.
+          enable_jekyll: false
+

acoular-24.3/.zenodo.json

@@ -0,0 +1,47 @@
+{
+  "metadata": {
+    "title": "Acoular – Acoustic testing and source mapping software",
+    "license": "BSD",
+    "keywords": [
+      "acoustics",
+      "beamforming",
+      "microphone array"
+    ],
+    "upload_type": "software",
+    "creators": [
+      {
+        "affiliation": "Department of Engineering Acoustics, TU Berlin",
+        "name": "Sarradj, Ennes",
+        "orcid": "0000-0002-0274-8456"
+      },
+      {
+        "affiliation": "Department of Engineering Acoustics, TU Berlin",
+        "name": "Herold, Gert",
+        "orcid": "0000-0001-5284-051X"
+      },
+      {
+        "affiliation": "Department of Engineering Acoustics, TU Berlin",
+        "name": "Kujawski, Adam",
+        "orcid": "0000-0003-4579-8813"
+      },
+      {
+        "affiliation": "Department of Engineering Acoustics, TU Berlin",
+        "name": "Jekosch, Simon"
+      },
+      {
+        "affiliation": "Department of Engineering Acoustics, TU Berlin",
+        "name": "Pelling, Art J. R.",
+        "orcid": "0000-0003-3228-6069"
+
+      },
+      {
+        "affiliation": "Department of Engineering Acoustics, TU Berlin",
+        "name": "Czuchaj, Mikolaj"
+      },
+      {
+        "affiliation": "Department of Engineering Acoustics, TU Berlin",
+        "name": "Gensch, Tom"
+      }
+    ]
+  }
+}

{acoular-23.11 → acoular-24.3}/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2006-2023 The acoular developers.
+Copyright (c) Acoular Development Team.
 All rights reserved.
 
 

{acoular-23.11 → acoular-24.3}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.1
 Name: acoular
-Version: 23.11
+Version: 24.3
 Summary: Python library for acoustic beamforming
 Project-URL: homepage, https://acoular.org
 Project-URL: documentation, https://acoular.org
 Project-URL: repository, https://github.com/acoular/acoular
 Author-email: Acoular Development Team <info@acoular.org>
-Maintainer-email: Adam Kujawski <adam.kujawski@tu-berlin.de>, Art Pelling <a.pelling@tu-berlin.de>, Ennes Sarradj <ennes.sarradj@tu-berlin.de>, Gert Herlod <gert.herold@tu-berlin.de>, Mikolaj Czuchaj <mikolaj.czuchaj@tu-berlin.de>, Simon Jekosch <s.jekosch@tu-berlin.de>
-License: Copyright (c) 2006-2023 The acoular developers.
+Maintainer-email: Adam Kujawski <adam.kujawski@tu-berlin.de>, Art Pelling <a.pelling@tu-berlin.de>, Ennes Sarradj <ennes.sarradj@tu-berlin.de>, Gert Herold <gert.herold@tu-berlin.de>, Mikolaj Czuchaj <mikolaj.czuchaj@tu-berlin.de>, Simon Jekosch <s.jekosch@tu-berlin.de>
+License: Copyright (c) Acoular Development Team.
         All rights reserved.
         
         
@@ -57,10 +57,18 @@ Requires-Dist: scipy>=1.1.0
 Requires-Dist: tables>=3.4.4
 Requires-Dist: traits>=6.0
 Provides-Extra: dev
+Requires-Dist: graphviz; extra == 'dev'
+Requires-Dist: ipython; extra == 'dev'
+Requires-Dist: matplotlib; extra == 'dev'
 Requires-Dist: nox; extra == 'dev'
+Requires-Dist: numpydoc; extra == 'dev'
+Requires-Dist: pickleshare; extra == 'dev'
+Requires-Dist: sounddevice; extra == 'dev'
+Requires-Dist: sphinx; extra == 'dev'
 Provides-Extra: full
 Requires-Dist: matplotlib; extra == 'full'
 Requires-Dist: pylops; extra == 'full'
+Requires-Dist: sounddevice; extra == 'full'
 Description-Content-Type: text/markdown
 
 ![Acoular Logo](./docs/source/_static/Acoular_logo.png)

{acoular-23.11 → acoular-24.3}/acoular/fbeamform.py

@@ -43,13 +43,20 @@ invert, dot, newaxis, zeros, linalg, \
 searchsorted, pi, sign, diag, arange, sqrt, log10, \
 reshape, hstack, vstack, eye, tril, size, clip, tile, round, delete, \
 absolute, argsort, sum, hsplit, fill_diagonal, zeros_like, \
-einsum, ndarray, isscalar, inf, real, unique
+einsum, ndarray, isscalar, inf, real, unique, atleast_2d, einsum_path,trace
 
 from numpy.linalg import norm
 
 from sklearn.linear_model import LassoLars, LassoLarsCV, LassoLarsIC,\
 OrthogonalMatchingPursuitCV, LinearRegression
 
+#check for sklearn version to account for incompatible behavior
+import sklearn
+from packaging.version import parse
+sklearn_ndict = {}
+if parse(sklearn.__version__)<parse('1.4'):
+    sklearn_ndict['normalize'] = False
+
 from scipy.optimize import nnls, linprog, fmin_l_bfgs_b, shgo
 from scipy.linalg import inv, eigh, eigvals, fractional_matrix_power
 from warnings import warn
@@ -170,7 +177,7 @@ class SteeringVector( HasPrivateTraits ):
 
     @property_depends_on('grid.digest, mics.digest, env.digest')
     def _get_rm ( self ):
-        return self.env._r(self.grid.pos(), self.mics.mpos)
+        return atleast_2d(self.env._r(self.grid.pos(), self.mics.mpos))
  
     @cached_property
     def _get_digest( self ):
@@ -1547,7 +1554,7 @@ class BeamformerOrth( BeamformerBase ):
                                                 self.r_diag, 
                                                 normFactor, 
                                                 steer_vector(f[i]), 
-                                                (ones(1), eve[:, n:n+1]))[0]
+                                                (ones(1), eve[:, n].reshape((-1,1))))[0]
                     ac[i, beamformerOutput.argmax()]+=eva[n]/numchannels
                 fr[i] = 1
 
@@ -1890,16 +1897,16 @@ class BeamformerCMF ( BeamformerBase ):
                 # choose method
                 if self.method == 'LassoLars':
                     model = LassoLars(alpha = self.alpha * unit,
-                                      max_iter = self.max_iter, 
-                                      normalize=False)
+                                      max_iter = self.max_iter,
+                                      **sklearn_ndict)
                 elif self.method == 'LassoLarsBIC':
                     model = LassoLarsIC(criterion = 'bic',
-                                        max_iter = self.max_iter, 
-                                        normalize=False,)
+                                        max_iter = self.max_iter,
+                                        **sklearn_ndict)
                 elif self.method == 'OMPCV':
-                    model = OrthogonalMatchingPursuitCV(normalize=False)
+                    model = OrthogonalMatchingPursuitCV(**sklearn_ndict)
                 elif self.method == 'NNLS':
-                    model = LinearRegression(normalize=False, positive=True)
+                    model = LinearRegression(positive=True)
 
                 if self.method == 'Split_Bregman' and PYLOPS_TRUE:   
                     Oop = MatrixMult(A) #tranfer operator 
@@ -2041,7 +2048,8 @@ class BeamformerSODIX( BeamformerBase ):
                                           group)
             ac = self.h5f.get_data_by_reference('result','/'+nodename)
             fr = self.h5f.get_data_by_reference('freqs','/'+nodename)
-            return (ac,fr)    
+            gpos = None
+            return (ac,fr,gpos) 
     
     @property_depends_on('ext_digest')
     def _get_sodix_result ( self ):
@@ -2059,7 +2067,7 @@ class BeamformerSODIX( BeamformerBase ):
                     config.global_caching == 'none' or 
                     (config.global_caching == 'individual' and self.cached == False)
                 ):
-                (ac,fr) = self._get_filecache() 
+                (ac,fr,gpos) = self._get_filecache() 
                 if ac and fr: 
                     if not fr[f.ind_low:f.ind_high].all():                       
                         if config.global_caching == 'readonly': 
@@ -2216,21 +2224,28 @@ class BeamformerSODIX( BeamformerBase ):
 
                         '''           
                         #### the sodix function ####
-                        Djm = D.reshape([numpoints,num_mics])                           
-                        csmmod = einsum('jm,jm,jn,jn->mn',h.T,Djm,Djm,h.T.conj() )        
-                        func = sum(absolute((csm - csmmod)))**2 + self.alpha*norm(Djm,self.pnorm)
-                        ####the sodix  derivitaive ####
-                        inner = csm - einsum('jl,jl,jm,jm->lm',h.T,Djm,Djm,h.T.conj() )      
-                        derdrl = -4 *  Djm * real(einsum('rm,rl,lm->rl',h.T,h.T.conj(),inner)) + \
-                            self.alpha * (abs(Djm)/norm(Djm,self.pnorm))**(1-self.pnorm)*sign(Djm)
-
-                        return  func, derdrl[:].flatten()  #func[0]
-                    
+                        Djm = D.reshape([numpoints,num_mics])
+                        p = h.T * Djm
+                        csm_mod = dot(p.T, p.conj())
+                        Q = csm - csm_mod
+                        func = sum((absolute(Q))**2)
+
+                        # subscripts and operands for numpy einsum and einsum_path
+                        subscripts = 'rl,rm,ml->rl'
+                        operands = (h.T,h.T.conj()*Djm,Q)
+                        es_path = einsum_path(subscripts, *operands, optimize='greedy')[0]
+
+                        #### the sodix derivative ####
+                        derdrl = einsum(subscripts, *operands, optimize=es_path)
+                        derdrl = -4 * real(derdrl)
+                        return func, derdrl.ravel()
+
                     ##### initial guess #### 
                     if all(ac[(i-1)]==0):
                          D0 = ones([numpoints,num_mics])
                     else:
-                         D0 = ac[(i-1)]
+                         D0 = sqrt(ac[(i-1)]*
+                             real((trace(csm)/trace(array(self.freq_data.csm[i-1], dtype='complex128',copy=1)))))
                     
                     #boundarys - set to non negative [2*(numpoints*num_mics)]
                     boundarys = tile((0, +inf), (numpoints*num_mics,1))
@@ -2239,11 +2254,11 @@ class BeamformerSODIX( BeamformerBase ):
                     # see https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.fmin_l_bfgs_b.html                    
 
                     qi = ones([numpoints,num_mics])
-                    qi, yval, dicts =  fmin_l_bfgs_b(function, D0, fprime=None, args=(),  #None  
-                                                         approx_grad=0, bounds=boundarys, #approx_grad 0 or True
-                                                         factr=100.0, pgtol=1e-09, epsilon=1e-08,
-                                                          iprint=0, maxfun=1500000, maxiter=self.max_iter,
-                                                          disp=None, callback=None, maxls=20)
+                    qi, yval, dicts =  fmin_l_bfgs_b(function, D0, fprime=None, args=(),
+                                                         approx_grad=0, bounds=boundarys, 
+                                                         factr=100.0, pgtol=1e-12, epsilon=1e-08,
+                                                          iprint=-1, maxfun=1500000, maxiter=self.max_iter,
+                                                          disp=-1, callback=None, maxls=20)
                     #squared pressure
                     ac[i]=qi**2
                 else:

{acoular-23.11 → acoular-24.3}/acoular/tests/test_beamformer_results.py

@@ -21,7 +21,14 @@ RectGrid, BeamformerBase, BeamformerEig, BeamformerOrth, BeamformerCleansc, \
 MaskedTimeSamples, BeamformerCMF, \
 BeamformerCapon, BeamformerMusic, BeamformerDamas, BeamformerClean, \
 BeamformerFunctional, BeamformerDamasPlus, BeamformerGIB, BeamformerGridlessOrth,\
-SteeringVector, Environment
+SteeringVector, Environment, BeamformerSODIX
+
+# copy CMF classes as workaround so that reference data name is unique later
+class BeamformerCMFLassoLarsBIC (BeamformerCMF):
+    pass
+
+class BeamformerCMFNNLS (BeamformerCMF):
+    pass
 
 # if this flag is set to True
 WRITE_NEW_REFERENCE_DATA = False
@@ -70,12 +77,14 @@ def fbeamformers():
     bdp = BeamformerDamasPlus(beamformer=bb, n_iter=100, cached = False)
     bo = BeamformerOrth(freq_data=f, steer=st, r_diag=True, eva_list=list(range(38,54)), cached = False)
     bs = BeamformerCleansc(freq_data=f, steer=st, r_diag=True, cached = False)
-    bcmf = BeamformerCMF(freq_data=f, steer=st, method='LassoLarsBIC', cached = False)
+    bcmflassobic = BeamformerCMFLassoLarsBIC(freq_data=f, steer=st, method='LassoLarsBIC', cached = False)
+    bcmfnnls = BeamformerCMFNNLS(freq_data=f, steer=st, method='NNLS', cached = False)
     bl = BeamformerClean(beamformer=bb, n_iter=10, cached = False)
     bf = BeamformerFunctional(freq_data=f, steer=st, r_diag=False, gamma=3, cached = False)
     bgib = BeamformerGIB(freq_data=f, steer=st, method= 'LassoLars', n=2, cached = False)
     bgo = BeamformerGridlessOrth(freq_data=f, steer=st, r_diag=False, n=1,  shgo={'n':16}, cached = False)
-    return (bbase, bc, beig, bm, bl, bo, bs, bd, bcmf, bf, bdp, bgib, bgo)
+    bsodix = BeamformerSODIX(freq_data=f, steer=st,max_iter=10, cached = False)
+    return (bbase, bc, beig, bm, bl, bo, bs, bd, bcmflassobic, bcmfnnls, bf, bdp, bgib, bgo,bsodix)
 
 class acoular_beamformer_test(unittest.TestCase):
 

{acoular-23.11 → acoular-24.3}/acoular/tools.py

@@ -24,11 +24,11 @@ from numpy import array, concatenate, newaxis, where,arctan2,sqrt,pi,mod,zeros,\
 from numpy.linalg import norm
 from numpy.ma import masked_where
 from .spectra import synthetic
-from traits.api import Bool, CArray, Float, HasPrivateTraits, Instance, Property, Either
+from traits.api import Bool, CArray, HasPrivateTraits, Instance, Property, Any
 
 from scipy.special import spherical_yn, spherical_jn, sph_harm
 from scipy.spatial.distance import cdist
-
+from copy import copy
 
 class MetricEvaluator(HasPrivateTraits):
     """Evaluate the reconstruction performance of source mapping methods.
@@ -104,8 +104,11 @@ class MetricEvaluator(HasPrivateTraits):
         sectors = []
         for i in range(ns):
             loc = self.target_grid.gpos[:,i]
-            sectors.append(
-                ac.CircSector(r=r[i],x=loc[0],y=loc[1]))
+            sector = copy(self.sector)
+            sector.r = r[i]
+            sector.x = loc[0]
+            sector.y = loc[1]
+            sectors.append(sector)
         return sectors
 
     def _integrate_sectors(self):
@@ -116,11 +119,12 @@ class MetricEvaluator(HasPrivateTraits):
         array (num_freqs,num_sources)
             returns the integrated Pa**2 values for each sector
         """
+        sectors = self.sectors
         results = empty(shape=self.target_data.shape)
         for f in range(self.target_data.shape[0]):
             data = self.data[f]
             for i in range(self.target_data.shape[1]):
-                sector = self.sectors[i]
+                sector = sectors[i]
                 results[f,i] = ac.integrate(data,self.grid,sector)
                 if not self.multi_assignment:
                     indices = self.grid.subdomain(sector)

{acoular-23.11 → acoular-24.3}/acoular/tprocess.py

@@ -40,7 +40,7 @@
 from numpy import array, empty, empty_like, pi, sin, sqrt, zeros, newaxis, unique, \
 int16, nan, concatenate, sum, float64, identity, argsort, interp, arange, append, \
 linspace, flatnonzero, argmin, argmax, delete, mean, inf, asarray, stack, sinc, exp, \
-polymul, arange, cumsum, ceil, split
+polymul, arange, cumsum, ceil, split, array_equal
 
 from numpy.linalg import norm
 from numpy.matlib import repmat
@@ -957,7 +957,7 @@ class SpatialInterpolator(TimeInOut):
         # Interpolation for 1D Arrays 
         if self.array_dimension =='1D' or self.array_dimension =='ring':
             #for rotation add phidelay
-            if not phiDelay == []:
+            if not array_equal(phiDelay,[]):
                 xInterpHelp = repmat(virtNewCoord[0, :], nTime, 1) + repmat(phiDelay, virtNewCoord.shape[1], 1).T
                 xInterp = ((xInterpHelp + pi ) % (2 * pi)) - pi #  shifting phi cootrdinate into feasible area [-pi, pi]
             #if no rotation given
@@ -1001,7 +1001,7 @@ class SpatialInterpolator(TimeInOut):
         # Interpolation for arbitrary 2D Arrays
         elif self.array_dimension =='2D':
             #check rotation
-            if not phiDelay == []:
+            if not array_equal(phiDelay,[]):
                 xInterpHelp = repmat(virtNewCoord[0, :], nTime, 1) + repmat(phiDelay, virtNewCoord.shape[1], 1).T
                 xInterp = ((xInterpHelp + pi ) % (2 * pi)) - pi #shifting phi cootrdinate into feasible area [-pi, pi]
             else:
@@ -1081,7 +1081,7 @@ class SpatialInterpolator(TimeInOut):
         # Interpolation for arbitrary 3D Arrays             
         elif self.array_dimension =='3D':
             #check rotation
-            if not phiDelay == []:
+            if not array_equal(phiDelay,[]):
                 xInterpHelp = repmat(virtNewCoord[0, :], nTime, 1) + repmat(phiDelay, virtNewCoord.shape[1], 1).T
                 xInterp = ((xInterpHelp + pi  ) % (2 * pi)) - pi  #shifting phi cootrdinate into feasible area [-pi, pi]
             else:

{acoular-23.11 → acoular-24.3}/acoular/version.py

@@ -5,5 +5,5 @@
 
 # separate file to find out about version without importing the acoular lib
 __author__ = "Acoular Development Team"
-__date__ = "20 November 2023"
-__version__ = "23.11"
+__date__ = "11 March 2024"
+__version__ = "24.03"

{acoular-23.11 → acoular-24.3}/docs/source/get_started/index.rst

@@ -7,10 +7,11 @@ Prerequisites
 -------------
 This "Getting started" tutorial assumes that the Acoular library is :doc:`installed<../install/index>` together with its dependencies and matplotlib, and that the demo finished successfully. If you did not run the demo yet, you should do so by typing into your python console
 
-.. code-block:: console
+.. ipython:: 
 
-    > import acoular
-    > acoular.demo.acoular_demo.run()
+    In [1]: import acoular
+    
+    In [1]: acoular.demo.acoular_demo.run()
 
 This should, after some seconds, produce two pictures (a 64 microphone arrangement and a beamforming map with three sources). You may close the pictures in order to continue. 
 

{acoular-23.11 → acoular-24.3}/docs/source/news/index.rst

@@ -1,5 +1,24 @@
 What's new
 ============
+24.03
+------------
+    * Improve test coverage for :class:`~acoular.fbeamform.BeamformerCMF`
+    * Changes to :class:`~acoular.fbeamform.BeamformerSODIX`:
+        * correction of wrong cost-function 
+        * speedups through the use of `numpy.einsum_path` together with `numpy.einsum`
+        * changed start value `pgtol` for the optimization with `scipy.optimize.fmin_l_bfgs_b` solver
+    * Bugfixes:
+        * fixes unrecognized sector arguments in :class:`~acoular.tools.MetricEvaluator`
+        * handles version-dependent default values for `normalize` attribute in sklearn solvers (relevant for :class:`~acoular.fbeamform.BeamformerCMF` )
+        * fixes bug in :class:`~acoular.fbeamform.BeamformerOrth`: assigned strongest source at grid index 0 when instead of `eva_list` the trait `n` was given
+        * fixes broken :class:`~acoular.tprocess.SpatialInterpolator` 
+        * minor bugfix for single microphone transfer functions calculated with :class:`~acoular.fbeamform.SteeringVector` 
+        * fixes broken `NNLS` method in :class:`~acoular.fbeamform.BeamformerCMF` (wrong keyword argument `normalize`)
+    * Internal:
+        * new GitHub workflow for CI of the documentation 
+        * added Zenodo metadata file
+        * changes to author name in `pyproject.toml`
+
 
 23.11
 ------------

{acoular-23.11 → acoular-24.3}/pyproject.toml

@@ -4,7 +4,7 @@
 
 [project]
 name = "acoular"
-version = "23.11"
+version = "24.03"
 description = "Python library for acoustic beamforming"
 requires-python = ">=3.7,<=11"
 authors = [
@@ -41,7 +41,7 @@ maintainers = [
     {name = "Adam Kujawski", email = "adam.kujawski@tu-berlin.de"},
     {name = "Art Pelling", email = "a.pelling@tu-berlin.de"},
     {name = "Ennes Sarradj", email = "ennes.sarradj@tu-berlin.de"},
-    {name = "Gert Herlod", email = "gert.herold@tu-berlin.de"},
+    {name = "Gert Herold", email = "gert.herold@tu-berlin.de"},
     {name = "Mikolaj Czuchaj", email = "mikolaj.czuchaj@tu-berlin.de"},
     {name = "Simon Jekosch", email = "s.jekosch@tu-berlin.de"},
 ]
@@ -49,10 +49,18 @@ maintainers = [
 [project.optional-dependencies]
 dev = [
     "nox",
+    "sphinx", # docs
+    "matplotlib", # docs
+    "ipython", # docs
+    "numpydoc", # docs
+    "sounddevice", # docs 
+    "graphviz", #docs
+    "pickleshare", #docs
 ]
 full = [
     "matplotlib",
-    "pylops"
+    "pylops",
+    "sounddevice"
 ]
 
 [project.urls]