Version 1.6.1 patch (#222)

* Add support for tensorflow backend which allows for differentiability (#112) * Added support for tensorflow * Updates to get tests passing * Or --> And * Moving modopt to allow working with tensorflow * Fix issues with wos * Fix all flakes finally! * Update modopt/base/backend.py Co-authored-by: Samuel Farrens <[email protected]> * Update modopt/base/backend.py Co-authored-by: Samuel Farrens <[email protected]> * Minute updates to codes * Add dynamic module * Fix docu * Fix PEP Co-authored-by: chaithyagr <[email protected]> Co-authored-by: Samuel Farrens <[email protected]> * Fix 115 (#116) * Fix issues * Add right tests * Fix PEP Co-authored-by: chaithyagr <[email protected]> * Minor bug fix, remove elif (#124) Co-authored-by: chaithyagr <[email protected]> * Add tests for modopt.base.backend and fix minute bug uncovered (#126) * Minor bug fix, remove elif * Add tests for backend * Fix tests * Add tests * Remove cupy * PEP fixes * Fix PEP * Fix PEP and update * Final PEP * Update setup.cfg Co-authored-by: Samuel Farrens <[email protected]> * Update test_base.py Co-authored-by: chaithyagr <[email protected]> Co-authored-by: Samuel Farrens <[email protected]> * Release cleanup (#128) * updated GPU dependencies * added logo to manifest * updated package version and release date * Unpin package dependencies (#189) * unpinned dependencies * updated pinned documentation dependency versions * Add Gradient descent algorithms (#196) * Version 1.5.1 patch release (#114) * Add support for tensorflow backend which allows for differentiability (#112) * Added support for tensorflow * Updates to get tests passing * Or --> And * Moving modopt to allow working with tensorflow * Fix issues with wos * Fix all flakes finally! * Update modopt/base/backend.py Co-authored-by: Samuel Farrens <[email protected]> * Update modopt/base/backend.py Co-authored-by: Samuel Farrens <[email protected]> * Minute updates to codes * Add dynamic module * Fix docu * Fix PEP Co-authored-by: chaithyagr <[email protected]> Co-authored-by: Samuel Farrens <[email protected]> * Fix 115 (#116) * Fix issues * Add right tests * Fix PEP Co-authored-by: chaithyagr <[email protected]> * Minor bug fix, remove elif (#124) Co-authored-by: chaithyagr <[email protected]> * Add tests for modopt.base.backend and fix minute bug uncovered (#126) * Minor bug fix, remove elif * Add tests for backend * Fix tests * Add tests * Remove cupy * PEP fixes * Fix PEP * Fix PEP and update * Final PEP * Update setup.cfg Co-authored-by: Samuel Farrens <[email protected]> * Update test_base.py Co-authored-by: chaithyagr <[email protected]> Co-authored-by: Samuel Farrens <[email protected]> * Release cleanup (#128) * updated GPU dependencies * added logo to manifest * updated package version and release date Co-authored-by: Chaithya G R <[email protected]> Co-authored-by: chaithyagr <[email protected]> * make algorithms a module. * add Gradient Descent Algorithms * enforce WPS compliance. * add test for gradient descent * Docstrings improvements * Add See Also and minor corrections * add idx initialisation for all algorithms. * fix merge error * fix typo Co-authored-by: Samuel Farrens <[email protected]> Co-authored-by: Chaithya G R <[email protected]> Co-authored-by: chaithyagr <[email protected]> * Release cleanup (#198) * started clean up for next release * update progress * further clean up * additional clean up * cleaned up link to logo * fixed index.rst * fixed conflict * Fast Singular Value Thresholding (#209) * add SingularValueThreshold This Method provides 10x faster SVT estimation than the LowRankMatrix Operator. * linting * add test for fast computation. * flake8 compliance * Ignore DAR000 Error. * Update modopt/signal/svd.py tuples in docstring Co-authored-by: Samuel Farrens <[email protected]> * Update modopt/signal/svd.py typo Co-authored-by: Samuel Farrens <[email protected]> * Update modopt/opt/proximity.py typo Co-authored-by: Samuel Farrens <[email protected]> * update docstring * fix isort * Update modopt/signal/svd.py Co-authored-by: Samuel Farrens <[email protected]> * Update modopt/signal/svd.py Co-authored-by: Samuel Farrens <[email protected]> * run isort Co-authored-by: Samuel Farrens <[email protected]> * added writeable input data array feature for benchopt (#213) * removed flake8 limit Co-authored-by: Chaithya G R <[email protected]> Co-authored-by: chaithyagr <[email protected]> Co-authored-by: Pierre-Antoine Comby <[email protected]>
CEA-COSMIC · Apr 8, 2022 · dbf0959 · dbf0959
1 parent c3db304
commit dbf0959
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Showing 6 changed files with 105 additions and 7 deletions.
diff --git a/develop.txt b/develop.txt
@@ -1,5 +1,5 @@
 coverage>=5.5
-flake8<4
+flake8>=4
 nose>=1.3.7
 pytest>=6.2.2
 pytest-cov>=2.11.1

diff --git a/modopt/opt/gradient.py b/modopt/opt/gradient.py
@@ -34,6 +34,8 @@ class GradParent(object):
         Method for calculating the cost (default is ``None``)
     data_type : type, optional
         Expected data type of the input data (default is ``None``)
+    input_data_writeable: bool, optional
+        Option to make the observed data writeable (default is ``False``)
     verbose : bool, optional
         Option for verbose output (default is ``True``)
 
@@ -66,10 +68,12 @@ def __init__(
         get_grad=None,
         cost=None,
         data_type=None,
+        input_data_writeable=False,
         verbose=True,
     ):
 
         self.verbose = verbose
+        self._input_data_writeable = input_data_writeable
         self._grad_data_type = data_type
         self.obs_data = input_data
         self.op = op
@@ -102,7 +106,7 @@ def obs_data(self, input_data):
         check_npndarray(
             input_data,
             dtype=self._grad_data_type,
-            writeable=False,
+            writeable=self._input_data_writeable,
             verbose=self.verbose,
         )
 

diff --git a/modopt/opt/proximity.py b/modopt/opt/proximity.py
@@ -28,7 +28,7 @@
 from modopt.math.matrix import nuclear_norm
 from modopt.signal.noise import thresh
 from modopt.signal.positivity import positive
-from modopt.signal.svd import svd_thresh, svd_thresh_coef
+from modopt.signal.svd import svd_thresh, svd_thresh_coef, svd_thresh_coef_fast
 
 
 class ProximityParent(object):
@@ -237,6 +237,9 @@ class LowRankMatrix(ProximityParent):
     lowr_type : {'standard', 'ngole'}
         Low-rank implementation (options are 'standard' or 'ngole', default is
         'standard')
+    initial_rank: int, optional
+        Initial guess of the rank of future input_data.
+        If provided this will save computation time.
     operator : class
         Operator class ('ngole' only)
 
@@ -268,6 +271,7 @@ def __init__(
         threshold,
         thresh_type='soft',
         lowr_type='standard',
+        initial_rank=None,
         operator=None,
     ):
 
@@ -277,8 +281,9 @@ def __init__(
         self.operator = operator
         self.op = self._op_method
         self.cost = self._cost_method
+        self.rank = initial_rank
 
-    def _op_method(self, input_data, extra_factor=1.0):
+    def _op_method(self, input_data, extra_factor=1.0, rank=None):
         """Operator.
 
         This method returns the input data after the singular values have been
@@ -290,22 +295,37 @@ def _op_method(self, input_data, extra_factor=1.0):
             Input data array
         extra_factor : float
             Additional multiplication factor (default is ``1.0``)
+        rank: int, optional
+            Estimation of the rank to save computation time in standard mode,
+            if not set an internal estimation is used.
 
         Returns
         -------
         numpy.ndarray
             SVD thresholded data
 
+        Raises
+        ------
+        ValueError
+            if lowr_type is not in ``{'standard', 'ngole'}``
         """
         # Update threshold with extra factor.
         threshold = self.thresh * extra_factor
-
-        if self.lowr_type == 'standard':
+        if self.lowr_type == 'standard' and self.rank is None and rank is None:
             data_matrix = svd_thresh(
                 cube2matrix(input_data),
                 threshold,
                 thresh_type=self.thresh_type,
             )
+        elif self.lowr_type == 'standard':
+            data_matrix, update_rank = svd_thresh_coef_fast(
+                cube2matrix(input_data),
+                threshold,
+                n_vals=rank or self.rank,
+                extra_vals=5,
+                thresh_type=self.thresh_type,
+            )
+            self.rank = update_rank  # save for future use
 
         elif self.lowr_type == 'ngole':
             data_matrix = svd_thresh_coef(
@@ -314,6 +334,8 @@ def _op_method(self, input_data, extra_factor=1.0):
                 threshold,
                 thresh_type=self.thresh_type,
             )
+        else:
+            raise ValueError('lowr_type should be standard or ngole')
 
         # Return updated data.
         return matrix2cube(data_matrix, input_data.shape[1:])

diff --git a/modopt/signal/svd.py b/modopt/signal/svd.py
@@ -10,6 +10,7 @@
 
 import numpy as np
 from scipy.linalg import svd
+from scipy.sparse.linalg import svds
 
 from modopt.base.transform import matrix2cube
 from modopt.interface.errors import warn
@@ -200,6 +201,64 @@ def svd_thresh(input_data, threshold=None, n_pc=None, thresh_type='hard'):
     return np.dot(u_vec, np.dot(s_new, v_vec))
 
 
+def svd_thresh_coef_fast(
+    input_data,
+    threshold,
+    n_vals=-1,
+    extra_vals=5,
+    thresh_type='hard',
+):
+    """Threshold the singular values coefficients.
+
+    This method thresholds the input data by using singular value
+    decomposition, but only computing the the greastest ``n_vals``
+    values.
+
+    Parameters
+    ----------
+    input_data : numpy.ndarray
+        Input data array, 2D matrix
+        Operator class instance
+    threshold : float or numpy.ndarray
+        Threshold value(s)
+    n_vals: int, optional
+        Number of singular values to compute.
+        If None, compute all singular values.
+    extra_vals: int, optional
+        If the number of values computed is not enough to perform thresholding,
+        recompute by using ``n_vals + extra_vals`` (default is ``5``)
+    thresh_type : {'hard', 'soft'}
+        Type of noise to be added (default is ``'hard'``)
+
+    Returns
+    -------
+    tuple
+        The thresholded data (numpy.ndarray) and the estimated rank after
+        thresholding (int)
+    """
+    if n_vals == -1:
+        n_vals = min(input_data.shape) - 1
+    ok = False
+    while not ok:
+        (u_vec, s_values, v_vec) = svds(input_data, k=n_vals)
+        ok = (s_values[0] <= threshold or n_vals == min(input_data.shape) - 1)
+        n_vals = min(n_vals + extra_vals, *input_data.shape)
+
+    s_values = thresh(
+        s_values,
+        threshold,
+        threshold_type=thresh_type,
+    )
+    rank = np.count_nonzero(s_values)
+    return (
+        np.dot(
+            u_vec[:, -rank:] * s_values[-rank:],
+            v_vec[-rank:, :],
+        ),
+        rank,
+    )
+
+
 def svd_thresh_coef(input_data, operator, threshold, thresh_type='hard'):
     """Threshold the singular values coefficients.
 

diff --git a/modopt/tests/test_opt.py b/modopt/tests/test_opt.py
@@ -675,6 +675,11 @@ def setUp(self):
             weights,
         )
         self.lowrank = proximity.LowRankMatrix(10.0, thresh_type='hard')
+        self.lowrank_rank = proximity.LowRankMatrix(
+            10.0,
+            initial_rank=1,
+            thresh_type='hard',
+        )
         self.lowrank_ngole = proximity.LowRankMatrix(
             10.0,
             lowr_type='ngole',
@@ -763,6 +768,8 @@ def tearDown(self):
         self.positivity = None
         self.sparsethresh = None
         self.lowrank = None
+        self.lowrank_rank = None
+        self.lowrank_ngole = None
         self.combo = None
         self.data1 = None
         self.data2 = None
@@ -841,6 +848,11 @@ def test_low_rank_matrix(self):
             err_msg='Incorrect low rank operation: standard',
         )
 
+        npt.assert_almost_equal(
+            self.lowrank_rank.op(self.data3),
+            self.data4,
+            err_msg='Incorrect low rank operation: standard with rank',
+        )
         npt.assert_almost_equal(
             self.lowrank_ngole.op(self.data3),
             self.data5,

diff --git a/setup.cfg b/setup.cfg
@@ -58,7 +58,8 @@ per-file-ignores =
   #Justification: Needed to import matplotlib.pyplot
   modopt/plot/cost_plot.py: N802,WPS301
   #Todo: Investigate possible bug in find_n_pc function
-  modopt/signal/svd.py: WPS345
+  #Todo: Investigate darglint error
+  modopt/signal/svd.py: WPS345, DAR000
   #Todo: Check security of using system executable call
   modopt/signal/wavelet.py: S404,S603
   #Todo: Clean up tests