Merge pull request #74 from lanl/73_trinmfk

73 trinmfk
lanl · Dec 5, 2023 · 52b74e5 · 52b74e5
2 parents 42b5e63 + c66d57a
commit 52b74e5
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diff --git a/CITATION.cff b/CITATION.cff
@@ -20,7 +20,7 @@ authors:
   - family-names: Alexandrov
     given-names: Boian
 title: "Tensor Extraction of Latent Features (T-ELF)"
-version: 0.0.4
+version: 0.0.5
 url: https://github.com/lanl/T-ELF
 doi: 10.5281/zenodo.10257897
 date-released: 2023-12-04
diff --git a/README.md b/README.md
@@ -150,7 +150,7 @@ If you use T-ELF please cite.
 
 **APA:**
 ```latex
-Eren, M., Solovyev, N., Barron, R., Bhattarai, M., Truong, D., Boureima, I., Skau, E., Rasmussen, K., & Alexandrov, B. (2023). Tensor Extraction of Latent Features (T-ELF) (Version 0.0.4) [Computer software]. https://doi.org/10.5281/zenodo.10257897
+Eren, M., Solovyev, N., Barron, R., Bhattarai, M., Truong, D., Boureima, I., Skau, E., Rasmussen, K., & Alexandrov, B. (2023). Tensor Extraction of Latent Features (T-ELF) (Version 0.0.5) [Computer software]. https://doi.org/10.5281/zenodo.10257897
 ```
 
 **BibTeX:**

diff --git a/TELF/factorization/TriNMFk.py b/TELF/factorization/TriNMFk.py
@@ -19,8 +19,8 @@
 import numpy as np
 import warnings
 import scipy.sparse
-import numpy as np
 import os
+from pathlib import Path
 
 try:
     import cupy as cp
@@ -87,6 +87,7 @@ class TriNMFk():
     def __init__(self,
                  experiment_name="TriNMFk",
                  nmfk_params={},
+                 save_path = "TriNMFk",
                  nmf_verbose=False,
                  use_gpu=False,
                  n_jobs=-1,
@@ -108,6 +109,8 @@ def __init__(self,
             Name used for the experiment. Default is "TriNMFk".
         nmfk_params : str, optional
             Parameters for NMFk. See documentation for NMFk for the options.
+        save_path : str, optional
+            Used for save location when NMFk fit is not performed first, and TriNMFk fit is done.
         nmf_verbose : bool, optional
             If True, shows progress in each NMF operation. The default is False.
         use_gpu : bool, optional
@@ -151,8 +154,9 @@ def __init__(self,
         self.nmfk_fit = False
         self.pruned = pruned
         self.transpose = transpose
-        self.save_path = "",
+        self.save_path = save_path
         self.verbose = verbose
+        self.save_path_full = ""
 
         # organize n_jobs
         n_jobs, self.use_gpu = organize_n_jobs(use_gpu, n_jobs)
@@ -206,7 +210,7 @@ def fit_nmfk(self, X, Ks, note=""):
 
         # Do NMFk
         nmfk_results = self.nmfk.fit(X, Ks, self.experiment_name, note)
-        self.save_path = os.path.join(self.nmfk.save_path, self.nmfk.experiment_name)
+        self.save_path_full = self.nmfk.save_path_full
 
         # Do nmfk here
         self.nmfk_fit = True
@@ -215,7 +219,8 @@ def fit_nmfk(self, X, Ks, note=""):
 
     def fit_tri_nmfk(self, X, k1k2:tuple):
         """
-        Factorize the input matrix ``X``, after applying ``fit_nmfk()`` to select the ``Wk`` and ``Hk``, to factorize the given matrix with ``k1k2=(Wk, Hk)``.
+        Factorize the input matrix ``X``.\n
+        after applying ``fit_nmfk()`` to select the ``Wk`` and ``Hk``, to factorize the given matrix with ``k1k2=(Wk, Hk)``.
 
         Parameters
         ----------
@@ -233,8 +238,20 @@ def fit_tri_nmfk(self, X, k1k2:tuple):
 
 
         if not self.nmfk_fit:
-            warnings.warn("NMFk needs to be fit first. Use fit_nmfk function!")
-            return
+            name = (
+                str(self.experiment_name)
+                + "_"
+                + str(self.n_iters)
+                + "iters_"
+                + str(self.n_inits)
+                + "inits"
+            )
+            self.save_path_full = os.path.join(self.save_path, name)
+            try:
+                if not Path(self.save_path_full).is_dir():
+                    Path(self.save_path_full).mkdir(parents=True)
+            except Exception as e:
+                print(e)
 
         if self.transpose:
             if isinstance(X, np.ndarray):
@@ -306,7 +323,7 @@ def fit_tri_nmfk(self, X, k1k2:tuple):
 
         # save the results
         np.savez_compressed(
-                    self.save_path
+                    self.save_path_full
                     + "/WSH"
                     + "_k="
                     + str(k1k2)

diff --git a/TELF/version.py b/TELF/version.py
@@ -1 +1 @@
-__version__ = '0.0.4'
+__version__ = '0.0.5'
diff --git a/docs/Beaver.html b/docs/Beaver.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.pre_processing.Beaver: Fast matrix and tensor building tool &#8212; TELF 0.0.4 documentation</title>
+    <title>TELF.pre_processing.Beaver: Fast matrix and tensor building tool &#8212; TELF 0.0.5 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=dfd84850"></script>
+    <script src="_static/documentation_options.js?v=6424ca4d"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.4 documentation</p>
+    <p class="title logo__title">TELF 0.0.5 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">

diff --git a/docs/NMFk.html b/docs/NMFk.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.factorization.NMFk: Non-negative Matrix Factorization with Automatic Model Determination &#8212; TELF 0.0.4 documentation</title>
+    <title>TELF.factorization.NMFk: Non-negative Matrix Factorization with Automatic Model Determination &#8212; TELF 0.0.5 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=dfd84850"></script>
+    <script src="_static/documentation_options.js?v=6424ca4d"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.4 documentation</p>
+    <p class="title logo__title">TELF 0.0.5 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">

diff --git a/docs/RESCALk.html b/docs/RESCALk.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.factorization.RESCALk: RESCAL with Automatic Model Determination &#8212; TELF 0.0.4 documentation</title>
+    <title>TELF.factorization.RESCALk: RESCAL with Automatic Model Determination &#8212; TELF 0.0.5 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=dfd84850"></script>
+    <script src="_static/documentation_options.js?v=6424ca4d"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.4 documentation</p>
+    <p class="title logo__title">TELF 0.0.5 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">

diff --git a/docs/SymNMFk.html b/docs/SymNMFk.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.factorization.SymNMFk: Symmetric Non-negative Matrix Factorization with Automatic Model Determination &#8212; TELF 0.0.4 documentation</title>
+    <title>TELF.factorization.SymNMFk: Symmetric Non-negative Matrix Factorization with Automatic Model Determination &#8212; TELF 0.0.5 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=dfd84850"></script>
+    <script src="_static/documentation_options.js?v=6424ca4d"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.4 documentation</p>
+    <p class="title logo__title">TELF 0.0.5 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">

diff --git a/docs/TELF.factorization.decompositions.html b/docs/TELF.factorization.decompositions.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.factorization.decompositions package &#8212; TELF 0.0.4 documentation</title>
+    <title>TELF.factorization.decompositions package &#8212; TELF 0.0.5 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=dfd84850"></script>
+    <script src="_static/documentation_options.js?v=6424ca4d"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -128,7 +128,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.4 documentation</p>
+    <p class="title logo__title">TELF 0.0.5 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">

diff --git a/docs/TELF.factorization.decompositions.utilities.html b/docs/TELF.factorization.decompositions.utilities.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.factorization.decompositions.utilities package &#8212; TELF 0.0.4 documentation</title>
+    <title>TELF.factorization.decompositions.utilities package &#8212; TELF 0.0.5 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=dfd84850"></script>
+    <script src="_static/documentation_options.js?v=6424ca4d"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.4 documentation</p>
+    <p class="title logo__title">TELF 0.0.5 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">