nmrdenoise 0.2.0__tar.gz → 0.2.2__tar.gz

{nmrdenoise-0.2.0/src/nmrdenoise.egg-info → nmrdenoise-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nmrdenoise
-Version: 0.2.0
+Version: 0.2.2
 Summary: A Python API for deep learning-based NMR denoising
 Author: Kinkini
 Classifier: Programming Language :: Python :: 3

{nmrdenoise-0.2.0 → nmrdenoise-0.2.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nmrdenoise"
-version = "0.2.0"
+version = "0.2.2"
 authors = [
   { name="Kinkini"},
 ]

{nmrdenoise-0.2.0 → nmrdenoise-0.2.2}/src/nmrdenoise/__init__.py

@@ -1,4 +1,4 @@
  # src/nmrdenoise/__init__.py
 from .core import read_bruker, load_denoising_checkpoint, denoise_component, Autoencoder, Desperate
 
-__version__ = "0.2.0"
+__version__ = "0.2.2"

{nmrdenoise-0.2.0 → nmrdenoise-0.2.2}/src/nmrdenoise/core.py

@@ -258,19 +258,19 @@ class Desperate:
         ### from each using the chosen thresholding method
         for i in range(len(coeffs)):
             temp = coeffs[i]
-            lam = calc_lamb(temp[0], region_spec) #lam comes from approx. component
+            lam = self.calc_lamb(temp[0], region_spec) #lam comes from approx. component
             if threshold == 'soft':
-                fincomp0 = soft_threshold(temp[0], lam)
-                fincomp1 = soft_threshold(temp[1], lam)
+                fincomp0 = self.soft_threshold(temp[0], lam)
+                fincomp1 = self.soft_threshold(temp[1], lam)
             if threshold == 'hard':
-                fincomp0 = hard_threshold(temp[0], lam)
-                fincomp1 = hard_threshold(temp[1], lam)
+                fincomp0 = self.hard_threshold(temp[0], lam)
+                fincomp1 = self.hard_threshold(temp[1], lam)
             if threshold == 'mod':
-                fincomp0 = mod_thresh(temp[0], lam, alpha)
-                fincomp1 = mod_thresh(temp[1], lam, alpha)
+                fincomp0 = self.mod_thresh(temp[0], lam, alpha)
+                fincomp1 = self.mod_thresh(temp[1], lam, alpha)
             if threshold == 'gar':
-                fincomp0 = gar_threshold(temp[0], lam)
-                fincomp1 = gar_threshold(temp[1], lam)
+                fincomp0 = self.gar_threshold(temp[0], lam)
+                fincomp1 = self.gar_threshold(temp[1], lam)
             coeffs[i] = (fincomp0, fincomp1)
         #print('Lambda = %5.3f'%lam)
         final = pywt.iswt(coeffs, wave) #recontrusct the final denoised spectrum
@@ -287,12 +287,12 @@ class Desperate:
         coeffin = np.copy(coeffs)
         for i in range(len(coeffs)):
             temp = coeffs[i]
-            lam = calc_lamb(temp[0], region_spec) #lam comes from approx. component
+            lam = self.calc_lamb(temp[0], region_spec) #lam comes from approx. component
             if threshold == 'mod':
-                fincomp0 = mod_thresh(temp[0], lam, alpha)
-                fincomp1 = mod_thresh(temp[1][0], lam, alpha)
-                fincomp2 = mod_thresh(temp[1][1], lam, alpha)
-                fincomp3 = mod_thresh(temp[1][2], lam, alpha)
+                fincomp0 = self.mod_thresh(temp[0], lam, alpha)
+                fincomp1 = self.mod_thresh(temp[1][0], lam, alpha)
+                fincomp2 = self.mod_thresh(temp[1][1], lam, alpha)
+                fincomp3 = self.mod_thresh(temp[1][2], lam, alpha)
             coeffs[i] = (fincomp0, (fincomp1, fincomp2, fincomp3))
 
         final = pywt.iswt2(coeffs, wave)
@@ -330,14 +330,14 @@ class Desperate:
         lam = sig*np.sqrt(2*np.log(len(data)))
         return lam
 
-    def hard_threshold(data, lam):
+    def hard_threshold(self, data, lam):
         """Hard Thresholding"""
         data_thr = np.copy(data)
         neg_idx = np.where(np.abs(data) < lam)
         data_thr[neg_idx] = 0
         return data_thr
         
-    def soft_threshold(data, lam):
+    def soft_threshold(self, data, lam):
         """Soft Thresholding"""
         data_thr = np.copy(data)
         pos_idx = np.where(data > lam)
@@ -348,7 +348,7 @@ class Desperate:
         data_thr[neg_idx] = data[neg_idx] + lam
         return data_thr
 
-    def mod_thresh(data, lam, alpha):
+    def mod_thresh(self, data, lam, alpha):
         """Modified thresholding using algorithm in:
         Wang and Dai, Proceedings of the 2018 International Symposium 
         on Communication Engineering & Computer Science (CECS 2018), 2018, 481"""
@@ -359,7 +359,7 @@ class Desperate:
         data_thr[neg_idx] = (1-alpha)*(data[neg_idx]**5/lam**4)
         return data_thr
 
-    def gar_threshold(data, lam):
+    def gar_threshold(self, data, lam):
         "garrote thresholding"
         data_thr = np.copy(data)
         pos_idx = np.where(np.abs(data) > lam)
@@ -368,7 +368,7 @@ class Desperate:
         data_thr[neg_idx] = 0
         return data_thr
 
-    def consecutive(data, stepsize=1):
+    def consecutive(self, data, stepsize=1):
         """"
         basic function to blocks of consecutive number in an array
         """

{nmrdenoise-0.2.0 → nmrdenoise-0.2.2/src/nmrdenoise.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nmrdenoise
-Version: 0.2.0
+Version: 0.2.2
 Summary: A Python API for deep learning-based NMR denoising
 Author: Kinkini
 Classifier: Programming Language :: Python :: 3