v. 0.9.12

metabolabpy/__init__.py

@@ -1,4 +1,4 @@
 __author__ = 'Christian Ludwig ([email protected])'
 __credits__ = 'Christian Ludwig ([email protected])'
-__version__ = '0.9.11'
+__version__ = '0.9.12'
 __license__ = 'GPLv3'

metabolabpy/exampleScripts/example1DScript.py

@@ -4,7 +4,9 @@
 self.read_spcs([data_path],data_sets)				# reading Bruker spectra
 msg = self.nd.set_zero_fill([131072])				# zero fill to 131072 data points
 msg = self.nd.set_lb([0.3])						# 0.3 Hz line broadening
-msg = self.nd.set_window_type([1])					# exponential window function
+msg = self.nd.set_window_type(['Exponential'])			# window function ('None', 'Exponential', 'Gaussian', 'Sine', 'QSine', 'SEM')
+msg = self.nd.set_water_suppression('None')				# set water suppression ('None', 'Conv', 'Poly', 'WaveWat')
+msg = self.nd.set_autobaseline(False)				# perform automatic baseline correction (False, True) 
 msg = self.nd.ft_all()							# Fourier Transform all NMR spectra
 msg = self.nd.auto_ref_all()						# automatically reference to TMSP
 self.nd.e = 0						 		# make first spectrum the current experiment

metabolabpy/nmr/nmrDataSet.py

@@ -237,8 +237,7 @@ def baseline1d_all(self):
     def bucket_spectra(self):
         self.pp.bucket_points = np.diff(self.nmrdat[self.s][self.e].ppm2points([0.0, self.pp.bucket_ppm]))
         idx1 = np.arange(len(self.nmrdat[self.s][0].ppm1))
-        print(f'self.pp.bucket_points: {self.pp.bucket_points}')
-        idx2 = idx1[::int(self.pp.bucket_points)]
+        idx2 = idx1[::int(self.pp.bucket_points[0])]
         idx2 = np.append(idx2, len(idx1))
         ppm = np.array([])
         for k in range(len(idx2) - 1):
@@ -1572,6 +1571,15 @@ def select_plot_clear(self): # pragma: no cover
         self.plot_spc()
         # end select_plot_clear
 
+    def set_autobaseline(self, autobaseline=False):
+        n_exp = len(self.nmrdat[self.s])
+        for k in range(n_exp):
+            self.nmrdat[self.s][k].proc.autobaseline = autobaseline
+
+        return "set_autobaseline"
+
+        # set_autobaseline
+
     def set_loadings_from_excel(self, file_name='', worksheet='', columns=['']): # pragma: no cover
         if len(file_name) == 0:
             return
@@ -1728,9 +1736,16 @@ def set_water_suppression(self, ws='None'):
 
     def set_window_type(self, wt):
         n_exp = len(self.nmrdat[self.s])
+        wt2 = []
+        for k in range(len(wt)):
+            if isinstance(wt[0], int):
+                wt2.append(wt[k])
+            else:
+                wt2.append(self.nmrdat[self.s][self.e].proc.window_functions[wt[k]])
+
         for k in range(n_exp):
-            for l in range(len(wt)):
-                self.nmrdat[self.s][k].proc.window_type[l] = wt[l]
+            for l in range(len(wt2)):
+                self.nmrdat[self.s][k].proc.window_type[l] = wt2[l]
 
         return "set_window_type"
 

metabolabpy/nmr/procPars.py

@@ -85,11 +85,11 @@ def __init__(self):
             0: "None",
             1: "Conv",
             2: "Poly",
-            3: "Wavewat",
+            3: "WaveWat",
             "None": 0,
             "Conv": 1,
             "Poly": 2,
-            "Wavewat": 3
+            "WaveWat": 3
         }
         self.data_type = ''
         self.autobaseline_alg = 'rolling_ball'