add sigmoid function to basic models

fixes #304

Co-authored-by: Dominik Demuth <dominik.demuth@physik.tu-darmstadt.de>
Reviewed-on: #305

src/gui_qt/io/asciireader.py

@@ -133,7 +133,7 @@ class QAsciiReader(QtWidgets.QDialog, Ui_ascii_reader):
         if self.column_checkBox.isChecked() and self.line_spinBox.isEnabled():
             header_line = self.reader.header[self.line_spinBox.value()-1]
             header_line = header_line.strip('\n\t\r, ')
-            header_line = re.sub(r'[\t ;,]+', ';', header_line)
+            header_line = re.sub(r'[\t, ;]+(?!\w*})', ';', header_line)
 
             self.ascii_table.setHorizontalHeaderLabels(header_line.split(';'))
 

src/nmreval/io/asciireader.py

@@ -49,7 +49,7 @@ class AsciiReader:
         with self.fname.open('r') as f:
             for i, line in enumerate(islice(f, len(self.header)+len(self.lines), num_lines)):
                 line = line.strip('\n\t\r, ')
-                line = re.sub(r'[\t ;,]+', ';', line)
+                line = re.sub(r'[\t, ;]+(?!\w*})', ';', line)
                 line = line.split(';')
 
                 try:
@@ -146,10 +146,11 @@ class AsciiReader:
             raw_data = raw_data.reshape((1, *raw_data.shape))
 
         if len(x) == 0 or raw_data.shape[2] == 1:
-            _temp = np.zeros((raw_data.shape[0], raw_data.shape[1], raw_data.shape[2]+1))
+            raw_data = raw_data.reshape(raw_data.shape[0], raw_data.shape[2], raw_data.shape[1])
-            _temp[:, :, 0] = np.arange(raw_data.shape[1])
+            # _temp = np.zeros((raw_data.shape[0], raw_data.shape[2], raw_data.shape[1]))
-            _temp[:, :, 1:] = raw_data
+            # _temp[:, :, 0] = np.arange(raw_data.shape[1])
-            raw_data = _temp
+            # _temp[:, :, 1:] = raw_data
+            # raw_data = _temp
 
             if y:
                 y = [i+1 for i in y]

src/nmreval/models/basic.py

@@ -203,6 +203,31 @@ class Sinc:
         return c * np.sinc(((x-x0)/w)/np.pi)
 
 
+class Sigmoid:
+    type = 'Basic'
+    name = 'Sigmoid'
+    equation = 'C / [1 + exp(-a * (x - x_{0})] + y_{0}'
+    params = ['C', 'a', 'x_{0}', 'y_{0}']
+
+    @staticmethod
+    def func(x, c, a, x0, y0):
+        """
+        Sigmoid function
+
+        .. math::
+            y = C / [1 + exp(-a * (x - x_0))] + y_0
+
+        Args:
+            x (array_like): Input values
+            c (float): Prefactor
+            a (float): Steepness of the sigmoid
+            x0 (float): x position of the sigmoid's midpoint
+            y0 (float): y position of the sigmoid's midpoint
+
+        """
+        return c / (1 + np.exp(-a * (x - x0))) + y0
+
+
 class Sine:
     """
     Wavy sine function

src/nmreval/models/diffusion.py

@@ -116,7 +116,7 @@ class Peschier:
     name = 'Diffusion + Cross-Relaxation'
     type = 'Diffusion'
     equation = r'Diffusion with cross-relax f(ast) \rightarrow s(low)'
-    params = ['M_{0}', 'D', 'T_{1,f}', 'T_{1,s}', 'k', 'p_{f}', 't_{ev}', 'g']
+    params = ['M_{0}', 'D', 'T_{1f}', 'T_{1s}', 'k', 'p_{f}', 't_{ev}', 'g']
     bounds = [(0, None), (0, None), (0, None), (0, None), (0, None), (0, None)]
     choices = [(r'\gamma', 'nucleus', gamma)]
 

src/nmreval/models/relaxation.py

@@ -75,7 +75,7 @@ class TwoSatRecAbsolute:
     type = 'Relaxation'
     name = 'Two-step relaxation (abs. int)'
     equation = r'M_{0} + \Sigma \DeltaM_{i}(1-exp(-(x/T_{1,i})^{\beta_{i}}))'
-    params = [r'\DeltaM_{1}', 'T_{1,1}', r'\beta_{1}', r'\DeltaM_{2}', 'T_{1,2}', r'\beta_{2}', 'M_{0}']
+    params = [r'\DeltaM_{1}', 'T_{11}', r'\beta_{1}', r'\DeltaM_{2}', 'T_{12}', r'\beta_{2}', 'M_{0}']
     choices = [('Type', 'is_inv', {'Saturation': False, 'Inversion': True})]
     bounds = [(0, None), (0, None), (0, 1), (0, None), (0, None), (0, 1), (None, None)]
 
@@ -92,7 +92,7 @@ class TwoSatRecRelative:
     name = 'Two-step relaxation (rel. int)'
     equation = r'M_{0} + \DeltaM[R(1-exp(-(x/T_{1,1})^{\beta_{1}})) + \n'\
                r'(1-R)(1-exp(-(x/T_{1,2})^{\beta_{2}}))]'
-    params = [r'\DeltaM', 'M_{0}', 'T_{1,1}', r'\beta_{1}', 'T_{1,2}', r'\beta_{2}', 'R']
+    params = [r'\DeltaM', 'M_{0}', 'T_{11}', r'\beta_{1}', 'T_{12}', r'\beta_{2}', 'R']
     choices = [('Type', 'kind', {'Saturation': 'sat', 'Inversion': 'inv'})]
     bounds = [(0, None), (None, None), (0, None), (0, 1), (0, None), (0, 1), (0, 1)]