Support for stress based ascii files.

Changed manual picking procedure.

RSTpicking/RST_Func.py

@@ -18,9 +18,9 @@ import matplotlib.gridspec as gridspec
 import matplotlib.pyplot as plt
 import nptdms
 import numpy as np
-from scipy.optimize import least_squares, curve_fit
-from scipy.stats import norm
+from scipy.optimize import curve_fit, least_squares
 from scipy.signal import medfilt, resample
+from scipy.stats import norm
 
 
 # %%==============CONVERSION===================================================
@@ -42,10 +42,17 @@ def convert(path, file_in, var):
                     '.dat': _readdat,
                     '.tdms': _readtdms}
 
-    (_, ext) = os.path.splitext(path+file_in)
+    (_, ext) = os.path.splitext(os.path.join(path, file_in))
     data = file_convert[ext](path, file_in)  # data contains basic content
     nsamples = int(var['nsamples'])
 
+    # check if stress data was imported instead of force
+    if 'normalstress' in data.keys():
+        data['normalforce'] = data['normalstress'] * var['A']
+        data['shearforce'] = (
+            (data['shearstress'] * (var['li']*var['A'])) / var['lo']
+        )
+
     if len(data['time']) > nsamples:
         data['time'] = np.linspace(0, data['time'][-1], nsamples)
         data['velocity'] = downsample(
@@ -72,6 +79,8 @@ def convert(path, file_in, var):
     data['normalstress'] = data['normalforce']/var['A']
     data['displacement'] = np.cumsum(data['time'][1]*data['velocity'])
 
+    data['name'] = file_in
+
     print(file_in+' read')
     return data
 
@@ -359,10 +368,20 @@ def eval_shearstress(cur_dat, var, review=None):
         closest = prednorms[np.argmin(np.abs(differences))]
         return closest
 
+    print('Picking %s' % cur_dat['name'])
     if not review:
-        picks = _auto_pick(cur_dat, var)
+        try:
+            picks = _auto_pick(cur_dat, var)
+        except IndexError as _:
+            print('Auto picking failed ... starting manual pick')
+            picks = _manual_pick(cur_dat, var)
+
     elif review == 'auto':
-        picks = _auto_pick(cur_dat, var)
+        try:
+            picks = _auto_pick(cur_dat, var)
+        except IndexError as _:
+            print('Auto picking failed ... starting manual pick')
+            picks = _manual_pick(cur_dat, var)
         (fig, ax) = _pick_base_plot(cur_dat, var)
         (fig, ax) = _review_picks(fig, ax, picks)
         plt.close()
@@ -995,9 +1014,32 @@ def dilation(path, name, lid_pos, exp_data, prop_file, cfg):
     plt.close()
 
 
+def _check_for_type(filepath):
+    """
+    Checks what kind of dat file we have.
+
+    Returns:
+        0: if it is unkown
+        1: if data is in Newton
+        2: if data is in Pascal
+    """
+    with open(filepath, 'rt') as fhandle:
+        for i, row in enumerate(csv.reader(fhandle)):
+            if i == 2:
+                row = row[0]
+                if '[N]' in row:
+                    return 1
+                elif '[Pa]' in row:
+                    return 2
+                else:
+                    return 0
+            elif i > 2:
+                break
+
+
 def _readasc(path, file_in):
     """ Helper function to read *.asc file """
-    with codecs.open(path+file_in, encoding='utf-8-sig') as f:
+    with codecs.open(os.path.join(path, file_in), encoding='utf-8-sig') as f:
         data_load = np.loadtxt(f)  # load file for further calculations
 
     # extract data and convert to SI-units
@@ -1017,33 +1059,84 @@ def _readasc(path, file_in):
 
 def _readdat(path, file_in):
     """ Helper function to read *.dat file  """
-    with codecs.open(path+file_in, encoding='utf-8-sig') as f:
-        try:
-            data_load = np.loadtxt(f, delimiter=';', skiprows=3)
-            time = data_load[:, 0]  # in s
-            normalforce = data_load[:, 1]  # in N
-            shearforce = data_load[:, 2]  # in N
-            liddispl = data_load[:, 3]  # in mm
-            velocity = data_load[:, 4]  # in mm/s
-
-            data = {'time': time,
-                    'velocity': velocity,
-                    'normalforce': normalforce,
-                    'shearforce': shearforce,
-                    'liddispl': liddispl,
-                    'name': file_in.split('.')[0]}
-        except ValueError as _:
-            data_load = np.loadtxt(f, delimiter='\t', skiprows=1)
-            time = data_load[:, 0]  # in s
-            velocity = data_load[:, 1]  # in mm/s
-            normalforce = data_load[:, 2]  # in N
-            shearforce = data_load[:, 3]  # in N
-
-            data = {'time': time,
-                    'velocity': velocity,
-                    'normalforce': normalforce,
-                    'shearforce': shearforce,
-                    'name': file_in.split('.')[0]}
+
+    def standardload(f):
+        """
+        Standard loading
+        """
+        data_load = np.loadtxt(f, delimiter=';', skiprows=3)
+        time = data_load[:, 0]  # in s
+        normalforce = data_load[:, 1]  # in N
+        shearforce = data_load[:, 2]  # in N
+        liddispl = data_load[:, 3]  # in mm
+        velocity = data_load[:, 4]  # in mm/s
+
+        data = {
+            'time': time,
+            'velocity': velocity,
+            'normalforce': normalforce,
+            'shearforce': shearforce,
+            'liddispl': liddispl,
+            'name': file_in.split('.')[0]
+        }
+        return data
+
+    def alternativeload(f):
+        """
+        Loads data in a slightly different way to ensure backwards
+        compatability
+        """
+        data_load = np.loadtxt(f, delimiter='\t', skiprows=1)
+        time = data_load[:, 0]  # in s
+        velocity = data_load[:, 1]  # in mm/s
+        normalforce = data_load[:, 2]  # in N
+        shearforce = data_load[:, 3]  # in N
+
+        data = {
+            'time': time,
+            'velocity': velocity,
+            'normalforce': normalforce,
+            'shearforce': shearforce,
+            'name': file_in.split('.')[0]
+        }
+        return data
+
+    def pascalload(f):
+        """
+        Loads a file with Pascal as main units
+        """
+        data_load = np.loadtxt(f, delimiter=';', skiprows=3)
+        time = data_load[:, 0]  # in s
+        normalforce = data_load[:, 1]  # in Pa
+        shearforce = data_load[:, 2]  # in Pa
+        liddispl = data_load[:, 3]  # in mm
+        velocity = data_load[:, 4]  # in mm/s
+
+        data = {
+            'time': time,
+            'velocity': velocity,
+            'normalstress': normalforce,
+            'shearstress': shearforce,
+            'liddispl': liddispl,
+            'name': file_in.split('.')[0]
+        }
+        return data
+
+    load_fun = [
+        alternativeload, standardload, pascalload
+    ]
+    filetype = _check_for_type(os.path.join(path, file_in))
+    print('%s of type: %s' % (file_in, filetype))
+
+    if filetype:  # if filetype is non zero:
+        with codecs.open(
+            os.path.join(path, file_in),
+            encoding='utf-8-sig'
+        ) as f:
+            try:
+                data = load_fun[filetype](f)
+            except ValueError as _:
+                data = alternativeload(f)
     return data
 
 
@@ -1051,7 +1144,7 @@ def _readtdms(path, file_in):
     """ Helper function to read *.tdms file """
 
     try:
-        f = nptdms.TdmsFile(path+file_in)
+        f = nptdms.TdmsFile(os.path.join(path, file_in))
         time = f.group_channels('Untitled')[0].time_track()  # in [s]
         df_raw = dict()
         for channel in f.group_channels('Untitled'):
@@ -1062,7 +1155,7 @@ def _readtdms(path, file_in):
         liddispl = df_raw['Lid Displacement']  # in [mm]
         velocity = df_raw['Velocity']  # in [mm/s]
     except AttributeError as _:
-        with nptdms.TdmsFile.open(path+file_in) as f:
+        with nptdms.TdmsFile.open(os.path.join(path, file_in)) as f:
             time = f['Untitled']['Shear Force'].time_track()  # in [s]
             shearforce = f['Untitled']['Shear Force'][:]  # in [N]
             normalforce = f['Untitled']['Normal Force'][:]  # in [N]