Fixed saving of data in CV (#40)

* Added a recursive funciton to get rid of internal pd in the saving dict
* Fixed the cli
* Make the logo smaller

README.rst

@@ -1,9 +1,12 @@
-.. image:: logo.png
-    :align: center
+
 
 MADAP
 ~~~~~
 
+.. image:: logo.png
+    :align: center
+    :width: 240px
+
 Modular and Autonomous Data Analysis Platform (MADAP) is a
 well-documented python package which can be used for electrochmeical
 data analysis.

madap/echem/voltammetry/voltammetry_CV.py

@@ -34,7 +34,6 @@ def __init__(self, current, voltage, time_params, cycle_list, args, scan_rate=No
         self.cathodic_peak_params = {}
         self.E_half_params = {}
         self.smoothing_window_size = 1
-        self.fitting_window_size = int(args.fitting_window_size) if args.fitting_window_size is not None else 30
         self.data = None
         self.temperature = float(args.temperature) if args.temperature is not None else 298.15 # Unit: K
         self.cycle_list = cycle_list
@@ -245,10 +244,10 @@ def _calculate_diffusion_coefficient(self, i_peak, scan_rate):
     def _find_peak_and_tafel_params(self):
         """ Find the peak parameters for each anodic and cathodic peak.
         """
-        for cycle, tafel_data in self.E_half_params.items():
-            tafel_data = {}
+        for cycle, _ in self.E_half_params.items():
+            self.tafel_data[cycle] = {}
             for pair in self.E_half_params[cycle].keys():
-                tafel_data[pair] = {}
+                self.tafel_data[cycle][pair] = {}
                 peak_anodic_number = self.E_half_params[cycle][pair]['anodic_peak']
                 peak_cathodic_number = self.E_half_params[cycle][pair]['cathodic_peak']
 
@@ -323,7 +322,7 @@ def _find_height_of_cathodic_peak_current(self, cycle, pair, peak_cathodic_numbe
         # find the index of the voltage where the current is half of the peak current
         index_of_I_half_voltage = max(filter_cathodic_data.index[filter_cathodic_data['voltage'] >= self.E_half_params[cycle][pair]['E_half']])
         # find the fitting window size
-        fitting_window = int(len(filter_cathodic_data[:index_of_I_half_voltage]) / 6) #self.fitting_window_size)
+        fitting_window = int(len(filter_cathodic_data[:index_of_I_half_voltage]) / 6)
 
         for i in range(len(smoothened_data.loc[:index_of_I_half_voltage])):
             # select two points and fit a line
@@ -374,7 +373,7 @@ def _find_height_of_anodic_peak_current(self, cycle, pair, peak_anodic_number, f
         # Smoothen the filtered data
         filter_anodic_data['current'] = filter_anodic_data['current'].rolling(window=self.smoothing_window_size).mean()
         index_of_I_half_voltage = max(filter_anodic_data.index[filter_anodic_data['voltage'] <= self.E_half_params[cycle][pair]['E_half']])
-        fitting_window = int(len(filter_anodic_data[:index_of_I_half_voltage]) / 6) #self.fitting_window_size)
+        fitting_window = int(len(filter_anodic_data[:index_of_I_half_voltage]) / 6)
 
         for i in range(len(filter_anodic_data.loc[:index_of_I_half_voltage-fitting_window])):
             # select two points and fit a line
@@ -733,10 +732,10 @@ def save_data(self, save_dir:str, optional_name:str = None):
 
         added_data = {**self.E_half_params, **self.anodic_peak_params, **self.cathodic_peak_params,
                     "Smoothing window size": self.smoothing_window_size,
-                    "Fitting window size": self.fitting_window_size,
                     "Temperature [K]": self.temperature}
 
         processed_data = utils.convert_numpy_to_python(added_data)
+        processed_data = utils.convert_from_pd(processed_data)
         utils.save_data_as_json(save_dir, processed_data, name)
 
         self._save_data_with_name(optional_name, self.__class__.__name__, save_dir, self.data)
@@ -760,7 +759,7 @@ def perform_all_actions(self, save_dir:str, plots:list, optional_name:str = None
             self.plot(save_dir, plots, optional_name=optional_name)
         except ValueError as e:
             raise e
-        #self.save_data(save_dir=save_dir, optional_name=optional_name)
+        self.save_data(save_dir=save_dir, optional_name=optional_name)
 
 
     @property

madap/utils/utils.py

@@ -103,6 +103,25 @@ def append_to_save_data(directory, added_data, name):
     save_data_as_json(directory, data, name)
 
 
+def convert_from_pd(obj):
+    """Helper to convert pandas data to python data
+
+    Args:
+        obj (pandas.DataFrame): The data that should be converted
+    Returns:
+        dict: The converted data
+    """
+
+    if isinstance(obj, pd.Series):
+        return obj.to_dict()
+    if isinstance(obj, dict):
+        return {k: convert_from_pd(v) for k, v in obj.items()}
+    if isinstance(obj, list):
+        return [convert_from_pd(x) for x in obj]
+    else:
+        return obj
+
+
 def convert_numpy_to_python(data):
     """Convert numpy data to python data
 

madap_cli.py

@@ -83,8 +83,7 @@ def _analyze_parser_args():
         if proc.voltammetry_procedure == "cv":
             cv = first_parser.add_argument_group("Options for the CV procedure")
             cv.add_argument("-plcy", "--cycle_list", required=False, default=None,
-                            help="list of cycles to be plotted. \n format: [1, 2, 3] \n if it is not specified, all cycles will be plotted",
-                            required=False, default=None)
+                            help="list of cycles to be plotted. \n format: [1, 2, 3] \n if it is not specified, all cycles will be plotted")
             cv.add_argument("-pl", "--plots", required=True, choices=["E-t", "I-t", "Peak Scan", "CV", "Tafel"],
                             nargs="+", help="plots to be generated")
             cv.add_argument("-temp", "--temperature", type=float, required=False, default=None,