ararpy 0.1.198__py3-none-any.whl → 0.2.1__py3-none-any.whl

ararpy/smp/raw.py

@@ -22,7 +22,7 @@ RawData = samples.RawData
 Sequence = samples.Sequence
 
 
-def to_raw(file_path: Union[str, List[str]], input_filter_path: Union[str, List[str]], **kwargs):
+def to_raw(file_path: Union[str, List[str]], input_filter_path: Union[str, List[str]], file_name=None, **kwargs):
     """ Read raw data from files, can create raw data instance based on the given files
     Raw data will have the structure like:
         [
@@ -35,6 +35,7 @@ def to_raw(file_path: Union[str, List[str]], input_filter_path: Union[str, List[
     ----------
     file_path
     input_filter_path
+    file_name
     kwargs
 
     Returns
@@ -42,22 +43,18 @@ def to_raw(file_path: Union[str, List[str]], input_filter_path: Union[str, List[
 
     """
     if isinstance(file_path, list) and isinstance(input_filter_path, list):
-        raw = concatenate([to_raw(file, input_filter_path[index]) for index, file in enumerate(file_path)])
+        raw = concatenate([to_raw(file, input_filter_path[index],
+            file_name[index] if isinstance(file_name, list) else file_name) for index, file in enumerate(file_path)])
     elif isinstance(file_path, str) and isinstance(input_filter_path, str):
         input_filter = read_params(input_filter_path)
-        file_name = str(os.path.split(file_path)[-1]).split('.')[0]
-        res = raw_file.open_file(file_path, input_filter)
+        file_name = str(os.path.split(file_path)[-1]).split('.')[0] if file_name is None else file_name
+        res = raw_file.open_file(file_path, input_filter, file_name)
         data = res.get('data', None)
         sequences = res.get('sequences', None)
         sequence_num = len(data) if data is not None else len(sequences)
-        # default fitting method, all exponential
-        # <option value=0>Linear</option>
-        # <option value=1>Quadratic</option>
-        # <option value=2>Exponential</option>
-        # <option value=3>Power</option>
-        # <option value=4>Average</option>
-        fitting_method = [2, 0, 2, 2, 2]
-        raw = RawData(name=file_name, data=data, isotopic_num=10, sequence_num=sequence_num, source=[file_path],
+        experiment_name = data[0][0][2]['ExpName'] if data is not None else file_name
+        fitting_method = [2, 0, 2, 2, 2]  # 0 - linear, 1 - quadratic, 2 - exponential, 3 - power, 4 - average
+        raw = RawData(name=experiment_name, data=data, isotopic_num=10, sequence_num=sequence_num, source=[file_path],
                       sequence=sequences, unit=str(input_filter[30]), fitting_method=[*fitting_method])
     else:
         raise ValueError("File path and input filter should be both string or list with a same length.")
@@ -156,11 +153,10 @@ def do_regression(raw: RawData, sequence_index: Optional[List] = None, isotopic_
         # unselected: list = [unselected[[isotopic_index*2 + 1, 2 * (isotopic_index + 1)]].dropna().values.tolist()
         #                     for isotopic_index in list(range(5))]
 
-        for index, isotope in enumerate(selected):
+        for index, isotopic_data in enumerate(selected):
             if hasattr(isotopic_index, '__getitem__') and index not in isotopic_index:
                 continue
-            # print(f"regression for {sequence.name = }, isotope {index = }")
-            res = raw_funcs.get_raw_data_regression_results(isotope)
+            res = raw_funcs.get_raw_data_regression_results(isotopic_data)
             try:
                 sequence.results[index] = res[1]
                 sequence.coefficients[index] = res[2]