feat: add cv data with offset

chem_spectra/lib/composer/ni.py

@@ -16,7 +16,7 @@
     extrac_dic, calc_npoints, BaseComposer
 )
 from chem_spectra.lib.shared.calc import (  # noqa: E402
-    calc_mpy_center, calc_ks, get_curve_endpoint, cal_slope, cal_xyIntegration
+    calc_mpy_center, calc_ks, get_curve_endpoint, cal_slope, cal_xyIntegration, cal_cyclic_volta_shift_offset_at_index
 )
 
 
@@ -141,6 +141,9 @@ def __gen_cyclic_voltammetry_data_peaks(self):
         content = ['##$CSCYCLICVOLTAMMETRYDATA=\n']
         if self.core.is_cyclic_volta:
             listMaxMinPeaks = self.core.max_min_peaks_table
+            cyclicvolta_data = self.core.params['cyclicvolta']
+            current_jcamp_idx = self.core.params['jcamp_idx']
+            offset = cal_cyclic_volta_shift_offset_at_index(cyclicvolta_data, current_jcamp_idx)
             if self.core.params['list_max_min_peaks'] is not None:
                 listMaxMinPeaks = self.core.params['list_max_min_peaks']
 
@@ -163,6 +166,8 @@ def __gen_cyclic_voltammetry_data_peaks(self):
                 if (x_max_peak == '' or x_min_peak == ''):
                     delta = ''
                 else:
+                    x_max_peak += offset
+                    x_min_peak += offset
                     delta = abs(x_max_peak - x_min_peak)
 
                 x_pecker = ''
@@ -174,6 +179,7 @@ def __gen_cyclic_voltammetry_data_peaks(self):
                         pecker = peak['pecker']
                         x_pecker = pecker['x']
                         y_pecker = pecker['y']
+                    x_pecker += offset
                     first_expr = abs(y_min_peak) / abs(y_max_peak)
                     second_expr = 0.485 * abs(y_pecker) / abs(y_max_peak)
                     ratio = first_expr + second_expr + 0.086

chem_spectra/lib/converter/share.py

@@ -21,6 +21,8 @@ def parse_params(params):
             'fname': '',
             'waveLength': default_wavelength,
             'list_max_min_peaks': None,
+            'cyclicvolta': None,
+            'jcamp_idx': 0,
         }
 
     select_x = params.get('select_x', None)
@@ -75,6 +77,8 @@ def parse_params(params):
         'fname': fname,
         'waveLength': waveLength,
         'list_max_min_peaks': listMaxMinPeaks,
+        'cyclicvolta': cyclicvolta,
+        'jcamp_idx': jcamp_idx,
     }
 
 

chem_spectra/lib/shared/calc.py

@@ -100,3 +100,59 @@ def cal_area_multiplicity(xL, xU, data_xs, data_ys):
     lower_value = Decimal(str(ks[iL]))
 
     return float(abs(upper_value - lower_value))
+
+def cal_cyclic_volta_shift_offset(cyclic_data):
+    if cyclic_data is None:
+        return []
+    if isinstance(cyclic_data, dict) ==  False:
+        return []
+    if 'spectraList' not in cyclic_data:
+        return []
+
+    spectra_list = cyclic_data['spectraList']
+    if isinstance(spectra_list, list) ==  False:
+        return []
+
+    list_offsets = []
+
+    for spectra in spectra_list:
+        offset = 0.0
+        analysed_data = spectra['list']
+        arr_has_ref_value = list(filter(lambda x: x['isRef'] == True,  analysed_data))
+        if len(arr_has_ref_value) > 0:
+            shift = spectra['shift']
+            val = shift['val']
+            ref_value = arr_has_ref_value[0]
+            e12 = ref_value['e12']
+            offset = e12 - val
+        list_offsets.append(offset)
+
+    return list_offsets
+
+def cal_cyclic_volta_shift_offset_at_index(cyclic_data, index=0):
+    if cyclic_data is None:
+        return 0.0
+    if isinstance(cyclic_data, dict) ==  False:
+        return 0.0
+    if 'spectraList' not in cyclic_data:
+        return 0.0
+
+    spectra_list = cyclic_data['spectraList']
+    if isinstance(spectra_list, list) ==  False:
+        return 0.0
+    if len(spectra_list) <  index:
+        return 0.0
+
+    offset = 0.0
+
+    spectra = spectra_list[index]
+    analysed_data = spectra['list']
+    arr_has_ref_value = list(filter(lambda x: x['isRef'] == True,  analysed_data))
+    if len(arr_has_ref_value) > 0:
+        shift = spectra['shift']
+        val = shift['val']
+        ref_value = arr_has_ref_value[0]
+        e12 = ref_value['e12']
+        offset = e12 - val
+
+    return offset

tests/lib/shared/test_calc.py

@@ -101,3 +101,25 @@ def test_cal_area_multiplicity():
     data_ys = [2.0, 4.0]
     area = cal_area_multiplicity(xL, xU, data_xs=data_xs, data_ys=data_ys)
     assert area == 1.0
+
+def test_cal_cyclic_volta_shift_offset_when_cyclic_data_is_none():
+    list_expected_offsets = []
+    list_offsets = cal_cyclic_volta_shift_offset(None)
+    assert list_offsets == list_expected_offsets
+
+def test_cal_cyclic_volta_shift_offset_when_invalid_cyclic_data():
+    list_expected_offsets = []
+    list_offsets = cal_cyclic_volta_shift_offset({'test': []})
+    assert list_offsets == list_expected_offsets
+
+def test_cal_cyclic_volta_shift_offset():
+    cyclic_data = {'spectraList':[{'list':[{'min':{'x':-1.48904,'y':-1.10686e-05},'max':{'x':1.80895,'y':9.51171e-06},'isRef':True,'e12':0.15995500000000007,'pecker':{'x':-0.129871,'y':7.78418e-07}}],'selectedIdx':0,'isWorkMaxPeak':True,'jcampIdx':0,'shift':{'ref':None,'val':0}},{'list':[{'min':{'x':-1.48904,'y':-3.3747399999999995e-05},'max':{'x':0.929483,'y':0.00023741},'isRef':True,'e12':-0.27977849999999993}],'selectedIdx':0,'isWorkMaxPeak':True,'jcampIdx':1,'shift':{'ref':None,'val':5}},{'list':[{'min':{'x':0.45977,'y':-0.000226347},'max':{'x':1.00943,'y':0.000371349},'isRef':False,'e12':0.7346}],'selectedIdx':0,'isWorkMaxPeak':True,'jcampIdx':2,'shift':{'ref':None,'val':0}}]}
+    list_expected_offsets = [0.15995500000000007, -5.2797785, 0.0]
+    list_offsets = cal_cyclic_volta_shift_offset(cyclic_data)
+    assert list_offsets == list_expected_offsets
+
+def test_cal_cyclic_volta_shift_offset_at_index():
+    cyclic_data = {'spectraList':[{'list':[{'min':{'x':-1.48904,'y':-1.10686e-05},'max':{'x':1.80895,'y':9.51171e-06},'isRef':True,'e12':0.15995500000000007,'pecker':{'x':-0.129871,'y':7.78418e-07}}],'selectedIdx':0,'isWorkMaxPeak':True,'jcampIdx':0,'shift':{'ref':None,'val':0}},{'list':[{'min':{'x':-1.48904,'y':-3.3747399999999995e-05},'max':{'x':0.929483,'y':0.00023741},'isRef':True,'e12':-0.27977849999999993}],'selectedIdx':0,'isWorkMaxPeak':True,'jcampIdx':1,'shift':{'ref':None,'val':5}},{'list':[{'min':{'x':0.45977,'y':-0.000226347},'max':{'x':1.00943,'y':0.000371349},'isRef':False,'e12':0.7346}],'selectedIdx':0,'isWorkMaxPeak':True,'jcampIdx':2,'shift':{'ref':None,'val':0}}]}
+    expected_offset = 0.15995500000000007
+    offset = cal_cyclic_volta_shift_offset_at_index(cyclic_data, 0)
+    assert offset == expected_offset