ararpy 0.1.12__py3-none-any.whl → 0.1.14__py3-none-any.whl

ararpy/smp/corr.py

@@ -20,54 +20,53 @@ from .sample import Sample
 
 
 # =======================
-# Corr Blank
+# Corr Gain
 # =======================
-def corr_blank(sample: Sample):
+def corr_gain(sample: Sample):
     """Blank Correction"""
-    corrBlank = sample.TotalParam[102][0]
-    # if not corrBlank:
-    #     sample.BlankCorrected = copy.deepcopy(sample.SampleIntercept)
-    #     sample.CorrectedValues = copy.deepcopy(sample.BlankCorrected)
-    #     return
-    blank_corrected = [[]] * 10
+    corrGain = True
+    gain_corrected = np.zeros([10, len(sample.SequenceName)])
     try:
         for i in range(5):
-            blank_corrected[i * 2:2 + i * 2] = calc.corr.blank(
-                *sample.SampleIntercept[i * 2:2 + i * 2], *sample.BlankIntercept[i * 2:2 + i * 2])
+            f, sf = np.array(sample.TotalParam[126 + i * 2:128 + i * 2])
+            sf = f * sf / 100
+            gain_corrected[i * 2:2 + i * 2] = calc.corr.gain(*sample.SampleIntercept[i * 2:2 + i * 2], f, sf)
     except Exception as e:
+        print(f"Gain correction failed")
         print(traceback.format_exc())
-        raise ValueError('Blank correction error')
+        return
     for i in range(0, 10, 2):
-        blank_corrected[i] = [blank_corrected[i][index] if sample.TotalParam[102][index] else j for index, j in enumerate(sample.SampleIntercept[i])]
-        blank_corrected[i + 1] = [blank_corrected[i + 1][index] if sample.TotalParam[102][index] else j for index, j in enumerate(sample.SampleIntercept[i + 1])]
-        blank_corrected[i] = [0 if j < 0 and sample.TotalParam[101][index] else j for index, j in enumerate(blank_corrected[i])]
-    sample.BlankCorrected = blank_corrected
-    sample.CorrectedValues = copy.deepcopy(sample.BlankCorrected)
+        gain_corrected[i] = [gain_corrected[i][index] if corrGain else j for index, j in enumerate(sample.SampleIntercept[i])]
+        gain_corrected[i + 1] = [gain_corrected[i + 1][index] if corrGain else j for index, j in enumerate(sample.SampleIntercept[i + 1])]
+    sample.CorrectedValues = copy.deepcopy(gain_corrected)
 
 
 # =======================
 # Corr Blank
 # =======================
-def corr_gain(sample: Sample):
+def corr_blank(sample: Sample):
     """Blank Correction"""
-    corrGain = True
-    # if not corrBlank:
-    #     sample.BlankCorrected = copy.deepcopy(sample.SampleIntercept)
-    #     sample.CorrectedValues = copy.deepcopy(sample.BlankCorrected)
-    #     return
-    gain_corrected = [[]] * 10
+    blank_corrected = np.zeros([10, len(sample.SequenceName)])
     try:
         for i in range(5):
-            gain_corrected[i * 2:2 + i * 2] = calc.corr.gain(
-                *sample.BlankCorrected[i * 2:2 + i * 2], *sample.TotalParam[126 + i * 2:128 + i * 2])
+            b, sb = copy.deepcopy(sample.BlankIntercept[i * 2: i * 2 + 2])
+            f, sf = np.array(sample.TotalParam[126 + i * 2:128 + i * 2])
+            sf = f * sf / 100
+            _ = calc.corr.gain(*sample.BlankIntercept[i * 2:2 + i * 2], f, sf)
+            for index in range(len(sample.BlankIntercept[i * 2])):
+                if sample.TotalParam[111][index]:  # use same parameters to correct blank intercepts
+                    b[index] = _[0][index]
+                    sb[index] = _[1][index]
+            blank_corrected[i * 2:2 + i * 2] = calc.corr.blank(
+                *sample.CorrectedValues[i * 2:2 + i * 2], b, sb)
     except Exception as e:
-        print(f"Gain correction failed")
         print(traceback.format_exc())
-        return
+        raise ValueError('Blank correction error')
     for i in range(0, 10, 2):
-        gain_corrected[i] = [gain_corrected[i][index] if corrGain else j for index, j in enumerate(sample.BlankCorrected[i])]
-        gain_corrected[i + 1] = [gain_corrected[i + 1][index] if corrGain else j for index, j in enumerate(sample.BlankCorrected[i + 1])]
-    sample.BlankCorrected = copy.deepcopy(gain_corrected)
+        blank_corrected[i] = [blank_corrected[i][index] if sample.TotalParam[102][index] else j for index, j in enumerate(sample.CorrectedValues[i])]
+        blank_corrected[i + 1] = [blank_corrected[i + 1][index] if sample.TotalParam[102][index] else j for index, j in enumerate(sample.CorrectedValues[i + 1])]
+        blank_corrected[i] = [0 if j < 0 and sample.TotalParam[101][index] else j for index, j in enumerate(blank_corrected[i])]
+    sample.BlankCorrected = blank_corrected
     sample.CorrectedValues = copy.deepcopy(sample.BlankCorrected)
 
 
@@ -82,7 +81,7 @@ def corr_massdiscr(sample: Sample):
         sample.CorrectedValues = copy.deepcopy(sample.MassDiscrCorrected)
         return
     MASS = sample.TotalParam[71:81]
-    mdf_corrected = [[]] * 10
+    mdf_corrected = np.zeros([10, len(sample.SequenceName)])
     try:
         for i in range(5):
             if len(sample.BlankCorrected[i * 2:2 + i * 2]) == 0:
@@ -111,7 +110,7 @@ def corr_decay(sample: Sample):
     -------
 
     """
-    decay_corrected = [[]] * 10
+    decay_corrected = np.zeros([10, len(sample.SequenceName)])
     try:
         irradiation_cycles = [list(filter(None, re.split(r'[DS]', each_step))) for each_step in sample.TotalParam[27]]
         t1 = [re.findall(r"\d+", i) for i in sample.TotalParam[31]]  # t1: experimental times
@@ -265,7 +264,6 @@ def calc_degas_cl(sample: Sample):
         # 38ArCl
         ar38cl = [[], []]
         ar38cl[1] = [calc.err.mul((ar36cl[0][i], ar36cl[1][i]), (v3[i], s3[i])) for i in range(len(ar36cl[0]))]
-        ar38cl[0] = [ar36cl[0][i] * v3[i] for i in range(len(ar36cl[0]))]
 
         # Negative number set to zero
         ar36cl[0] = [0 if i < 0 and set_negative_zero else i for i in ar36cl[0]]
@@ -273,11 +271,13 @@ def calc_degas_cl(sample: Sample):
         ar36cl[0] = [0 if ar36acl[0][i] - item < 0 and set_negative_zero else item
                      for i, item in enumerate(ar36cl[0])]
 
+        ar38cl[0] = [ar36cl[0][i] * v3[i] for i in range(len(ar36cl[0]))]
+
     except Exception as e:
         print('Error in corr Cl: {}, lines: {}'.format(e, e.__traceback__.tb_lineno))
         n = len(ar36acl[0])
-        ar36cl = [[0] * n, [0] * n]
-        ar38cl = [[0] * n, [0] * n]
+        ar36cl = np.zeros([2, n])
+        ar38cl = np.zeros([2, n])
 
     # sample.DegasValues[6:8] = ar36cl
     # sample.DegasValues[10:12] = ar38cl
@@ -357,6 +357,57 @@ def calc_degas_r(sample: Sample):
 # =======================
 # Calc ratio
 # =======================
+def calc_nor_inv_isochrons(sample: Sample):
+    n = len(sample.SequenceName)
+    try:
+        isochron_1 = calc.isochron.get_data(*sample.DegasValues[20:22], *calc.arr.sub(
+            sample.CorrectedValues[8:10], sample.DegasValues[30:32]), *sample.DegasValues[0:2])
+        isochron_2 = calc.isochron.get_data(*sample.DegasValues[20:22], *sample.DegasValues[0:2], *calc.arr.sub(
+            sample.CorrectedValues[8:10], sample.DegasValues[30:32]))
+    except:
+        return np.zeros([5, n]), np.zeros([5, n])
+    else:
+        return isochron_1, isochron_2
+
+
+def calc_cl_isochrons(sample: Sample):
+    n = len(sample.SequenceName)
+    try:
+        isochron_3 = calc.isochron.get_data(
+            *sample.DegasValues[20:22], *sample.DegasValues[24:26], *sample.DegasValues[10:12])
+        isochron_4 = calc.isochron.get_data(
+            *sample.DegasValues[20:22], *sample.DegasValues[10:12], *sample.DegasValues[24:26])
+        isochron_5 = calc.isochron.get_data(
+            *sample.DegasValues[10:12], *sample.DegasValues[24:26], *sample.DegasValues[20:22])
+    except:
+        return np.zeros([5, n]), np.zeros([5, n]), np.zeros([5, n])
+    else:
+        return isochron_3, isochron_4, isochron_5
+
+
+def calc_3D_isochrons(sample: Sample):
+    n = len(sample.SequenceName)
+    try:
+        # === Ar values ===
+        # 3D ratio, 36Ar(a+cl)/40Ar(a+r), 38Ar(a+cl)/40Ar(a+r), 39Ar(k)/40Ar(a+r),
+        ar40ar = calc.arr.sub(sample.CorrectedValues[8:10], sample.DegasValues[30:32])
+        # 36Ar deduct Ca, that is sum of 36Ara and 36ArCl (and also 36Arc)
+        ar36acl = calc.arr.sub(sample.CorrectedValues[0:2], sample.DegasValues[4:6])
+        # 38Ar deduct K and Ca, that is sum of 38Ara and 38ArCl (and also 38Arc)
+        ar38acl = calc.arr.sub(calc.arr.sub(sample.CorrectedValues[4:6], sample.DegasValues[16:18]),
+                               sample.DegasValues[18:20])
+        # 38ArCl
+        ar38cl = sample.DegasValues[10:12]
+        # 39ArK
+        ar39k = sample.DegasValues[20:22]
+        # isochron_6 = calc.isochron.get_3d_data(*ar36acl, *ar38acl, *ar40ar, *ar39k)
+        isochron_6 = calc.isochron.get_3d_data(*ar36acl, *ar38acl, *ar39k, *ar40ar)  # Points on the plot will be more disperse than the above
+    except:
+        return np.zeros([9, n])
+    else:
+        return isochron_6
+
+
 def calc_ratio(sample: Sample, monte_carlo: bool = False):
     """ Calculate isochron ratio data, 40Arr/39ArK, Ar40r percentage,
         Ar39K released percentage, Ca/K
@@ -372,57 +423,36 @@ def calc_ratio(sample: Sample, monte_carlo: bool = False):
     ar40r_percent = [item / sample.CorrectedValues[8][index] * 100 if sample.CorrectedValues[8][index] != 0 else 0
                      for index, item in enumerate(sample.DegasValues[24])]
     sum_ar39k = sum(sample.DegasValues[20])
-    ar39k_percent = [item / sum_ar39k * 100 if sum_ar39k != 0 else 0 for item in sample.DegasValues[20]]
     sum_ar36a = sum(sample.DegasValues[ 0])
-    ar36a_percent = [item / sum_ar36a * 100 if sum_ar36a != 0 else 0 for item in sample.DegasValues[ 0]]
-    ar40rar39k = calc.arr.mul_factor(
-        sample.DegasValues[24:26], calc.arr.rec_factor(sample.DegasValues[20:22], isRelative=False),
-        isRelative=False)
-    ar40aar36a = calc.arr.mul_factor(
-        sample.DegasValues[26:28], calc.arr.rec_factor(sample.DegasValues[0:2], isRelative=False),
-        isRelative=False)
     CaK = calc.arr.mul_factor(calc.arr.mul_factor(
         sample.DegasValues[8:10], calc.arr.rec_factor(sample.DegasValues[20:22], isRelative=False)),
         calc.arr.rec_factor(sample.TotalParam[20:22], isRelative=True))
-    isochron_1 = calc.isochron.get_data(*sample.DegasValues[20:22], *calc.arr.sub(
-        sample.CorrectedValues[8:10], sample.DegasValues[30:32]), *sample.DegasValues[0:2])
-    isochron_2 = calc.isochron.get_data(*sample.DegasValues[20:22], *sample.DegasValues[0:2], *calc.arr.sub(
-        sample.CorrectedValues[8:10], sample.DegasValues[30:32]))
-    isochron_3 = calc.isochron.get_data(
-        *sample.DegasValues[20:22], *sample.DegasValues[24:26], *sample.DegasValues[10:12])
-    isochron_4 = calc.isochron.get_data(
-        *sample.DegasValues[20:22], *sample.DegasValues[10:12], *sample.DegasValues[24:26])
-    isochron_5 = calc.isochron.get_data(
-        *sample.DegasValues[10:12], *sample.DegasValues[24:26], *sample.DegasValues[20:22])
 
     # assignation
-    sample.ApparentAgeValues[0:2] = ar40aar36a if sample.Info.sample.type == "Air" else ar40rar39k
+    if sample.Info.sample.type == "Air":
+        ar40aar36a = calc.arr.mul_factor(
+            sample.DegasValues[26:28], calc.arr.rec_factor(sample.DegasValues[0:2], isRelative=False),
+            isRelative=False)
+        ar36a_percent = [item / sum_ar36a * 100 if sum_ar36a != 0 else 0 for item in sample.DegasValues[0]]
+        sample.ApparentAgeValues[0:2] = ar40aar36a
+        sample.ApparentAgeValues[7] = ar36a_percent
+    else:
+        ar40rar39k = calc.arr.mul_factor(
+            sample.DegasValues[24:26], calc.arr.rec_factor(sample.DegasValues[20:22], isRelative=False),
+            isRelative=False)
+        ar39k_percent = [item / sum_ar39k * 100 if sum_ar39k != 0 else 0 for item in sample.DegasValues[20]]
+        sample.ApparentAgeValues[0:2] = ar40rar39k
+        sample.ApparentAgeValues[7] = ar39k_percent
+
     sample.ApparentAgeValues[6] = ar40r_percent
-    sample.ApparentAgeValues[7] = ar36a_percent if sample.Info.sample.type == "Air" else ar39k_percent
-    sample.PublishValues[7:11] = [ar40r_percent, ar39k_percent, *CaK]
-    sample.IsochronValues[0:5] = isochron_1
-    sample.IsochronValues[6:11] = isochron_2
-    sample.IsochronValues[12:17] = isochron_3
-    sample.IsochronValues[18:23] = isochron_4
-    sample.IsochronValues[24:29] = isochron_5
+    sample.PublishValues[7:11] = copy.deepcopy([*sample.ApparentAgeValues[6:8], *CaK])
+
+    sample.IsochronValues[0:5], sample.IsochronValues[6:11] = calc_nor_inv_isochrons(sample)
+    sample.IsochronValues[12:17], sample.IsochronValues[18:23], sample.IsochronValues[24:29] = \
+        calc_cl_isochrons(sample)
 
     # === Cl-Atm-Correlation Plot ===
-    # === Ar values ===
-    # 3D ratio, 36Ar(a+cl)/40Ar(a+r), 38Ar(a+cl)/40Ar(a+r), 39Ar(k)/40Ar(a+r),
-    ar40ar = calc.arr.sub(sample.CorrectedValues[8:10], sample.DegasValues[30:32])
-    # 36Ar deduct Ca, that is sum of 36Ara and 36ArCl (and also 36Arc)
-    ar36acl = calc.arr.sub(sample.CorrectedValues[0:2], sample.DegasValues[4:6])
-    # 38Ar deduct K and Ca, that is sum of 38Ara and 38ArCl (and also 38Arc)
-    ar38acl = calc.arr.sub(calc.arr.sub(sample.CorrectedValues[4:6], sample.DegasValues[16:18]),
-                           sample.DegasValues[18:20])
-    # 38ArCl
-    ar38cl = sample.DegasValues[10:12]
-    # 39ArK
-    ar39k = sample.DegasValues[20:22]
-    # isochron_6 = calc.isochron.get_3d_data(*ar36acl, *ar38acl, *ar40ar, *ar39k)
-    isochron_6 = calc.isochron.get_3d_data(*ar36acl, *ar38acl, *ar39k,
-                                           *ar40ar)  # Points on the plot will be more disperse than the above
-    sample.IsochronValues[30:39] = isochron_6
+    sample.IsochronValues[30:39] = calc_3D_isochrons(sample)
 
     # Turner 1988 3D cake mix plots
     # ar40 = sample.CorrectedValues[8:10]  # ar40 = atm + r + k