ararpy 0.1.18__py3-none-any.whl → 0.1.20__py3-none-any.whl

ararpy/smp/corr.py

@@ -25,16 +25,15 @@ from .sample import Sample
 def corr_gain(sample: Sample):
     """Blank Correction"""
     corrGain = True
-    gain_corrected = np.zeros([10, len(sample.SequenceName)])
+    gain_corrected = np.zeros([10, sample.Info.experiment.step_num])
     try:
         for i in range(5):
             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())
-        return
+    except (Exception, BaseException) as e:
+        print(f"Gain correction failed: \n{traceback.format_exc()}")
+        raise
     for i in range(0, 10, 2):
         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])]
@@ -156,15 +155,12 @@ def calc_degas_ca(sample: Sample):
     ar39ca = calc.arr.mul_factor(ar37ca, sample.TotalParam[8:10], isRelative=True)
     ar38ca = calc.arr.mul_factor(ar37ca, sample.TotalParam[10:12], isRelative=True)
     ar36ca = calc.arr.mul_factor(ar37ca, sample.TotalParam[12:14], isRelative=True)
-    sample.DegasValues[8:10] = copy.deepcopy(ar37ca)
-    # sample.DegasValues[22:24] = ar39ca if corrDecasCa else [[0] * n, [0] * n]
-    # sample.DegasValues[18:20] = ar38ca if corrDecasCa else [[0] * n, [0] * n]
-    # sample.DegasValues[4:6] = ar36ca if corrDecasCa else [[0] * n, [0] * n]
-    sample.DegasValues[ 4] = [val if corrDecasCa[idx] else 0 for idx, val in enumerate(ar36ca[0])]
+    sample.DegasValues[8:10] = copy.deepcopy(ar37ca)  # 37Ca
+    sample.DegasValues[ 4] = [val if corrDecasCa[idx] else 0 for idx, val in enumerate(ar36ca[0])]  # 36Ca
     sample.DegasValues[ 5] = [val if corrDecasCa[idx] else 0 for idx, val in enumerate(ar36ca[1])]
-    sample.DegasValues[18] = [val if corrDecasCa[idx] else 0 for idx, val in enumerate(ar38ca[0])]
+    sample.DegasValues[18] = [val if corrDecasCa[idx] else 0 for idx, val in enumerate(ar38ca[0])]  # 38Ca
     sample.DegasValues[19] = [val if corrDecasCa[idx] else 0 for idx, val in enumerate(ar38ca[1])]
-    sample.DegasValues[22] = [val if corrDecasCa[idx] else 0 for idx, val in enumerate(ar39ca[0])]
+    sample.DegasValues[22] = [val if corrDecasCa[idx] else 0 for idx, val in enumerate(ar39ca[0])]  # 39Ca
     sample.DegasValues[23] = [val if corrDecasCa[idx] else 0 for idx, val in enumerate(ar39ca[1])]
     sample.PublishValues[1] = copy.deepcopy(ar37ca[0])
 
@@ -241,43 +237,51 @@ def calc_degas_cl(sample: Sample):
     try:
         if not corrDecasCl:
             raise ValueError("Do not apply degas chlorine")
-        v3 = [cl36_cl38_p[0][i] * (1 - np.exp(-1 * decay_const[0][i] * stand_time_year[i])) for i in
+        vDecay = [cl36_cl38_p[0][i] * (1 - np.exp(-1 * decay_const[0][i] * stand_time_year[i])) for i in
               range(len(stand_time_year))]
-        s3 = [pow((cl36_cl38_p[1][i] * (1 - np.exp(-1 * decay_const[0][i] * stand_time_year[i]))) ** 2 +
+        sDecay = [pow((cl36_cl38_p[1][i] * (1 - np.exp(-1 * decay_const[0][i] * stand_time_year[i]))) ** 2 +
                   (cl36_cl38_p[0][i] * stand_time_year[i] * (np.exp(-1 * decay_const[0][i] * stand_time_year[i])) *
                    decay_const[1][i]) ** 2, 0.5) for i in range(len(stand_time_year))]
-        s3 = [calc.err.div((1, 0), (v3[i], s3[i])) for i in range(len(s3))]
-        v3 = [1 / v3[i] for i in range(len(v3))]
+        sDecay = [calc.err.div((1, 0), (vDecay[i], sDecay[i])) for i in range(len(sDecay))]
+        vDecay = [1 / vDecay[i] for i in range(len(vDecay))]
+
         # 36ArCl
         ar36cl = [[], []]
-        ar36cl[0] = [(ar36acl[0][i] * ar38ar36[0][i] - ar38acl[0][i]) / (ar38ar36[0][i] - v3[i])
-                     for i in range(len(ar36acl[0]))]
-        s1 = [(ar36acl[1][i] * ar38ar36[0][i] / (ar38ar36[0][i] - v3[i])) ** 2 for i in range(len(ar36cl[0]))]
-        s2 = [(ar38acl[1][i] / (ar38ar36[0][i] - v3[i])) ** 2 for i in range(len(ar36cl[0]))]
-        s3 = [(s3[i] * (ar36acl[0][i] * ar38ar36[0][i] - ar38acl[0][i]) / (ar38ar36[0][i] - v3[i]) ** 2) ** 2
-              for i in range(len(ar36cl[0]))]
-        s4 = [(ar36acl[0][i] / (ar38ar36[0][i] - v3[i]) -
-               (ar36acl[0][i] * ar38ar36[0][i] - ar38acl[0][i]) / (ar38ar36[0][i] - v3[i]) ** 2) ** 2 *
-              (ar38ar36[1][i]) ** 2 for i in range(len(ar36cl[0]))]
-        ar36cl[1] = [pow(s1[i] + s2[i] + s3[i] + s4[i], 0.5) for i in range(len(ar36cl[0]))]
-
         # 38ArCl
         ar38cl = [[], []]
-        ar38cl[1] = [calc.err.mul((ar36cl[0][i], ar36cl[1][i]), (v3[i], s3[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]]
-        # force 36ArCl to zero if 36Ar - 36ArCa - 36Cl < 0
-        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]))]
+        for i in range(len(vDecay)):
+            a1 = sample.CorrectedValues[0][i]; s1 = sample.CorrectedValues[1][i]
+            a2 = sample.DegasValues[4][i]; s2 = sample.DegasValues[5][i];
+            a3 =  sample.DegasValues[16][i]; s3 = sample.DegasValues[17][i]
+            a4 =  sample.DegasValues[18][i]; s4 = sample.DegasValues[19][i]
+            a5 =  sample.CorrectedValues[4][i]; s5 = sample.CorrectedValues[5][i]
+            a6 = vDecay[i]; s6 = sDecay[i]
+            a7 = ar38ar36[0][i]; s7 = ar38ar36[1][i]
+
+            d1 = 1 / (1 - a6 / a7)
+            d2 = - 1 / (1 - a6 / a7)
+            d3 = 1 / (a7 - a6)
+            d4 = 1 / (a7 - a6)
+            d5 = - 1 / (a7 - a6)
+            d6 = (a1 - a2 + (a3 + a4) / a7 - a5 / a7) / a7 / (1 - a6 / a7) ** 2
+            d7 = -(a1 - a2) * (a6) / (a7 - a6) ** 2 - (a3 + a4 - a5) / (a7 - a6) ** 2
+
+            v1 = (a1 - a2 + (a3 + a4) / a7 - a5 / a7) / (1 - a6 / a7)
+            s1 = (d1**2*s1**2 + d2**2*s2**2 + d3**2*s3**2 + d4**2*s4**2+ d5**2*s5**2 + d6**2*s6**2 + d7**2*s7**2) ** .5
+            s2 = calc.err.mul((v1, s1), (vDecay[i], sDecay[i]))
+            v1 = 0 if (ar36acl[0][i] - v1 < 0 or v1 < 0) and set_negative_zero[i] else v1
+            v2 = v1 * vDecay[i]
+
+            # Note: Ar36Cl uncertainty is differen with ArArCALC. All calculation was conducted separately considering they are independent
+            # s1 = calc.err.div((a1 - a2 + (a3 + a4) / a7 - a5 / a7, calc.err.add(s1, s2, calc.err.div((a3 + a4, calc.err.add(s3, s4)), (a7, s7)), calc.err.div((a5, s5), (a7, s7)))), (1 - a6 / a7, calc.err.div((a6, s6), (a7, s7))))
+
+            ar36cl[0].append(v1); ar36cl[1].append(s1)
+            ar38cl[0].append(v2); ar38cl[1].append(s2)
 
     except Exception as e:
         print('Error in corr Cl: {}, lines: {}'.format(e, e.__traceback__.tb_lineno))
-        n = len(ar36acl[0])
-        ar36cl = np.zeros([2, n])
-        ar38cl = np.zeros([2, n])
+        ar36cl = np.zeros([2, len(ar36acl[0])])
+        ar38cl = np.zeros([2, len(ar36acl[0])])
 
     # sample.DegasValues[6:8] = ar36cl
     # sample.DegasValues[10:12] = ar38cl
@@ -349,7 +353,7 @@ def calc_degas_r(sample: Sample):
     """
     ar40ar = calc.arr.sub(sample.CorrectedValues[8:10], sample.DegasValues[30:32])
     ar40r = calc.arr.sub(ar40ar, sample.DegasValues[26:28])
-    ar40r[0] = [item if item >= 0 else 0 for item in ar40r[0]]
+    ar40r[0] = [0 if item < 0 and sample.TotalParam[101][index] else item for index, item in enumerate(ar40r[0])]
     sample.DegasValues[24:26] = copy.deepcopy(ar40r)
     sample.PublishValues[4] = copy.deepcopy(ar40r[0])
 
@@ -360,11 +364,16 @@ def calc_degas_r(sample: Sample):
 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:
+        isochron_1 = calc.isochron.get_data(
+            *calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor),
+            *calc.arr.sub(sample.CorrectedValues[8:10], sample.DegasValues[30:32]),
+            *sample.DegasValues[0:2]
+        )
+        isochron_2 = calc.isochron.get_data(
+            *calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor),
+            *sample.DegasValues[0:2],
+            *calc.arr.sub(sample.CorrectedValues[8:10], sample.DegasValues[30:32]))
+    except (BaseException, Exception):
         return np.zeros([5, n]), np.zeros([5, n])
     else:
         return isochron_1, isochron_2
@@ -374,12 +383,18 @@ 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])
+            *calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor),
+            *sample.DegasValues[24:26],
+            *calc.arr.mul(sample.DegasValues[10:12], sample.NormalizeFactor))
         isochron_4 = calc.isochron.get_data(
-            *sample.DegasValues[20:22], *sample.DegasValues[10:12], *sample.DegasValues[24:26])
+            *calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor),
+            *calc.arr.mul(sample.DegasValues[10:12], sample.NormalizeFactor),
+            *sample.DegasValues[24:26])
         isochron_5 = calc.isochron.get_data(
-            *sample.DegasValues[10:12], *sample.DegasValues[24:26], *sample.DegasValues[20:22])
-    except:
+            *calc.arr.mul(sample.DegasValues[10:12], sample.NormalizeFactor),
+            *sample.DegasValues[24:26],
+            *calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor))
+    except (BaseException, Exception):
         return np.zeros([5, n]), np.zeros([5, n]), np.zeros([5, n])
     else:
         return isochron_3, isochron_4, isochron_5
@@ -422,7 +437,6 @@ 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])
     sum_ar36a = sum(sample.DegasValues[ 0])
     CaK = calc.arr.mul_factor(calc.arr.mul_factor(
         sample.DegasValues[8:10], calc.arr.rec_factor(sample.DegasValues[20:22], isRelative=False)),
@@ -437,10 +451,12 @@ def calc_ratio(sample: Sample, monte_carlo: bool = False):
         sample.ApparentAgeValues[0:2] = ar40aar36a
         sample.ApparentAgeValues[7] = ar36a_percent
     else:
+        ar39k, sar39k = calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor)
+        sum_ar39k = sum(ar39k)
+        ar39k_percent = [item / sum_ar39k * 100 if sum_ar39k != 0 else 0 for item in ar39k]
         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
 
@@ -529,6 +545,7 @@ def monte_carlo_f(sample: Sample):
     R36v38clp = np.transpose(sample.TotalParam[56:58])
 
     stand_time_year = np.transpose(sample.TotalParam[32])
+    JNFactor = sample.NormalizeFactor
 
     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
@@ -562,6 +579,7 @@ def monte_carlo_f(sample: Sample):
             L37ar=L37ar[i], L39ar=L39ar[i], L36cl=L36cl[i],
             MDFunc=None,
             MDF=MDF[i], stand_time_year=stand_time_year[i],
+            JNFactor=JNFactor,
             blank_gain_corr=sample.TotalParam[111][i]
         )