ararpy 0.1.193__tar.gz → 0.1.197__tar.gz

{ararpy-0.1.193 → ararpy-0.1.197}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.193
+Version: 0.1.197
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.193 → ararpy-0.1.197}/ararpy/__init__.py

@@ -16,7 +16,7 @@ from . import calc, smp, files, thermo, test
 """ Information """
 
 name = 'ararpy'
-version = '0.1.193'
+version = '0.1.197'
 __version__ = version
 full_version = version
 last_update = '2024-03-28'

{ararpy-0.1.193 → ararpy-0.1.197}/ararpy/calc/age.py

@@ -61,15 +61,18 @@ def calc_age_min(F, sF, **kwargs) -> tuple:
     Lb = arr.array_as_float(kwargs.pop('Lb'))
     sLb = arr.array_as_float(kwargs.pop('sLb') * Lb / 100)
     t = arr.array_as_float(kwargs.pop('t'))
-    st = arr.array_as_float(kwargs.pop('st') * t / 100)
+    st = arr.array_as_float(kwargs.pop('st'))
     # Ap = arr.array_as_float(kwargs.pop('Ap'))
     # sAp = arr.array_as_float(kwargs.pop('sAp') * Ap / 100)
     # Kp = arr.array_as_float(kwargs.pop('Kp'))
     # sKp = arr.array_as_float(kwargs.pop('sKp') * Kp / 100)
 
+    print(f"{t = }, {st = }")
+
     # recalculation using Min et al.(2000) equation
     # lmd = A * W * Y / (f * No)
     V = f * No / ((Ab + Ae) * W * Y)
+    sf = 0
     sV = pow((V / f * sf) ** 2 + (V / No * sNo) ** 2 + (V / (Ab + Ae)) ** 2 * (sAb ** 2 + sAe ** 2) +
              (V / W * sW) ** 2 + (V / Y * sY) ** 2, 0.5)
     # standard age in year, change to Ma

{ararpy-0.1.193 → ararpy-0.1.197}/ararpy/calc/arr.py

@@ -38,7 +38,7 @@ def mul(*args):
 
     Returns
     -------
-    2D list, [values, errors]
+    two-D list, [values, errors]
     """
     v = np.array(args)
     res = np.zeros([2, v.shape[-1]], dtype=np.float64)
@@ -575,7 +575,7 @@ def wtd_mean(a: list, e: list, sf: int = 1, adjust_error: bool = True):
     k0 = sum(a * wt) / sum(wt)  # error weighting
     k4 = sum((a - k0) ** 2 * wt)  # Chi square
     k3 = k4 / df  # MSWD mentioned in Min et al., 2000
-    if adjust_error:
+    if adjust_error and k3 > 1:
         k1 = (k3 / sum(wt)) ** .5
     else:
         k1 = (1 / sum(wt)) ** .5

{ararpy-0.1.193 → ararpy-0.1.197}/ararpy/calc/corr.py

@@ -268,7 +268,7 @@ def Monte_Carlo_F(ar40m: Tuple[float, float], ar39m: Tuple[float, float], ar38m:
                   M37: Tuple[float, float], M36: Tuple[float, float],
                   G40: Tuple[float, float], G39: Tuple[float, float], G38: Tuple[float, float],
                   G37: Tuple[float, float], G36: Tuple[float, float],
-                  stand_time_year: float,
+                  stand_time_year: float, JNFactor: Tuple[float, float],
                   **options):
     """
 
@@ -294,6 +294,7 @@ def Monte_Carlo_F(ar40m: Tuple[float, float], ar39m: Tuple[float, float], ar38m:
     L36cl
     MDFunc
     MDF
+    JNFactor
     options
 
     Returns
@@ -307,9 +308,7 @@ def Monte_Carlo_F(ar40m: Tuple[float, float], ar39m: Tuple[float, float], ar38m:
     Monte_Carlo_Size = 10000
 
     # generate random
-    print(ar40m)
     ar40m = random_normal_absolute(*ar40m, size=Monte_Carlo_Size)
-    print(ar40m)
     ar39m = random_normal_absolute(*ar39m, size=Monte_Carlo_Size)
     ar38m = random_normal_absolute(*ar38m, size=Monte_Carlo_Size)
     ar37m = random_normal_absolute(*ar37m, size=Monte_Carlo_Size)
@@ -347,6 +346,8 @@ def Monte_Carlo_F(ar40m: Tuple[float, float], ar39m: Tuple[float, float], ar38m:
     R38v39k = random_normal_relative(*R38v39k, size=Monte_Carlo_Size)
     R36v38clp = random_normal_relative(*R36v38clp, size=Monte_Carlo_Size)
 
+    JNFactor = random_normal_absolute(*JNFactor, size=Monte_Carlo_Size)
+
     blank_gain_corr = options.get('blank_gain_corr', True)
 
     def do_simulation():
@@ -376,6 +377,7 @@ def Monte_Carlo_F(ar40m: Tuple[float, float], ar39m: Tuple[float, float], ar38m:
             _ar36a = _ar36res - _ar36cl
             _ar40r = _ar40 - _ar36a * R40v36a[i] - _ar39k * R40v39k[i]
             _ar40ar = _ar40 - _ar39k * R40v39k[i]
+            _ar39k = _ar39k * JNFactor[i]
             _f = _ar40r / _ar39k
             i += 1
             # yield _f, _ar36, _ar37, _ar38, _ar39, _ar40, _ar36a, _ar37ca, _ar39k, _ar40r, _ar36cl

{ararpy-0.1.193 → ararpy-0.1.197}/ararpy/smp/basic.py

@@ -500,10 +500,16 @@ def set_params(smp: Sample, params: Union[List, str], flag: Optional[str] = None
             flag = params.split(".")[-1]
         return set_params(smp, read_params(params), flag=flag)
 
+    def isValid(item):
+        valid = True
+        if isinstance(item, (float, int)):
+            valid = not np.isnan(item)
+        return valid and item is not None and item != ""
+
     def remove_none(old_params, new_params, row_list, length):
         res = [[old_params[i][j] if j < len(old_params[i]) else None for j in range(max(len(old_params[i]), length))] for i in range(len(old_params))]
         for index, item in enumerate(new_params):
-            if item is not None:
+            if isValid(item):
                 for row in row_list:
                     res[index][row] = item
         return res

{ararpy-0.1.193 → ararpy-0.1.197}/ararpy/smp/corr.py

@@ -156,15 +156,12 @@ 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 +238,51 @@ 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 +354,7 @@ 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 +365,16 @@ 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 +384,18 @@ 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 +438,6 @@ 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 +452,12 @@ 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
 
@@ -528,6 +545,8 @@ def monte_carlo_f(sample: Sample):
     R38v36a = np.transpose(sample.TotalParam[4:6])
     R36v38clp = np.transpose(sample.TotalParam[56:58])
 
+    JNFactor = np.transpose(sample.NormalizeFactor)
+
     stand_time_year = np.transpose(sample.TotalParam[32])
 
     irradiation_cycles = [list(filter(None, re.split(r'[DS]', each_step))) for each_step in sample.TotalParam[27]]
@@ -562,6 +581,7 @@ 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]
         )
 

{ararpy-0.1.193 → ararpy-0.1.197}/ararpy/smp/export.py

@@ -1069,7 +1069,7 @@ class WritingWorkbook:
         material = self.sample.Info.sample.material
         weight = self.sample.Info.sample.weight
         J_value = self.sample.TotalParam[67][0]
-        J_error = self.sample.TotalParam[68][0]
+        J_error = self.sample.TotalParam[68][0] * self.sample.TotalParam[67][0] / 100
         sigma = self.sample.Info.preference['confidenceLevel']
         sequence_type = {"StepLaser": "Laser", "StepFurnace": "Temperature", "StepCrusher": "Drop", }.get(method, "Step Value")
         sequence_unit = self.sample.Info.sample.sequence_unit if self.sample.Info.sample.sequence_unit != "" else "Unit"

{ararpy-0.1.193 → ararpy-0.1.197}/ararpy/smp/initial.py

@@ -16,7 +16,7 @@ import pandas as pd
 import numpy as np
 import copy
 from typing import List, Union, Optional
-from ..calc import arr
+from ..calc import arr, err
 from ..files import calc_file
 from . import (sample as samples, basic, table, raw as smp_raw)
 
@@ -268,10 +268,10 @@ def initial_plot_styles(sample: Sample, except_attrs=None):
             set_attr(plot, key, attr)
 
 
-def re_set_smp(sample: Sample):
+def re_set_smp(smp: Sample):
     std = initial(Sample())
-    basic.get_merged_smp(sample, std)
-    return sample
+    basic.get_merged_smp(smp, std)
+    return check_version(smp)
 
 
 def check_version(smp: Sample):
@@ -286,10 +286,28 @@ def check_version(smp: Sample):
 
     """
     if smp.version != samples.VERSION:
-        re_set_smp(smp)
-    if int(smp.version) <= 20250328:  # Experiment info
-        smp.Info.experiment.name = smp.name()
-        smp.Info.experiment.step_num = smp.sequence().size
+        std = initial(Sample())
+        basic.get_merged_smp(smp, std)
+
+    # 20250328:  # Experiment info
+    smp.Info.experiment.name = smp.name()
+    smp.Info.experiment.step_num = smp.sequence().size
+
+    # 20250404
+    doNormalize = True
+    v, sv = [], []
+    if smp.Info.sample.type.lower() != "unknown":
+        v, sv = smp.TotalParam[67:69]
+        sv = np.multiply(v, sv) / 100
+    elif smp.Info.sample.type.lower() != "air":
+        v, sv = smp.TotalParam[95:97]
+        sv = np.multiply(v, sv) / 100
+    elif smp.Info.sample.type.lower() != "standard":
+        v, sv = smp.TotalParam[59:61]
+    smp.NormalizeFactor = [
+        [1 if v[0] == each or not doNormalize else v[0] / each for each in v],
+        [0 if v[0] == v[i] or not doNormalize else err.div((v[0], sv[0]), (v[i], sv[i])) for i in range(len(v))]
+    ]
     return smp
 
 
@@ -356,7 +374,7 @@ def from_calc_files(file_path: str, **kwargs):
     """
     file = calc_file.ArArCalcFile(file_path=file_path, **kwargs).open()
     sample = create_sample_from_df(file.get_content(), file.get_smp_info())
-    return sample
+    return check_version(sample)
 
 
 # create
@@ -375,7 +393,7 @@ def from_full_files(file_path: str, sample_name: str = None):
         sample_name = str(os.path.split(file_path)[-1]).split('.')[0]
     content, sample_info = calc_file.open_full_xls(file_path, sample_name)
     sample = create_sample_from_dict(content=content, smp_info=sample_info)
-    return sample
+    return check_version(sample)
 
 
 # create
@@ -453,4 +471,4 @@ def from_raw_data(raw: RawData, mapping: Optional[List[dict]] = None) -> Sample:
 
     # sample.TotalParam[31] = [raw.get_sequence(row['unknown'], flag='name').datetime for row in mapping]
 
-    return sample
+    return check_version(sample)

{ararpy-0.1.193 → ararpy-0.1.197}/ararpy/smp/plots.py

@@ -405,6 +405,9 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
     -------
     None
     """
+    ar39k, sar39k = calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor)
+    ar40r, sar40r = sample.DegasValues[24:26]
+    ar40rar39k = calc.arr.div([ar40r, sar40r], [ar39k, sar39k])
     params_initial_ratio = calc.arr.partial(sample.TotalParam, cols=list(range(115, 120)))
     ratio_set1 = [[], []]
     ratio_set2 = [[], []]
@@ -430,10 +433,12 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
             ratio_set2[0].append(298.56)
             ratio_set2[1].append(0.31)
 
-    # Get ages and line data points for each set
+    # Weighted mean ages of two sets with the given initial ratios
     try:
-        set1_res, set1_age, set1_data = \
-            get_plateau_results(sample, sample.SelectedSequence1, calc_ar40ar39(*ratio_set1, smp=sample), **kwargs)
+        set1_res, set1_age, set1_data = get_plateau_results(
+            sample, sample.SelectedSequence1, calc_ar40ar39(*ratio_set1, smp=sample),
+            ar39k_percentage=np.cumsum(ar39k) / np.sum(ar39k),
+            **kwargs)
     except ValueError:
         # print(traceback.format_exc())
         pass
@@ -443,8 +448,10 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
         sample.AgeSpectraPlot.set1.data = calc.arr.transpose(set1_data)
         sample.AgeSpectraPlot.text1.text = ""  # 注意和js的配合，js那边根据text是否为空判断是否重新生成文字
     try:
-        set2_res, set2_age, set2_data = \
-            get_plateau_results(sample, sample.SelectedSequence2, calc_ar40ar39(*ratio_set2, smp=sample), **kwargs)
+        set2_res, set2_age, set2_data = get_plateau_results(
+            sample, sample.SelectedSequence2, calc_ar40ar39(*ratio_set2, smp=sample),
+            ar39k_percentage=np.cumsum(ar39k) / np.sum(ar39k),
+            **kwargs)
     except ValueError:
         # print(traceback.format_exc())
         pass
@@ -454,16 +461,18 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
         sample.AgeSpectraPlot.set2.data = calc.arr.transpose(set2_data)
         sample.AgeSpectraPlot.text2.text = ""  # 注意和js的配合，js那边根据text是否为空判断是否重新生成文字
 
-    # Get weighted mean ages of two sets
+    # Weighted mean ages of two sets with 298.56 (defoult air ratio)
     try:
-        set1_res = get_wma_results(sample, sample.SelectedSequence1)
+        set1_res = get_wma_results(
+            sample, sample.SelectedSequence1, ar40rar39k=ar40rar39k, ar39k_percentage=np.cumsum(ar39k) / np.sum(ar39k))
     except ValueError:
         pass
         # raise ValueError(f"Set 1 WMA calculation error.")
     else:
         sample.Info.results.age_spectra.update({0: set1_res})
     try:
-        set2_res = get_wma_results(sample, sample.SelectedSequence2)
+        set2_res = get_wma_results(
+            sample, sample.SelectedSequence2, ar40rar39k=ar40rar39k, ar39k_percentage=np.cumsum(ar39k) / np.sum(ar39k))
     except ValueError:
         pass
         # raise ValueError(f"Set 2 WMA calculation error.")
@@ -558,7 +567,7 @@ def calc_ar40ar39(r, sr, smp):
     """
     try:
         ar36a = np.array(smp.DegasValues[0:2])
-        ar39k = smp.DegasValues[20:22]
+        ar39k = calc.arr.mul(smp.DegasValues[20:22], smp.NormalizeFactor)
         ar40 = smp.CorrectedValues[8:10]
         ar40k = smp.DegasValues[30:32]
         size = ar36a.shape[-1]
@@ -568,8 +577,6 @@ def calc_ar40ar39(r, sr, smp):
             ratio = np.array([r, sr])
         else:
             raise ValueError(f"Initial ratio is unsupported.")
-        # print(f"{ratio = }")
-        # print(f"{ar36a = }")
         ar40a = calc.arr.mul(ar36a, ratio)
         ar40r = calc.arr.sub(ar40, ar40k, ar40a)
         ar40rar39k: list = calc.arr.div(ar40r, ar39k)
@@ -627,13 +634,15 @@ def get_plateau_results(sample: Sample, sequence: list, ar40rar39k: list = None,
     return plateau_res, age, plot_data
 
 
-def get_wma_results(sample: Sample, sequence: list):
+def get_wma_results(sample: Sample, sequence: list, ar40rar39k: list = None, ar39k_percentage: list = None):
     """
     Get initial ratio re-corrected plateau results
     Parameters
     ----------
     sample : sample instance
     sequence : data slice index
+    ar40rar39k :
+    ar39k_percentage :
 
     Returns
     -------
@@ -642,6 +651,11 @@ def get_wma_results(sample: Sample, sequence: list):
         'age', 's1', 's2', 's3', 'Ar39', 'rs'
     ]
     """
+    if ar40rar39k is None:
+        ar40rar39k = sample.ApparentAgeValues[0:2]
+    if ar39k_percentage is None:
+        ar39k_percentage = sample.ApparentAgeValues[7]
+
     spectra_res = initial.SPECTRA_RES.copy()
     # spectra_res = initial.SPECTRA_RES
 
@@ -649,9 +663,9 @@ def get_wma_results(sample: Sample, sequence: list):
         return [arg[min(points): max(points) + 1] for arg in args]
 
     if len(sequence) > 0:
-        sum_ar39k = sum(_get_partial(sequence, sample.ApparentAgeValues[7])[0])
-        fs = _get_partial(sequence, sample.ApparentAgeValues[0])[0]
-        sfs = _get_partial(sequence, sample.ApparentAgeValues[1])[0]
+        sum_ar39k = sum(_get_partial(sequence, ar39k_percentage)[0])
+        fs = _get_partial(sequence, ar40rar39k[0])[0]
+        sfs = _get_partial(sequence, ar40rar39k[1])[0]
 
         wmf, swmf, num, mswd, chisq, p = calc.arr.wtd_mean(fs, sfs)
         age, s1, s2, s3 = basic.calc_age([wmf, swmf], smp=sample)

{ararpy-0.1.193 → ararpy-0.1.197}/ararpy/smp/sample.py

@@ -115,9 +115,9 @@ TOTAL_PARAMS_HEADERS = [
     'Mass \u00B3\u2078Ar', '%1\u03C3', 'Mass \u00B3\u2079Ar', '%1\u03C3',
     'Mass \u2074\u2070', '%1\u03C3', 'K Mass', '%1\u03C3',  # 73-84
     'No', '%1\u03C3', 'Year', '%1\u03C3', '\u2074\u2070K/K', '%1\u03C3',
-    '\u00B3\u2075/\u00B3\u2077Cl', '%1\u03C3', 'HCl/Cl', '%1\u03C3',  # 85-94
-    '\u2074\u2070Ar/\u00B3\u2076Ar air', '%1\u03C3',
-    '\u00B3\u2078Ar/\u00B3\u2076Ar air', '%1\u03C3',  # 95-98
+    '\u00B3\u2075Cl/\u00B3\u2077Cl', '%1\u03C3', 'HCl/Cl', '%1\u03C3',  # 85-94
+    '\u2074\u2070Ar/\u00B3\u2076Ar air', '%1\u03C3',  # 95-96
+    '\u00B3\u2078Ar/\u00B3\u2076Ar air', '%1\u03C3',  # 97-98
     'Isochron Fitting', 'Convergence', 'Iteration', 'Discrimination',  # 99-102
     'Not Zero', 'Corr Blank', 'Corr Discr', 'Corr \u00B3\u2077Ar Decay',  # 103-106
     'Corr \u00B3\u2079Ar Decay',  # 107
@@ -743,7 +743,7 @@ DEFAULT_PLOT_STYLES = {
     },
 }
 
-VERSION = '20250328'
+VERSION = '20250404'
 
 NAMED_DICT = {
     "unknown": {"header": SAMPLE_INTERCEPT_HEADERS.copy()},
@@ -812,6 +812,7 @@ class Sample:
         self.SelectedSequence2 = []
         self.UnselectedSequence = []
         self.IsochronMark = []
+        self.NormalizeFactor = [[], []]
 
         # Tables and Plots
         self.UnknownTable = Table()
@@ -849,7 +850,8 @@ class Sample:
         # self.__version = '20250102'  # gain correction to blanks
         # self.__version = '20250301'  # update sample info
         # self.__version = '20250321'  # error sigma adjustment
-        self.__version = '20250328'  # Experiment info
+        # self.__version = '20250328'  # Experiment info
+        self.__version = '20250404'  # J normalization factor
 
     @property
     def version(self):

{ararpy-0.1.193 → ararpy-0.1.197}/ararpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.193
+Version: 0.1.197
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.193 → ararpy-0.1.197}/setup.py

@@ -16,7 +16,7 @@ long_description = (here / 'README.md').read_text(encoding='utf-8')
 
 setuptools.setup(
     name='ararpy',  #
-    version='0.1.193',  # version
+    version='0.1.197',  # version
     author='Yang Wu',
     author_email='wuycug@hotmail.com',
     description='A project for Ar-Ar geochronology',  # short description