ararpy 0.1.20__py3-none-any.whl → 0.1.22__py3-none-any.whl

ararpy/__init__.py

@@ -16,7 +16,7 @@ from . import calc, smp, files, thermo, test
 """ Information """
 
 name = 'ararpy'
-version = '0.1.20'
+version = '0.1.22'
 __version__ = version
 full_version = version
 last_update = '2024-03-28'

ararpy/calc/age.py

@@ -41,11 +41,13 @@ def calc_age_min(F, sF, **kwargs) -> tuple:
     J = arr.array_as_float(kwargs.pop('J'))
     sJ = arr.array_as_float(kwargs.pop('sJ') * J / 100)
     A = arr.array_as_float(kwargs.pop('A'))
-    sA = arr.array_as_float(kwargs.pop('sA') * A / 100)
+    sA = arr.array_as_float(kwargs.pop('sA') * A / 100)  # total A, A = Aec + (Ab+) + (Ab-). Ab- for Ca
     Ae = arr.array_as_float(kwargs.pop('Ae'))
-    sAe = arr.array_as_float(kwargs.pop('sAe') * Ae / 100)
+    sAe = arr.array_as_float(kwargs.pop('sAe') * Ae / 100)  # Aec
     Ab = arr.array_as_float(kwargs.pop('Ab'))
-    sAb = arr.array_as_float(kwargs.pop('sAb') * Ab / 100)
+    sAb = arr.array_as_float(kwargs.pop('sAb') * Ab / 100)  # Ab-
+    Abp = arr.array_as_float(kwargs.pop('Abp'))
+    sAbp = arr.array_as_float(kwargs.pop('sAbp') * Ab / 100)  # Ab+
     W = arr.array_as_float(kwargs.pop('W'))
     sW = arr.array_as_float(kwargs.pop('sW') * W / 100)
     Y = arr.array_as_float(kwargs.pop('Y'))
@@ -62,21 +64,21 @@ def calc_age_min(F, sF, **kwargs) -> tuple:
     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'))
-    # 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)
+    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)
 
-    # recalculation using Min et al.(2000) equation
+    # calculating 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
     t = t * 1000000
     st = st * 1000000
-    # back-calculating Ar40/Ar39 ration for the standard
+    # back-calculating Ar40/Ar39 of the standard
     stdR = (np.exp(t * L) - 1) / J
     # errors of standard age and decay constants were not applied
     sStdR = pow((stdR / J) ** 2 * sJ ** 2, 0.5)
@@ -85,31 +87,27 @@ def calc_age_min(F, sF, **kwargs) -> tuple:
     sR_1 = np.sqrt((sF / stdR) ** 2 + (F * sStdR / stdR ** 2) ** 2)  # errors of measured 40Ar/39Ar and J value
     sR_2 = np.sqrt((sF / stdR) ** 2)  # error of measured 40Ar/39Ar only
 
-    BB = 1
-    KK = np.exp(t / V) - 1  # 40Arr / 40K Use standard age
+    useStandardAge = True
+    if useStandardAge:
+        # ln part in Min 2000 equation
+        BB = 1
+        KK = np.exp(t / V) - 1  # 40Arr / 40K Use standard age
+    else:  # use Ar40* and K concentrations of primary standard
+        # not fanished, this function is wrong
+        BB = (Ab + Ae) / Ae
+        KK = Ap / Kp / f
+        raise TypeError(f"Not use standard age. Not supported.")
+
     XX = BB * KK * R + 1
     k0 = V * np.log(XX)
-    e1 = (np.log(XX) * V / f - V * BB * KK * R / (f * XX)) ** 2 * sf ** 2  # sF
-    e2 = (np.log(XX) * V / No) ** 2 * sNo ** 2  # sNo
-    e3 = (-1 * np.log(XX) * V / A + BB * KK * R / (A * XX)) ** 2 * sAb ** 2  # sAb
-    e4 = (-1 * np.log(XX) * V / A - Ab * KK * R / (Ae ** 2 * XX)) ** 2 * sAe ** 2  # sAe
-    e5 = (-1 * np.log(XX) * V / W - V * BB * KK * R / (W * XX)) ** 2 * sW ** 2  # sW
-    e6 = (np.log(XX) * V / Y) ** 2 * sY ** 2  # sY
-    e7 = (V * BB * KK / XX) ** 2 * sR_1 ** 2  # sR
-    # e8 = (V * BB * KK * R / (Ap * XX)) ** 2 * sAp ** 2  # sAp
-    # e9 = (V * BB * KK * R / (Kp * XX)) ** 2 * sKp ** 2  # sKp
-    e8, e9 = 0, 0
-    # useDecayConst = False
-    # if useDecayConst:  # k0 = log(L / Le * KK * R + 1) / L
-    #     e1 = (V * BB * KK * R / (f * XX)) ** 2 * sf ** 2
-    #     e2 = 0
-    #     e3 = (-1 * np.log(XX) * V / L + BB * KK * R / (L * XX)) ** 2 * sLb ** 2
-    #     e4 = (-1 * np.log(XX) * V / L - Lb * KK * R / (Le ** 2 * XX)) ** 2 * sLe ** 2
-    #     e5 = (V * BB * KK * R / (W * XX)) ** 2 * sW ** 2
-    #     e6 = 0
-    useStandardAge = True
+
     if useStandardAge:
-        e1, e9 = 0, 0
+        # k0 =  V * ln(exp(t/V) - 1 * R + 1)
+        e1 = (np.log(XX) - R * (KK + 1) * t / (V * XX)) ** 2 * sV ** 2  # sV
+        e2 = (BB * (KK + 1) * R / XX) ** 2 * st ** 2  # st
+        e3 = (V * BB * KK / XX) ** 2 * sR_1 ** 2  # sR
+    else:
+        e1, e2, e3 = 0, 0, 0
 
     # change to Ma
     # analytical error, error of 40Ar/39Ar only
@@ -117,7 +115,7 @@ def calc_age_min(F, sF, **kwargs) -> tuple:
     # internal error, errors of 40Ar/39Ar and J value
     s2 = np.sqrt((V * KK * BB / XX) ** 2 * sR_1 ** 2)
     # total external error
-    s3 = np.sqrt(e1 + e2 + e3 + e4 + e5 + e6 + e7 + e8 + e9)
+    s3 = np.sqrt(e1 + e2 + e3)
     age = k0
     return age, s1, s2, s3
 
@@ -146,7 +144,7 @@ def calc_age_general(F, sF, J, sJ, L, sL, **kwargs):
     v1 = sF ** 2 * (J / (L * (1 + J * F))) ** 2
     v2 = sJ ** 2 * (F / (L * (1 + J * F))) ** 2
     v3 = sL ** 2 * (np.log(1 + J * F) / (L ** 2)) ** 2
-    s1 = v1 ** .5  # analytical error
-    s2 = (v1 + v2) ** .5  # internal error
-    s3 = (v1 + v2 + v3) ** .5  # full external error
+    s1 = v1 ** .5  # analytical error, F only
+    s2 = (v1 + v2) ** .5  # internal error, F and J
+    s3 = (v1 + v2 + v3) ** .5  # full external error. F, J and L
     return age, s1, s2, s3

ararpy/calc/corr.py

@@ -61,10 +61,10 @@ def mdf(rm: float, srm: float, m1: float, m2: float, ra: float = 298.56,
     sratio_m = err.div((m2, sm2), (m1, sm1))
     useRyu = False
     if not useRyu:
-        # line
-        k1 = (ra / rm + delta_m - 1) / delta_m
-        k2 = err.div(((ra / rm + delta_m - 1), err.div((ra, sra), (rm, srm))), (delta_m, sdelta_m))
-        # exp
+        # line, D = 1 + (ra / rm - 1) / dm  # Renne2009
+        k1 = 1 + (ra / rm - 1) / delta_m
+        k2 = err.div(((ra / rm - 1), err.div((ra, sra), (rm, srm))), (delta_m, sdelta_m))
+        # exp, D = 1 + ln(ra / rm) / (m1 * ln(m2/m1))  # Renne2009
         try:
             k3 = (np.log(ra / rm) / np.log(ratio_m)) * (1 / m1) + 1
             v1 = err.log((ra / rm, err.div((ra, sra), (rm, srm))))
@@ -73,7 +73,7 @@ def mdf(rm: float, srm: float, m1: float, m2: float, ra: float = 298.56,
             k4 = err.div((np.log(ra / rm) / np.log(ratio_m), v3), (m1, sm1))
         except Exception:
             k3, k4 = 0, 0
-        # pow
+        # pow, D = pow(ra / rm, 1 / dm)  # Renne2009
         try:
             k5 = pow((ra / rm), (1 / delta_m))  # Renne2009, B.D. Turrin2010
             k6 = err.pow((ra / rm, err.div((ra, sra), (rm, srm))),
@@ -105,18 +105,17 @@ def discr(a0: list, e0: list, mdf: list, smdf: list, m: list, m40: list,
     if isRelative:
         smdf = [smdf[i] * mdf[i] / 100 for i in range(len(smdf))]
     for i in range(min([len(arg) for arg in [a0, e0, mdf, smdf]])):
-        delta_mass = abs(m40[i] - m[i])
-        ratio_mass = abs(m40[i] / m[i]) if m[i] != 0 else 1
-        if method.lower().startswith("l"):
-            k0 = 1 / (delta_mass * mdf[i] - delta_mass + 1) if (delta_mass * mdf[i] - delta_mass + 1) != 0 else 0
-            k1 = err.div((1, 0), (delta_mass * mdf[i] - delta_mass + 1, smdf[i] * delta_mass))
-        elif method.lower().startswith("e"):
-            k0 = 1 / (ratio_mass ** (mdf[i] * m40[i] - m[i]))
-            k1 = err.div((1, 0), (ratio_mass ** (mdf[i] * m40[i] - m[i]), err.pow((ratio_mass, 0), (
-                mdf[i] * m40[i] - m[i], err.mul((mdf[i], smdf[i]), (m40[i], 0))))))
-        elif method.lower().startswith("p"):
-            k0 = 1 / (mdf[i] ** delta_mass)
-            k1 = err.div((1, 0), (mdf[i] ** delta_mass, err.pow((mdf[i], smdf[i]), (delta_mass, 0))))
+        delta_m = abs(m40[i] - m[i])
+        ratio_m = abs(m40[i] / m[i]) if m[i] != 0 else 1
+        if method.lower().startswith("l"):  # linear
+            k0 = 1 / (delta_m * mdf[i] - delta_m + 1) if (delta_m * mdf[i] - delta_m + 1) != 0 else 0
+            k1 = err.rec((delta_m * mdf[i] - delta_m + 1, smdf[i] * delta_m))
+        elif method.lower().startswith("e"):  # exponential
+            k0 = 1 / np.exp((mdf - 1) * m * np.log(m40 / m))
+            k1 = err.rec((1 / k0, err.pow((np.e, 0), ((mdf - 1) * m * np.log(m40 / m), err.mul((mdf - 1, smdf), (m * np.log(m40 / m), 0))))))
+        elif method.lower().startswith("p"):  # power
+            k0 = 1 / (mdf[i] ** delta_m)
+            k1 = err.rec((mdf[i] ** delta_m, err.pow((mdf[i], smdf[i]), (delta_m, 0))))
         else:
             k0 = 1
             k1 = 0

ararpy/smp/basic.py

@@ -153,7 +153,8 @@ def calc_age(ar40ar39=None, params: dict = None, smp: Sample = None, index: list
     """
     params_index_dict = {
         34: 'L', 35: 'sL', 36: 'Le', 37: 'sLe', 38: 'Lb', 39: 'sLb', 48: 'A', 49: 'sA',
-        50: 'Ae', 51: 'sAe', 52: 'Ab', 53: 'sAb', 59: 't', 60: 'st', 67: 'J', 68: 'sJ',
+        50: 'Ae', 51: 'sAe', 52: 'Ab', 53: 'sAb', 54: 'Abp', 55: 'sAbp', 59: 't', 60: 'st',
+        61: 'Ap', 62: 'sAp', 63: 'Kp', 64: 'sKp', 67: 'J', 68: 'sJ',
         81: 'W', 82: 'sW', 83: 'No', 84: 'sNo', 85: 'Y', 86: 'sY', 87: 'f', 88: 'sf', 110: 'Min'
     }
 

ararpy/smp/corr.py

@@ -545,7 +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
+    JNFactor = np.transpose(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
@@ -579,7 +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,
+            JNFactor=JNFactor[i],
             blank_gain_corr=sample.TotalParam[111][i]
         )
 

ararpy/smp/sample.py

@@ -248,8 +248,8 @@ TOTAL_PARAMS_SHORT_HEADERS = [
     'DAb-K40', '%1s',  # 54-55
     'DAb+K40', '%1s',  # 56-57
     'Cl36/Cl38P', '%1s',  # 58-59
-    'StdName', 'StdAge', '1s', 'Ar40%', '1s', 'K%', '1s',
-    'F', '1s',  # 60-68
+    'StdName', 'StdAge', '1s', 'Ar40%', '1s', 'K%', '1s',  # 60-66
+    'F', '1s',  # 67-68
     'J', '%1s', 'MDF', '%1s',  # 69-72
     'MassAr36', '%1s', 'MassAr37', '%1s',
     'MassAr38', '%1s', 'MassAr39', '%1s',

{ararpy-0.1.20.dist-info → ararpy-0.1.22.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.20
+Version: 0.1.22
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.20.dist-info → ararpy-0.1.22.dist-info}/RECORD

@@ -1,10 +1,10 @@
-ararpy/__init__.py,sha256=V5si5FQDT72N9e7Nf_GuCgS_ZNJdcFEdGAvhIDS_E2I,6857
+ararpy/__init__.py,sha256=eXot2SznEPD-wmJMnxjnESJes1ehgJafSapnCxoKwxc,6857
 ararpy/test.py,sha256=4F46-JJ1Ge12HGae0qO44Qc6kiEMHBgn2MsY_5LlHDo,3973
 ararpy/calc/__init__.py,sha256=kUjRuLE8TLuKOv3i976RnGJoEMj23QBZDu37LWs81U4,322
-ararpy/calc/age.py,sha256=OcStt55LoYW1brs7a5_Ovv1NUSR5uZVQHDVGGmA_Pqg,5784
+ararpy/calc/age.py,sha256=WOZs70zXiBWDIEhXJLIaNiYTOFJNk0NDbH5e5zCbCks,5435
 ararpy/calc/arr.py,sha256=jD1Fd0Cj3xc7NqgnG4cp3VWQWxUlV0qCtPBZZokDG8o,15246
 ararpy/calc/basic.py,sha256=uJCCUFaPd9zvfkggrdbFYSGLl2pt7UJ7ENgXanzHy68,4036
-ararpy/calc/corr.py,sha256=6hlBlFIM8HyN6CDuWPGqiLpVM88pZJLEuRm8vAyg9ng,18747
+ararpy/calc/corr.py,sha256=QDitvLf6y5IBpHtVEJfOUVjWSlIP9qJ4Jhluk9eDEDE,18801
 ararpy/calc/err.py,sha256=63LtprqjemlIb1QGDst4Ggcv5KMSDHdlAIL-nyQs1eA,2691
 ararpy/calc/histogram.py,sha256=0GVbDdsjd91KQ1sa2B7NtZ4KGo0XpRIJapgIrzAwQUo,5777
 ararpy/calc/isochron.py,sha256=ej9G2e68k6yszonWHsLcEubh3TA7eh1upTJP_X0ttAA,5726
@@ -41,10 +41,10 @@ ararpy/files/raw_file.py,sha256=5hnZMS7r78lA0ZXrBEN5SWVurQyl0QsHOI9rJz5BQv8,2230
 ararpy/files/xls.py,sha256=DVcZ_yRnc19p-m4leGGjt-YPDpSa2udYKmGyrM0qub0,640
 ararpy/smp/EXPORT_TO_PDF_DATA_PROPERTIES.py,sha256=baDM437tu6hsPv0uYfod0TREXlPd6kvMBFT1S9ZZlkk,3024
 ararpy/smp/__init__.py,sha256=k6_fa27UJsQK7K7oC5GYlwMo6l0Xd8af3QtOrZz2XJk,478
-ararpy/smp/basic.py,sha256=FjntKS61vdUFtwrBJcL2HTiTJthR288Q-DDNuFoUND4,24825
+ararpy/smp/basic.py,sha256=PMvlSoToY8CJEORRrhEo4rYM2-VfSmjg0IuDpGFOGUM,24899
 ararpy/smp/calculation.py,sha256=LCFJWjLVLEKEQ5b7RFUIxsMahEzgLdodW4kCYXV5Z34,2919
 ararpy/smp/consts.py,sha256=XIdjdz8cYxspG2jMnoItdlUsxr3hKbNFJjMZJh1bpzw,393
-ararpy/smp/corr.py,sha256=tE8nVv7DrL9ktou_HvxfYQaYwhJ3MA4l0fAXasKVph8,26499
+ararpy/smp/corr.py,sha256=L4YwCzu14Zot9tm9ijOgYzMbZEYEZGXArACrquIrfDg,26516
 ararpy/smp/diffusion_funcs.py,sha256=4-PMMIZWzjk2HOYYWNgSp4GmApygp1MmOxJ2g3xrqWc,175049
 ararpy/smp/export.py,sha256=s89L5B1aHoCeJIjcw6nXA6NtV0j_5XXaWnOETWnomCs,115043
 ararpy/smp/info.py,sha256=iKUELm-BuUduDlJKC1d8tKKNHbwwbNmhUg2pi6bcBvA,489
@@ -52,15 +52,15 @@ ararpy/smp/initial.py,sha256=VSNku2fYD1xGkpHxMqnSJCAhSQawfsDCdqYCxtDJryQ,17196
 ararpy/smp/json.py,sha256=BTZCjVN0aj9epc700nwkYEYMKN2lHBYo-pLmtnz5oHY,2300
 ararpy/smp/plots.py,sha256=rF0vrFu9dMt2Eu1EHiDfDRC9232M6dH0Unc_3qNDxLY,33579
 ararpy/smp/raw.py,sha256=51n-rrbW2FqeZHQyevuG7iObPLGvIBzTe414QDVM1FE,6523
-ararpy/smp/sample.py,sha256=ZOrQt3Ilm6tJbQCwh_btoZOXdkCngZFHCt10Nh0UmpI,57727
+ararpy/smp/sample.py,sha256=dEgy2--RxfS4vXYqlBjD5MlLpw2SaZPDyPxRyiQXjgU,57736
 ararpy/smp/style.py,sha256=wCygwtpCflhzwmI7u08X-feYGPytOyfR98YcgJx813c,7678
 ararpy/smp/table.py,sha256=9bNAOqAIOc0nSC3LNeqjJKUYSJSM28Ji3o9VimwMU8A,6645
 ararpy/thermo/__init__.py,sha256=6VBuqTRFl403PVqOuMkVrut0nKaQsAosBmfW91X1dMg,263
 ararpy/thermo/arrhenius.py,sha256=Ass1ichHfqIAtpv8eLlgrUc1UOb3Urh1qzr1E3gLB4U,233
 ararpy/thermo/atomic_level_random_walk.py,sha256=Q97zfe2h2RaxADkoBAqd0uEiP16BFOajrTmXHMkL2EQ,25502
 ararpy/thermo/basic.py,sha256=nBGHI9uK7VdJwThwBIOcKAzdnYqPyQseFoY6s4zKizk,11504
-ararpy-0.1.20.dist-info/licenses/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
-ararpy-0.1.20.dist-info/METADATA,sha256=-3UiJOtxnZz1wNj81B591579TjQq3rzQ5K5DlVvHxyA,24516
-ararpy-0.1.20.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-ararpy-0.1.20.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
-ararpy-0.1.20.dist-info/RECORD,,
+ararpy-0.1.22.dist-info/licenses/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
+ararpy-0.1.22.dist-info/METADATA,sha256=BD8UulpdJ0OOiH2cSJaEwfB6qWjavqDcc6XnVZF8OEI,24516
+ararpy-0.1.22.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+ararpy-0.1.22.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
+ararpy-0.1.22.dist-info/RECORD,,