ararpy 0.0.1a1__py3-none-any.whl

ararpy/smp/calculation.py

@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2023 Yang
+# ararpy - smp - calculation
+# 2023-12-4
+# ==========================================
+#
+# ArArPy.smp.smp_funcs
+#
+"""
+
+from . import (
+    basic, corr, initial, plots, style, table
+)
+from .sample import Sample
+
+
+def recalculate(
+        sample: Sample, re_initial: bool = False,
+        re_corr_blank: bool = False, re_corr_massdiscr: bool = False,
+        re_corr_decay: bool = False, re_degas_ca: bool = False, re_degas_k: bool = False,
+        re_degas_cl: bool = False, re_degas_atm: bool = False, re_degas_r: bool = False,
+        re_calc_ratio: bool = False, re_calc_apparent_age: bool = False,
+        re_plot: bool = False, re_plot_style: bool = False, re_set_table: bool = False,
+        re_table_style: bool = False, **kwargs
+):
+    """
+    Assign recalculate functions based on selections
+    Parameters
+    ----------
+    sample
+    re_initial
+    re_corr_blank
+    re_corr_massdiscr
+    re_corr_decay
+    re_degas_ca
+    re_degas_k
+    re_degas_cl
+    re_degas_atm
+    re_degas_r
+    re_calc_ratio
+    re_calc_apparent_age
+    re_plot
+    re_plot_style
+    re_set_table
+    re_table_style
+    kwargs
+
+    Returns
+    -------
+    Sample
+    """
+    if len(sample.UnselectedSequence) == len(sample.SelectedSequence1) == len(sample.SelectedSequence2) == 0:
+        sample.UnselectedSequence = list(range(len(sample.SequenceName)))
+    # print(f"{sample.UnselectedSequence = }")
+    # print(f"{sample.SelectedSequence1 = }")
+    # print(f"{sample.SelectedSequence2 = }")
+    # --- initializing ---
+    if re_initial:  # 1
+        initial.re_set_smp(sample)
+    # --- calculating ---
+    if re_corr_blank:  # 2
+        corr.corr_blank(sample)
+    if re_corr_massdiscr:  # 3
+        corr.corr_massdiscr(sample)
+    if re_corr_decay:  # 4
+        corr.corr_decay(sample)
+    if re_degas_ca:  # 5
+        corr.calc_degas_ca(sample)
+    if re_degas_k:  # 6
+        corr.calc_degas_k(sample)
+    if re_degas_cl:  # 7
+        corr.calc_degas_cl(sample)
+    if re_degas_atm:  # 8
+        corr.calc_degas_atm(sample)
+    if re_degas_r:  # 9
+        corr.calc_degas_r(sample)
+    if re_calc_ratio:  # 10
+        corr.calc_ratio(sample)
+    if re_calc_apparent_age:  # 11
+        basic.calc_apparent_ages(sample)
+    # --- plot and table ---
+    if re_plot:  # 12
+        plots.set_plot_data(sample, **kwargs)
+    if re_plot_style:  # 13
+        style.set_plot_style(sample)
+    if re_set_table:  # 14
+        table.update_table_data(sample)
+    if re_table_style:  # 15
+        style.set_table_style(sample)
+    return sample
+

ararpy/smp/consts.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2023 Yang 
+# webarar - consts
+# ==========================================
+#
+#
+# 
+"""
+
+# unicode for superscript numbers
+sup_35 = '\u00B3\u2075'
+sup_36 = '\u00B3\u2076'
+sup_37 = '\u00B3\u2077'
+sup_38 = '\u00B3\u2078'
+sup_39 = '\u00B3\u2079'
+sup_40 = '\u2074\u2070'
+

ararpy/smp/corr.py

@@ -0,0 +1,376 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2023 Yang
+# ararpy - smp - corr
+# ==========================================
+#
+#
+#
+"""
+
+import traceback
+import numpy as np
+import copy
+import re
+
+from .. import calc
+from .sample import Sample
+
+
+# =======================
+# Corr Blank
+# =======================
+def corr_blank(sample: Sample):
+    """Blank Correction"""
+    corrBlank = sample.TotalParam[102][0]
+    set_negative_zero = sample.TotalParam[101][0]
+    if not corrBlank:
+        sample.BlankCorrected = copy.deepcopy(sample.SampleIntercept)
+        sample.CorrectedValues = copy.deepcopy(sample.BlankCorrected)
+        return
+    blank_corrected = [[]]*10
+    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])
+    except Exception as e:
+        print(traceback.format_exc())
+        raise ValueError('Blank correction error')
+    if set_negative_zero:
+        blank_corrected[0] = [i if i >= 0 else 0 for i in blank_corrected[0]]
+    sample.BlankCorrected = blank_corrected
+    sample.CorrectedValues = copy.deepcopy(sample.BlankCorrected)
+
+
+# =======================
+# Mass Discrimination
+# =======================
+def corr_massdiscr(sample: Sample):
+    """Mass Discrimination Correction"""
+    corrMassdiscr = sample.TotalParam[103][0]
+    if not corrMassdiscr:
+        sample.MassDiscrCorrected = copy.deepcopy(sample.BlankCorrected)
+        sample.CorrectedValues = copy.deepcopy(sample.MassDiscrCorrected)
+        return
+    MASS = sample.TotalParam[71:81]
+    mdf_corrected = [[]]*10
+    try:
+        for i in range(5):
+            mdf_corrected[i * 2:2 + i * 2] = calc.corr.discr(
+                *sample.BlankCorrected[i * 2:2 + i * 2],
+                *sample.TotalParam[69:71], m=MASS[i*2], m40=MASS[8], isRelative=True,
+                method=sample.TotalParam[100][0])
+    except Exception as e:
+        print(traceback.format_exc())
+        raise ValueError('Mass discrimination correction error')
+    sample.MassDiscrCorrected = mdf_corrected
+    sample.CorrectedValues = copy.deepcopy(sample.MassDiscrCorrected)
+
+
+# =======================
+# Decay correction
+# =======================
+def corr_decay(sample: Sample):
+    """ Ar37 and Ar39 Decay Correction
+    Parameters
+    ----------
+    sample
+
+    Returns
+    -------
+
+    """
+    decay_corrected = [[]]*10
+    try:
+        irradiation_cycles = [list(filter(None, re.split(r'[DS]', each_step))) for each_step in sample.TotalParam[27]]
+        t1 = [i.split('-') for i in sample.TotalParam[31]]  # t1: experimental times
+        t2, t3 = [], []  # t2: irradiation times, t3: irradiation durations
+        for each_step in irradiation_cycles:
+            t2.append([item.split('-') for i, item in enumerate(each_step) if i % 2 == 0])
+            t3.append([item for i, item in enumerate(each_step) if i % 2 == 1])
+        decay_corrected[2:4] = calc.corr.decay(
+            *sample.MassDiscrCorrected[2:4], t1, t2, t3, *sample.TotalParam[44:46], isRelative=True)
+        decay_corrected[6:8] = calc.corr.decay(
+            *sample.MassDiscrCorrected[6:8], t1, t2, t3, *sample.TotalParam[42:44], isRelative=True)
+        # Negative number set to zero in decay correction
+        decay_corrected[2] = [0 if i < 0 else i for i in decay_corrected[2]]
+        decay_corrected[6] = [0 if i < 0 else i for i in decay_corrected[6]]
+    except Exception as e:
+        print(traceback.format_exc())
+        raise ValueError('Decay correction correction error')
+
+    corrDecay37 = sample.TotalParam[104][0]
+    corrDecay39 = sample.TotalParam[105][0]
+    if corrDecay37:
+        sample.CorrectedValues[2:4] = copy.deepcopy(decay_corrected[2:4])
+    if corrDecay39:
+        sample.CorrectedValues[6:8] = copy.deepcopy(decay_corrected[6:8])
+
+
+# =======================
+# Degas Calcium derived 37Ar 36Ar 38Ar 39Ar
+# =======================
+def calc_degas_ca(sample: Sample):
+    """ Degas Pattern for Ca
+    Parameters
+    ----------
+    sample
+
+    Returns
+    -------
+
+    """
+    corrDecasCa = sample.TotalParam[106][0]
+    n = len(sample.CorrectedValues[2])
+    ar37ca = sample.CorrectedValues[2:4]
+    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] = 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.PublishValues[1] = ar37ca[0]
+
+
+# =======================
+# Degas Potassium derived 39Ar 38Ar 40Ar
+# =======================
+def calc_degas_k(sample: Sample):
+    """ Degas Pattern for K
+    Parameters
+    ----------
+    sample
+
+    Returns
+    -------
+
+    """
+    corrDecasK = sample.TotalParam[107][0]
+    set_negative_zero = sample.TotalParam[101][0]
+    n = len(sample.CorrectedValues[6])
+    ar39k = calc.arr.sub(sample.CorrectedValues[6:8], sample.DegasValues[22:24])
+    ar39k[0] = [0 if i < 0 and set_negative_zero else i for i in ar39k[0]]
+    ar40k = calc.arr.mul_factor(ar39k, sample.TotalParam[14:16], isRelative=True)
+    ar38k = calc.arr.mul_factor(ar39k, sample.TotalParam[16:18], isRelative=True)
+
+    sample.PublishValues[3] = ar39k[0]
+    sample.DegasValues[20:22] = ar39k
+    sample.DegasValues[30:32] = ar40k if corrDecasK else [[0] * n, [0] * n]
+    sample.DegasValues[16:18] = ar38k if corrDecasK else [[0] * n, [0] * n]
+
+
+# =======================
+# Degas Chlorine derived 36Ar 38Ar
+# =======================
+def calc_degas_cl(sample: Sample):
+    """ Degas Pattern for Cl
+    Parameters
+    ----------
+    sample
+
+    Returns
+    -------
+
+    """
+    corrDecasCl = sample.TotalParam[108][0]
+    decay_const = sample.TotalParam[46:48]
+    cl36_cl38_p = sample.TotalParam[56:58]
+    ar38ar36 = sample.TotalParam[4:6]
+    stand_time_year = sample.TotalParam[32]
+    set_negative_zero = sample.TotalParam[101][0]
+    # ============
+    decay_const[1] = [decay_const[0][i] * decay_const[1][i] / 100 for i in
+                      range(len(decay_const[0]))]  # convert to absolute error
+    cl36_cl38_p[1] = [cl36_cl38_p[0][i] * cl36_cl38_p[1][i] / 100 for i in
+                      range(len(cl36_cl38_p[0]))]  # convert to absolute error
+    # convert to absolute error
+    ar38ar36[1] = [ar38ar36[0][i] * ar38ar36[1][i] / 100 for i in range(len(ar38ar36[0]))]
+    # ============
+    # 36Ar deduct Ca, that is sum of 36Ara and 36ArCl
+    ar36acl = calc.arr.sub(sample.CorrectedValues[0:2], sample.DegasValues[4:6])
+    # 38Ar deduct K and Ca, that is sum of 38Ara and 38ArCl
+    ar38acl = calc.arr.sub(calc.arr.sub(
+        sample.CorrectedValues[4:6], sample.DegasValues[16:18]), sample.DegasValues[18:20])
+    if set_negative_zero:
+        for index, item in enumerate(ar36acl[0]):
+            if item < 0:
+                ar36acl[0][index] = 0
+            if ar38acl[0][index] < 0:
+                ar38acl[0][index] = 0
+    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
+              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 +
+                  (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))]
+        # 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]))]
+        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]]
+        # 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])]
+
+    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]
+    sample.DegasValues[6:8] = ar36cl
+    sample.DegasValues[10:12] = ar38cl
+    sample.PublishValues[2] = ar38cl[0]
+
+
+# =======================
+# Degas atmospheric 36Ar 38Ar 40Ar
+# =======================
+def calc_degas_atm(sample: Sample):
+    """ Degas for Atmospheric Gas
+    Parameters
+    ----------
+    sample
+
+    Returns
+    -------
+
+    """
+    corrDecasAtm = sample.TotalParam[109][0]
+    set_negative_zero = sample.TotalParam[101][0]
+    n = len(sample.CorrectedValues[0])
+    # 36Ar deduct Ca, that is sum of 36Ara and 36ArCl
+    ar36acl = calc.arr.sub(sample.CorrectedValues[0:2], sample.DegasValues[4:6])
+    if set_negative_zero:
+        ar36acl[0] = [i if i >= 0 else 0 for i in ar36acl[0]]
+    # 38Ar deduct K and Ca, that is sum of 38Ara and 38ArCl
+    # ar38acl = calc.arr.sub()(
+    #     calc.arr.sub()(sample.CorrectedValues[2:4], sample.DegasValues[16:18]), sample.DegasValues[18:20])
+    # 36ArAir
+    ar36a = calc.arr.sub(ar36acl, sample.DegasValues[6:8])
+    # If ar36acl - ar36cl < 0, let ar36a = ar36 - ar36ca
+    if set_negative_zero:
+        ar36a[0] = [item if item >= 0 else ar36acl[index] for index, item in enumerate(ar36a[0])]
+    # 38ArAir
+    ar38a = calc.arr.mul_factor(ar36a, sample.TotalParam[4:6], isRelative=True)
+    # 40ArAir
+    ar40a = calc.arr.mul_factor(ar36a, sample.TotalParam[0:2], isRelative=True)
+    sample.DegasValues[0:2] = ar36a
+    sample.DegasValues[12:14] = ar38a if corrDecasAtm else [[0] * n, [0] * n]
+    sample.DegasValues[26:28] = ar40a if corrDecasAtm else [[0] * n, [0] * n]
+    sample.PublishValues[0] = ar36a[0]
+
+
+# =======================
+# Degas radiogenic 40Ar
+# =======================
+def calc_degas_r(sample: Sample):
+    """ Degas for Radiogenic Ar40
+    Parameters
+    ----------
+    sample
+
+    Returns
+    -------
+
+    """
+    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]]
+    sample.DegasValues[24:26] = ar40r
+    sample.PublishValues[4] = ar40r[0]
+
+
+# =======================
+# Calc ratio
+# =======================
+def calc_ratio(sample: Sample):
+    """ Calculate isochron ratio data, 40Arr/39ArK, Ar40r percentage,
+        Ar39K released percentage, Ca/K
+    Parameters
+    ----------
+    sample : Sample instance
+
+    Returns
+    -------
+    None
+    """
+    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]]
+    ar40rar39k = calc.arr.mul_factor(
+        sample.DegasValues[24:26], calc.arr.rec_factor(sample.DegasValues[20:22], 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] = ar40rar39k
+    sample.ApparentAgeValues[6:8] = [ar40r_percent, 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
+
+    # === 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
+
+    # Turner 1988 3D cake mix plots
+    # ar40 = sample.CorrectedValues[8:10]  # ar40 = atm + r + k
+    # ar36a = sample.DegasValues[0:2]  # ar36a
+    # isochron_6 = calc.isochron.get_3d_data(*ar39k, *ar38cl, *ar40, *ar36a)
+    # sample.IsochronValues[30:39] = isochron_6
+
+    # Note that the difference between Turner 3D plots and our 3D plots.
+
+