ararpy 0.0.1a1__py3-none-any.whl

ararpy/files/calc_file.py

@@ -0,0 +1,683 @@
+
+"""
+# ==========================================
+# Copyright 2023 Yang
+# ararpy - files - calc_file
+# ==========================================
+
+Open age files from ArArCALC. It currently supports version: 25.2 and 24.0.
+Version 25.2 is preferred to 24.0 as containing more detailed parameters than 24.0.
+
+ArArCalcFile(file_path, file_name: optional)
+    -> open()
+        -> get content and sample info ()
+
+"""
+import traceback
+import pandas as pd
+import numpy as np
+import re
+from xlrd import open_workbook, biffh
+import os
+import msoffcrypto
+# from programs.ararpy.calc.basic import get_datetime
+# from programs.ararpy import smp, calc
+# from programs.ararpy.files import xls
+from ..files import xls
+from ..smp.initial import create_sample_from_df, create_sample_from_dict
+from ..calc.basic import get_datetime
+from ..calc import arr, err, isochron
+
+
+def to_sample(file_path: str, **kwargs):
+    """
+
+    Parameters
+    ----------
+    file_path
+
+    Returns
+    -------
+
+    """
+    file = ArArCalcFile(file_path=file_path, **kwargs).open()
+    sample = create_sample_from_df(file.get_content(), file.get_smp_info())
+    return sample
+
+
+def read_calc_file(file_path: str):
+    """
+    :param file_path: file with suffix of .age or .air
+    :return: dict, keys are sheet name, value are list of [[col 0], [col 1], ...] of corresponding sheet
+    """
+    PASSWORD = 'aapkop'  # password to open age file, the password to unhide worksheets is boris
+    decrypt_file_path = file_path + '_decrypt.xls'
+    try:
+        # opening excel in decrypt function would reveal the hidden sheet without protect
+        with open(file_path, 'rb') as age_file:
+            office_file = msoffcrypto.OfficeFile(age_file)
+            office_file.load_key(password=PASSWORD)
+            office_file.decrypt(open(decrypt_file_path, 'wb'))
+        wb = open_workbook(decrypt_file_path)
+        worksheets = wb.sheet_names()
+        book_contents = dict()
+        for each_sheet in worksheets:
+            sheet = wb.sheet_by_name(each_sheet)
+            sheet_contents = [
+                [sheet.cell(row, col).value for col in range(sheet.ncols)]
+                for row in range(sheet.nrows)
+            ]
+            book_contents[each_sheet] = sheet_contents
+        os.remove(decrypt_file_path)
+    except Exception as e:
+        print(traceback.format_exc())
+        return False
+    else:
+        return book_contents
+
+
+def open_252(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
+    """
+    Open 25.2 version ArArCALC files
+    :param data:
+    :param logs01:
+    :param logs02:
+    :return:
+    """
+    # add default columns for 999, -999, and -1 index
+    data[-999] = [0] * data.index.size
+    data[999] = [1] * data.index.size
+    data[-1] = [np.nan] * data.index.size
+    # rows_unm --> 样品阶段数
+    sequence_index = [1, 2, ]
+    sample_values_index = [16, 17, 21, 22, 26, 27, 31, 32, 36, 37,]
+    blank_values_index = [3, 4, 5, 6, 7, 8, 9, 10, 11, 12,]
+    corrected_values_index = [
+        188, 189, 190, 191, 192, 193, 194, 195, 196, 197,]
+    degas_values_index = [
+        138, 139, 140, 141, 142, 143, 144, 145,  # 36 a, c, ca, cl    0-9
+        146, 147,  # 37 ca    10-11
+        156, 157, 148, 149, 150, 151, 152, 153, 154, 155,  # 38 cl, a, c, k, ca   12-21
+        158, 159, 160, 161,  # 39 k, ca    22-25
+        162, 163, 164, 165, 166, 167, 168, 169,  # 40 r, a, c, k    26-33
+    ]
+    publish_values_index = [
+        101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,
+    ]
+    apparent_age_values_index = [
+        198, 199, 200, 201, -999, -999, 202, 203,  # f, sf, ages, s, s, s, 40Arr%, 39Ar%
+    ]
+    isochron_values_index = [
+        116, 117, 118, 119, 122,  # normal isochron
+        -1, 127, 128, 129, 130, 133,  # inverse
+        -1, -999, -999, -999, -999, -999,  # 39/38 vs 40/38
+        -1, -999, -999, -999, -999, -999,  # 39/40 vs 39/40
+        -1, -999, -999, -999, -999, -999,  # 38/39 vs 40/39
+        -1, -999, -999, -999, -999, -999, -999,  # 3D isochron, 36/39, 38/39, 40/39
+    ]
+    isochron_mark_index = [115,]
+    total_param_index = [
+        71, 72, 73, 74, 75, 76, 77, 78, 79, 80,  # 0-9
+        81, 82, 83, 84, 85, 86, 87, 88, 89, 90,  # 10-19
+        91, 92, 93, 94, 95, 96, -999, -999, 63, -999,  # 20-29
+        -999, -999, -1, -1, -999, -999, -999, -999, -999, -999,  # 30-39
+        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 40-49
+        -999, -999, -999, -999, -999, -999, -999, -999, 67, 49,  # 50-59
+        50, -999, -999, -999, -999, -999, -999, 51, 52, 53,  # 60-69
+        54, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 70-79
+        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 80-89
+        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 90-99
+        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 100-109
+        -999, -999, -999, -999, -1,  # 110-114
+        -999, -999, -999, -999, -999, -999, -999, -999,  # 115-122
+    ]
+
+    # double transpose to remove keys
+    get_data = lambda df, index: pd.concat([df[index].transpose()], ignore_index=True).transpose()
+
+    sample_values = get_data(data, sample_values_index)
+    blank_values = get_data(data, blank_values_index)
+    corrected_values = get_data(data, corrected_values_index)
+    degas_values = get_data(data, degas_values_index)
+    publish_values = get_data(data, publish_values_index)
+    apparent_age_values = get_data(data, apparent_age_values_index)
+    isochron_values = get_data(data, isochron_values_index)
+    total_param = get_data(data, total_param_index)
+    isochron_mark = get_data(data, isochron_mark_index)
+    sequence = get_data(data, sequence_index)
+
+    # adjustment
+    isochron_mark.replace({4.0: 1}, inplace=True)
+    total_param[83] = logs01[1][9]  # No
+    total_param[84] = logs01[1][10]  # %SD
+    total_param[81] = logs01[1][11]  # K mass
+    total_param[82] = logs01[1][12]  # K mass %SD
+
+    total_param[85] = logs01[1][13]  # How many seconds in a year
+    total_param[86] = 0  # %SD
+
+    total_param[87] = logs01[1][14]  # The constant of 40K/K
+    total_param[88] = logs01[1][15]  # %SD
+
+    total_param[89] = logs01[1][16]  # The constant of 35Cl/37Cl
+    total_param[90] = logs01[1][17]  # %SD
+    total_param[56] = logs01[1][18]  # The constant of 36/38Cl productivity
+    total_param[57] = logs01[1][19]  # %SD
+    total_param[91] = logs01[1][24]  # The constant of HCl/Cl
+    total_param[92] = logs01[1][25]  # %SD
+
+    total_param[50] = logs01[1][26]  # 40K(EC) activities param
+    total_param[51] = logs01[1][27]  # %SD
+    total_param[52] = logs01[1][28]  # 40K(\beta-) activities param
+    total_param[53] = logs01[1][29]  # %SD
+    total_param[48] = logs01[1][26] + logs01[1][28]  # 40K(EC) activities param
+    total_param[49] = 100 / total_param[48] * pow(
+        (logs01[1][27] / 100 * logs01[1][26]) ** 2 + (logs01[1][29] / 100 * logs01[1][28]) ** 2, 0.5)  # %SD
+
+    total_param[34] = logs01[1][36]  # decay constant of 40K total
+    total_param[35] = logs01[1][37]  # %SD
+    total_param[36] = logs01[1][30]  # decay constant of 40K EC
+    total_param[37] = logs01[1][31]  # %SD
+    total_param[38] = logs01[1][32]  # decay constant of 40K \beta-
+    total_param[39] = logs01[1][33]  # %SD
+    total_param[40] = 0  # decay constant of 40K \beta+
+    total_param[41] = 0  # %SD
+    total_param[46] = logs01[1][34]  # decay constant of 36Cl
+    total_param[47] = logs01[1][35]  # %SD
+    total_param[42] = logs01[1][38]  # decay constant of 39Ar
+    total_param[43] = logs01[1][39]  # %SD
+    total_param[44] = logs01[1][40]  # decay constant of 37Ar
+    total_param[45] = logs01[1][41]  # %SD
+
+    # logs01[1][49]]  # 1 for using weighted YORK isochron regression, 2 for unweighted
+    # logs01[1][50]]  # True for including errors on irradiation constants, False for excluding those
+    # [logs01[1][67]]  # MDF method, 'LIN'
+    total_param[93] = logs01[1][70]  # 40Ar/36Ar air
+    total_param[94] = logs01[1][71]  # %SD
+
+    total_param[97] = 'York-2'  # Fitting method
+    total_param[98] = logs01[1][0]  # Convergence
+    total_param[99] = logs01[1][1]  # Iterations number
+    total_param[100] = logs01[1][67]  # MDF method
+    total_param[101] = logs01[1][65]  # force negative to zero when correct blank
+    total_param[102] = True  # Apply 37Ar decay
+    total_param[103] = True  # Apply 39Ar decay
+    total_param[104] = logs01[1][6]  # Apply 37Ar decay
+    total_param[105] = logs01[1][7]  # Apply 39Ar decay
+    total_param[106] = True  # Apply K degas
+    total_param[107] = True  # Apply Ca degas
+    total_param[108] = True  # Apply Air degas
+    total_param[109] = logs01[1][8]  # Apply Cl degas
+
+    total_param[110] = True if logs01[1][5] == 'MIN' else False  # Calculating ages using Min equation [True] or conventional equation [False]
+    total_param[111] = logs01[1][89]  # Use primary standard or not
+    total_param[112] = logs01[1][91]  # Use standard age or not
+    total_param[113] = logs01[1][92]  # Use primary ratio or not
+
+    # irradiation time
+    total_param = general_adjustment(
+        total_param.copy(), logs02, get_data(data, [59, 58, 57, 60, 61]), data[63][0]
+    )
+    return [
+        sample_values, blank_values, corrected_values, degas_values, publish_values,
+        apparent_age_values, isochron_values, total_param, isochron_mark,
+        sequence,
+    ]
+
+
+def open_240(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
+    """
+    Open 24.0 version ArArCALC files
+    :param data:
+    :param logs01:
+    :param logs02:
+    :return:
+    """
+    # add default columns for 999, -999, and -1 index
+    data[-999] = [0] * data.index.size
+    data[999] = [1] * data.index.size
+    data[-1] = [np.nan] * data.index.size
+    # values index
+    sequence_index = [1, 2, ]
+    sample_values_index = [16, 17, 21, 22, 26, 27, 31, 32, 36, 37,]
+    blank_values_index = [3, 4, 5, 6, 7, 8, 9, 10, 11, 12,]
+    corrected_values_index = [
+        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,]
+    degas_values_index = [
+        # 36 a, c, ca, cl
+        136, -999, 137, -999, 139, -999, 138, -999,
+        # 37 ca,
+        140, -999,
+        # 38 cl, a, c, k, ca,
+        145, -999, 141, -999, 142, -999, 143, -999, 144, -999,
+        # 39 k, ca
+        146, -999, 147, -999,
+        # 40 r, a, c, k
+        148, -999, 149, -999, 150, -999, 151, -999,
+    ]
+    publish_values_index = [
+        99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109,
+    ]
+    apparent_age_values_index = [
+        # f, sf, ages, s, s, s, 39Ar%
+        156, 157, 104, 105, -999, -999, 106, 107,
+    ]
+    isochron_values_index = [
+        # normal isochron
+        114, 115, 116, 117, 120,
+        # inverse
+        -1, 125, 126, 127, 128, 131,
+        # 39/38 vs 40/38
+        -1, -999, -999, -999, -999, -999,
+        # 39/40 vs 39/40
+        -1, -999, -999, -999, -999, -999,
+        # 38/39 vs 40/39
+        -1, -999, -999, -999, -999, -999,
+        # 3D isochron, 36/39, 38/39, 40/39, r1, r2, r3
+        -1, -999, -999, -999, -999, -999, -999, -999, -999, -999,
+    ]
+    isochron_mark_index = [113,]
+    total_param_index = [
+        # 0-9
+        69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
+        # 10-19
+        79, 80, 81, 82, 83, 84, 85, 86, 87, 88,
+        # 20-29
+        89, 90, 91, 92, 93, 94, -999, -999, 63, -999,
+        # 30-39
+        -999, -999, -1, -1, -999, -999, -999, -999, -999, -999,
+        # 40-49
+        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,
+        # 50-59
+        -999, -999, -999, -999, -999, -999, -999, -999, 65, 49,
+        # 60-69
+        50, -999, -999, -999, -999, -999, -999, 51, 52, 53,
+        # 70-79
+        54, -999, -999, -999, -999, -999, -999, -999, -999, -999,
+        # 80-89
+        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,
+        # 90-99
+        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,
+        # 100-99909
+        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,
+        # 110-114
+        -999, -999, -999, -999, -1,
+        # 115-122
+        -999, -999, -999, -999, -999, -999, -999, -999,
+    ]
+
+    # double transpose to remove keys
+    get_data = lambda df, index: pd.concat([df[index].transpose()], ignore_index=True).transpose()
+
+    sample_values = get_data(data, sample_values_index)
+    blank_values = get_data(data, blank_values_index)
+    corrected_values = get_data(data, corrected_values_index)
+    degas_values = get_data(data, degas_values_index)
+    publish_values = get_data(data, publish_values_index)
+    apparent_age_values = get_data(data, apparent_age_values_index)
+    isochron_values = get_data(data, isochron_values_index)
+    total_param = get_data(data, total_param_index)
+    isochron_mark = get_data(data, isochron_mark_index)
+    sequence = get_data(data, sequence_index)
+
+    # irradiation time
+    total_param = general_adjustment(
+        total_param.copy(), logs02, get_data(data, [59, 58, 57, 60, 61]), data[63][0]
+    )
+    # Do adjustment
+    isochron_mark.replace({4.0: 1}, inplace=True)
+    total_param[44] = logs01[1][40]
+    total_param[45] = logs01[1][41]
+    total_param[42] = logs01[1][38]
+    total_param[43] = logs01[1][39]
+    total_param[34] = logs01[1][36]
+    total_param[35] = logs01[1][37]
+
+    return [
+        sample_values, blank_values, corrected_values, degas_values, publish_values,
+        apparent_age_values, isochron_values, total_param, isochron_mark,
+        sequence,
+    ]
+
+
+def change_error_type(data: pd.DataFrame, header: pd.Series):
+    """
+    :param data: 2D DataFrame
+    :param header: 1D Series, headers
+    :return:
+    """
+    # 2 sigma to 1 sigma
+    tochange = np.flatnonzero(header.where(header.str.contains('2s'), other=False))
+    data[tochange.tolist()] = data[tochange.tolist()] / 2
+
+    # 2 sigma to 1 sigma
+    tochange = np.flatnonzero(header.where(header.str.contains('%1s|%2s', regex=True), other=False))
+    data[tochange.tolist()] = \
+        data[tochange.tolist()] * abs(data[(tochange - 1).tolist()].rename(lambda x: x + 1, axis='columns')) / 100
+
+    return data
+
+
+def general_adjustment(
+        total_param: pd.DataFrame, logs02: pd.DataFrame, experimental_time: pd.DataFrame,
+        irradiation_name: str
+):
+    """
+        General handle for all age files, including set irradiaition time, initial ratios, error display
+    :param total_param:
+    :param logs02:
+    :param experimental_time:
+    :param irradiation_name:
+    :return:
+    """
+    irra_project = pd.Series(logs02[1].copy())
+    irradiation_index = np.flatnonzero(irra_project.where(irra_project.str.fullmatch(irradiation_name), other=False))[0]
+    irradiation_info = logs02[32][irradiation_index].split('\n')
+    # 处理辐照时间
+    month_convert = {
+        r'^(?i)Jan$': '01', r'^(?i)Feb$': '02', r'^(?i)Mar$': '03', r'^(?i)Apr$': '04', r'^(?i)May$': '05', r'^(?i)Jun$': '06',
+        r'^(?i)Jul$': '07', r'^(?i)Aug$': '08', r'^(?i)Sep$': '09', r'^(?i)Oct$': '10', r'^(?i)Nov$': '11', r'^(?i)Dec$': '12'}
+    duration_hour = []
+    end_time_second = []
+    irradiation_end_time = []
+    last_time = []
+    for each_date in irradiation_info:
+        if '/' in each_date:
+            _year = each_date.split(' ')[1].split('/')[2]
+            _month = each_date.split(' ')[1].split('/')[1].capitalize()
+            for pat, val in month_convert.items():
+                if re.match(pat, _month):
+                    _month = val
+                    break
+            _day = each_date.split(' ')[1].split('/')[0]
+            _hour = each_date.split(' ')[2].split('.')[0]
+            _min = each_date.split(' ')[2].split('.')[1]
+            end_time_second.append(get_datetime(
+                t_year=int(_year), t_month=int(_month), t_day=int(_day),
+                t_hour=int(_hour), t_min=int(_min)))
+            each_duration_hour = each_date.split(' ')[0].split('.')[0]
+            each_duration_min = each_date.split(' ')[0].split('.')[1]
+            each_duration = int(each_duration_hour) + round(int(each_duration_min) / 60, 2)
+            duration_hour.append(each_duration)
+            irradiation_end_time.append(f"{_year}-{_month}-{_day}-{_hour}-{_min}D{each_duration}")
+            last_time = [_year, _month, _day, _hour, _min]
+
+    experimental_time: pd.DataFrame = experimental_time.apply(pd.to_numeric, errors='ignore', downcast='integer')
+    experimental_time: pd.DataFrame = experimental_time.replace(to_replace=month_convert, regex=True)
+    total_param[31] = [f"{i[0]}-{i[1]}-{i[2]}T{i[3]}:{i[4]}Z" for i in experimental_time.values.tolist()]
+    total_param[26] = len(irradiation_end_time)
+    total_param[27] = 'S'.join(irradiation_end_time)
+    total_param[29] = sum(duration_hour)
+    total_param[30] = '-'.join(last_time)
+
+    stand_time_second = [
+        get_datetime(*i) - get_datetime(*last_time) for i in experimental_time.values.tolist()]
+    total_param[32] = [i / (3600 * 24 * 365.242) for i in stand_time_second]  # stand year
+
+    # initial ratios & error display settings
+    total_param[115] = 0
+    total_param[116] = 298.56
+    total_param[117] = 0.31
+    total_param[118] = 298.56
+    total_param[119] = 0.31
+    total_param[120] = 1
+    total_param[121] = 1
+    total_param[122] = 1
+
+    return total_param
+
+
+def full_to_sample(file_path: str, sample_name: str = None):
+    """
+    Parameters
+    ----------
+    file_path
+    sample_name
+
+    Returns
+    -------
+
+    """
+    if sample_name is None:
+        sample_name = str(os.path.split(file_path)[-1]).split('.')[0]
+    content, sample_info = open_full_xls(file_path, sample_name)
+    sample = create_sample_from_dict(content=content, smp_info=sample_info)
+    return sample
+
+
+def open_full_xls(file_path: str, sample_name: str = ''):
+    """
+    filepath: absolute full path of input file
+    return sample instance
+    """
+    try:
+        res = xls.open_xls(file_path)
+    except (Exception, BaseException) as e:
+        return e
+    start_row = 5
+    rows_num = len(res['Sample Parameters']) - 5
+    for key, val in res.items():
+        res[key] = arr.transpose(val[:start_row + rows_num])
+        # 2倍误差改回1倍
+        for i in range(len(res[key])):
+            if res[key][i][2] in ['2s', '%2s', '± 2s']:
+                _temp = []
+                for j in range(rows_num):
+                    try:
+                        _temp.append(res[key][i][start_row + j] / 2)
+                    except TypeError:
+                        _temp.append('')
+                res[key][i][start_row: start_row + rows_num] = _temp
+    if res['Incremental Heating Summary'][13][2] == 'K/Ca':
+        _temp, _s = [], []
+        for j in range(rows_num):
+            try:
+                _temp.append(1 / res['Relative Abundances'][13][start_row + j])
+                _s.append(err.div((1, 0), (
+                    res['Relative Abundances'][13][start_row + j], res['Relative Abundances'][14][start_row + j])))
+            except TypeError:
+                _temp.append(None)
+                _s.append(None)
+        res['Incremental Heating Summary'][13][start_row: start_row + rows_num] = _temp
+        res['Incremental Heating Summary'][13][start_row: start_row + rows_num] = _s
+
+    # degas相对误差改为绝对误差
+    for i in range(len(res['Degassing Patterns'])):
+        if res['Degassing Patterns'][i][2] in ['%1s', '%2s']:
+            _temp = []
+            for j in range(rows_num):
+                try:
+                    _temp.append(res['Degassing Patterns'][i][start_row + j] * res['Degassing Patterns'][i - 1][
+                        start_row + j] / 100)
+                except TypeError:
+                    _temp.append('')
+            res['Degassing Patterns'][i][start_row: start_row + rows_num] = _temp
+    rows = list(range(start_row, rows_num))
+    sequence_name = arr.partial(res['Procedure Blanks'], rows, 1)
+    sequence_value = arr.partial(res['Procedure Blanks'], rows, 2)
+    blank_values = arr.partial(
+        res['Procedure Blanks'], rows, [3, 4, 5, 6, 7, 8, 9, 10, 11, 12])
+    sample_values = arr.partial(
+        res['Intercept Values'], rows, [3, 4, 8, 9, 13, 14, 18, 19, 23, 24])
+    corrected_values = arr.partial(
+        res['Relative Abundances'], rows, [4, 5, 6, 7, 8, 9, 10, 11, 12, 13])
+    degas_values = arr.partial(
+        res['Degassing Patterns'], rows, [
+            4, 5, 6, 7, 8, 9, 10, 11,
+            12, 13,
+            22, 23, 14, 15, 16, 17, 18, 19, 20, 21,
+            24, 25, 26, 27,
+            28, 29, 30, 31, 32, 33, 34, 35])
+    publish_values = arr.partial(
+        res['Incremental Heating Summary'], rows, [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14])
+    apparent_age_values = arr.partial(
+        res['Relative Abundances'], rows, [14, 15, 16, 17, -1, -1, 18, 19])
+    isochron_values = [[np.nan] * len(rows)] * 39
+    isochron_values[0:5] = arr.partial(
+        res['Normal Isochron Table'], rows, [4, 5, 6, 7, 10])
+    isochron_values[6:11] = arr.partial(
+        res['Inverse Isochron Table'], rows, [4, 5, 6, 7, 10])
+    total_param = arr.partial(
+        res['Sample Parameters'], rows, [
+            # 1, 2,  # 0-1
+            -1, -1, -1, -1,  # 2-5
+            -1, -1, -1, -1,  # 6-9
+            -1, -1, -1, -1, -1, -1,  # 10-15
+            -1, -1, -1, -1,  # 16-19
+            -1, -1,  # 20-21
+            23, 24, -1, -1, -1, -1,  # 22-27
+            -1, -1,  # 28-29
+            22, -1, -1, -1,  # 30-33
+            -1, -1,  # 34-35
+            -1, -1,  # 36-37
+            -1, -1,  # 38-39
+            -1, -1,  # 40-41
+            -1, -1,  # 42-43
+            -1, -1,  # 44-45
+            -1, -1,  # 46-47
+            -1, -1,  # 48-49
+            -1, -1,  # 50-51
+            -1, -1,  # 52-53
+            -1, -1,  # 54-55
+            -1, -1,  # 56-57
+            -1, -1,  # 58-59
+            -1, -1, -1, -1, -1, -1, -1, -1, -1,  # 60-68
+            10, 11, 12, 13,  #
+            -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  #
+            -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  #
+            -1, -1, -1, -1,  #
+            -1, -1, -1, -1,  #
+            -1, -1, -1, -1, -1,  #
+            -1, -1, -1, -1,  #
+            -1, -1, -1, -1,  #
+            -1,  #
+        ])
+
+    month_convert = {'Jan': '01', 'Feb': '02', 'Mar': '03', 'Apr': '04', 'May': '05', 'Jun': '06',
+                     'Jul': '07', 'Aug': '08', 'Sep': '09', 'Oct': '10', 'Nov': '11', 'Dec': '12'}
+    experiment_start_time = []
+    for i in arr.transpose(
+            arr.partial(res['Sample Parameters'], rows, [18, 17, 16, 19, 20])):
+        _year = str(i[0]) if '.' not in str(i[0]) else str(i[0]).split('.')[0]
+        _month = str(month_convert[str(i[1]).capitalize()]) if str(i[1]).capitalize() in month_convert.keys() else str(
+            i[1]).capitalize()
+        _day = str(i[2]) if '.' not in str(i[2]) else str(i[2]).split('.')[0]
+        _hour = str(i[3]) if '.' not in str(i[3]) else str(i[3]).split('.')[0]
+        _min = str(i[4]) if '.' not in str(i[4]) else str(i[4]).split('.')[0]
+        experiment_start_time.append([_year, _month, _day, _hour, _min])
+
+    total_param[31] = ['-'.join(i) for i in experiment_start_time]
+    total_param[0:26] = arr.partial(
+        res['Irradiation Constants'], rows,
+        [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
+
+    isochron_values[11] = [''] * len(isochron_values[0])
+    isochron_values[17] = [''] * len(isochron_values[0])
+    isochron_values[23] = [''] * len(isochron_values[0])
+    isochron_values[12:17] = isochron.get_data(
+        degas_values[20], degas_values[21], degas_values[24], degas_values[25], degas_values[10], degas_values[11]
+    )  # 39/38, 40/38
+    isochron_values[18:23] = isochron.get_data(
+        degas_values[20], degas_values[21], degas_values[10], degas_values[11], degas_values[24], degas_values[25]
+    )  # 39/40, 38/40
+    isochron_values[24:29] = isochron.get_data(
+        degas_values[10], degas_values[11], degas_values[24], degas_values[25], degas_values[20], degas_values[21]
+    )  # 38/39, 40/39
+    isochron_mark = [1 if i == 'P' else '' for i in arr.partial(
+        res['Normal Isochron Table'], rows, 3)]
+
+    sample_info = {
+        'sample': {'name': sample_name, 'material': 'MATERIAL', 'location': 'LOCATION'},
+        'researcher': {'name': 'RESEARCHER', 'addr': 'ADDRESS'},
+        'laboratory': {'name': 'LABORATORY', 'addr': 'ADDRESS', 'analyst': 'ANALYST'}
+    }
+
+    res = [sample_values, blank_values, corrected_values, degas_values, publish_values,
+           apparent_age_values, isochron_values, total_param, [isochron_mark],
+           [sequence_name, sequence_value]]
+
+    return dict(zip(['smp', 'blk', 'cor', 'deg', 'pub', 'age', 'iso', 'pam', 'mak', 'seq'], res)), sample_info
+
+
+class ArArCalcFile:
+    def __init__(self, file_path: str, sample_name: str = ""):
+        self.file_path = file_path
+        self.sample_name = sample_name
+        self.supported_versions = ['25.2', '24.0']
+        self.content = pd.DataFrame([])
+        self.sample_info = {
+            'sample': {'name': 'undefined', 'material': 'undefined',},
+            'researcher': {'name': 'undefined'},
+            'laboratory': {'name': 'undefined', 'analyst': 'undefined', 'info': 'undefined',}
+        }
+
+    def open(self):
+        book_contents = read_calc_file(self.file_path)
+        if not book_contents:
+            raise ValueError('Fail to open the file')
+        # create data frames for book values
+        content = pd.DataFrame(book_contents['Data Tables'])
+        logs01 = pd.DataFrame(book_contents['Logs01'])
+        logs02 = pd.DataFrame(book_contents['Logs02'])
+        logs03 = pd.DataFrame(book_contents['Logs03'])
+
+        start_row = 5
+        sequence_num = int(logs03[2][0])
+        header = content.loc[2]
+        data = pd.concat([content.loc[list(range(start_row, start_row + sequence_num))]], ignore_index=True).apply(
+            pd.to_numeric, errors='ignore'
+        )
+
+        # check version
+        version = logs03[3][0]
+        if version == '25.2':
+            handler = open_252
+            material = data[45][0]
+            analyst = data[47][0]
+        elif version == '24.0':
+            handler = open_240
+            material = data[46][0]
+            analyst = data[48][0]
+        else:
+            raise ValueError(f'non-supported version: {version}')
+
+        # change error type, 2sigma to 1sigma...
+        data = change_error_type(data, header)
+
+        # get full data frames
+        # ['smp', 'blk', 'cor', 'deg', 'pub', 'age', 'iso', 'pam', 'inf', 'mak', 'seq',] are abbreviations for
+        #     [sample_values, blank_values, corrected_values, degas_values, publish_values,
+        #      apparent_age_values, isochron_values, total_param, sample_info, isochron_mark,
+        #      sequence_name, sequence_value]
+        self.content = pd.concat(
+            handler(data.copy(), logs01, logs02), axis=1,
+            keys=['smp', 'blk', 'cor', 'deg', 'pub', 'age', 'iso', 'pam', 'mak', 'seq', ],
+        )
+
+        # sample info
+        self.sample_info = {
+            'sample': {
+                'name': self.sample_name or data[44][0],
+                'material': material, 'location': 'LOCATION'
+            },
+            'researcher': {'name': data[64][0]},
+            'laboratory': {
+                'name': logs01[1][44],
+                'analyst': analyst,
+                'info': '\n'.join([logs01[1][45], logs01[1][46], logs01[1][47]]),
+            }
+        }
+
+        return self
+
+    def get_content(self):
+        return self.content
+
+    def get_smp_info(self):
+        return self.sample_info
+
+    def get_df(self):
+        return self.content
+
+    def get_list(self):
+        return self.content