ararpy 0.2.3__tar.gz → 0.2.4__tar.gz

{ararpy-0.2.3 → ararpy-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.2.3
+Version: 0.2.4
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.2.3 → ararpy-0.2.4}/ararpy/__init__.py

@@ -16,10 +16,10 @@ from . import calc, smp, files, thermo, test
 """ Information """
 
 name = 'ararpy'
-version = '0.2.3'
+version = '0.2.4'
 __version__ = version
 full_version = version
-last_update = '2026-01-01'
+last_update = '2026-01-07'
 
 """ ArArPy Functions """
 
@@ -97,24 +97,6 @@ Sample.set_params = smp.basic.set_params
 Sample.set_info = lambda _smp, info: setattr(_smp, 'Info', smp.basic.update_plot_from_dict(_smp.Info, info))
 
 Sample.recalculate = lambda _smp, *args, **kwargs: smp.calculation.recalculate(_smp, *args, **kwargs)
-Sample.plot_init = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=False, isInit=True, isPlateau=False)
-Sample.plot_isochron = lambda _smp, **kwargs: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, **kwargs)
-Sample.plot_age_plateau = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=False, isInit=False, isPlateau=True)
-Sample.plot_normal = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_2'])
-Sample.plot_inverse = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_3'])
-Sample.plot_cl_1 = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_4'])
-Sample.plot_cl_2 = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_5'])
-Sample.plot_cl_3 = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_6'])
-Sample.plot_3D = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_7'])
 
 Sample.to_excel = lambda _smp, file_path, *args, **kwargs: smp.export.to_excel(_smp, file_path=file_path, *args, **kwargs)
 

{ararpy-0.2.3 → ararpy-0.2.4}/ararpy/calc/arr.py

@@ -311,7 +311,10 @@ def multi_append(a, *args):
 
     """
     for arg in args:
-        a.append(arg)
+        if isinstance(a, list):
+            a.append(arg)
+        if isinstance(a, np.ndarray):
+            a = np.append(a, arg)
     return a
 
 
@@ -351,7 +354,7 @@ def create_arr(shape: tuple):
 
     """
     if len(shape) == 1:
-        return []
+        return [0 for i in range(shape[0])]
     return [create_arr(shape[1:]) for i in range(shape[0])]
 
 

{ararpy-0.2.3 → ararpy-0.2.4}/ararpy/smp/basic.py

@@ -35,15 +35,16 @@ pd.options.mode.chained_assignment = None  # default='warn'
 # =======================
 class ParamsInvalid(Exception):
     """    """
-    def __init__(self, code, message, context=None):
+    def __init__(self, code=400, message="", context=None, fatal=True):
         self.code = code
         self.message = message
         self.context = context or {}
+        self.fatal = fatal
         # 调用父类构造函数，确保异常能正常抛出
         super().__init__(f"{self.message}")
 
 
-def validate_params(**kwargs):
+def validate_params(fatal=True, **kwargs):
 
     def check(data, dtype, **kwargs):
         k = np.array(data, dtype=dtype)
@@ -65,7 +66,7 @@ def validate_params(**kwargs):
                     if not kwargs.get('func')(each):
                         raise ValueError
                 except (Exception, BaseException) as e:
-                    raise ValueError(f"{type(e).__name__}: invalid value, {each}")
+                    raise ValueError(f"invalid value, {each}")
 
     context = {'names': [], 'classnames': [], 'messages': []}
     for index, (name, content) in enumerate(kwargs.items(), 1):
@@ -83,7 +84,7 @@ def validate_params(**kwargs):
     if not context['names']:
         return True
     else:
-        raise ParamsInvalid(400, '. '.join(context['messages']), context)
+        raise ParamsInvalid(400, '. '.join(context['messages']), context, fatal=fatal)
 
 
 # =======================
@@ -268,7 +269,7 @@ def calc_age(ar40ar39=None, params: dict = None, smp: Sample = None, index: list
             age_unit_factor = 1
 
     # check if using Min equation
-    params['Min'] = [i if isinstance(i, bool) else False for i in params['Min']]
+    params['Min'] = [bool(i) for i in params['Min']]
 
     idx1 = np.flatnonzero(np.where(params['Min'], True, False))  # True, using Min equation
     idx2 = np.flatnonzero(np.where(params['Min'], False, True))  # False
@@ -668,6 +669,10 @@ def set_params(smp: Sample, params: Union[List, str], flag: Optional[str] = None
         else:
             smp.TotalParam[32] = [item / (3600 * 24 * 365.242) if index in rows else smp.TotalParam[32][index] for index, item in enumerate(stand_time_second)]  # stand year
 
+        smp.Info.irradiation.label = params[-3]
+        smp.Info.irradiation.location = params[-2]
+        smp.Info.irradiation.info = params[-1]
+
     elif flag == 'smp':
         smp.TotalParam[67:71] = remove_none(smp.TotalParam[67:71], params[0:4], rows, n)
         smp.TotalParam[58:67] = remove_none(smp.TotalParam[58:67], params[4:13], rows, n)
@@ -702,6 +707,7 @@ def get_sequence(smp: Sample):
     smp.Info.results.selection[0]['data'] = smp.SelectedSequence1
     smp.Info.results.selection[1]['data'] = smp.SelectedSequence2
     smp.Info.results.selection[2]['data'] = smp.UnselectedSequence
+    smp.Info.experiment.step_num = len(smp.SequenceName)
     return ArArBasic(
         size=len(smp.SequenceName), name=smp.SequenceName, value=smp.SequenceValue, unit=smp.SequenceUnit,
         mark=ArArBasic(

{ararpy-0.2.3 → ararpy-0.2.4}/ararpy/smp/corr.py

@@ -153,10 +153,13 @@ def corr_decay(sample: Sample):
     corrDecay37 = sample.TotalParam[104]
     corrDecay39 = sample.TotalParam[105]
     sample.CorrectedValues = copy.deepcopy(sample.MassDiscrCorrected)
-    sample.CorrectedValues[2] = [val if corrDecay37[idx] else 0 for idx, val in enumerate(decay_corrected[2])]
-    sample.CorrectedValues[3] = [val if corrDecay37[idx] else 0 for idx, val in enumerate(decay_corrected[3])]
-    sample.CorrectedValues[6] = [val if corrDecay39[idx] else 0 for idx, val in enumerate(decay_corrected[6])]
-    sample.CorrectedValues[7] = [val if corrDecay39[idx] else 0 for idx, val in enumerate(decay_corrected[7])]
+    for idx in range(sample.Info.experiment.step_num):
+        if corrDecay37[idx]:
+            sample.CorrectedValues[2][idx] = decay_corrected[2][idx]
+            sample.CorrectedValues[3][idx] = decay_corrected[3][idx]
+        if corrDecay39[idx]:
+            sample.CorrectedValues[6][idx] = decay_corrected[6][idx]
+            sample.CorrectedValues[7][idx] = decay_corrected[7][idx]
 
     data = np.array(sample.CorrectedValues)
     data[1:10:2] = data[1:10:2] = np.abs(np.divide(data[1:10:2], data[0:10:2])) * 100
@@ -769,7 +772,7 @@ def monte_carlo_f(sample: Sample):
             blank_gain_corr=sample.TotalParam[111][i],
             MDF_method=sample.TotalParam[100][i],
             force_to_zero=sample.TotalParam[101][i],
-            monte_carlo_size=1000,
+            monte_carlo_size=4000,
         )
 
         yield res

{ararpy-0.2.3 → ararpy-0.2.4}/ararpy/smp/initial.py

@@ -191,7 +191,7 @@ def initial(smp: Sample):
         ),
         preference=ArArBasic(**PREFERENCE_RES),
         irradiation= ArArBasic(
-            label='', pos_h='', pos_x='', pos_y='',
+            label='', pos_h='', pos_x='', pos_y='', location='', info=''
         )
     ))
 
@@ -234,7 +234,7 @@ def initial(smp: Sample):
     ))
     setattr(smp, 'TotalParamsTable', Table(
         id='8', name='Total Params', header=samples.TOTAL_PARAMS_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1, 2, 30, 31, 33, 34, 61, 100, 103, *list(range(104, 118))],
+        text_indexes=[0, 1, 2, 29, 30, 31, 33, 34, 61, 100, 103, 118],
         # numeric_indexes=list(range(1, 120)),
     ))
 
@@ -359,10 +359,25 @@ def check_version(smp: Sample):
             smp.TotalParam[32] = [np.nan for index in range(smp.Info.experiment.step_num)]
         else:
             smp.TotalParam[32] = [item / (3600 * 24 * 365.242) for item in stand_time_second]  # stand year
-        smp = smp.recalculate(re_table_style=True)
-        smp = smp.recalculate(re_set_table=True)
         smp.version = "20251001"
 
+    # 20251231 change publish table
+    if version < 20251231:
+        smp.PublishValues = arr.create_arr((len(samples.PUBLISH_TABLE_HEADERS) - 3, smp.Info.experiment.step_num))
+        try:
+            data = np.array(smp.CorrectedValues)
+            data[1:10:2] = np.abs(np.divide(data[1:10:2], data[0:10:2])) * 100
+            smp.PublishValues[0:10] = copy.deepcopy(data.tolist())
+            smp.PublishValues[10:14] = copy.deepcopy(smp.ApparentAgeValues[0:4])
+            smp.PublishValues[14:16] = copy.deepcopy(smp.ApparentAgeValues[6:8])
+        except (BaseException, Exception) as e:
+            print(f"{type(e).__name__}: {str(e)}")
+            pass
+        else:
+            smp = smp.recalculate(re_table_style=True)
+            smp = smp.recalculate(re_set_table=True)
+            smp.version = "20251231"
+
     return smp
 
 

{ararpy-0.2.3 → ararpy-0.2.4}/ararpy/smp/plots.py

@@ -36,182 +36,176 @@ ISOCHRON_INDEX_DICT = {
 }
 
 
-# =======================
-# Reset plot data
-# =======================
-def set_plot_data(sample: Sample, isInit: bool = True, isIsochron: bool = True,
-                  isPlateau: bool = True, **kwargs):
+def set_plot_data(sample: Sample, isInit: bool = True, **kwargs):
     """
     Parameters
     ----------
     sample
-    isInit
-    isIsochron
-    isPlateau
     kwargs
 
     Returns
     -------
 
     """
-    # print(f"isInit: {isInit}, isIsochron: {isIsochron}, isPlateau: {isPlateau}")
-
-    # Initialization, apply age spectra data and isochron plot data
-    if isInit:
-        initial_plot_data(sample)
-        # try:
-        #     initial_plot_data(sample)
-        # except (Exception, BaseException):
-        #     print("initial_plot_data(sample) error:\n", traceback.format_exc())
-        #     pass
-
-    # Recalculate isochron lines
-    if isIsochron:
-        recalc_isochrons(sample, **kwargs)
-        reset_isochron_line_data(sample)
-        # try:
-        #     recalc_isochrons(sample, **kwargs)
-        # except (Exception, BaseException):
-        #     print("recalc_isochrons(sample, **kwargs) error:\n", traceback.format_exc())
-        #     pass
-        # try:
-        #     reset_isochron_line_data(sample)
-        # except (Exception, BaseException):
-        #     print("reset_isochron_line_data(sample):\n", traceback.format_exc())
-        #     pass
-
-    # Recalculate plateaus
-    if isPlateau:
-        recalc_plateaus(sample)
-        # try:
-        #     recalc_plateaus(sample)
-        # except (Exception, BaseException):
-        #     print("recalc_plateaus(sample) error:\n", traceback.format_exc())
-        #     pass
-
-
-# =======================
-# Initialize plot data
-# =======================
-def initial_plot_data(smp: Sample):
+    all_figures = ['figure_2', 'figure_3', 'figure_4', 'figure_5', 'figure_6', 'figure_7',  'figure_8',  'figure_9', 'figure_1', ]
+    figures = kwargs.get('figures', all_figures)
+    for idx, fig_id in enumerate(all_figures):
+        if fig_id not in figures:
+            continue
+        if fig_id == 'figure_1':
+            if isInit:
+                init_age_spec_plot(sample)
+            recalc_plateaus(sample)
+        if fig_id == 'figure_2':
+            plot_normal_iso(sample, isInit=isInit)
+        if fig_id == 'figure_3':
+            plot_inverse_iso(sample, isInit=isInit)
+        if fig_id == 'figure_4':
+            plot_cl1_iso(sample, isInit=isInit)
+        if fig_id == 'figure_5':
+            plot_cl2_iso(sample, isInit=isInit)
+        if fig_id == 'figure_6':
+            plot_cl3_iso(sample, isInit=isInit)
+        if fig_id == 'figure_7':
+            plot_3D_iso(sample, isInit=isInit)
+        if fig_id == 'figure_8':
+            recalc_degassing_plot(sample)
+        if fig_id == 'figure_9':
+            recalc_agedistribution(sample)
+
+
+# Isochrons
+def get_iso_res(sample: Sample, figure: Plot):
     """
-    Assign initial data for plots
+
     Parameters
     ----------
-    smp : Sample instance
+    sample
+    kwargs
 
     Returns
     -------
-    None
-    """
-    try:
-        params_to_check = {
-            'normal': {'data': smp.IsochronValues[0:5], 'dtype': float, 'class': 'k1', },
-            'inverse': {'data': smp.IsochronValues[6:11], 'dtype': float, 'class': 'k2', },
-            'K-Cl-Ar 1': {'data': smp.IsochronValues[12:17], 'dtype': float, 'class': 'k3', },
-            'K-Cl-Ar 2': {'data': smp.IsochronValues[18:23], 'dtype': float, 'class': 'k4', },
-            'K-Cl-Ar 3': {'data': smp.IsochronValues[24:29], 'dtype': float, 'class': 'k5', },
-            '3D': {'data': smp.IsochronValues[30:39], 'dtype': float, 'class': 'k6', },
-            'age spectra': [
-                {'data': smp.ApparentAgeValues[2:4], 'dtype': float, 'class': 'k7', },
-                {'data': smp.ApparentAgeValues[7], 'dtype': float, 'class': 'k7', },
-            ],
-            'degas pattern': {'data': smp.IsochronValues[30:39], 'dtype': float, 'class': 'k8', },
-            'age distribution': {'data': smp.IsochronValues[30:39], 'dtype': float, 'class': 'k9', },
-        }
-    except (IndexError, AttributeError) as e:
-        raise
-    if not basic.validate_params(**params_to_check):
-        return
 
-    # Isochron plots
-    for key, val in ISOCHRON_INDEX_DICT.items():
-        figure = basic.get_component_byid(smp, key)
-        figure.data = [
-            *smp.IsochronValues[val['data_index'][0]:val['data_index'][1]],
-            list(range(smp.Info.experiment.step_num))
-        ]
-        # Ellipse
-        if key != 'figure_7':
-            ellipse_data = []
-            for point in calc.arr.transpose(figure.data[:5]):
-                if '' not in point and None not in point:
-                    ellipse_data.append(calc.isochron.get_ellipse(*point))
-                    getattr(figure, 'ellipse', Set(id='ellipse')).data = ellipse_data
-
-    # Age spectra plot
-    # Try to calculate total gas age
-    try:
-        if str(smp.Info.sample.type).lower() == "unknown":
-            a0, e0 = sum(smp.DegasValues[24]), pow(sum([i ** 2 for i in smp.DegasValues[25]]), 0.5)
-            a1, e1 = sum(smp.DegasValues[20]), pow(sum([i ** 2 for i in smp.DegasValues[21]]), 0.5)
-            handle = basic.calc_age
-        elif str(smp.Info.sample.type).lower() == "standard":
-            a0, e0 = sum(smp.DegasValues[24]), pow(sum([i ** 2 for i in smp.DegasValues[25]]), 0.5)
-            a1, e1 = sum(smp.DegasValues[20]), pow(sum([i ** 2 for i in smp.DegasValues[21]]), 0.5)
-            handle = basic.calc_j
-        elif str(smp.Info.sample.type).lower() == "air":
-            a0, e0 = sum(smp.DegasValues[26]), pow(sum([i ** 2 for i in smp.DegasValues[27]]), 0.5)
-            a1, e1 = sum(smp.DegasValues[ 0]), pow(sum([i ** 2 for i in smp.DegasValues[ 1]]), 0.5)
-            handle = basic.calc_mdf
+    """
+    figure.set3.data, figure.set1.data, figure.set2.data = \
+        sample.UnselectedSequence.copy(), sample.SelectedSequence1.copy(), sample.SelectedSequence2.copy()
+    for index, sequence in enumerate([figure.set1.data, figure.set2.data, figure.set3.data]):
+        set_data = calc.arr.partial(
+            sample.IsochronValues, rows=sequence, cols=list(range(*ISOCHRON_INDEX_DICT[figure.id]['data_index'])))
+        if figure.id != 'figure_7':
+            iso_res = get_isochron_results(
+                set_data, figure_type=ISOCHRON_INDEX_DICT[figure.id]["figure_type"], smp=sample, sequence=sequence)
+            sample.Info.results.isochron[figure.id].update({index: iso_res})
         else:
-            raise TypeError(f"Sample type is not supported: {smp.Info.sample.type}")
-        total_f = [a0 / a1, calc.err.div((a0, e0), (a1, e1))]
-        total_age = handle(total_f[:2], smp=smp)
-    except (Exception, BaseException):
-        print(traceback.format_exc())
-        total_f = [np.nan] * 2
-        total_age = [np.nan] * 4
-    smp.Info.results.age_spectra['TGA'].update(
-        {'Ar39': 100, 'F': total_f[0], 'sF': total_f[1], 'age': total_age[0],
-         's1': total_age[1], 's2': total_age[2], 's3': total_age[3], 'Num': len(smp.DegasValues[24])}
-    )
-    try:
-        smp.AgeSpectraPlot.data = calc.spectra.get_data(*smp.ApparentAgeValues[2:4], smp.ApparentAgeValues[7])
-        smp.AgeSpectraPlot.data = calc.arr.transpose(smp.AgeSpectraPlot.data)
-    except (Exception, BaseException):
-        print(traceback.format_exc())
-        smp.AgeSpectraPlot.data = []
+            iso_res = get_3D_results(data=set_data, sequence=sequence, sample=sample)
+            sample.Info.results.isochron[figure.id].update({index: iso_res})
 
-    # Degassing plot
-    recalc_degassing_plot(smp)
 
-    # Age distribution plot
-    recalc_agedistribution(smp)
-
-
-# =======================
-# Isochron results
-# =======================
-def recalc_isochrons(sample: Sample, **kwargs):
+def set_iso_line_data(sample: Sample, figure: Plot):
     """
-
+    Set isochron regression lines
     Parameters
     ----------
-    sample
-    kwargs
+    sample : sample instance
 
     Returns
     -------
-
+    None, set regression lines data to sample instance.
     """
-    figures = kwargs.pop('figures', ['figure_2', 'figure_3', 'figure_4', 'figure_5', 'figure_6', 'figure_7', ])
-    for key, val in ISOCHRON_INDEX_DICT.items():
-        if key not in figures:
-            continue
-        figure = basic.get_component_byid(sample, key)
-        figure.set3.data, figure.set1.data, figure.set2.data = \
-            sample.UnselectedSequence.copy(), sample.SelectedSequence1.copy(), sample.SelectedSequence2.copy()
-        for index, sequence in enumerate([figure.set1.data, figure.set2.data, figure.set3.data]):
-            set_data = calc.arr.partial(
-                sample.IsochronValues, rows=sequence, cols=list(range(*val['data_index'])))
-            if key != 'figure_7':
-                iso_res = get_isochron_results(
-                    set_data, figure_type=val["figure_type"], smp=sample, sequence=sequence)
-                sample.Info.results.isochron[figure.id].update({index: iso_res})
-            else:
-                iso_res = get_3D_results(data=set_data, sequence=sequence, sample=sample)
-                sample.Info.results.isochron[figure.id].update({index: iso_res})
+    for index in [0, 1]:
+        xscale, yscale = [figure.xaxis.min, figure.xaxis.max], [figure.yaxis.min, figure.yaxis.max]
+        coeffs = [sample.Info.results.isochron[figure.id][index]['k'], sample.Info.results.isochron[figure.id][index]['m1']]
+        line_point = calc.isochron.get_line_points(xscale, yscale, coeffs)
+        setattr(getattr(figure, ['line1', 'line2'][index]), 'data', line_point)
+        setattr(getattr(figure, ['text1', 'text2'][index]), '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
+
+
+def get_iso_init(sample: Sample, figure: Plot):
+    # data
+    val = ISOCHRON_INDEX_DICT.get(figure.id)['data_index']
+    data = [*sample.IsochronValues[val[0]:val[1]], list(range(sample.Info.experiment.step_num))]
+    # ellipse
+    ellipse_data = []
+    if figure.id != 'figure_7':
+        for point in calc.arr.transpose(data[:5]):
+            if '' not in point and None not in point:
+                ellipse_data.append(calc.isochron.get_ellipse(*point))
+    return data, ellipse_data
+
+
+def plot_normal_iso(sample: Sample, isInit: bool = False):
+    figure = sample.NorIsochronPlot
+    # data
+    if isInit:
+        data, ellipse_data = get_iso_init(sample, figure)
+        figure.data = data
+        getattr(figure, 'ellipse', Set(id='ellipse')).data = ellipse_data
+    # iso res
+    get_iso_res(sample, figure)
+    # line data
+    set_iso_line_data(sample, figure)
+
+
+def plot_inverse_iso(sample: Sample, isInit: bool = False):
+    figure = sample.InvIsochronPlot
+    # data
+    if isInit:
+        data, ellipse_data = get_iso_init(sample, figure)
+        figure.data = data
+        getattr(figure, 'ellipse', Set(id='ellipse')).data = ellipse_data
+    # iso res
+    get_iso_res(sample, figure)
+    # line data
+    set_iso_line_data(sample, figure)
+
+
+def plot_cl1_iso(sample: Sample, isInit: bool = False):
+    figure = sample.KClAr1IsochronPlot
+    # data
+    if isInit:
+        data, ellipse_data = get_iso_init(sample, figure)
+        figure.data = data
+        getattr(figure, 'ellipse', Set(id='ellipse')).data = ellipse_data
+    # iso res
+    get_iso_res(sample, figure)
+    # line data
+    set_iso_line_data(sample, figure)
+
+
+def plot_cl2_iso(sample: Sample, isInit: bool = False):
+    figure = sample.KClAr2IsochronPlot
+    # data
+    if isInit:
+        data, ellipse_data = get_iso_init(sample, figure)
+        figure.data = data
+        getattr(figure, 'ellipse', Set(id='ellipse')).data = ellipse_data
+    # iso res
+    get_iso_res(sample, figure)
+    # line data
+    set_iso_line_data(sample, figure)
+
+
+def plot_cl3_iso(sample: Sample, isInit: bool = False):
+    figure = sample.KClAr3IsochronPlot
+    # data
+    if isInit:
+        data, ellipse_data = get_iso_init(sample, figure)
+        figure.data = data
+        getattr(figure, 'ellipse', Set(id='ellipse')).data = ellipse_data
+    # iso res
+    get_iso_res(sample, figure)
+    # line data
+    set_iso_line_data(sample, figure)
+
+
+def plot_3D_iso(sample: Sample, isInit: bool = False):
+    figure = sample.ThreeDIsochronPlot
+    # data
+    if isInit:
+        data, ellipse_data = get_iso_init(sample, figure)
+        figure.data = data
+    # iso res
+    get_iso_res(sample, figure)
 
 
 def get_isochron_results(data: list, smp: Sample, sequence, figure_type: int = 0):
@@ -331,33 +325,55 @@ def get_3D_results(data: list, sequence: list, sample: Sample):
     return iso_res
 
 
-def reset_isochron_line_data(smp: Sample):
-    """
-    Set isochron regression lines
-    Parameters
-    ----------
-    smp : sample instance
+# Spectra
+def init_age_spec_plot(sample: Sample):
 
-    Returns
-    -------
-    None, set regression lines data to sample instance.
-    """
-    for k, v in basic.get_components(smp).items():
-        if not isinstance(v, Plot):
-            continue
-        if k not in ['figure_2', 'figure_3', 'figure_4', 'figure_5', 'figure_6', ]:
-            continue
-        for index in [0, 1]:
-            xscale, yscale = [v.xaxis.min, v.xaxis.max], [v.yaxis.min, v.yaxis.max]
-            coeffs = [smp.Info.results.isochron[k][index]['k'], smp.Info.results.isochron[k][index]['m1']]
-            line_point = calc.isochron.get_line_points(xscale, yscale, coeffs)
-            setattr(getattr(v, ['line1', 'line2'][index]), 'data', line_point)
-            setattr(getattr(v, ['text1', 'text2'][index]), '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
+    figure = sample.AgeSpectraPlot
+
+    try:
+        params_to_check = {
+            '40Arr/39ArK': {'data': sample.ApparentAgeValues[2:4], 'dtype': float, 'func': lambda x: np.isfinite(x), 'class': 'k1', },
+            '39ArK%': {'data': sample.ApparentAgeValues[7], 'dtype': float, 'func': lambda x: np.isfinite(x), 'class': 'k1', },
+        }
+    except (IndexError, AttributeError) as e:
+        raise
+    if not basic.validate_params(fatal=False, **params_to_check):
+        return
+
+    try:
+        if str(sample.Info.sample.type).lower() == "unknown":
+            a0, e0 = sum(sample.DegasValues[24]), pow(sum([i ** 2 for i in sample.DegasValues[25]]), 0.5)
+            a1, e1 = sum(sample.DegasValues[20]), pow(sum([i ** 2 for i in sample.DegasValues[21]]), 0.5)
+            handler = basic.calc_age
+        elif str(sample.Info.sample.type).lower() == "standard":
+            a0, e0 = sum(sample.DegasValues[24]), pow(sum([i ** 2 for i in sample.DegasValues[25]]), 0.5)
+            a1, e1 = sum(sample.DegasValues[20]), pow(sum([i ** 2 for i in sample.DegasValues[21]]), 0.5)
+            handler = basic.calc_j
+        elif str(sample.Info.sample.type).lower() == "air":
+            a0, e0 = sum(sample.DegasValues[26]), pow(sum([i ** 2 for i in sample.DegasValues[27]]), 0.5)
+            a1, e1 = sum(sample.DegasValues[ 0]), pow(sum([i ** 2 for i in sample.DegasValues[ 1]]), 0.5)
+            handler = basic.calc_mdf
+        else:
+            msg = f"Sample type is not supported: {sample.Info.sample.type}"
+            context = {'names': [figure.name], 'classnames': [f'k7'], 'messages': [msg]}
+            raise basic.ParamsInvalid(400, msg, context=context, fatal=False)
+
+        total_f = [a0 / a1, calc.err.div((a0, e0), (a1, e1))]
+        total_age = handler(total_f[:2], smp=sample)
+    except (Exception, BaseException) as e:
+        total_f = [np.nan] * 2
+        total_age = [np.nan] * 4
+
+    sample.Info.results.age_spectra['TGA'].update(
+        {'Ar39': 100, 'F': total_f[0], 'sF': total_f[1], 'age': total_age[0],
+         's1': total_age[1], 's2': total_age[2], 's3': total_age[3], 'Num': len(sample.DegasValues[24])}
+    )
+
+    figure.data = calc.arr.transpose(
+        calc.spectra.get_data(*sample.ApparentAgeValues[2:4], sample.ApparentAgeValues[7])
+    )
 
 
-# =======================
-# Age spectra results
-# =======================
 def recalc_plateaus(sample: Sample, **kwargs):
     if sample.Info.sample.type == "Unknown":
         return recalc_age_plateaus(sample, **kwargs)
@@ -379,6 +395,19 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
     -------
     None
     """
+
+    try:
+        params_to_check = {
+            '39ArK': {'data': sample.DegasValues[20:22], 'dtype': float, 'func': lambda x: np.isfinite(x), 'class': 'k1', },
+            '40Arr': {'data': sample.DegasValues[24:26], 'dtype': float, 'func': lambda x: np.isfinite(x), 'class': 'k1', },
+            'J Factor': {'data': sample.TotalParam[136], 'dtype': float, 'func': lambda x: np.isfinite(x) and x > 0, 'class': 'k1', },
+            'J Factor': {'data': sample.TotalParam[137], 'dtype': float, 'func': lambda x: np.isfinite(x), 'class': 'k1', },
+        }
+    except (IndexError, AttributeError) as e:
+        raise
+    if not basic.validate_params(fatal=False, **params_to_check):
+        return
+
     ar39k, sar39k = calc.arr.mul(sample.DegasValues[20:22], sample.TotalParam[136:138])
     ar40r, sar40r = sample.DegasValues[24:26]
     ar40rar39k = calc.arr.div([ar40r, sar40r], [ar39k, sar39k])
@@ -561,6 +590,30 @@ def recalc_mdf_plateaus(sample: Sample, **kwargs):
         sample.AgeSpectraPlot.text2.text = ""
 
 
+def recalc_j_plateaus(sample: Sample, **kwargs):
+
+    ar40rar39k = sample.ApparentAgeValues[0:2]
+    j = sample.ApparentAgeValues[2:4]
+
+    try:
+        set1_res, _, set1_data = get_plateau_results(sample, sample.SelectedSequence1, ar40rar39k=ar40rar39k)
+    except ValueError:
+        pass
+    else:
+        sample.Info.results.age_plateau.update({0: set1_res})
+        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_data = get_plateau_results(sample, sample.SelectedSequence2, ar40rar39k=ar40rar39k)
+    except ValueError:
+        pass
+    else:
+        sample.Info.results.age_plateau.update({1: set2_res})
+        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
+
+
 def calc_ar40ar39(r, sr, smp):
     """
     Calculate Ar40r / Ar39K based on passed initial ratio.
@@ -693,33 +746,7 @@ def get_wma_results(sample: Sample, sequence: list, ar40rar39k: list = None, ar3
     return spectra_res
 
 
-def recalc_j_plateaus(sample: Sample, **kwargs):
-
-    ar40rar39k = sample.ApparentAgeValues[0:2]
-    j = sample.ApparentAgeValues[2:4]
-
-    try:
-        set1_res, _, set1_data = get_plateau_results(sample, sample.SelectedSequence1, ar40rar39k=ar40rar39k)
-    except ValueError:
-        pass
-    else:
-        sample.Info.results.age_plateau.update({0: set1_res})
-        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_data = get_plateau_results(sample, sample.SelectedSequence2, ar40rar39k=ar40rar39k)
-    except ValueError:
-        pass
-    else:
-        sample.Info.results.age_plateau.update({1: set2_res})
-        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
-
-
-# =======================
 # Age Distribution Plot
-# =======================
 def recalc_agedistribution(smp: Sample, **kwargs):
     try:
         ages = smp.ApparentAgeValues[2]
@@ -769,14 +796,32 @@ def recalc_agedistribution(smp: Sample, **kwargs):
         plot.set2.data = [[], []]
 
 
-# =======================
 # Age Distribution Plot
-# =======================
 def recalc_degassing_plot(smp: Sample, **kwargs):
+    figure = smp.DegasPatternPlot
+
+    try:
+        params_to_check = {
+            'degas pattern': [
+                {'data': smp.DegasValues[0], 'dtype': float, 'class': 'k8', },
+                {'data': smp.DegasValues[8], 'dtype': float, 'class': 'k8', },
+                {'data': smp.DegasValues[10], 'dtype': float, 'class': 'k8', },
+                {'data': smp.DegasValues[20], 'dtype': float, 'class': 'k8', },
+                {'data': smp.DegasValues[24], 'dtype': float, 'class': 'k8', },
+                {'data': smp.CorrectedValues[0:10:2], 'dtype': float, 'class': 'k8', },
+            ],
+        }
+    except (IndexError, AttributeError) as e:
+        context = {'names': [figure.name], 'classnames': [f'k8'], 'messages': [f"{figure.name}: {str(e)}"]}
+        raise basic.ParamsInvalid(400, f"{figure.name}: {str(e)}", context=context, fatal=False)
+
+    if not basic.validate_params(fatal=False, **params_to_check):
+        return
+
     if not hasattr(smp, 'DegasPatternPlot'):
         setattr(smp, 'DegasPatternPlot', Plot(id='figure_8', name='Degas Pattern Plot'))
     isotope_percentage = lambda l: [e / sum(l) * 100 if sum(l) != 0 else 0 for e in l]
-    smp.DegasPatternPlot.data = [
+    figure.data = [
         isotope_percentage(smp.DegasValues[0]),  # Ar36a
         isotope_percentage(smp.DegasValues[8]),  # Ar37Ca
         isotope_percentage(smp.DegasValues[10]),  # Ar38Cl
@@ -788,4 +833,4 @@ def recalc_degassing_plot(smp: Sample, **kwargs):
         isotope_percentage(smp.CorrectedValues[6]),  # Ar39
         isotope_percentage(smp.CorrectedValues[8]),  # Ar40
     ]
-    smp.DegasPatternPlot.info = [True] * 10
+    figure.info = [True] * 10

{ararpy-0.2.3 → ararpy-0.2.4}/ararpy/smp/sample.py

@@ -855,7 +855,8 @@ class Sample:
         # self.__version = '20250328'  # Experiment info
         # self.__version = '20250404'  # J normalization factor
         # self.__version = '20251001'  # add marker col for all tables
-        self.__version = '20251231'  # move montecarlo to params-112
+        # self.__version = '20251231'  # move montecarlo to params-112
+        self.__version = '20260101'  #
 
         self.Doi = ""
         self.RawData = RawData()

{ararpy-0.2.3 → ararpy-0.2.4}/ararpy/smp/style.py

@@ -60,8 +60,6 @@ def set_plot_style(smp: Sample):
     initial.initial_plot_styles(smp, except_attrs=['data'])
     # Auto scale
     reset_plot_scale(smp)
-    # Reset isochron data
-    plots.reset_isochron_line_data(smp)
     # Auto position and contents of texts
     reset_text(smp)
     # Set title, which are deleted in initializing
@@ -69,8 +67,16 @@ def set_plot_style(smp: Sample):
     smp_name = smp.Info.sample.name
     name = f"{exp_name} {smp_name}" if str(exp_name).lower().strip() != str(smp_name).lower().strip() else exp_name
     suffix = f"{name} {smp.Info.sample.material}"
+
     for figure_id, figure in basic.get_components(smp).items():
+        if not isinstance(figure, Plot):
+            continue
+
         if isinstance(figure, Plot):
+            # Reset isochron line
+            if figure_id in ['figure_2', 'figure_3', 'figure_4', 'figure_5', 'figure_6', ]:
+                plots.set_iso_line_data(smp, figure)
+            # name and title
             if not hasattr(figure, 'title'):
                 setattr(figure, 'title', Plot.Text())
             setattr(getattr(figure, 'title'), 'text', f"{suffix} {getattr(figure, 'name', '')}")
@@ -111,8 +117,8 @@ def reset_plot_scale(smp: Sample, only_figure: str = None):
         if k == 'figure_1':
             try:
                 k0 = calc.arr.transpose(v.data)
-                k1 = calc.arr.transpose(v.set1.data) if len(v.set1.data) != 0 else [[]] * 3
-                k2 = calc.arr.transpose(v.set2.data) if len(v.set2.data) != 0 else [[]] * 3
+                k1 = calc.arr.transpose(v.set1.data) if len(v.set1.data) != 0 else [[] for i in range(3)]
+                k2 = calc.arr.transpose(v.set2.data) if len(v.set2.data) != 0 else [[] for i in range(3)]
                 data = np.concatenate([k0, k1, k2], axis=1)
                 ylist = np.concatenate([data[1], data[2]])
                 yscale = calc.plot.get_axis_scale(ylist, min_interval=5, extra_count=1)

{ararpy-0.2.3 → ararpy-0.2.4}/ararpy/smp/table.py

@@ -60,7 +60,10 @@ def update_table_data(smp: Sample, only_table: str = None):
         elif key == '8':
             data = [smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.TotalParam]
         else:
-            data = [['']]
+            raise KeyError(f"Invalid table id")
+
+        data = _normalize_data(
+            data, len(comp.header), smp.Info.experiment.step_num, text_col_indexes=comp.text_indexes)
 
         try:
             params_to_check = {
@@ -94,61 +97,46 @@ def update_handsontable(smp: Sample, data: list, id: str):
 
     """
 
-    def _normalize_data(a, cols, start_col=0):
-        if len(a) >= cols:
-            return a[start_col:cols]
-        else:
-            return a[start_col:] + [[''] * len(a[0])] * (cols - len(a))
-
-    def _strToBool(cols):
-        bools_dict = {
-            'true': True, 'false': False, 'True': True, 'False': False, '1': True, '0': False, 'none': False,
-        }
-        return [bools_dict.get(str(col).lower(), False) for col in cols]
-
-    def _digitize_data(a):
-        # pattern = r'^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?$'
-        # return [[ast.literal_eval(str(cell)) if re.fullmatch(pattern, str(cell)) else np.nan if str(cell) == "" else cell for cell in row] for row in a]
-        return a
 
     try:
-        smp.SequenceName = data[0]
+        col3 = _normalize_data(data[0:3], cols=3, rows=len(data[0]), text_col_indexes=[0, 1, 2])
     except IndexError:
-        pass
+        raise
 
     update_all_table = False
     try:
-        if data[1] != smp.SequenceValue or data[2] != smp.IsochronMark:
+        if col3[0] != smp.SequenceName or col3[1] != smp.SequenceValue or col3[2] != smp.IsochronMark:
             update_all_table = True
-            smp.SequenceValue = data[1]
-            smp.IsochronMark = data[2]
+            smp.SequenceName = col3[0]
+            smp.SequenceValue = col3[1]
+            smp.IsochronMark = col3[2]
     except IndexError:
         print(f"Check sequence value / isochron mark failed")
-        pass
-
+        raise
+    n = len(data[0])
     if id == '1':  # 样品值
-        data = _normalize_data(data, len(samples.SAMPLE_INTERCEPT_HEADERS), 3)
+        data = _normalize_data(data, len(samples.SAMPLE_INTERCEPT_HEADERS), n, 3)
         smp.SampleIntercept = _digitize_data(data)
     elif id == '2':  # 本底值
-        data = _normalize_data(data, len(samples.BLANK_INTERCEPT_HEADERS), 3)
+        data = _normalize_data(data, len(samples.BLANK_INTERCEPT_HEADERS), n, 3)
         smp.BlankIntercept = _digitize_data(data)
     elif id == '3':  # 校正值
-        data = _normalize_data(data, len(samples.CORRECTED_HEADERS), 3)
+        data = _normalize_data(data, len(samples.CORRECTED_HEADERS), n, 3)
         smp.CorrectedValues = _digitize_data(data)
     elif id == '4':  # Degas table
-        data = _normalize_data(data, len(samples.DEGAS_HEADERS), 3)
+        data = _normalize_data(data, len(samples.DEGAS_HEADERS), n, 3)
         smp.DegasValues = _digitize_data(data)
     elif id == '5':  # 发行表
-        data = _normalize_data(data, len(samples.PUBLISH_TABLE_HEADERS), 3)
+        data = _normalize_data(data, len(samples.PUBLISH_TABLE_HEADERS), n, 3)
         smp.PublishValues = _digitize_data(data)
     elif id == '6':  # 年龄谱
-        data = _normalize_data(data, len(samples.SPECTRUM_TABLE_HEADERS), 3)
+        data = _normalize_data(data, len(samples.SPECTRUM_TABLE_HEADERS), n, 3)
         smp.ApparentAgeValues = _digitize_data(data)
     elif id == '7':  # 等时线
-        data = _normalize_data(data, len(samples.ISOCHRON_TABLE_HEADERS), 3)
+        data = _normalize_data(data, len(samples.ISOCHRON_TABLE_HEADERS), n, 3)
         smp.IsochronValues = _digitize_data(data)
     elif id == '8':  # 总参数
-        data = _normalize_data(data, len(samples.TOTAL_PARAMS_HEADERS), 3)
+        data = _normalize_data(data, len(samples.TOTAL_PARAMS_HEADERS), n, 3)
         data = _digitize_data(data)
         data[101: 112] = [_strToBool(i) for i in data[101: 112]]
         smp.TotalParam = data
@@ -198,4 +186,50 @@ def update_data_from_table(smp: Sample, only_table: str = None):
             pass
 
 
+def _normalize_data(a, cols, rows, start_col=0, start_row=0, text_col_indexes=[]):
+    if isinstance(a, np.ndarray):
+        a = a.tolist()
+    if not isinstance(a, list):
+        raise ValueError(f"List required, but {type(a)} given.")
+    if len(a) >= cols:
+        a = a[start_col:cols]
+    else:
+        a = a[start_col:] + [[] for j in range(cols - len(a))]
+
+    def f(_, _i):
+        if _i in text_col_indexes:
+            if isinstance(_, type(None)):
+                return ""
+            if isinstance(_, float) and np.isnan(_):
+                return ""
+            return str(_)
+        else:
+            if _ in ["", None, np.nan]:
+                return np.nan
+            elif isinstance(_, str):
+                if _.lower() == 'true':
+                    return 1
+                elif _.lower() == 'false':
+                    return 0
+            return float(_)
+
+    for i in range(cols - start_col):
+        if len(a[i]) >= rows:
+            a[i] = [f(each, i + start_col) for each in a[i][start_row:rows]]
+        else:
+            a[i] = [f(each, i + start_col) for each in a[i][start_row:]] + [f("", i + start_col) for j in range(rows - len(a[i]))]
+
+    return a
+
+
+def _digitize_data(a):
+    # pattern = r'^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?$'
+    # return [[ast.literal_eval(str(cell)) if re.fullmatch(pattern, str(cell)) else np.nan if str(cell) == "" else cell for cell in row] for row in a]
+    return a
+
 
+def _strToBool(cols):
+    bools_dict = {
+        'true': True, 'false': False, 'True': True, 'False': False, '1': True, '0': False, 'none': False,
+    }
+    return [bools_dict.get(str(col).lower(), False) for col in cols]

{ararpy-0.2.3 → ararpy-0.2.4}/ararpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.2.3
+Version: 0.2.4
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.2.3 → ararpy-0.2.4}/setup.py

@@ -16,7 +16,7 @@ long_description = (here / 'README.md').read_text(encoding='utf-8')
 
 setuptools.setup(
     name='ararpy',  #
-    version='0.2.3',  # version
+    version='0.2.4',  # version
     author='Yang Wu',
     author_email='wuycug@hotmail.com',
     description='A project for Ar-Ar geochronology',  # short description