ararpy 0.1.19__py3-none-any.whl → 0.1.21__py3-none-any.whl

ararpy/smp/plots.py

@@ -89,27 +89,27 @@ def set_plot_data(sample: Sample, isInit: bool = True, isIsochron: bool = True,
 # =======================
 # Initialize plot data
 # =======================
-def initial_plot_data(sample: Sample):
+def initial_plot_data(smp: Sample):
     """
     Assign initial data for plots
     Parameters
     ----------
-    sample : Sample instance
+    smp : Sample instance
 
     Returns
     -------
     None
     """
     for key, val in ISOCHRON_INDEX_DICT.items():
-        figure = basic.get_component_byid(sample, key)
+        figure = basic.get_component_byid(smp, key)
         try:
             # data = [x, sx, y, sy, (z, sz,) r1, (r2, r3,), index from 1]
-            figure.data = sample.IsochronValues[val['data_index'][0]:val['data_index'][1]] + \
-                          [[i + 1 for i in range(len(sample.SequenceName))]]
+            figure.data = smp.IsochronValues[val['data_index'][0]:val['data_index'][1]] + \
+                          [[i + 1 for i in range(len(smp.SequenceName))]]
         except (Exception, BaseException):
             print(traceback.format_exc())
             figure.data = [[]] * (val['data_index'][1] - val['data_index'][0]) + \
-                          [[i + 1 for i in range(len(sample.SequenceName))]]
+                          [[i + 1 for i in range(len(smp.SequenceName))]]
         finally:
             # Ellipse
             if key != 'figure_7':
@@ -122,51 +122,62 @@ def initial_plot_data(sample: Sample):
     # Set age spectra lines
     # Try to calculate total gas age
     try:
-        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)
+        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
+        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 = basic.calc_age(total_f[:2], smp=sample)
+        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
-    sample.Info.results.age_spectra['TGA'].update(
+    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(sample.DegasValues[24])}
+         's1': total_age[1], 's2': total_age[2], 's3': total_age[3], 'Num': len(smp.DegasValues[24])}
     )
     try:
-        sample.AgeSpectraPlot.data = calc.spectra.get_data(
-            *sample.ApparentAgeValues[2:4], sample.ApparentAgeValues[7])
-        sample.AgeSpectraPlot.data = calc.arr.transpose(sample.AgeSpectraPlot.data)
+        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())
-        sample.AgeSpectraPlot.data = []
+        smp.AgeSpectraPlot.data = []
 
     # Degassing plot
     try:
-        if not hasattr(sample, 'DegasPatternPlot'):
-            setattr(sample, 'DegasPatternPlot', Plot(id='figure_8', name='Degas Pattern Plot'))
+        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]
-        sample.DegasPatternPlot.data = [
-            isotope_percentage(sample.DegasValues[0]),  # Ar36a
-            isotope_percentage(sample.DegasValues[8]),  # Ar37Ca
-            isotope_percentage(sample.DegasValues[10]),  # Ar38Cl
-            isotope_percentage(sample.DegasValues[20]),  # Ar39K
-            isotope_percentage(sample.DegasValues[24]),  # Ar40r
-            isotope_percentage(sample.CorrectedValues[0]),  # Ar36
-            isotope_percentage(sample.CorrectedValues[2]),  # Ar37
-            isotope_percentage(sample.CorrectedValues[4]),  # Ar38
-            isotope_percentage(sample.CorrectedValues[6]),  # Ar39
-            isotope_percentage(sample.CorrectedValues[8]),  # Ar40
+        smp.DegasPatternPlot.data = [
+            isotope_percentage(smp.DegasValues[0]),  # Ar36a
+            isotope_percentage(smp.DegasValues[8]),  # Ar37Ca
+            isotope_percentage(smp.DegasValues[10]),  # Ar38Cl
+            isotope_percentage(smp.DegasValues[20]),  # Ar39K
+            isotope_percentage(smp.DegasValues[24]),  # Ar40r
+            isotope_percentage(smp.CorrectedValues[0]),  # Ar36
+            isotope_percentage(smp.CorrectedValues[2]),  # Ar37
+            isotope_percentage(smp.CorrectedValues[4]),  # Ar38
+            isotope_percentage(smp.CorrectedValues[6]),  # Ar39
+            isotope_percentage(smp.CorrectedValues[8]),  # Ar40
         ]
-        sample.DegasPatternPlot.info = [True] * 10
+        smp.DegasPatternPlot.info = [True] * 10
     except Exception as e:
         print(traceback.format_exc())
         pass
 
     # Set age distribution plot data
     try:
-        recalc_agedistribution(sample)
+        recalc_agedistribution(smp)
     except Exception as e:
         print(traceback.format_exc())
 
@@ -390,7 +401,7 @@ def recalc_plateaus(sample: Sample, **kwargs):
     if sample.Info.sample.type == "Standard":
         return recalc_j_plateaus(sample, **kwargs)
     if sample.Info.sample.type == "Air":
-        return recalc_j_plateaus(sample, **kwargs)
+        return recalc_mdf_plateaus(sample, **kwargs)
 
 
 def recalc_age_plateaus(sample: Sample, **kwargs):
@@ -405,6 +416,9 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
     -------
     None
     """
+    ar39k, sar39k = calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor)
+    ar40r, sar40r = sample.DegasValues[24:26]
+    ar40rar39k = calc.arr.div([ar40r, sar40r], [ar39k, sar39k])
     params_initial_ratio = calc.arr.partial(sample.TotalParam, cols=list(range(115, 120)))
     ratio_set1 = [[], []]
     ratio_set2 = [[], []]
@@ -430,10 +444,12 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
             ratio_set2[0].append(298.56)
             ratio_set2[1].append(0.31)
 
-    # Get ages and line data points for each set
+    # Weighted mean ages of two sets with the given initial ratios
     try:
-        set1_res, set1_age, set1_data = \
-            get_plateau_results(sample, sample.SelectedSequence1, calc_ar40ar39(*ratio_set1, smp=sample), **kwargs)
+        set1_res, set1_age, set1_data = get_plateau_results(
+            sample, sample.SelectedSequence1, calc_ar40ar39(*ratio_set1, smp=sample),
+            ar39k_percentage=np.array(ar39k) / np.sum(ar39k),
+            **kwargs)
     except ValueError:
         # print(traceback.format_exc())
         pass
@@ -443,8 +459,10 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
         sample.AgeSpectraPlot.set1.data = calc.arr.transpose(set1_data)
         sample.AgeSpectraPlot.text1.text = ""  # 注意和js的配合，js那边根据text是否为空判断是否重新生成文字
     try:
-        set2_res, set2_age, set2_data = \
-            get_plateau_results(sample, sample.SelectedSequence2, calc_ar40ar39(*ratio_set2, smp=sample), **kwargs)
+        set2_res, set2_age, set2_data = get_plateau_results(
+            sample, sample.SelectedSequence2, calc_ar40ar39(*ratio_set2, smp=sample),
+            ar39k_percentage=np.array(ar39k) / np.sum(ar39k),
+            **kwargs)
     except ValueError:
         # print(traceback.format_exc())
         pass
@@ -454,16 +472,18 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
         sample.AgeSpectraPlot.set2.data = calc.arr.transpose(set2_data)
         sample.AgeSpectraPlot.text2.text = ""  # 注意和js的配合，js那边根据text是否为空判断是否重新生成文字
 
-    # Get weighted mean ages of two sets
+    # Weighted mean ages of two sets with 298.56 (defoult air ratio)
     try:
-        set1_res = get_wma_results(sample, sample.SelectedSequence1)
+        set1_res = get_wma_results(
+            sample, sample.SelectedSequence1, ar40rar39k=ar40rar39k, ar39k_percentage=np.array(ar39k) / np.sum(ar39k))
     except ValueError:
         pass
         # raise ValueError(f"Set 1 WMA calculation error.")
     else:
         sample.Info.results.age_spectra.update({0: set1_res})
     try:
-        set2_res = get_wma_results(sample, sample.SelectedSequence2)
+        set2_res = get_wma_results(
+            sample, sample.SelectedSequence2, ar40rar39k=ar40rar39k, ar39k_percentage=np.array(ar39k) / np.sum(ar39k))
     except ValueError:
         pass
         # raise ValueError(f"Set 2 WMA calculation error.")
@@ -543,6 +563,41 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
     # # """end"""
 
 
+def recalc_mdf_plateaus(sample: Sample, **kwargs):
+    """
+    Calculate age plateaus results
+    Parameters
+    ----------
+    sample : sample instance
+    kwargs : optional args, keys in [r1, sr1, r2, sr2]
+
+    Returns
+    -------
+    None
+    """
+    ar36a, sar36a = calc.arr.mul(sample.DegasValues[0:2], sample.NormalizeFactor)
+    ar40aar36a = sample.ApparentAgeValues[0:2]
+    mdf = sample.ApparentAgeValues[2:4]
+
+    try:
+        set1_res, _, set1_data = get_plateau_results(sample, sample.SelectedSequence1, ar40rar39k=ar40aar36a)
+    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 = ""
+
+    try:
+        set2_res, _, set2_data = get_plateau_results(sample, sample.SelectedSequence2, ar40rar39k=ar40aar36a)
+    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 = ""
+
+
 def calc_ar40ar39(r, sr, smp):
     """
     Calculate Ar40r / Ar39K based on passed initial ratio.
@@ -558,7 +613,7 @@ def calc_ar40ar39(r, sr, smp):
     """
     try:
         ar36a = np.array(smp.DegasValues[0:2])
-        ar39k = smp.DegasValues[20:22]
+        ar39k = calc.arr.mul(smp.DegasValues[20:22], smp.NormalizeFactor)
         ar40 = smp.CorrectedValues[8:10]
         ar40k = smp.DegasValues[30:32]
         size = ar36a.shape[-1]
@@ -568,8 +623,6 @@ def calc_ar40ar39(r, sr, smp):
             ratio = np.array([r, sr])
         else:
             raise ValueError(f"Initial ratio is unsupported.")
-        # print(f"{ratio = }")
-        # print(f"{ar36a = }")
         ar40a = calc.arr.mul(ar36a, ratio)
         ar40r = calc.arr.sub(ar40, ar40k, ar40a)
         ar40rar39k: list = calc.arr.div(ar40r, ar39k)
@@ -579,20 +632,20 @@ def calc_ar40ar39(r, sr, smp):
         return ar40rar39k
 
 
-def get_plateau_results(sample: Sample, sequence: list, ar40rar39k: list = None,
+def get_plateau_results(smp: Sample, sequence: list, ar40rar39k: list = None,
                         ar39k_percentage: list = None, **kwargs):
     """
     Get initial ratio re-corrected plateau results
     Parameters
     ----------
-    sample : sample instance
+    smp : sample instance
     sequence : data slice index
     ar40rar39k :
     ar39k_percentage : Ar39K released
 
     Returns
     -------
-    three itmes tuple, result dict, age, and plot data, results keys = [
+    three items tuple, result dict, age, and plot data, results keys = [
         'F', 'sF', 'Num', 'MSWD', 'Chisq', 'Pvalue',
         'age', 's1', 's2', 's3', 'Ar39', 'rs'
     ]
@@ -609,31 +662,40 @@ def get_plateau_results(sample: Sample, sequence: list, ar40rar39k: list = None,
     if len(sequence) == 0:
         return plateau_res, [], []
     if ar40rar39k is None:
-        ar40rar39k = sample.ApparentAgeValues[0:2]
+        ar40rar39k = smp.ApparentAgeValues[0:2]
     if ar39k_percentage is None:
-        ar39k_percentage = sample.ApparentAgeValues[7]
+        ar39k_percentage = smp.ApparentAgeValues[7]
+
+    if str(smp.Info.sample.type).lower() == "unknown":
+        handle = basic.calc_age
+    elif str(smp.Info.sample.type).lower() == "standard":
+        handle = basic.calc_j
+    elif str(smp.Info.sample.type).lower() == "air":
+        handle = basic.calc_mdf
+    else:
+        raise TypeError(f"Sample type is not supported: {smp.Info.sample.type}")
 
-    age = basic.calc_age(ar40ar39=ar40rar39k, smp=sample)[0:2]
+    age = handle(ar40ar39=ar40rar39k, smp=smp)[0:2]
     plot_data = calc.spectra.get_data(*age, ar39k_percentage, indices=sequence, **kwargs)
     f_values = _get_partial(sequence, *ar40rar39k)
     age = _get_partial(sequence, *age)
     sum_ar39k = sum(_get_partial(sequence, ar39k_percentage)[0])
     wmf = calc.arr.wtd_mean(*f_values)
-    wmage = basic.calc_age(wmf[0:2], smp=sample)
+    wmage = handle(wmf[0:2], smp=smp)
 
-    plateau_res.update(dict(zip(
-        plateau_res_keys, [*wmf, *wmage, sum_ar39k, np.nan]
-    )))
+    plateau_res.update(dict(zip(plateau_res_keys, [*wmf, *wmage, sum_ar39k, np.nan])))
     return plateau_res, age, plot_data
 
 
-def get_wma_results(sample: Sample, sequence: list):
+def get_wma_results(sample: Sample, sequence: list, ar40rar39k: list = None, ar39k_percentage: list = None):
     """
     Get initial ratio re-corrected plateau results
     Parameters
     ----------
     sample : sample instance
     sequence : data slice index
+    ar40rar39k :
+    ar39k_percentage :
 
     Returns
     -------
@@ -642,6 +704,11 @@ def get_wma_results(sample: Sample, sequence: list):
         'age', 's1', 's2', 's3', 'Ar39', 'rs'
     ]
     """
+    if ar40rar39k is None:
+        ar40rar39k = sample.ApparentAgeValues[0:2]
+    if ar39k_percentage is None:
+        ar39k_percentage = sample.ApparentAgeValues[7]
+
     spectra_res = initial.SPECTRA_RES.copy()
     # spectra_res = initial.SPECTRA_RES
 
@@ -649,9 +716,9 @@ def get_wma_results(sample: Sample, sequence: list):
         return [arg[min(points): max(points) + 1] for arg in args]
 
     if len(sequence) > 0:
-        sum_ar39k = sum(_get_partial(sequence, sample.ApparentAgeValues[7])[0])
-        fs = _get_partial(sequence, sample.ApparentAgeValues[0])[0]
-        sfs = _get_partial(sequence, sample.ApparentAgeValues[1])[0]
+        sum_ar39k = sum(_get_partial(sequence, ar39k_percentage)[0])
+        fs = _get_partial(sequence, ar40rar39k[0])[0]
+        sfs = _get_partial(sequence, ar40rar39k[1])[0]
 
         wmf, swmf, num, mswd, chisq, p = calc.arr.wtd_mean(fs, sfs)
         age, s1, s2, s3 = basic.calc_age([wmf, swmf], smp=sample)
@@ -665,13 +732,11 @@ def get_wma_results(sample: Sample, sequence: list):
 
 def recalc_j_plateaus(sample: Sample, **kwargs):
 
-    print(f"Recalc J plateau")
-
+    ar40rar39k = sample.ApparentAgeValues[0:2]
     j = sample.ApparentAgeValues[2:4]
 
     try:
-        set1_res, _, set1_data = \
-            get_j_plateau_results(sample, sample.SelectedSequence1, j)
+        set1_res, _, set1_data = get_plateau_results(sample, sample.SelectedSequence1, ar40rar39k=ar40rar39k)
     except ValueError:
         pass
     else:
@@ -680,8 +745,7 @@ def recalc_j_plateaus(sample: Sample, **kwargs):
         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_j_plateau_results(sample, sample.SelectedSequence2, j)
+        set2_res, _, set2_data = get_plateau_results(sample, sample.SelectedSequence2, ar40rar39k=ar40rar39k)
     except ValueError:
         pass
     else:
@@ -690,31 +754,6 @@ def recalc_j_plateaus(sample: Sample, **kwargs):
         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 get_j_plateau_results(sample: Sample, sequence: list, j: list, ar39k_percentage: list = None):
-
-    def _get_partial(points, *args):
-        # return [arg[min(points): max(points) + 1] for arg in args]
-        return [[arg[i] for i in points] for arg in args]
-
-    if ar39k_percentage is None:
-        ar39k_percentage = sample.ApparentAgeValues[7]
-    sum_ar39k = sum(_get_partial(sequence, ar39k_percentage)[0])
-
-    j_values = _get_partial(sequence, *j)
-    wmj = calc.arr.wtd_mean(*j_values)
-    plot_data = [[sum(ar39k_percentage[:min(sequence)]), sum(ar39k_percentage[:max(sequence) + 1])],
-                 [wmj[0], wmj[0]]]
-
-    plateau_res_keys = [
-        'F', 'sF', 'Num', 'MSWD', 'Chisq', 'Pvalue', 'age', 's1', 's2', 's3', 'Ar39',
-        'rs',  # 'rs' means relative error of the total sum
-    ]
-    plateau_res = dict(zip(plateau_res_keys, [np.nan for i in plateau_res_keys]))
-    plateau_res.update(dict(zip(plateau_res_keys, [*wmj, np.nan, np.nan, np.nan, np.nan, sum_ar39k, np.nan])))
-
-    return plateau_res, 0, plot_data
-
-
 # =======================
 # Age Distribution Plot
 # =======================

ararpy/smp/sample.py

@@ -54,7 +54,21 @@ PUBLISH_TABLE_HEADERS = [
     'Sequence', '',  # 0-1
     '\u00B3\u2076Ar[a]', '\u00B3\u2077Ar[Ca]', '\u00B3\u2078Ar[Cl]',  # 2-4
     '\u00B3\u2079Ar[K]', '\u2074\u2070Ar[r]',  # 5-6
-    'Apparent Age', '1\u03C3', '\u2074\u2070Arr%', '\u00B3\u2079ArK%',  # 7-10
+    'Apparent Age', '1\u03C3', '\u2074\u2070Ar[r]%', '\u00B3\u2079Ar[K]%',  # 7-10
+    'Ca/K', '1\u03C3',  # 11-12
+]
+PUBLISH_TABLE_HEADERS_AIR = [
+    'Sequence', '',  # 0-1
+    '\u00B3\u2076Ar[a]', '\u00B3\u2077Ar[Ca]', '\u00B3\u2078Ar[Cl]',  # 2-4
+    '\u00B3\u2079Ar[K]', '\u2074\u2070Ar[r]',  # 5-6
+    'MDF', '1\u03C3', '\u2074\u2070Ar[r]%', '\u00B3\u2076Ar%',  # 7-10
+    'Ca/K', '1\u03C3',  # 11-12
+]
+PUBLISH_TABLE_HEADERS_STD = [
+    'Sequence', '',  # 0-1
+    '\u00B3\u2076Ar[a]', '\u00B3\u2077Ar[Ca]', '\u00B3\u2078Ar[Cl]',  # 2-4
+    '\u00B3\u2079Ar[K]', '\u2074\u2070Ar[r]',  # 5-6
+    'J', '1\u03C3', '\u2074\u2070Ar[r]%', '\u00B3\u2076Ar%',  # 7-10
     'Ca/K', '1\u03C3',  # 11-12
 ]
 SPECTRUM_TABLE_HEADERS = [
@@ -63,6 +77,18 @@ SPECTRUM_TABLE_HEADERS = [
     'Apparent Age', '1\u03C3', '1\u03C3', '1\u03C3',  # 4-7
     '\u2074\u2070Ar[r]%', '\u00B3\u2079Ar[K]%',  # 8-9
 ]
+SPECTRUM_TABLE_HEADERS_AIR = [
+    'Sequence', '',  # 0-1
+    '\u2074\u2070Ar/\u00B3\u2076Ar', '1\u03C3',  # 2-3
+    'MDF', '1\u03C3', '1\u03C3', '1\u03C3',  # 4-7
+    '\u2074\u2070Ar[r]%', '\u00B3\u2076Ar%',  # 8-9
+]
+SPECTRUM_TABLE_HEADERS_STD = [
+    'Sequence', '',  # 0-1
+    '\u2074\u2070Ar/\u00B3\u2076Ar', '1\u03C3',  # 2-3
+    'J', '1\u03C3', '1\u03C3', '1\u03C3',  # 4-7
+    '\u2074\u2070Ar[r]%', '\u00B3\u2076Ar%',  # 8-9
+]
 ISOCHRON_TABLE_HEADERS = [
     'Sequence', '', 'Mark',  # 0-2
     '\u00B3\u2079Ar[K]/\u00B3\u2076Ar[a]', '1\u03C3',  # 3-4
@@ -108,16 +134,16 @@ TOTAL_PARAMS_HEADERS = [
     'Decay Activity \u2074\u2070K(\u03B2<sup>-</sup>)', '%1\u03C3',  # 54-55
     'Decay Activity \u2074\u2070K(\u03B2<sup>+</sup>)', '%1\u03C3',  # 56-57
     '\u00B3\u2076Cl/\u00B3\u2078Cl Productivity', '%1\u03C3',  # 58-59
-    'Std Name', 'Std Age', '1\u03C3', '\u2074\u2070Ar%', '1\u03C3', 'K%', '1\u03C3',
-    '\u2074\u2070Ar<sup>*</sup>/K', '1\u03C3',  # 60-68
+    'Std Name', 'Std Age', '1\u03C3', '\u2074\u2070Ar%', '1\u03C3', 'K%', '1\u03C3',  # 60-66
+    '\u2074\u2070Ar<sup>*</sup>/K', '1\u03C3',  # 67-68
     'J', '%1\u03C3', 'MDF', '%1\u03C3',  # 69-72
-    'Mass \u00B3\u2076Ar', '%1\u03C3', 'Mass \u00B3\u2077Ar', '%1\u03C3',
-    'Mass \u00B3\u2078Ar', '%1\u03C3', 'Mass \u00B3\u2079Ar', '%1\u03C3',
-    'Mass \u2074\u2070', '%1\u03C3', 'K Mass', '%1\u03C3',  # 73-84
+    'Mass \u00B3\u2076Ar', '%1\u03C3', 'Mass \u00B3\u2077Ar', '%1\u03C3',  # 73-76
+    'Mass \u00B3\u2078Ar', '%1\u03C3', 'Mass \u00B3\u2079Ar', '%1\u03C3',  # 77-80
+    'Mass \u2074\u2070', '%1\u03C3', 'K Mass', '%1\u03C3',  # 81-84
     'No', '%1\u03C3', 'Year', '%1\u03C3', '\u2074\u2070K/K', '%1\u03C3',
-    '\u00B3\u2075/\u00B3\u2077Cl', '%1\u03C3', 'HCl/Cl', '%1\u03C3',  # 85-94
-    '\u2074\u2070Ar/\u00B3\u2076Ar air', '%1\u03C3',
-    '\u00B3\u2078Ar/\u00B3\u2076Ar air', '%1\u03C3',  # 95-98
+    '\u00B3\u2075Cl/\u00B3\u2077Cl', '%1\u03C3', 'HCl/Cl', '%1\u03C3',  # 85-94
+    '\u2074\u2070Ar/\u00B3\u2076Ar air', '%1\u03C3',  # 95-96
+    '\u00B3\u2078Ar/\u00B3\u2076Ar air', '%1\u03C3',  # 97-98
     'Isochron Fitting', 'Convergence', 'Iteration', 'Discrimination',  # 99-102
     'Not Zero', 'Corr Blank', 'Corr Discr', 'Corr \u00B3\u2077Ar Decay',  # 103-106
     'Corr \u00B3\u2079Ar Decay',  # 107
@@ -222,8 +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',
@@ -259,19 +285,26 @@ TOTAL_PARAMS_SHORT_HEADERS = [
     '40Gain', '%1s',  # 136-137
 ]
 
-DEFAULT_PLOT_STYLES = {
+DEFAULT_PLOT_STYLES = lambda sample_type, age_unit: {
     'figure_1': {
-        'id': 'figure_1', 'name': 'Age Spectra', 'type': 'spectra', 'attr_name': 'AgeSpectraPlot',
+        'id': 'figure_1', 'name': 'Age Spectra' if sample_type == "Unknown" else 'J Spectra' if sample_type == "Standard" else "MDF" if sample_type == "Air" else "Unkown Title",
+        'type': 'spectra', 'attr_name': 'AgeSpectraPlot',
         'rightside_text': [],
-        'title': {'id': 'title', 'show': True, 'text': 'Age Spectra', 'position': 'center',
+        'title': {'id': 'title', 'show': True,
+                  'text': 'Age Spectra' if sample_type == "Unknown" else 'J Spectra' if sample_type == "Standard" else "MDF" if sample_type == "Air" else "Unkown Title",
+                  'position': 'center',
                   'font_size': 18, 'color': '#333333', 'opacity': 1, 'type': 'text', 'font_weight': 'bolder',
                   'font_family': 'Microsoft Sans Serif', },
         'xaxis': {
-            'title': {'text': 'Cumulative {sup|39}Ar Released (%)', 'type': 'text', }, 'type': 'axis',
+            'title': {'text': 'Cumulative {sup|39}Ar Released (%)' if sample_type == "Unknown" or sample_type == "Standard" else "Cumulative {sup|36}Ar Released (%)" if sample_type == "Air" else "Unkown Title",
+                      'type': 'text', }, 'type': 'axis',
             'min': 0, 'max': 100, 'show_splitline': False, 'ticks_inside': False, 'split_number': 5, 'interval': 10,
         },
         'yaxis': {
-            'title': {'text': 'Apparent Age (Ma)', 'type': 'text', }, 'type': 'axis',
+            'title': {
+                'text': f'Apparent Age ({age_unit})' if sample_type == "Unknown" else 'J Values' if sample_type == "Standard" else "MDF" if sample_type == "Air" else "Unkown Title",
+                'type': 'text',
+            }, 'type': 'axis',
             'min': 0, 'max': 100, 'show_splitline': False, 'ticks_inside': False, 'split_number': 5, 'interval': 10,
         },
         'set1': {'id': 'Points Set 1', 'type': 'set', },
@@ -743,7 +776,7 @@ DEFAULT_PLOT_STYLES = {
     },
 }
 
-VERSION = '20250321'
+VERSION = '20250404'
 
 NAMED_DICT = {
     "unknown": {"header": SAMPLE_INTERCEPT_HEADERS.copy()},
@@ -812,6 +845,7 @@ class Sample:
         self.SelectedSequence2 = []
         self.UnselectedSequence = []
         self.IsochronMark = []
+        self.NormalizeFactor = [[], []]
 
         # Tables and Plots
         self.UnknownTable = Table()
@@ -847,8 +881,10 @@ class Sample:
         # self.__version = '20240730'  # change parameter table for thermo calculation
         # self.__version = '20241028'  # gain correction
         # self.__version = '20250102'  # gain correction to blanks
+        # self.__version = '20250301'  # update sample info
         # self.__version = '20250321'  # error sigma adjustment
-        self.__version = '20250301'  # update sample info
+        # self.__version = '20250328'  # Experiment info
+        self.__version = '20250404'  # J normalization factor
 
     @property
     def version(self):
@@ -930,7 +966,7 @@ class Sample:
 
     def show_data(self): ...
 
-    def set_params(self, params: Union[List, str], flag: Optional[str] = None): ...
+    def set_params(self, params: Union[List, str], flag: Optional[str] = None, rows: Optional[List] = None): ...
 
     def set_info(self, info: dict): ...
 
@@ -938,6 +974,8 @@ class Sample:
 
     def to_pdf(self, file_path: str, figure: str = "figure_3"): ...
 
+    def to_excel(self, file_path: str, *args, **kwargs): ...
+
 
 class Table:
     def __init__(self, id='', name='Table', colcount=None, rowcount=None, header=None,

ararpy/smp/style.py

@@ -19,13 +19,26 @@ Sample = samples.Sample
 Table = samples.Table
 Plot = samples.Plot
 
-TABLEHEADER = lambda index: [
-    '',
-    samples.SAMPLE_INTERCEPT_HEADERS, samples.BLANK_INTERCEPT_HEADERS,
-    samples.CORRECTED_HEADERS, samples.DEGAS_HEADERS, samples.PUBLISH_TABLE_HEADERS,
-    samples.SPECTRUM_TABLE_HEADERS, samples.ISOCHRON_TABLE_HEADERS,
-    samples.TOTAL_PARAMS_HEADERS
-][index]
+TABLEHEADER = lambda sample_type, index: {
+    'Unknown': ['',
+                samples.SAMPLE_INTERCEPT_HEADERS, samples.BLANK_INTERCEPT_HEADERS,
+                samples.CORRECTED_HEADERS, samples.DEGAS_HEADERS, samples.PUBLISH_TABLE_HEADERS,
+                samples.SPECTRUM_TABLE_HEADERS, samples.ISOCHRON_TABLE_HEADERS,
+                samples.TOTAL_PARAMS_HEADERS
+                ],
+    'Standard': ['',
+                samples.SAMPLE_INTERCEPT_HEADERS, samples.BLANK_INTERCEPT_HEADERS,
+                samples.CORRECTED_HEADERS, samples.DEGAS_HEADERS, samples.PUBLISH_TABLE_HEADERS_STD,
+                samples.SPECTRUM_TABLE_HEADERS_STD, samples.ISOCHRON_TABLE_HEADERS,
+                samples.TOTAL_PARAMS_HEADERS
+                ],
+    'Air': ['',
+            samples.SAMPLE_INTERCEPT_HEADERS, samples.BLANK_INTERCEPT_HEADERS,
+            samples.CORRECTED_HEADERS, samples.DEGAS_HEADERS, samples.PUBLISH_TABLE_HEADERS_AIR,
+            samples.SPECTRUM_TABLE_HEADERS_AIR, samples.ISOCHRON_TABLE_HEADERS,
+            samples.TOTAL_PARAMS_HEADERS
+            ],
+}[sample_type][index]
 
 
 # =======================
@@ -58,13 +71,6 @@ def set_plot_style(smp: Sample):
                 setattr(figure, 'title', Plot.Text())
             setattr(getattr(figure, 'title'), 'text', f"{suffix} {getattr(figure, 'name', '')}")
 
-    age_unit = "Undefined"
-    try:
-        age_unit = str(smp.Info.preference['ageUnit']).capitalize()
-    except:
-        print(traceback.format_exc())
-    smp.AgeSpectraPlot.yaxis.title.text = f"Apparent Age ({age_unit})"
-
 
 def reset_plot_scale(smp: Sample, only_figure: str = None):
     """
@@ -160,7 +166,8 @@ def reset_text(smp: Sample, only_figure: str = None):
     -------
     None
     """
-    for figure_id in list(samples.DEFAULT_PLOT_STYLES.keys()):
+    default_styles = initial.get_default_plot_style(smp)
+    for figure_id in list(default_styles.keys()):
         if only_figure is not None and figure_id != only_figure:
             continue
         figure = basic.get_component_byid(smp, figure_id)
@@ -190,7 +197,7 @@ def set_table_style(sample: Sample):
     """
     for key, comp in basic.get_components(sample).items():
         if isinstance(comp, Table):
-            comp.header = TABLEHEADER(index=int(comp.id))
+            comp.header = TABLEHEADER(sample_type=sample.Info.sample.type, index=int(comp.id))
             comp.set_coltypes()
             # comp.colcount = len(comp.header)
             # comp.coltypes = [{'type': 'numeric'}] * (comp.colcount)

{ararpy-0.1.19.dist-info → ararpy-0.1.21.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.19
+Version: 0.1.21
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu