ararpy 0.1.197__py3-none-any.whl → 0.1.199__py3-none-any.whl

ararpy/__init__.py

@@ -16,7 +16,7 @@ from . import calc, smp, files, thermo, test
 """ Information """
 
 name = 'ararpy'
-version = '0.1.197'
+version = '0.1.199'
 __version__ = version
 full_version = version
 last_update = '2024-03-28'

ararpy/calc/age.py

@@ -67,8 +67,6 @@ def calc_age_min(F, sF, **kwargs) -> tuple:
     # Kp = arr.array_as_float(kwargs.pop('Kp'))
     # sKp = arr.array_as_float(kwargs.pop('sKp') * Kp / 100)
 
-    print(f"{t = }, {st = }")
-
     # recalculation using Min et al.(2000) equation
     # lmd = A * W * Y / (f * No)
     V = f * No / ((Ab + Ae) * W * Y)

ararpy/calc/arr.py

@@ -67,10 +67,11 @@ def div(a, b):
     n = np.shape([a, b])[-1]
     k0, k1 = [], []
     for i in range(n):
-        k0.append(np.divide(a[0][i], b[0][i]))
-        k1.append(
-            (np.divide(a[1][i] ** 2, b[0][i] ** 2) +
-             np.divide(a[0][i] ** 2 * b[1][i] ** 2, b[0][i] ** 4)) ** .5)
+        try:
+            k0.append(np.divide(a[0][i], b[0][i]))
+            k1.append((np.divide(a[1][i] ** 2, b[0][i] ** 2) + np.divide(a[0][i] ** 2 * b[1][i] ** 2, b[0][i] ** 4)) ** .5)
+        except TypeError as e:
+            raise TypeError(f"a = {a[0][i]}, b = {b[0][i]},  {e}")
     return [k0, k1]
 
 

ararpy/calc/corr.py

@@ -72,18 +72,18 @@ def mdf(rm: float, srm: float, m1: float, m2: float, ra: float = 298.56,
             v3 = err.div((np.log(ra / rm), v1), (np.log(ratio_m), v2))
             k4 = err.div((np.log(ra / rm) / np.log(ratio_m), v3), (m1, sm1))
         except Exception:
-            k3, k4 = "Null", "Null"
+            k3, k4 = 0, 0
         # pow
         try:
             k5 = pow((ra / rm), (1 / delta_m))  # Renne2009, B.D. Turrin2010
             k6 = err.pow((ra / rm, err.div((ra, sra), (rm, srm))),
                          (1 / delta_m, err.div((1, 0), (delta_m, sdelta_m))))
         except Exception:
-            k5, k6 = "Null", "Null"
-        return k1, k2, k3, k4, k5, k6
+            k5, k6 = 0, 0
+        return k1, k2, k2, k2, k3, k4, k4, k4, k5, k6, k6, k6
     else:
         mdf_line_2 = (rm / ra - 1) / delta_m  # Ryu et al., 2013
-        return mdf_line_2, 0, 0, 0, 0, 0
+        return mdf_line_2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
 
 
 def discr(a0: list, e0: list, mdf: list, smdf: list, m: list, m40: list,

ararpy/calc/jvalue.py

@@ -36,4 +36,4 @@ def j_value(age, sage, r, sr, f, rsf):
     v2 = sage ** 2 * (f * np.exp(f * age) / r) ** 2
     v3 = sr ** 2 * ((1 - np.exp(f * age)) / r ** 2) ** 2
     k1 = np.sqrt(v1 + v2 + v3)
-    return k0, k1
+    return k0, k1, k1, k1

ararpy/calc/plot.py

@@ -39,8 +39,11 @@ def get_axis_scale(data: list, count=6, increment=None, extra_count=0, min_inter
     """
     if len(data) == 0:
         return 0, 1, 5, 0.2  # Default return
-    _max = float(np.ma.masked_invalid(data).max())
-    _min = float(np.ma.masked_invalid(data).min())
+    _max = np.ma.masked_invalid(data).max()
+    _min = np.ma.masked_invalid(data).min()
+    if isinstance(_max, np.ma.core.MaskedConstant) or isinstance(_min, np.ma.core.MaskedConstant):
+        return 0, 1, 5, 0.2  # Default return
+    _max = float(_max); _min = float(_min)
     interval = (_max - _min) / count
     if interval == 0:
         interval = 10

ararpy/smp/basic.py

@@ -59,24 +59,81 @@ def calc_apparent_ages(smp: Sample):
 
 
 def calc_j(ar40ar39=None, params: dict = None, smp: Sample = None, index: list = None):
-    std_age, std_err = smp.TotalParam[59:61]
-    r, sr = smp.ApparentAgeValues[0:2]  # ar40ar39, error
-    f, rsf = smp.TotalParam[34:36]  # L, sL
-    j, sj = calc.jvalue.j_value(std_age, std_err, r, sr, f, rsf)
-    return [j.tolist(), sj.tolist()]
+    params_index_dict = {
+        34: 'L', 35: 'rsL', 59: 'Age', 60: 'sAge'
+    }
+    if ar40ar39 is None and smp is not None:
+        ar40ar39 = smp.ApparentAgeValues[0:2]  # ar40ar39 air, error
+    if len(np.shape(ar40ar39)) == 1:
+        ar40ar39 = np.reshape(ar40ar39, (2, 1))
+    if index is None:
+        index = list(range(np.shape(ar40ar39)[-1]))
+    if smp is None and params is None:
+        raise ValueError(f"Parameters are required for calculating mdf, or it is empty.")
+    if params is not None:
+        for key, val in params.items():
+            if not isinstance(val, list):
+                params[key] = list(val)
+    if smp is not None:
+        try:
+            params_from_smp = dict(zip(
+                list(params_index_dict.values()),
+                [[smp.TotalParam[i][j] for j in index] for i in params_index_dict.keys()]
+            ))
+        except Exception:
+            print(traceback.format_exc())
+            raise ValueError(f"Parameters cannot be found in the given sample object")
+        if params is not None:
+            params_from_smp.update(params)
+        params = params_from_smp
+
+    j = calc.jvalue.j_value(params['Age'], params['sAge'], *ar40ar39, params['L'], params['rsL'])
+
+    if len(index) == 1:
+        return np.array(j).squeeze().tolist()
+    else:
+        return np.array(j).tolist()
 
 
 def calc_mdf(ar40ar36=None, params: dict = None, smp: Sample = None, index: list = None):
-    std_air, std_err = smp.TotalParam[93:95]
-    m36, sm36 = smp.TotalParam[71:73]
-    m40, sm40 = smp.TotalParam[79:81]
-    air, sair = smp.ApparentAgeValues[0:2]  # ar40ar36 air, error
-    discrimination_method = smp.TotalParam[100]  # L, sL
+    params_index_dict = {
+        71: 'M36', 72: 'sM36', 79: 'M40', 80: 'sM40', 93: 'Air', 94: 'sAir', 100: 'Discr'
+    }
+    if ar40ar36 is None and smp is not None:
+        ar40ar36 = smp.ApparentAgeValues[0:2]  # ar40ar36 air, error
+    if len(np.shape(ar40ar36)) == 1:
+        ar40ar36 = np.reshape(ar40ar36, (2, 1))
+    if index is None:
+        index = list(range(np.shape(ar40ar36)[-1]))
+    if smp is None and params is None:
+        raise ValueError(f"Parameters are required for calculating mdf, or it is empty.")
+    if params is not None:
+        for key, val in params.items():
+            if not isinstance(val, list):
+                params[key] = list(val)
+    if smp is not None:
+        try:
+            params_from_smp = dict(zip(
+                list(params_index_dict.values()),
+                [[smp.TotalParam[i][j] for j in index] for i in params_index_dict.keys()]
+            ))
+        except Exception:
+            print(traceback.format_exc())
+            raise ValueError(f"Parameters cannot be found in the given sample object")
+        if params is not None:
+            params_from_smp.update(params)
+        params = params_from_smp
+
     mdf = []
-    for i in range(len(std_air)):
-        k = calc.corr.mdf(air[i], sair[i], m36[i], m40[i], std_air[i], std_err[i])  # linear, exp, pow
-        mdf.append({"linear": k[0:2], "exp": k[2:4], "pow": k[4:6]}[discrimination_method[i].lower()])
-    return np.transpose(mdf).tolist()
+    for i in range(len(index)):
+        k = calc.corr.mdf(ar40ar36[0][i], ar40ar36[1][i], params['M36'][i], params['M40'][i],
+                          params['Air'][i], params['sAir'][i])  # linear, exp, pow
+        mdf.append({"linear": k[0:4], "exp": k[4:8], "pow": k[8:12]}[params['Discr'][i].lower()])
+
+    if len(index) == 1:
+        return np.transpose(mdf).squeeze().tolist()
+    else:
+        return np.transpose(mdf).tolist()
 
 
 def calc_age(ar40ar39=None, params: dict = None, smp: Sample = None, index: list = None):

ararpy/smp/corr.py

@@ -25,16 +25,15 @@ from .sample import Sample
 def corr_gain(sample: Sample):
     """Blank Correction"""
     corrGain = True
-    gain_corrected = np.zeros([10, len(sample.SequenceName)])
+    gain_corrected = np.zeros([10, sample.Info.experiment.step_num])
     try:
         for i in range(5):
             f, sf = np.array(sample.TotalParam[126 + i * 2:128 + i * 2])
             sf = f * sf / 100
             gain_corrected[i * 2:2 + i * 2] = calc.corr.gain(*sample.SampleIntercept[i * 2:2 + i * 2], f, sf)
-    except Exception as e:
-        print(f"Gain correction failed")
-        print(traceback.format_exc())
-        return
+    except (Exception, BaseException) as e:
+        print(f"Gain correction failed: \n{traceback.format_exc()}")
+        raise
     for i in range(0, 10, 2):
         gain_corrected[i] = [gain_corrected[i][index] if corrGain else j for index, j in enumerate(sample.SampleIntercept[i])]
         gain_corrected[i + 1] = [gain_corrected[i + 1][index] if corrGain else j for index, j in enumerate(sample.SampleIntercept[i + 1])]

ararpy/smp/initial.py

@@ -237,7 +237,7 @@ def initial(smp: Sample):
     return smp
 
 
-def initial_plot_styles(sample: Sample, except_attrs=None):
+def initial_plot_styles(smp: Sample, except_attrs=None):
     """
     Initialize plot components styles based on Default Styles. Except attrs is a list containing attrs
     that are not expected to be initialized.
@@ -261,13 +261,22 @@ def initial_plot_styles(sample: Sample, except_attrs=None):
             for k, v in value.items():
                 set_attr(getattr(obj, name), k, v)
 
-    default_styles = copy.deepcopy(samples.DEFAULT_PLOT_STYLES)
+    default_styles = get_default_plot_style(smp)
     for figure_index, figure_attr in default_styles.items():
-        plot = getattr(sample, figure_attr['attr_name'], Plot())
+        plot = getattr(smp, figure_attr['attr_name'], Plot())
         for key, attr in figure_attr.items():
             set_attr(plot, key, attr)
 
 
+def get_default_plot_style(smp: Sample):
+    sample_type = smp.Info.sample.type
+    try:
+        age_unit = str(smp.Info.preference['ageUnit']).capitalize()
+    except:
+        age_unit = "Undefined"
+    return copy.deepcopy(samples.DEFAULT_PLOT_STYLES(sample_type, age_unit))
+
+
 def re_set_smp(smp: Sample):
     std = initial(Sample())
     basic.get_merged_smp(smp, std)
@@ -296,13 +305,13 @@ def check_version(smp: Sample):
     # 20250404
     doNormalize = True
     v, sv = [], []
-    if smp.Info.sample.type.lower() != "unknown":
+    if smp.Info.sample.type.lower() == "unknown":
         v, sv = smp.TotalParam[67:69]
         sv = np.multiply(v, sv) / 100
-    elif smp.Info.sample.type.lower() != "air":
-        v, sv = smp.TotalParam[95:97]
+    elif smp.Info.sample.type.lower() == "air":
+        v, sv = smp.TotalParam[93:95]
         sv = np.multiply(v, sv) / 100
-    elif smp.Info.sample.type.lower() != "standard":
+    elif smp.Info.sample.type.lower() == "standard":
         v, sv = smp.TotalParam[59:61]
     smp.NormalizeFactor = [
         [1 if v[0] == each or not doNormalize else v[0] / each for each in v],

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 +122,64 @@ 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(
+    print(f"{total_f = }")
+    print(f"{total_age = }")
+    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 +403,7 @@ 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):
@@ -437,7 +450,7 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
     try:
         set1_res, set1_age, set1_data = get_plateau_results(
             sample, sample.SelectedSequence1, calc_ar40ar39(*ratio_set1, smp=sample),
-            ar39k_percentage=np.cumsum(ar39k) / np.sum(ar39k),
+            ar39k_percentage=np.array(ar39k) / np.sum(ar39k),
             **kwargs)
     except ValueError:
         # print(traceback.format_exc())
@@ -450,7 +463,7 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
     try:
         set2_res, set2_age, set2_data = get_plateau_results(
             sample, sample.SelectedSequence2, calc_ar40ar39(*ratio_set2, smp=sample),
-            ar39k_percentage=np.cumsum(ar39k) / np.sum(ar39k),
+            ar39k_percentage=np.array(ar39k) / np.sum(ar39k),
             **kwargs)
     except ValueError:
         # print(traceback.format_exc())
@@ -464,7 +477,7 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
     # Weighted mean ages of two sets with 298.56 (defoult air ratio)
     try:
         set1_res = get_wma_results(
-            sample, sample.SelectedSequence1, ar40rar39k=ar40rar39k, ar39k_percentage=np.cumsum(ar39k) / np.sum(ar39k))
+            sample, sample.SelectedSequence1, ar40rar39k=ar40rar39k, ar39k_percentage=np.array(ar39k) / np.sum(ar39k))
     except ValueError:
         pass
         # raise ValueError(f"Set 1 WMA calculation error.")
@@ -472,7 +485,7 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
         sample.Info.results.age_spectra.update({0: set1_res})
     try:
         set2_res = get_wma_results(
-            sample, sample.SelectedSequence2, ar40rar39k=ar40rar39k, ar39k_percentage=np.cumsum(ar39k) / np.sum(ar39k))
+            sample, sample.SelectedSequence2, ar40rar39k=ar40rar39k, ar39k_percentage=np.array(ar39k) / np.sum(ar39k))
     except ValueError:
         pass
         # raise ValueError(f"Set 2 WMA calculation error.")
@@ -552,6 +565,41 @@ 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.
@@ -586,20 +634,20 @@ 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'
     ]
@@ -616,21 +664,28 @@ 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
 
 
@@ -679,13 +734,11 @@ def get_wma_results(sample: Sample, sequence: list, ar40rar39k: list = None, ar3
 
 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:
@@ -694,8 +747,7 @@ 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:
@@ -704,31 +756,6 @@ 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
@@ -108,12 +134,12 @@ 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\u2075Cl/\u00B3\u2077Cl', '%1\u03C3', 'HCl/Cl', '%1\u03C3',  # 85-94
     '\u2074\u2070Ar/\u00B3\u2076Ar air', '%1\u03C3',  # 95-96
@@ -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', },

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 index, sample_type: {
+    '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-0.1.197.dist-info → ararpy-0.1.199.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.197
+Version: 0.1.199
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.197.dist-info → ararpy-0.1.199.dist-info}/RECORD

@@ -1,15 +1,15 @@
-ararpy/__init__.py,sha256=8plcttpvAfTMr8fz0s7MHbFPgXcSoPKBQySFBrr4q1c,6858
+ararpy/__init__.py,sha256=pYgGSZqLShU0gpXzw0ACDxxCRJRm2Y78YlZxBAkes00,6858
 ararpy/test.py,sha256=4F46-JJ1Ge12HGae0qO44Qc6kiEMHBgn2MsY_5LlHDo,3973
 ararpy/calc/__init__.py,sha256=kUjRuLE8TLuKOv3i976RnGJoEMj23QBZDu37LWs81U4,322
-ararpy/calc/age.py,sha256=mNHsW41vCarKnVqP1s79XWIAAYZjtDEQhsCk0AX2mAA,5817
-ararpy/calc/arr.py,sha256=fe_nCo5zjD8HK9jNIsKXmsRKZ73GMipKK7dogVk5Ubk,15152
+ararpy/calc/age.py,sha256=OcStt55LoYW1brs7a5_Ovv1NUSR5uZVQHDVGGmA_Pqg,5784
+ararpy/calc/arr.py,sha256=jD1Fd0Cj3xc7NqgnG4cp3VWQWxUlV0qCtPBZZokDG8o,15246
 ararpy/calc/basic.py,sha256=uJCCUFaPd9zvfkggrdbFYSGLl2pt7UJ7ENgXanzHy68,4036
-ararpy/calc/corr.py,sha256=Ps_AYgHSYjJNfb1PgPoYBa5eGc6eT9KLIiIiP0Q81as,18725
+ararpy/calc/corr.py,sha256=6hlBlFIM8HyN6CDuWPGqiLpVM88pZJLEuRm8vAyg9ng,18747
 ararpy/calc/err.py,sha256=63LtprqjemlIb1QGDst4Ggcv5KMSDHdlAIL-nyQs1eA,2691
 ararpy/calc/histogram.py,sha256=0GVbDdsjd91KQ1sa2B7NtZ4KGo0XpRIJapgIrzAwQUo,5777
 ararpy/calc/isochron.py,sha256=ej9G2e68k6yszonWHsLcEubh3TA7eh1upTJP_X0ttAA,5726
-ararpy/calc/jvalue.py,sha256=zHUhJ1iYe5mPrY95mGYxoUPAp7hwu4coUgiHKiruKfM,1138
-ararpy/calc/plot.py,sha256=iWxPYIaT0OmJBiho7X9wFY7m-QrvYexu6nWHp24T_VY,1962
+ararpy/calc/jvalue.py,sha256=OL5zPYU8Pac-wOxUWPCgu3onh2n01xDnhpi2mlUsjJM,1146
+ararpy/calc/plot.py,sha256=sUqjKBdAEjFarUoSCLqf8cbUM0rEAdZhmtyXB2K7LkA,2139
 ararpy/calc/raw_funcs.py,sha256=UC01lvA6GyZ5FJv43jgoUULAFoLnZJMxeSa0BeVFCAM,2637
 ararpy/calc/regression.py,sha256=w5kni6LGqvISvlvbBZnJ3N2c5eQjgkz3bBbj0PXPyGs,40251
 ararpy/calc/spectra.py,sha256=_Q23eP9necHlaCoHf3_UfW1N3JmVZj5rcWFro8GS-CA,1995
@@ -41,26 +41,26 @@ ararpy/files/raw_file.py,sha256=5hnZMS7r78lA0ZXrBEN5SWVurQyl0QsHOI9rJz5BQv8,2230
 ararpy/files/xls.py,sha256=DVcZ_yRnc19p-m4leGGjt-YPDpSa2udYKmGyrM0qub0,640
 ararpy/smp/EXPORT_TO_PDF_DATA_PROPERTIES.py,sha256=baDM437tu6hsPv0uYfod0TREXlPd6kvMBFT1S9ZZlkk,3024
 ararpy/smp/__init__.py,sha256=k6_fa27UJsQK7K7oC5GYlwMo6l0Xd8af3QtOrZz2XJk,478
-ararpy/smp/basic.py,sha256=k9Vk_LP6P9HO68gMvPQ-adkvaVXEobg1FY-rF5YG7HQ,22588
+ararpy/smp/basic.py,sha256=slRu3VnnQ4zCaA5GFqcd_N_Pby1_8lIsvhhLhHIJ7As,24821
 ararpy/smp/calculation.py,sha256=LCFJWjLVLEKEQ5b7RFUIxsMahEzgLdodW4kCYXV5Z34,2919
 ararpy/smp/consts.py,sha256=XIdjdz8cYxspG2jMnoItdlUsxr3hKbNFJjMZJh1bpzw,393
-ararpy/smp/corr.py,sha256=ZS9hlRkBYhtuyT7HovEYIjBWBTLkHqJuQzT0vN4GNwg,26503
+ararpy/smp/corr.py,sha256=s1t8VCM7M8WnwfIxWNIRva4ofGJPEPYpKxlb25skH8E,26515
 ararpy/smp/diffusion_funcs.py,sha256=4-PMMIZWzjk2HOYYWNgSp4GmApygp1MmOxJ2g3xrqWc,175049
 ararpy/smp/export.py,sha256=s89L5B1aHoCeJIjcw6nXA6NtV0j_5XXaWnOETWnomCs,115043
 ararpy/smp/info.py,sha256=iKUELm-BuUduDlJKC1d8tKKNHbwwbNmhUg2pi6bcBvA,489
-ararpy/smp/initial.py,sha256=xaKQHEiOv-pS6U3CtVqhXopyFm8vBEr3VFqQnpBZAu0,16929
+ararpy/smp/initial.py,sha256=VSNku2fYD1xGkpHxMqnSJCAhSQawfsDCdqYCxtDJryQ,17196
 ararpy/smp/json.py,sha256=BTZCjVN0aj9epc700nwkYEYMKN2lHBYo-pLmtnz5oHY,2300
-ararpy/smp/plots.py,sha256=mF2ORen2KcPMkWkq-98-2QocmCeA2oJrwT6V_-4cAlE,32495
+ararpy/smp/plots.py,sha256=Grx4GY2kh5KtvAwUV1iIDvQNQSrQd7IaliQ4cT6w01Y,33637
 ararpy/smp/raw.py,sha256=51n-rrbW2FqeZHQyevuG7iObPLGvIBzTe414QDVM1FE,6523
-ararpy/smp/sample.py,sha256=FGJ98J_bZr4QY7q3i8VMY_NJKjP83KvhYaIRVLqKcRU,55970
-ararpy/smp/style.py,sha256=Z4exOAdtvw5xwDf6nyIjPxuvww2U5JK6H_Ql02DBSyM,7030
+ararpy/smp/sample.py,sha256=ZOrQt3Ilm6tJbQCwh_btoZOXdkCngZFHCt10Nh0UmpI,57727
+ararpy/smp/style.py,sha256=gCJ3F_vHnetrfbzEt-KgG5clRfosvJ00RJg6tN53QsQ,7678
 ararpy/smp/table.py,sha256=9bNAOqAIOc0nSC3LNeqjJKUYSJSM28Ji3o9VimwMU8A,6645
 ararpy/thermo/__init__.py,sha256=6VBuqTRFl403PVqOuMkVrut0nKaQsAosBmfW91X1dMg,263
 ararpy/thermo/arrhenius.py,sha256=Ass1ichHfqIAtpv8eLlgrUc1UOb3Urh1qzr1E3gLB4U,233
 ararpy/thermo/atomic_level_random_walk.py,sha256=Q97zfe2h2RaxADkoBAqd0uEiP16BFOajrTmXHMkL2EQ,25502
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