ararpy 0.1.1__py3-none-any.whl → 0.1.12__py3-none-any.whl

ararpy/smp/__init__.py

@@ -1,6 +1,6 @@
 
 from . import (
-    sample as samples, consts, json, basic, corr, raw, initial,
+    sample as samples, info, consts, json, basic, corr, raw, initial,
     plots, style, table, calculation, export, diffusion_funcs
 )
 

ararpy/smp/basic.py

@@ -534,10 +534,11 @@ def set_params(smp: Sample, params: Union[List, str], flag: Optional[str] = None
         smp.TotalParam[58:67] = remove_none(smp.TotalParam[58:67], params[4:13], n, 67 - 58)
         smp.TotalParam[97:100] = remove_none(smp.TotalParam[97:100], params[13:16], n, 100 - 97)
         smp.TotalParam[115:120] = remove_none(smp.TotalParam[115:120], params[16:21], n, 120 - 115)
-        smp.TotalParam[120:123] = remove_none(smp.TotalParam[120:123], params[21:24], n, 123 - 120)
+        smp.TotalParam[126:136] = remove_none(smp.TotalParam[126:136], params[21:31], n, 136 - 126)
+        smp.TotalParam[120:123] = remove_none(smp.TotalParam[120:123], params[31:34], n, 123 - 120)
         smp.TotalParam[100:114] = remove_none(
             smp.TotalParam[100:114],
-            [['Linear', 'Exponential', 'Power'][params[24:27].index(True)] if True in params[24:27] else '', *params[27:]], n, 114 - 100)
+            [['Linear', 'Exponential', 'Power'][params[34:37].index(True)] if True in params[34:37] else '', *params[37:]], n, 114 - 100)
     else:
         raise KeyError(f"{flag = } is not supported. It must be 'calc' for Calc Params, "
                        f"'irra' for Irradiation Params, or 'smp' for Sample Params.")

ararpy/smp/calculation.py

@@ -47,6 +47,7 @@ def recalculate(
     re_plot_style
     re_set_table
     re_table_style
+    re_corr_gain
     kwargs
 
     Returns
@@ -59,11 +60,14 @@ def recalculate(
     # print(f"{sample.SelectedSequence1 = }")
     # print(f"{sample.SelectedSequence2 = }")
     # --- initializing ---
+    re_corr_gain = re_corr_blank
     if re_initial:  # 1
         initial.re_set_smp(sample)
     # --- calculating ---
     if re_corr_blank:  # 2
         corr.corr_blank(sample)
+    if re_corr_gain:  # 2 2024-10-04 add
+        corr.corr_gain(sample)
     if re_corr_massdiscr:  # 3
         corr.corr_massdiscr(sample)
     if re_corr_decay:  # 4

ararpy/smp/corr.py

@@ -45,6 +45,32 @@ def corr_blank(sample: Sample):
     sample.CorrectedValues = copy.deepcopy(sample.BlankCorrected)
 
 
+# =======================
+# Corr Blank
+# =======================
+def corr_gain(sample: Sample):
+    """Blank Correction"""
+    corrGain = True
+    # if not corrBlank:
+    #     sample.BlankCorrected = copy.deepcopy(sample.SampleIntercept)
+    #     sample.CorrectedValues = copy.deepcopy(sample.BlankCorrected)
+    #     return
+    gain_corrected = [[]] * 10
+    try:
+        for i in range(5):
+            gain_corrected[i * 2:2 + i * 2] = calc.corr.gain(
+                *sample.BlankCorrected[i * 2:2 + i * 2], *sample.TotalParam[126 + i * 2:128 + i * 2])
+    except Exception as e:
+        print(f"Gain correction failed")
+        print(traceback.format_exc())
+        return
+    for i in range(0, 10, 2):
+        gain_corrected[i] = [gain_corrected[i][index] if corrGain else j for index, j in enumerate(sample.BlankCorrected[i])]
+        gain_corrected[i + 1] = [gain_corrected[i + 1][index] if corrGain else j for index, j in enumerate(sample.BlankCorrected[i + 1])]
+    sample.BlankCorrected = copy.deepcopy(gain_corrected)
+    sample.CorrectedValues = copy.deepcopy(sample.BlankCorrected)
+
+
 # =======================
 # Mass Discrimination
 # =======================

ararpy/smp/diffusion_funcs.py

@@ -167,7 +167,7 @@ class DiffArrmultiFunc(DiffSample):
         print(f"{self.telab = }")
         print(f"{self.tilab = }")
 
-    def main(self):
+    def main(self, **params):
 
         print(f"\n======================================")
         print(f"Run Arrmulti Main | ")
@@ -1436,7 +1436,7 @@ class DiffArrmultiFunc(DiffSample):
         return xran, yran
 
     def arr(self, e, ord, dzx, fmod, f, telab, tilab, xlogd,
-            ns=200, r=1.987e-3, pi=3.141592654, ee=0.4342944879, acut=0, b=1, imp=1):
+            ns=200, r=1.987e-3, pi=3.141592654, ee=0.4342944879, acut=0.5, b=8, imp=2):
 
         # print(f"{e = }")
         # print(f"{ord = }")
@@ -3677,13 +3677,10 @@ class InsideTemperatureCalibration:
 
 
 class SmpTemperatureCalibration:
-    def __init__(self, arr_path="", helix_log_path="", libano_log_path=None,
+    def __init__(self, helix_log_path="", libano_log_path=None,
                  name="smp_example", loc=r'D:\DjangoProjects\webarar\static\settings'):
 
         self.name = name
-        self.smp = ap.from_arr(file_path=arr_path)
-        if isinstance(self.smp, Sample):
-            self.name = self.smp.name()
 
         self.loc = loc
 
@@ -3858,27 +3855,28 @@ class SmpTemperatureCalibration:
 
         file_out.close()
 
+        np.savetxt(os.path.join(self.loc, f"{self.name}-temp.txt"), libano_log, delimiter=',')
+        heating_out = open(os.path.join(self.loc, f"{self.name}-heated-index.txt"), "w")
+        heating_out.writelines([f'{min(i)},{max(i)}\n' for i in yellow_data_index])
+        heating_out.close()
 
-        fig, ax = plt.subplots()
-        fig.set_size_inches(w=12, h=10)
+        plt_plot = False
+        if plt_plot:
 
-        ax.plot(libano_log[0], libano_log[1], c='green')
-        ax.plot(libano_log[0], libano_log[2], c='blue')
-        ax.plot(libano_log[0], libano_log[4], c='red')
-        ax.plot(libano_log[0], libano_log[5], c='red')
-        for i in range(nstep):
-            _index = yellow_data_index[i]
-            ax.plot(libano_log[0, _index], libano_log[4, _index], c='yellow')
-            ax.plot(libano_log[0, _index], libano_log[5, _index], c='yellow')
+            fig, ax = plt.subplots()
+            fig.set_size_inches(w=12, h=10)
 
-        fig.tight_layout()
-        plt.show()
+            ax.plot(libano_log[0], libano_log[1], c='green')
+            ax.plot(libano_log[0], libano_log[2], c='blue')
+            ax.plot(libano_log[0], libano_log[4], c='red')
+            ax.plot(libano_log[0], libano_log[5], c='red')
+            for i in range(nstep):
+                _index = yellow_data_index[i]
+                ax.plot(libano_log[0, _index], libano_log[4, _index], c='yellow')
+                ax.plot(libano_log[0, _index], libano_log[5, _index], c='yellow')
 
-
-        np.savetxt(os.path.join(self.loc, f"{self.name}-temp.txt"), libano_log, delimiter=',')
-        heating_out = open(os.path.join(self.loc, f"{self.name}-heated-index.txt"), "w")
-        heating_out.writelines([','.join([str(j) for j in i]) for i in yellow_data_index])
-        heating_out.close()
+            fig.tight_layout()
+            plt.show()
 
 
         #
@@ -4613,15 +4611,15 @@ def dr2_lovera(f, ti, ar, sar):
     # Lovera
     f = np.array(f)
     ti = np.array(ti)
-    ar = np.array(ar)
-    sar = np.array(sar)
+    # ar = np.array(ar)
+    # sar = np.array(sar)
     ti = ti * 60  # in seconds
     pi = math.pi
     pi = 3.141592654
 
     # sf = sqrt(b ** 2 * siga ** 2 + a ** 2 * sigb ** 2) / (a + b) ** 2
-    sf = [math.sqrt(sar[i + 1:].sum() ** 2 * (sar[:i + 1] ** 2).sum() + ar[:i + 1].sum() ** 2 * (sar[i + 1:] ** 2).sum()) / ar.sum() ** 2 for i in range(len(ar) - 1)]
-    sf.append(0)
+    # sf = [math.sqrt(sar[i + 1:].sum() ** 2 * (sar[:i + 1] ** 2).sum() + ar[:i + 1].sum() ** 2 * (sar[i + 1:] ** 2).sum()) / ar.sum() ** 2 for i in range(len(ar) - 1)]
+    # sf.append(0)
 
     f = np.where(f >= 1, 0.9999999999999999, f)
 
@@ -4631,41 +4629,67 @@ def dr2_lovera(f, ti, ar, sar):
     dr2 = [(dtr2[i] - (dtr2[i - 1] if i > 0 else 0)) / ti[i] * imp ** 2 for i in range(len(dtr2))]
     xlogd = [np.log10(i) for i in dr2]
 
-    wt = errcal(f, ti, a39=ar, sig39=sar)
+    wt = errcal(f, ti, ar, sar)
 
     return dr2, xlogd, wt
 
 
-def dr2_yang(f, ti):
+def dr2_yang(f, ti, ar, sar):
+    """
+
+        if i == 0:
+            dr2[i] = _dr2(f[i]) / ti[i]
+        else:
+            dr2[i] = _dr2((f[i] - f[i - 1]) / (1 - f[i - 1])) / ti[i]
+
+    Parameters
+    ----------
+    f: array NOTE：这里的 f 既不是释放百分数也不是累积百分数，而是各个阶段释放量占其及后续所有气体的分数，即占释放前的比例
+    ti
+
+    Returns
+    -------
+
+    """
     f = np.array(f)
     ti = np.array(ti)
     n = min(len(f), len(ti))
     ti = ti * 60  # in seconds
+    sti = 5.
     pi = math.pi
     pi = 3.141592654
+    ee = 0.4342944819
     dr2 = np.zeros(n)
+    sdr2 = np.zeros(n)
 
-    if f[-1] >= 1:
-        f[-1] = 0.99999999
+    f = np.where(f >= 1, 0.9999999999999999, f)
 
     def _dr2(_fi):
+        # return: dr2, dy/df
         if _fi <= 0.85:
-            return (1 - math.sqrt(1 - pi * _fi / 3)) ** 2 / pi
+            return (1 - math.sqrt(1 - pi * _fi / 3)) ** 2 / pi, 1 / (3 * math.sqrt(1 - pi * _fi / 3)) - 1 / 3
         else:
-            return math.log((1 - _fi) / (6 / pi ** 2)) / - (pi ** 2)
+            return math.log((1 - _fi) / (6 / pi ** 2)) / - (pi ** 2), 1 / (pi ** 2 * (1 - _fi))
 
-    for i in range(len(f)):
-        if i == 0:
-            dr2[i] = _dr2(f[i]) / ti[i]
-        else:
-            dr2[i] = _dr2((f[i] - f[i - 1]) / (1 - f[i - 1])) / ti[i]
+    for i in range(n):
+        dtr2, d = _dr2((f[i] - (f[i-1] if i > 0 else 0)) / (1 - (f[i-1] if i > 0 else 0)))
+        # sf 中 f = (f[i] - f[i - 1]) / (1 - f[i - 1])
+        sf = sum([ar[i] ** 2 * sar[j] ** 2 / sum(ar[i:]) ** 4 for j in range(i+1, n)]) + sum(ar[i+1:]) ** 2 * sar[i] ** 2 / sum(ar[i:]) ** 4
+        sdtr2 = math.sqrt(d ** 2 * sf)
+        dr2[i] = dtr2 / ti[i]
+        sdr2[i] = ap.calc.err.div((dtr2, sdtr2), (ti[i], sti))
+
+    xlogd = np.log(dr2)
+    sxlogd = np.abs(sdr2 / dr2)
 
     print(f"yang {dr2 = }")
+    print(f"yang {xlogd = }")
+    print(f"yang {sxlogd = }")
 
-    return dr2, np.log(dr2)
+    return dr2, xlogd, sxlogd
 
 
-def errcal(f, ti, a39, sig39):
+def errcal(f, ti, ar, sar):
 
     # ns = 200
     # r = 1.987E-3
@@ -4681,9 +4705,9 @@ def errcal(f, ti, a39, sig39):
     sigt0 = 90.
 
     ni = len(f)
-    sumat = sum(a39)
-    sigsm = [i / sumat for i in sig39]
-    siga = [sig39[i] / a39[i] for i in range(ni)]
+    sumat = sum(ar)
+    sigsm = [i / sumat for i in sar]
+    siga = [sar[i] / ar[i] for i in range(ni)]
 
     an1 = math.pi ** 2
     sigat = 0.

ararpy/smp/export.py

@@ -41,6 +41,52 @@ def to_pdf(file_path: str, figure: str, smp: Sample):
     pdf.save(figure=figure)
 
 
+def export_chart_to_pdf(data: dict):
+    # create a canvas
+    cv = pm.Canvas(width=17, height=12, unit="cm", show_frame=True, clip_outside_plot_areas=False)
+    # change frame outline style
+    cv.show_frame(color="grey", line_width=0.5)
+    sc = (*data['xAxis'][0]['extent'], *data['yAxis'][0]['extent'])
+    pt = cv.add_plot_area(name="Plot1", plot_area=(0.15, 0.15, 0.8, 0.8), plot_scale=sc, show_frame=True)
+    # draw axis
+    for stick in data['xAxis'][0]['interval']:
+        start = pt.scale_to_points(stick, sc[2])
+        end = pt.scale_to_points(stick, sc[2])
+        end = (end[0], end[1] - 5)
+        pt.line(start=start, end=end, width=1, line_style="solid", y_clip=False, coordinate="pt", z_index=100)
+        pt.text(x=start[0], y=end[1] - 15, text=f"{stick}", clip=False,
+                coordinate="pt", h_align="middle", z_index=150)
+    for stick in data['yAxis'][0]['interval']:
+        start = pt.scale_to_points(sc[0], stick)
+        end = pt.scale_to_points(sc[0], stick)
+        end = (end[0] - 5, end[1])
+        pt.line(start=start, end=end, width=1, line_style="solid", x_clip=False, coordinate="pt", z_index=100)
+        pt.text(x=end[0] - 5, y=end[1], text=f"{stick}", clip=False,
+                coordinate="pt", h_align="right", v_align="center", z_index=150)
+    # axis titles
+    nameLocation = pt.scale_to_points(sum(sc[:2]) / 2, sc[2])
+    pt.text(x=nameLocation[0], y=nameLocation[1] - 30, text=data['xAxis'][0]['title'], clip=False, coordinate="pt",
+            h_align="middle", v_align="top", z_index=150)
+    nameLocation = pt.scale_to_points(sc[0], sum(sc[2:4]) / 2)
+    pt.text(x=nameLocation[0] - 50, y=nameLocation[1], text=data['yAxis'][0]['title'], clip=False, coordinate="pt",
+            h_align="middle", v_align="bottom", rotate=90, z_index=150)
+    # draw series
+    for se in data['series']:
+        data = se.get('data', [])
+        if 'line' in se['type']:
+            for index in range(1, len(data)):
+                pt.line(start=data[index - 1], end=data[index], width=1, line_style='solid', name=se['name'],
+                        color=se.get('color', 'black'), clip=True, line_caps=se.get('line_caps', 'none'), z_index=9)
+        if 'scatter' in se['type'] and se['name'] != 'Text':
+            for each in data:
+                pt.scatter(each[0], each[1], fill_color=se.get('color', 'black'), size=2)
+        if 'scatter' in se['type'] and se['name'] == 'Text' or 'text' in se['type']:
+            for each in data:
+                pt.text(*each[:2], **se)
+
+    return cv
+
+
 class ExcelTemplate:
     def __init__(self, **kwargs):
         self.name = ""

ararpy/smp/info.py

@@ -0,0 +1,23 @@
+#  Copyright (C) 2024 Yang. - All Rights Reserved
+
+# !/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2024 Yang 
+# ararpy - info
+# ==========================================
+#
+#
+# 
+"""
+
+
+def name(smp, n: str = None):
+    if n is None:
+        return smp.Info.sample.name
+    elif isinstance(n, str):
+        smp.Info.sample.name = n
+        return n
+    else:
+        raise ValueError(f"{n} is not a string")

ararpy/smp/json.py

@@ -22,7 +22,8 @@ def dumps(a):
 
 
 def loads(a):
-    return json.loads(a)
+    # null will be converted to None by default, replace None with np.nan
+    return json.loads(a, object_hook=myHook)
 
 
 class MyEncoder(json.JSONEncoder):
@@ -51,3 +52,13 @@ class MyEncoder(json.JSONEncoder):
         if not isinstance(obj, (int, str, list, dict, tuple, float)):
             print(f"Special type, {type(obj) = }, {obj = }")
         return super(MyEncoder, self).default(obj)
+
+
+def myHook(obj):
+    if isinstance(obj, dict):
+        return {k: myHook(v) for k, v in obj.items()}
+    elif isinstance(obj, list):
+        return [myHook(v) for v in obj]
+    elif obj is None:
+        return np.nan
+    return obj

ararpy/smp/plots.py

@@ -61,16 +61,20 @@ def set_plot_data(sample: Sample, isInit: bool = True, isIsochron: bool = True,
         try:
             initial_plot_data(sample)
         except (Exception, BaseException):
-            print(traceback.format_exc())
+            # print(traceback.format_exc())
             pass
 
     # Recalculate isochron lines
     if isIsochron:
         try:
             recalc_isochrons(sample, **kwargs)
+        except (Exception, BaseException):
+            # print(traceback.format_exc())
+            pass
+        try:
             reset_isochron_line_data(sample)
         except (Exception, BaseException):
-            print(traceback.format_exc())
+            # print(traceback.format_exc())
             pass
 
     # Recalculate plateaus
@@ -78,7 +82,7 @@ def set_plot_data(sample: Sample, isInit: bool = True, isIsochron: bool = True,
         try:
             recalc_plateaus(sample)
         except (Exception, BaseException):
-            print(traceback.format_exc())
+            # print(traceback.format_exc())
             pass
 
 
@@ -237,7 +241,7 @@ def get_isochron_results(data: list, smp: Sample, sequence, figure_type: int = 0
     try:
         regression_res = regression_method(*data[:5])
     except (Exception, BaseException):
-        print(f"Warning: {traceback.format_exc()}")
+        # print(f"Warning: {traceback.format_exc()}")
         return iso_res
     else:
         iso_res.update(dict(zip(reg_res_index, regression_res)))
@@ -305,11 +309,11 @@ def get_3D_results(data: list, sequence: list, sample: Sample):
             Q = 1 - np.exp(-1 * sample.TotalParam[46][0] * sum(sample.TotalParam[32]) / len(sample.TotalParam[32]))
             P = PQ / Q
         except:
-            print(f"Warning: {traceback.format_exc()}")
+            # print(f"Warning: {traceback.format_exc()}")
             P = 0
         age = basic.calc_age([f, sf], smp=sample)
     except:
-        print(f"Warning: {traceback.format_exc()}")
+        # print(f"Warning: {traceback.format_exc()}")
         k = [0] * 15
         age = [0] * 4
         ar40ar36, sar40ar36, P = 0, 0, 0

ararpy/smp/sample.py

@@ -119,8 +119,8 @@ TOTAL_PARAMS_HEADERS = [
     '\u2074\u2070Ar/\u00B3\u2076Ar air', '%1\u03C3',
     '\u00B3\u2078Ar/\u00B3\u2076Ar air', '%1\u03C3',  # 95-98
     'Isochron Fitting', 'Convergence', 'Iteration', 'Discrimination',  # 99-102
-    'Not Zero', 'Corr Blank', 'Corr Discr', 'Corr \u00B3\u2077Ar Decay',
-    'Corr \u00B3\u2079Ar Decay',  # 103-107
+    'Not Zero', 'Corr Blank', 'Corr Discr', 'Corr \u00B3\u2077Ar Decay',  # 103-106
+    'Corr \u00B3\u2079Ar Decay',  # 107
     'Ca Degassing', 'K Degassing', 'Cl Degassing', 'Trap Degassing',  # 108-111
     'Using Min Equation',
     # 'Recalibration', 'Using Std Age', 'Use Std Ratio',  # 112-115  to be completed
@@ -137,6 +137,11 @@ TOTAL_PARAMS_HEADERS = [
     'Heating Time (s)',  # 125
     'Heating Actual Temp (C)',  # 126
     'Heating AT 1\u03C3',  # 127
+    '36Ar Gain', '1\u03C3',  # 128-129
+    '37Ar Gain', '1\u03C3',  # 130-131
+    '38Ar Gain', '1\u03C3',  # 132-133
+    '39Ar Gain', '1\u03C3',  # 134-135
+    '40Ar Gain', '1\u03C3',  # 136-137
 ]
 
 SAMPLE_INTERCEPT_SHORT_HEADERS = [
@@ -245,6 +250,11 @@ TOTAL_PARAMS_SHORT_HEADERS = [
     'HeatingTime',  # 125
     'HeatingActualTemp',  # 126
     'HeatingActualTempError',  # 127
+    '36Gain', '1s',  # 128-129
+    '37Gain', '1s',  # 130-131
+    '38Gain', '1s',  # 132-133
+    '39Gain', '1s',  # 134-135
+    '40Gain', '1s',  # 136-137
 ]
 
 DEFAULT_PLOT_STYLES = {
@@ -731,7 +741,7 @@ DEFAULT_PLOT_STYLES = {
     },
 }
 
-VERSION = '20240730'
+VERSION = '20240930'
 
 NAMED_DICT = {
     "unknown": {"header": SAMPLE_INTERCEPT_HEADERS.copy()},
@@ -839,7 +849,7 @@ class Sample:
         return self.__version
 
     def help(self) -> str: ...
-
+    
     def name(self) -> str: ...
 
     def doi(self) -> str: ...
@@ -854,7 +864,7 @@ class Sample:
 
     def sequence(self) -> ArArBasic: ...
 
-    def recalculate(self, *args): ...
+    def recalculate(self, *args, **kwargs): ...
 
     def plot_age_plateau(self): ...
 

ararpy/smp/table.py

@@ -9,6 +9,7 @@
 #
 #
 """
+import copy
 from .. import calc
 from . import (sample as samples, basic)
 
@@ -47,6 +48,13 @@ def update_table_data(smp: Sample, only_table: str = None):
             data = calc.arr.merge(
                 smp.SequenceName, smp.SequenceValue, *smp.DegasValues)
         elif key == '5':
+            smp.PublishValues[0] = copy.deepcopy(smp.DegasValues[ 0])
+            smp.PublishValues[1] = copy.deepcopy(smp.DegasValues[ 8])
+            smp.PublishValues[2] = copy.deepcopy(smp.DegasValues[10])
+            smp.PublishValues[3] = copy.deepcopy(smp.DegasValues[20])
+            smp.PublishValues[4] = copy.deepcopy(smp.DegasValues[24])
+            smp.PublishValues[5:7] = copy.deepcopy(smp.ApparentAgeValues[2:4])
+            smp.PublishValues[7:9] = copy.deepcopy(smp.ApparentAgeValues[6:8])
             data = calc.arr.merge(
                 smp.SequenceName, smp.SequenceValue, *smp.PublishValues)
         elif key == '6':