ararpy 0.1.191__py3-none-any.whl → 0.1.195__py3-none-any.whl

ararpy/__init__.py

@@ -16,10 +16,10 @@ from . import calc, smp, files, thermo, test
 """ Information """
 
 name = 'ararpy'
-version = '0.0.1.a4'
+version = '0.1.195'
 __version__ = version
 full_version = version
-last_update = '2024-01-04'
+last_update = '2024-03-28'
 
 """ ArArPy Functions """
 
@@ -116,6 +116,8 @@ Sample.plot_cl_3 = lambda _smp: smp.calculation.recalculate(
 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)
+
 Sample.show_data = lambda _smp: \
     f"Sample Name: \n\t{_smp.name()}\n" \
     f"Doi: \n\t{_smp.doi()}\n" \

ararpy/calc/arr.py

@@ -514,6 +514,15 @@ def transpose(obj, ignore: bool = True):
             raise ValueError
 
 
+def remove_empty(a: list):
+    index = 0
+    for i in range(len(a)):
+        if not is_empty(a[-(i + 1)]):
+            index = len(a) - i
+            break
+    return transpose(a[:index])
+
+
 def get_item(obj: list, loc: (list, tuple, int), default: Union[str, int, float, bool] = None,
              base: Union[int, tuple, list] = 0) -> Union[str, int, float, bool]:
     """ Get item from a n-dimension list
@@ -566,7 +575,7 @@ def wtd_mean(a: list, e: list, sf: int = 1, adjust_error: bool = True):
     k0 = sum(a * wt) / sum(wt)  # error weighting
     k4 = sum((a - k0) ** 2 * wt)  # Chi square
     k3 = k4 / df  # MSWD mentioned in Min et al., 2000
-    if adjust_error:
+    if adjust_error and k3 > 1:
         k1 = (k3 / sum(wt)) ** .5
     else:
         k1 = (1 / sum(wt)) ** .5

ararpy/files/calc_file.py

@@ -49,8 +49,7 @@ def read_calc_file(file_path: str):
             book_contents[each_sheet] = sheet_contents
         os.remove(decrypt_file_path)
     except Exception as e:
-        print(traceback.format_exc())
-        return False
+        raise
     else:
         return book_contents
 
@@ -420,7 +419,7 @@ def open_full_xls(file_path: str, sample_name: str = ''):
     try:
         res = xls.open_xls(file_path)
     except (Exception, BaseException) as e:
-        return e
+        raise 
     start_row = 5
     rows_num = len(res['Sample Parameters']) - 5
 
@@ -583,8 +582,6 @@ class ArArCalcFile:
 
     def open(self):
         book_contents = read_calc_file(self.file_path)
-        if not book_contents:
-            raise ValueError('Fail to open the file')
         # create data frames for book values
         content = pd.DataFrame(book_contents['Data Tables'])
         logs01 = pd.DataFrame(book_contents['Logs01'])

ararpy/files/raw_file.py

@@ -274,7 +274,7 @@ def get_raw_data(file_contents: List[List[Union[int, float, str, bool, list]]],
                 raise ValueError(f"Step name not found")
         except (TypeError, ValueError, IndexError):
             # When parsing the step name fails, the end of the file has been reached
-            break
+            raise
 
         # other information
         options = get_sample_info(file_contents, optional_info_index, default="", base=[1, 1 - idx, 1])

ararpy/files/xls.py

@@ -20,8 +20,7 @@ def open_xls(filepath: str):
             sheet = wb.sheet_by_name(sheet_name)
             res[sheet_name] = [[sheet.cell(row, col).value for col in range(sheet.ncols)] for row in range(sheet.nrows)]
     except biffh.XLRDError as e:
-        print('Error in opening excel file: %s' % str(e))
-        return e
+        raise
     else:
         return res
 

ararpy/smp/basic.py

@@ -477,7 +477,7 @@ def get_diff_smp(backup: (dict, Sample), smp: (dict, Sample)):
 # =======================
 # Set parameters
 # =======================
-def set_params(smp: Sample, params: Union[List, str], flag: Optional[str] = None):
+def set_params(smp: Sample, params: Union[List, str], flag: Optional[str] = None, rows: Optional[List] =None):
     """
     Parameters
     ----------
@@ -485,84 +485,76 @@ def set_params(smp: Sample, params: Union[List, str], flag: Optional[str] = None
     params
     flag : optional, should be one of 'calc', 'irra', and 'smp'. If it is not given,
         the text of the extension without a dot will be used
+    rows
 
     Returns
     -------
 
     """
+    if rows is None:
+        rows = []
+    rows = list(set(rows))
+
     if isinstance(params, str) and os.path.isfile(params):
         if flag is None:
             flag = params.split(".")[-1]
         return set_params(smp, read_params(params), flag=flag)
 
-    def remove_none(old_params, new_params, rows, length):
-        res = [[] for _ in range(length)]
+    def isValid(item):
+        valid = True
+        if isinstance(item, (float, int)):
+            valid = not np.isnan(item)
+        return valid and item is not None and item != ""
+
+    def remove_none(old_params, new_params, row_list, length):
+        res = [[old_params[i][j] if j < len(old_params[i]) else None for j in range(max(len(old_params[i]), length))] for i in range(len(old_params))]
         for index, item in enumerate(new_params):
-            if item is None:
-                res[index] = old_params[index]
-            else:
-                res[index] = [item] * rows
+            if isValid(item):
+                for row in row_list:
+                    res[index][row] = item
         return res
 
     n = len(smp.SequenceName)
-
     if n == 0:
-        raise ValueError(f"The number of sample sequences is undefined.")
+        raise ValueError(f"The number of sample sequences is zero")
 
     if flag == 'calc':
-        smp.TotalParam[34:56] = remove_none(smp.TotalParam[34:56], params[0:22], n, 56 - 34)
-        smp.TotalParam[71:97] = remove_none(smp.TotalParam[71:97], params[22:48], n, 97 - 71)
+        smp.TotalParam[34:56] = remove_none(smp.TotalParam[34:56], params[0:22], rows, n)
+        smp.TotalParam[71:97] = remove_none(smp.TotalParam[71:97], params[22:48], rows, n)
     elif flag == 'irra':
-        smp.TotalParam[0:20] = remove_none(smp.TotalParam[0:20], params[0:20], n, 20 - 0)
-        smp.TotalParam[56:58] = remove_none(smp.TotalParam[56:58], params[20:22], n, 57 - 55)  # Cl36/38 productivity
-        smp.TotalParam[20:27] = remove_none(smp.TotalParam[20:27], params[22:29], n, 27 - 20)
-        # smp.TotalParam[26] = [params[26]] * n
+        smp.TotalParam[0:20] = remove_none(smp.TotalParam[0:20], params[0:20], rows, n)
+        smp.TotalParam[56:58] = remove_none(smp.TotalParam[56:58], params[20:22], rows, n)  # Cl36/38 productivity
+        smp.TotalParam[20:27] = remove_none(smp.TotalParam[20:27], params[22:29], rows, n)
         irradiation_time = []
         duration = []
         if None not in params[29:-3] and '' not in params[29:-3]:
             for i in range(len(params[29:-3])):
                 if i % 2 == 0:
-                    # [d, t] = params[29:-3][i].split('T')
-                    # [t1, t2] = t.split(':')
-                    # irradiation_time.append(d + '-' + t1 + '-' + t2 + 'D' + str(params[29:-3][i + 1]))
-                    text = params[29:-3][i]
-                    for char in ['T', ':']:
-                        text = text.replace(char, '-')
                     irradiation_time.append(params[29:-3][i] + 'D' + str(params[29:-3][i + 1]))
                     duration.append(float(params[29:-3][i + 1]))
-            smp.TotalParam[27] = ['S'.join(irradiation_time)] * n
-            smp.TotalParam[28] = [params[-3]] * n
-            smp.TotalParam[29] = [sum(duration)] * n
+            smp.TotalParam[27:30] = remove_none(smp.TotalParam[27:30], ['S'.join(irradiation_time), params[-3], sum(duration)], rows, n)
         if params[-5] != '':
-            # [a, b] = params[-5].split('T')
-            # [b, c] = b.split(':')
-            # smp.TotalParam[30] = [a + '-' + b + '-' + c] * n
-            text = params[-5]
-            for char in ['T', ':']:
-                text = text.replace(char, '-')
-            # smp.TotalParam[30] = [text] * n
-            smp.TotalParam[30] = [params[-5]] * n
+            smp.TotalParam[30:32] = remove_none(smp.TotalParam[30:32], [params[-5], None], rows, n)
         try:
             stand_time_second = [
                 calc.basic.get_datetime(*re.findall(r"\d+", smp.TotalParam[31][i])) - calc.basic.get_datetime(
-                    *re.findall(r"\d+", smp.TotalParam[30][i])) for i in range(n)]
+                    *re.findall(r"\d+", smp.TotalParam[30][i])) for i in range(len(smp.TotalParam[30]))]
         except (BaseException, Exception):
             print(f'Error in calculate standing duration: {traceback.format_exc()}')
-            raise
+            smp.TotalParam[32] = [None for index in range(n)]
         else:
-            smp.TotalParam[32] = [i / (3600 * 24 * 365.242) for i in stand_time_second]  # stand year
+            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
 
     elif flag == 'smp':
-        print(dict(zip([i for i in range(len(params))], params)))
-        smp.TotalParam[67:71] = remove_none(smp.TotalParam[67:71], params[0:4], n, 71 - 67)
-        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[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[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)
+        smp.TotalParam[97:100] = remove_none(smp.TotalParam[97:100], params[13:16], rows, n)
+        smp.TotalParam[115:120] = remove_none(smp.TotalParam[115:120], params[16:21], rows, n)
+        smp.TotalParam[126:136] = remove_none(smp.TotalParam[126:136], params[21:31], rows, n)
+        # smp.TotalParam[120:123] = remove_none(smp.TotalParam[120:123], params[31:34], rows, n)
         smp.TotalParam[100:114] = remove_none(
             smp.TotalParam[100:114],
-            [['Linear', 'Exponential', 'Power'][params[35:38].index(True)] if True in params[35:38] else '', *params[38:]], n, 114 - 100)
+            [['Linear', 'Exponential', 'Power'][params[35:38].index(True)] if True in params[35:38] else '', *params[38:]], rows, n)
         pref = dict(zip(preference_keys, params[31:35]))
         smp.Info.preference.update(pref)
         for key, comp in get_components(smp).items():
@@ -570,7 +562,6 @@ def set_params(smp: Sample, params: Union[List, str], flag: Optional[str] = None
                 comp.decimal_places = pref['decimalPlaces']
                 comp.set_coltypes()
         smp.AgeSpectraPlot.yaxis.title.text = f"Apparent Age ({str(pref['ageUnit']).capitalize()})"
-        print(smp.Info.preference)
 
     else:
         raise KeyError(f"{flag = } is not supported. It must be 'calc' for Calc Params, "

ararpy/smp/corr.py

@@ -349,7 +349,7 @@ def calc_degas_r(sample: Sample):
     """
     ar40ar = calc.arr.sub(sample.CorrectedValues[8:10], sample.DegasValues[30:32])
     ar40r = calc.arr.sub(ar40ar, sample.DegasValues[26:28])
-    ar40r[0] = [item if item >= 0 else 0 for item in ar40r[0]]
+    ar40r[0] = [0 if item < 0 and sample.TotalParam[101][index] else item for index, item in enumerate(ar40r[0])]
     sample.DegasValues[24:26] = copy.deepcopy(ar40r)
     sample.PublishValues[4] = copy.deepcopy(ar40r[0])
 

ararpy/smp/export.py

@@ -38,8 +38,8 @@ except ModuleNotFoundError:
     SETTINGS_ROOT = ""
 
 
-def to_excel(file_path: str):
-    excel = WritingWorkbook(filepath=file_path)
+def to_excel(smp: Sample, file_path: str, *args, **kwargs):
+    excel = WritingWorkbook(sample=smp, filepath=file_path, *args, **kwargs)
     excel.get_xls()
 
 
@@ -297,6 +297,24 @@ def get_plot_series_data(smp: Sample, diagram: str = 'age spectra', **options):
     return series
 
 
+def spectraData2Sgima(data, sigma=2):
+    return list(map(lambda row: [row[0], (row[1] - row[2]) / 2 * (sigma - 1) + row[1], (row[2] - row[1]) / 2 * (sigma - 1) + row[2]], data))
+
+
+def getRectFromSpectra(data):
+    """
+    Parameters
+    ----------
+    data: [x, y1, y2]
+
+    Returns
+    -------
+
+    """
+    data = np.array(data)
+    return list(map(lambda index: [data[index,0], min(data[index,[1,2]]), np.diff(data[[index,index+1],0])[0], np.diff(data[index,[1,2]])[0]], list(range(len(data) - 1))))
+
+
 def _get_additional_text_series(name):
     return {
         'type': 'text', 'id': f'text-{name}-{get_random_digits()}',
@@ -330,22 +348,42 @@ def _get_plot_data_age_spectra_series(smp: sample, **options):
     })
     text1 = smp.AgeSpectraPlot.text1
     text2 = smp.AgeSpectraPlot.text2
+    sigma = 1
+    set_data = [spectraData2Sgima(smp.AgeSpectraPlot.set1.data, sigma),
+                spectraData2Sgima(smp.AgeSpectraPlot.set2.data, sigma)]
     for index, text in enumerate([text1, text2]):
-        if not np.isnan(smp.Info.results.age_spectra[index]['age']):
+        res = smp.Info.results.age_plateau[index]
+        if not np.isnan(res['age']):
             selection = np.array(smp.Info.results.selection[index]['data']) * 2 + 1
-            set_data = list(map(lambda each: [data[0][each - 1], min(data[1][each], data[2][each]), data[0][each + 1] - data[0][each], sigma * abs(data[1][each] - data[2][each])], selection))
+            plateau_data = np.array(set_data[index])
+            # spectra_fill_data = list(map(lambda each: [data[0][each - 1], min(data[1][each], data[2][each]), data[0][each + 1] - data[0][each], sigma * abs(data[1][each] - data[2][each])], selection))
+            spectra_fill_data = getRectFromSpectra(plateau_data)
             series.append({
                 'type': 'series.rect', 'id': f'rect-{smp.name()}-{get_random_digits()}', 'name': f'rect-{smp.name()}-{get_random_digits()}',
-                'color': 'none', 'fill_color': ['red', 'blue'][index], 'line_width': 1, 'line_style': 'solid', 'z_index': 9,
-                'data': set_data, 'line_caps': 'square', 'fill': True,
+                'color': ['red', 'blue'][index], 'fill_color': ['red', 'blue'][index], 'line_width': 0, 'line_style': 'solid', 'z_index': 9,
+                'data': spectra_fill_data, 'line_caps': 'square', 'fill': True,
+                'axis_index': 0,
+            })
+            series.append({
+                'type': 'series.line', 'id': f'line-{smp.name()}-{get_random_digits()}',
+                'name': f'line-{smp.name()}-{get_random_digits()}',
+                'color': ['red', 'blue'][index], 'line_width': 1, 'line_style': 'solid', 'z_index': 9,
+                'data': plateau_data[:,[0,1]].tolist(), 'line_caps': 'square',
+                'axis_index': 0,
+            })
+            series.append({
+                'type': 'series.line', 'id': f'line-{smp.name()}-{get_random_digits()}',
+                'name': f'line-{smp.name()}-{get_random_digits()}',
+                'color': ['red', 'blue'][index], 'line_width': 1, 'line_style': 'solid', 'z_index': 9,
+                'data': plateau_data[:,[0,2]].tolist(), 'line_caps': 'square',
                 'axis_index': 0,
             })
             series.append({
                 'type': 'text', 'id': f'text-{smp.name()}-{get_random_digits()}', 'name': f'text-{smp.name()}-{get_random_digits()}',
                 'color': ['red', 'blue'][index], 'fill_color': ['red', 'blue'][index],
-                'text': f"WMPA = {smp.Info.results.age_spectra[index]['age']:.2f} ± {(sigma * smp.Info.results.age_spectra[index]['s3']):.2f} Ma<r>"
-                        f"MSWD = {smp.Info.results.age_spectra[index]['MSWD']:.2f}, n = {smp.Info.results.age_spectra[index]['Num']:.0f}<r>"
-                        f"<sup>39</sup>Ar = {smp.Info.results.age_spectra[index]['Ar39']:.2f}%",
+                'text': f"WMPA = {res['age']:.2f} ± {(sigma * res['s3']):.2f} Ma<r>"
+                        f"MSWD = {res['MSWD']:.2f}, n = {res['Num']:.0f}<r>"
+                        f"<sup>39</sup>Ar = {res['Ar39']:.2f}%",
                 'size': title_size,
                 'data': [text.pos],
                 'axis_index': 1,
@@ -386,10 +424,15 @@ def _get_plot_data_age_spectra_axis(smp: sample, **options):
     y_low_limit, y_up_limit, stick_num, inc = get_axis_scale(np.array(data[1:3]).flatten())
     y_extent = [y_low_limit, y_up_limit]
     y_interval = [y_low_limit + i * inc for i in range(stick_num + 1)]
+    y_interval.extend([y_up_limit * 10] * 3)
+    dp = int(np.log10(abs(y_up_limit - y_low_limit)) - 1)
+    dp = 0 if dp >= 0 else abs(dp)
+    print(f"{dp = }")
+    y_interval = [f"{i:.{dp}f}" for i in y_interval]
 
-    y_extent = [4, 12]
-    y_interval = ['0', '10', '20', '30', '40', '50', '60', '70', '80', '90', '100']
-    y_interval = ['0', '4', '6', '8', '10', '12', '60', '70', '80', '90', '100']
+    # y_extent = [4, 12]
+    # y_interval = ['0', '10', '20', '30', '40', '50', '60', '70', '80', '90', '100']
+    # y_interval = ['0', '4', '6', '8', '10', '12', '60', '70', '80', '90', '100']
 
     xAxis.append({
         'extent': [0, 100], 'interval': [0, 20, 40, 60, 80, 100], 'id': 0, 'show_frame': True,
@@ -762,16 +805,6 @@ class WritingWorkbook:
 
         if self.template_filepath is not None:
             self.read_template()
-        if self.style is None:
-            self.style = {
-                'font_size': 10, 'font_name': 'Microsoft Sans Serif', 'bold': False,
-                'bg_color': '#FFFFFF',  # back ground
-                'font_color': '#000000', 'align': 'left',
-                'top': 1, 'left': 1, 'right': 1, 'bottom': 1  # border width
-            }
-
-    def spectraData2Sgima(self, data, sigma=2):
-        return list(map(lambda row: [row[0], (row[1] - row[2]) / 2 * (sigma - 1) + row[1], (row[2] - row[1]) / 2 * (sigma - 1) + row[2]], data))
 
     def read_template(self):
         # print(self.template_filepath)
@@ -781,7 +814,7 @@ class WritingWorkbook:
         # TypeError: NAN/INF not supported in write_number() without 'nan_inf_to_errors' Workbook() option
         xls = Workbook(self.filepath, {"nan_inf_to_errors": True})
 
-        style = xls.add_format(self.style)
+        style = xls.add_format(self.default_fmt_prop)
 
         sigma = int(self.sample.Info.preference['confidenceLevel'])
 
@@ -809,9 +842,9 @@ class WritingWorkbook:
 
         # Data for age spectra
         try:
-            spectra_data = arr.transpose(self.spectraData2Sgima(self.sample.AgeSpectraPlot.data, sigma))
-            spectra_set1_data = arr.transpose(self.spectraData2Sgima(self.sample.AgeSpectraPlot.set1.data, sigma)) or [[]] * 3
-            spectra_set2_data = arr.transpose(self.spectraData2Sgima(self.sample.AgeSpectraPlot.set2.data, sigma)) or [[]] * 3
+            spectra_data = arr.transpose(spectraData2Sgima(self.sample.AgeSpectraPlot.data, sigma))
+            spectra_set1_data = arr.transpose(spectraData2Sgima(self.sample.AgeSpectraPlot.set1.data, sigma)) or [[]] * 3
+            spectra_set2_data = arr.transpose(spectraData2Sgima(self.sample.AgeSpectraPlot.set2.data, sigma)) or [[]] * 3
             sht_reference.write_column(f"A{start_row}", spectra_data[0], style)
             sht_reference.write_column(f"B{start_row}", spectra_data[1], style)
             sht_reference.write_column(f"C{start_row}", spectra_data[2], style)
@@ -1036,7 +1069,7 @@ class WritingWorkbook:
         material = self.sample.Info.sample.material
         weight = self.sample.Info.sample.weight
         J_value = self.sample.TotalParam[67][0]
-        J_error = self.sample.TotalParam[68][0]
+        J_error = self.sample.TotalParam[68][0] * self.sample.TotalParam[67][0] / 100
         sigma = self.sample.Info.preference['confidenceLevel']
         sequence_type = {"StepLaser": "Laser", "StepFurnace": "Temperature", "StepCrusher": "Drop", }.get(method, "Step Value")
         sequence_unit = self.sample.Info.sample.sequence_unit if self.sample.Info.sample.sequence_unit != "" else "Unit"
@@ -1046,27 +1079,27 @@ class WritingWorkbook:
         set2_ratio = [self.sample.Info.results.isochron['figure_3'][1]['initial'], self.sample.Info.results.isochron['figure_2'][1]['initial'], self.sample.TotalParam[118][0]][int(self.sample.TotalParam[115][0])]
 
         content = [
-            [(0, 0, 0, 14), f"Table 1. 40Ar/39Ar dating results", {'bold': 1, 'top': 1, 'bottom': 1, 'align': 'left'}],
-            [(1, 0, 2, 0), f"Step", {'bold': 1}],
-            [(1, 1), f"{sequence_type}", {'bold': 1}],
-            [(2, 1), f"({sequence_unit})", {'bold': 1}],
-            [(1, 2, 2, 2), f"Set", {'bold': 1}],
-            [(1, 3, 2, 3), f"36Arair", {'bold': 1}],
-            [(1, 4, 2, 4), f"36ArCa", {'bold': 1}],
-            [(1, 5, 2, 5), f"36ArCl", {'bold': 1}],
-            [(1, 6, 2, 6), f"36ArK", {'bold': 1}],
-            [(1, 7, 2, 7), f"36Ar*", {'bold': 1}],
-            [(1, 8, 2, 8), f"39Ar/40Ar", {'bold': 1}],
-            [(1, 9, 2, 9), f"36Ar/40Ar", {'bold': 1}],
-            [(1, 10), f"Apparent Age", {'bold': 1}],
-            [(1, 11), f"± {sigma} σ", {'bold': 1}],
-            [(2, 10, 2, 11), f"({age_unit})", {'bold': 1}],
-            [(1, 12), f"40Ar*", {'bold': 1}],
-            [(2, 12), f"(%)", {'bold': 1}],
-            [(1, 13), f"39ArK", {'bold': 1}],
-            [(2, 13), f"(%)", {'bold': 1}],
-            [(1, 14, 2, 14), f"Ca/K", {'bold': 1}],
-            [(3, 0, 3, 14), f"Sample {name} ({material}){' by ' if method != '' else ''}{method}, weight = {weight} mg, J = {J_value} ± {J_error}", {'bold': 1, 'italic': 1, 'top': 6, 'align': 'left'}],
+            [(0, 0), f"Table 1. 40Ar/39Ar dating results", {'bold': 1, 'top': 1, 'align': 'left'}],
+            [(1, 0, 2, 0), f"Step", {'bold': 1, 'top': 1, 'bottom': 6}],
+            [(1, 1), f"{sequence_type}", {'bold': 1, 'top': 1}],
+            [(2, 1), f"({sequence_unit})", {'bold': 1, 'bottom': 6}],
+            [(1, 2, 2, 2), f"Set", {'bold': 1, 'top': 1, 'bottom': 6}],
+            [(1, 3, 2, 3), f"36Arair", {'bold': 1, 'top': 1, 'bottom': 6}],
+            [(1, 4, 2, 4), f"37ArCa", {'bold': 1, 'top': 1, 'bottom': 6}],
+            [(1, 5, 2, 5), f"38ArCl", {'bold': 1, 'top': 1, 'bottom': 6}],
+            [(1, 6, 2, 6), f"39ArK", {'bold': 1, 'top': 1, 'bottom': 6}],
+            [(1, 7, 2, 7), f"40Ar*", {'bold': 1, 'top': 1, 'bottom': 6}],
+            [(1, 8, 2, 8), f"39Ar/40Ar", {'bold': 1, 'top': 1, 'bottom': 6}],
+            [(1, 9, 2, 9), f"36Ar/40Ar", {'bold': 1, 'top': 1, 'bottom': 6}],
+            [(1, 10), f"Apparent Age", {'bold': 1, 'top': 1}],
+            [(1, 11), f"± {sigma} σ", {'bold': 1, 'top': 1}],
+            [(2, 10, 2, 11), f"({age_unit})", {'bold': 1, 'bottom': 6}],
+            [(1, 12), f"40Ar*", {'bold': 1, 'top': 1}],
+            [(2, 12), f"(%)", {'bold': 1, 'bottom': 6}],
+            [(1, 13), f"39ArK", {'bold': 1, 'top': 1}],
+            [(2, 13), f"(%)", {'bold': 1, 'bottom': 6}],
+            [(1, 14, 2, 14), f"Ca/K", {'bold': 1, 'top': 1, 'bottom': 6}],
+            [(3, 0), f"Sample {name} ({material}){' by ' if method != '' else ''}{method}, weight = {weight} mg, J = {J_value} ± {J_error}", {'bold': 1, 'italic': 1, 'align': 'left'}],
             [(4, 0, 1), self.sample.SequenceName, {'align': 'left'}],
             [(4, 1, 1), self.sample.SequenceValue, {'num_format': 'General'}],
             [(4, 2, 1), list(map(lambda x: int(x) if str(x).isnumeric() else "", self.sample.IsochronMark)), {'num_format': 'General'}],
@@ -1084,7 +1117,7 @@ class WritingWorkbook:
             [(4, 14, 1), self.sample.PublishValues[9], {}],
             [(4 + num_step, 0, 0), [''] * 15, {'bold': 1, 'top': 1}],
 
-            [(5 + num_step, 0, 5 + num_step, 8), "Table 2. 40Ar/39Ar age summary", {'bold': 1, 'align': 'left'}],
+            [(5 + num_step, 0), "Table 2. 40Ar/39Ar age summary", {'bold': 1, 'align': 'left'}],
             [(6 + num_step, 0, 7 + num_step, 0), "Group", {'bold': 1, 'top': 1}],
             [(6 + num_step, 1, 7 + num_step, 1), "40Arr/39K", {'bold': 1, 'top': 1}],
             [(6 + num_step, 2, 7 + num_step, 2), f"± {sigma} σ", {'bold': 1, 'top': 1}],

ararpy/smp/initial.py

@@ -183,7 +183,10 @@ def initial(smp: Sample):
         reference=ArArBasic(
             name='REFERENCE', journal='JOURNAL', doi='DOI'
         ),
-        preference=copy.deepcopy(PREFERENCE_RES)
+        preference=copy.deepcopy(PREFERENCE_RES),
+        experiment=ArArBasic(
+            name='', mass_spec='', collectors='', step_num=0
+        ),
     ))
 
     decimal_places = PREFERENCE_RES['decimalPlaces']
@@ -265,10 +268,10 @@ def initial_plot_styles(sample: Sample, except_attrs=None):
             set_attr(plot, key, attr)
 
 
-def re_set_smp(sample: Sample):
+def re_set_smp(smp: Sample):
     std = initial(Sample())
-    basic.get_merged_smp(sample, std)
-    return sample
+    basic.get_merged_smp(smp, std)
+    return check_version(smp)
 
 
 def check_version(smp: Sample):
@@ -283,7 +286,11 @@ def check_version(smp: Sample):
 
     """
     if smp.version != samples.VERSION:
-        re_set_smp(smp)
+        std = initial(Sample())
+        basic.get_merged_smp(smp, std)
+    # if int(smp.version) <= 20250328:  # Experiment info
+    smp.Info.experiment.name = smp.name()
+    smp.Info.experiment.step_num = smp.sequence().size
     return smp
 
 
@@ -329,11 +336,8 @@ def from_arr_files(file_path, sample_name: str = ""):
     def renamed_load(file_obj):
         return RenameUnpickler(file_obj).load()
 
-    try:
-        with open(file_path, 'rb') as f:
-            sample = renamed_load(f)
-    except (Exception, BaseException):
-        raise ValueError(f"Fail to open arr file: {file_path}")
+    with open(file_path, 'rb') as f:
+        sample = renamed_load(f)
     # Check arr version
     # recalculation will not be applied automatically
     return check_version(sample)
@@ -353,7 +357,7 @@ def from_calc_files(file_path: str, **kwargs):
     """
     file = calc_file.ArArCalcFile(file_path=file_path, **kwargs).open()
     sample = create_sample_from_df(file.get_content(), file.get_smp_info())
-    return sample
+    return check_version(sample)
 
 
 # create
@@ -372,7 +376,7 @@ def from_full_files(file_path: str, sample_name: str = None):
         sample_name = str(os.path.split(file_path)[-1]).split('.')[0]
     content, sample_info = calc_file.open_full_xls(file_path, sample_name)
     sample = create_sample_from_dict(content=content, smp_info=sample_info)
-    return sample
+    return check_version(sample)
 
 
 # create
@@ -450,4 +454,4 @@ def from_raw_data(raw: RawData, mapping: Optional[List[dict]] = None) -> Sample:
 
     # sample.TotalParam[31] = [raw.get_sequence(row['unknown'], flag='name').datetime for row in mapping]
 
-    return sample
+    return check_version(sample)

ararpy/smp/sample.py

@@ -743,7 +743,7 @@ DEFAULT_PLOT_STYLES = {
     },
 }
 
-VERSION = '20250321'
+VERSION = '20250328'
 
 NAMED_DICT = {
     "unknown": {"header": SAMPLE_INTERCEPT_HEADERS.copy()},
@@ -847,8 +847,9 @@ 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
 
     @property
     def version(self):
@@ -930,7 +931,7 @@ 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 +939,8 @@ 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-0.1.191.dist-info → ararpy-0.1.195.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.191
+Version: 0.1.195
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.191.dist-info → ararpy-0.1.195.dist-info}/RECORD

@@ -1,8 +1,8 @@
-ararpy/__init__.py,sha256=abmIxFaRq9m7mUI66xHbMGD2wRdzV9v8FAgvlViIlTc,6733
+ararpy/__init__.py,sha256=kHlsop1f9Gs6d_F7G0JhTvhjwahHtgf73991YlqIAWs,6858
 ararpy/test.py,sha256=4F46-JJ1Ge12HGae0qO44Qc6kiEMHBgn2MsY_5LlHDo,3973
 ararpy/calc/__init__.py,sha256=kUjRuLE8TLuKOv3i976RnGJoEMj23QBZDu37LWs81U4,322
 ararpy/calc/age.py,sha256=POBF_UxfXM_GCfXR_sTE__-fOvYZleNXXSuR_SIrFrI,5782
-ararpy/calc/arr.py,sha256=w31bn6MXF8I8qPXYo5kI-TfMKCYspx1rZ5g_UpwwSd8,14939
+ararpy/calc/arr.py,sha256=vrjerWuP-2VlMshoOPyOYvBnbHifkhdRISYfOD06ZZk,15149
 ararpy/calc/basic.py,sha256=uJCCUFaPd9zvfkggrdbFYSGLl2pt7UJ7ENgXanzHy68,4036
 ararpy/calc/corr.py,sha256=HnCbf_84gKD6vMX7PflZym-I1MezRKfNHYfEtkDCCaI,18598
 ararpy/calc/err.py,sha256=63LtprqjemlIb1QGDst4Ggcv5KMSDHdlAIL-nyQs1eA,2691
@@ -35,32 +35,32 @@ ararpy/examples/sample-default.smp,sha256=YNkoQGgPrsL_fXS7ZHxfRtLQWekCDqT9czS6vB
 ararpy/files/__init__.py,sha256=l5B5ZQ01WdtvjjN0aMkyAFNgpwANdM_1I0tQbqnRuEY,69
 ararpy/files/arr_file.py,sha256=KqksGlEA6nmMQofTgi7v45flscQZVtefxaNCKrV3Am4,837
 ararpy/files/basic.py,sha256=nc7Hgo_qLSkdmtKzZmd5SQ8Jy0dhW46ly4gh-oisUDs,2095
-ararpy/files/calc_file.py,sha256=Mww0R1RH3BpTCo6EetW9jikd19G6-Ljhgak5PXccRfA,28341
+ararpy/files/calc_file.py,sha256=nqv_VfbOzz8ejcnjNoHJafGiYldhYSOLusUGtuZ8jR0,28207
 ararpy/files/new_file.py,sha256=efblARIBROVLWS2w3-98BxLX5VZ8grRpiTkJFtf_rAk,214
-ararpy/files/raw_file.py,sha256=A0DnCn7dL5eUZTgEwevlDgLsEMWrRmtuBzzPlWoBxAQ,22302
-ararpy/files/xls.py,sha256=8ibT4ZRY2grK34ikKm1pDmlWFlVTgDL7vSMO6mphzrY,702
+ararpy/files/raw_file.py,sha256=5hnZMS7r78lA0ZXrBEN5SWVurQyl0QsHOI9rJz5BQv8,22302
+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=1zsBznVojY-SFAjq_1tkHxvpI9-mD_uotcrd9aDd6n4,22923
+ararpy/smp/basic.py,sha256=k9Vk_LP6P9HO68gMvPQ-adkvaVXEobg1FY-rF5YG7HQ,22588
 ararpy/smp/calculation.py,sha256=LCFJWjLVLEKEQ5b7RFUIxsMahEzgLdodW4kCYXV5Z34,2919
 ararpy/smp/consts.py,sha256=XIdjdz8cYxspG2jMnoItdlUsxr3hKbNFJjMZJh1bpzw,393
-ararpy/smp/corr.py,sha256=1MDH41TsBVyuyI45mqaqP2IvEm_jAUMZgR0MG7uNiu4,25598
+ararpy/smp/corr.py,sha256=D3Ac2iUq3FjzKZR8yhnMLpG__YVEbtyVVfly873m6xc,25649
 ararpy/smp/diffusion_funcs.py,sha256=4-PMMIZWzjk2HOYYWNgSp4GmApygp1MmOxJ2g3xrqWc,175049
-ararpy/smp/export.py,sha256=V_7BsWAQq0I8no3ME62Tva-8DwlCa7LP3xuyz5oYE1Y,113455
+ararpy/smp/export.py,sha256=s89L5B1aHoCeJIjcw6nXA6NtV0j_5XXaWnOETWnomCs,115043
 ararpy/smp/info.py,sha256=iKUELm-BuUduDlJKC1d8tKKNHbwwbNmhUg2pi6bcBvA,489
-ararpy/smp/initial.py,sha256=bB_bJcUx8DkjXQsM77jgD68pWK-4KFr9sjobCgSNN6w,16064
+ararpy/smp/initial.py,sha256=x4zBFXnNKFzuQEWrfBp9Z7LMHxtzr9ASBf-Dnqc_IEA,16304
 ararpy/smp/json.py,sha256=BTZCjVN0aj9epc700nwkYEYMKN2lHBYo-pLmtnz5oHY,2300
 ararpy/smp/plots.py,sha256=u4gUSTfLO6rErQDp3N0hyBf2uc-8CUfITlAtnpN3DG8,31722
 ararpy/smp/raw.py,sha256=51n-rrbW2FqeZHQyevuG7iObPLGvIBzTe414QDVM1FE,6523
-ararpy/smp/sample.py,sha256=6ly0Y9OKtrAADm6yx0nOf4rwjRyK5DPF6DYenb_dda4,55702
+ararpy/smp/sample.py,sha256=Mt6SC8p0AOiuafvwsTsW3IM4BDfV2GL2yunTvffELvM,55853
 ararpy/smp/style.py,sha256=Z4exOAdtvw5xwDf6nyIjPxuvww2U5JK6H_Ql02DBSyM,7030
 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
 ararpy/thermo/basic.py,sha256=nBGHI9uK7VdJwThwBIOcKAzdnYqPyQseFoY6s4zKizk,11504
-ararpy-0.1.191.dist-info/licenses/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
-ararpy-0.1.191.dist-info/METADATA,sha256=MMszQhjI3GBNB83U8dhpQFnvVPZ72q7p2qHgwahMbjA,24517
-ararpy-0.1.191.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
-ararpy-0.1.191.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
-ararpy-0.1.191.dist-info/RECORD,,
+ararpy-0.1.195.dist-info/licenses/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
+ararpy-0.1.195.dist-info/METADATA,sha256=GVX2BTS_XSVYOwfWyGP1wcRbtly3ESqicOA-g_Afxao,24517
+ararpy-0.1.195.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+ararpy-0.1.195.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
+ararpy-0.1.195.dist-info/RECORD,,

{ararpy-0.1.191.dist-info → ararpy-0.1.195.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (77.0.3)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any