ararpy 0.1.26__tar.gz → 0.1.28__tar.gz

{ararpy-0.1.26 → ararpy-0.1.28}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.26
+Version: 0.1.28
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.26 → ararpy-0.1.28}/ararpy/calc/basic.py

@@ -129,3 +129,11 @@ def monte_carlo(func, inputs, confidence_level, **kwargs):
     limits = values[:, [l_range, r_range]]
 
     return np.concatenate((means, limits), axis=1), cov
+
+
+def parser(v: str, t: type):
+    if t == bool:
+        if str(v).lower().rstrip() in ["true", "1"]:
+            return True
+    return t(v)
+

{ararpy-0.1.26 → ararpy-0.1.28}/ararpy/files/calc_file.py

@@ -22,7 +22,7 @@ import os
 import msoffcrypto
 
 from . import xls
-from ..calc.basic import get_datetime
+from ..calc.basic import get_datetime, parser
 from ..calc import arr, err, isochron
 
 
@@ -107,9 +107,8 @@ def open_252(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
         -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 90-99
         -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 100-109
         -999, -999, -999, -999, -1,  # 110-114
-        -999, -999, -999, -999, -999, -999, -999, -999,  # 115-122
-        -999, -999, -999, -999, -999, -999, -999, -999,  # 123-130
-        -999, -999, -999, -999, -999,  # 131-135
+        -999, -999, -999, -999, -999, -999, -999, -999, -999, -999, -999,  # 115-125
+        999, -999, 999, -999, 999, -999, 999, -999, 999, -999,  # 126-135
     ]
 
     # double transpose to remove keys
@@ -128,6 +127,13 @@ def open_252(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
 
     # adjustment
     isochron_mark.replace({4.0: '1'}, inplace=True)
+
+    total_param[71] = 35.96754628
+    total_param[73] = 36.9667759
+    total_param[75] = 37.9627322
+    total_param[77] = 38.964313
+    total_param[79] = 39.962383123
+
     total_param[83] = logs01[1][9]  # No
     total_param[84] = logs01[1][10]  # %SD
     total_param[81] = logs01[1][11]  # K mass
@@ -150,9 +156,9 @@ def open_252(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
     total_param[51] = logs01[1][27]  # %SD
     total_param[52] = logs01[1][28]  # 40K(\beta-) activities param
     total_param[53] = logs01[1][29]  # %SD
-    total_param[48] = logs01[1][26] + logs01[1][28]  # 40K(EC) activities param
-    total_param[49] = 100 / total_param[48] * pow(
-        (logs01[1][27] / 100 * logs01[1][26]) ** 2 + (logs01[1][29] / 100 * logs01[1][28]) ** 2, 0.5)  # %SD
+    total_param[48] = logs01[1][26] + logs01[1][28]  # 40K total activities param
+    total_param[49] = round(100 / total_param[48] * pow(
+        (logs01[1][27] / 100 * logs01[1][26]) ** 2 + (logs01[1][29] / 100 * logs01[1][28]) ** 2, 0.5), 6)  # %SD
 
     total_param[34] = logs01[1][36]  # decay constant of 40K total
     total_param[35] = logs01[1][37]  # %SD
@@ -169,30 +175,29 @@ def open_252(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
     total_param[44] = logs01[1][40]  # decay constant of 37Ar
     total_param[45] = logs01[1][41]  # %SD
 
-    # logs01[1][49]]  # 1 for using weighted YORK isochron regression, 2 for unweighted
-    # logs01[1][50]]  # True for including errors on irradiation constants, False for excluding those
-    # [logs01[1][67]]  # MDF method, 'LIN'
+    # logs01[1][49]  # 1 for using weighted YORK isochron regression, 2 for unweighted
+    # logs01[1][50]  # True for including errors on irradiation constants, False for excluding those
+    # logs01[1][67]  # MDF method, 'LIN'
     total_param[93] = logs01[1][70]  # 40Ar/36Ar air
     total_param[94] = logs01[1][71]  # %SD
-
-    total_param[97] = 'York-2'  # Fitting method
+    total_param[97] = 'York-2' if int(logs01[1][49]) == 1 else ""   # Fitting method
     total_param[98] = logs01[1][0]  # Convergence
     total_param[99] = logs01[1][1]  # Iterations number
     total_param[100] = logs01[1][67]  # MDF method
-    total_param[101] = logs01[1][65]  # force negative to zero when correct blank
+    total_param[101] = parser(logs01[1][65], bool)  # force negative to zero when correct blank
     total_param[102] = True  # Apply 37Ar decay
     total_param[103] = True  # Apply 39Ar decay
-    total_param[104] = logs01[1][6]  # Apply 37Ar decay
-    total_param[105] = logs01[1][7]  # Apply 39Ar decay
-    total_param[106] = True  # Apply K degas
-    total_param[107] = True  # Apply Ca degas
-    total_param[108] = True  # Apply Air degas
-    total_param[109] = logs01[1][8]  # Apply Cl degas
+    total_param[104] = parser(logs01[1][6], bool)  # Apply 37Ar decay
+    total_param[105] = parser(logs01[1][7], bool)  # Apply 39Ar decay
+    total_param[106] = True  # Apply Ca degas
+    total_param[107] = True  # Apply K degas
+    total_param[108] = parser(logs01[1][8], bool)  # Apply Cl degas
+    total_param[109] = True  # Apply Trap degas
 
     total_param[110] = True if logs01[1][5] == 'MIN' else False  # Calculating ages using Min equation [True] or conventional equation [False]
-    total_param[111] = logs01[1][89]  # Use primary standard or not
-    total_param[112] = logs01[1][91]  # Use standard age or not
-    total_param[113] = logs01[1][92]  # Use primary ratio or not
+    total_param[111] = parser(logs01[1][89], bool)  # Use primary standard or not
+    total_param[112] = parser(logs01[1][91], bool)  # Use standard age or not
+    total_param[113] = parser(logs01[1][92], bool)  # Use primary ratio or not
 
     # irradiation time
     total_param = general_adjustment(
@@ -310,12 +315,12 @@ def open_240(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
     )
     # Do adjustment
     isochron_mark.replace({4.0: '1'}, inplace=True)
-    total_param[44] = logs01[1][40]
-    total_param[45] = logs01[1][41]
-    total_param[42] = logs01[1][38]
-    total_param[43] = logs01[1][39]
     total_param[34] = logs01[1][36]
     total_param[35] = logs01[1][37]
+    total_param[42] = logs01[1][38]
+    total_param[43] = logs01[1][39]
+    total_param[44] = logs01[1][40]
+    total_param[45] = logs01[1][41]
 
     return [
         sample_values, blank_values, corrected_values, degas_values, publish_values,
@@ -399,6 +404,8 @@ def general_adjustment(
     total_param[32] = [i / (3600 * 24 * 365.242) for i in stand_time_second]  # stand year
 
     # initial ratios & error display settings
+    total_param[95] = logs02[9][irradiation_index]  # 38Ar/36Ar air
+    total_param[96] = logs02[10][irradiation_index]  # %SD
     total_param[115] = 0
     total_param[116] = 298.56
     total_param[117] = 0.31
@@ -624,10 +631,10 @@ class ArArCalcFile:
         # list(range(1, 26, 2)) irradiation correction constants
         # list(range(39, 58, 2)) decay constants
         # list(range(68, 97, 2)) J, MDF, other constants
-        for column in list(range(1, 26, 2)) + list(range(68, 71, 2)):
+        for column in list(range(1, 26, 2)) + list(range(68, 71, 2)):  # irradiation constants and J, MDF uncertainties
             self.content.loc[:, ('pam', column)] = \
-                (self.content['pam', column].astype("float") / (
-                    self.content['pam', column - 1].astype("float")) * 100).replace(np.nan, 0)
+                round(self.content['pam', column].astype("float") / (
+                    self.content['pam', column - 1].astype("float")) * 100, 6).replace(np.nan, 0)
 
         # sample info
         self.sample_info = {

{ararpy-0.1.26 → ararpy-0.1.28}/ararpy/files/raw_file.py

@@ -97,7 +97,6 @@ def open_file(file_path: str, input_filter: List[Union[str, int, bool]]):
                    'Qtegra Exported XLS': open_qtegra_exported_xls, 'Seq': open_raw_seq}[
             ['txt', 'excel', 'Qtegra Exported XLS', 'Seq'][int(input_filter[1])]]
     except KeyError:
-        print(traceback.format_exc())
         raise FileNotFoundError("Wrong File.")
     return handler(file_path, input_filter)
 
@@ -302,6 +301,7 @@ def get_raw_data(file_contents: List[List[Union[int, float, str, bool, list]]],
 
         # ============ Zero datetime ============
         timezone = strings_index[7] if strings_index[7] != "" else "utc"
+        options.update({'TimeZone': timezone})
         try:
             if check_box_index[3]:  # date in one string
                 zero_date = datetime_parse(options.get('ZeroYear'), strings_index[5])
@@ -319,10 +319,11 @@ def get_raw_data(file_contents: List[List[Union[int, float, str, bool, list]]],
                 zero_date.year, zero_date.month, zero_date.day, zero_time.hour, zero_time.minute, zero_time.second)
             # adjust to UTC
             zero_datetime = utc_dt(zero_datetime, tz=timezone).isoformat(timespec='seconds')
-        except (TypeError, ValueError, IndexError):
-            # print(f"Cannot parse zero datetime")
-            zero_datetime = datetime(1970, 1, 1, 0, 0, 0).isoformat(timespec='seconds')
-
+            options.update({'ZeroDT': zero_datetime})
+        except (TypeError, ValueError, IndexError) as e:
+            print(traceback.format_exc())
+            raise ValueError(f"Failed to parse zero datetime: {e}")
+            # zero_datetime = datetime(1970, 1, 1, 0, 0, 0).isoformat(timespec='seconds')
         current_step = [[step_name, zero_datetime, options]]
 
         # ============ isotope data ============
@@ -395,6 +396,9 @@ def get_raw_data(file_contents: List[List[Union[int, float, str, bool, list]]],
         if not check_box_index[0] or len(step_list) >= 500:  # check_box_index[0]: multiple sequences
             break
 
+    if not step_list:
+        raise ValueError("Failed to read the original file. It might be because the names of the experiments or steps were not recognized.")
+
     return step_list
 
 

{ararpy-0.1.26 → ararpy-0.1.28}/ararpy/smp/corr.py

@@ -266,7 +266,7 @@ def calc_degas_cl(sample: Sample):
             d6 = (a1 - a2 + (a3 + a4) / a7 - a5 / a7) / a7 / (1 - a6 / a7) ** 2
             d7 = -(a1 - a2) * (a6) / (a7 - a6) ** 2 - (a3 + a4 - a5) / (a7 - a6) ** 2
 
-            v1 = (a1 - a2 + (a3 + a4) / a7 - a5 / a7) / (1 - a6 / a7)
+            v1 = (a1 - a2 + (a3 + a4 - a5) / a7) / (1 - a6 / a7)
             s1 = (d1**2*s1**2 + d2**2*s2**2 + d3**2*s3**2 + d4**2*s4**2+ d5**2*s5**2 + d6**2*s6**2 + d7**2*s7**2) ** .5
             s2 = calc.err.mul((v1, s1), (vDecay[i], sDecay[i]))
             v1 = 0 if (ar36acl[0][i] - v1 < 0 or v1 < 0) and set_negative_zero[i] else v1

{ararpy-0.1.26 → ararpy-0.1.28}/ararpy/smp/export.py

@@ -19,6 +19,7 @@ import pickle
 import traceback
 import pdf_maker as pm
 import numpy as np
+from math import log
 from decimal import Decimal
 
 from ..calc import arr, isochron, spectra, err
@@ -63,19 +64,19 @@ def get_cv_from_dict(data: dict, **kwargs):
         scale = (float(scale[0]), float(scale[1]), float(scale[2]), float(scale[3]))
         # create plot area based on axis scale
         plot_area = (kwargs.get("pt_left", 0.15), kwargs.get("pt_bottom", 0.15), kwargs.get("pt_width", 0.8), kwargs.get("pt_height", 0.8))
-        pt = cv.add_plot_area(name=f"PlotArea{i}", plot_area=plot_area, plot_scale=scale, show_frame=True)
+        pt = cv.add_plot_area(name=f"PlotArea{i}", plot_area=plot_area, plot_scale=scale, **data['xAxis'][i])
         for stick in data['xAxis'][i]['interval']:
             start = pt.scale_to_points(float(stick), scale[2])
             end = pt.scale_to_points(float(stick), scale[2])
             end = (end[0], end[1] - 5)
-            if pt.line(start=start, end=end, width=1, line_style="solid", y_clip=False, coordinate="pt", z_index=100):
+            if pt.line(start=start, end=end, width=data['xAxis'][i]['line_width'], 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, size=int(data['xAxis'][i]['label_size']),
                         coordinate="pt", h_align="middle", z_index=150)
         for stick in data['yAxis'][i]['interval']:
             start = pt.scale_to_points(scale[0], float(stick))
             end = pt.scale_to_points(scale[0], float(stick))
             end = (end[0] - 5, end[1])
-            if pt.line(start=start, end=end, width=1, line_style="solid", x_clip=False, coordinate="pt", z_index=100):
+            if pt.line(start=start, end=end, width=data['xAxis'][i]['line_width'], 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, size=int(data['yAxis'][i]['label_size']),
                         coordinate="pt", h_align="right", v_align="center", z_index=150)
         # axis titles
@@ -107,13 +108,13 @@ def get_cv_from_dict(data: dict, **kwargs):
                     start=data[index - 1], end=data[index], width=se.get('line_width', 1),
                     line_style=se.get('line_style', 'solid'), name=se['name'],
                     color=se.get('color', 'black'), clip=True, line_caps=se.get('line_caps', 'none'),
-                    z_index=se.get('z_index', 9))
+                    z_index=int(se.get('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('fill_color', 'black'), size=se.get('size', 5),
                     stroke_color=se.get('stroke_color', se.get('color', 'black')),
-                    z_index=se.get('z_index', 9)
+                    z_index=int(se.get('z_index', 9))
                 )
         if 'scatter' in se['type'] and se['name'] == 'Text' or 'text' in se['type']:
             for each in data:
@@ -181,6 +182,12 @@ def export_chart_to_pdf(cvs, file_name: str = "", file_path: str = "", **kwargs)
     -------
 
     """
+    # capital letter for label
+    def get_label(l="", num=0):
+        if num // 26 > 0:
+            return get_label(get_label(l, num // 26 - 1), num % 26)
+        return l + chr(num % 26 + 65)
+
     # write pdf
     show_label = kwargs.get('show_label', False)
     num_cols = kwargs.get('num_columns', 2)
@@ -195,21 +202,12 @@ def export_chart_to_pdf(cvs, file_name: str = "", file_path: str = "", **kwargs)
         file.del_obj(i)
     file.add_page(size=page_size[kwargs.get('page_size', 'a4').lower()], unit='mm')
     for page_index, page in enumerate(cvs):
-
-        # for x in range(0, 600, 10):
-        #     file.line(page_index, start=(x, 0), end=(x, 900), style='dash', color='grey')
-        # for y in range(0, 900, 10):
-        #     file.line(page_index, start=(0, y), end=(800, y), style='dash', color='grey')
-
-        numbers = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N']
-
         for cv_index, cv in enumerate(page):
             left = 10 + cv_index % num_cols * cv.width()
             top = 20 + cv_index // num_cols * cv.height()
             if show_label:
-                # file.text(page=page_index, x=left + 65, y=810 - top, text=numbers[cv_index])
                 cv._plot_areas[1].text(
-                    x=5, y=95, text=numbers[cv_index],
+                    x=5, y=95, text=f"({get_label(num=cv_index)})",
                     id=f'text-label-{page_index}-{cv_index}',
                     name=f'text-label-{page_index}-{cv_index}',
                     color='black', size=title_size, axis_index=1, h_align='middle', v_align='center'
@@ -312,7 +310,7 @@ def getRectFromSpectra(data):
 
     """
     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))))
+    return list(filter(lambda rect: rect[2] != 0 and rect[3] != 0, map(lambda index: [data[index,0], min(data[index,[1,2]]), abs(data[index+1,0] - data[index,0]), abs(data[index,1] - data[index,2])], list(range(len(data) - 1)))))
 
 
 def _get_additional_text_series(name):
@@ -327,28 +325,36 @@ def _get_additional_text_series(name):
 
 def _get_plot_data_age_spectra_series(smp: sample, **options):
     color = options.get('color', 'black')
-    sigma = options.get('sigma', 1)
+    sigma = options.get('sigma', smp.Info.preference['confidenceLevel'])
+    unit = options.get('unit', smp.Info.preference['ageUnit'])
     xAxis = options.get('xAxis', [{}])
     yAxis = options.get('yAxis', [{}])
+    line_width = options.get('line_width', 1)
+    line_caps = options.get('line_caps', 'square')
     series = []
+    # apparent spectra lines
     age = smp.ApparentAgeValues[2:4]
     ar = smp.DegasValues[20]
-    data = spectra.get_data(*age, ar, cumulative=False)
+    data = spectra.get_data(*age, ar, cumulative=False, sigma=sigma)
     series.append({
         'type': 'series.line', 'id': f'line-{smp.name()}-{get_random_digits()}', 'name': f'line-{smp.name()}-{get_random_digits()}',
-        'color': color, 'fill_color': color, 'line_width': 1, 'line_style': 'solid', 'z_index': 9,
-        'data': np.transpose([data[0], data[1]]).tolist(), 'line_caps': 'square',
+        'color': color, 'fill_color': color, 'line_width': line_width, 'line_style': 'solid', 'z_index': 19,
+        'data': np.transpose([data[0], data[1]]).tolist(),
+        'line_caps': line_caps,
+        # 'line_caps': 'none',
         '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': color, 'fill_color': color, 'line_width': 1, 'line_style': 'solid', 'z_index': 9,
-        'data': np.transpose([data[0], data[2]]).tolist(), 'line_caps': 'square',
+        'color': color, 'fill_color': color, 'line_width': line_width, 'line_style': 'solid', 'z_index': 19,
+        'data': np.transpose([data[0], data[2]]).tolist(),
+        'line_caps': line_caps,
+        # 'line_caps': 'none',
         'axis_index': 0,
     })
+    # initial values corrected spectra lines and rect
     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]):
@@ -360,54 +366,60 @@ def _get_plot_data_age_spectra_series(smp: sample, **options):
             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': ['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,
+                'color': ['red', 'blue'][index], 'fill_color': ['red', 'blue'][index], 'line_width': 0, 'line_style': 'none', 'z_index': 9,
+                'data': spectra_fill_data, 'line_caps': 'none', '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',
+                'color': ['red', 'blue'][index], 'line_width': line_width, 'line_style': 'solid', 'z_index': 9,
+                'data': plateau_data[:,[0,1]].tolist(),
+                'line_caps': line_caps,
+                # 'line_caps': 'none',
                 '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',
+                'color': ['red', 'blue'][index], 'line_width': line_width, 'line_style': 'solid', 'z_index': 9,
+                'data': plateau_data[:,[0,2]].tolist(),
+                'line_caps': line_caps,
+                # 'line_caps': 'none',
                 '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 = {res['age']:.2f} ± {(sigma * res['s3']):.2f} Ma<r>"
+                'text': f"WMPA = {res['age']:.2f} ± {(sigma * res['s3']):.2f} {unit} ({sigma}s)<r>"
                         f"MSWD = {res['MSWD']:.2f}, n = {res['Num']:.0f}<r>"
-                        f"<sup>39</sup>Ar = {res['Ar39']:.2f}%",
+                        f"<sup>39</sup>Ar = {res['Ar39']*100:.2f}%",
                 'size': title_size,
-                'data': [text.pos],
-                'axis_index': 1,
+                # 'data': [text.pos],
+                'data': [[50, 50]],
+                'axis_index': 1, 'z_index': 29,
                 'h_align': "middle",
                 'v_align': "center",
             })
+    # TGA
     tga = smp.Info.results.age_spectra['TGA']
     if not np.isnan(tga['age']):
         series.append({
             'type': 'text', 'id': f'text-{smp.name()}-{get_random_digits()}', 'name': f'text-{smp.name()}-{get_random_digits()}',
             'color': color, 'fill_color': color,
-            'text': f"TGA = {tga['age']:.2f} ± {(sigma * tga['s3']):.2f} Ma",
+            'text': f"TGA = {tga['age']:.2f} ± {(sigma * tga['s3']):.2f} {unit} ({sigma}s)",
             'size': title_size,
             'data': [[50, 3]],
             'axis_index': 1,
             'h_align': "middle",
             'v_align': "bottom",
         })
-
+    # title
     series.append({
         'type': 'text', 'id': f'text-{smp.name()}-{get_random_digits()}',
         'name': f'text-{smp.name()}-{get_random_digits()}', 'color': color,
         'text': smp.name(), 'size': title_size,
-        'data': [[50, 95]], 'axis_index': 1,
+        'data': [[50, 95]], 'axis_index': 1, 'z_index': 29,
         'h_align': "middle", 'v_align': "center",
     })
 
@@ -416,50 +428,60 @@ def _get_plot_data_age_spectra_series(smp: sample, **options):
 
 def _get_plot_data_age_spectra_axis(smp: sample, **options):
     color = options.get('color', 'black')
+    line_width = options.get('line_width', 1)
     xAxis, yAxis = [], []
     age = smp.ApparentAgeValues[2:4]
     ar = smp.DegasValues[20]
     data = spectra.get_data(*age, ar, cumulative=False)
 
-    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_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)
+    # y_interval = [f"{i:.{dp}f}" for i in y_interval]
+    try:
+        y_low_limit = float(smp.AgeSpectraPlot.yaxis.min)
+        y_up_limit = float(smp.AgeSpectraPlot.yaxis.max)
+        y_extent = [y_low_limit, y_up_limit]
+        stick_num = int(smp.AgeSpectraPlot.yaxis.split_number)
+        inc = float(smp.AgeSpectraPlot.yaxis.interval)
+        y_interval = [y_low_limit + i * inc for i in range(stick_num + 1)]
+        dp = int(np.log10(abs(y_up_limit - y_low_limit)) - 1)
+        dp = 0 if dp >= 0 else abs(dp)
+        y_interval = [f"{i:.{dp}f}" for i in y_interval]
+    except (BaseException, Exception):
+        y_extent = [0, 250]
+        y_interval = ['0', '50', '100', '150', '200', '250', '600', '700', '800', '900', '1000']
 
     xAxis.append({
         'extent': [0, 100], 'interval': [0, 20, 40, 60, 80, 100], 'id': 0, 'show_frame': True,
-        'title': 'Cumulative <sup>39</sup>Ar Released (%)', 'name_location': 'middle',
-        'line_width': 1, 'line_style': 'solid', 'z_index': 9, 'label_size': label_size, 'title_size': title_size,
+        'title': 'Cumulative <sup>39</sup>Ar released (%)', 'name_location': 'middle',
+        'line_width': line_width, 'line_style': 'solid', 'z_index': 9, 'label_size': label_size, 'title_size': title_size,
     })
     xAxis.append({
         'extent': [0, 100], 'interval': [], 'id': 1, 'show_frame': False,
         'title': '', 'name_location': 'middle',
-        'line_width': 1, 'line_style': 'solid', 'z_index': 0, 'label_size': label_size, 'title_size': title_size,
+        'line_width': 0, 'line_style': 'none', 'z_index': 0, 'label_size': label_size, 'title_size': title_size,
     })
     yAxis.append({
         'extent': y_extent, 'interval': y_interval,
         'id': 0, 'show_frame': True,
-        'title': 'Apparent Age (Ma)', 'name_location': 'middle',
-        'line_width': 1, 'line_style': 'solid', 'z_index': 9, 'label_size': label_size, 'title_size': title_size,
+        'title': 'Apparent age (Ma)', 'name_location': 'middle',
+        'line_width': line_width, 'line_style': 'solid', 'z_index': 9, 'label_size': label_size, 'title_size': title_size,
     })
     yAxis.append({
         'extent': [0, 100], 'interval': [], 'id': 1, 'show_frame': False,
         'title': '', 'name_location': 'middle',
-        'line_width': 1, 'line_style': 'solid', 'z_index': 0, 'label_size': label_size, 'title_size': title_size,
+        'line_width': 0, 'line_style': 'none', 'z_index': 0, 'label_size': label_size, 'title_size': title_size,
     })
     return xAxis, yAxis
 
 
 def _get_plot_data_inv_isochron_axis(smp: sample, **options):
     color = options.get('color', 'black')
+    line_width = options.get('line_width', 1)
     xAxis, yAxis = [], []
     data = np.array(smp.InvIsochronPlot.data)
     set1 = smp.InvIsochronPlot.set1.data
@@ -478,10 +500,12 @@ def _get_plot_data_inv_isochron_axis(smp: sample, **options):
         'interval': interval,
         'id': 0, 'show_frame': True, 'z_index': 9, 'label_size': label_size, 'title_size': title_size,
         'title': '<sup>39</sup>Ar<sub>K</sub> / <sup>40</sup>Ar<sup>*</sup>', 'name_location': 'middle',
+        'line_width': line_width,
     })
     xAxis.append({
         'extent': [0, 100], 'interval': [], 'id': 1, 'show_frame': False,
         'title': '', 'name_location': 'middle', 'z_index': 0, 'label_size': label_size, 'title_size': title_size,
+        'line_width': 0,
     })
 
     low_limit, up_limit, stick_num, inc = get_axis_scale(data[2])
@@ -1164,7 +1188,6 @@ class WritingWorkbook:
         ]:
             for index, _ in enumerate(['Set 1', 'Set 2']):
                 ar39[index] = res[index].get('Ar39', ar39[index] * 100) / 100
-                print(res[index])
                 try:
                     content.extend([
                         [(row + num_step, 0, row + 1 + num_step, 0), _, {'bold': 1, 'align': 'center'}],

{ararpy-0.1.26 → ararpy-0.1.28}/ararpy/smp/initial.py

@@ -302,17 +302,20 @@ def check_version(smp: Sample):
     smp.Info.experiment.name = smp.name()
     smp.Info.experiment.step_num = smp.sequence().size
 
-    # 20250404
+    # 20250404:  # Normalization for steps with different J values
     doNormalize = True
     v, sv = [], []
-    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[93:95]
-        sv = np.multiply(v, sv) / 100
-    elif smp.Info.sample.type.lower() == "standard":
-        v, sv = smp.TotalParam[59:61]
+    try:
+        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[93:95]
+            sv = np.multiply(v, sv) / 100
+        elif smp.Info.sample.type.lower() == "standard":
+            v, sv = smp.TotalParam[59:61]
+    except:
+        doNormalize = False
     smp.NormalizeFactor = [
         [1 if v[0] == each or not doNormalize else v[0] / each for each in v],
         [0 if v[0] == v[i] or not doNormalize else err.div((v[0], sv[0]), (v[i], sv[i])) for i in range(len(v))]

{ararpy-0.1.26 → ararpy-0.1.28}/ararpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.26
+Version: 0.1.28
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.26 → ararpy-0.1.28}/setup.py

@@ -16,7 +16,7 @@ long_description = (here / 'README.md').read_text(encoding='utf-8')
 
 setuptools.setup(
     name='ararpy',  #
-    version='0.1.26',  # version
+    version='0.1.28',  # version
     author='Yang Wu',
     author_email='wuycug@hotmail.com',
     description='A project for Ar-Ar geochronology',  # short description