ararpy 0.1.30__py3-none-any.whl → 0.1.33__py3-none-any.whl

ararpy/smp/export.py

@@ -23,15 +23,22 @@ from math import log
 from decimal import Decimal
 
 from ..calc import arr, isochron, spectra, err
-from ..calc.basic import get_random_digits
+from ..calc.basic import get_random_digits, merge_dicts
 from ..calc.plot import get_axis_scale
 from . import basic, sample, consts
 
 Sample = sample.Sample
 Plot = sample.Plot
 
-title_size = 11
-label_size = 11
+title_size = 8
+label_size = 8
+
+colors_map = {
+    'red': "#EF661B",
+    'blue': "#189CCA",
+    'red80': "#FFB593",
+    'blue80': "#6BD2FF",
+}
 
 try:
     from webarar.settings import SETTINGS_ROOT
@@ -54,8 +61,12 @@ def get_cv_from_dict(data: dict, **kwargs):
     cv = pm.Canvas(width=kwargs.get("width", 17), height=kwargs.get("height", 12),
                    unit="cm", show_frame=False, clip_outside_plot_areas=False)
     # change frame outline style
-    if kwargs.get("show_frame", True):
+    if kwargs.get("show_frame", False):
         cv.show_frame(color="grey", line_width=0.5)
+    # stick length
+    stick_length = kwargs.get("stick_length", 3)
+    ylabel_offset = kwargs.get("ylabel_offset", 2)
+    xlabel_offset = kwargs.get("xlabel_offset", 8)
     axis_num = min([len(data['xAxis']), len(data['yAxis'])])
     # draw axis
     plots = []
@@ -68,24 +79,24 @@ def get_cv_from_dict(data: dict, **kwargs):
         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=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']),
+            end = (end[0], end[1] - stick_length)
+            if pt.line(start=start, end=end, width=data['xAxis'][i].get('line_width', 1), line_style="solid", y_clip=False, coordinate="pt", z_index=100):
+                pt.text(x=start[0], y=end[1] - xlabel_offset, text=f"{stick}", clip=False, size=int(data['xAxis'][i].get('label_size', 8)),
                         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=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']),
+            end = (end[0] - stick_length, end[1])
+            if pt.line(start=start, end=end, width=data['xAxis'][i].get('line_width', 1), line_style="solid", x_clip=False, coordinate="pt", z_index=100):
+                pt.text(x=end[0] - ylabel_offset, y=end[1], text=f"{stick}", clip=False, size=int(data['yAxis'][i].get('label_size', 8)),
                         coordinate="pt", h_align="right", v_align="center", z_index=150)
         # axis titles
         nloc = pt.scale_to_points(sum(scale[:2]) / 2, scale[2])
-        pt.text(x=nloc[0], y=nloc[1] - kwargs.get("offset_bottom", 30), text=data['xAxis'][i]['title'], clip=False, coordinate="pt",
-                h_align="middle", v_align="center", z_index=150, size=int(data['xAxis'][i]['title_size']))
+        pt.text(x=nloc[0], y=nloc[1] - kwargs.get("offset_bottom", 30), text=data['xAxis'][i].get('title', 'title'), clip=False, coordinate="pt",
+                h_align="middle", v_align="center", z_index=150, size=int(data['xAxis'][i].get('title_size', 8)))
         nloc = pt.scale_to_points(scale[0], sum(scale[2:4]) / 2)
-        pt.text(x=nloc[0] - kwargs.get("offset_left", 50), y=nloc[1], text=data['yAxis'][i]['title'], clip=False, coordinate="pt",
-                h_align="middle", v_align="center", rotate=90, z_index=150, size=int(data['yAxis'][i]['title_size']))
+        pt.text(x=nloc[0] - kwargs.get("offset_left", 50), y=nloc[1], text=data['yAxis'][i].get('title', 'title'), clip=False, coordinate="pt",
+                h_align="middle", v_align="center", rotate=90, z_index=150, size=int(data['yAxis'][i].get('title_size', 8)))
         plots.append(pt)
     # draw series
     for se in data['series']:
@@ -103,20 +114,23 @@ def get_cv_from_dict(data: dict, **kwargs):
         except IndexError:
             continue
         if 'line' in se['type']:
+            se['width'] = se.get('line_width', 1)
+            se['line_style'] = se.get('line_style', 'solid')
+            se['color'] = se.get('color', 'black')
+            se['line_caps'] = se.get('line_caps', 'none')
+            se['z_index'] = int(se.get('z_index', 9))
             for index in range(1, len(data)):
-                pt.line(
-                    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=int(se.get('z_index', 9)))
+                pt.line(start=data[index - 1], end=data[index], **se)
         if 'scatter' in se['type'] and se['name'] != 'Text':
+            se['fill_color'] = se.get('fill_color', 'black')
+            se['size'] = se.get('size', 5)
+            se['stroke_color'] = se.get('stroke_color', se.get('color', 'black'))
+            se['z_index'] = int(se.get('z_index', 9))
+            se['marker'] = se.get('marker', 'rec')
             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=int(se.get('z_index', 9))
-                )
+                pt.scatter(each[0], each[1], **se)
         if 'scatter' in se['type'] and se['name'] == 'Text' or 'text' in se['type']:
+            se.update({'size': 10})
             for each in data:
                 pt.text(*each[:2], **se)
         if 'rect' in se['type']:
@@ -207,7 +221,7 @@ def export_chart_to_pdf(cvs, file_name: str = "", file_path: str = "", **kwargs)
             top = 20 + cv_index // num_cols * cv.height()
             if show_label:
                 cv._plot_areas[1].text(
-                    x=5, y=95, text=f"({get_label(num=cv_index)})",
+                    x=5, y=95, text=f"({str(get_label(num=cv_index)).lower()})",
                     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'
@@ -330,24 +344,18 @@ def _get_plot_data_age_spectra_series(smp: sample, **options):
     xAxis = options.get('xAxis', [{}])
     yAxis = options.get('yAxis', [{}])
     line_width = options.get('line_width', 1)
-    line_caps = options.get('line_caps', 'square')
+    line_caps = options.get('line_caps', 'none')
     series = []
     # apparent spectra lines
     age = smp.ApparentAgeValues[2:4]
     ar = smp.DegasValues[20]
-    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': 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,
-    })
+    x, y1, y2 = spectra.get_data(*age, ar, cumulative=False, sigma=sigma)
+    X = x + list(reversed(x))
+    Y = y1 + list(reversed(y2))
     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': line_width, 'line_style': 'solid', 'z_index': 19,
-        'data': np.transpose([data[0], data[2]]).tolist(),
+        'data': np.transpose([X, Y]).tolist(),
         'line_caps': line_caps,
         # 'line_caps': 'none',
         'axis_index': 0,
@@ -366,34 +374,38 @@ 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': 'none', 'z_index': 9,
+                'color': [colors_map['red'], colors_map['blue']][index], 'fill_color': [colors_map['red'], colors_map['blue']][index],   'line_style': 'none', 'z_index': 9,
                 'data': spectra_fill_data, 'line_caps': 'none', 'fill': True,
                 'axis_index': 0,
             })
+            x, y1, y2 = np.transpose(plateau_data).tolist()[:3]
+            X = x + list(reversed(x))
+            Y = y1 + list(reversed(y2))
             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': line_width, 'line_style': 'solid', 'z_index': 9,
-                'data': plateau_data[:,[0,1]].tolist(),
+                'color': [colors_map['red'], colors_map['blue']][index], 'line_width': line_width, 'line_style': 'solid', 'z_index': 9,
+                'data': np.transpose([X, Y]).tolist(),
                 'line_caps': line_caps,
                 # 'line_caps': 'none',
                 'axis_index': 0,
             })
+            # plateau line
             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': line_width, 'line_style': 'solid', 'z_index': 9,
-                'data': plateau_data[:,[0,2]].tolist(),
+                'color': '#A9A9A9', 'line_width': line_width, 'line_style': 'solid', 'z_index': 9,
+                'data': [[0, res['age']], [100, res['age']]],
                 '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} {unit} ({sigma}s)<r>"
+                'color': [colors_map['red'], colors_map['blue']][index], 'fill_color': [colors_map['red'], colors_map['blue']][index],
+                'text': f"Corrected = {res['age']:.2f} ± {(sigma * res['s2']):.2f} {unit} ({sigma}s)<r>"
                         f"MSWD = {res['MSWD']:.2f}, n = {res['Num']:.0f}<r>"
-                        f"<sup>39</sup>Ar = {res['Ar39']*100:.2f}%",
+                        f"<sup>39</sup>Ar = {res['Ar39']:.2f}%",
                 'size': title_size,
                 # 'data': [text.pos],
                 'data': [[50, 50]],
@@ -401,19 +413,87 @@ def _get_plot_data_age_spectra_series(smp: sample, **options):
                 'h_align': "middle",
                 'v_align': "center",
             })
+        spe = smp.Info.results.age_spectra[index]
+        if not np.isnan(res['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"WMPA = {spe['age']:.2f} ± {(sigma * spe['s2']):.2f} {unit} ({sigma}s)",
+                'size': title_size,
+                'data': [[50, 10+10*index]],
+                'axis_index': 1,
+                'h_align': "middle",
+                'v_align': "bottom",
+            })
+
     # 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} {unit} ({sigma}s)",
+            'text': f"TGA = {tga['age']:.2f} ± {(sigma * tga['s2']):.2f} {unit} ({sigma}s)",
             'size': title_size,
             'data': [[50, 3]],
             'axis_index': 1,
             'h_align': "middle",
             'v_align': "bottom",
         })
+    # Max
+    age = np.array(smp.ApparentAgeValues[2:8]).transpose()
+    age = np.where(age is None, np.nan, age)
+    valid_mask = np.isfinite(age[:, 0])
+    age = age[valid_mask]
+    age = age[age[:, 5] >= 0.1]
+    try:
+        max_index = np.argmax(age[20:, 0]) + 20
+    except ValueError:
+        max_index = np.argmax(age[10:, 0]) + 10
+    min_index = np.argmin(age[:20, 0])
+    # print(f"{max_index = }")
+    # print(f"{min_index = }")
+
+    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"Max. = {age[max_index, 0]:.2f} ± {(sigma * age[max_index, 2]):.2f} {unit}",
+        'size': title_size,
+        'data': [[50, 70]],
+        'axis_index': 1,
+        'h_align': "middle",
+        'v_align': "bottom",
+    })
+
+    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"Min. = {age[min_index, 0]:.2f} ± {(sigma * age[min_index, 2]):.2f} {unit}",
+        'size': title_size,
+        'data': [[50, 75]],
+        'axis_index': 1,
+        'h_align': "middle",
+        'v_align': "bottom",
+    })
+
+    series.append({
+        'type': 'series.line', 'id': f'line-{smp.name()}-{get_random_digits()}',
+        'name': f'line-{smp.name()}-{get_random_digits()}',
+        'color': '#A9A9A9', 'line_width': line_width, 'line_style': 'solid', 'z_index': 9,
+        'data': [[0, age[max_index, 0]], [100, age[max_index, 0]]],
+        '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': '#A9A9A9', 'line_width': line_width, 'line_style': 'solid', 'z_index': 9,
+        'data': [[0, age[min_index, 0]], [100, age[min_index, 0]]],
+        'line_caps': line_caps,
+        # 'line_caps': 'none',
+        'axis_index': 0,
+    })
     # title
     series.append({
         'type': 'text', 'id': f'text-{smp.name()}-{get_random_digits()}',
@@ -531,9 +611,10 @@ def _get_plot_data_inv_isochron_axis(smp: sample, **options):
 
 def _get_plot_data_inv_isochron_series(smp: sample, **options):
     color = options.get('color', 'black')
+    marker_size = options.get('marker_szie', 2)
     xAxis = options.get('xAxis', [{}])
     yAxis = options.get('yAxis', [{}])
-    sigma = options.get('sigma', 1)
+    sigma = options.get('sigma', 2)
     series = []
     age = smp.ApparentAgeValues[2:4]
     ar = smp.DegasValues[20]
@@ -544,21 +625,21 @@ def _get_plot_data_inv_isochron_series(smp: sample, **options):
     # set 1
     series.append({
         'type': 'series.scatter', 'id': f'scatter-{smp.name()}-{get_random_digits()}', 'name': f'scatter-{smp.name()}-{get_random_digits()}',
-        'stroke_color': 'red', 'fill_color': 'red', 'myType': 'scatter', 'size': 3, 'line_width': 0,
+        'stroke_color': colors_map['red'], 'fill_color': colors_map['red80'], 'myType': 'scatter', 'size': marker_size, 'line_width': 0,
         'data': (data[[0, 2], :][:, set1]).transpose().tolist(),
         'axis_index': 0, 'z_index': 99
     })
     # set 2
     series.append({
         'type': 'series.scatter', 'id': f'scatter-{smp.name()}-{get_random_digits()}', 'name': f'scatter-{smp.name()}-{get_random_digits()}',
-        'stroke_color': 'blue', 'fill_color': 'blue', 'myType': 'scatter', 'size': 3, 'line_width': 0,
+        'stroke_color': colors_map['blue'], 'fill_color': colors_map['blue80'], 'myType': 'scatter', 'size': marker_size, 'line_width': 0,
         'data': (data[[0, 2], :][:, set2]).transpose().tolist(),
         'axis_index': 0, 'z_index': 99
     })
     # set 3
     series.append({
         'type': 'series.scatter', 'id': f'scatter-{smp.name()}-{get_random_digits()}', 'name': f'scatter-{smp.name()}-{get_random_digits()}',
-        'stroke_color': 'black', 'fill_color': 'white', 'myType': 'scatter', 'size': 3, 'line_width': 0,
+        'stroke_color': 'black', 'fill_color': 'white', 'myType': 'scatter', 'size': marker_size, 'line_width': 0,
         'data': (data[[0, 2], :][:, set3]).transpose().tolist(),
         'axis_index': 0, 'z_index': 0
     })
@@ -573,17 +654,17 @@ def _get_plot_data_inv_isochron_series(smp: sample, **options):
             ]
             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], 'fill_color': ['red', 'blue'][index],
-                'line_width': 1.5, 'line_style': 'solid',
+                'color': [colors_map['red'], colors_map['blue']][index], 'fill_color': [colors_map['red'], colors_map['blue']][index],
+                'line_width': 1, 'line_style': 'solid',
                 'data': isochron_data,
                 '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"IIA = {smp.Info.results.isochron['figure_3'][index]['age']:.2f} ± {(sigma * smp.Info.results.isochron['figure_3'][index]['s3']):.2f} Ma<r>"
-                        f"[<sup>40</sup>Ar/<sup>36</sup>Ar]<sub>i</sub> = {smp.Info.results.isochron['figure_3'][index]['initial']:.2f} ± {(sigma * smp.Info.results.isochron['figure_3'][index]['sinitial']):.2f}<r>"
-                        f"MSWD = {smp.Info.results.isochron['figure_3'][index]['MSWD']:.2f}, r<sup>2</sup> = {smp.Info.results.isochron['figure_3'][index]['R2']:.4f}<r>",
+                'color': [colors_map['red'], colors_map['blue']][index], 'fill_color': [colors_map['red'], colors_map['blue']][index],
+                'text': f"IIA = {smp.Info.results.isochron['figure_3'][index]['age']:.2f} ± {(sigma * smp.Info.results.isochron['figure_3'][index]['s2']):.2f} Ma ({sigma}s)<r>"
+                        f"(40Ar/36Ar)0 = {smp.Info.results.isochron['figure_3'][index]['initial']:.2f} ± {(sigma * smp.Info.results.isochron['figure_3'][index]['sinitial']):.2f}<r>"
+                        f"MSWD = {smp.Info.results.isochron['figure_3'][index]['MSWD']:.2f}<r>",
                 'size': title_size,
                 'data': [text.pos],
                 'axis_index': 1,
@@ -1168,7 +1249,7 @@ class WritingWorkbook:
         tga_res = self.sample.Info.results.age_spectra['TGA']
         content.extend([
             [(9 + num_step, 1, 10 + num_step, 1), tga_res['F'], {'num_format': '0.00000'}],
-            [(9 + num_step, 2, 10 + num_step, 2), tga_res['sF'], {'num_format': '0.00000'}],
+            [(9 + num_step, 2, 10 + num_step, 2), tga_res['sF'] * sigma, {'num_format': '0.00000'}],
             [(9 + num_step, 3, 10 + num_step, 3), tga_res['age'], {'num_format': '0.00'}],
             [(9 + num_step, 4), tga_res['s1'] * sigma, {'num_format': '± 0.00', 'align': 'left'}],
             [(9 + num_step, 5), tga_res['s2'] * sigma, {'num_format': '± 0.00', 'align': 'left'}],
@@ -1878,7 +1959,7 @@ class CreatePDF:
         yaxis_max = float(yaxis.max)
 
         plot_scale = (xaxis_min, xaxis_max, yaxis_min, yaxis_max)
-        colors = ['red', 'color']
+        colors = [colors_map['red'], 'color']
 
         # create a canvas
         cv = pm.Canvas(width=17, height=12, unit="cm", show_frame=True, clip_outside_plot_areas=False)
@@ -2017,10 +2098,10 @@ class CreatePDF:
         for index in range(len(data) - 1):
             pt.line(start=(data[index][0], data[index][1]), end=(data[index + 1][0], data[index + 1][1]),
                     width=widths[0], line_style=styles[0], color=colors[0],
-                    clip=True, line_caps="square", z_index=9)
+                    clip=True, line_caps="none", z_index=9)
             pt.line(start=(data[index][0], data[index][2]), end=(data[index + 1][0], data[index + 1][2]),
                     width=widths[1], line_style=styles[1], color=colors[1],
-                    clip=True, line_caps="square", z_index=9)
+                    clip=True, line_caps="none", z_index=9)
 
         colors = [
             [self.color_rgb_normalized(self.color_hex_to_rgb(plot.line3.color)),
@@ -2114,8 +2195,6 @@ class CreatePDF:
         yaxis_max = float(yaxis.max)
         plot_scale = (xaxis_min, xaxis_max, yaxis_min, yaxis_max)
 
-        colors = ['red', 'color']
-
         # data
         data = plot.data  # 36a, 37ca, 38cl, 39k, 40r, 36, 37, 38, 39, 40
 

ararpy/smp/initial.py

@@ -123,14 +123,14 @@ def create_sample_from_dict(content: dict, smp_info: dict):
 
 def initial(smp: Sample):
     # 已更新 2023/7/4
-    smp.TotalParam = arr.create_arr((len(samples.TOTAL_PARAMS_HEADERS) - 2, 0))
-    smp.BlankIntercept = arr.create_arr((len(samples.BLANK_INTERCEPT_HEADERS) - 2, 0))
-    smp.SampleIntercept = arr.create_arr((len(samples.SAMPLE_INTERCEPT_HEADERS) - 2, 0))
-    smp.PublishValues = arr.create_arr((len(samples.PUBLISH_TABLE_HEADERS) - 2, 0))
+    smp.TotalParam = arr.create_arr((len(samples.TOTAL_PARAMS_HEADERS) - 3, 0))
+    smp.BlankIntercept = arr.create_arr((len(samples.BLANK_INTERCEPT_HEADERS) - 3, 0))
+    smp.SampleIntercept = arr.create_arr((len(samples.SAMPLE_INTERCEPT_HEADERS) - 3, 0))
+    smp.PublishValues = arr.create_arr((len(samples.PUBLISH_TABLE_HEADERS) - 3, 0))
     smp.DecayCorrected = arr.create_arr((10, 0))
-    smp.CorrectedValues = arr.create_arr((len(samples.CORRECTED_HEADERS) - 2, 0))
-    smp.DegasValues = arr.create_arr((len(samples.DEGAS_HEADERS) - 2, 0))
-    smp.ApparentAgeValues = arr.create_arr((len(samples.SPECTRUM_TABLE_HEADERS) - 2, 0))
+    smp.CorrectedValues = arr.create_arr((len(samples.CORRECTED_HEADERS) - 3, 0))
+    smp.DegasValues = arr.create_arr((len(samples.DEGAS_HEADERS) - 3, 0))
+    smp.ApparentAgeValues = arr.create_arr((len(samples.SPECTRUM_TABLE_HEADERS) - 3, 0))
     smp.IsochronValues = arr.create_arr((len(samples.ISOCHRON_TABLE_HEADERS) - 3, 0))
 
     # Doi
@@ -193,32 +193,32 @@ def initial(smp: Sample):
     # Plots and Tables
     setattr(smp, 'UnknownTable', Table(
         id='1', name='Unknown', header=samples.SAMPLE_INTERCEPT_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 20))
     ))
     setattr(smp, 'BlankTable', Table(
         id='2', name='Blank', header=samples.BLANK_INTERCEPT_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 20))
     ))
     setattr(smp, 'CorrectedTable', Table(
         id='3', name='Corrected', header=samples.CORRECTED_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 35))
     ))
     setattr(smp, 'DegasPatternTable', Table(
         id='4', name='Degas Pattern', header=samples.DEGAS_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 35))
     ))
     setattr(smp, 'PublishTable', Table(
         id='5', name='Publish', header=samples.PUBLISH_TABLE_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 20))
     ))
     setattr(smp, 'AgeSpectraTable', Table(
         id='6', name='Age Spectra', header=samples.SPECTRUM_TABLE_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 26))
     ))
     setattr(smp, 'IsochronsTable', Table(
@@ -228,7 +228,7 @@ def initial(smp: Sample):
     ))
     setattr(smp, 'TotalParamsTable', Table(
         id='8', name='Total Params', header=samples.TOTAL_PARAMS_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1, 29, 30, 32, 33, 60, 99, *list(range(100, 115))],
+        text_indexes=[0, 1, 2, 29, 30, 32, 33, 60, 99, *list(range(100, 115))],
         # numeric_indexes=list(range(1, 120)),
     ))
 
@@ -334,10 +334,13 @@ def check_version(smp: Sample):
             v, sv = smp.TotalParam[59:61]
     except:
         doNormalize = False
-    smp.NormalizeFactor = [
+    smp.TotalParam[136:138] = [
         [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))]
     ]
+
+    # 20251001:  # add marks for every table
+    smp = smp.recalculate(re_set_table=True, re_table_style=True)
     return smp
 
 

ararpy/smp/plots.py

@@ -416,7 +416,7 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
     -------
     None
     """
-    ar39k, sar39k = calc.arr.mul(sample.DegasValues[20:22], sample.NormalizeFactor)
+    ar39k, sar39k = calc.arr.mul(sample.DegasValues[20:22], sample.TotalParam[136:138])
     ar40r, sar40r = sample.DegasValues[24:26]
     ar40rar39k = calc.arr.div([ar40r, sar40r], [ar39k, sar39k])
     params_initial_ratio = calc.arr.partial(sample.TotalParam, cols=list(range(115, 120)))
@@ -575,7 +575,7 @@ def recalc_mdf_plateaus(sample: Sample, **kwargs):
     -------
     None
     """
-    ar36a, sar36a = calc.arr.mul(sample.DegasValues[0:2], sample.NormalizeFactor)
+    ar36a, sar36a = calc.arr.mul(sample.DegasValues[0:2], sample.TotalParam[136:138])
     ar40aar36a = sample.ApparentAgeValues[0:2]
     mdf = sample.ApparentAgeValues[2:4]
 
@@ -613,7 +613,7 @@ def calc_ar40ar39(r, sr, smp):
     """
     try:
         ar36a = np.array(smp.DegasValues[0:2])
-        ar39k = calc.arr.mul(smp.DegasValues[20:22], smp.NormalizeFactor)
+        ar39k = calc.arr.mul(smp.DegasValues[20:22], smp.TotalParam[136:138])
         ar40 = smp.CorrectedValues[8:10]
         ar40k = smp.DegasValues[30:32]
         size = ar36a.shape[-1]
@@ -675,7 +675,7 @@ def get_plateau_results(smp: Sample, sequence: list, ar40rar39k: list = None,
     else:
         raise TypeError(f"Sample type is not supported: {smp.Info.sample.type}")
 
-    age = handle(ar40ar39=ar40rar39k, smp=smp)[0:2]
+    age = handle(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)