ararpy 0.1.199__py3-none-any.whl → 0.2.2__py3-none-any.whl

ararpy/smp/plots.py

@@ -58,32 +58,36 @@ def set_plot_data(sample: Sample, isInit: bool = True, isIsochron: bool = True,
 
     # Initialization, apply age spectra data and isochron plot data
     if isInit:
-        try:
-            initial_plot_data(sample)
-        except (Exception, BaseException):
-            print("initial_plot_data(sample) error:\n", traceback.format_exc())
-            pass
+        initial_plot_data(sample)
+        # try:
+        #     initial_plot_data(sample)
+        # except (Exception, BaseException):
+        #     print("initial_plot_data(sample) error:\n", traceback.format_exc())
+        #     pass
 
     # Recalculate isochron lines
     if isIsochron:
-        try:
-            recalc_isochrons(sample, **kwargs)
-        except (Exception, BaseException):
-            print("recalc_isochrons(sample, **kwargs) error:\n", traceback.format_exc())
-            pass
-        try:
-            reset_isochron_line_data(sample)
-        except (Exception, BaseException):
-            print("reset_isochron_line_data(sample):\n", traceback.format_exc())
-            pass
+        recalc_isochrons(sample, **kwargs)
+        reset_isochron_line_data(sample)
+        # try:
+        #     recalc_isochrons(sample, **kwargs)
+        # except (Exception, BaseException):
+        #     print("recalc_isochrons(sample, **kwargs) error:\n", traceback.format_exc())
+        #     pass
+        # try:
+        #     reset_isochron_line_data(sample)
+        # except (Exception, BaseException):
+        #     print("reset_isochron_line_data(sample):\n", traceback.format_exc())
+        #     pass
 
     # Recalculate plateaus
     if isPlateau:
-        try:
-            recalc_plateaus(sample)
-        except (Exception, BaseException):
-            print("recalc_plateaus(sample) error:\n", traceback.format_exc())
-            pass
+        recalc_plateaus(sample)
+        # try:
+        #     recalc_plateaus(sample)
+        # except (Exception, BaseException):
+        #     print("recalc_plateaus(sample) error:\n", traceback.format_exc())
+        #     pass
 
 
 # =======================
@@ -100,26 +104,42 @@ def initial_plot_data(smp: Sample):
     -------
     None
     """
+    try:
+        params_to_check = {
+            'normal': {'data': smp.IsochronValues[0:5], 'dtype': float, 'class': 'k1', },
+            'inverse': {'data': smp.IsochronValues[6:11], 'dtype': float, 'class': 'k2', },
+            'K-Cl-Ar 1': {'data': smp.IsochronValues[12:17], 'dtype': float, 'class': 'k3', },
+            'K-Cl-Ar 2': {'data': smp.IsochronValues[18:23], 'dtype': float, 'class': 'k4', },
+            'K-Cl-Ar 3': {'data': smp.IsochronValues[24:29], 'dtype': float, 'class': 'k5', },
+            '3D': {'data': smp.IsochronValues[30:39], 'dtype': float, 'class': 'k6', },
+            'age spectra': [
+                {'data': smp.ApparentAgeValues[2:4], 'dtype': float, 'class': 'k7', },
+                {'data': smp.ApparentAgeValues[7], 'dtype': float, 'class': 'k7', },
+            ],
+            'degas pattern': {'data': smp.IsochronValues[30:39], 'dtype': float, 'class': 'k8', },
+            'age distribution': {'data': smp.IsochronValues[30:39], 'dtype': float, 'class': 'k9', },
+        }
+    except (IndexError, AttributeError) as e:
+        raise
+    if not basic.validate_params(**params_to_check):
+        return
+
+    # Isochron plots
     for key, val in ISOCHRON_INDEX_DICT.items():
         figure = basic.get_component_byid(smp, key)
-        try:
-            # data = [x, sx, y, sy, (z, sz,) r1, (r2, r3,), index from 1]
-            figure.data = smp.IsochronValues[val['data_index'][0]:val['data_index'][1]] + \
-                          [[i + 1 for i in range(len(smp.SequenceName))]]
-        except (Exception, BaseException):
-            print(traceback.format_exc())
-            figure.data = [[]] * (val['data_index'][1] - val['data_index'][0]) + \
-                          [[i + 1 for i in range(len(smp.SequenceName))]]
-        finally:
-            # Ellipse
-            if key != 'figure_7':
-                ellipse_data = []
-                for point in calc.arr.transpose(figure.data[:5]):
-                    if '' not in point and None not in point:
-                        ellipse_data.append(calc.isochron.get_ellipse(*point))
-                        getattr(figure, 'ellipse', Set(id='ellipse')).data = ellipse_data
-
-    # Set age spectra lines
+        figure.data = [
+            *smp.IsochronValues[val['data_index'][0]:val['data_index'][1]],
+            list(range(smp.Info.experiment.step_num))
+        ]
+        # Ellipse
+        if key != 'figure_7':
+            ellipse_data = []
+            for point in calc.arr.transpose(figure.data[:5]):
+                if '' not in point and None not in point:
+                    ellipse_data.append(calc.isochron.get_ellipse(*point))
+                    getattr(figure, 'ellipse', Set(id='ellipse')).data = ellipse_data
+
+    # Age spectra plot
     # Try to calculate total gas age
     try:
         if str(smp.Info.sample.type).lower() == "unknown":
@@ -142,8 +162,6 @@ def initial_plot_data(smp: Sample):
         print(traceback.format_exc())
         total_f = [np.nan] * 2
         total_age = [np.nan] * 4
-    print(f"{total_f = }")
-    print(f"{total_age = }")
     smp.Info.results.age_spectra['TGA'].update(
         {'Ar39': 100, 'F': total_f[0], 'sF': total_f[1], 'age': total_age[0],
          's1': total_age[1], 's2': total_age[2], 's3': total_age[3], 'Num': len(smp.DegasValues[24])}
@@ -156,32 +174,10 @@ def initial_plot_data(smp: Sample):
         smp.AgeSpectraPlot.data = []
 
     # Degassing plot
-    try:
-        if not hasattr(smp, 'DegasPatternPlot'):
-            setattr(smp, 'DegasPatternPlot', Plot(id='figure_8', name='Degas Pattern Plot'))
-        isotope_percentage = lambda l: [e / sum(l) * 100 if sum(l) != 0 else 0 for e in l]
-        smp.DegasPatternPlot.data = [
-            isotope_percentage(smp.DegasValues[0]),  # Ar36a
-            isotope_percentage(smp.DegasValues[8]),  # Ar37Ca
-            isotope_percentage(smp.DegasValues[10]),  # Ar38Cl
-            isotope_percentage(smp.DegasValues[20]),  # Ar39K
-            isotope_percentage(smp.DegasValues[24]),  # Ar40r
-            isotope_percentage(smp.CorrectedValues[0]),  # Ar36
-            isotope_percentage(smp.CorrectedValues[2]),  # Ar37
-            isotope_percentage(smp.CorrectedValues[4]),  # Ar38
-            isotope_percentage(smp.CorrectedValues[6]),  # Ar39
-            isotope_percentage(smp.CorrectedValues[8]),  # Ar40
-        ]
-        smp.DegasPatternPlot.info = [True] * 10
-    except Exception as e:
-        print(traceback.format_exc())
-        pass
+    recalc_degassing_plot(smp)
 
-    # Set age distribution plot data
-    try:
-        recalc_agedistribution(smp)
-    except Exception as e:
-        print(traceback.format_exc())
+    # Age distribution plot
+    recalc_agedistribution(smp)
 
 
 # =======================
@@ -249,13 +245,14 @@ def get_isochron_results(data: list, smp: Sample, sequence, figure_type: int = 0
 
     if len(sequence) < 3:
         return iso_res
-    regression_method = {
-        "york-2": calc.regression.york2, "olst": calc.regression.olst
-    }.get(smp.TotalParam[97][min(sequence)].lower(), calc.regression.york2)
     try:
+        regression_method = {
+            "york-2": calc.regression.york2, "olst": calc.regression.olst
+        }.get(smp.TotalParam[97][min(sequence)].lower(), calc.regression.york2)
         regression_res = regression_method(*data[:5])
     except (Exception, BaseException):
-        # print(f"Warning: {traceback.format_exc()}")
+        # print(f"{data[:5] = }")
+        # print(f"Warning Isochron Regression: {traceback.format_exc()}")
         return iso_res
     else:
         iso_res.update(dict(zip(reg_res_index, regression_res)))
@@ -348,50 +345,14 @@ def reset_isochron_line_data(smp: Sample):
     for k, v in basic.get_components(smp).items():
         if not isinstance(v, Plot):
             continue
+        if k not in ['figure_2', 'figure_3', 'figure_4', 'figure_5', 'figure_6', ]:
+            continue
         for index in [0, 1]:
-            try:
-                xscale, yscale = [v.xaxis.min, v.xaxis.max], [v.yaxis.min, v.yaxis.max]
-                coeffs = [smp.Info.results.isochron[k][index]['k'], smp.Info.results.isochron[k][index]['m1']]
-                line_point = calc.isochron.get_line_points(xscale, yscale, coeffs)
-                setattr(getattr(v, ['line1', 'line2'][index]), 'data', line_point)
-                setattr(getattr(v, ['text1', 'text2'][index]), 'text', "")  # 注意和js的配合，js那边根据text是否为空判断是否重新生成文字
-            except Exception:
-                # print(traceback.format_exc())
-                continue
-
-
-def set_selection(smp: Sample, index: int, mark: int):
-    """
-    Parameters
-    ----------
-    smp : sample instance
-    index : int, data point index
-    mark : int, 0 for unselected, 1 for set1, 2 for set2
-
-    Returns
-    -------
-
-    """
-    if mark not in [1, 2, '1', '2']:
-        raise ValueError(f"{mark = }, mark must be 1 or 2.")
-
-    def seq(_i): return [smp.UnselectedSequence, smp.SelectedSequence1, smp.SelectedSequence2][_i]
-
-    if index in seq(mark):
-        seq(mark).remove(index)
-        smp.UnselectedSequence.append(index)
-    else:
-        for i in [0, [0, 2, 1][mark]]:
-            if index in seq(i):
-                seq(i).remove(index)
-        seq(mark).append(index)
-    smp.IsochronMark = [
-        '1' if i in smp.SelectedSequence1 else '2' if i in smp.SelectedSequence2 else '' for i in
-        range(len(smp.IsochronValues[2]))]
-    #
-    smp.Info.results.selection[0]['data'] = smp.SelectedSequence1
-    smp.Info.results.selection[1]['data'] = smp.SelectedSequence2
-    smp.Info.results.selection[2]['data'] = smp.UnselectedSequence
+            xscale, yscale = [v.xaxis.min, v.xaxis.max], [v.yaxis.min, v.yaxis.max]
+            coeffs = [smp.Info.results.isochron[k][index]['k'], smp.Info.results.isochron[k][index]['m1']]
+            line_point = calc.isochron.get_line_points(xscale, yscale, coeffs)
+            setattr(getattr(v, ['line1', 'line2'][index]), 'data', line_point)
+            setattr(getattr(v, ['text1', 'text2'][index]), 'text', "")  # 注意和js的配合，js那边根据text是否为空判断是否重新生成文字
 
 
 # =======================
@@ -418,7 +379,7 @@ 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)))
@@ -577,7 +538,7 @@ 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]
 
@@ -615,7 +576,7 @@ 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]
@@ -677,7 +638,7 @@ 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)
@@ -759,53 +720,72 @@ def recalc_j_plateaus(sample: Sample, **kwargs):
 # =======================
 # Age Distribution Plot
 # =======================
-def recalc_agedistribution(sample: Sample, **kwargs):
-    for i in range(2):
-        try:
-            # Age bars
-            sample.AgeDistributionPlot.set3.data = calc.arr.remove(sample.ApparentAgeValues[2:4], (None, np.nan))
-            # Set histogram data
-            s = getattr(sample.AgeDistributionPlot.set1, 'bin_start', None)
-            w = getattr(sample.AgeDistributionPlot.set1, 'bin_width', None)
-            c = getattr(sample.AgeDistributionPlot.set1, 'bin_count', None)
-            r = getattr(sample.AgeDistributionPlot.set1, 'bin_rule', None)
-            # print(f's = {s}, r = {r}, w = {w}, c = {c}')
-            histogram_data = calc.histogram.get_data(sample.ApparentAgeValues[2], s=s, r=r, w=w, c=c)
-            sample.AgeDistributionPlot.set1.data = [histogram_data[1], histogram_data[0], histogram_data[2]]  # [half_bins, counts]
-            setattr(sample.AgeDistributionPlot.set1, 'bin_start', histogram_data[3])
-            setattr(sample.AgeDistributionPlot.set1, 'bin_rule', histogram_data[4])
-            setattr(sample.AgeDistributionPlot.set1, 'bin_width', histogram_data[5])
-            setattr(sample.AgeDistributionPlot.set1, 'bin_count', histogram_data[6])
-            h = getattr(sample.AgeDistributionPlot.set2, 'band_width', None)
-            k = getattr(sample.AgeDistributionPlot.set2, 'band_kernel', 'normal')
-            t = getattr(sample.AgeDistributionPlot.set2, 'band_extend', False)
-            a = getattr(sample.AgeDistributionPlot.set2, 'auto_width', 'Scott')
-            n = getattr(sample.AgeDistributionPlot.set2, 'band_points', 1000)
-            # print(f'h = {h}, k = {k}, a = {a}, n = {n}, extend = {t}')
-            kda_data = calc.histogram.get_kde(
-                sample.ApparentAgeValues[2], h=h, k=k, n=n, a=a,
-                s=float(getattr(sample.AgeDistributionPlot.xaxis, 'min')) if t else histogram_data[3],
-                e=float(getattr(sample.AgeDistributionPlot.xaxis, 'max')) if t else histogram_data[7],
-            )
-            sample.AgeDistributionPlot.set2.data = kda_data[0]  # [values, kda]
-            setattr(sample.AgeDistributionPlot.set2, 'band_width', kda_data[1])
-            setattr(sample.AgeDistributionPlot.set2, 'band_kernel', kda_data[2])
-            setattr(sample.AgeDistributionPlot.set2, 'auto_width', kda_data[3])
-            # sorted_data = [i[0] for i in sorted(zipped_data, key=lambda x: x[1])]
-            text = f'n = {len(sample.ApparentAgeValues[2])}'
-            peaks = find_peaks(kda_data[0][1])
-            for index, peak in enumerate(peaks[0].tolist()):
-                text = text + f'\nPeak {index}: {kda_data[0][0][peak]:.2f}'
-            setattr(sample.AgeDistributionPlot.text1, 'text', text)
-        except AttributeError:
-            print(traceback.format_exc())
-            initial.re_set_smp(sample)
-            continue
-        except (Exception, BaseException):
-            print(traceback.format_exc())
-            sample.AgeDistributionPlot.data = [[], []]
-            sample.AgeDistributionPlot.set1.data = [[], []]
-            sample.AgeDistributionPlot.set2.data = [[], []]
-        break
+def recalc_agedistribution(smp: Sample, **kwargs):
+    try:
+        ages = smp.ApparentAgeValues[2]
+        plot = smp.AgeDistributionPlot
+        # Set3: Age bars
+        plot.set3.data = calc.arr.remove(smp.ApparentAgeValues[2:4], (None, np.nan))
+
+        # Set1: Histogram data
+        s = getattr(plot.set1, 'bin_start', None)
+        w = getattr(plot.set1, 'bin_width', None)
+        c = getattr(plot.set1, 'bin_count', None)
+        r = getattr(plot.set1, 'bin_rule', None)
+        # print(f's = {s}, r = {r}, w = {w}, c = {c}')
+        histogram_data = calc.histogram.get_data(ages, s=s, r=r, w=w, c=c)
+        plot.set1.data = [histogram_data[1], histogram_data[0], histogram_data[2]]  # [half_bins, counts]
+        setattr(plot.set1, 'bin_start', histogram_data[3])
+        setattr(plot.set1, 'bin_rule', histogram_data[4])
+        setattr(plot.set1, 'bin_width', histogram_data[5])
+        setattr(plot.set1, 'bin_count', histogram_data[6])
+        h = getattr(plot.set2, 'band_width', None)
+        k = getattr(plot.set2, 'band_kernel', 'normal')
+        t = getattr(plot.set2, 'band_extend', False)
+        a = getattr(plot.set2, 'auto_width', 'Scott')
+        n = getattr(plot.set2, 'band_points', 1000)
+        # print(f'h = {h}, k = {k}, a = {a}, n = {n}, extend = {t}')
+        kda_data = calc.histogram.get_kde(
+            ages, h=h, k=k, n=n, a=a,
+            s=float(getattr(plot.xaxis, 'min')) if t else histogram_data[3],
+            e=float(getattr(plot.xaxis, 'max')) if t else histogram_data[7],
+        )
+
+        # Set2: KDA data
+        plot.set2.data = kda_data[0]  # [values, kda]
+        setattr(plot.set2, 'band_width', kda_data[1])
+        setattr(plot.set2, 'band_kernel', kda_data[2])
+        setattr(plot.set2, 'auto_width', kda_data[3])
+        # sorted_data = [i[0] for i in sorted(zipped_data, key=lambda x: x[1])]
+        text = f'n = {len(ages)}'
+        peaks = find_peaks(kda_data[0][1])
+        for index, peak in enumerate(peaks[0].tolist()):
+            text = text + f'\nPeak {index}: {kda_data[0][0][peak]:.2f}'
+        setattr(plot.text1, 'text', text)
+    except (Exception, BaseException):
+        print(traceback.format_exc())
+        plot.data = [[], []]
+        plot.set1.data = [[], []]
+        plot.set2.data = [[], []]
 
 
+# =======================
+# Age Distribution Plot
+# =======================
+def recalc_degassing_plot(smp: Sample, **kwargs):
+    if not hasattr(smp, 'DegasPatternPlot'):
+        setattr(smp, 'DegasPatternPlot', Plot(id='figure_8', name='Degas Pattern Plot'))
+    isotope_percentage = lambda l: [e / sum(l) * 100 if sum(l) != 0 else 0 for e in l]
+    smp.DegasPatternPlot.data = [
+        isotope_percentage(smp.DegasValues[0]),  # Ar36a
+        isotope_percentage(smp.DegasValues[8]),  # Ar37Ca
+        isotope_percentage(smp.DegasValues[10]),  # Ar38Cl
+        isotope_percentage(smp.DegasValues[20]),  # Ar39K
+        isotope_percentage(smp.DegasValues[24]),  # Ar40r
+        isotope_percentage(smp.CorrectedValues[0]),  # Ar36
+        isotope_percentage(smp.CorrectedValues[2]),  # Ar37
+        isotope_percentage(smp.CorrectedValues[4]),  # Ar38
+        isotope_percentage(smp.CorrectedValues[6]),  # Ar39
+        isotope_percentage(smp.CorrectedValues[8]),  # Ar40
+    ]
+    smp.DegasPatternPlot.info = [True] * 10

ararpy/smp/raw.py

@@ -22,7 +22,7 @@ RawData = samples.RawData
 Sequence = samples.Sequence
 
 
-def to_raw(file_path: Union[str, List[str]], input_filter_path: Union[str, List[str]], **kwargs):
+def to_raw(file_path: Union[str, List[str]], input_filter_path: Union[str, List[str]], file_name=None, **kwargs):
     """ Read raw data from files, can create raw data instance based on the given files
     Raw data will have the structure like:
         [
@@ -35,6 +35,7 @@ def to_raw(file_path: Union[str, List[str]], input_filter_path: Union[str, List[
     ----------
     file_path
     input_filter_path
+    file_name
     kwargs
 
     Returns
@@ -42,22 +43,18 @@ def to_raw(file_path: Union[str, List[str]], input_filter_path: Union[str, List[
 
     """
     if isinstance(file_path, list) and isinstance(input_filter_path, list):
-        raw = concatenate([to_raw(file, input_filter_path[index]) for index, file in enumerate(file_path)])
+        raw = concatenate([to_raw(file, input_filter_path[index],
+            file_name[index] if isinstance(file_name, list) else file_name) for index, file in enumerate(file_path)])
     elif isinstance(file_path, str) and isinstance(input_filter_path, str):
         input_filter = read_params(input_filter_path)
-        file_name = str(os.path.split(file_path)[-1]).split('.')[0]
-        res = raw_file.open_file(file_path, input_filter)
+        file_name = str(os.path.split(file_path)[-1]).split('.')[0] if file_name is None else file_name
+        res = raw_file.open_file(file_path, input_filter, file_name)
         data = res.get('data', None)
         sequences = res.get('sequences', None)
         sequence_num = len(data) if data is not None else len(sequences)
-        # default fitting method, all exponential
-        # <option value=0>Linear</option>
-        # <option value=1>Quadratic</option>
-        # <option value=2>Exponential</option>
-        # <option value=3>Power</option>
-        # <option value=4>Average</option>
-        fitting_method = [2, 0, 2, 2, 2]
-        raw = RawData(name=file_name, data=data, isotopic_num=10, sequence_num=sequence_num, source=[file_path],
+        experiment_name = data[0][0][2]['ExpName'] if data is not None else file_name
+        fitting_method = [2, 0, 2, 2, 2]  # 0 - linear, 1 - quadratic, 2 - exponential, 3 - power, 4 - average
+        raw = RawData(name=experiment_name, data=data, isotopic_num=10, sequence_num=sequence_num, source=[file_path],
                       sequence=sequences, unit=str(input_filter[30]), fitting_method=[*fitting_method])
     else:
         raise ValueError("File path and input filter should be both string or list with a same length.")
@@ -156,11 +153,10 @@ def do_regression(raw: RawData, sequence_index: Optional[List] = None, isotopic_
         # unselected: list = [unselected[[isotopic_index*2 + 1, 2 * (isotopic_index + 1)]].dropna().values.tolist()
         #                     for isotopic_index in list(range(5))]
 
-        for index, isotope in enumerate(selected):
+        for index, isotopic_data in enumerate(selected):
             if hasattr(isotopic_index, '__getitem__') and index not in isotopic_index:
                 continue
-            # print(f"regression for {sequence.name = }, isotope {index = }")
-            res = raw_funcs.get_raw_data_regression_results(isotope)
+            res = raw_funcs.get_raw_data_regression_results(isotopic_data)
             try:
                 sequence.results[index] = res[1]
                 sequence.coefficients[index] = res[2]