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

ararpy/smp/style.py

@@ -19,7 +19,7 @@ Sample = samples.Sample
 Table = samples.Table
 Plot = samples.Plot
 
-TABLEHEADER = lambda index, sample_type: {
+TABLEHEADER = lambda sample_type, index: {
     'Unknown': ['',
                 samples.SAMPLE_INTERCEPT_HEADERS, samples.BLANK_INTERCEPT_HEADERS,
                 samples.CORRECTED_HEADERS, samples.DEGAS_HEADERS, samples.PUBLISH_TABLE_HEADERS,
@@ -55,6 +55,7 @@ def set_plot_style(smp: Sample):
     -------
 
     """
+
     # Reset styles
     initial.initial_plot_styles(smp, except_attrs=['data'])
     # Auto scale
@@ -64,7 +65,10 @@ def set_plot_style(smp: Sample):
     # Auto position and contents of texts
     reset_text(smp)
     # Set title, which are deleted in initializing
-    suffix = f"{smp.Info.sample.name} {smp.Info.sample.material}"
+    exp_name = smp.Info.experiment.name
+    smp_name = smp.Info.sample.name
+    name = f"{exp_name} {smp_name}" if str(exp_name).lower().strip() != str(smp_name).lower().strip() else exp_name
+    suffix = f"{name} {smp.Info.sample.material}"
     for figure_id, figure in basic.get_components(smp).items():
         if isinstance(figure, Plot):
             if not hasattr(figure, 'title'):
@@ -84,15 +88,28 @@ def reset_plot_scale(smp: Sample, only_figure: str = None):
     -------
     tuple of two tuples, (xscale, yscale)
     """
+
+
+
     for k, v in basic.get_components(smp).items():
         if not isinstance(v, Plot):
             continue
         if only_figure is not None and k != only_figure:
             continue
+
+        try:
+            params_to_check = {
+                v.name: [
+                    {'data': v.data, 'dtype': float, 'class': 'k1', },
+                ],
+            }
+        except (IndexError, AttributeError) as e:
+            raise ValueError(f"{v.name}, {str(e)}")
+        if not basic.validate_params(**params_to_check):
+            return
+
         if k == 'figure_1':
             try:
-                # data = calc.arr.transpose(
-                #     v.data + v.data + v.set1.data + v.set1.data + v.set2.data + v.set2.data)
                 k0 = calc.arr.transpose(v.data)
                 k1 = calc.arr.transpose(v.set1.data) if len(v.set1.data) != 0 else [[]] * 3
                 k2 = calc.arr.transpose(v.set2.data) if len(v.set2.data) != 0 else [[]] * 3
@@ -109,7 +126,7 @@ def reset_plot_scale(smp: Sample, only_figure: str = None):
                 xscale = calc.plot.get_axis_scale(xlist)
                 yscale = [0, 0.004, 4, 0.001]
             except (Exception, BaseException):
-                # print(traceback.format_exc())
+                print(traceback.format_exc())
                 continue
         elif k == 'figure_7':
             try:
@@ -121,7 +138,7 @@ def reset_plot_scale(smp: Sample, only_figure: str = None):
                 setattr(getattr(v, 'zaxis'), 'max', zscale[1])
                 setattr(getattr(v, 'zaxis'), 'split_number', zscale[2])
             except (Exception, BaseException):
-                # print(traceback.format_exc())
+                print(traceback.format_exc())
                 continue
         elif k == 'figure_9':
             try:
@@ -141,7 +158,7 @@ def reset_plot_scale(smp: Sample, only_figure: str = None):
                 xscale = calc.plot.get_axis_scale(xlist)
                 yscale = calc.plot.get_axis_scale(ylist)
             except (Exception, BaseException):
-                # print(traceback.format_exc())
+                print(traceback.format_exc())
                 continue
         setattr(getattr(v, 'xaxis', Plot.Axis()), 'min', xscale[0])
         setattr(getattr(v, 'xaxis', Plot.Axis()), 'max', xscale[1])
@@ -195,9 +212,11 @@ def set_table_style(sample: Sample):
     -------
 
     """
+    std = initial.initial(Sample())
     for key, comp in basic.get_components(sample).items():
         if isinstance(comp, Table):
             comp.header = TABLEHEADER(sample_type=sample.Info.sample.type, index=int(comp.id))
+            comp.text_indexes = basic.get_component_byid(std, comp.id).text_indexes
             comp.set_coltypes()
             # comp.colcount = len(comp.header)
             # comp.coltypes = [{'type': 'numeric'}] * (comp.colcount)

ararpy/smp/table.py

@@ -38,17 +38,13 @@ def update_table_data(smp: Sample, only_table: str = None):
         if only_table is not None and key != only_table:
             continue
         if key == '1':
-            data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.SampleIntercept)
+            data = [smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.SampleIntercept]
         elif key == '2':
-            data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.BlankIntercept)
+            data = [smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.BlankIntercept]
         elif key == '3':
-            data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.CorrectedValues)
+            data = [smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.CorrectedValues]
         elif key == '4':
-            data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.DegasValues)
+            data = [smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.DegasValues]
         elif key == '5':
             smp.PublishValues[0] = copy.deepcopy(smp.DegasValues[ 0])
             smp.PublishValues[1] = copy.deepcopy(smp.DegasValues[ 8])
@@ -57,19 +53,31 @@ def update_table_data(smp: Sample, only_table: str = None):
             smp.PublishValues[4] = copy.deepcopy(smp.DegasValues[24])
             smp.PublishValues[5:7] = copy.deepcopy(smp.ApparentAgeValues[2:4])
             smp.PublishValues[7:9] = copy.deepcopy(smp.ApparentAgeValues[6:8])
-            data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.PublishValues)
+            data = [smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.PublishValues]
         elif key == '6':
-            data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.ApparentAgeValues)
+            data = [smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.ApparentAgeValues]
         elif key == '7':
-            data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.IsochronValues)
+            data = [smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.IsochronValues]
         elif key == '8':
-            data = calc.arr.merge(
-                smp.SequenceName, smp.SequenceValue, *smp.TotalParam)
+            data = [smp.SequenceName, smp.SequenceValue, smp.IsochronMark, *smp.TotalParam]
         else:
             data = [['']]
+
+        try:
+            params_to_check = {
+                comp.name: [
+                    {'data': [data[i] for i in comp.text_indexes], 'dtype': str, 'class': 'k1', },
+                    {'data': [data[i] for i in range(len(data)) if i not in comp.text_indexes], 'dtype': float, 'class': 'k1', },
+                ],
+                'step num': {'data': len(smp.SequenceName), 'dtype': int,
+                             'func': lambda x: x == smp.Info.experiment.step_num >= 0, 'class': 'k2', },
+            }
+        except (IndexError, AttributeError) as e:
+            raise ValueError(f"{type(e).__name__}, {str(e)}")
+        if not basic.validate_params(**params_to_check):
+            return
+
+        comp.set_colcount(len(data))
         # calc.arr.replace(data, pd.isnull, None)
         setattr(comp, 'data', calc.arr.transpose(data))
 
@@ -111,42 +119,43 @@ def update_handsontable(smp: Sample, data: list, id: str):
 
     update_all_table = False
     try:
-        if data[1] != smp.SequenceValue:
+        if data[1] != smp.SequenceValue or data[2] != smp.IsochronMark:
             update_all_table = True
             smp.SequenceValue = data[1]
+            smp.IsochronMark = data[2]
     except IndexError:
+        print(f"Check sequence value / isochron mark failed")
         pass
 
     if id == '1':  # 样品值
-        data = _normalize_data(data, len(samples.SAMPLE_INTERCEPT_HEADERS), 2)
+        data = _normalize_data(data, len(samples.SAMPLE_INTERCEPT_HEADERS), 3)
         smp.SampleIntercept = _digitize_data(data)
     elif id == '2':  # 本底值
-        data = _normalize_data(data, len(samples.BLANK_INTERCEPT_HEADERS), 2)
+        data = _normalize_data(data, len(samples.BLANK_INTERCEPT_HEADERS), 3)
         smp.BlankIntercept = _digitize_data(data)
     elif id == '3':  # 校正值
-        data = _normalize_data(data, len(samples.CORRECTED_HEADERS), 2)
+        data = _normalize_data(data, len(samples.CORRECTED_HEADERS), 3)
         smp.CorrectedValues = _digitize_data(data)
     elif id == '4':  # Degas table
-        data = _normalize_data(data, len(samples.DEGAS_HEADERS), 2)
+        data = _normalize_data(data, len(samples.DEGAS_HEADERS), 3)
         smp.DegasValues = _digitize_data(data)
     elif id == '5':  # 发行表
-        data = _normalize_data(data, len(samples.PUBLISH_TABLE_HEADERS), 2)
+        data = _normalize_data(data, len(samples.PUBLISH_TABLE_HEADERS), 3)
         smp.PublishValues = _digitize_data(data)
     elif id == '6':  # 年龄谱
-        data = _normalize_data(data, len(samples.SPECTRUM_TABLE_HEADERS), 2)
+        data = _normalize_data(data, len(samples.SPECTRUM_TABLE_HEADERS), 3)
         smp.ApparentAgeValues = _digitize_data(data)
     elif id == '7':  # 等时线
-        smp.IsochronMark = _digitize_data(data)[2]
         data = _normalize_data(data, len(samples.ISOCHRON_TABLE_HEADERS), 3)
         smp.IsochronValues = _digitize_data(data)
-        smp.sequence()
     elif id == '8':  # 总参数
-        data = _normalize_data(data, len(samples.TOTAL_PARAMS_HEADERS), 2)
+        data = _normalize_data(data, len(samples.TOTAL_PARAMS_HEADERS), 3)
         data = _digitize_data(data)
         data[101: 112] = [_strToBool(i) for i in data[101: 112]]
         smp.TotalParam = data
     else:
         raise ValueError(f"{id = }, The table id is not supported.")
+    smp.sequence()
     if update_all_table:
         update_table_data(smp)
     else:
@@ -171,21 +180,21 @@ def update_data_from_table(smp: Sample, only_table: str = None):
         if only_table is not None and key != only_table:
             continue
         if key == '1':
-            smp.SampleIntercept = calc.arr.transpose(comp.data)[2:]
+            smp.SampleIntercept = calc.arr.transpose(comp.data)[3:]
         elif key == '2':
-            smp.BlankIntercept = calc.arr.transpose(comp.data)[2:]
+            smp.BlankIntercept = calc.arr.transpose(comp.data)[3:]
         elif key == '3':
-            smp.CorrectedValues = calc.arr.transpose(comp.data)[2:]
+            smp.CorrectedValues = calc.arr.transpose(comp.data)[3:]
         elif key == '4':
-            smp.DegasValues = calc.arr.transpose(comp.data)[2:]
+            smp.DegasValues = calc.arr.transpose(comp.data)[3:]
         elif key == '5':
-            smp.PublishValues = calc.arr.transpose(comp.data)[2:]
+            smp.PublishValues = calc.arr.transpose(comp.data)[3:]
         elif key == '6':
-            smp.ApparentAgeValues = calc.arr.transpose(comp.data)[2:]
+            smp.ApparentAgeValues = calc.arr.transpose(comp.data)[3:]
         elif key == '7':
             smp.IsochronValues = calc.arr.transpose(comp.data)[3:]
         elif key == '8':
-            smp.TotalParam = calc.arr.transpose(comp.data)[2:]
+            smp.TotalParam = calc.arr.transpose(comp.data)[3:]
         else:
             pass
 

ararpy/thermo/atomic_level_random_walk.py

@@ -127,8 +127,9 @@ def walker2(pos: np.ndarray, duration, step_length, min_bound, max_bound, time_s
     :return:
     """
 
-    if len(pos) == 0:
-        return pos
+    # Ar40模拟时不能判断，因为会增加
+    # if len(pos) == 0:
+    #     return pos
 
     dimension = pos.shape[-1] if len(pos.shape) > 1 else 1
 
@@ -141,7 +142,6 @@ def walker2(pos: np.ndarray, duration, step_length, min_bound, max_bound, time_s
             conditions = np.array([[-50, -50, 50, 50, 1]])
 
     for step in range(int(1e16)):
-
         n = parent - int(parent * math.exp(-1 * decay * dt / (3600 * 24 * 365.2425)))
         # print(f"number of new pos = {n}")
         parent = parent - n
@@ -288,6 +288,8 @@ class DiffSimulation:
         self.end_at = 0
         self.dimension = 3
 
+        self.thermal_log = []
+
         self.size_scale = 1
         self.length_scale = 1
 
@@ -373,7 +375,7 @@ class DiffSimulation:
                         boundary_factor = 0.1 ** (k * math.log10(1 + (max(conditions[:, -1]) // 1000)))
                     step_length = self.step_length / np.sqrt(pos.shape[1] if len(pos.shape) > 1 else 1)
                     scale = int(total_steps)
-                    # print(f"调整后: {nsteps_factor = }, gamma = {conditions[0][-1]}, {total_steps = }, {compensation = }, {boundary_factor = }")
+                    print(f"调整后: {nsteps_factor = }, gamma = {conditions[0][-1]}, {total_steps = }, {compensation = }, {boundary_factor = }")
 
                     _pos = walker(
                         copy.deepcopy(pos), step_length=step_length, total_nsteps=total_steps,
@@ -437,7 +439,7 @@ class DiffSimulation:
                 self.remained_per_step.append(len(pos))
                 self.released_per_step.append(self.natoms - len(pos))
 
-            print(f"{index = } {duration} - {heating_duration = } - {temperature = } - {total_steps = } - conc = {len(pos) / self.natoms * 100:.2f}% - {time.time() - _start:.5f}s")
+            print(f"{index = } {duration = }s - {heating_duration = }s - {temperature = }K - {total_steps = } - conc = {len(pos) / self.natoms * 100:.2f}% - {time.time() - _start:.5f}s")
 
         self.positions = copy.deepcopy(pos)
 
@@ -452,6 +454,49 @@ class DiffSimulation:
         return self.run_sequence(*seq, domains=domains, nsteps_factor=scale, simulating=simulation,
                                  epsilon=epsilon, start_time=start_time)
 
+def demo_init(n, es, fs, di, gs, ds, fr, ss=1):
+    demo = DiffSimulation()
+    # fs 应从大到小，父空间在前，子空间在后
+
+    # demo.grain_size = 300
+    # demo.size_scale = 0.05
+    # demo.atom_density = 1e14  # 原子密度 个/立方厘米
+
+    demo.dimension = di                 # dimension, 1 or 3
+    demo.size_scale = 1                 # size_scale
+    demo.grain_size = gs                # grain_szie
+    demo.frequency = fr                 # frequency
+
+    # domains应该从外到内
+    domains = []
+    for i in range(n-1, 0-1, -1):
+        size = int(demo.grain_size * fs[i]) * demo.size_scale
+        center = np.zeros(demo.dimension)
+        if isinstance(ds, (int, float)) or len(ds) == 1:
+            demo.atom_density = ds              # atom_density  # 原子密度 个/立方厘米
+            if i == 2:
+                ad = ds * 5 / 4
+            else:
+                ad = ds
+        else:
+            ad = ds[i]
+        dom = Domain(
+            dimension=demo.dimension, atom_density=ad, min_bound=center - size / 2, max_bound=center + size / 2,
+            energy=es[i], fraction=fs[i], inclusions=[domains[-1]] if len(domains) >= 1 else []
+        )
+        domains.append(dom)
+    # domains应该从外到内, 上面为了inclusion以及方便不同扩散域设置不同的密度，要按照从小到大的顺序生成，但是后面行走的时候要根据不同条件设置系数，要从外到内
+    demo.domains = sorted(domains, key=lambda dom: dom.fraction, reverse=True)
+
+    demo.setup()
+
+    a = [f"{dom.fraction = }, {dom.energy = }, {dom.natoms = }, {dom.atom_density = }" for dom in demo.domains]
+
+    print(
+        f"Total Atoms: {demo.natoms}\n" + "\n".join(a)
+    )
+
+    return demo
 
 def run(times, temps, statuses, energies, fractions, ndoms: int = 1, grain_szie=275, atom_density=1e10, frequency=1e13,
         dimension: int = 3, targets: list = None, epsilon: float = 0.001, simulation: bool = False,
@@ -472,43 +517,12 @@ def run(times, temps, statuses, energies, fractions, ndoms: int = 1, grain_szie=
     :return:
     """
 
-    demo = DiffSimulation()
-
-    def _(n, es, fs):
-        # fs 应从大到小，父空间在前，子空间在后
-
-        # demo.grain_size = 300
-        # demo.size_scale = 0.05
-        # demo.atom_density = 1e14  # 原子密度 个/立方厘米
-        demo.dimension = dimension
-
-        demo.size_scale = 1
-        demo.grain_size = grain_szie
-        demo.atom_density = atom_density  # 原子密度 个/立方厘米
-        demo.frequency = frequency
-
-        # domains应该从外到内
-        domains = []
-        for i in range(n-1, 0-1, -1):
-            size = int(demo.grain_size * fs[i]) * demo.size_scale
-            center = np.zeros(demo.dimension)
-            if i == 2:
-                ad = demo.atom_density * 5 / 4
-            else:
-                ad = demo.atom_density
-            dom = Domain(
-                dimension=demo.dimension, atom_density=ad, min_bound=center - size / 2, max_bound=center + size / 2,
-                energy=es[i], fraction=fs[i], inclusions=[domains[-1]] if len(domains) >= 1 else []
-            )
-            domains.append(dom)
-        # domains应该从外到内, 上面为了inclusion以及方便不同扩散域设置不同的密度，要按照从小到大的顺序生成，但是后面行走的时候要根据不同条件设置系数，要从外到内
-        demo.domains = sorted(domains, key=lambda dom: dom.fraction, reverse=True)
-
-        demo.setup()
-
+    try:
+        # demo.run_persecond(times=times, temperatures=temps, domains=demo.domains, targets=target,
+        #                    epsilon=epsilon, simulation=simulation)
+        demo = demo_init(ndoms, energies, fractions, dimension, grain_szie, atom_density, frequency, ss=1)
         demo.name = f"{file_name}"
-
-        print(f"Total Atoms: {demo.natoms}, atoms in each dom: {[dom.natoms for dom in demo.domains]} filename: {demo.name}")
+        demo.thermal_log = list(zip(times, temps))
 
         if positions is not None:
             demo.positions = positions
@@ -516,13 +530,7 @@ def run(times, temps, statuses, energies, fractions, ndoms: int = 1, grain_szie=
 
         demo.run_sequence(times=times, temperatures=temps, statuses=statuses, targets=targets, domains=demo.domains,
                           epsilon=epsilon, simulating=simulation, **kwargs)
-        # demo.run_persecond(times=times, temperatures=temps, domains=demo.domains, targets=target,
-        #                    epsilon=epsilon, simulation=simulation)
-
-        return demo
-
-    try:
-        return _(ndoms, energies, fractions), True
+        return demo, True
     except OverEpsilonError as e:
         if ignore_error:
             return demo, False

ararpy/thermo/basic.py

@@ -235,7 +235,7 @@ def get_tc(da2, sda2, E, sE, cooling_rate=10, temp_in_celsius=True, temp=None, A
     R = 8.314 if R is None else R # in J/K mol
     Tc = 600
     sTc = 0
-    Tm = 99999999 if temp is None else temp
+    Tm = 9999999999 if temp is None else temp
     Tm = Tm + 273.15 if temp_in_celsius else Tm
     cooling_rate = cooling_rate / 1000000
 
@@ -243,8 +243,8 @@ def get_tc(da2, sda2, E, sE, cooling_rate=10, temp_in_celsius=True, temp=None, A
     iter_diff = 100
     while abs(iter_diff) > 0.01 and iter_num < 100:
         tau = R * Tc ** 2 / (E * cooling_rate)
-        # new_Tc = (E/R) / log(A * tau * da2)
         new_Tc = (R / E) * log(A * tau * da2) + 1 / Tm  #
+        # new_Tc = (R / E) * log(A * tau * da2)
         d1 = cooling_rate / (A * da2 * Tc ** 2)
         s1 = d1 ** 2 * sda2 ** 2  # da2
         d2 = R / E ** 2 * (log(A * tau * da2) + 1)

{ararpy-0.1.199.dist-info → ararpy-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.199
+Version: 0.2.2
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu
@@ -12,6 +12,14 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.5
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: chardet
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: parse
+Requires-Dist: scipy
+Requires-Dist: xlrd
+Requires-Dist: XlsxWriter
+Requires-Dist: pdf_maker
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -20,6 +28,7 @@ Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: license
 Dynamic: license-file
+Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
 

ararpy-0.2.2.dist-info/RECORD

@@ -0,0 +1,73 @@
+ararpy/Example - Check arr.py,sha256=c9HUUZySUXOYk4eCqiPSp124G2sYpFP5zoMl0FXdalE,1709
+ararpy/Example - Granite Cooling History.py,sha256=V4V63RVp1gocOZX0T3OOGOiVhCA1DqrCyJnXgFvEcUs,14917
+ararpy/Example - Plot temperature calibration.py,sha256=8pR-WKqdaIKQTuuSbfwXuxoEkCop4zhmZUMJSARWDOg,10879
+ararpy/Example - Show MDD results.py,sha256=YFkiQual60lyCClsfvivr4REY6waSYuomf0uo5soUHE,22635
+ararpy/Example - Show all Kfs age spectra.py,sha256=1edPtBpFfS0lC7vLnLu34mDHt_xjbc8ptk6rZ--pf-I,12304
+ararpy/Example - Show random walk results.py,sha256=8WWvbAI7ySiMR-XwtFe5kTQihW3mcqzL3S7EUZdoxYo,15477
+ararpy/Example - Tc calculation.py,sha256=sD9pu3IaZ8mBV95rV2wOEhlQUexFNqBUoBqnNMdUBis,19617
+ararpy/__init__.py,sha256=wz69XzhfcI0QMPU2QJ8gZoWEsG2vHeSE7b5E7GytwI0,6767
+ararpy/test.py,sha256=4F46-JJ1Ge12HGae0qO44Qc6kiEMHBgn2MsY_5LlHDo,3973
+ararpy/calc/__init__.py,sha256=kUjRuLE8TLuKOv3i976RnGJoEMj23QBZDu37LWs81U4,322
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