ararpy 0.1.14__tar.gz → 0.1.15__tar.gz

{ararpy-0.1.14 → ararpy-0.1.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: ararpy
-Version: 0.1.14
+Version: 0.1.15
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.14 → ararpy-0.1.15}/ararpy/argon_diffusion_simulator/main.py

@@ -53,7 +53,7 @@ def _uniform_sphere_step(step_length, shape):
 
 
 def walker(pos, step_length, total_nsteps, min_bound, max_bound, scale=0., compensation=0, remove=True,
-           conditions=None, boundary_factor=1):
+           conditions=None, boundary_factor=1, decay=0, parent=0):
 
     if len(pos) == 0:
         return pos
@@ -122,7 +122,7 @@ def walker(pos, step_length, total_nsteps, min_bound, max_bound, scale=0., compe
 
 
 def walker2(pos: np.ndarray, duration, step_length, min_bound, max_bound, time_scale, frequency,
-            conditions=None, remove: bool = True):
+            conditions=None, remove: bool = True, decay=0, parent=0):
     """
     :return:
     """
@@ -132,6 +132,7 @@ def walker2(pos: np.ndarray, duration, step_length, min_bound, max_bound, time_s
 
     dimension = pos.shape[-1] if len(pos.shape) > 1 else 1
 
+
     dt = time_scale
     if conditions is None:
         if dimension == 3:
@@ -141,6 +142,13 @@ def walker2(pos: np.ndarray, duration, step_length, min_bound, max_bound, time_s
 
     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
+        new_pos = np.random.uniform(max(max_bound), min(min_bound), size=(int(n), dimension))
+        new_pos = new_pos[np.all((new_pos >= min_bound) & (new_pos <= max_bound), axis=1)]
+        pos = np.concatenate((pos, new_pos), axis=0)
+
         res = np.zeros(0).reshape(0, dimension)
         for index, each in enumerate(conditions):
             # each = (x1, y1, z1, x2, y2, z2, gamma)
@@ -235,6 +243,7 @@ class Domain:
         # 初始化粒子位置，随机分布在网格内
         # 初始原子个数  1e14 原子密度 个/立方厘米   1e-4是单位换算 cm/µm
         natoms = int(self.atom_density ** (self.dimension / 3) * (abs(max(self.max_bound) - min(self.min_bound)) * 1e-4) ** self.dimension)
+        natoms = 1 if natoms == 0 else natoms
         self.positions = np.random.uniform(max(self.max_bound), min(self.min_bound), size=(int(natoms), self.dimension))
         self.positions = self.positions[np.all((self.positions >= self.min_bound) & (self.positions <= self.max_bound), axis=1)]
         for dom in self.inclusions:
@@ -320,7 +329,7 @@ class DiffSimulation:
 
     def run_sequence(self, times, temperatures, statuses, targets, domains: List[Domain], nsteps_factor=None,
                      simulating: bool = False, epsilon=0.001, start_time=0, k=1.2, use_walker1=True,
-                     scoring: bool = False):
+                     scoring: bool = False, decay=0, parent=0):
         pos = copy.deepcopy(self.positions)
         self.seq = []  # 用于记录参数
 
@@ -369,7 +378,8 @@ class DiffSimulation:
                     _pos = walker(
                         copy.deepcopy(pos), step_length=step_length, total_nsteps=total_steps,
                         min_bound=self.min_bound, max_bound=self.max_bound, scale=scale,
-                        compensation=compensation, remove=True, conditions=conditions, boundary_factor=boundary_factor
+                        compensation=compensation, remove=True, conditions=conditions, boundary_factor=boundary_factor,
+                        decay=decay, parent=parent
                     )
 
                     # self.seq[index].update({
@@ -383,7 +393,7 @@ class DiffSimulation:
                     scale = k
                     _pos = walker2(copy.deepcopy(pos), duration=heating_duration, step_length=step_length,
                                    min_bound=self.min_bound, max_bound=self.max_bound, time_scale=scale,
-                                   frequency=self.frequency, conditions=conditions, remove=True)
+                                   frequency=self.frequency, conditions=conditions, remove=True, decay=decay, parent=parent)
                     boundary_factor = 1
                     compensation = 0
 
@@ -429,6 +439,8 @@ class DiffSimulation:
 
             print(f"{index = } {duration} - {heating_duration = } - {temperature = } - {total_steps = } - conc = {len(pos) / self.natoms * 100:.2f}% - {time.time() - _start:.5f}s")
 
+        self.positions = copy.deepcopy(pos)
+
     def run_persecond(self, times, temperatures, statuses, targets, domains: List[Domain], scale=None,
                      simulation: bool = False, epsilon=0.001, start_time=0):
         seq = []
@@ -442,6 +454,83 @@ class DiffSimulation:
 
 
 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,
+        file_name: str = "Y70", ignore_error: bool = False, positions=None, **kwargs):
+    """
+    :param times:
+    :param temps:
+    :param statuses:
+    :param energies:
+    :param fractions:
+    :param dimension:
+    :param ndoms:
+    :param targets:
+    :param epsilon:
+    :param simulation:
+    :param file_name:
+    :param ignore_error:
+    :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()
+
+        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}")
+
+        if positions is not None:
+            demo.positions = positions
+            demo.natoms = len(positions)
+
+        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
+    except OverEpsilonError as e:
+        if ignore_error:
+            return demo, False
+        else:
+            raise
+
+
+def run_40ar(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,
         file_name: str = "Y70", ignore_error: bool = False, **kwargs):
     """

{ararpy-0.1.14 → ararpy-0.1.15}/ararpy/calc/age.py

@@ -20,6 +20,7 @@ import numpy as np
 def calc_age_min(F, sF, **kwargs) -> tuple:
     """
     Calculate ArAr ages using Min et al. (2000) equation.
+    Note that the Ar/K of primary standards is not working currently
     Parameters
     ----------
     F : array-like
@@ -68,7 +69,6 @@ def calc_age_min(F, sF, **kwargs) -> tuple:
     # recalculation using Min et al.(2000) equation
     # lmd = A * W * Y / (f * No)
     V = f * No / ((Ab + Ae) * W * Y)
-    sf = 0  # the error of f was not considered by Koppers
     sV = pow((V / f * sf) ** 2 + (V / No * sNo) ** 2 + (V / (Ab + Ae)) ** 2 * (sAb ** 2 + sAe ** 2) +
              (V / W * sW) ** 2 + (V / Y * sY) ** 2, 0.5)
     # standard age in year, change to Ma
@@ -87,7 +87,7 @@ def calc_age_min(F, sF, **kwargs) -> tuple:
     KK = np.exp(t / V) - 1  # 40Arr / 40K Use standard age
     XX = BB * KK * R + 1
     k0 = V * np.log(XX)
-    e1 = (np.log(XX) * V / f - V * BB * KK * R / (f * XX)) ** 2 * sf ** 2  # sFr
+    e1 = (np.log(XX) * V / f - V * BB * KK * R / (f * XX)) ** 2 * sf ** 2  # sF
     e2 = (np.log(XX) * V / No) ** 2 * sNo ** 2  # sNo
     e3 = (-1 * np.log(XX) * V / A + BB * KK * R / (A * XX)) ** 2 * sAb ** 2  # sAb
     e4 = (-1 * np.log(XX) * V / A - Ab * KK * R / (Ae ** 2 * XX)) ** 2 * sAe ** 2  # sAe

{ararpy-0.1.14 → ararpy-0.1.15}/ararpy/calc/basic.py

@@ -66,7 +66,7 @@ def merge_dicts(a: dict, b: dict):
     """
     res = copy.deepcopy(a)
     for key, val in b.items():
-        if key not in res.keys() and key.isnumeric():
+        if key not in res.keys() and str(key).isnumeric():
             key = int(key)
         if key not in res.keys():
             res[key] = val

{ararpy-0.1.14 → ararpy-0.1.15}/ararpy/calc/corr.py

@@ -59,14 +59,14 @@ def mdf(rm: float, srm: float, m1: float, m2: float, ra: float = 298.56,
     sdelta_m = err.add(sm2, sm1)
     ratio_m = m2 / m1
     sratio_m = err.div((m2, sm2), (m1, sm1))
-    isAapkop = True
-    if isAapkop:
+    useRyu = False
+    if not useRyu:
         # line
-        k1 = (ra / rm + delta_m - 1) / delta_m  # A.A.P.Koppers
+        k1 = (ra / rm + delta_m - 1) / delta_m
         k2 = err.div(((ra / rm + delta_m - 1), err.div((ra, sra), (rm, srm))), (delta_m, sdelta_m))
         # exp
         try:
-            k3 = (np.log(ra / rm) / np.log(ratio_m)) * (1 / m1) + 1  # A.A.P.Koppers
+            k3 = (np.log(ra / rm) / np.log(ratio_m)) * (1 / m1) + 1
             v1 = err.log((ra / rm, err.div((ra, sra), (rm, srm))))
             v2 = err.log((ratio_m, sratio_m))
             v3 = err.div((np.log(ra / rm), v1), (np.log(ratio_m), v2))
@@ -75,7 +75,7 @@ def mdf(rm: float, srm: float, m1: float, m2: float, ra: float = 298.56,
             k3, k4 = "Null", "Null"
         # pow
         try:
-            k5 = pow((ra / rm), (1 / delta_m))  # A.A.P.Koppers, also Renne2009, B.D. Turrin2010
+            k5 = pow((ra / rm), (1 / delta_m))  # Renne2009, B.D. Turrin2010
             k6 = err.pow((ra / rm, err.div((ra, sra), (rm, srm))),
                          (1 / delta_m, err.div((1, 0), (delta_m, sdelta_m))))
         except Exception:

{ararpy-0.1.14 → ararpy-0.1.15}/ararpy/files/calc_file.py

@@ -109,6 +109,8 @@ def open_252(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
         -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
     ]
 
     # double transpose to remove keys
@@ -283,6 +285,10 @@ def open_240(data: pd.DataFrame, logs01: pd.DataFrame, logs02: pd.DataFrame):
         -999, -999, -999, -999, -1,
         # 115-122
         -999, -999, -999, -999, -999, -999, -999, -999,
+        # 123-130
+        -999, -999, -999, -999, -999, -999, -999, -999,
+        # 131-135
+        -999, -999, -999, -999, -999,
     ]
 
     # double transpose to remove keys
@@ -503,15 +509,17 @@ def open_full_xls(file_path: str, sample_name: str = ''):
             -1, -1,  # 56-57
             -1, -1,  # 58-59
             -1, -1, -1, -1, -1, -1, -1, -1, -1,  # 60-68
-            10, 11, 12, 13,  #
-            -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  #
-            -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  #
-            -1, -1, -1, -1,  #
-            -1, -1, -1, -1,  #
-            -1, -1, -1, -1, -1,  #
-            -1, -1, -1, -1,  #
-            -1, -1, -1, -1,  #
-            -1,  #
+            10, 11, 12, 13,  # 69-72
+            -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  # 73-84
+            -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  # 85-94
+            -1, -1, -1, -1,  # 95-98
+            -1, -1, -1, -1,  # 99-102
+            -1, -1, -1, -1,  # 103-106
+            -1, -1, -1, -1,  # 107-110
+            -1, -1, -1, -1,  # 111-114
+            -1, -1, -1, -1, -1, -1, -1, -1,  # 115-122
+            -1, -1, -1, -1, -1, -1, -1, -1,  # 123-130
+            -1, -1, -1, -1, -1,  # 131-135
         ])
 
     month_convert = {'Jan': '01', 'Feb': '02', 'Mar': '03', 'Apr': '04', 'May': '05', 'Jun': '06',

{ararpy-0.1.14 → ararpy-0.1.15}/ararpy/smp/initial.py

@@ -49,6 +49,12 @@ spectra_res_keys = [
 SPECTRA_RES = dict(zip(
     spectra_res_keys, [np.nan for i in spectra_res_keys])
 )
+settings_keys = [
+    'sigma_level'
+]
+SETTINGS_RES = dict(zip(
+    settings_keys, [np.nan for i in settings_keys])
+)
 
 
 # create sample instance
@@ -176,8 +182,11 @@ def initial(smp: Sample):
         reference=ArArBasic(
             name='REFERENCE', journal='JOURNAL', doi='DOI'
         ),
+        settings=copy.deepcopy(SETTINGS_RES)
     ))
 
+    smp.Info.settings.update({'sigma_level': 1})
+
     # Plots and Tables
     setattr(smp, 'UnknownTable', Table(
         id='1', name='Unknown', header=samples.SAMPLE_INTERCEPT_HEADERS,

{ararpy-0.1.14 → ararpy-0.1.15}/ararpy/smp/plots.py

@@ -59,7 +59,7 @@ 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, **kwargs)
+            initial_plot_data(sample)
         except (Exception, BaseException):
             # print(traceback.format_exc())
             pass
@@ -80,7 +80,7 @@ def set_plot_data(sample: Sample, isInit: bool = True, isIsochron: bool = True,
     # Recalculate plateaus
     if isPlateau:
         try:
-            recalc_plateaus(sample, **kwargs)
+            recalc_plateaus(sample)
         except (Exception, BaseException):
             # print(traceback.format_exc())
             pass
@@ -89,7 +89,7 @@ def set_plot_data(sample: Sample, isInit: bool = True, isIsochron: bool = True,
 # =======================
 # Initialize plot data
 # =======================
-def initial_plot_data(sample: Sample, **kwargs):
+def initial_plot_data(sample: Sample):
     """
     Assign initial data for plots
     Parameters
@@ -136,7 +136,7 @@ def initial_plot_data(sample: Sample, **kwargs):
     )
     try:
         sample.AgeSpectraPlot.data = calc.spectra.get_data(
-            *sample.ApparentAgeValues[2:4], sample.ApparentAgeValues[7], **kwargs)
+            *sample.ApparentAgeValues[2:4], sample.ApparentAgeValues[7])
         sample.AgeSpectraPlot.data = calc.arr.transpose(sample.AgeSpectraPlot.data)
     except (Exception, BaseException):
         print(traceback.format_exc())

{ararpy-0.1.14 → ararpy-0.1.15}/ararpy/smp/sample.py

@@ -743,7 +743,7 @@ DEFAULT_PLOT_STYLES = {
     },
 }
 
-VERSION = '20250102'
+VERSION = '20250301'
 
 NAMED_DICT = {
     "unknown": {"header": SAMPLE_INTERCEPT_HEADERS.copy()},
@@ -846,7 +846,8 @@ class Sample:
         # self.__version = '20231116'  # change smp parameters
         # self.__version = '20240730'  # change parameter table for thermo calculation
         # self.__version = '20241028'  # gain correction
-        self.__version = '20250102'  # gain correction to blanks
+        # self.__version = '20250102'  # gain correction to blanks
+        self.__version = '20250301'  # error sigma adjustment
 
     @property
     def version(self):
@@ -943,7 +944,7 @@ class Table:
         if header is None:
             header = ['']
         if data is None:
-            data = [['']]
+            data = [['' for i in range(len(header))]]
         if colcount is None:
             colcount = len(header)
         if rowcount is None:

{ararpy-0.1.14 → ararpy-0.1.15}/ararpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: ararpy
-Version: 0.1.14
+Version: 0.1.15
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.14 → ararpy-0.1.15}/setup.py

@@ -16,7 +16,7 @@ long_description = (here / 'README.md').read_text(encoding='utf-8')
 
 setuptools.setup(
     name='ararpy',  #
-    version='0.1.14',  # version
+    version='0.1.15',  # version
     author='Yang Wu',
     author_email='wuycug@hotmail.com',
     description='A project for Ar-Ar geochronology',  # short description