ararpy 0.1.13__tar.gz → 0.1.14__tar.gz

{ararpy-0.1.13 → ararpy-0.1.14}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: ararpy
-Version: 0.1.13
+Version: 0.1.14
 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
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: requires-python
+Dynamic: summary
 
 # ArArPy
 

ararpy-0.1.14/ararpy/argon_diffusion_simulator/__init__.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2025 Yang 
+# webarar - __init__.py
+# ==========================================
+#
+#
+# 
+"""
+from . import main

ararpy-0.1.14/ararpy/argon_diffusion_simulator/main.py

@@ -0,0 +1,542 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2024 Yang
+# ArgonDiffusionRandomWalk - main
+# ==========================================
+#
+#
+#
+"""
+import os
+import pickle
+import numpy as np
+import math
+import copy
+import time
+from typing import List
+
+np.set_printoptions(precision=18, threshold=10000, linewidth=np.inf)
+
+SETUP_PRINT = "natoms = {0}, nsteps = {1}, grain_size = {2}, time_scale = {3}, size_scale = {4}, number_scale = {5}"
+
+
+def _uniform_sphere_step(step_length, shape):
+    """
+    在三维空间中生成均匀分布的球面样本，且步长严格为指定长度。
+
+    Parameters:
+        step_length (array, float): 步长的固定长度, (n, m)
+        num_samples (tuple): 步长shape, (n, m)
+
+    Returns:
+        np.ndarray: 形状为 (num_samples, 3) 的数组，每行是一个随机步长向量
+    """
+    # 随机生成方位角 phi 和极角的 cos(theta)
+    num_samples, dimension = shape
+    phi = np.random.uniform(0, 2 * np.pi, num_samples)
+    cos_theta = np.random.uniform(-1, 1, num_samples)
+    sin_theta = np.sqrt(1 - cos_theta ** 2)  # sin(theta) = sqrt(1 - cos^2(theta))
+
+    # 将球面坐标转换为笛卡尔坐标
+    x = sin_theta * np.cos(phi)
+    y = sin_theta * np.sin(phi)
+    z = cos_theta
+
+    # 构建单位向量
+    unit_vectors = np.vstack((x, y, z)).T
+
+    # 乘以步长，得到最终的步长向量
+    steps = step_length * unit_vectors
+    return steps
+
+
+def walker(pos, step_length, total_nsteps, min_bound, max_bound, scale=0., compensation=0, remove=True,
+           conditions=None, boundary_factor=1):
+
+    if len(pos) == 0:
+        return pos
+
+    dimension = pos.shape[1] if len(pos.shape) > 1 else 1
+
+    sigma = step_length * math.sqrt(scale)
+
+    if conditions is None:
+        if dimension == 3:
+            conditions = np.array([[-50, -50, -50, 50, 50, 50, 1]])
+        else:
+            conditions = np.array([[-50, -50, 50, 50, 1]])
+
+    num_big_steps = int(total_nsteps // scale) if int(scale) > 1 else 0
+    num_small_steps = int(total_nsteps % scale) if int(scale) > 1 else int(total_nsteps)
+
+    for _ in range(num_big_steps):
+        # print(f"new walker {_ = } {len(pos) = }")
+        # 边界判断（布尔掩码）
+        in_boundary_mask = np.all(
+            (pos >= (min_bound + sigma * compensation)) & (pos <= (max_bound - sigma * compensation)), axis=1)
+        in_core = pos[in_boundary_mask]
+        in_boundary = pos[~in_boundary_mask]
+
+        # 核心粒子随机行走
+        coefficients = np.ones(len(in_core))
+        for each in conditions:
+            # each = x1, y1, z1, x2, y2, z2, coeff for dimension=3
+            cond = np.all(
+                (in_core >= np.array(each[:dimension])) & (in_core <= np.array(each[dimension:int(2*dimension)])),
+                axis=1)
+            coefficients = np.where(cond, each[-1] ** 0.5, coefficients)
+        steps = np.random.normal(0, sigma, size=in_core.shape)
+        in_core += steps * coefficients[:, None]
+
+        # 将边界粒子以更小 scale 的步长模拟
+        if scale > 1:
+            in_boundary = walker(in_boundary, step_length, scale, min_bound, max_bound, scale // 2,
+                                 compensation, remove, conditions, boundary_factor)
+
+        # 拼接核心和边界粒子
+        pos = np.concatenate((in_boundary, in_core))
+
+        # 移除超出范围的粒子
+        if remove:
+            pos = pos[np.all((pos >= min_bound) & (pos <= max_bound), axis=1)]
+
+    # 最后处理 scale < 1 的小步模拟, boundary_factor用来缩放这里的处理步数，1 < boundary_factor <= 1如果 boundary_factor=1，将完全吻合实际
+    # boundary_factor < 1 将加快一些速度， boundary_factor=0 将忽略小步数
+    k = boundary_factor * max(conditions[:, -1])
+    for _ in range(int(num_small_steps * k)):
+        coefficients = np.ones(len(pos))
+        for each in conditions:
+            cond = np.all((pos >= np.array(each[:dimension])) & (pos <= np.array(each[dimension:int(2*dimension)])),
+                          axis=1)
+            coefficients = np.where(cond, (each[-1] / k) ** 0.5, coefficients)
+            # coefficients = np.where(cond, coeff ** 0.5, coefficients)
+        steps = np.random.normal(0, step_length, size=np.shape(pos))
+        pos += steps * coefficients[:, None]
+
+        if remove:
+            pos = pos[np.all((pos >= min_bound) & (pos <= max_bound), axis=1)]
+
+    return pos
+
+
+def walker2(pos: np.ndarray, duration, step_length, min_bound, max_bound, time_scale, frequency,
+            conditions=None, remove: bool = True):
+    """
+    :return:
+    """
+
+    if len(pos) == 0:
+        return pos
+
+    dimension = pos.shape[-1] if len(pos.shape) > 1 else 1
+
+    dt = time_scale
+    if conditions is None:
+        if dimension == 3:
+            conditions = np.array([[-50, -50, -50, 50, 50, 50, 1]])
+        else:
+            conditions = np.array([[-50, -50, 50, 50, 1]])
+
+    for step in range(int(1e16)):
+
+        res = np.zeros(0).reshape(0, dimension)
+        for index, each in enumerate(conditions):
+            # each = (x1, y1, z1, x2, y2, z2, gamma)
+            d = step_length * math.sqrt(each[-1] * frequency * time_scale)
+
+            locs = np.ones(len(pos)) * 999
+            for _index, _each in enumerate(conditions):
+                cond = np.all((pos >= np.array(_each[:dimension])) & (pos <= np.array(_each[dimension:int(2*dimension)])), axis=1)
+                locs = np.where(cond, _index, locs)
+
+            partial_pos = pos[locs == index]
+
+            # c = len(partial_pos)
+            # # 初始化步长
+            # steps = np.zeros(partial_pos.shape, dtype=float)
+            # # 移动方向, x or y or z
+            # directions = np.random.choice(list(range(dimension)), size=c)
+            # # 方向, positive or negative, 步长
+            # steps[np.arange(c), directions] = np.random.choice([-d, d], size=c, p=[0.5, 0.5])
+            steps = np.random.normal(0, d, size=partial_pos.shape)
+
+            partial_pos += steps
+
+            if remove:
+                partial_pos = partial_pos[np.all((partial_pos >= min_bound) & (partial_pos <= max_bound), axis=1)]
+
+            res = np.concatenate((res, partial_pos))
+
+        pos = copy.deepcopy(res)
+
+        _t = (step + 1) * dt
+
+        if abs(_t - duration) < dt:
+            break
+
+    return pos
+
+
+class OverEpsilonError(Exception):
+    def __init__(self, i, d, e):
+        self.i = i
+        self.d = d
+        self.e = e
+
+    def __str__(self):
+        return f"OverEpsilonError: Index = {self.i}, d = {self.d} > e = {self.e}"
+
+
+class Domain:
+    def __init__(self, dimension: int = 3, atom_density: float = 1e14, fraction: float = 1.0,
+                 min_bound=None, max_bound=None, **kwargs):
+
+        self.dimension = dimension
+        self.size = ...
+        self.atom_density = atom_density
+        self.fraction = fraction
+        self.time_scale = 1
+        self.size_scale = 0.05
+
+        self.energy = 120 * 1000  # J/mol
+        self.density = 0
+        self.fracture = 0
+        self.boundary = 0
+        self.defect = 0
+        self.pho = 1
+        self.step_length = 0.0001  # 1 A = 0.1 nm = 0.0001 μm
+
+        self.current_temp = 273.15
+
+        self.inclusions: List[Domain] = []
+        self.natoms: int = 0
+        self.positions = []
+        self.min_bound = min_bound
+        self.max_bound = max_bound
+        self.remained_per_step = []
+        self.released_per_step = []
+
+        self.attr = {}
+
+        for key, val in kwargs.items():
+            if hasattr(self, key):
+                setattr(self, key, val)
+
+        self.setup()
+
+    def setup(self):
+        """
+        Used to set or reset positions of atoms
+        :return:
+        """
+
+        # 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)
+        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:
+            self.positions = self.positions[~np.all((self.positions >= dom.min_bound) & (self.positions <= dom.max_bound), axis=1)]
+        self.natoms = len(self.positions)
+
+        self.remained_per_step = []
+        self.released_per_step = []
+
+    def get_gamma(self, energy: float = None, temperature: float = None):
+        r = 8.31446261815324  # J / (K * mol)
+        T = self.current_temp if temperature is None else temperature
+        e = self.energy if energy is None else energy
+        alpha = 1 - self.density
+        p1 = math.exp(- e / (r * T))
+        p2 = math.exp(- e / 2 / (r * T))  # p2是给定活化能的一半，用于假定晶面扩散的活化能
+        gamma = p1 * alpha * (1 - self.fracture) + self.fracture * p2 + self.boundary + self.defect
+        return gamma
+
+    def get_natoms(self, pos=None):
+        if pos is None:
+            return len(self.positions)
+        pos = pos[np.all((pos >= self.min_bound) & (pos <= self.max_bound), axis=1)]
+        for dom in self.inclusions:
+            pos = pos[~np.all((pos >= dom.min_bound) & (pos <= dom.max_bound), axis=1)]
+        return len(pos)
+
+    def set_attr(self, name, value, index=None):
+        if index is None:
+            self.attr.update({name: value})
+        else:
+            if name not in self.attr.keys():
+                self.attr.update({name: {}})
+            self.attr[name].update({index: value})
+
+
+class DiffSimulation:
+    def __init__(self):
+        self.name = "example"
+        self.loc = "examples"
+        self.score = 0
+        self.end_at = 0
+        self.dimension = 3
+
+        self.size_scale = 1
+        self.length_scale = 1
+
+        self.atom_density = 1e14  # 原子密度 个/立方厘米
+        self.frequency = 1e13  # 每秒振动的次数, Debye frequency
+
+        self.grain_size = 300  # 0.3 mm = 300 μm = 300000 nm
+        self.grid_size = self.grain_size * self.size_scale  # 网格大小
+        self.nsteps: int = ...
+        self.natoms: int = ...
+        self.epsilon = 1e-5
+        self.step_length = 0.0001 * 2.5  # 1 A = 0.1 nm = 0.0001 μm
+
+        self.seq: [List, np.ndarray] = []
+        self.domains: List[Domain] = []
+        self.positions: [List, np.ndarray] = []
+
+        self.remained_per_step = []
+        self.released_per_step = []
+
+    def setup(self):
+        """
+        Used to set or reset positions of atoms
+        :return:
+        """
+        # 网格大小和颗粒边界
+        self.grid_size = self.grain_size * self.size_scale  # 网格大小
+        center = np.array([0 for i in range(self.dimension)])
+        self.min_bound = center - self.grid_size / 2
+        self.max_bound = center + self.grid_size / 2
+
+        # 粒子位置
+        self.positions = np.concatenate([dom.positions for dom in self.domains])
+        # 粒子数目
+        self.natoms = len(self.positions)
+
+        self.remained_per_step = []
+        self.released_per_step = []
+
+    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):
+        pos = copy.deepcopy(self.positions)
+        self.seq = []  # 用于记录参数
+
+        for index, (duration, temperature, target, status) in enumerate(zip(times, temperatures, targets, statuses)):
+
+            self.seq.append({})
+
+            loop = 0
+            e_low = 100 * 1000
+            e_up = 300 * 1000
+
+            _start = time.time()
+            heating_duration = duration - start_time  # in seconds
+            start_time = duration
+            temperature = temperature + 273.15  # in Kelvin
+
+            while loop < 50:
+
+                e = (e_low + e_up) / 2
+
+                total_steps = self.frequency * heating_duration  # 振动次数
+                conditions = np.array(
+                    [[*dom.min_bound, *dom.max_bound,
+                      dom.get_gamma(temperature=temperature, energy=e if simulating else None)] for dom in domains if dom.energy != 0 and not simulating])
+
+                if use_walker1:
+
+                    # print(f"调整前: {nsteps_factor = }, gamma = {conditions[0][-1]}, {total_steps = }")
+                    nsteps_factor = 10 ** math.floor(
+                        -math.log10(max(conditions[:, -1]))) * 1000  # 用来调节次数和步长的巨大差异，次数太大，但步程太小
+                    while int(total_steps / nsteps_factor) < 1:
+                        nsteps_factor /= 10
+                    while int(total_steps / nsteps_factor) > 10000:
+                        nsteps_factor *= 10
+                    total_steps = int(total_steps / nsteps_factor)  # 振动次数
+                    conditions[:, -1] *= nsteps_factor
+                    compensation = max(3, *(np.ceil(np.sqrt(conditions[:, -1])) * 3))
+                    boundary_factor = 1
+                    if max(conditions[:, -1]) > 1000:
+                        # k = 0时，bf = 1, 完全无缩放 # k = 1时，bf <= 0.5 小步行走将至少缩放一半   # 推荐值 k = 1.2
+                        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 = }")
+
+                    _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
+                    )
+
+                    # self.seq[index].update({
+                    #     "duration": duration, "temperature": temperature, "target": target, "step_length": step_length,
+                    #     "scale": scale, "compensation": compensation, "boundary_factor": boundary_factor, "e": e,
+                    #     "simulation": simulating, "nsteps_factor": nsteps_factor, "conditions": conditions
+                    # })
+
+                else:
+                    step_length = self.step_length / np.sqrt(pos.shape[1] if len(pos.shape) > 1 else 1)
+                    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)
+                    boundary_factor = 1
+                    compensation = 0
+
+                self.seq[index].update({
+                    "duration": duration, "temperature": temperature, "target": target, "step_length": step_length,
+                    "scale": scale, "compensation": compensation, "boundary_factor": boundary_factor, "e": e,
+                    "simulation": simulating, "nsteps_factor": nsteps_factor, "conditions": conditions
+                })
+
+                released = 1 - len(_pos) / self.natoms
+                d = released - target
+                if simulating:
+                    loop += 1
+                    print(f"{e = }, {d = }, {abs(d) <= epsilon}")
+                    if abs(d) <= epsilon:
+                        break
+                    elif d > 0:
+                        e_low = e
+                    else:
+                        e_up = e
+                elif scoring:
+                    self.score += (d * 100) ** 2
+                    print(f"{self.score = }, {d = }")
+                    if self.score > 4 * (index + 1):
+                        raise OverEpsilonError(index, self.score, 4 * (index + 1))
+                    else:
+                        break
+                else:
+                    break
+
+            pos = _pos
+
+            if status:
+                # status == True: argon collection, False: pumping
+                for dom in self.domains:
+                    _c = dom.get_natoms(pos)
+                    dom.remained_per_step.append(_c)
+                    dom.released_per_step.append(dom.natoms - _c)
+                    dom.set_attr("energy", float(e), index=index)
+
+                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")
+
+    def run_persecond(self, times, temperatures, statuses, targets, domains: List[Domain], scale=None,
+                     simulation: bool = False, epsilon=0.001, start_time=0):
+        seq = []
+        for i in range(1, int(times[-1] + 1), 300):
+            for index, time in enumerate(times):
+                if (times[index-1] if index > 0 else 0) < i <= times[index]:
+                    seq.append([i, temperatures[index], statuses[index], targets[index]])
+        seq = np.transpose(seq)
+        return self.run_sequence(*seq, domains=domains, nsteps_factor=scale, simulating=simulation,
+                                 epsilon=epsilon, start_time=start_time)
+
+
+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, **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)
+            dom = Domain(
+                dimension=demo.dimension, atom_density=demo.atom_density, 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}")
+
+        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 save_ads(ads: DiffSimulation, dir_path: str = None, name: str = None):
+    if dir_path is None:
+        dir_path = ""
+    if name is None:
+        name = ads.name
+    if not name.endswith(".ads"):
+        name = f"{name}.ads"
+    dir_path = os.path.join(dir_path, name)
+    with open(dir_path, 'wb') as f:
+        f.write(pickle.dumps(ads))
+    return name
+
+
+def read_ads(file_path: str) -> DiffSimulation:
+
+    class RenameUnpickler(pickle.Unpickler):
+        def find_class(self, module: str, name: str):
+            if "argon_diffusion_simulator" in module:
+                return super(RenameUnpickler, self).find_class(DiffSimulation().__module__, name)
+            else:
+                return super(RenameUnpickler, self).find_class(module, name)
+
+    def renamed_load(file_obj) -> DiffSimulation:
+        return RenameUnpickler(file_obj).load()
+
+    try:
+        with open(file_path, 'rb') as f:
+            return renamed_load(f)
+    except (Exception, BaseException):
+        raise ValueError(f"ModuleNotFoundError")

{ararpy-0.1.13 → ararpy-0.1.14}/ararpy/calc/corr.py

@@ -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
+            k5 = pow((ra / rm), (1 / delta_m))  # A.A.P.Koppers, also 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:
@@ -107,14 +107,14 @@ def discr(a0: list, e0: list, mdf: list, smdf: list, m: list, m40: list,
     for i in range(min([len(arg) for arg in [a0, e0, mdf, smdf]])):
         delta_mass = abs(m40[i] - m[i])
         ratio_mass = abs(m40[i] / m[i]) if m[i] != 0 else 1
-        if method.lower()[0] == 'l':
+        if method.lower().startswith("l"):
             k0 = 1 / (delta_mass * mdf[i] - delta_mass + 1) if (delta_mass * mdf[i] - delta_mass + 1) != 0 else 0
             k1 = err.div((1, 0), (delta_mass * mdf[i] - delta_mass + 1, smdf[i] * delta_mass))
-        elif method.lower()[0] == 'e':
+        elif method.lower().startswith("e"):
             k0 = 1 / (ratio_mass ** (mdf[i] * m40[i] - m[i]))
             k1 = err.div((1, 0), (ratio_mass ** (mdf[i] * m40[i] - m[i]), err.pow((ratio_mass, 0), (
                 mdf[i] * m40[i] - m[i], err.mul((mdf[i], smdf[i]), (m40[i], 0))))))
-        elif method.lower()[0] == 'p':
+        elif method.lower().startswith("p"):
             k0 = 1 / (mdf[i] ** delta_mass)
             k1 = err.div((1, 0), (mdf[i] ** delta_mass, err.pow((mdf[i], smdf[i]), (delta_mass, 0))))
         else:

{ararpy-0.1.13 → ararpy-0.1.14}/ararpy/calc/plot.py

@@ -13,9 +13,9 @@ import traceback
 
 import decimal
 from math import exp, log, cos, acos, ceil, sqrt, atan, sin, gamma
-from typing import List, Any
-from scipy.optimize import fsolve
-from scipy.stats import distributions
+# from typing import List, Any
+# from scipy.optimize import fsolve
+# from scipy.stats import distributions
 import numpy as np
 
 math_e = 2.718281828459045

{ararpy-0.1.13 → ararpy-0.1.14}/ararpy/calc/raw_funcs.py

@@ -46,6 +46,8 @@ def get_raw_data_regression_results(points_data, unselected: list = None):
             # line_data = transpose([lines_x, res[7](lines_x)])
             line_results = res[0:4]
             reg_coeffs = res[5]
+            if any(np.isnan(line_results)):
+                raise ValueError
             # if np.isin(np.inf, line_data) or np.isin(np.nan, line_data):
             #     raise ZeroDivisionError(f"Infinite value or nan value.")
             if abs(res[0] - min(y)) > 5 * (max(y) - min(y)):

{ararpy-0.1.13 → ararpy-0.1.14}/ararpy/calc/regression.py

@@ -966,11 +966,6 @@ def exponential(a0: list, a1: list):
     se_intercept = sec / errfz * errfx
     rse_intercept = se_intercept / intercept * 100
 
-    if abs(intercept) > 10 * max(a0):
-        raise ValueError
-    if intercept < 0:
-        raise ValueError
-
     return intercept, se_intercept, rse_intercept, r2, 'mswd', [a, b, c], 'se', \
            lambda x: [_exp_func(i, a, b, c) for i in x], m_ssresid
 

{ararpy-0.1.13 → ararpy-0.1.14}/ararpy/calc/spectra.py

@@ -13,7 +13,7 @@ import numpy as np
 
 
 def get_data(y: list, sy: list, x: list, f: int = 1, indices: list = None,
-             cumulative: bool = False, successive: bool = True):
+             cumulative: bool = False, successive: bool = True, sigma: int = 1):
     """
     Get spectra data based on passed x, y, and sy.
 
@@ -28,6 +28,7 @@ def get_data(y: list, sy: list, x: list, f: int = 1, indices: list = None,
     cumulative : bool, default False.
         This parameter should be True if x is already cumulative.
     successive : If setting indices successive
+    sigma:
 
     Returns
     -------
@@ -35,6 +36,7 @@ def get_data(y: list, sy: list, x: list, f: int = 1, indices: list = None,
     """
     if np.issubdtype(type(f), np.integer) and f > 1:
         sy = np.divide(sy, f)
+    sy = np.array(sy) * sigma
     dp = np.shape([y, sy, x])[-1]
     if indices is None:
         indices = list(range(dp))

{ararpy-0.1.13 → ararpy-0.1.14}/ararpy/smp/corr.py

@@ -49,8 +49,16 @@ def corr_blank(sample: Sample):
     blank_corrected = np.zeros([10, len(sample.SequenceName)])
     try:
         for i in range(5):
+            b, sb = copy.deepcopy(sample.BlankIntercept[i * 2: i * 2 + 2])
+            f, sf = np.array(sample.TotalParam[126 + i * 2:128 + i * 2])
+            sf = f * sf / 100
+            _ = calc.corr.gain(*sample.BlankIntercept[i * 2:2 + i * 2], f, sf)
+            for index in range(len(sample.BlankIntercept[i * 2])):
+                if sample.TotalParam[111][index]:  # use same parameters to correct blank intercepts
+                    b[index] = _[0][index]
+                    sb[index] = _[1][index]
             blank_corrected[i * 2:2 + i * 2] = calc.corr.blank(
-                *sample.CorrectedValues[i * 2:2 + i * 2], *sample.BlankIntercept[i * 2:2 + i * 2])
+                *sample.CorrectedValues[i * 2:2 + i * 2], b, sb)
     except Exception as e:
         print(traceback.format_exc())
         raise ValueError('Blank correction error')