ararpy 0.1.1__py3-none-any.whl → 0.1.11__py3-none-any.whl

ararpy/smp/__init__.py

@@ -1,6 +1,6 @@
 
 from . import (
-    sample as samples, consts, json, basic, corr, raw, initial,
+    sample as samples, info, consts, json, basic, corr, raw, initial,
     plots, style, table, calculation, export, diffusion_funcs
 )
 

ararpy/smp/info.py

@@ -0,0 +1,23 @@
+#  Copyright (C) 2024 Yang. - All Rights Reserved
+
+# !/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2024 Yang 
+# ararpy - info
+# ==========================================
+#
+#
+# 
+"""
+
+
+def name(smp, n: str = None):
+    if n is None:
+        return smp.Info.sample.name
+    elif isinstance(n, str):
+        smp.Info.sample.name = n
+        return n
+    else:
+        raise ValueError(f"{n} is not a string")

ararpy/smp/sample.py

@@ -839,7 +839,7 @@ class Sample:
         return self.__version
 
     def help(self) -> str: ...
-
+    
     def name(self) -> str: ...
 
     def doi(self) -> str: ...

ararpy/test.py

@@ -10,287 +10,28 @@
 """
 import ararpy as ap
 import os
-import ctypes
-import numpy as np
-import time
-
-def is_number(s):
-    try:
-        float(s)
-        return True
-    except ValueError:
-        return False
-
-
-class DiffSample:
-    def __init__(self, smp = None, name: str = None):
-
-        if smp is not None:
-            self.smp = smp
-            self.sname = self.smp.name()
-
-            self.sequence = self.smp.sequence()
-            self.ni = self.sequence.size  # sequence number
-
-            # self.telab = np.linspace(600, 1500, self.ni, dtype=np.float64)
-            self.telab = np.array(self.smp.TotalParam[124], dtype=np.float64)
-
-            ### 这里用真实的加热温度之后 a1 > 0，导致后面无法计算
-            ### 原因：telab不能为 0
-
-
-            self.telab = self.telab + 275.13
-            # self.tilab = np.array([15*60 for i in range(self.ni)], dtype=np.float64)
-            self.tilab = np.array(self.smp.TotalParam[123], dtype=np.float64)
-            self.a39 = np.array(self.smp.DegasValues[20], dtype=np.float64)
-            self.sig39 = np.array(self.smp.DegasValues[21], dtype=np.float64)
-            self.f = np.cumsum(self.a39) / self.a39.sum()
-            self.f[-1] = 0.999999999
-            # self.f = np.insert(self.f, 0, 0)
-            self.ya = np.array(self.smp.ApparentAgeValues[2], dtype=np.float64)
-            self.sig = np.array(self.smp.ApparentAgeValues[3], dtype=np.float64)
-
-            loc = "D:\\PythonProjects\\ararpy_package\\ararpy\\examples"
-            self.file_age_in = open(os.path.join(loc, f"{self.sname}_age.in"), "w")
-            self.file_sig_in = open(os.path.join(loc, f"{self.sname}_sig.in"), "w")
-            self.file_tmp_in = open(os.path.join(loc, f"{self.sname}_tmp.in"), "w")
-            self.file_fj_in = open(os.path.join(loc, f"{self.sname}_fj.in"), "w")
-            self.file_a39_in = open(os.path.join(loc, f"{self.sname}_a39.in"), "w")
-
-            self.file_age_in.writelines("\n".join([f"  {self.f[i] * 100}  {self.ya[i]}" for i in range(self.ni)]))
-            self.file_sig_in.writelines("\n".join([f"{self.sig[i]}" for i in range(self.ni)]))
-            self.file_tmp_in.writelines(f"{str(self.ni)}\n")
-            self.file_tmp_in.writelines("\n".join([f"{self.telab[i]}\n{self.tilab[i]}" for i in range(self.ni)]))
-            self.file_fj_in.writelines("\n".join([f"{self.f[i]}" for i in range(self.ni)]))
-            self.file_a39_in.writelines("\n".join([f"  {self.a39[i]}  {self.sig39[i]}" for i in range(self.ni)]))
-
-            self.file_age_in.close()
-            self.file_sig_in.close()
-            self.file_tmp_in.close()
-            self.file_fj_in.close()
-            self.file_a39_in.close()
-
-
-        elif name is not None:
-            self.sname = name
-        else:
-            raise ValueError("Sample not found")
-
-        self.pi = 3.141592654
-        self.nloop = 1
-        self.ngauss = 10
-        self.zi = [0.]
-        self.b = 8
-        self.imp = 2
-        self.acut = 0.5
-        self.dchmin = 0.01
-        self.ncons = 0
-        self.ndom = 8
-        self.mdom = 8
-        self.iset = 0
-        self.gset = 0
-        self.wt = []
-
-
-class DiffAgemonFuncs(DiffSample):
-
-    def __init__(self, ni=10, mmax=100, ochisq=0, **kwargs):
-
-        self.ni = ni
-        self.mmax = mmax
-        self.ochisq = ochisq
-
-        super().__init__(**kwargs)
-
-        self.nca = 200
-        self.da = np.zeros(self.ni, dtype=np.float64)
-        self.beta = np.zeros(self.mmax, dtype=np.float64)
-        self.atry = np.zeros(self.mmax, dtype=np.float64)
-
-        # constants
-        self.nwcy = 10
-        self.ncyc = 1
-        self.ntst = 1001
-        self.ns = 200
-        self.nmaxi = np.zeros(self.nwcy, dtype=int)
-        self.nmaxo = np.zeros(self.nwcy, dtype=int)
-        self.tti = np.zeros([self.nwcy, 2, self.ntst], dtype=np.float64)
-        self.tto = np.zeros([self.nwcy, 2, self.ntst], dtype=np.float64)
-        self.agei = np.zeros([self.nwcy, 2, self.ns], dtype=np.float64)
-        self.ageo = np.zeros([self.nwcy, 2, self.ns], dtype=np.float64)
-
-        self.loc = "D:\\PythonProjects\\ararpy_package\\ararpy\\examples"
-
-        self.file_ame_in = open(os.path.join(self.loc, f"{self.sname}.ame"), "r")  # from arrmulti
-        self.file_age_in = open(os.path.join(self.loc, f"{self.sname}_age.in"), "r")
-        self.file_sig_in = open(os.path.join(self.loc, f"{self.sname}_sig.in"), "r")
-        self.file_tmp_in = open(os.path.join(self.loc, f"{self.sname}_tmp.in"), "r")
-
-        self.file_output_mch = open(os.path.join(self.loc, f"{self.sname}_mch-out.dat"), "w")
-        self.file_output_mages = open(os.path.join(self.loc, f"{self.sname}_mages-out.dat"), "w")
-        self.file_output_agesd = open(os.path.join(self.loc, f"{self.sname}_ages-sd.samp"), "w")
-
-        self.file_output_mch.close()
-        self.file_output_mages.close()
-        self.file_output_agesd.close()
-
-        # parameters
-        self.ns = 200
-        self.nc = 100
-        self.ntst = 1001
-        self.mxi = 350
-        self.nn = 319
-        self.mfit = 10
-        self.nwcy = 10
-        self.nd = 10
-        self.xlambd = 0.0005543
-        self.a = 0
-        self.perc = 0.01
-        self.cht0 = 1.0e-4
-        self.nrun = 5
-        self.maxrun = 15
-        self.nemax = 10
-
-        # 读取加热温度和时间
-        self.ni = int(self.file_tmp_in.readline())
-        self.nit = self.ni
-        self.r39 = np.zeros(self.ni, dtype=np.float64)
-        self.telab = np.zeros(self.ni, dtype=np.float64)
-        self.tilab = np.zeros(self.ni, dtype=np.float64)
-        for i in range(self.ni):
-            self.telab[i] = float(self.file_tmp_in.readline())
-            self.tilab[i] = float(self.file_tmp_in.readline())
-            if self.telab[i] > 1373:
-                # go to 11
-                self.ni = i
-                break
-            self.tilab[i] /= 5.256E+11  # 1 Ma = 525600000000 minutes
-
-        # 读取
-        nemax = 0
-        self.nst_arr = np.zeros(100, dtype=int)
-        self.e_arr = np.zeros(100, dtype=np.float64)
-        self.d0_arr = np.zeros([100, 20], dtype=np.float64)
-        self.vc_arr = np.zeros([100, 20], dtype=np.float64)
-        self.e = 0
-        self.d0 = np.zeros(self.nd, dtype=np.float64)
-        self.vc = np.zeros(self.nd, dtype=np.float64)
-        kk = 0
-        while True:
-            try:
-                self.nst_arr[kk] = int(self.file_ame_in.readline())  # sequence number
-                # self.nst = int(self.file_ame_in.readline())  # sequence number
-                for i in range(self.nst_arr[kk]):
-                    self.e_arr[kk] = float(self.file_ame_in.readline())
-                    self.d0_arr[kk, i] = 10 ** float(self.file_ame_in.readline()) / 4 * (24 * 3600 * 365e+6)
-                    self.vc_arr[kk, i] = float(self.file_ame_in.readline())
-                    # self.e = float(self.file_ame_in.readline())
-                    # self.d0[i] = float(self.file_ame_in.readline())
-                    # self.vc[i] = float(self.file_ame_in.readline())
-                    # self.d0[i] = 10 ** self.d0[i] / 4 * (24 * 3600 * 365e+6)
-                    nemax += 1
-                self.atmp = self.file_ame_in.readline()
-                self.atmp = self.file_ame_in.readline()
-                self.atmp = self.file_ame_in.readline()
-                kk += 1
-            except ValueError:
-                break
-        self.kk = kk
-        print(f"{self.kk = }")
-
-        # 读取sig
-        self.sig = np.zeros(self.ns, dtype=np.float64)
-        self.xs = np.zeros(self.ns + 1, dtype=np.float64)
-        self.ya = np.zeros(self.ns + 1, dtype=np.float64)
-        for i in range(self.nit + 1):
-            try:
-                self.sig[i] = float(self.file_sig_in.readline())
-                if self.sig[i] <= 0:
-                    raise ValueError("Sigma less than 0")
-                self.xs[i + 1], self.ya[i + 1] = [float(j) for j in filter(lambda x: is_number(x),
-                                                                           self.file_age_in.readline().split(' '))]
-                self.xs[i + 1] /= 100
-                if self.ya[i] < 0:
-                    self.ya[i] = 0
-            except ValueError:
-                print(f"{i = } error in reading sig file")
-            continue
-
-        self.max_plateau_age = 30
-
-        self.file_ame_in.close()
-        self.file_tmp_in.close()
-        self.file_age_in.close()
-        self.file_sig_in.close()
-
-
-
-
 
 
 def test():
     example_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), r'examples')
     print(f"Running: ararpy.test()")
     print(f"============= Open an example .arr file =============")
-    # file_path = os.path.join(example_dir, r'22WHA0433.arr')
-    # sample = ap.from_arr(file_path=file_path)
-    # # file_path = os.path.join(example_dir, r'22WHA0433.age')
-    # # sample = ap.from_age(file_path=file_path)
-    # print(f"{file_path = }")
-    # print(f"sample = from_arr(file_path=file_path)")
-    # print(f"{sample.name() = }")
-    # print(f"{sample.help = }")
-    # print(f"sample.parameters() = {sample.parameters()}")
-    # print(f"sample.parameters().to_df() = \n{sample.parameters().to_df()}")
-    # print(sample.show_data())
-    # print(sample.sample())
-    # print(sample.blank().to_df().iloc[:, [1, 2, 3]])
-
-    # diff_smp = ap.calc.diffusion_funcs.DiffArrmultiFunc(smp=sample)
-    # diff_smp = ap.calc.diffusion_funcs.DiffArrmultiFunc(name='12h')
-    # e, sige, ordi, sigo = diff_smp.main()
-    # diff_smp = ap.calc.diffusion_funcs.DiffAgemonFuncs(smp=sample)
-    # diff_smp = ap.calc.diffusion_funcs.DiffAgemonFuncs(name='12h')
-    # diff_smp.main()
-    # diff_smp = ap.calc.diffusion_funcs.DiffDraw(name='12h')
-    # diff_smp.main()
-
-
-    # diff_smp = ap.calc.diffusion_funcs.InsideTemperatureCalibration()
-    #
-    # # k1, k2 = diff_smp.get_calibrated_temp(45 * 60, 600)
-    # # print(round((k1 + k2) / 2, 2), round(abs(k2 - k1) / 2, 2))
-    #
-    # ## 显示每个设定温度的所有空载加热测试结果，红蓝线为上下95%置信区间
-    # diff_smp.plot()
-    #
-    # ## 显示用于校正的温度曲线
-    # diff_smp.plot_confidence()
-
-    ## 显示实际样品的 libano 记录，并给出校正的温度曲线
-    # diff_smp.plot_libano_log(r"C:\Users\Young\OneDrive\Documents\Libano Data\2024-03-26\202403260941-libano.log")
-    # diff_smp.plot_libano_log(r"C:\Users\Young\OneDrive\00-Projects\【2】个人项目\2022-05论文课题\【3】分析测试\ArAr\01-VU实验数据和记录\20240717-Y53\202407171832-libano.log")
-    # diff_smp.plot_libano_log(r"C:\Users\Young\OneDrive\00-Projects\【2】个人项目\2022-05论文课题\【3】分析测试\ArAr\01-VU实验数据和记录\20240714-Y52\202407142127-libano.log")
-
-    name = "20240909-Y86"
-    arr_name = "20240909_24BY86"
-
-    libano_log_path = f"C:\\Users\\Young\\OneDrive\\00-Projects\\【2】个人项目\\2022-05论文课题\\【3】分析测试\\ArAr\\01-VU实验数据和记录\\{name}\\Libano-log"
-    # libano_log_path = r"C:\Users\Young\OneDrive\00-Projects\【2】个人项目\2022-05论文课题\【3】分析测试\ArAr\01-VU实验数据和记录\20240705-Y50\Libano-log"
-    libano_log_path = [os.path.join(libano_log_path, i) for i in os.listdir(libano_log_path)]
-    print(libano_log_path)
-    helix_log_path = f"C:\\Users\\Young\\OneDrive\\00-Projects\\【2】个人项目\\2022-05论文课题\\【3】分析测试\\ArAr\\01-VU实验数据和记录\\{name}\\LogFiles"
-    # helix_log_path = r"C:\Users\Young\OneDrive\00-Projects\【2】个人项目\2022-05论文课题\【3】分析测试\ArAr\01-VU实验数据和记录\20240621-Y56\LogFiles-20240621"
-    helix_log_path = [os.path.join(helix_log_path, i) for i in os.listdir(helix_log_path)]
-    print(helix_log_path)
-
-    loc = f"C:\\Users\\Young\\OneDrive\\00-Projects\\【2】个人项目\\2022-05论文课题\\【3】分析测试\\ArAr\\01-VU实验数据和记录\\{name}"
-    arr_path = f"C:\\Users\\Young\\OneDrive\\00-Projects\\【2】个人项目\\2022-05论文课题\\【3】分析测试\\ArAr\\01-VU实验数据和记录\\Arr Data\\{arr_name}.arr"
-    diff_smp = ap.calc.diffusion_funcs.SmpTemperatureCalibration(libano_log_path=libano_log_path, helix_log_path=helix_log_path, arr_path=arr_path, loc=loc)
-
-
+    file_path = os.path.join(example_dir, r'22WHA0433.arr')
+    sample = ap.from_arr(file_path=file_path)
+    # file_path = os.path.join(example_dir, r'22WHA0433.age')
+    # sample = ap.from_age(file_path=file_path)
+    print(f"{file_path = }")
+    print(f"sample = from_arr(file_path=file_path)")
+    print(f"{sample.name() = }")
+    sample.name("new name")
+    print(f"{sample.name() = }")
+    print(f"{sample.help() = }")
+    print(f"{sample.parameters() = }")
+    print(f"{sample.parameters().to_df() = }")
+    print(sample.show_data())
+    print(sample.sample())
+    print(sample.blank().to_df().iloc[:, [1, 2, 3]])
 
-###  梳理这些函数  用numba加速
 
 if __name__ == "__main__":
     test()

{ararpy-0.1.1.dist-info → ararpy-0.1.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ararpy
-Version: 0.1.1
+Version: 0.1.11
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.1.dist-info → ararpy-0.1.11.dist-info}/RECORD

@@ -1,5 +1,5 @@
 ararpy/__init__.py,sha256=XKlsgklkzGfvqQkt59y-UST9aVhgCf-eXpEDiaZaynQ,6725
-ararpy/test.py,sha256=wrXLWejJ7HEBIEy3Eq1Xt5LFd4r_5VM3gf9HtR_BTzo,12805
+ararpy/test.py,sha256=jdHhBvMbvDlxi0o2eRVG99nsUBNDA-0s2bbGbnXweo8,1130
 ararpy/calc/__init__.py,sha256=kUjRuLE8TLuKOv3i976RnGJoEMj23QBZDu37LWs81U4,322
 ararpy/calc/age.py,sha256=CUex9UxZbYinl9ypd7o86R3VRQFzahku3gW__fBeoss,5811
 ararpy/calc/arr.py,sha256=ntu6p3lUcF654SxLnFNrToLubXRWl101LRNFVJFulTQ,14871
@@ -38,22 +38,23 @@ ararpy/files/calc_file.py,sha256=b4bzPsoVD9y5wDqFw-2HmhK6Rd7qwufnEjaYz_FLxos,278
 ararpy/files/new_file.py,sha256=efblARIBROVLWS2w3-98BxLX5VZ8grRpiTkJFtf_rAk,214
 ararpy/files/raw_file.py,sha256=B2k4RjAp4EViwHKv6CbI5400Liaa7OW_eBjGSPlN9Ek,22768
 ararpy/files/xls.py,sha256=8ibT4ZRY2grK34ikKm1pDmlWFlVTgDL7vSMO6mphzrY,702
-ararpy/smp/__init__.py,sha256=Go-NQjPgDOrIqYOuRCHAeCgx5xBGtAf3rzyECt56gJA,472
+ararpy/smp/__init__.py,sha256=k6_fa27UJsQK7K7oC5GYlwMo6l0Xd8af3QtOrZz2XJk,478
 ararpy/smp/basic.py,sha256=1OgPXk-2OysJOZ9e_HuqB__fp3TNm844y0KKSlF5Wz0,21405
 ararpy/smp/calculation.py,sha256=JXo6vS-HcBhOe7b8OMLds-Sn9vofFjV6maY5u3E-X3c,2793
 ararpy/smp/consts.py,sha256=XIdjdz8cYxspG2jMnoItdlUsxr3hKbNFJjMZJh1bpzw,393
 ararpy/smp/corr.py,sha256=3lvs-2A3WjK_yfRnQRCG1Tb_QNhI4j82HU6a5OAN4Q8,23402
 ararpy/smp/diffusion_funcs.py,sha256=u7cEH7sac5tw0Z9Yvh7AuH93ZYEENJVtZ3Npni8dWUE,167616
 ararpy/smp/export.py,sha256=MBcisVfPwmdMyYqE7Tm3oLAMsVA5Rk0fl3Tqn0LxouI,78231
+ararpy/smp/info.py,sha256=iKUELm-BuUduDlJKC1d8tKKNHbwwbNmhUg2pi6bcBvA,489
 ararpy/smp/initial.py,sha256=nZNrV4fv_PlNXYfqqIOOOkcQjnSOTLymVpJyJ9d_QtM,15359
 ararpy/smp/json.py,sha256=87zMMopD5eL3VsemDYTEAfhSWXO_1Z7Y782S4GR2UUs,1740
 ararpy/smp/plots.py,sha256=s6xDZyxeGl512Wn4knquhzFeECucZCWNAsfI70OInqI,31362
 ararpy/smp/raw.py,sha256=KtAmzTAwCDK4x1dRgvwj2TbOzHRv7LFwaU2hHCknF3c,6173
-ararpy/smp/sample.py,sha256=aRTrIpJTgj67-QexJZNH-Z2a-nkOTAO5rlR3wLgqjfY,54607
+ararpy/smp/sample.py,sha256=S1vgt0LRihcAiqpXhuLLJnkft3kVp0QwzjH_JQkMyc0,54611
 ararpy/smp/style.py,sha256=NZwTeodhtHBBdCyjvupF64nh2B5EDdMHzlT8oE360zg,6746
 ararpy/smp/table.py,sha256=fyITVbj0JrPoB4SPW4dHoJl2jliKEZ_HpS2FSF9FQx4,6274
-ararpy-0.1.1.dist-info/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
-ararpy-0.1.1.dist-info/METADATA,sha256=BHMmwMCYAge-00gmPor6gseIYpjtqavxbQZ5YdpWfxQ,24330
-ararpy-0.1.1.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-ararpy-0.1.1.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
-ararpy-0.1.1.dist-info/RECORD,,
+ararpy-0.1.11.dist-info/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
+ararpy-0.1.11.dist-info/METADATA,sha256=uLONl17cQulcXUYmJ4BvhpxHyYrhIOs3i8Z9uOb6zD0,24331
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+ararpy-0.1.11.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
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