ararpy 0.1.1__tar.gz → 0.1.11__tar.gz

{ararpy-0.1.1 → ararpy-0.1.11}/PKG-INFO

@@ -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 → ararpy-0.1.11}/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-0.1.11/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-0.1.1 → ararpy-0.1.11}/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-0.1.11/ararpy/test.py

@@ -0,0 +1,37 @@
+#  Copyright (C) 2024 Yang. - All Rights Reserved
+"""
+# ==========================================
+# Copyright 2024 Yang
+# ararpy - test.py
+# ==========================================
+#
+#
+#
+"""
+import ararpy as ap
+import os
+
+
+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() = }")
+    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]])
+
+
+if __name__ == "__main__":
+    test()

{ararpy-0.1.1 → ararpy-0.1.11}/ararpy.egg-info/PKG-INFO

@@ -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 → ararpy-0.1.11}/ararpy.egg-info/SOURCES.txt

@@ -52,6 +52,7 @@ ararpy/smp/consts.py
 ararpy/smp/corr.py
 ararpy/smp/diffusion_funcs.py
 ararpy/smp/export.py
+ararpy/smp/info.py
 ararpy/smp/initial.py
 ararpy/smp/json.py
 ararpy/smp/plots.py

{ararpy-0.1.1 → ararpy-0.1.11}/setup.py

@@ -16,7 +16,7 @@ long_description = (here / 'README.md').read_text(encoding='utf-8')
 
 setuptools.setup(
     name='ararpy',  #
-    version='0.1.1',  # version
+    version='0.1.11',  # version
     author='Yang Wu',
     author_email='wuycug@hotmail.com',
     description='A project for Ar-Ar geochronology',  # short description

ararpy-0.1.1/ararpy/test.py

@@ -1,296 +0,0 @@
-#  Copyright (C) 2024 Yang. - All Rights Reserved
-"""
-# ==========================================
-# Copyright 2024 Yang
-# ararpy - test.py
-# ==========================================
-#
-#
-#
-"""
-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)
-
-
-
-###  梳理这些函数  用numba加速
-
-if __name__ == "__main__":
-    test()