ararpy 0.1.34__tar.gz → 0.1.36__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {ararpy-0.1.34 → ararpy-0.1.36}/PKG-INFO +1 -1
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/__init__.py +2 -2
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/basic.py +3 -4
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/raw_funcs.py +3 -3
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/regression.py +94 -82
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/files/basic.py +0 -22
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/files/calc_file.py +35 -34
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/files/raw_file.py +27 -70
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/diffusion_funcs.py +1 -1
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/export.py +32 -32
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/raw.py +7 -11
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/sample.py +55 -55
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy.egg-info/PKG-INFO +1 -1
- {ararpy-0.1.34 → ararpy-0.1.36}/setup.py +1 -1
- {ararpy-0.1.34 → ararpy-0.1.36}/LICENSE +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/README.md +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/Example - Check arr.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/Example - Granite Cooling History.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/Example - Plot temperature calibration.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/Example - Show MDD results.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/Example - Show all Kfs age spectra.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/Example - Show random walk results.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/Example - Tc calculation.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/__init__.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/age.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/arr.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/corr.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/err.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/histogram.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/isochron.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/jvalue.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/plot.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/calc/spectra.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/022_VU124-M11a.ahd +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/20WHA0103.age +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/22WHA0078.xls +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/22WHA0433.age +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/22WHA0433.arr +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/22WHA0433.full.xls +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/24WHN0001-51-592.XLS +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/AHD.input-filter +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/ArAr.calc +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/ArArCALC.age +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/NGX-600 - Copy.TXT +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/NGX-600.TXT +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/NGX-XLS.input-filter +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/Qtegra-exported-xls.input-filter +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/S01-239.csv +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/WH01.irra +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/WHA.pdf +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/raw_example.xls +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/examples/sample-default.smp +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/files/__init__.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/files/arr_file.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/files/new_file.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/files/xls.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/EXPORT_TO_PDF_DATA_PROPERTIES.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/__init__.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/basic.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/calculation.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/consts.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/corr.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/info.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/initial.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/json.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/plots.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/style.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/smp/table.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/test.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/thermo/__init__.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/thermo/arrhenius.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/thermo/atomic_level_random_walk.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy/thermo/basic.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy.egg-info/SOURCES.txt +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy.egg-info/dependency_links.txt +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/ararpy.egg-info/top_level.txt +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/setup.cfg +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/tests/test.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/tests/test2.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/tests/test_error_correlation.py +0 -0
- {ararpy-0.1.34 → ararpy-0.1.36}/tests/test_regression_methods.py +0 -0
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@@ -16,10 +16,10 @@ from . import calc, smp, files, thermo, test
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""" Information """
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name = 'ararpy'
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version = '0.1.
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version = '0.1.36'
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__version__ = version
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full_version = version
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last_update = '2025-
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last_update = '2025-12-08'
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""" ArArPy Functions """
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#
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"""
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import copy
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import
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import string
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import secrets
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import numpy as np
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from scipy import stats
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from datetime import datetime, timezone, timedelta
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return res
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def
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return
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def get_random_string(length: int = 8) -> str:
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return secrets.token_hex(max(int(length/2), 1))
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def monte_carlo(func, inputs, confidence_level, **kwargs):
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"""
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def power(a0, a1):
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return regression.power(a0, a1)
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# return regression.power(a0, a1)
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raise ValueError("Deprecated regression")
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# if unselected is None:
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# unselected = []
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# linesData = []
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power, regression.average]
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# size = 50
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# lines_x = [(max(x + un_x) - 0) / size * i for i in range(size + 1)]
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x, y = transpose(points_data, ignore=False)
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for i in range(len(reg_handler)):
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try:
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x, y = transpose(points_data, ignore=False)
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res = reg_handler[i](a0=y, a1=x)
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# line_data = transpose([lines_x, res[7](lines_x)])
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line_results = res[0:4]
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import numpy as np
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import pandas as pd
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from scipy.stats import distributions
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from scipy.optimize import
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from scipy.optimize import minimize_scalar
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import warnings
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warnings.simplefilter(action="ignore", category=RuntimeWarning)
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# calculate Y values base on the fitted formula
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estimate_y = np.matmul(x, beta)
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ssresid = resid.sum() # 残差平方和
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ssreg = reg.sum() # 回归平方和
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beta = beta.flatten()
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def get_adjusted_y(*args):
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k1 = pow(sum([(i - k0) ** 2 for i in a0]) / df, 0.5) # standard deviation
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:return: intercept | standard error of intercept | relative error | R2 | MSWD | [m, c, b] | [sem, sec, seb]
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b, count = newton_minimize_1d(_get_s, x0=ini_b, h=1e-5, tol=1e-8, max_iter=30)
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except Exception as e:
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# 使用 scipy 一维优化
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res = minimize_scalar(_get_s, bounds=(-2, 2), method='bounded', options={'xatol': 1e-8})
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b, count = res.x, res.nfev
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932
|
-
a, sea, c, sec = f[5][1], f[6][1], f[0], f[1]
|
|
909
|
+
# print(f"{b = }, {count = }")
|
|
933
910
|
|
|
934
|
-
|
|
935
|
-
|
|
936
|
-
|
|
937
|
-
|
|
938
|
-
|
|
939
|
-
|
|
940
|
-
|
|
941
|
-
|
|
942
|
-
|
|
911
|
+
x = np.concatenate(([np.ones(len(a1))], [np.exp(b * np.array(a1))]), axis=0).transpose()
|
|
912
|
+
m, n = x.shape # number of data, number of unknown x
|
|
913
|
+
try:
|
|
914
|
+
inv_xtx = np.linalg.inv(np.matmul(x.transpose(), x))
|
|
915
|
+
except np.linalg.LinAlgError:
|
|
916
|
+
raise np.linalg.LinAlgError(f"The determinant of the given matrix must not be zero ")
|
|
917
|
+
beta = np.matmul(inv_xtx, np.matmul(x.transpose(), y))
|
|
918
|
+
estimate_y = np.matmul(x, beta)
|
|
919
|
+
resid = (estimate_y - y) ** 2
|
|
920
|
+
reg = (estimate_y - np.mean(y)) ** 2
|
|
921
|
+
ssresid = resid.sum() # 残差平方和
|
|
922
|
+
ssreg = reg.sum() # 回归平方和
|
|
923
|
+
sstotal = ((y - np.mean(y)) ** 2).sum()
|
|
943
924
|
r2 = ssreg / sstotal if sstotal != 0 else 1
|
|
944
925
|
|
|
945
|
-
|
|
926
|
+
df = m - n
|
|
927
|
+
m_ssresid = ssresid / df # 均方残差,与加权平均中的MSWD对应
|
|
928
|
+
cov_beta = m_ssresid * inv_xtx
|
|
929
|
+
|
|
930
|
+
sc, sa = np.diagonal(cov_beta) ** .5
|
|
931
|
+
c, a = beta.flatten()
|
|
946
932
|
intercept = a + c
|
|
947
|
-
|
|
948
|
-
# calculate error of intercept
|
|
949
|
-
errfz = pow(sum([i ** 2 for i in z]) / (dp * sum([i ** 2 for i in z]) - sum(z) ** 2), 0.5)
|
|
950
|
-
errfx = pow(sum([i ** 2 for i in a1]) / (dp * sum([i ** 2 for i in a1]) - sum(a1) ** 2), 0.5)
|
|
951
|
-
# seb = errfz * sey = errfz * ssresid / df -> se_intercept = sey * errfx = seb / errfz * errfx
|
|
952
|
-
se_intercept = sec / errfz * errfx
|
|
953
|
-
rse_intercept = se_intercept / intercept * 100
|
|
933
|
+
se_intercept = pow(sa ** 2 + sc ** 2 + 2 * cov_beta[0][1] , 0.5)
|
|
954
934
|
|
|
955
|
-
return intercept, se_intercept,
|
|
956
|
-
lambda x: [_exp_func(
|
|
935
|
+
return intercept, se_intercept, se_intercept / intercept * 100, r2, m_ssresid, [a, b, c], 'se', \
|
|
936
|
+
lambda x: [_exp_func(xi, a, b, c) for xi in x], m_ssresid
|
|
937
|
+
|
|
938
|
+
|
|
939
|
+
def newton_minimize_1d(func, x0, h=1e-5, tol=1e-8, max_iter=20):
|
|
940
|
+
x = x0
|
|
941
|
+
for i in range(max_iter):
|
|
942
|
+
fx = func(x)
|
|
943
|
+
if not np.isfinite(fx):
|
|
944
|
+
raise ValueError("Newton Minimize: Function returned non-finite value at x={}".format(x))
|
|
945
|
+
|
|
946
|
+
# 一阶导数(中心差分)
|
|
947
|
+
f_plus = func(x + h)
|
|
948
|
+
f_minus = func(x - h)
|
|
949
|
+
if not (np.isfinite(f_plus) and np.isfinite(f_minus)):
|
|
950
|
+
raise ValueError("Newton Minimize: Non-finite values in derivative computation")
|
|
951
|
+
|
|
952
|
+
df = (f_plus - f_minus) / (2 * h)
|
|
953
|
+
d2f = (f_plus - 2 * fx + f_minus) / (h * h)
|
|
954
|
+
|
|
955
|
+
# 牛顿步长
|
|
956
|
+
if abs(d2f) < 1e-12: # 避免除零或平坦区域
|
|
957
|
+
print("Newton Minimize: Second derivative too small, stopping.")
|
|
958
|
+
break
|
|
959
|
+
|
|
960
|
+
step = df / d2f
|
|
961
|
+
x_new = x - step
|
|
962
|
+
|
|
963
|
+
if abs(step) < tol:
|
|
964
|
+
x = x_new
|
|
965
|
+
break
|
|
966
|
+
|
|
967
|
+
x = x_new
|
|
957
968
|
|
|
969
|
+
return x, i + 1
|
|
958
970
|
|
|
959
971
|
""" line functions """
|
|
960
972
|
|
|
@@ -12,31 +12,9 @@
|
|
|
12
12
|
|
|
13
13
|
import os
|
|
14
14
|
import pickle
|
|
15
|
-
import traceback
|
|
16
15
|
import json
|
|
17
16
|
|
|
18
17
|
|
|
19
|
-
def upload(file, media_dir):
|
|
20
|
-
try:
|
|
21
|
-
name, suffix = os.path.splitext(file.name)
|
|
22
|
-
if suffix.lower() not in [
|
|
23
|
-
'.xls', '.age', '.xlsx', '.arr', '.jpg', '.png', '.txt',
|
|
24
|
-
'.log', '.seq', '.json', '.ahd', '.csv', '.ngxdp']:
|
|
25
|
-
raise TypeError(f"The imported file is not supported: {suffix}")
|
|
26
|
-
web_file_path = os.path.join(media_dir, file.name)
|
|
27
|
-
with open(web_file_path, 'wb') as f:
|
|
28
|
-
for chunk in file.chunks():
|
|
29
|
-
f.write(chunk)
|
|
30
|
-
print("File path on the server: %s" % web_file_path)
|
|
31
|
-
except PermissionError:
|
|
32
|
-
raise ValueError(f'Permission denied')
|
|
33
|
-
except (Exception, BaseException) as e:
|
|
34
|
-
print(traceback.format_exc())
|
|
35
|
-
raise ValueError(f'Error in opening file: {e}')
|
|
36
|
-
else:
|
|
37
|
-
return web_file_path, name, suffix
|
|
38
|
-
|
|
39
|
-
|
|
40
18
|
def read(file_path):
|
|
41
19
|
""" Read text files, default 'r', 'rb'
|
|
42
20
|
Parameters
|
|
@@ -493,40 +493,41 @@ def open_full_xls(file_path: str, sample_name: str = ''):
|
|
|
493
493
|
res['Inverse Isochron Table'], rows, [4, 5, 6, 7, 10])
|
|
494
494
|
total_param = arr.partial(
|
|
495
495
|
res['Sample Parameters'], rows, [
|
|
496
|
-
# 1, 2,
|
|
497
|
-
-1, -1, -1, -1, #
|
|
498
|
-
-1, -1, -1, -1, #
|
|
499
|
-
-1, -1, -1, -1, -1, -1, #
|
|
500
|
-
-1, -1, -1, -1, #
|
|
501
|
-
-1, -1, #
|
|
502
|
-
23, 24, -1, -1, -1, -1, #
|
|
503
|
-
-1, -1, #
|
|
504
|
-
22, -1, -1, -1, #
|
|
505
|
-
-1, -1, #
|
|
506
|
-
-1, -1, #
|
|
507
|
-
-1, -1, #
|
|
508
|
-
-1, -1, #
|
|
509
|
-
-1, -1, #
|
|
510
|
-
-1, -1, #
|
|
511
|
-
-1, -1, #
|
|
512
|
-
-1, -1, #
|
|
513
|
-
-1, -1, #
|
|
514
|
-
-1, -1, #
|
|
515
|
-
-1, -1, #
|
|
516
|
-
-1, -1, #
|
|
517
|
-
-1, -1, #
|
|
518
|
-
-1, -1, -1, -1, -1, -1, -1, -1, -1, #
|
|
519
|
-
10, 11, 12, 13, #
|
|
520
|
-
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, #
|
|
521
|
-
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, #
|
|
522
|
-
-1, -1, -1, -1, #
|
|
523
|
-
-1, -1, -1, -1, #
|
|
524
|
-
-1, -1, -1, -1, #
|
|
525
|
-
-1, -1, -1, -1, #
|
|
526
|
-
-1, -1, -1, -1, #
|
|
527
|
-
-1, -1, -1, -1, -1, -1, -1, -1, #
|
|
528
|
-
-1, -1, -1, -1, -1, -1, -1, -1, #
|
|
529
|
-
-1, -1, -1, -1, -1, #
|
|
496
|
+
# 1, 2, -1, # 0-2
|
|
497
|
+
-1, -1, -1, -1, # 3-6
|
|
498
|
+
-1, -1, -1, -1, # 7-10
|
|
499
|
+
-1, -1, -1, -1, -1, -1, # 11-16
|
|
500
|
+
-1, -1, -1, -1, # 17-20
|
|
501
|
+
-1, -1, # 21-22
|
|
502
|
+
23, 24, -1, -1, -1, -1, # 23-28
|
|
503
|
+
-1, -1, # 29-30
|
|
504
|
+
22, -1, -1, -1, # 31-34
|
|
505
|
+
-1, -1, # 35-36
|
|
506
|
+
-1, -1, # 37-38
|
|
507
|
+
-1, -1, # 39-40
|
|
508
|
+
-1, -1, # 41-42
|
|
509
|
+
-1, -1, # 43-44
|
|
510
|
+
-1, -1, # 45-46
|
|
511
|
+
-1, -1, # 47-48
|
|
512
|
+
-1, -1, # 49-50
|
|
513
|
+
-1, -1, # 51-52
|
|
514
|
+
-1, -1, # 53-54
|
|
515
|
+
-1, -1, # 55-56
|
|
516
|
+
-1, -1, # 57-58
|
|
517
|
+
-1, -1, # 59-60
|
|
518
|
+
-1, -1, -1, -1, -1, -1, -1, -1, -1, # 61-69
|
|
519
|
+
10, 11, 12, 13, # 70-73
|
|
520
|
+
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, # 74-85
|
|
521
|
+
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, # 86-95
|
|
522
|
+
-1, -1, -1, -1, # 96-99
|
|
523
|
+
-1, -1, -1, -1, # 100-103
|
|
524
|
+
-1, -1, -1, -1, # 104-107
|
|
525
|
+
-1, -1, -1, -1, # 108-111
|
|
526
|
+
-1, -1, -1, -1, # 112-115
|
|
527
|
+
-1, -1, -1, -1, -1, -1, -1, -1, # 116-123
|
|
528
|
+
-1, -1, -1, -1, -1, -1, -1, -1, # 124-131
|
|
529
|
+
-1, -1, -1, -1, -1, # 132-136
|
|
530
|
+
-1, -1, -1, -1, # 137-140
|
|
530
531
|
])
|
|
531
532
|
|
|
532
533
|
month_convert = {'Jan': '01', 'Feb': '02', 'Mar': '03', 'Apr': '04', 'May': '05', 'Jun': '06',
|
|
@@ -65,7 +65,7 @@ DEFAULT_SAMPLE_INFO = {
|
|
|
65
65
|
|
|
66
66
|
|
|
67
67
|
|
|
68
|
-
def open_file(file_path: str, input_filter: List[Union[str, int, bool]]):
|
|
68
|
+
def open_file(file_path: str, input_filter: List[Union[str, int, bool]], name=None):
|
|
69
69
|
"""
|
|
70
70
|
Parameters
|
|
71
71
|
----------
|
|
@@ -94,63 +94,14 @@ def open_file(file_path: str, input_filter: List[Union[str, int, bool]]):
|
|
|
94
94
|
"""
|
|
95
95
|
extension = str(os.path.split(file_path)[-1]).split('.')[-1]
|
|
96
96
|
try:
|
|
97
|
-
handler = {'txt': open_raw_txt, 'excel': open_raw_xls,
|
|
98
|
-
|
|
99
|
-
['txt', 'excel', 'Qtegra Exported XLS', 'Seq'][int(input_filter[1])]]
|
|
97
|
+
handler = {'txt': open_raw_txt, 'excel': open_raw_xls, 'Seq': open_raw_seq}[
|
|
98
|
+
['txt', 'excel', 'Qtegra Excel (deleted)', 'Seq'][int(input_filter[1])]]
|
|
100
99
|
except KeyError:
|
|
101
100
|
raise FileNotFoundError("Wrong File.")
|
|
102
|
-
return handler(file_path, input_filter)
|
|
101
|
+
return handler(file_path, input_filter, name)
|
|
103
102
|
|
|
104
103
|
|
|
105
|
-
def
|
|
106
|
-
if input_filter is None:
|
|
107
|
-
input_filter = []
|
|
108
|
-
try:
|
|
109
|
-
wb = open_workbook(filepath)
|
|
110
|
-
sheets = wb.sheet_names()
|
|
111
|
-
sheet = wb.sheet_by_name(sheets[0])
|
|
112
|
-
value, step_header, step_list = [], [], []
|
|
113
|
-
for row in range(sheet.nrows):
|
|
114
|
-
row_set = []
|
|
115
|
-
for col in range(sheet.ncols):
|
|
116
|
-
if sheet.cell(row, col).value == '':
|
|
117
|
-
pass
|
|
118
|
-
else:
|
|
119
|
-
row_set.append(sheet.cell(row, col).value)
|
|
120
|
-
if row_set != [] and len(row_set) > 1:
|
|
121
|
-
value.append(row_set)
|
|
122
|
-
for each_row in value:
|
|
123
|
-
# if the first item of each row is float (1.0, 2.0, ...) this row is the header of a step.
|
|
124
|
-
if isinstance(each_row[0], float):
|
|
125
|
-
each_row[0] = int(each_row[0])
|
|
126
|
-
if "M" in each_row[1].upper():
|
|
127
|
-
each_row[1] = datetime.strptime(each_row[1], '%m/%d/%Y %I:%M:%S %p').isoformat(timespec='seconds')
|
|
128
|
-
else:
|
|
129
|
-
each_row[1] = datetime.strptime(each_row[1], '%m/%d/%Y %H:%M:%S').isoformat(timespec='seconds')
|
|
130
|
-
step_header.append(each_row)
|
|
131
|
-
for step_index, each_step_header in enumerate(step_header):
|
|
132
|
-
row_start_number = value.index(each_step_header)
|
|
133
|
-
try:
|
|
134
|
-
row_stop_number = value.index(step_header[step_index + 1])
|
|
135
|
-
except IndexError:
|
|
136
|
-
row_stop_number = len(value) + 1
|
|
137
|
-
step_values = [
|
|
138
|
-
each_step_header[0:4],
|
|
139
|
-
*list(map(
|
|
140
|
-
# lambda x: [x[0], x[1], x[2], x[1], x[3], x[1], x[4], x[1], x[5], x[1], x[6]],
|
|
141
|
-
# x[1] = time, x[2] = H2:40, x[3] = H1: 39, x[4] = AX: 38, x[5] = L1: 37, x[6] = L2: 36
|
|
142
|
-
lambda x: [x[0], x[1], x[6], x[1], x[5], x[1], x[4], x[1], x[3], x[1], x[2]],
|
|
143
|
-
# in sequence: Ar36, Ar37, Ar38, Ar39, Ar40
|
|
144
|
-
[value[i] for i in range(row_start_number + 2, row_stop_number - 7, 1)]))
|
|
145
|
-
]
|
|
146
|
-
step_list.append(step_values)
|
|
147
|
-
except Exception as e:
|
|
148
|
-
raise ValueError('Error in opening the original file: %s' % str(e))
|
|
149
|
-
else:
|
|
150
|
-
return {'data': step_list}
|
|
151
|
-
|
|
152
|
-
|
|
153
|
-
def open_raw_txt(file_path, input_filter: List[Union[str, int]]):
|
|
104
|
+
def open_raw_txt(file_path, input_filter: List[Union[str, int]], name=None):
|
|
154
105
|
"""
|
|
155
106
|
Parameters
|
|
156
107
|
----------
|
|
@@ -173,12 +124,12 @@ def open_raw_txt(file_path, input_filter: List[Union[str, int]]):
|
|
|
173
124
|
lines = [line.strip().split(['\t', ';', " ", ",", input_filter[3]][int(input_filter[2])])
|
|
174
125
|
for line in contents.decode(encoding=encoding["encoding"]).split('\r\n')]
|
|
175
126
|
|
|
176
|
-
file_name = os.path.basename(file_path).rstrip(os.path.splitext(file_path)[-1])
|
|
127
|
+
file_name = os.path.basename(file_path).rstrip(os.path.splitext(file_path)[-1]) if name is None else name
|
|
177
128
|
step_list = get_raw_data([lines], input_filter, file_name=file_name)
|
|
178
129
|
return {'data': step_list}
|
|
179
130
|
|
|
180
131
|
|
|
181
|
-
def open_raw_xls(file_path, input_filter: List[Union[str, int]]):
|
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132
|
+
def open_raw_xls(file_path, input_filter: List[Union[str, int]], name):
|
|
182
133
|
"""
|
|
183
134
|
Parameters
|
|
184
135
|
----------
|
|
@@ -205,13 +156,13 @@ def open_raw_xls(file_path, input_filter: List[Union[str, int]]):
|
|
|
205
156
|
|
|
206
157
|
wb = open_workbook(file_path)
|
|
207
158
|
contents = [_get_content_from_sheet(i) for i in range(100)]
|
|
208
|
-
file_name = os.path.basename(file_path).rstrip(os.path.splitext(file_path)[-1])
|
|
159
|
+
file_name = os.path.basename(file_path).rstrip(os.path.splitext(file_path)[-1]) if name is None else name
|
|
209
160
|
step_list = get_raw_data(contents, input_filter, file_name=file_name)
|
|
210
161
|
|
|
211
162
|
return {'data': step_list}
|
|
212
163
|
|
|
213
164
|
|
|
214
|
-
def open_raw_seq(file_path, input_filter=None):
|
|
165
|
+
def open_raw_seq(file_path, input_filter=None, name=None):
|
|
215
166
|
|
|
216
167
|
class RenameUnpickler(pickle.Unpickler):
|
|
217
168
|
def find_class(self, module: str, name: str):
|
|
@@ -257,20 +208,29 @@ def get_raw_data(file_contents: List[List[Union[int, float, str, bool, list]]],
|
|
|
257
208
|
|
|
258
209
|
"""
|
|
259
210
|
|
|
260
|
-
def datetime_parse(string, f):
|
|
211
|
+
def datetime_parse(string: str, f: str):
|
|
261
212
|
try:
|
|
262
213
|
return datetime.strptime(string, f)
|
|
263
214
|
except ValueError as v:
|
|
215
|
+
print(traceback.format_exc())
|
|
264
216
|
if f.strip() == "":
|
|
265
217
|
return datetime_parser.parse(string)
|
|
266
218
|
elif len(v.args) > 0 and v.args[0].startswith('unconverted data remains: '):
|
|
267
|
-
|
|
268
|
-
return
|
|
219
|
+
# %f handles microseconds (6 digits), remove the remains
|
|
220
|
+
return datetime_parse(string[:-(len(v.args[0]) - 26)], f)
|
|
221
|
+
# elif f.upper()[-2:] in ['PM', 'AM']:
|
|
222
|
+
# return datetime_parse(string, f[:-2])
|
|
269
223
|
else:
|
|
270
224
|
raise
|
|
271
225
|
|
|
226
|
+
def step_num_parse(s: str):
|
|
227
|
+
try:
|
|
228
|
+
return f"{round(float(s)):02d}"
|
|
229
|
+
except (ValueError, TypeError):
|
|
230
|
+
return s
|
|
231
|
+
|
|
272
232
|
step_list = []
|
|
273
|
-
idx = step_index
|
|
233
|
+
idx = 0 # step_index
|
|
274
234
|
|
|
275
235
|
header = input_filter[5]
|
|
276
236
|
isotope_index = input_filter[8:28]
|
|
@@ -293,13 +253,10 @@ def get_raw_data(file_contents: List[List[Union[int, float, str, bool, list]]],
|
|
|
293
253
|
if res is not None and "en" in res.named.keys():
|
|
294
254
|
experiment_name = res.named.get("en")
|
|
295
255
|
if res is not None and "sn" in res.named.keys():
|
|
296
|
-
|
|
297
|
-
|
|
298
|
-
|
|
299
|
-
|
|
300
|
-
step_name = f"{experiment_name}-{step_index}"
|
|
301
|
-
if step_name == "":
|
|
302
|
-
raise ValueError(f"Step name not found")
|
|
256
|
+
step_name = res.named.get("sn")
|
|
257
|
+
if str(step_name) == "":
|
|
258
|
+
raise ValueError(f"Step name not found, break reading steps")
|
|
259
|
+
step_name = f"{experiment_name}-{step_num_parse(step_name)}"
|
|
303
260
|
except (TypeError, ValueError, IndexError):
|
|
304
261
|
# When parsing the step name fails, the end of the file has been reached
|
|
305
262
|
# raise
|
|
@@ -417,7 +374,7 @@ def get_raw_data(file_contents: List[List[Union[int, float, str, bool, list]]],
|
|
|
417
374
|
step_list.append(current_step)
|
|
418
375
|
idx = data_index[28] * len(step_list)
|
|
419
376
|
if not check_box_index[0] or len(step_list) >= 500: # check_box_index[0]: multiple sequences
|
|
420
|
-
print(f"Multiple Sequence = {check_box_index[0]}, Step number = {len(step_list)}")
|
|
377
|
+
# print(f"Multiple Sequence = {check_box_index[0]}, Step number = {len(step_list)}")
|
|
421
378
|
break
|
|
422
379
|
|
|
423
380
|
if not step_list:
|
|
@@ -4436,7 +4436,7 @@ def get_random_dir(path: str, length=7, random_index=""):
|
|
|
4436
4436
|
try:
|
|
4437
4437
|
exist_ok = random_index != ""
|
|
4438
4438
|
if random_index == "":
|
|
4439
|
-
random_index = calc.basic.
|
|
4439
|
+
random_index = calc.basic.get_random_string(length=length)
|
|
4440
4440
|
destination_folder = os.path.join(path, random_index)
|
|
4441
4441
|
os.makedirs(destination_folder, exist_ok=exist_ok)
|
|
4442
4442
|
return destination_folder, random_index
|