ararpy 0.1.13__py3-none-any.whl → 0.1.15__py3-none-any.whl

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
+            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:
@@ -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/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/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/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/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/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/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')

ararpy/smp/diffusion_funcs.py

@@ -743,6 +743,8 @@ class DiffArrmultiFunc(DiffSample):
         for j in range(0, na, 2):
             a1[j + 1] = a1[j + 1] / sum
 
+            # 生成体积浓度分数随机值，归一到总和为1
+
         # Definition of sizes (start with random order numbers greater to smaller)
         sum = 0.0
         for j in range(0, na - 2, 2):
@@ -753,11 +755,15 @@ class DiffArrmultiFunc(DiffSample):
         for j in range(0, na - 2, 2):
             a1[j] = a1[j] / sum * xro
 
+            # 从后到前随机生成尺寸，归一化到最大值为xro
+
         sum = a1[na - 1] + a1[na - 3]
         for j in range(2, na - 3, 2):
             a1[j] = a1[j] - np.log10(sum)
             sum = sum + a1[na - (j + 1) - 2]
 
+            # 调整尺寸的值，为什么？
+
         ro = 10.0 ** a1[0]
 
         for j in range(2, na - 3, 2):
@@ -3716,7 +3722,7 @@ class SmpTemperatureCalibration:
                 if line == "":
                     break
                 k = line.split(";")
-                time = dt.strptime(k[0], "%Y-%m-%dT%H:%M:%S%z").timestamp()
+                time = dt.strptime(k[0], "%Y-%m-%dT%H:%M:%S%z").timestamp()  # UTC datetime
                 cumulative_time = 0
                 if int(k[1]) != last_sp:
                     last_sp = int(k[1])
@@ -3731,11 +3737,12 @@ class SmpTemperatureCalibration:
                 except KeyError:
                     inside_temp = [0, 0]
 
-                libano_log.append([time, int(k[1]), int(k[2]), cumulative_time, inside_temp[0], inside_temp[1]])
+                # timestamp, cumulative_time of the current temperature, SP, AP, Inside, Inside error
+                libano_log.append([time, cumulative_time, int(k[1]), int(k[2]), (inside_temp[0] + inside_temp[1]) / 2,
+                                   abs(inside_temp[0] - inside_temp[1]) / 2, 9999])
                 n += 1
 
             libano_file.close()
-        libano_log = np.array(libano_log).transpose()
 
         # # set time starts with zero
         # log_time = [i - log_time[0] for i in log_time]
@@ -3749,10 +3756,13 @@ class SmpTemperatureCalibration:
         helix_log = [[], [], [], [], [], [], [], [], [], [], [], []]
         nstep = 0
 
+        time_difference = 147  # helix time - libano time 时间差
+
         keys = {
             "start_buildup": "GenWorkflow-BuildUp.cs: line 1: Clock reset",
             "set_temp": "GenWorkflow-Sampling.cs: Target temperature: key = Intensity, value = ",
             "end_sampling": "GenWorkflow-Prepare.cs: line 1: CLOSE for VUcleaningline/VINL2",
+            # "start_sampling": "GenWorkflow-Prepare.cs: line 15: CLOSE for VUcleaningline/VGP5",  # Y01样品之后发现VPL1漏气，多加了一步关闭VPL1因此，在那之后是line 15
             "start_sampling": "GenWorkflow-Prepare.cs: line 14: CLOSE for VUcleaningline/VGP5",
             "end_sequence": "GenWorkflow-PostAcquisition.cs: line 7: Starting Acquisition",
             "get_setpoint": "GenWorkflow-Sampling.cs: Target temperature: key = Intensity, value = ",
@@ -3781,7 +3791,9 @@ class SmpTemperatureCalibration:
                 dt_utc = dt_str[:26] + dt_str[27:]  # dt_utc will be like 2024-10-23T19:58:59.666214+02:00
                 dt_utc = dt.fromisoformat(str(dt_utc)).timestamp()
 
-                if not (self.start_time <= dt_utc <= self.end_time):
+                dt_utc  = dt_utc - time_difference
+
+                if not (self.start_time <= int(dt_utc) <= self.end_time):
                     continue
                 if message1.startswith(keys["start_buildup"]):
                     ### start buildup
@@ -3795,6 +3807,16 @@ class SmpTemperatureCalibration:
                     # 关闭vinlet2，60秒进质谱，之后开vinlet2，90秒抽气
                     gas_collection_end = dt_utc
                     helix_log[1].append(dt_utc)
+                    try:
+                        gas_collection_start = gas_collection_start
+                    except NameError:
+                        gas_collection_start = buildup_start
+                    # 添加阶段标记
+                    for each_row in libano_log:
+                        # 时间在集气过程中
+                        if gas_collection_start <= each_row[0] <= gas_collection_end:
+                            each_row[6] = nstep
+
                 if message1.startswith(keys["start_sampling"]):
                     # Close VGP5, start peak centering and measurement, IMPORTANT: start to sampling
                     gas_collection_start = dt_utc
@@ -3815,6 +3837,8 @@ class SmpTemperatureCalibration:
         for i in helix_log:
             print(len(i))
             print(i)
+
+        libano_log = np.array(libano_log).transpose()
         helix_log = np.array(helix_log)
 
 
@@ -3843,12 +3867,12 @@ class SmpTemperatureCalibration:
             yellow_data_index.append(_index)
 
             med = int((_index[0] + _index[-1]) / 2)
-            helix_log[4, i] = (libano_log[4, _index][0] + libano_log[5, _index][0]) / 2
-            helix_log[5, i] = abs(libano_log[4, _index][0] - libano_log[5, _index][0]) / 2
-            helix_log[6, i] = (libano_log[4, _index][-1] + libano_log[5, _index][-1]) / 2
-            helix_log[7, i] = abs(libano_log[4, _index][-1] - libano_log[5, _index][-1]) / 2
-            helix_log[8, i] = (libano_log[4, med] + libano_log[5, med]) / 2
-            helix_log[9, i] = abs(libano_log[4, med] - libano_log[5, med]) / 2
+            helix_log[4, i] = libano_log[4, _index][0]
+            helix_log[5, i] = libano_log[5, _index][0]
+            helix_log[6, i] = libano_log[4, _index][-1]
+            helix_log[7, i] = libano_log[5, _index][-1]
+            helix_log[8, i] = libano_log[4, med]
+            helix_log[9, i] = libano_log[5, med]
             helix_log[11, i] = gas_in_end - gas_in_start
 
             line = f"{i + 1}\t{helix_log[10, i]}\t{helix_log[11, i]}\t" + '\t'.join(
@@ -3871,11 +3895,9 @@ class SmpTemperatureCalibration:
             ax.plot(libano_log[0], libano_log[1], c='green')
             ax.plot(libano_log[0], libano_log[2], c='blue')
             ax.plot(libano_log[0], libano_log[4], c='red')
-            ax.plot(libano_log[0], libano_log[5], c='red')
             for i in range(nstep):
                 _index = yellow_data_index[i]
                 ax.plot(libano_log[0, _index], libano_log[4, _index], c='yellow')
-                ax.plot(libano_log[0, _index], libano_log[5, _index], c='yellow')
 
             fig.tight_layout()
             plt.show()