ararpy 0.1.12__py3-none-any.whl → 0.1.14__py3-none-any.whl

ararpy/smp/json.py

@@ -14,6 +14,7 @@ import json
 import numpy as np
 import pandas as pd
 from .sample import Sample, Table, Plot, RawData, Sequence, ArArBasic
+from django.db.models import QuerySet
 
 
 def dumps(a):
@@ -31,6 +32,9 @@ class MyEncoder(json.JSONEncoder):
         # np.array
         if isinstance(obj, np.ndarray):
             return obj.tolist()
+        # np.array
+        if isinstance(obj, QuerySet):
+            return list(obj)
         # pd.DataFrame
         if isinstance(obj, pd.DataFrame):
             print(obj)
@@ -49,6 +53,9 @@ class MyEncoder(json.JSONEncoder):
                     'is_blank': obj.is_blank(), 'is_unknown': obj.is_unknown(),
                     'is_air': obj.is_air()})
             return obj.__dict__
+        # Error
+        if isinstance(obj, BaseException):
+            return obj.args[0]
         if not isinstance(obj, (int, str, list, dict, tuple, float)):
             print(f"Special type, {type(obj) = }, {obj = }")
         return super(MyEncoder, self).default(obj)

ararpy/smp/plots.py

@@ -59,7 +59,7 @@ def set_plot_data(sample: Sample, isInit: bool = True, isIsochron: bool = True,
     # Initialization, apply age spectra data and isochron plot data
     if isInit:
         try:
-            initial_plot_data(sample)
+            initial_plot_data(sample, **kwargs)
         except (Exception, BaseException):
             # print(traceback.format_exc())
             pass
@@ -80,7 +80,7 @@ def set_plot_data(sample: Sample, isInit: bool = True, isIsochron: bool = True,
     # Recalculate plateaus
     if isPlateau:
         try:
-            recalc_plateaus(sample)
+            recalc_plateaus(sample, **kwargs)
         except (Exception, BaseException):
             # print(traceback.format_exc())
             pass
@@ -89,7 +89,7 @@ def set_plot_data(sample: Sample, isInit: bool = True, isIsochron: bool = True,
 # =======================
 # Initialize plot data
 # =======================
-def initial_plot_data(sample: Sample):
+def initial_plot_data(sample: Sample, **kwargs):
     """
     Assign initial data for plots
     Parameters
@@ -136,7 +136,7 @@ def initial_plot_data(sample: Sample):
     )
     try:
         sample.AgeSpectraPlot.data = calc.spectra.get_data(
-            *sample.ApparentAgeValues[2:4], sample.ApparentAgeValues[7])
+            *sample.ApparentAgeValues[2:4], sample.ApparentAgeValues[7], **kwargs)
         sample.AgeSpectraPlot.data = calc.arr.transpose(sample.AgeSpectraPlot.data)
     except (Exception, BaseException):
         print(traceback.format_exc())
@@ -434,8 +434,9 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
     # Get ages and line data points for each set
     try:
         set1_res, set1_age, set1_data = \
-            get_plateau_results(sample, sample.SelectedSequence1, calc_ar40ar39(*ratio_set1, smp=sample))
+            get_plateau_results(sample, sample.SelectedSequence1, calc_ar40ar39(*ratio_set1, smp=sample), **kwargs)
     except ValueError:
+        # print(traceback.format_exc())
         pass
         # raise ValueError(f"Set 1 Plateau results calculation error.")
     else:
@@ -444,8 +445,9 @@ def recalc_age_plateaus(sample: Sample, **kwargs):
         sample.AgeSpectraPlot.text1.text = ""  # 注意和js的配合，js那边根据text是否为空判断是否重新生成文字
     try:
         set2_res, set2_age, set2_data = \
-            get_plateau_results(sample, sample.SelectedSequence2, calc_ar40ar39(*ratio_set2, smp=sample))
+            get_plateau_results(sample, sample.SelectedSequence2, calc_ar40ar39(*ratio_set2, smp=sample), **kwargs)
     except ValueError:
+        # print(traceback.format_exc())
         pass
         # raise ValueError(f"Set 2 Plateau results calculation error.")
     else:
@@ -579,7 +581,7 @@ def calc_ar40ar39(r, sr, smp):
 
 
 def get_plateau_results(sample: Sample, sequence: list, ar40rar39k: list = None,
-                        ar39k_percentage: list = None):
+                        ar39k_percentage: list = None, **kwargs):
     """
     Get initial ratio re-corrected plateau results
     Parameters
@@ -613,7 +615,7 @@ def get_plateau_results(sample: Sample, sequence: list, ar40rar39k: list = None,
         ar39k_percentage = sample.ApparentAgeValues[7]
 
     age = basic.calc_age(ar40ar39=ar40rar39k, smp=sample)[0:2]
-    plot_data = calc.spectra.get_data(*age, ar39k_percentage, indices=sequence)
+    plot_data = calc.spectra.get_data(*age, ar39k_percentage, indices=sequence, **kwargs)
     f_values = _get_partial(sequence, *ar40rar39k)
     age = _get_partial(sequence, *age)
     sum_ar39k = sum(_get_partial(sequence, ar39k_percentage)[0])

ararpy/smp/raw.py

@@ -50,8 +50,15 @@ def to_raw(file_path: Union[str, List[str]], input_filter_path: Union[str, List[
         data = res.get('data', None)
         sequences = res.get('sequences', None)
         sequence_num = len(data) if data is not None else len(sequences)
-        raw = RawData(name=file_name, data=data, isotopic_num=10, sequence_num=sequence_num,
-                      source=[file_path], sequence=sequences, unit=str(input_filter[30]))
+        # default fitting method, all exponential
+        # <option value=0>Linear</option>
+        # <option value=1>Quadratic</option>
+        # <option value=2>Exponential</option>
+        # <option value=3>Power</option>
+        # <option value=4>Average</option>
+        fitting_method = [2, 0, 2, 2, 2]
+        raw = RawData(name=file_name, data=data, isotopic_num=10, sequence_num=sequence_num, source=[file_path],
+                      sequence=sequences, unit=str(input_filter[30]), fitting_method=[*fitting_method])
     else:
         raise ValueError("File path and input filter should be both string or list with a same length.")
     return raw

ararpy/smp/sample.py

@@ -122,9 +122,10 @@ TOTAL_PARAMS_HEADERS = [
     'Not Zero', 'Corr Blank', 'Corr Discr', 'Corr \u00B3\u2077Ar Decay',  # 103-106
     'Corr \u00B3\u2079Ar Decay',  # 107
     'Ca Degassing', 'K Degassing', 'Cl Degassing', 'Trap Degassing',  # 108-111
-    'Using Min Equation',
+    'Using Min Equation',  # 112
     # 'Recalibration', 'Using Std Age', 'Use Std Ratio',  # 112-115  to be completed
-    '', '', '',  # 112-115
+    'Apply Gain Corr to Blanks',  # 113
+    '', '',  # 114-115
     'Auto Plateau Method',  # 116 the index includes sequence name and unit
     'Initial Ratio Model',  # 117
     'Set1 initial Ratio',  # 118
@@ -137,11 +138,11 @@ TOTAL_PARAMS_HEADERS = [
     'Heating Time (s)',  # 125
     'Heating Actual Temp (C)',  # 126
     'Heating AT 1\u03C3',  # 127
-    '36Ar Gain', '1\u03C3',  # 128-129
-    '37Ar Gain', '1\u03C3',  # 130-131
-    '38Ar Gain', '1\u03C3',  # 132-133
-    '39Ar Gain', '1\u03C3',  # 134-135
-    '40Ar Gain', '1\u03C3',  # 136-137
+    '36Ar Gain', '%1\u03C3',  # 128-129
+    '37Ar Gain', '%1\u03C3',  # 130-131
+    '38Ar Gain', '%1\u03C3',  # 132-133
+    '39Ar Gain', '%1\u03C3',  # 134-135
+    '40Ar Gain', '%1\u03C3',  # 136-137
 ]
 
 SAMPLE_INTERCEPT_SHORT_HEADERS = [
@@ -235,9 +236,10 @@ TOTAL_PARAMS_SHORT_HEADERS = [
     'NotZero', 'CorrBlank', 'CorrDiscr', 'CorrAr37Decay',
     'CorrAr39Decay',  # 103-107
     'CaDegassing', 'KDegassing', 'ClDegassing', 'TrapDegassing',  # 108-111
-    'UsingMin',
+    'UsingMin',  # 112
     # 'Recalibration', 'Using Std Age', 'Use Std Ratio',  # 112-115  to be completed
-    '', '', '',  # 112-115
+    'BlankGainCorr',  # 113
+    '', '',  # 114-115
     'AutoPlateauMethod',  # 116 the index includes sequence name and unit
     'InitialRatioModel',  # 117
     'Set1InitialRatio',  # 118
@@ -250,11 +252,11 @@ TOTAL_PARAMS_SHORT_HEADERS = [
     'HeatingTime',  # 125
     'HeatingActualTemp',  # 126
     'HeatingActualTempError',  # 127
-    '36Gain', '1s',  # 128-129
-    '37Gain', '1s',  # 130-131
-    '38Gain', '1s',  # 132-133
-    '39Gain', '1s',  # 134-135
-    '40Gain', '1s',  # 136-137
+    '36Gain', '%1s',  # 128-129
+    '37Gain', '%1s',  # 130-131
+    '38Gain', '%1s',  # 132-133
+    '39Gain', '%1s',  # 134-135
+    '40Gain', '%1s',  # 136-137
 ]
 
 DEFAULT_PLOT_STYLES = {
@@ -741,7 +743,7 @@ DEFAULT_PLOT_STYLES = {
     },
 }
 
-VERSION = '20240930'
+VERSION = '20250102'
 
 NAMED_DICT = {
     "unknown": {"header": SAMPLE_INTERCEPT_HEADERS.copy()},
@@ -842,7 +844,9 @@ class Sample:
         # self.__version = '20230730'  # delete calcparams attribute
         # self.__version = '20230827'  # using merge smp to update arr version
         # self.__version = '20231116'  # change smp parameters
-        self.__version = '20240730'  # change parameter table for thermo calculation
+        # self.__version = '20240730'  # change parameter table for thermo calculation
+        # self.__version = '20241028'  # gain correction
+        self.__version = '20250102'  # gain correction to blanks
 
     @property
     def version(self):
@@ -1154,16 +1158,21 @@ class RawData:
         self.isotopic_num = isotopic_num
         self.sequence_num = sequence_num
         self.interpolated_blank = None
-        if data is not None:
+        if sequence is not None:
+            self.sequence = sequence
+        elif data is not None:
             self.sequence: List[Sequence] = [
-                Sequence(index=index, name=item[0][0] if isinstance(item[0][0], str) and item[0][
-                    0] != '' else f"{self.name}-{index + 1:02d}", data=item[1:], datetime=item[0][1], type_str=item[0][2],
-                         fitting_method=[0] * 5, options=item[0][3])
-                for index, item in enumerate(data)]
+                Sequence(
+                    index=index,
+                    name=item[0][0] if isinstance(item[0][0], str) and item[0][0] != '' else f"{self.name}-{index + 1:02d}",
+                    data=item[1:],
+                    datetime=item[0][1],
+                    type_str=item[0][2],
+                    fitting_method=[*kwargs.get("fitting_method", [0] * 5)],
+                    options=item[0][3]
+                ) for index, item in enumerate(data)]
         else:
             self.sequence: List[Sequence] = []
-        if sequence is not None:
-            self.sequence = sequence
         for k, v in kwargs.items():
             if hasattr(self, k) and type(getattr(self, k)) is MethodType:
                 continue

{ararpy-0.1.12.dist-info → ararpy-0.1.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: ararpy
-Version: 0.1.12
+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-0.1.12.dist-info → ararpy-0.1.14.dist-info}/RECORD

@@ -1,18 +1,20 @@
 ararpy/__init__.py,sha256=XKlsgklkzGfvqQkt59y-UST9aVhgCf-eXpEDiaZaynQ,6725
 ararpy/test.py,sha256=4F46-JJ1Ge12HGae0qO44Qc6kiEMHBgn2MsY_5LlHDo,3973
+ararpy/argon_diffusion_simulator/__init__.py,sha256=8VEdUP7sh17lNg6FcRVVK0JynthEsSk_qcTQtwisqU8,229
+ararpy/argon_diffusion_simulator/main.py,sha256=TaULfYZCKkbotIxt0wMuRlSCg0OuG0sy1V4fdzY8VMk,21920
 ararpy/calc/__init__.py,sha256=kUjRuLE8TLuKOv3i976RnGJoEMj23QBZDu37LWs81U4,322
 ararpy/calc/age.py,sha256=CUex9UxZbYinl9ypd7o86R3VRQFzahku3gW__fBeoss,5811
-ararpy/calc/arr.py,sha256=P0DdYMXXnN69tNGL9NpB0hftNN03EEB_KFmfmZdIy-A,14922
-ararpy/calc/basic.py,sha256=wPzUXmrHAXdFkvd53JsH9Vae-o7O3LxYWztGQ5OpDhw,2871
-ararpy/calc/corr.py,sha256=mQd5_CfDP2aBQrkQHKTV5R-zKbNOjXh8a21zHNrRNmU,19102
+ararpy/calc/arr.py,sha256=w31bn6MXF8I8qPXYo5kI-TfMKCYspx1rZ5g_UpwwSd8,14939
+ararpy/calc/basic.py,sha256=0K0rbm9GpDpEZjQ1r7N-6w-dU-S3UzByOTrefLmjT0c,3231
+ararpy/calc/corr.py,sha256=mFo_j2YGUS4U3dwIkcYO6QrffcODvnzS_IgB6m2qeK4,17979
 ararpy/calc/err.py,sha256=63LtprqjemlIb1QGDst4Ggcv5KMSDHdlAIL-nyQs1eA,2691
 ararpy/calc/histogram.py,sha256=0GVbDdsjd91KQ1sa2B7NtZ4KGo0XpRIJapgIrzAwQUo,5777
 ararpy/calc/isochron.py,sha256=ej9G2e68k6yszonWHsLcEubh3TA7eh1upTJP_X0ttAA,5726
 ararpy/calc/jvalue.py,sha256=zHUhJ1iYe5mPrY95mGYxoUPAp7hwu4coUgiHKiruKfM,1138
-ararpy/calc/plot.py,sha256=v-vJwciJIhKrdXKWAUZbYslez0zBrIa6awI-DopmRZg,1956
-ararpy/calc/raw_funcs.py,sha256=fhAmqpvTvWUegbLi2PNbFRIbKgbDmycDIWNic3z25hU,2536
-ararpy/calc/regression.py,sha256=UQ7e6_u_FUpIllKTUgPa6-HqFvRBI7qDqyKli7fFInE,40172
-ararpy/calc/spectra.py,sha256=iBhuQ03PyIKHbAQSexx3fZ6ZYaxM6P_uMyWdUeeMck4,1936
+ararpy/calc/plot.py,sha256=iWxPYIaT0OmJBiho7X9wFY7m-QrvYexu6nWHp24T_VY,1962
+ararpy/calc/raw_funcs.py,sha256=UC01lvA6GyZ5FJv43jgoUULAFoLnZJMxeSa0BeVFCAM,2637
+ararpy/calc/regression.py,sha256=Xes0rvIX5a9e_gje3n6iTXYbNtRuZZMKRcADp2b-5Dw,40091
+ararpy/calc/spectra.py,sha256=_Q23eP9necHlaCoHf3_UfW1N3JmVZj5rcWFro8GS-CA,1995
 ararpy/examples/022_VU124-M11a.ahd,sha256=3m0Gd-ZObou3KsnRNFMf77QwzT1Uz3nu3vA33Sqeyng,5414
 ararpy/examples/20WHA0103.age,sha256=cT-a4d7Wt77aotx6v0G47vulY_TZIcZUcaVHB3pqTPM,380416
 ararpy/examples/22WHA0078.xls,sha256=1XAAHmIhuswwZ3toCT-qTLrYzqXNDYWGjDyCTI3xaMY,2611729
@@ -35,27 +37,28 @@ ararpy/examples/sample-default.smp,sha256=YNkoQGgPrsL_fXS7ZHxfRtLQWekCDqT9czS6vB
 ararpy/files/__init__.py,sha256=l5B5ZQ01WdtvjjN0aMkyAFNgpwANdM_1I0tQbqnRuEY,69
 ararpy/files/arr_file.py,sha256=KqksGlEA6nmMQofTgi7v45flscQZVtefxaNCKrV3Am4,837
 ararpy/files/basic.py,sha256=nc7Hgo_qLSkdmtKzZmd5SQ8Jy0dhW46ly4gh-oisUDs,2095
-ararpy/files/calc_file.py,sha256=b4bzPsoVD9y5wDqFw-2HmhK6Rd7qwufnEjaYz_FLxos,27865
+ararpy/files/calc_file.py,sha256=fYPwJxazhxxHS1BCI9q7CJW-VIyJZ8UAh6Z8bO9DmLY,27864
 ararpy/files/new_file.py,sha256=efblARIBROVLWS2w3-98BxLX5VZ8grRpiTkJFtf_rAk,214
-ararpy/files/raw_file.py,sha256=B2k4RjAp4EViwHKv6CbI5400Liaa7OW_eBjGSPlN9Ek,22768
+ararpy/files/raw_file.py,sha256=aVHlebiGpxHGj_z9mrTR-Y2JEivxa4k1MJZ1TFXyMnA,22319
 ararpy/files/xls.py,sha256=8ibT4ZRY2grK34ikKm1pDmlWFlVTgDL7vSMO6mphzrY,702
+ararpy/smp/EXPORT_TO_PDF_DATA_PROPERTIES.py,sha256=baDM437tu6hsPv0uYfod0TREXlPd6kvMBFT1S9ZZlkk,3024
 ararpy/smp/__init__.py,sha256=k6_fa27UJsQK7K7oC5GYlwMo6l0Xd8af3QtOrZz2XJk,478
-ararpy/smp/basic.py,sha256=DrwU4ApXOkxYNMwax7B-ErBndJnUwG5n64fLU6zR63Y,21506
-ararpy/smp/calculation.py,sha256=1dUKYbq83j0YpZ9Nbb5rM0wbaEXezDKqcbUCc9TRKng,2919
+ararpy/smp/basic.py,sha256=Jufv_4zXO1-XbmwM4UUrvZsp4tRGD05ec-035u8CiEs,21533
+ararpy/smp/calculation.py,sha256=LCFJWjLVLEKEQ5b7RFUIxsMahEzgLdodW4kCYXV5Z34,2919
 ararpy/smp/consts.py,sha256=XIdjdz8cYxspG2jMnoItdlUsxr3hKbNFJjMZJh1bpzw,393
-ararpy/smp/corr.py,sha256=MXF04dLYGcZN7JHFq8OJqawkZ-yUjN45qG0NJX_kBB0,24528
-ararpy/smp/diffusion_funcs.py,sha256=5yDlyVVcaKQDMPLd7ZvyCetyiQNBR57XtrJkLT_Hsww,168544
-ararpy/smp/export.py,sha256=SEUySwBnDm6ao0Ujc93y98FamUx_UmEsqnd3cmFgKPA,80817
+ararpy/smp/corr.py,sha256=ga3OsRSwPeLd4VV7DbOjZ3T4qlOYweUZhFfAM9MkM5s,25484
+ararpy/smp/diffusion_funcs.py,sha256=_8SchTD27CAS8SmQVDoXJscTRB7M-BqtpASEgg_izBM,175748
+ararpy/smp/export.py,sha256=4RtoDvItQ2ysWXY78gS_tDocTgSY9ftP9Vb-YKrOGQI,107646
 ararpy/smp/info.py,sha256=iKUELm-BuUduDlJKC1d8tKKNHbwwbNmhUg2pi6bcBvA,489
 ararpy/smp/initial.py,sha256=nZNrV4fv_PlNXYfqqIOOOkcQjnSOTLymVpJyJ9d_QtM,15359
-ararpy/smp/json.py,sha256=Y7xoTZczSTrvVHlhfLmpu-zoxgLw9MFn2lgRYkjgHTY,2079
-ararpy/smp/plots.py,sha256=bM4ofS12NedBUXXleEy7-xcK9C8svVuSrTXYmeiMY3k,31495
-ararpy/smp/raw.py,sha256=KtAmzTAwCDK4x1dRgvwj2TbOzHRv7LFwaU2hHCknF3c,6173
-ararpy/smp/sample.py,sha256=KPysezU7avqUBu6ykIEtP3_2wa5a16n0gC0iF_kqSoU,54988
+ararpy/smp/json.py,sha256=BTZCjVN0aj9epc700nwkYEYMKN2lHBYo-pLmtnz5oHY,2300
+ararpy/smp/plots.py,sha256=AuL-cUU9hdzTOGsf764c-nCyhnq0k8Mv4MTGs2Eb0IU,31657
+ararpy/smp/raw.py,sha256=51n-rrbW2FqeZHQyevuG7iObPLGvIBzTe414QDVM1FE,6523
+ararpy/smp/sample.py,sha256=w_ev8lXgpU7A7dIH-uVhteuL6UG4GXJZNp6LdB8yR-Y,55336
 ararpy/smp/style.py,sha256=NZwTeodhtHBBdCyjvupF64nh2B5EDdMHzlT8oE360zg,6746
 ararpy/smp/table.py,sha256=yNr4PLxbH4ezeUXpKBxLjRfq4RuYiW-G3sMWFDtjlVM,6802
-ararpy-0.1.12.dist-info/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
-ararpy-0.1.12.dist-info/METADATA,sha256=BiPSBAkyiLpDd-5VsJm14TqeH58VkFf1G1mpQh3Xx4E,24331
-ararpy-0.1.12.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-ararpy-0.1.12.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
-ararpy-0.1.12.dist-info/RECORD,,
+ararpy-0.1.14.dist-info/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
+ararpy-0.1.14.dist-info/METADATA,sha256=ei5CYPYIF-nGHQrn3BvfqpzDcGy79ekVX2N1Ra9dcjM,24513
+ararpy-0.1.14.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+ararpy-0.1.14.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
+ararpy-0.1.14.dist-info/RECORD,,

{ararpy-0.1.12.dist-info → ararpy-0.1.14.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any