ararpy 0.1.21__py3-none-any.whl → 0.1.24__py3-none-any.whl

ararpy/__init__.py

@@ -16,7 +16,7 @@ from . import calc, smp, files, thermo, test
 """ Information """
 
 name = 'ararpy'
-version = '0.1.21'
+version = '0.1.24'
 __version__ = version
 full_version = version
 last_update = '2024-03-28'

ararpy/calc/corr.py

@@ -61,10 +61,10 @@ def mdf(rm: float, srm: float, m1: float, m2: float, ra: float = 298.56,
     sratio_m = err.div((m2, sm2), (m1, sm1))
     useRyu = False
     if not useRyu:
-        # line
-        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
+        # line, D = 1 + (ra / rm - 1) / dm  # Renne2009
+        k1 = 1 + (ra / rm - 1) / delta_m
+        k2 = err.div(((ra / rm - 1), err.div((ra, sra), (rm, srm))), (delta_m, sdelta_m))
+        # exp, D = 1 + ln(ra / rm) / (m1 * ln(m2/m1))  # Renne2009
         try:
             k3 = (np.log(ra / rm) / np.log(ratio_m)) * (1 / m1) + 1
             v1 = err.log((ra / rm, err.div((ra, sra), (rm, srm))))
@@ -73,7 +73,7 @@ def mdf(rm: float, srm: float, m1: float, m2: float, ra: float = 298.56,
             k4 = err.div((np.log(ra / rm) / np.log(ratio_m), v3), (m1, sm1))
         except Exception:
             k3, k4 = 0, 0
-        # pow
+        # pow, D = pow(ra / rm, 1 / dm)  # Renne2009
         try:
             k5 = pow((ra / rm), (1 / delta_m))  # Renne2009, B.D. Turrin2010
             k6 = err.pow((ra / rm, err.div((ra, sra), (rm, srm))),
@@ -105,18 +105,17 @@ def discr(a0: list, e0: list, mdf: list, smdf: list, m: list, m40: list,
     if isRelative:
         smdf = [smdf[i] * mdf[i] / 100 for i in range(len(smdf))]
     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().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().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().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))))
+        delta_m = abs(m40[i] - m[i])
+        ratio_m = abs(m40[i] / m[i]) if m[i] != 0 else 1
+        if method.lower().startswith("l"):  # linear
+            k0 = 1 / (delta_m * mdf[i] - delta_m + 1) if (delta_m * mdf[i] - delta_m + 1) != 0 else 0
+            k1 = err.rec((delta_m * mdf[i] - delta_m + 1, smdf[i] * delta_m))
+        elif method.lower().startswith("e"):  # exponential
+            k0 = 1 / np.exp((mdf - 1) * m * np.log(m40 / m))
+            k1 = err.rec((1 / k0, err.pow((np.e, 0), ((mdf - 1) * m * np.log(m40 / m), err.mul((mdf - 1, smdf), (m * np.log(m40 / m), 0))))))
+        elif method.lower().startswith("p"):  # power
+            k0 = 1 / (mdf[i] ** delta_m)
+            k1 = err.rec((mdf[i] ** delta_m, err.pow((mdf[i], smdf[i]), (delta_m, 0))))
         else:
             k0 = 1
             k1 = 0

ararpy/files/raw_file.py

@@ -224,24 +224,23 @@ def get_raw_data(file_contents: List[List[Union[int, float, str, bool, list]]],
 
     timezone = sample_info_index[3] if sample_info_index[3] != "" else "utc"
     while True:  # measurment steps sloop
+
+        # all text information
+        options = get_sample_info(file_contents, optional_info_index, default="", base=[1, 1 - idx, 1])
+
         # Zero datetime
         try:
             if check_box_index[2]:  # input_filter[134]: date in one string
-                zero_date = datetime_parse(
-                    get_item(file_contents, sample_info_index[16:19], base=[1, 1 - idx, 1]), sample_info_index[1])
+                zero_date = datetime_parse(options.get('ZeroYear'), sample_info_index[1])
             else:
-                zero_date = datetime(year=get_item(file_contents, sample_info_index[16:19], base=1),
-                                     month=get_item(file_contents, sample_info_index[22:25], base=[1, 1 - idx, 1]),
-                                     day=get_item(file_contents, sample_info_index[28:31], base=[1, 1 - idx, 1]))
+                zero_date = datetime(year=options.get('ZeroYear'), month=options.get('ZeroMon'),
+                                     day=options.get('ZeroDay'))
 
             if check_box_index[3]:  # input_filter[135]: time in one string
-                zero_time = datetime_parse(
-                    get_item(file_contents, sample_info_index[19:22], base=[1, 1 - idx, 1]), sample_info_index[2])
+                zero_time = datetime_parse(options.get('ZeroHour'), sample_info_index[2])
             else:
-                zero_time = datetime(year=2020, month=12, day=31,
-                                     hour=get_item(file_contents, sample_info_index[19:22], base=[1, 1 - idx, 1]),
-                                     minute=get_item(file_contents, sample_info_index[25:28], base=[1, 1 - idx, 1]),
-                                     second=get_item(file_contents, sample_info_index[31:34], base=[1, 1 - idx, 1]))
+                zero_time = datetime(year=2020, month=12, day=31, hour=options.get('ZeroHour'),
+                                     minute=options.get('ZeroMin'), second=options.get('ZeroSec'))
 
             zero_datetime = datetime(
                 zero_date.year, zero_date.month, zero_date.day, zero_time.hour, zero_time.minute, zero_time.second)
@@ -251,16 +250,10 @@ def get_raw_data(file_contents: List[List[Union[int, float, str, bool, list]]],
             # print(f"Cannot parse zero datetime")
             zero_datetime = datetime(1970, 1, 1, 0, 0, 0).isoformat(timespec='seconds')
 
-        # Experiment name
-        try:
-            experiment_name = get_item(file_contents, sample_info_index[4:7], default="", base=[1, 1 - idx, 1])
-        except (TypeError, ValueError, IndexError):
-            # print(f"Cannot parse experiment name")
-            experiment_name = "ExpName"
-
         # Step name
         try:
-            step_name = get_item(file_contents, sample_info_index[7:10], default="", base=[1, 1 - idx, 1]) if input_filter[7] > 0 else ""
+            step_name = options.get('StepName')
+            experiment_name = options.get('ExpName')
             if check_box_index[1] and sample_info_index[0].strip() != "":
                 _res = string_parser(sample_info_index[0], file_name)
                 if _res is not None:
@@ -274,12 +267,13 @@ def get_raw_data(file_contents: List[List[Union[int, float, str, bool, list]]],
                 raise ValueError(f"Step name not found")
         except (TypeError, ValueError, IndexError):
             # When parsing the step name fails, the end of the file has been reached
-            raise
-
-        # other information
-        options = get_sample_info(file_contents, optional_info_index, default="", base=[1, 1 - idx, 1])
+            # raise
+            break
+        else:
+            options.update({'StepName': step_name})
+            options.update({'ExpName': experiment_name})
 
-        current_step = [[step_name, zero_datetime, experiment_name, options]]
+        current_step = [[step_name, zero_datetime, options]]
 
         break_num = 0
         cycle_num = 0
@@ -370,7 +364,7 @@ def get_sample_info(file_contents: list, index_list: list, default="", base: Uni
     sample_info.update({
         "ExpName": get_item(file_contents, index_list[0:3], default=default, base=base),
         "StepName": get_item(file_contents, index_list[3:6], default=default, base=base),
-        "SmpType": get_item(file_contents, index_list[6:9], default=default, base=base),
+        "StepType": get_item(file_contents, index_list[6:9], default=default, base=base),
         "StepLabel": get_item(file_contents, index_list[9:12], default=default, base=base),
         "ZeroYear": get_item(file_contents, index_list[12:15], default=default, base=base),  # year
         "ZeroHour": get_item(file_contents, index_list[15:18], default=default, base=base),  # hour
@@ -402,7 +396,7 @@ def get_sample_info(file_contents: list, index_list: list, default="", base: Uni
         "StdAgeSig": get_item(file_contents, index_list[93:96], default=default, base=base),
         # "Experiment Name": get_item(file_contents, sample_info_index[0:3], default=default, base=base),
         # "Step Name": get_item(file_contents, sample_info_index[3:6], default=default, base=base),
-        # "Sample Type": get_item(file_contents, sample_info_index[6:9], default=default, base=base),
+        # "Step Type": get_item(file_contents, sample_info_index[6:9], default=default, base=base),
         # "Step Label": get_item(file_contents, sample_info_index[9:12], default=default, base=base),
         # "Zero Date Year": get_item(file_contents, sample_info_index[12:15], default=default, base=base),
         # "Zero Time Hour": get_item(file_contents, sample_info_index[15:18], default=default, base=base),

ararpy/smp/sample.py

@@ -1110,27 +1110,33 @@ class Plot:
 
 class Sequence:
     def __init__(self, index=None, data=None, flag=None, name=None, datetime=None,
-                 type_str=None, results=None, coefficients=None, fitting_method=None,
+                 type_str=None, label=None, results=None, coefficients=None, fitting_method=None,
                  is_estimated=False, options=None, **kwargs):
         if options is None:
             options = {}
-        self.index = index
         if name is None or not isinstance(name, str):
-            name = ""
-        self.name = name.strip()
-        self.datetime = datetime
-        self.data = data
+            name = options.get('StepName', "")
         # flag is to check if the data point is selected
         if flag is None and data is not None:
             flag = [[j if i == 0 else True for i, j in enumerate(_m)] for _m in data]
-        self.flag = flag
-        self.type_str = type_str
+        if type_str is None:
+            type_str = options.get('StepType', "Unknown")
+        if label is None:
+            label = options.get('StepLabel', "")
         if results is None:
             results = []
         if fitting_method is None:
             fitting_method = []
         if coefficients is None:
             coefficients = []
+
+        self.index = index
+        self.datetime = datetime
+        self.data = data
+        self.name = name.strip()
+        self.flag = flag
+        self.type_str = type_str.strip()
+        self.label = str(label).strip()
         self.results = results
         self.coefficients = coefficients
         self.fitting_method = fitting_method
@@ -1211,9 +1217,8 @@ class RawData:
                     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]
+                    options=item[0][2]
                 ) for index, item in enumerate(data)]
         else:
             self.sequence: List[Sequence] = []

{ararpy-0.1.21.dist-info → ararpy-0.1.24.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.1.21
+Version: 0.1.24
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.1.21.dist-info → ararpy-0.1.24.dist-info}/RECORD

@@ -1,10 +1,10 @@
-ararpy/__init__.py,sha256=WlCsGj-l5qvzTG5kZM0QFGPSwLZlYoeBv9yftCZZj40,6857
+ararpy/__init__.py,sha256=QEp5L28BpSsG8M5Od5bV8kEffBsktW19SvENTbtQ_v4,6857
 ararpy/test.py,sha256=4F46-JJ1Ge12HGae0qO44Qc6kiEMHBgn2MsY_5LlHDo,3973
 ararpy/calc/__init__.py,sha256=kUjRuLE8TLuKOv3i976RnGJoEMj23QBZDu37LWs81U4,322
 ararpy/calc/age.py,sha256=WOZs70zXiBWDIEhXJLIaNiYTOFJNk0NDbH5e5zCbCks,5435
 ararpy/calc/arr.py,sha256=jD1Fd0Cj3xc7NqgnG4cp3VWQWxUlV0qCtPBZZokDG8o,15246
 ararpy/calc/basic.py,sha256=uJCCUFaPd9zvfkggrdbFYSGLl2pt7UJ7ENgXanzHy68,4036
-ararpy/calc/corr.py,sha256=6hlBlFIM8HyN6CDuWPGqiLpVM88pZJLEuRm8vAyg9ng,18747
+ararpy/calc/corr.py,sha256=QDitvLf6y5IBpHtVEJfOUVjWSlIP9qJ4Jhluk9eDEDE,18801
 ararpy/calc/err.py,sha256=63LtprqjemlIb1QGDst4Ggcv5KMSDHdlAIL-nyQs1eA,2691
 ararpy/calc/histogram.py,sha256=0GVbDdsjd91KQ1sa2B7NtZ4KGo0XpRIJapgIrzAwQUo,5777
 ararpy/calc/isochron.py,sha256=ej9G2e68k6yszonWHsLcEubh3TA7eh1upTJP_X0ttAA,5726
@@ -37,7 +37,7 @@ ararpy/files/arr_file.py,sha256=KqksGlEA6nmMQofTgi7v45flscQZVtefxaNCKrV3Am4,837
 ararpy/files/basic.py,sha256=nc7Hgo_qLSkdmtKzZmd5SQ8Jy0dhW46ly4gh-oisUDs,2095
 ararpy/files/calc_file.py,sha256=nqv_VfbOzz8ejcnjNoHJafGiYldhYSOLusUGtuZ8jR0,28207
 ararpy/files/new_file.py,sha256=efblARIBROVLWS2w3-98BxLX5VZ8grRpiTkJFtf_rAk,214
-ararpy/files/raw_file.py,sha256=5hnZMS7r78lA0ZXrBEN5SWVurQyl0QsHOI9rJz5BQv8,22302
+ararpy/files/raw_file.py,sha256=FScTqZzMPinNSCew86ETyDEcTjhbV-FQ3o4mWrbiBbU,21564
 ararpy/files/xls.py,sha256=DVcZ_yRnc19p-m4leGGjt-YPDpSa2udYKmGyrM0qub0,640
 ararpy/smp/EXPORT_TO_PDF_DATA_PROPERTIES.py,sha256=baDM437tu6hsPv0uYfod0TREXlPd6kvMBFT1S9ZZlkk,3024
 ararpy/smp/__init__.py,sha256=k6_fa27UJsQK7K7oC5GYlwMo6l0Xd8af3QtOrZz2XJk,478
@@ -52,15 +52,15 @@ ararpy/smp/initial.py,sha256=VSNku2fYD1xGkpHxMqnSJCAhSQawfsDCdqYCxtDJryQ,17196
 ararpy/smp/json.py,sha256=BTZCjVN0aj9epc700nwkYEYMKN2lHBYo-pLmtnz5oHY,2300
 ararpy/smp/plots.py,sha256=rF0vrFu9dMt2Eu1EHiDfDRC9232M6dH0Unc_3qNDxLY,33579
 ararpy/smp/raw.py,sha256=51n-rrbW2FqeZHQyevuG7iObPLGvIBzTe414QDVM1FE,6523
-ararpy/smp/sample.py,sha256=dEgy2--RxfS4vXYqlBjD5MlLpw2SaZPDyPxRyiQXjgU,57736
+ararpy/smp/sample.py,sha256=N0ChOxMgNYLU_EwJvGXJARWnubsaKXmvS7jmM-uW7mg,57948
 ararpy/smp/style.py,sha256=wCygwtpCflhzwmI7u08X-feYGPytOyfR98YcgJx813c,7678
 ararpy/smp/table.py,sha256=9bNAOqAIOc0nSC3LNeqjJKUYSJSM28Ji3o9VimwMU8A,6645
 ararpy/thermo/__init__.py,sha256=6VBuqTRFl403PVqOuMkVrut0nKaQsAosBmfW91X1dMg,263
 ararpy/thermo/arrhenius.py,sha256=Ass1ichHfqIAtpv8eLlgrUc1UOb3Urh1qzr1E3gLB4U,233
 ararpy/thermo/atomic_level_random_walk.py,sha256=Q97zfe2h2RaxADkoBAqd0uEiP16BFOajrTmXHMkL2EQ,25502
 ararpy/thermo/basic.py,sha256=nBGHI9uK7VdJwThwBIOcKAzdnYqPyQseFoY6s4zKizk,11504
-ararpy-0.1.21.dist-info/licenses/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
-ararpy-0.1.21.dist-info/METADATA,sha256=L-HbEUtFqNu8W2jo_CXlH1wIM9TikBrhyVZpedtLmIM,24516
-ararpy-0.1.21.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-ararpy-0.1.21.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
-ararpy-0.1.21.dist-info/RECORD,,
+ararpy-0.1.24.dist-info/licenses/LICENSE,sha256=cvG5t_C1qY_zUyJI7sNOa7gCArdngNPaOrfujl2LYuc,1085
+ararpy-0.1.24.dist-info/METADATA,sha256=ugp-dLJNZMSuugSyvAvFUrki9T4VUfys5Cv9lpz8DIM,24516
+ararpy-0.1.24.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
+ararpy-0.1.24.dist-info/top_level.txt,sha256=9iTpsPCYuRYq09yQTk9d2lqB8JtTEOmbN-IcGB-K3vY,7
+ararpy-0.1.24.dist-info/RECORD,,

{ararpy-0.1.21.dist-info → ararpy-0.1.24.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.7.1)
 Root-Is-Purelib: true
 Tag: py3-none-any