ararpy 0.2.3__tar.gz → 0.2.5__tar.gz

{ararpy-0.2.3 → ararpy-0.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ararpy
-Version: 0.2.3
+Version: 0.2.5
 Summary: A project for Ar-Ar geochronology
 Home-page: https://github.com/wuyangchn/ararpy.git
 Author: Yang Wu

{ararpy-0.2.3 → ararpy-0.2.5}/ararpy/__init__.py

@@ -16,10 +16,10 @@ from . import calc, smp, files, thermo, test
 """ Information """
 
 name = 'ararpy'
-version = '0.2.3'
+version = '0.2.5'
 __version__ = version
 full_version = version
-last_update = '2026-01-01'
+last_update = '2026-01-08'
 
 """ ArArPy Functions """
 
@@ -97,24 +97,6 @@ Sample.set_params = smp.basic.set_params
 Sample.set_info = lambda _smp, info: setattr(_smp, 'Info', smp.basic.update_plot_from_dict(_smp.Info, info))
 
 Sample.recalculate = lambda _smp, *args, **kwargs: smp.calculation.recalculate(_smp, *args, **kwargs)
-Sample.plot_init = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=False, isInit=True, isPlateau=False)
-Sample.plot_isochron = lambda _smp, **kwargs: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, **kwargs)
-Sample.plot_age_plateau = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=False, isInit=False, isPlateau=True)
-Sample.plot_normal = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_2'])
-Sample.plot_inverse = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_3'])
-Sample.plot_cl_1 = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_4'])
-Sample.plot_cl_2 = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_5'])
-Sample.plot_cl_3 = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_6'])
-Sample.plot_3D = lambda _smp: smp.calculation.recalculate(
-    _smp, re_plot=True, isIsochron=True, isInit=False, isPlateau=False, figures=['figure_7'])
 
 Sample.to_excel = lambda _smp, file_path, *args, **kwargs: smp.export.to_excel(_smp, file_path=file_path, *args, **kwargs)
 

{ararpy-0.2.3 → ararpy-0.2.5}/ararpy/calc/arr.py

@@ -311,7 +311,10 @@ def multi_append(a, *args):
 
     """
     for arg in args:
-        a.append(arg)
+        if isinstance(a, list):
+            a.append(arg)
+        if isinstance(a, np.ndarray):
+            a = np.append(a, arg)
     return a
 
 
@@ -351,7 +354,7 @@ def create_arr(shape: tuple):
 
     """
     if len(shape) == 1:
-        return []
+        return [0 for i in range(shape[0])]
     return [create_arr(shape[1:]) for i in range(shape[0])]
 
 

{ararpy-0.2.3 → ararpy-0.2.5}/ararpy/files/arr_file.py

@@ -27,7 +27,7 @@ def save(file_path, sample):
     str, file name
     """
     if not file_path.endswith(".arr"):
-        file_path = os.path.join(file_path, f"{sample.Info.sample.name}.arr")
+        file_path = os.path.join(file_path, f"{sample.Info.experiment.name}.arr")
     with open(file_path, 'wb') as f:
         f.write(pickle.dumps(sample))
     # with open(file_path, 'w') as f:

{ararpy-0.2.3 → ararpy-0.2.5}/ararpy/files/raw_file.py

@@ -411,39 +411,42 @@ def get_sample_info(file_contents: list, index_list: list, default="", base: Uni
     """
     sample_info = DEFAULT_SAMPLE_INFO.copy()
     sample_info.update({
-        "ExpName": get_item(file_contents, index_list[0:3], default=default, base=base).strip(),
-        "StepName": get_item(file_contents, index_list[3:6], default=default, base=base).strip(),
-        "StepType": get_item(file_contents, index_list[6:9], default=default, base=base).strip(),
-        "StepLabel": get_item(file_contents, index_list[9:12], default=default, base=base).strip(),
-        "ZeroYear": get_item(file_contents, index_list[12:15], default=default, base=base).strip(),
-        "ZeroHour": get_item(file_contents, index_list[15:18], default=default, base=base).strip(),
-        "ZeroMon": get_item(file_contents, index_list[18:21], default=default, base=base).strip(),
-        "ZeroMin": get_item(file_contents, index_list[21:24], default=default, base=base).strip(),
-        "ZeroDay": get_item(file_contents, index_list[24:27], default=default, base=base).strip(),
-        "ZeroSec": get_item(file_contents, index_list[27:30], default=default, base=base).strip(),
-        "SmpName": get_item(file_contents, index_list[30:33], default=default, base=base).strip(),
-        "SmpLoc": get_item(file_contents, index_list[33:36], default=default, base=base).strip(),
-        "SmpMatr": get_item(file_contents, index_list[36:39], default=default, base=base).strip(),
-        "ExpType": get_item(file_contents, index_list[39:42], default=default, base=base).strip(),
-        "SmpWeight": get_item(file_contents, index_list[42:45], default=default, base=base).strip(),
-        "Stepunit": get_item(file_contents, index_list[45:48], default=default, base=base).strip(),
-        "HeatingTime": get_item(file_contents, index_list[48:51], default=default, base=base).strip(),
-        "InstrName": get_item(file_contents, index_list[51:54], default=default, base=base).strip(),
-        "Researcher": get_item(file_contents, index_list[54:57], default=default, base=base).strip(),
-        "Analyst": get_item(file_contents, index_list[57:60], default=default, base=base).strip(),
-        "Lab": get_item(file_contents, index_list[60:63], default=default, base=base).strip(),
-        "Jv": get_item(file_contents, index_list[63:66], default=default, base=base).strip(),
-        "Jsig": get_item(file_contents, index_list[66:69], default=default, base=base).strip(),
-        "MDF": get_item(file_contents, index_list[69:72], default=default, base=base).strip(),
-        "MDFSig": get_item(file_contents, index_list[72:75], default=default, base=base).strip(),
-        "CalcName": get_item(file_contents, index_list[75:78], default=default, base=base).strip(),
-        "IrraName": get_item(file_contents, index_list[78:81], default=default, base=base).strip(),
-        "IrraLabel": get_item(file_contents, index_list[81:84], default=default, base=base).strip(),
-        "IrraPosH": get_item(file_contents, index_list[84:87], default=default, base=base).strip(),
-        "IrraPosX": get_item(file_contents, index_list[87:90], default=default, base=base).strip(),
-        "IrraPosY": get_item(file_contents, index_list[90:93], default=default, base=base).strip(),
-        "StdName": get_item(file_contents, index_list[93:96], default=default, base=base).strip(),
-        "StdAge": get_item(file_contents, index_list[96:99], default=default, base=base).strip(),
-        "StdAgeSig": get_item(file_contents, index_list[99:102], default=default, base=base).strip(),
+        "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),
+        "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),
+        "ZeroHour": get_item(file_contents, index_list[15:18], default=default, base=base),
+        "ZeroMon": get_item(file_contents, index_list[18:21], default=default, base=base),
+        "ZeroMin": get_item(file_contents, index_list[21:24], default=default, base=base),
+        "ZeroDay": get_item(file_contents, index_list[24:27], default=default, base=base),
+        "ZeroSec": get_item(file_contents, index_list[27:30], default=default, base=base),
+        "SmpName": get_item(file_contents, index_list[30:33], default=default, base=base),
+        "SmpLoc": get_item(file_contents, index_list[33:36], default=default, base=base),
+        "SmpMatr": get_item(file_contents, index_list[36:39], default=default, base=base),
+        "ExpType": get_item(file_contents, index_list[39:42], default=default, base=base),
+        "SmpWeight": get_item(file_contents, index_list[42:45], default=default, base=base),
+        "Stepunit": get_item(file_contents, index_list[45:48], default=default, base=base),
+        "HeatingTime": get_item(file_contents, index_list[48:51], default=default, base=base),
+        "InstrName": get_item(file_contents, index_list[51:54], default=default, base=base),
+        "Researcher": get_item(file_contents, index_list[54:57], default=default, base=base),
+        "Analyst": get_item(file_contents, index_list[57:60], default=default, base=base),
+        "Lab": get_item(file_contents, index_list[60:63], default=default, base=base),
+        "Jv": get_item(file_contents, index_list[63:66], default=default, base=base),
+        "Jsig": get_item(file_contents, index_list[66:69], default=default, base=base),
+        "MDF": get_item(file_contents, index_list[69:72], default=default, base=base),
+        "MDFSig": get_item(file_contents, index_list[72:75], default=default, base=base),
+        "CalcName": get_item(file_contents, index_list[75:78], default=default, base=base),
+        "IrraName": get_item(file_contents, index_list[78:81], default=default, base=base),
+        "IrraLabel": get_item(file_contents, index_list[81:84], default=default, base=base),
+        "IrraPosH": get_item(file_contents, index_list[84:87], default=default, base=base),
+        "IrraPosX": get_item(file_contents, index_list[87:90], default=default, base=base),
+        "IrraPosY": get_item(file_contents, index_list[90:93], default=default, base=base),
+        "StdName": get_item(file_contents, index_list[93:96], default=default, base=base),
+        "StdAge": get_item(file_contents, index_list[96:99], default=default, base=base),
+        "StdAgeSig": get_item(file_contents, index_list[99:102], default=default, base=base),
     })
+    for key, val in sample_info.items():
+        if isinstance(val, str):
+            sample_info[key] = val.strip()
     return sample_info

{ararpy-0.2.3 → ararpy-0.2.5}/ararpy/smp/basic.py

@@ -35,15 +35,16 @@ pd.options.mode.chained_assignment = None  # default='warn'
 # =======================
 class ParamsInvalid(Exception):
     """    """
-    def __init__(self, code, message, context=None):
+    def __init__(self, code=400, message="", context=None, fatal=True):
         self.code = code
         self.message = message
         self.context = context or {}
+        self.fatal = fatal
         # 调用父类构造函数，确保异常能正常抛出
         super().__init__(f"{self.message}")
 
 
-def validate_params(**kwargs):
+def validate_params(fatal=True, **kwargs):
 
     def check(data, dtype, **kwargs):
         k = np.array(data, dtype=dtype)
@@ -65,7 +66,7 @@ def validate_params(**kwargs):
                     if not kwargs.get('func')(each):
                         raise ValueError
                 except (Exception, BaseException) as e:
-                    raise ValueError(f"{type(e).__name__}: invalid value, {each}")
+                    raise ValueError(f"invalid value, {each}")
 
     context = {'names': [], 'classnames': [], 'messages': []}
     for index, (name, content) in enumerate(kwargs.items(), 1):
@@ -83,7 +84,7 @@ def validate_params(**kwargs):
     if not context['names']:
         return True
     else:
-        raise ParamsInvalid(400, '. '.join(context['messages']), context)
+        raise ParamsInvalid(400, '. '.join(context['messages']), context, fatal=fatal)
 
 
 # =======================
@@ -268,7 +269,7 @@ def calc_age(ar40ar39=None, params: dict = None, smp: Sample = None, index: list
             age_unit_factor = 1
 
     # check if using Min equation
-    params['Min'] = [i if isinstance(i, bool) else False for i in params['Min']]
+    params['Min'] = [bool(i) for i in params['Min']]
 
     idx1 = np.flatnonzero(np.where(params['Min'], True, False))  # True, using Min equation
     idx2 = np.flatnonzero(np.where(params['Min'], False, True))  # False
@@ -668,6 +669,10 @@ def set_params(smp: Sample, params: Union[List, str], flag: Optional[str] = None
         else:
             smp.TotalParam[32] = [item / (3600 * 24 * 365.242) if index in rows else smp.TotalParam[32][index] for index, item in enumerate(stand_time_second)]  # stand year
 
+        smp.Info.irradiation.label = params[-3]
+        smp.Info.irradiation.location = params[-2]
+        smp.Info.irradiation.info = params[-1]
+
     elif flag == 'smp':
         smp.TotalParam[67:71] = remove_none(smp.TotalParam[67:71], params[0:4], rows, n)
         smp.TotalParam[58:67] = remove_none(smp.TotalParam[58:67], params[4:13], rows, n)
@@ -702,6 +707,7 @@ def get_sequence(smp: Sample):
     smp.Info.results.selection[0]['data'] = smp.SelectedSequence1
     smp.Info.results.selection[1]['data'] = smp.SelectedSequence2
     smp.Info.results.selection[2]['data'] = smp.UnselectedSequence
+    smp.Info.experiment.step_num = len(smp.SequenceName)
     return ArArBasic(
         size=len(smp.SequenceName), name=smp.SequenceName, value=smp.SequenceValue, unit=smp.SequenceUnit,
         mark=ArArBasic(

{ararpy-0.2.3 → ararpy-0.2.5}/ararpy/smp/corr.py

@@ -153,10 +153,13 @@ def corr_decay(sample: Sample):
     corrDecay37 = sample.TotalParam[104]
     corrDecay39 = sample.TotalParam[105]
     sample.CorrectedValues = copy.deepcopy(sample.MassDiscrCorrected)
-    sample.CorrectedValues[2] = [val if corrDecay37[idx] else 0 for idx, val in enumerate(decay_corrected[2])]
-    sample.CorrectedValues[3] = [val if corrDecay37[idx] else 0 for idx, val in enumerate(decay_corrected[3])]
-    sample.CorrectedValues[6] = [val if corrDecay39[idx] else 0 for idx, val in enumerate(decay_corrected[6])]
-    sample.CorrectedValues[7] = [val if corrDecay39[idx] else 0 for idx, val in enumerate(decay_corrected[7])]
+    for idx in range(sample.Info.experiment.step_num):
+        if corrDecay37[idx]:
+            sample.CorrectedValues[2][idx] = decay_corrected[2][idx]
+            sample.CorrectedValues[3][idx] = decay_corrected[3][idx]
+        if corrDecay39[idx]:
+            sample.CorrectedValues[6][idx] = decay_corrected[6][idx]
+            sample.CorrectedValues[7][idx] = decay_corrected[7][idx]
 
     data = np.array(sample.CorrectedValues)
     data[1:10:2] = data[1:10:2] = np.abs(np.divide(data[1:10:2], data[0:10:2])) * 100
@@ -769,7 +772,7 @@ def monte_carlo_f(sample: Sample):
             blank_gain_corr=sample.TotalParam[111][i],
             MDF_method=sample.TotalParam[100][i],
             force_to_zero=sample.TotalParam[101][i],
-            monte_carlo_size=1000,
+            monte_carlo_size=4000,
         )
 
         yield res

{ararpy-0.2.3 → ararpy-0.2.5}/ararpy/smp/initial.py

@@ -191,7 +191,7 @@ def initial(smp: Sample):
         ),
         preference=ArArBasic(**PREFERENCE_RES),
         irradiation= ArArBasic(
-            label='', pos_h='', pos_x='', pos_y='',
+            label='', pos_h='', pos_x='', pos_y='', location='', info=''
         )
     ))
 
@@ -234,7 +234,7 @@ def initial(smp: Sample):
     ))
     setattr(smp, 'TotalParamsTable', Table(
         id='8', name='Total Params', header=samples.TOTAL_PARAMS_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1, 2, 30, 31, 33, 34, 61, 100, 103, *list(range(104, 118))],
+        text_indexes=[0, 1, 2, 29, 30, 31, 33, 34, 61, 100, 103, 118],
         # numeric_indexes=list(range(1, 120)),
     ))
 
@@ -300,14 +300,18 @@ def check_version(smp: Sample):
     -------
 
     """
-    if smp.version != samples.VERSION:
-        std = initial(Sample())
-        basic.get_merged_smp(smp, std)
 
     try:
         version = int(smp.version)
     except ValueError:
         return smp
+    except AttributeError:
+        smp.version = "20240701"
+        return check_version(smp)
+
+    if smp.version != samples.VERSION:
+        std = initial(Sample())
+        basic.get_merged_smp(smp, std)
 
     # 20250328:  # Experiment info
     smp.Info.experiment.name = smp.name()
@@ -328,7 +332,7 @@ def check_version(smp: Sample):
 
     # 20250404:  # Normalization for steps with different J values
     # always check
-    if version < 1120250405:
+    if version < 99990101:
         doNormalize = True
         v, sv = [], []
         try:
@@ -359,10 +363,25 @@ def check_version(smp: Sample):
             smp.TotalParam[32] = [np.nan for index in range(smp.Info.experiment.step_num)]
         else:
             smp.TotalParam[32] = [item / (3600 * 24 * 365.242) for item in stand_time_second]  # stand year
-        smp = smp.recalculate(re_table_style=True)
-        smp = smp.recalculate(re_set_table=True)
         smp.version = "20251001"
 
+    # 20251231 change publish table
+    if version < 20251231:
+        smp.PublishValues = arr.create_arr((len(samples.PUBLISH_TABLE_HEADERS) - 3, smp.Info.experiment.step_num))
+        try:
+            data = np.array(smp.CorrectedValues)
+            data[1:10:2] = np.abs(np.divide(data[1:10:2], data[0:10:2])) * 100
+            smp.PublishValues[0:10] = copy.deepcopy(data.tolist())
+            smp.PublishValues[10:14] = copy.deepcopy(smp.ApparentAgeValues[0:4])
+            smp.PublishValues[14:16] = copy.deepcopy(smp.ApparentAgeValues[6:8])
+        except (BaseException, Exception) as e:
+            print(f"{type(e).__name__}: {str(e)}")
+            pass
+        else:
+            smp = smp.recalculate(re_table_style=True)
+            smp = smp.recalculate(re_set_table=True)
+            smp.version = "20251231"
+
     return smp