ararpy 0.1.198__py3-none-any.whl → 0.2.1__py3-none-any.whl

ararpy/smp/info.py

@@ -15,9 +15,9 @@
 
 def name(smp, n: str = None):
     if n is None:
-        return smp.Info.sample.name
+        return smp.Info.experiment.name
     elif isinstance(n, str):
-        smp.Info.sample.name = n
+        smp.Info.experiment.name = n
         return n
     else:
         raise ValueError(f"{n} is not a string")

ararpy/smp/initial.py

@@ -10,13 +10,14 @@
 #
 """
 import os
+import re
 import pickle
 import uuid
 import pandas as pd
 import numpy as np
 import copy
 from typing import List, Union, Optional
-from ..calc import arr, err
+from ..calc import arr, err, basic as calc_basic
 from ..files import calc_file
 from . import (sample as samples, basic, table, raw as smp_raw)
 
@@ -50,7 +51,7 @@ SPECTRA_RES = dict(zip(
     spectra_res_keys, [np.nan for i in spectra_res_keys])
 )
 preference_keys = [
-    'decimalPlaces', 'toPrecision', 'confidenceLevel', 'ageUnit'
+    'decimal_places', 'to_precision', 'confidence_level', 'age_unit'
 ]
 PREFERENCE_RES = dict(zip(
     preference_keys, [6, 'fixed', 1, 'Ma'])
@@ -123,14 +124,14 @@ def create_sample_from_dict(content: dict, smp_info: dict):
 
 def initial(smp: Sample):
     # 已更新 2023/7/4
-    smp.TotalParam = arr.create_arr((len(samples.TOTAL_PARAMS_HEADERS) - 2, 0))
-    smp.BlankIntercept = arr.create_arr((len(samples.BLANK_INTERCEPT_HEADERS) - 2, 0))
-    smp.SampleIntercept = arr.create_arr((len(samples.SAMPLE_INTERCEPT_HEADERS) - 2, 0))
-    smp.PublishValues = arr.create_arr((len(samples.PUBLISH_TABLE_HEADERS) - 2, 0))
+    smp.TotalParam = arr.create_arr((len(samples.TOTAL_PARAMS_HEADERS) - 3, 0))
+    smp.BlankIntercept = arr.create_arr((len(samples.BLANK_INTERCEPT_HEADERS) - 3, 0))
+    smp.SampleIntercept = arr.create_arr((len(samples.SAMPLE_INTERCEPT_HEADERS) - 3, 0))
+    smp.PublishValues = arr.create_arr((len(samples.PUBLISH_TABLE_HEADERS) - 3, 0))
     smp.DecayCorrected = arr.create_arr((10, 0))
-    smp.CorrectedValues = arr.create_arr((len(samples.CORRECTED_HEADERS) - 2, 0))
-    smp.DegasValues = arr.create_arr((len(samples.DEGAS_HEADERS) - 2, 0))
-    smp.ApparentAgeValues = arr.create_arr((len(samples.SPECTRUM_TABLE_HEADERS) - 2, 0))
+    smp.CorrectedValues = arr.create_arr((len(samples.CORRECTED_HEADERS) - 3, 0))
+    smp.DegasValues = arr.create_arr((len(samples.DEGAS_HEADERS) - 3, 0))
+    smp.ApparentAgeValues = arr.create_arr((len(samples.SPECTRUM_TABLE_HEADERS) - 3, 0))
     smp.IsochronValues = arr.create_arr((len(samples.ISOCHRON_TABLE_HEADERS) - 3, 0))
 
     # Doi
@@ -140,15 +141,18 @@ def initial(smp: Sample):
     # Info
     setattr(smp, 'Info', ArArBasic(
         id='0', name='info', attr_name='Info', arr_version=samples.VERSION,
+        experiment=ArArBasic(
+            name='', type='', instrument='', mass_spec='', collectors='', step_num=0,
+        ),
         sample=ArArBasic(
             name='SAMPLE NAME', material='MATERIAL', location='LOCATION', type='Unknown', method='',
-            sequence_unit='', weight=''
+            sequence_unit='', weight='',
         ),
         researcher=ArArBasic(
-            name='RESEARCHER', addr='ADDRESS', email='EMAIL'
+            name='RESEARCHER', addr='ADDRESS', email='EMAIL',
         ),
         laboratory=ArArBasic(
-            name='LABORATORY', addr='ADDRESS', email='EMAIL', info='INFORMATION', analyst='ANALYST'
+            name='LABORATORY', addr='ADDRESS', email='EMAIL', info='INFORMATION', analyst='ANALYST',
         ),
         results=ArArBasic(
             name='RESULTS', plateau_F=[], plateau_age=[], total_F=[], total_age=[],
@@ -183,42 +187,42 @@ def initial(smp: Sample):
         reference=ArArBasic(
             name='REFERENCE', journal='JOURNAL', doi='DOI'
         ),
-        preference=copy.deepcopy(PREFERENCE_RES),
-        experiment=ArArBasic(
-            name='', mass_spec='', collectors='', step_num=0
-        ),
+        preference=ArArBasic(**PREFERENCE_RES),
+        irradiation= ArArBasic(
+            label='', pos_h='', pos_x='', pos_y='',
+        )
     ))
 
-    decimal_places = PREFERENCE_RES['decimalPlaces']
+    decimal_places = smp.Info.preference.decimal_places
     # Plots and Tables
     setattr(smp, 'UnknownTable', Table(
         id='1', name='Unknown', header=samples.SAMPLE_INTERCEPT_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 20))
     ))
     setattr(smp, 'BlankTable', Table(
         id='2', name='Blank', header=samples.BLANK_INTERCEPT_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 20))
     ))
     setattr(smp, 'CorrectedTable', Table(
         id='3', name='Corrected', header=samples.CORRECTED_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 35))
     ))
     setattr(smp, 'DegasPatternTable', Table(
         id='4', name='Degas Pattern', header=samples.DEGAS_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 35))
     ))
     setattr(smp, 'PublishTable', Table(
         id='5', name='Publish', header=samples.PUBLISH_TABLE_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 20))
     ))
     setattr(smp, 'AgeSpectraTable', Table(
         id='6', name='Age Spectra', header=samples.SPECTRUM_TABLE_HEADERS, decimal_places=decimal_places,
-        text_indexes=[0, 1],
+        text_indexes=[0, 1, 2],
         # numeric_indexes=list(range(1, 26))
     ))
     setattr(smp, 'IsochronsTable', Table(
@@ -228,7 +232,7 @@ 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, 29, 30, 32, 33, 60, 99, *list(range(100, 115))],
+        text_indexes=[0, 1, 2, 30, 31, 33, 34, 61, 100, 103, *list(range(104, 118))],
         # numeric_indexes=list(range(1, 120)),
     ))
 
@@ -237,7 +241,7 @@ def initial(smp: Sample):
     return smp
 
 
-def initial_plot_styles(sample: Sample, except_attrs=None):
+def initial_plot_styles(smp: Sample, except_attrs=None):
     """
     Initialize plot components styles based on Default Styles. Except attrs is a list containing attrs
     that are not expected to be initialized.
@@ -261,13 +265,22 @@ def initial_plot_styles(sample: Sample, except_attrs=None):
             for k, v in value.items():
                 set_attr(getattr(obj, name), k, v)
 
-    default_styles = copy.deepcopy(samples.DEFAULT_PLOT_STYLES)
+    default_styles = get_default_plot_style(smp)
     for figure_index, figure_attr in default_styles.items():
-        plot = getattr(sample, figure_attr['attr_name'], Plot())
+        plot = getattr(smp, figure_attr['attr_name'], Plot())
         for key, attr in figure_attr.items():
             set_attr(plot, key, attr)
 
 
+def get_default_plot_style(smp: Sample):
+    sample_type = smp.Info.sample.type
+    try:
+        age_unit = str(smp.Info.preference['ageUnit']).capitalize()
+    except:
+        age_unit = "Undefined"
+    return copy.deepcopy(samples.DEFAULT_PLOT_STYLES(sample_type, age_unit))
+
+
 def re_set_smp(smp: Sample):
     std = initial(Sample())
     basic.get_merged_smp(smp, std)
@@ -289,25 +302,65 @@ def check_version(smp: Sample):
         std = initial(Sample())
         basic.get_merged_smp(smp, std)
 
+    try:
+        version = int(smp.version)
+    except ValueError:
+        return smp
+
     # 20250328:  # Experiment info
     smp.Info.experiment.name = smp.name()
     smp.Info.experiment.step_num = smp.sequence().size
 
-    # 20250404
-    doNormalize = True
-    v, sv = [], []
-    if smp.Info.sample.type.lower() == "unknown":
-        v, sv = smp.TotalParam[67:69]
-        sv = np.multiply(v, sv) / 100
-    elif smp.Info.sample.type.lower() == "air":
-        v, sv = smp.TotalParam[93:95]
-        sv = np.multiply(v, sv) / 100
-    elif smp.Info.sample.type.lower() == "standard":
-        v, sv = smp.TotalParam[59:61]
-    smp.NormalizeFactor = [
-        [1 if v[0] == each or not doNormalize else v[0] / each for each in v],
-        [0 if v[0] == v[i] or not doNormalize else err.div((v[0], sv[0]), (v[i], sv[i])) for i in range(len(v))]
-    ]
+    # old version: add masses and gain factors
+    if version < 20240730:
+        gains = np.ones([10, smp.Info.experiment.step_num])
+        gains[[1, 3, 5, 7, 9], :] = 0
+        smp.TotalParam[126:136] = gains.tolist()
+        gains[0] = 35.96754628
+        gains[2] = 36.9667759
+        gains[4] = 37.9627322
+        gains[6] = 38.964313
+        gains[8] = 39.962383123
+        smp.TotalParam[71:81] = gains.tolist()
+        smp.version = "20240730"
+
+    # 20250404:  # Normalization for steps with different J values
+    # always check
+    if version < 1120250405:
+        doNormalize = True
+        v, sv = [], []
+        try:
+            if smp.Info.sample.type.lower() == "unknown":
+                v, sv = smp.TotalParam[67:69]
+                sv = np.multiply(v, sv) / 100
+            elif smp.Info.sample.type.lower() == "air":
+                v, sv = smp.TotalParam[93:95]
+                sv = np.multiply(v, sv) / 100
+            elif smp.Info.sample.type.lower() == "standard":
+                v, sv = smp.TotalParam[59:61]
+        except:
+            doNormalize = False
+        smp.TotalParam[136:138] = [
+            [1 if v[0] == each or not doNormalize else v[0] / each for each in v],
+            [0 if v[0] == v[i] or not doNormalize else err.div((v[0], sv[0]), (v[i], sv[i])) for i in range(len(v))]
+        ]
+        # smp.version = "20250405"
+
+    # 20251001:  # add marks for every table
+    if version < 20251002:
+        try:
+            stand_time_second = [
+                calc_basic.get_datetime(*re.findall(r"\d+", smp.TotalParam[31][i])) - calc_basic.get_datetime(
+                    *re.findall(r"\d+", smp.TotalParam[30][i])) for i in range(smp.Info.experiment.step_num)]
+        except (BaseException, Exception) as e:
+            print(f"{type(e).__name__}: {str(e)}")
+            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"
+
     return smp
 
 
@@ -439,14 +492,14 @@ def from_raw_data(raw: RawData, mapping: Optional[List[dict]] = None) -> Sample:
     for row in mapping:
         row_unknown_intercept = []
         row_blank_intercept = []
-
         unknown: Sequence = raw.get_sequence(row['unknown'], flag='name')
-        if row['blank'].lower() == "Interpolated Blank".lower():
+        try:
+            blank: Sequence = raw.get_sequence(row['blank'], flag='name')
+            if blank is None or blank == []: raise KeyError
+        except KeyError:
             blank: Sequence = arr.filter(
-                raw.interpolated_blank, func=lambda seq: seq.datetime == unknown.datetime,
+                raw.interpolated_blank, func=lambda seq: seq.datetime == unknown.datetime and seq.name == row['blank'],
                 get=None, unique=True)
-        else:
-            blank: Sequence = raw.get_sequence(row['blank'], flag='name')
         for i in range(5):
             row_unknown_intercept = arr.multi_append(row_unknown_intercept, *unknown.results[i][int(unknown.fitting_method[i])][:2])
             row_blank_intercept = arr.multi_append(row_blank_intercept, *blank.results[i][int(blank.fitting_method[i])][:2])
@@ -462,12 +515,16 @@ def from_raw_data(raw: RawData, mapping: Optional[List[dict]] = None) -> Sample:
     sample.UnselectedSequence = list(range(len(sample.SequenceName)))
     sample.SelectedSequence1 = []
     sample.SelectedSequence2 = []
+    sample.IsochronMark = ['' for i in range(len(sample.SequenceName))]
     #
     sample.Info.results.selection[0]['data'] = sample.SelectedSequence1
     sample.Info.results.selection[1]['data'] = sample.SelectedSequence2
     sample.Info.results.selection[2]['data'] = sample.UnselectedSequence
+    sample.Info.experiment.step_num = len(sample.SequenceName)
+
+    sample.recalculate(re_initial=True)
 
-    table.update_table_data(sample)  # Update table after submission row data and calculation
+    # table.update_table_data(sample)  # Update table after submission row data and calculation
 
     # sample.TotalParam[31] = [raw.get_sequence(row['unknown'], flag='name').datetime for row in mapping]
 

ararpy/smp/json.py

@@ -50,8 +50,8 @@ class MyEncoder(json.JSONEncoder):
                             Plot.Set, Plot.BasicAttr, RawData, Sequence, ArArBasic)):
             if isinstance(obj, Sequence):
                 return dict(obj.__dict__, **{
-                    'is_blank': obj.is_blank(), 'is_unknown': obj.is_unknown(),
-                    'is_air': obj.is_air()})
+                    'is_blank': obj.is_blank(), 'is_unknown': obj.is_unknown()
+                })
             return obj.__dict__
         # Error
         if isinstance(obj, BaseException):