ararpy 0.0.1a1__py3-none-any.whl

ararpy/smp/initial.py

@@ -0,0 +1,232 @@
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2023 Yang
+# ararpy - smp - initial
+# ==========================================
+#
+#
+#
+"""
+
+import uuid
+import pandas as pd
+import numpy as np
+import copy
+
+from . import (sample as samples, basic)
+
+Sample = samples.Sample
+Info = samples.Info
+Table = samples.Table
+Plot = samples.Plot
+
+plateau_res_keys = [
+    'F', 'sF', 'Num', 'MSWD', 'Chisq', 'Pvalue', 'age', 's1', 's2', 's3', 'Ar39',
+    'rs',  # 'rs' means relative error of the total sum
+]
+PLATEAU_RES = dict(zip(plateau_res_keys, [np.nan] * len(plateau_res_keys)))
+iso_res_keys = [
+    'k', 'sk', 'm1', 'sm1',
+    'MSWD', 'abs_conv', 'iter', 'mag', 'R2', 'Chisq', 'Pvalue',
+    'rs',  # 'rs' means relative error of the total sum
+    'age', 's1', 's2', 's3',
+    'conv', 'initial', 'sinitial', 'F', 'sF',
+]
+ISO_RES = dict(zip(
+    iso_res_keys, [np.nan] * len(iso_res_keys))
+)
+
+
+# create sample instance
+def create_sample_from_df(content: pd.DataFrame, smp_info: dict):
+    """
+
+    Parameters
+    ----------
+    content : [
+            sample_values, blank_values, corrected_values, degas_values, publish_values,
+            apparent_age_values, isochron_values, total_param, sample_info, isochron_mark,
+            sequence_name, sequence_value
+        ]
+    smp_info : dict
+
+    Returns
+    -------
+    Sample instance
+    """
+    content_dict = content.to_dict('list')
+    res = dict(zip([key[0] for key in content_dict.keys()], [[]] * len(content_dict)))
+    for key, val in content_dict.items():
+        res[key[0]] = res[key[0]] + [val]
+
+    return create_sample_from_dict(content=res, smp_info=smp_info)
+
+
+def create_sample_from_dict(content: dict, smp_info: dict):
+    """
+    content:
+        {
+            'smp': [], 'blk': [], 'cor': [], 'deg': [], 'pub': [],
+            'age': [], 'iso': [], 'pam': [], 'mak': [], 'seq': [],
+            'seq': []
+        }
+    return sample instance
+    """
+    # Create sample file
+    smp = Sample()
+    # Initializing
+    initial(smp)
+    smp.SampleIntercept = content['smp']
+    smp.BlankIntercept = content['blk']
+    smp.CorrectedValues = content['cor']
+    smp.DegasValues = content['deg']
+    smp.PublishValues = content['pub']
+    smp.ApparentAgeValues = content['age']
+    smp.IsochronValues = content['iso']
+    smp.TotalParam = content['pam']
+    smp.IsochronMark = content['mak'][0]
+    smp.SequenceName = content['seq'][0]
+    smp.SequenceValue = content['seq'][1]
+
+    basic.update_plot_from_dict(smp.Info, smp_info)
+
+    smp.SelectedSequence1 = [index for index, item in enumerate(smp.IsochronMark) if item == 1]
+    smp.SelectedSequence2 = [index for index, item in enumerate(smp.IsochronMark) if item == 2]
+    smp.UnselectedSequence = [index for index, item in enumerate(smp.IsochronMark) if item not in [1, 2]]
+
+    return smp
+
+
+def initial(smp: Sample):
+    # 已更新 2023/7/4
+    smp.TotalParam = [[]] * 123
+    smp.BlankIntercept = [[]] * 10
+    smp.SampleIntercept = [[]] * 10
+    smp.PublishValues = [[]] * 11
+    smp.DecayCorrected = [[]] * 10
+    smp.CorrectedValues = [[]] * 10
+    smp.DegasValues = [[]] * 32
+    smp.ApparentAgeValues = [[]] * 8
+    smp.IsochronValues = [[]] * 47
+
+    # Doi
+    if not hasattr(smp, 'Doi') or getattr(smp, 'Doi') in (None, ""):
+        setattr(smp, 'Doi', str(uuid.uuid4().hex))
+
+    # Info
+    setattr(smp, 'Info', Info(
+        id='0', name='info', attr_name='Info',
+        sample=Info(
+            name='SAMPLE NAME', material='MATERIAL', location='LOCATION'
+        ),
+        researcher=Info(
+            name='RESEARCHER', addr='ADDRESS', email='EMAIL'
+        ),
+        laboratory=Info(
+            name='LABORATORY', addr='ADDRESS', email='EMAIL', info='INFORMATION', analyst='ANALYST'
+        ),
+        results=Info(
+            name='RESULTS', plateau_F=[], plateau_age=[], total_F=[], total_age=[],
+            isochron_F=[], isochron_age=[], J=[],
+            # set1=result_set_1, set2=result_set_2,
+            isochron={
+                'figure_2': {
+                    0: copy.deepcopy(ISO_RES), 1: copy.deepcopy(ISO_RES), 2: copy.deepcopy(ISO_RES)},
+                'figure_3': {
+                    0: copy.deepcopy(ISO_RES), 1: copy.deepcopy(ISO_RES), 2: copy.deepcopy(ISO_RES)},
+                'figure_4': {
+                    0: copy.deepcopy(ISO_RES), 1: copy.deepcopy(ISO_RES), 2: copy.deepcopy(ISO_RES)},
+                'figure_5': {
+                    0: copy.deepcopy(ISO_RES), 1: copy.deepcopy(ISO_RES), 2: copy.deepcopy(ISO_RES)},
+                'figure_6': {
+                    0: copy.deepcopy(ISO_RES), 1: copy.deepcopy(ISO_RES), 2: copy.deepcopy(ISO_RES)},
+                'figure_7': {
+                    0: copy.deepcopy(ISO_RES), 1: copy.deepcopy(ISO_RES), 2: copy.deepcopy(ISO_RES)},
+            },
+            age_plateau={
+                0: copy.deepcopy(PLATEAU_RES), 1: copy.deepcopy(PLATEAU_RES), 2: copy.deepcopy(PLATEAU_RES)},
+            age_spectra={},
+        ),
+        reference=Info(
+            name='REFERENCE', journal='JOURNAL', doi='DOI'
+        ),
+    ))
+
+    # Plots and Tables
+    setattr(smp, 'UnknownTable', Table(
+        id='1', name='Unknown', header=samples.SAMPLE_INTERCEPT_HEADERS,
+        textindexs=[0], numericindexs=list(range(1, 20))
+    ))
+    setattr(smp, 'BlankTable', Table(
+        id='2', name='Blank', header=samples.BLANK_INTERCEPT_HEADERS,
+        textindexs=[0], numericindexs=list(range(1, 20))
+    ))
+    setattr(smp, 'CorrectedTable', Table(
+        id='3', name='Corrected', header=samples.CORRECTED_HEADERS,
+        textindexs=[0], numericindexs=list(range(1, 35))
+    ))
+    setattr(smp, 'DegasPatternTable', Table(
+        id='4', name='Degas Pattern', header=samples.DEGAS_HEADERS,
+        textindexs=[0], numericindexs=list(range(1, 35))
+    ))
+    setattr(smp, 'PublishTable', Table(
+        id='5', name='Publish', header=samples.PUBLISH_TABLE_HEADERS,
+        textindexs=[0], numericindexs=list(range(1, 20))
+    ))
+    setattr(smp, 'AgeSpectraTable', Table(
+        id='6', name='Age Spectra', header=samples.SPECTRUM_TABLE_HEADERS,
+        textindexs=[0], numericindexs=list(range(1, 26))
+    ))
+    setattr(smp, 'IsochronsTable', Table(
+        id='7', name='Isochrons', header=samples.ISOCHRON_TABLE_HEADERS,
+        textindexs=[0], numericindexs=list(range(1, 42))
+    ))
+    setattr(smp, 'TotalParamsTable', Table(
+        id='8', name='Total Params', header=samples.TOTAL_PARAMS_HEADERS,
+        textindexs=[0, 29, 30, 32, 33, 60, 99, 102, *list(range(103, 115))],
+        # numericindexs=list(range(1, 120)),
+        numericindexs=[1],
+    ))
+
+    initial_plot_styles(smp)
+
+    return smp
+
+
+def initial_plot_styles(sample: 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.
+    Judgment order:
+        1. The attr name is in except attrs and the sample has this attr: skip
+        2. The value is not a dict instance: setattr()
+        3. The sample has attr and it is a Set/Label/Text/Axis instance: iteration
+    """
+
+    if except_attrs is None:
+        except_attrs = []
+
+    def set_attr(obj, name, value):
+        if name in except_attrs and hasattr(obj, name):
+            pass
+        elif not isinstance(value, dict):
+            setattr(obj, name, value)
+        else:
+            if not (hasattr(obj, name) and isinstance(getattr(obj, name), Plot.BasicAttr)):
+                setattr(obj, name, getattr(Plot, value['type'].capitalize())())
+            for k, v in value.items():
+                set_attr(getattr(obj, name), k, v)
+
+    default_styles = copy.deepcopy(samples.DEFAULT_PLOT_STYLES)
+    for figure_index, figure_attr in default_styles.items():
+        plot = getattr(sample, figure_attr['attr_name'], Plot())
+        for key, attr in figure_attr.items():
+            set_attr(plot, key, attr)
+
+
+def re_set_smp(sample: Sample):
+    std = initial(Sample())
+    basic.get_merged_smp(sample, std)
+    return sample