ararpy 0.1.199__py3-none-any.whl → 0.2.1__py3-none-any.whl

ararpy/Example - Check arr.py

@@ -0,0 +1,52 @@
+#  Copyright (C) 2025 Yang. - All Rights Reserved
+
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2025 Yang 
+# ararpy - Example - Check arr
+# ==========================================
+#
+#
+# 
+"""
+import os
+import ararpy as ap
+import numpy as np
+import pdf_maker as pm
+
+
+def read_sample(arr_file_path):
+    # 读取样品信息
+    if not arr_file_path.endswith('.arr'):
+        for root, dirs, files in os.walk(arr_file_path):
+            for file in files:
+                if file.endswith('.arr'):
+                    arr_file_path = os.path.join(arr_file_path, file)
+                    break
+    print(f"arr file: {arr_file_path}")
+    sample = ap.from_arr(file_path=arr_file_path)
+    name = sample.name()
+    sequence = sample.sequence()
+    nsteps = sequence.size
+    arratio = sample.TotalParam[0][0]
+    if sample.Info.sample.type == "Unknown":
+        print(f"{name = }, {arratio = }")
+        # sample.TotalParam[0] = [298.56 for i in sample.TotalParam[0]]
+        sample.Info.preference["confidenceLevel"] = 2
+        # ap.smp.calculation.recalculate(sample, re_plot=True, re_plot_style=True, re_set_table=True, re_table_style=True)
+        ap.save(sample, arr_file_path)
+
+
+loc = r"C:\Users\Young\OneDrive\00-Projects\【2】个人项目\2022-05论文课题\【3】分析测试\ArAr\01-VU实验数据和记录\Arr Data"
+# read_sample(os.path.join(loc, "20240918_24FY87.arr"))
+# read_sample(loc)
+
+for root, dirs, files in os.walk(loc):
+    for file in files:
+        if file.endswith('.arr'):
+            arr_file_path = os.path.join(loc, file)
+            read_sample(arr_file_path)
+
+

ararpy/Example - Granite Cooling History.py

@@ -0,0 +1,411 @@
+#  Copyright (C) 2025 Yang. - All Rights Reserved
+
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2025 Yang 
+# ararpy - Example - Granite Cooling History
+# ==========================================
+#
+#
+# 
+"""
+
+#  Copyright (C) 2025 Yang. - All Rights Reserved
+
+#!/usr/bin/env python
+# -*- coding: UTF-8 -*-
+"""
+# ==========================================
+# Copyright 2025 Yang 
+# ararpy - Example - Show MDD results
+# ==========================================
+#
+#
+# 
+"""
+import ararpy as ap
+import numpy as np
+import pdf_maker as pm
+import os
+
+import matplotlib
+from matplotlib.collections import PathCollection
+
+matplotlib.use('TkAgg')
+matplotlib.rc('font',family='Arial', size=10)
+import matplotlib.pyplot as plt
+from matplotlib.patches import Rectangle
+# 设置全局字体，确保中文正常显示
+# plt.rcParams["font.family"] = ["SimHei"]  # 中文字体
+# plt.rcParams['axes.unicode_minus'] = False  # 解决负号显示问题
+
+
+
+def conf(input_x, input_y, num=None, using_binom=False, using_normal=False, start=None, end=None):
+    """
+    Calculate 90% confident interval of the given distribution of cooling histories.
+    Parameters
+    ----------
+    input_x: x, array like 2D
+    input_y: y, array like 2D
+    count:
+
+    Returns
+    -------
+
+    """
+
+    if len(input_x) != len(input_y):
+        raise ValueError("length of input x does not equal to that of input y")
+
+    ns = len(input_x)
+    if start is None:
+        start = min([min(i) for i in input_x])
+    if end is None:
+        end = max([max(i) for i in input_x])
+    nt = 18 if num is None else num
+
+    if not (using_normal or using_binom):
+        using_binom = True
+
+    x_conf = np.linspace(start, end, num=nt)
+    y_conf = np.zeros((nt, 4))
+    ytemp = np.zeros((nt, ns))
+    # 初始化数组
+    xmed = np.zeros(nt)
+    ave = np.zeros(nt)
+    adev = np.zeros(nt)
+    sdev = np.zeros(nt)
+    var = np.zeros(nt)
+    skew = np.zeros(nt)
+    curt = np.zeros(nt)
+
+    # 计算每个曲线的温度值
+    for k, out_x in enumerate(x_conf):
+        for i in range(ns):
+            xs = input_x[i]
+            ys = input_y[i]
+            for j in range(len(xs)-1):
+                if xs[j] >= out_x >= xs[j+1]:
+                    ytemp[k, i] = (ys[j+1] - ys[j]) / (xs[j+1] - xs[j]) * (out_x - xs[j]) + ys[j]
+                    break
+        # 排序
+        ytemp[k] = np.sort(ytemp[k])
+        # 计算均值、中位数
+        ave[k], adev[k], sdev[k], var[k], skew[k], curt[k], xmed[k] = stats = moment(ytemp[k])
+        # 计算置信区间索引
+        if using_binom:
+            j1, j2 = ap.smp.diffusion_funcs.binom(ns)  #
+            j3, j4 = int(round(ns * 0.05)) - 1, int(ns - round(ns * 0.05)) - 1  # 95%
+            y1, y2, y3, y4 = ytemp[k][j1], ytemp[k][j2], ytemp[k][j3], ytemp[k][j4]
+        elif using_normal:
+            y1, y2, y3, y4 = ave[k] - sdev[k], ave[k] + sdev[k], ave[k] - 2 * sdev[k], ave[k] + 2 * sdev[k]
+        else:
+            raise KeyError("use binom or using normal")
+        y_conf[k] = [y1, y2, y3, y4]
+    return x_conf, y_conf
+
+
+def moment(data):
+    """ 计算分布的统计矩阵：均值、平均偏差、标准差、方差、偏度、峰度、中位数 """
+    # 去除NaN值
+    data = data[~np.isnan(data)]
+    n = len(data)
+    if n == 0:
+        return [np.nan] * 7
+
+    mean = np.mean(data)
+    adev = np.mean(np.abs(data - mean))  # 平均偏差
+    sdev = np.std(data, ddof=1)  # 样本标准差
+    var = sdev ** 2  # 方差
+    med = np.median(data)  # 中位数
+
+    # 偏度 (三阶矩)
+    if sdev == 0:
+        skew = 0.0
+    else:
+        skew = np.sum(((data - mean) / sdev) ** 3) / n
+
+    # 峰度 (四阶矩)
+    if sdev == 0:
+        curt = 0.0
+    else:
+        curt = np.sum(((data - mean) / sdev) ** 4) / n - 3.0  # 减去3使正态分布峰度为0
+
+    return mean, adev, sdev, var, skew, curt, med
+
+
+def is_number(s):
+    try:
+        float(s)
+        return True
+    except:
+        return False
+
+
+def read_data(file):
+    data = []
+    rows = []
+    go = True
+    while go:
+        go = False
+        group = np.zeros([200, 20], dtype='<U64')
+        row = 0
+        while True:
+            try:
+                line = file.readline().rstrip("\n")
+                print(line)
+                if line == "":
+                    break
+                for col, _ in enumerate([str(l) for l in line.split(',')]):
+                    group[row][col] = _
+            except (Exception, BaseException) as e:
+                print(e)
+                break
+            else:
+                row += 1
+        data.append(group)
+        rows.append(row)
+    return data, rows
+
+
+def plot_CH(file, sname=None, title="", **params):
+
+    file_IN = open(file, "r")
+    [data], [nstep] = read_data(file_IN)
+
+
+    initial_age = params.pop("initial_age", 0)
+    final_age = params.pop("final_age", 20)
+    x1_extent = params.pop("x1_extent", [0, 50])
+    y1_extent = params.pop("y1_extent", [0, 900])
+    x2_extent = params.pop("x2_extent", [initial_age, final_age])
+    y2_extent = params.pop("y2_extent", [0, 500])
+    x3_extent = params.pop("x3_extent", [4, 16])
+    y3_extent = params.pop("y3_extent", [-10, 0])
+    x4_extent = params.pop("x4_extent", [0, 1000])
+    y4_extent = params.pop("y4_extent", [200, 1600])
+    autoscaling = params.pop("autoscaling", False)
+    export_PDF = params.pop("export_PDF", False)
+    index = params.pop("index", [])
+
+    main_color = ['#397DA1', '#BA5624', '#212121', '#3C6933', '#74757C', '#214193', '#524715']  # blue red black green
+    middle_color = ['#83CDFA', '#F1B595', '#737373', '#84B775', '#C1C3CB', '#6D8AE1', '#C0A737']
+    shallow_color = ['#E0F1FE', '#FBEBE3', '#DDDDDD', '#CFFEC0', '#EDEEF8', '#D6DFFC', '#FCF0BC']
+
+    print(f"{sname = }, {title = }")
+
+    fig, axs = plt.subplots(1, 1, figsize=(6, 4))
+
+    font_settings = {
+        # 'fontsize': 10,
+        # 'fontfamily': 'Arial'
+    }
+
+    colors = {
+        "biotite": {"facecolor": "#F1B595", "edgecolor": "#BA5624"},
+        "黑云母": {"facecolor": "#F1B595", "edgecolor": "#BA5624"},
+        "zircon": {"facecolor": "#737373", "edgecolor": "#212121"},
+        "锆石": {"facecolor": "#737373", "edgecolor": "#212121"},
+        "muscovite": {"facecolor": "#83CDFA", "edgecolor": "#397DA1"},
+        "白云母": {"facecolor": "#83CDFA", "edgecolor": "#397DA1"},
+        "monazite": {"facecolor": "#84B775", "edgecolor": "#3C6933"},
+        "独居石": {"facecolor": "#84B775", "edgecolor": "#3C6933"},
+        "apatite": {"facecolor": "#D6DFFC", "edgecolor": "#6D8AE1"},
+        "磷灰石": {"facecolor": "#D6DFFC", "edgecolor": "#6D8AE1"},
+        "xenotime": {"facecolor": "#C0A737", "edgecolor": "#524715"},
+        "磷钇矿": {"facecolor": "#C0A737", "edgecolor": "#524715"},
+        "电气石": {"facecolor": "white", "edgecolor": "#524715"},
+        "角闪石": {"facecolor": "white", "edgecolor": "#524715"},
+    }
+
+    axs.set_xlim(*x1_extent, auto=autoscaling)
+    axs.set_ylim(*y1_extent, auto=autoscaling)
+    body = data[:nstep, 0]
+    area = data[:nstep, 1]
+    lithology = data[:nstep, 2]
+    sample_number = data[:nstep, 3]
+    mineral = data[:nstep, 4]
+    method = data[:nstep, 5]
+    age = data[:nstep, 6].astype(np.float32)
+    sage = data[:nstep, 7].astype(np.float32)
+    reference = data[:nstep, 8]
+    tc = data[:nstep, 9].astype(np.float32)
+    stc = data[:nstep, 10].astype(np.float32)
+    print(f"{nstep = }")
+    for i in np.argsort(sage)[::-1]:
+        color = colors[mineral[i]]
+        print(f"age = {age[i]} +/- {sage[i]}, Tc = {tc[i]} +/- {stc[i]}")
+        linestyle = "solid"
+        rect = Rectangle(
+            (age[i]-sage[i], tc[i]-stc[i]), width=2 * sage[i], height=2 * stc[i], **color,
+            linestyle=linestyle
+        )
+        axs.add_patch(rect)
+    axs.set_title(f'{title}', loc='center', y=1, **font_settings)
+    axs.set_xlabel(f'Age (Ma)', **font_settings)
+    axs.set_ylabel(f'Temperature (°C)', **font_settings)
+
+    fig.tight_layout()
+    plt.show()
+
+    if not export_PDF:
+        return
+
+    filename = f"{title} - cooling history - matplotlib"
+
+    params_list = {
+        "page_size": 'a4', "ppi": 72, "width": 14, "height": 8,
+        "pt_width": 0.8, "pt_height": 0.8, "pt_left": 0.16, "pt_bottom": 0.18,
+        "offset_top": 0, "offset_right": 0, "offset_bottom": 20, "offset_left": 30,
+        "plot_together": False, "show_frame": False,
+        'xlabel_offset': 8, 'ylabel_offset': 2
+    }
+
+    plot_data = {
+        "data": [
+            transform(axs),
+        ],
+        "file_name": filename,
+        "plot_names": [f"plotname"],
+    }
+
+    filepath = os.path.join(r"C:\Users\Young\Downloads", f"{filename}.pdf")
+    cvs = [[ap.smp.export.get_cv_from_dict(plot, **params_list) for plot in plot_data['data']]]
+    for i in range(len(cvs[0])):
+        pt = cvs[0][i]._plot_areas[0]
+        title = pt.get_comp(comp_name="title")
+        title._y -= 2
+        title._z_index = 999
+    filepath = ap.smp.export.export_chart_to_pdf(cvs, filename, filepath)
+
+
+def transform(ax: plt.Axes):
+    xlabels = [i.get_text().replace('−', '-') for i in ax.get_xticklabels()]
+    ylabels = [i.get_text().replace('−', '-') for i in ax.get_yticklabels()]
+    linestyles = {'-': 'solid', '--': 'dashed', '-.': 'dashdot', ':': 'dotted'}
+
+    series = []
+    for i, line in enumerate(ax.lines):
+        xy_data = line.get_xydata()  # [[x1, y1], [x2, y2], ...]
+        line_style = linestyles.get(line.get_linestyle(), 'solid')
+        series.append({
+            'type': 'series.line', 'id': f'line-{i}', 'name': f'line-{i}',
+            'color': line.get_color(), 'line_width': 1, 'line_style': line_style,
+            'data': xy_data, 'line_caps': 'none'
+        })
+        if bool(line._marker):
+            series.append({
+                'type': 'series.scatter', 'id': f'line-marker-{i}', 'name': f'line-marker-{i}',
+                'stroke_color': line.get_markeredgecolor(), 'fill_color': line.get_markerfacecolor(),
+                'data': xy_data, 'size': 2,
+                # 'symbol': line._marker.markers.get(line.get_marker(), 'square'),
+                'symbol': 'rec'
+            })
+    for i, collection in enumerate(ax.collections):
+        series.append({
+            'type': 'series.scatter', 'id': f'scatter-{i}', 'name': f'{collection.get_label()}',
+            'stroke_color': collection.get_edgecolor()[0][:3], 'fill_color': collection.get_edgecolor()[0][:3],
+            'data': collection.get_offsets(), 'size': 2,
+            'symbol': 'rec'
+        })
+
+    for i, text in enumerate(ax.texts):
+        xy_data = text.get_position()  # [[x1, y1], [x2, y2], ...]
+        series.append({
+            'type': 'series.text', 'id': f'text-{i}', 'name': f'text-{i}',
+            'color': text.get_color(), 'data': [xy_data], 'text': text.get_text().replace('\n', '<r>'),
+            'size': 8
+        })
+
+    for child in ax._children:
+        if isinstance(child, Rectangle):
+            ld = [*child.get_xy(), child.get_width(), child.get_height()]
+            series.append({
+                'type': 'series.rect', 'id': f'rect-{child.get_gid()}', 'name': f'rect-{child.get_gid()}',
+                'color': child.get_edgecolor()[:3], 'fill_color': child.get_facecolor()[:3], 'fill': True,
+                'data': [ld], 'label': child.get_label(), 'clip': True
+            })
+
+    series.append({
+        'type': 'series.text', 'id': f'title', 'name': f'title',
+        'color': 'black', 'data': [[sum(ax.get_xlim()) / 2, ax.get_ylim()[1]]],
+        'h_align': "middle", 'v_align': "top",
+        'text': ax.get_title(), 'size': 8
+    })
+
+    if ax.legend_ is not None:
+        for handle, text in zip(ax.legend_.legend_handles, ax.legend_.texts):
+            series.append({
+                'type': 'series.text', 'id': f'legend', 'name': f'legend',
+                'color': text.get_color(), 'data': [[ax.get_xlim()[0], ax.get_ylim()[0]]],
+                'h_align': "left", 'v_align': "bottom",
+                'text': text.get_text(), 'size': 8
+            })
+            if isinstance(handle, plt.Line2D):
+                series.append({
+                    'type': 'series.line', 'id': f'legend-line', 'name': f'legend-line-{text.get_text()}',
+                    'color': handle.get_color(), 'data':[[ax.get_xlim()[0], ax.get_ylim()[0]], [ax.get_xlim()[1], ax.get_ylim()[1]]],
+                    'line_width': 1, 'line_style': linestyles.get(handle.get_linestyle(), 'solid')
+                })
+            if isinstance(handle, PathCollection):
+                stroke_c = handle.get_edgecolor()[0][:3]
+                stroke_c = f"#{int(stroke_c[0]*255):02x}{int(stroke_c[1]*255):02x}{int(stroke_c[2]*255):02x}"
+                fill_c = handle.get_facecolor()[0][:3]
+                fill_c = f"#{int(fill_c[0]*255):02x}{int(fill_c[1]*255):02x}{int(fill_c[2]*255):02x}"
+                series.append({
+                    'type': 'series.scatter', 'id': f'legend-scatter', 'name': f'legend-scatter-{text.get_text()}',
+                    'stroke_color': stroke_c, 'fill_color': fill_c,
+                    'data': [[sum(ax.get_xlim()) / 2, sum(ax.get_ylim()) / 2]],
+                    'size': 2, 'symbol': 'rec'
+                })
+
+    data = {
+        'xAxis': [{
+            'extent': ax.get_xlim(), 'interval': xlabels, 'title': ax.get_xlabel(),
+            'nameLocation': 'middle', 'show_frame': True, 'label_size': 8, 'title_size': 8,
+        }],
+        'yAxis': [{
+            'extent': ax.get_ylim(), 'interval': ylabels, 'title': ax.get_ylabel(),
+            'nameLocation': 'middle', 'show_frame': True, 'label_size': 8, 'title_size': 8,
+        }],
+        'series': series
+    }
+
+    # print(data)
+    return data
+
+
+
+if __name__ == "__main__":
+
+    params = {
+        "initial_age": 0,
+        "final_age": 11,
+        "x1_extent": [0, 60],
+        "y1_extent": [0, 900],
+        "x2_extent": [0, 11],
+        "y2_extent": [0, 500],
+        "x3_extent": [4, 16],
+        "y3_extent": [-10, 0],
+        "x4_extent": [0, 1800],
+        "y4_extent": [200, 1600],
+        "autoscaling": False,
+        # "autoscaling": True,
+        # "export_PDF": False,
+        "export_PDF": True,
+        "index": list(range(2, 17)),
+    }
+
+
+    s = 'yalaxiangbo'
+    s = 'paiku'
+    s = 'kuday'
+    s = 'ramba'
+    s = 'gaowu'
+    s = 'luozha'
+    loc = os.path.join("D:\DjangoProjects\webarar\private\mdd", f"{s}.txt")
+    plot_CH(file=loc, title=f"{s.capitalize()} - Cooling History", **params)
+