NepTrainKit 2.0.6.dev57__tar.gz → 2.1.1.dev37__tar.gz

neptrainkit-2.1.1.dev37/.gitignore

@@ -0,0 +1,8 @@
+**/__pycache__/
+/src/NepTrainKit.egg-info/
+/build
+/dist
+/docs/build
+.idea/
+/src/NepTrainKit/?.py
+/src/NepTrainKit/Log/*.log

{neptrainkit-2.0.6.dev57 → neptrainkit-2.1.1.dev37}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: NepTrainKit
-Version: 2.0.6.dev57
+Version: 2.1.1.dev37
 Summary: NepTrainKit is a Python package for visualizing and manipulating training datasets for NEP.
 Author: Chen Cheng bing
 Author-email: Chen Cheng bing <1747193328@qq.com>

{neptrainkit-2.0.6.dev57 → neptrainkit-2.1.1.dev37}/pyproject.toml

@@ -43,7 +43,7 @@ dependencies = [
 "numpy>=1.26.0",
 "vispy>=0.14.3",
 "ase",
-"scipy>=1.15.0"
+"scipy>=1.15.0",
 ]
 [project.optional-dependencies]
 test = [

{neptrainkit-2.0.6.dev57 → neptrainkit-2.1.1.dev37}/requirements.txt

@@ -4,6 +4,7 @@ loguru==0.7.2
 requests==2.32.3
 pyqtgraph==0.13.7
 PyOpenGL==3.1.7
-vispy==0.14.3
+vispy==0.15.2
 ase
-scipy==1.15.0
+scipy==1.15.0
+

{neptrainkit-2.0.6.dev57 → neptrainkit-2.1.1.dev37}/src/NepTrainKit/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2.0.6.dev57'
-__version_tuple__ = version_tuple = (2, 0, 6, 'dev57')
+__version__ = version = '2.1.1.dev37'
+__version_tuple__ = version_tuple = (2, 1, 1, 'dev37')

neptrainkit-2.1.1.dev37/src/NepTrainKit/core/canvas/pyqtgraph/__init__.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python 
+# -*- coding: utf-8 -*-
+# @Time    : 2025/5/20 14:20
+# @Author  : 兵
+# @email    : 1747193328@qq.com
+import pyqtgraph as pg
+pg.setConfigOption('background', 'w')  # 设置背景为白色
+pg.setConfigOption('foreground', 'k')  # 设置前景元素为黑色（如坐标轴）
+pg.setConfigOptions(antialias=False,useOpenGL=False)
+from .structure import StructurePlotWidget
+from .canvas import  PyqtgraphCanvas

{neptrainkit-2.0.6.dev57 → neptrainkit-2.1.1.dev37}/src/NepTrainKit/core/canvas/pyqtgraph/canvas.py

@@ -8,57 +8,55 @@
 from functools import partial
 
 import numpy as np
-import pyqtgraph as pg
+
 from PySide6.QtCore import Qt
-from pyqtgraph import GraphicsLayoutWidget,  ScatterPlotItem, PlotItem, ViewBox, TextItem
+from pyqtgraph import GraphicsLayoutWidget, ScatterPlotItem, PlotItem, ViewBox, TextItem
 
 from NepTrainKit import utils
 from NepTrainKit.core.types import Brushes, Pens
 from ..base.canvas import CanvasLayoutBase
 from ...io import NepTrainResultData
 
-pg.setConfigOption('background', 'w')  # 设置背景为白色
-pg.setConfigOption('foreground', 'k')  # 设置前景元素为黑色（如坐标轴）
-pg.setConfigOptions(antialias=False,useOpenGL=False)
 
 class MyPlotItem(PlotItem):
     """
     自定义Item 实例化即可创建一个axes
     """
+
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
         self.disableAutoRange()
 
-        self._scatter=ScatterPlotItem()
+        self._scatter = ScatterPlotItem()
         self.addItem(self._scatter)
 
-        self.text = TextItem(  color=(231, 63, 50))
+        self.text = TextItem(color=(231, 63, 50))
 
         self.addItem(self.text)
 
-        self.current_point=ScatterPlotItem()
+        self.current_point = ScatterPlotItem()
         self.current_point.setZValue(100)
         if "title" in kwargs:
             self.setTitle(kwargs["title"])
+
     def scatter(self, *args, **kargs):
         self._scatter.setData(*args, **kargs)
-    def set_current_point(self, x,y):
 
-        self.current_point.setData( x, y,brush=Brushes.Current ,pen=Pens.Current,
-                                      symbol='star',size=15 )
-        if self.current_point not in self.items:
+    def set_current_point(self, x, y):
 
+        self.current_point.setData(x, y, brush=Brushes.Current, pen=Pens.Current,
+                                   symbol='star', size=15)
+        if self.current_point not in self.items:
             self.addItem(self.current_point)
 
-
     def add_diagonal(self):
 
         self.addLine(angle=45, pos=(0.5, 0.5), pen=Pens.Line)
 
-    def item_clicked(self,scatter_item,items,event):
+    def item_clicked(self, scatter_item, items, event):
 
         if items.any():
-            item=items[0]
+            item = items[0]
 
             self.structureIndexChanged.emit(item.data())
 
@@ -70,42 +68,41 @@ class MyPlotItem(PlotItem):
     def title(self, t):
         if t == self.title:
             return
-        self.setTitle(  t)
+        self.setTitle(t)
         if t != "descriptor":
             self.add_diagonal()
 
 
-
 class CombinedMeta(type(CanvasLayoutBase), type(GraphicsLayoutWidget)):
     pass
 
-class PyqtgraphCanvas(CanvasLayoutBase,GraphicsLayoutWidget, metaclass=CombinedMeta):
+
+class PyqtgraphCanvas(CanvasLayoutBase, GraphicsLayoutWidget, metaclass=CombinedMeta):
     """
     pyqtgraph 绘图类
     """
-    def __init__(self,*args, **kwargs):
-        GraphicsLayoutWidget.__init__(self,*args,**kwargs)
+
+    def __init__(self, *args, **kwargs):
+        GraphicsLayoutWidget.__init__(self, *args, **kwargs)
 
         CanvasLayoutBase.__init__(self)
-        self.nep_result_data=None
-    def set_nep_result_data(self,dataset):
-        self.nep_result_data:NepTrainResultData=dataset
+        self.nep_result_data = None
 
+    def set_nep_result_data(self, dataset):
+        self.nep_result_data: NepTrainResultData = dataset
 
     def clear_axes(self):
         self.clear()
 
         super().clear_axes()
 
-
-
-    def init_axes(self,axes_num   ):
+    def init_axes(self, axes_num):
         self.clear_axes()
 
         for r in range(axes_num):
             plot = MyPlotItem(title="")
             self.addItem(plot)
-            plot.getViewBox().mouseDoubleClickEvent = partial(self.view_on_double_clicked,plot=plot)
+            plot.getViewBox().mouseDoubleClickEvent = partial(self.view_on_double_clicked, plot=plot)
             plot.getViewBox().setMouseEnabled(False, False)
             self.axes_list.append(plot)
 
@@ -113,11 +110,11 @@ class PyqtgraphCanvas(CanvasLayoutBase,GraphicsLayoutWidget, metaclass=CombinedM
 
         self.set_view_layout()
 
-    def view_on_double_clicked(self,event,plot):
+    def view_on_double_clicked(self, event, plot):
         self.set_current_axes(plot)
 
     def set_view_layout(self):
-        if len(self.axes_list)==0:
+        if len(self.axes_list) == 0:
             return
         if self.current_axes not in self.axes_list:
             self.set_current_axes(self.axes_list[0])
@@ -134,7 +131,6 @@ class PyqtgraphCanvas(CanvasLayoutBase,GraphicsLayoutWidget, metaclass=CombinedM
         for col, factor in enumerate([3, 1]):
             self.ci.layout.setRowStretchFactor(col, factor)
 
-
     @utils.timeit
     def plot_nep_result(self):
         """
@@ -142,174 +138,165 @@ class PyqtgraphCanvas(CanvasLayoutBase,GraphicsLayoutWidget, metaclass=CombinedM
         """
         self.nep_result_data.select_index.clear()
 
-        for index,_dataset in enumerate(self.nep_result_data.dataset):
-            plot=self.axes_list[index]
-            plot.title= _dataset.title
-            plot.scatter(_dataset.x,_dataset.y,data=_dataset.structure_index,
-                                      brush=Brushes.get(_dataset.title.upper()) ,pen=Pens.get(_dataset.title.upper()),
-                                      symbol='o',size=7,
+        for index, _dataset in enumerate(self.nep_result_data.dataset):
+            plot = self.axes_list[index]
+            plot.title = _dataset.title
+            plot.scatter(_dataset.x, _dataset.y, data=_dataset.structure_index,
+                         brush=Brushes.get(_dataset.title.upper()), pen=Pens.get(_dataset.title.upper()),
+                         symbol='o', size=7,
 
-                                      )
+                         )
             # 设置视图框更新模式
             self.auto_range(plot)
-            if _dataset.group_array.num !=0:
-                #更新结构
+            if _dataset.group_array.num != 0:
+                # 更新结构
                 if self.structure_index not in _dataset.group_array.now_data:
-                    self.structure_index=_dataset.group_array.now_data[0]
+                    self.structure_index = _dataset.group_array.now_data[0]
                     self.structureIndexChanged.emit(self.structure_index)
 
             else:
                 plot.set_current_point([], [])
 
-
             if _dataset.title not in ["descriptor"]:
-            #
-                pos=self.convert_pos(plot,(0 ,1))
-                text=f"rmse: {_dataset.get_formart_rmse()}"
+                #
+                pos = self.convert_pos(plot, (0, 1))
+                text = f"rmse: {_dataset.get_formart_rmse()}"
                 plot.text.setText(text)
                 plot.text.setPos(*pos)
 
-
-
-    def plot_current_point(self,structure_index):
+    def plot_current_point(self, structure_index):
         """
         鼠标点击后 在所有子图上绘制五角星标记当前点
         """
-        self.structure_index=structure_index
-
-        for plot in  self.axes_list :
-            dataset=self.get_axes_dataset(plot)
-            array_index=dataset.convert_index(structure_index)
-            if dataset.now_data.size!=0:
-                data=dataset.now_data[array_index,: ]
-                plot.set_current_point(data[:,dataset.cols:].flatten(),
+        self.structure_index = structure_index
+
+        for plot in self.axes_list:
+            dataset = self.get_axes_dataset(plot)
+            array_index = dataset.convert_index(structure_index)
+            if dataset.now_data.size != 0:
+                data = dataset.all_data[array_index, :]
+                plot.set_current_point(data[:, dataset.cols:].flatten(),
                                        data[:, :dataset.cols].flatten(),
                                        )
-    
-    def item_clicked(self,scatter_item,items,event):
+
+    def item_clicked(self, scatter_item, items, event):
 
         if items.any():
-            item=items[0]
+            item = items[0]
 
             self.structureIndexChanged.emit(item.data())
 
+    def select_point_from_polygon(self, polygon_xy, reverse):
 
-
-
-
-    def select_point_from_polygon(self,polygon_xy,reverse ):
-
-        index=self.is_point_in_polygon(np.column_stack([self.current_axes._scatter.data["x"],self.current_axes._scatter.data["y"]]),polygon_xy)
+        index = self.is_point_in_polygon(
+            np.column_stack([self.current_axes._scatter.data["x"], self.current_axes._scatter.data["y"]]), polygon_xy)
         index = np.where(index)[0]
-        select_index=self.current_axes._scatter.data[index]["data"].tolist()
-        self.select_index(select_index,reverse)
-
+        select_index = self.current_axes._scatter.data[index]["data"].tolist()
+        self.select_index(select_index, reverse)
 
-    def select_point(self,pos,reverse):
+    def select_point(self, pos, reverse):
         """
         鼠标单击选择结构
         """
-        items=self.current_axes._scatter.pointsAt(pos)
+        items = self.current_axes._scatter.pointsAt(pos)
         if len(items):
-            item=items[0]
-            index=item.index()
-            structure_index =item.data()
-            self.select_index(structure_index,reverse)
-
-
-
-    def update_scatter_color(self,structure_index,color=Brushes.Selected):
+            item = items[0]
+            index = item.index()
+            structure_index = item.data()
+            self.select_index(structure_index, reverse)
+    @utils.timeit
+    def update_scatter_color(self, structure_index, color=Brushes.Selected):
         """
         当结构点的状态发生变化的时候 通过该函数更改axes中散点的颜色
         """
 
-        for i,plot in enumerate(self.axes_list):
+        for i, plot in enumerate(self.axes_list):
 
             if not plot._scatter:
                 continue
-            structure_index_set= set(structure_index)
+            structure_index_set = set(structure_index)
             index_list = [i for i, val in enumerate(plot._scatter.data["data"]) if val in structure_index_set]
 
-            plot._scatter.data["brush"][index_list]=   color
+            plot._scatter.data["brush"][index_list] = color
             plot._scatter.data['sourceRect'][index_list] = (0, 0, 0, 0)
 
+            plot._scatter.updateSpots()
 
-            plot._scatter.updateSpots( )
-
-    def convert_pos(self,plot,pos):
+    def convert_pos(self, plot, pos):
         view_range = plot.viewRange()
         x_range = view_range[0]  # x轴范围 [xmin, xmax]
         y_range = view_range[1]  # y轴范围 [ymin, ymax]
 
         # 将百分比位置转换为坐标
-        x_percent = pos[0] # 50% 对应 x 轴中间
-        y_percent =  pos[1]  # 20% 对应 y 轴上的某个位置
+        x_percent = pos[0]  # 50% 对应 x 轴中间
+        y_percent = pos[1]  # 20% 对应 y 轴上的某个位置
 
         x_pos = x_range[0] + x_percent * (x_range[1] - x_range[0])  # 根据百分比计算实际位置
         y_pos = y_range[0] + y_percent * (y_range[1] - y_range[0])  # 根据百分比计算实际位置
-        return x_pos,y_pos
-    def auto_range(self,plot=None):
+        return x_pos, y_pos
+
+    def auto_range(self, plot=None):
 
         if plot is None:
-            plot=self.current_axes
+            plot = self.current_axes
         if plot:
 
             view = plot.getViewBox()
 
-            x_range=[10000,-10000]
-            y_range=[10000,-10000]
+            x_range = [10000, -10000]
+            y_range = [10000, -10000]
             for item in view.addedItems:
                 if isinstance(item, ScatterPlotItem):
 
-                    x=item.data["x"]
-                    y=item.data["y"]
+                    x = item.data["x"]
+                    y = item.data["y"]
 
-                    x=x[x>-10000]
-                    y=y[y>-10000]
-                    if x.size==0:
-                        x_range=[0,1]
-                        y_range=[0,1]
+                    x = x[x > -10000]
+                    y = y[y > -10000]
+                    if x.size == 0:
+                        x_range = [0, 1]
+                        y_range = [0, 1]
                         continue
-                    x_min = np.min(x )
-                    x_max = np.max(x )
-                    y_min = np.min(y )
-                    y_max = np.max(y )
+                    x_min = np.min(x)
+                    x_max = np.max(x)
+                    y_min = np.min(y)
+                    y_max = np.max(y)
                     if x_min < x_range[0]:
-                        x_range[0]=x_min
+                        x_range[0] = x_min
                     if x_max > x_range[1]:
-                        x_range[1]=x_max
-                    if y_min <y_range[0]:
-                        y_range[0]=y_min
+                        x_range[1] = x_max
+                    if y_min < y_range[0]:
+                        y_range[0] = y_min
                     if y_max > y_range[1]:
-                        y_range[1]=y_max
-            if plot.title!="descriptor":
+                        y_range[1] = y_max
+            if plot.title != "descriptor":
 
-                real_range=(min(x_range[0],y_range[0]),max(x_range[1],y_range[1]))
-                view.setRange(xRange=real_range,yRange=real_range)
+                real_range = (min(x_range[0], y_range[0]), max(x_range[1], y_range[1]))
+                view.setRange(xRange=real_range, yRange=real_range)
             else:
-                view.setRange(xRange=x_range,yRange=y_range)
+                view.setRange(xRange=x_range, yRange=y_range)
 
     def pan(self, checked):
 
         if self.current_axes:
-
             self.current_axes.setMouseEnabled(checked, checked)
             self.current_axes.getViewBox().setMouseMode(ViewBox.PanMode)
+
     def pen(self, checked):
         if self.current_axes is None:
-
             return False
 
         if checked:
-            self.draw_mode=True
+            self.draw_mode = True
             # 初始化鼠标状态和轨迹数据
             self.is_drawing = False
             self.x_data = []
             self.y_data = []
 
         else:
-            self.draw_mode=False
+            self.draw_mode = False
             pass
+
     #
     def mousePressEvent(self, event):
         if not self.draw_mode:
@@ -323,19 +310,18 @@ class PyqtgraphCanvas(CanvasLayoutBase,GraphicsLayoutWidget, metaclass=CombinedM
 
             self.curve.setData([], [])  # 清空绘制线条，避免对角线
 
-
     def mouseReleaseEvent(self, event):
 
         if not self.draw_mode:
             return super().mouseReleaseEvent(event)
-        if event.button() == Qt.MouseButton.LeftButton  or event.button() == Qt.MouseButton.RightButton:
+        if event.button() == Qt.MouseButton.LeftButton or event.button() == Qt.MouseButton.RightButton:
             self.is_drawing = False
-            reverse=event.button() == Qt.MouseButton.RightButton
+            reverse = event.button() == Qt.MouseButton.RightButton
             self.current_axes.removeItem(self.curve)
             # 创建鼠标轨迹的多边形
-            if len(self.x_data)>2:
+            if len(self.x_data) > 2:
 
-                self.select_point_from_polygon(np.column_stack((self.x_data, self.y_data)),reverse)
+                self.select_point_from_polygon(np.column_stack((self.x_data, self.y_data)), reverse)
             else:
                 # 右键的话  选中单个点
                 pass
@@ -343,10 +329,9 @@ class PyqtgraphCanvas(CanvasLayoutBase,GraphicsLayoutWidget, metaclass=CombinedM
                 mouse_point = self.current_axes.getViewBox().mapSceneToView(pos)
 
                 x = mouse_point.x()
-                self.select_point(mouse_point,reverse)
+                self.select_point(mouse_point, reverse)
             return
 
-
     def mouseMoveEvent(self, event):
         if not self.draw_mode:
             return super().mouseMoveEvent(event)
@@ -355,11 +340,11 @@ class PyqtgraphCanvas(CanvasLayoutBase,GraphicsLayoutWidget, metaclass=CombinedM
             pos = event.pos()
             if self.current_axes.sceneBoundingRect().contains(pos):
                 # 将场景坐标转换为视图坐标
-                mouse_point =self.current_axes.getViewBox().mapSceneToView(pos)
+                mouse_point = self.current_axes.getViewBox().mapSceneToView(pos)
                 x, y = mouse_point.x(), mouse_point.y()
                 # 记录轨迹数据
                 self.x_data.append(x)
                 self.y_data.append(y)
 
                 # 更新绘图
-                self.curve.setData(self.x_data, self.y_data)
+                self.curve.setData(self.x_data, self.y_data)

{neptrainkit-2.0.6.dev57/src/NepTrainKit/core/views → neptrainkit-2.1.1.dev37/src/NepTrainKit/core/canvas/pyqtgraph}/structure.py

@@ -1,27 +1,21 @@
 #!/usr/bin/env python 
 # -*- coding: utf-8 -*-
-# @Time    : 2025/3/15 13:44
+# @Time    : 2025/5/19 20:42
 # @Author  : 兵
 # @email    : 1747193328@qq.com
-
-import numpy as np
 #TODO: 这个导入慢 后面看能不能优化
 import pyqtgraph as pg
 import pyqtgraph.opengl as gl
 
-
-from OpenGL.GL import *  # noqa
+import numpy as np
+from OpenGL.GL import GL_PROJECTION, glLoadMatrixf, glMatrixMode
+from NepTrainKit.core import Config
 
 
 from PySide6.QtCore import Qt
 from PySide6.QtGui import QColor,QMatrix4x4
-from PySide6.QtWidgets import QApplication, QWidget, QGridLayout, QSizePolicy
 
-
-from NepTrainKit.core import Config
-from NepTrainKit.core.structure import table_info, Structure
-from NepTrainKit import utils
-from qfluentwidgets import BodyLabel
+from NepTrainKit.core.structure import table_info
 
 
 class StructurePlotWidget(gl.GLViewWidget):
@@ -399,66 +393,3 @@ class StructurePlotWidget(gl.GLViewWidget):
 
         # 示例：高亮第0个原子
         # self.highlight_atom(0)
-
-
-class StructureInfoWidget(QWidget):
-    def __init__(self, parent=None):
-        super(StructureInfoWidget, self).__init__(parent)
-        self.init_ui()
-    def init_ui(self):
-        self._layout = QGridLayout(self)  # 创建布局
-        self._layout.setContentsMargins(0, 0, 0, 0)  # 设置边距
-        self._layout.setSpacing(0)  # 设置间距
-        self.setLayout(self._layout)  # 设置布局
-
-
-        self.atom_label = BodyLabel(self)
-        self.atom_label.setText("Atoms:")
-        self.atom_num_text = BodyLabel(self)
-
-        self.formula_label = BodyLabel(self)
-        self.formula_label.setText("Formula:")
-        self.formula_text = BodyLabel(self)
-        self.formula_text.setSizePolicy(QSizePolicy.Policy.Preferred, QSizePolicy.Policy.Fixed)
-        self.formula_text.setWordWrap(True)
-
-        self.lattice_label=BodyLabel(self)
-        self.lattice_label.setText("Lattice:")
-        self.lattice_text = BodyLabel(self)
-        self.lattice_text.setWordWrap(True)
-
-        self.config_label = BodyLabel(self)
-        self.config_label.setText("Config Type:")
-        self.config_text = BodyLabel(self)
-        self.config_text.setSizePolicy(QSizePolicy.Policy.Preferred, QSizePolicy.Policy.Fixed)
-
-
-        self._layout.addWidget(self.atom_label, 0,0,1,1)
-        self._layout.addWidget(self.atom_num_text, 0, 1,1,3)
-        self._layout.addWidget(self.formula_label, 1,0,1,1)
-        self._layout.addWidget(self.formula_text, 1, 1,1,3)
-
-
-        self._layout.addWidget(self.config_label, 2, 0,1,1)
-        self._layout.addWidget(self.config_text, 2, 1,1,3)
-
-        self._layout.addWidget(self.lattice_label, 3, 0,1,1)
-        self._layout.addWidget(self.lattice_text, 3, 1,1,3)
-
-    def show_structure_info(self, structure):
-        pass
-        self.atom_num_text.setText(str(len(structure )))
-        self.formula_text.setText(structure.html_formula)
-        self.lattice_text.setText(str(np.round(structure.lattice,3)))
-        self.config_text.setText(structure.Config_type)
-
-if __name__ == '__main__':
-    app = QApplication([])
-    view = StructurePlotWidget()
-    view.show()
-    import time
-    start = time.time()
-    atoms = Structure.read_xyz("good.xyz")
-    view.show_structure(atoms)  # 修改为show_structure，与代码一致
-    print(time.time() - start)
-    QApplication.instance().exec_()

neptrainkit-2.1.1.dev37/src/NepTrainKit/core/canvas/vispy/__init__.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python 
+# -*- coding: utf-8 -*-
+# @Time    : 2025/5/20 14:18
+# @Author  : 兵
+# @email    : 1747193328@qq.com
+from vispy import use
+# 不要去掉
+from vispy.app.backends import _pyside6
+use("PySide6", "gl2")
+
+from .structure import StructurePlotWidget
+from .canvas import  VispyCanvas