Refine formula, docstring and code. (#353)

* refine losses formula and doc of loss

* refine docstring according to pydocstyle

docs/zh/api/autodiff.md

@@ -8,5 +8,6 @@
         - Jacobians
         - hessian
         - Hessians
+        - clear
       show_root_heading: false
       heading_level: 3

docs/zh/api/visualize.md

@@ -4,6 +4,7 @@
     handler: python
     options:
       members:
+        - Visualizer
         - VisualizerScatter1D
         - VisualizerScatter3D
         - VisualizerVtu
@@ -12,6 +13,7 @@
         - Visualizer3D
         - VisualizerWeather
         - save_vtu_from_dict
+        - save_vtu_to_mesh
         - save_plot_from_1d_dict
         - save_plot_from_3d_dict
       show_root_heading: false

ppsci/arch/afno.py

@@ -22,8 +22,8 @@
 
 import paddle
 import paddle.fft
-import paddle.nn as nn
 import paddle.nn.functional as F
+from paddle import nn
 
 from ppsci.arch import activation as act_mod
 from ppsci.arch import base
@@ -381,7 +381,7 @@ def __init__(
         )
 
     def forward(self, x):
-        B, C, H, W = x.shape
+        _, _, H, W = x.shape
         if not (H == self.img_size[0] and W == self.img_size[1]):
             raise ValueError(
                 f"Input image size ({H}*{W}) doesn't match model ({self.img_size[0]}*{self.img_size[1]})."
@@ -541,7 +541,7 @@ def forward(self, x):
 
         y = []
         input = x
-        for i in range(self.num_timestamps):
+        for _ in range(self.num_timestamps):
             out = self.forward_tensor(input)
             y.append(out)
             input = out
@@ -665,7 +665,7 @@ def forward(self, x):
 
         input_wind = x
         y = []
-        for i in range(self.num_timestamps):
+        for _ in range(self.num_timestamps):
             with paddle.no_grad():
                 out_wind = self.wind_model.forward_tensor(input_wind)
             out = self.forward_tensor(out_wind)

ppsci/arch/physx_transformer.py

@@ -114,8 +114,7 @@ def split_heads(self, x, k=False):
         x = x.reshape(new_x_shape)
         if k:
             return x.transpose([0, 2, 3, 1])
-        else:
-            return x.transpose([0, 2, 1, 3])
+        return x.transpose([0, 2, 1, 3])
 
     def forward(
         self,

ppsci/autodiff/ad.py

@@ -166,7 +166,7 @@ def __call__(
         j: int = 0,
         grad_y: Optional[paddle.Tensor] = None,
     ) -> paddle.Tensor:
-        """compute hessian matrix for given ys and xs.
+        """Compute hessian matrix for given ys and xs.
 
         Args:
             ys (paddle.Tensor): Output tensor.

ppsci/constraint/base.py

@@ -15,7 +15,7 @@
 from typing import Any
 from typing import Dict
 
-import paddle.io as io
+from paddle import io
 
 from ppsci import data
 from ppsci import loss

ppsci/data/dataset/array_dataset.py

@@ -95,6 +95,7 @@ def __init__(
         weight: Dict[str, np.ndarray],
         transforms: Optional[vision.Compose] = None,
     ):
+        super().__init__()
         self.input = {key: paddle.to_tensor(value) for key, value in input.items()}
         self.label = {key: paddle.to_tensor(value) for key, value in label.items()}
         self.weight = {key: paddle.to_tensor(value) for key, value in weight.items()}

ppsci/data/dataset/era5_dataset.py

@@ -90,8 +90,8 @@ def read_data(self, path: str, var="fields"):
         paths = [path] if path.endswith(".h5") else glob.glob(path + "/*.h5")
         paths.sort()
         files = []
-        for path in paths:
-            _file = h5py.File(path, "r")
+        for path_ in paths:
+            _file = h5py.File(path_, "r")
             files.append(_file[var])
         return files
 

ppsci/geometry/geometry.py

@@ -157,8 +157,8 @@ def sample_boundary(self, n, random="pseudo", criteria=None, evenly=False):
         ):
             area_dict = misc.convert_to_dict(area[:, 1:], ["area"])
             return {**x_dict, **normal_dict, **area_dict}
-        else:
-            return {**x_dict, **normal_dict}
+
+        return {**x_dict, **normal_dict}
 
     @abc.abstractmethod
     def random_points(self, n: int, random: str = "pseudo"):

ppsci/geometry/geometry_2d.py

@@ -455,7 +455,7 @@ def random_points(self, n, random="pseudo"):
         x = np.empty((0, 2), dtype=paddle.get_default_dtype())
         vbbox = self.bbox[1] - self.bbox[0]
         while len(x) < n:
-            x_new = sampler.sample(n, 2, sampler="pseudo") * vbbox + self.bbox[0]
+            x_new = sampler.sample(n, 2, "pseudo") * vbbox + self.bbox[0]
             x = np.vstack((x, x_new[self.is_inside(x_new)]))
         return x[:n]
 

ppsci/geometry/mesh.py

@@ -222,7 +222,7 @@ def inflated_random_boundary_points(
             all_points.append(normal)
             all_points.append(area)
 
-        all_point = np.concatenate(all_point, axis=0)
+        all_points = np.concatenate(all_points, axis=0)
         all_normal = np.concatenate(all_normal, axis=0)
         all_area = np.concatenate(all_area, axis=0)
         return all_points, all_normal, all_area
@@ -270,7 +270,7 @@ def random_boundary_points(self, n, random="pseudo", criteria=None):
             npoint_per_triangle, np.arange(len(triangle_prob) + 1) - 0.5
         )
 
-        all_point = []
+        all_points = []
         all_normal = []
         all_area = []
         for i, npoint in enumerate(npoint_per_triangle):
@@ -286,17 +286,17 @@ def random_boundary_points(self, n, random="pseudo", criteria=None):
                 dtype=paddle.get_default_dtype(),
             )
 
-            all_point.append(face_points)
+            all_points.append(face_points)
             all_normal.append(face_normal)
             all_area.append(valid_area)
 
-        all_point = np.concatenate(all_point, axis=0)
+        all_points = np.concatenate(all_points, axis=0)
         all_normal = np.concatenate(all_normal, axis=0)
         all_area = np.concatenate(all_area, axis=0)
 
         # NOTE: use global mean area instead of local mean area
         all_area = np.full_like(all_area, all_area.mean())
-        return all_point, all_normal, all_area
+        return all_points, all_normal, all_area
 
     def sample_boundary(
         self, n, random="pseudo", criteria=None, evenly=False, inflation_dist=None
@@ -311,11 +311,8 @@ def sample_boundary(
                 raise ValueError(
                     "Can't sample evenly on mesh now, please set evenly=False."
                 )
-                # points, normal, area = self.uniform_boundary_points(n, False)
-            else:
-                points, normals, areas = self.random_boundary_points(
-                    n, random, criteria
-                )
+            # points, normal, area = self.uniform_boundary_points(n, False)
+            points, normals, areas = self.random_boundary_points(n, random, criteria)
 
         x_dict = misc.convert_to_dict(points, self.dim_keys)
         normal_dict = misc.convert_to_dict(
@@ -362,9 +359,7 @@ def sample_interior(self, n, random="pseudo", criteria=None, evenly=False):
             raise NotImplementedError(
                 "uniformly sample for interior in mesh is not support yet"
             )
-            # points, area = self.uniform_points(n)
-        else:
-            points, areas = self.random_points(n, random, criteria)
+        points, areas = self.random_points(n, random, criteria)
 
         x_dict = misc.convert_to_dict(points, self.dim_keys)
         area_dict = misc.convert_to_dict(areas, ["area"])
@@ -375,45 +370,47 @@ def sample_interior(self, n, random="pseudo", criteria=None, evenly=False):
 
         return {**x_dict, **area_dict, **sdf_dict}
 
-    def union(self, rhs: "Mesh"):
+    def union(self, other: "Mesh"):
         if not checker.dynamic_import_to_globals(["pymesh"]):
             raise ModuleNotFoundError
         import pymesh
 
-        csg = pymesh.CSGTree({"union": [{"mesh": self.py_mesh}, {"mesh": rhs.py_mesh}]})
+        csg = pymesh.CSGTree(
+            {"union": [{"mesh": self.py_mesh}, {"mesh": other.py_mesh}]}
+        )
         return Mesh(csg.mesh)
 
-    def __or__(self, rhs: "Mesh"):
-        return self.union(rhs)
+    def __or__(self, other: "Mesh"):
+        return self.union(other)
 
-    def __add__(self, rhs: "Mesh"):
-        return self.union(rhs)
+    def __add__(self, other: "Mesh"):
+        return self.union(other)
 
-    def difference(self, rhs: "Mesh"):
+    def difference(self, other: "Mesh"):
         if not checker.dynamic_import_to_globals(["pymesh"]):
             raise ModuleNotFoundError
         import pymesh
 
         csg = pymesh.CSGTree(
-            {"difference": [{"mesh": self.py_mesh}, {"mesh": rhs.py_mesh}]}
+            {"difference": [{"mesh": self.py_mesh}, {"mesh": other.py_mesh}]}
         )
         return Mesh(csg.mesh)
 
-    def __sub__(self, rhs: "Mesh"):
-        return self.difference(rhs)
+    def __sub__(self, other: "Mesh"):
+        return self.difference(other)
 
-    def intersection(self, rhs: "Mesh"):
+    def intersection(self, other: "Mesh"):
         if not checker.dynamic_import_to_globals(["pymesh"]):
             raise ModuleNotFoundError
         import pymesh
 
         csg = pymesh.CSGTree(
-            {"intersection": [{"mesh": self.py_mesh}, {"mesh": rhs.py_mesh}]}
+            {"intersection": [{"mesh": self.py_mesh}, {"mesh": other.py_mesh}]}
         )
         return Mesh(csg.mesh)
 
-    def __and__(self, rhs: "Mesh"):
-        return self.intersection(rhs)
+    def __and__(self, other: "Mesh"):
+        return self.intersection(other)
 
     def __str__(self) -> str:
         """Return the name of class"""
@@ -429,7 +426,7 @@ def __str__(self) -> str:
 
 
 def area_of_triangles(v0, v1, v2):
-    """ref https://math.stackexchange.com/questions/128991/how-to-calculate-the-area-of-a-3d-triangle
+    """Ref https://math.stackexchange.com/questions/128991/how-to-calculate-the-area-of-a-3d-triangle
 
     Args:
         v0 (np.ndarray): Coordinates of the first vertex of the triangle surface with shape of [N, 3].

ppsci/geometry/pointcloud.py

@@ -18,8 +18,8 @@
 
 import numpy as np
 
-import ppsci.utils.misc as misc
 from ppsci.geometry import geometry
+from ppsci.utils import misc
 
 
 class PointCloud(geometry.Geometry):
@@ -148,32 +148,32 @@ def uniform_points(self, n: int, boundary=True):
         """Compute the equispaced points in the geometry."""
         return self.interior[:n]
 
-    def union(self, rhs):
+    def union(self, other):
         raise NotImplementedError(
             "Union operation for PointCloud is not supported yet."
         )
 
-    def __or__(self, rhs):
+    def __or__(self, other):
         raise NotImplementedError(
             "Union operation for PointCloud is not supported yet."
         )
 
-    def difference(self, rhs):
+    def difference(self, other):
         raise NotImplementedError(
             "Subtraction operation for PointCloud is not supported yet."
         )
 
-    def __sub__(self, rhs):
+    def __sub__(self, other):
         raise NotImplementedError(
             "Subtraction operation for PointCloud is not supported yet."
         )
 
-    def intersection(self, rhs):
+    def intersection(self, other):
         raise NotImplementedError(
             "Intersection operation for PointCloud is not supported yet."
         )
 
-    def __and__(self, rhs):
+    def __and__(self, other):
         raise NotImplementedError(
             "Intersection operation for PointCloud is not supported yet."
         )

ppsci/loss/base.py

@@ -16,7 +16,7 @@
 from typing import Optional
 from typing import Union
 
-import paddle.nn as nn
+from paddle import nn
 from typing_extensions import Literal
 
 

ppsci/loss/integral.py

@@ -28,12 +28,14 @@ class IntegralLoss(base.Loss):
     $$
     L =
     \begin{cases}
-        \dfrac{1}{N}\sum\limits_{i=1}^{N}{(\sum\limits_{j=1}^{M}{(x_i^j s_{j})}-y_i)^2}, & \text{if reduction='mean'} \\
-        \sum\limits_{i=1}^{N}{(\sum\limits_{j=1}^{M}{(x_i^j s_{j})}-y_i)^2}, & \text{if reduction='sum'}
+        \dfrac{1}{N} \Vert \mathbf{s} \circ \mathbf{x} - \mathbf{y} \Vert_2^2, & \text{if reduction='mean'} \\
+         \Vert \mathbf{s} \circ \mathbf{x} - \mathbf{y} \Vert_2^2, & \text{if reduction='sum'}
     \end{cases}
     $$
 
-    $M$ is the number of samples in Monte-Carlo integration.
+    $$
+    \mathbf{x}, \mathbf{y}, \mathbf{s} \in \mathcal{R}^{N}
+    $$
 
     Args:
         reduction (Literal["mean", "sum"], optional): Reduction method. Defaults to "mean".