plotfig 0.0.6__tar.gz → 0.0.7__tar.gz

{plotfig-0.0.6 → plotfig-0.0.7}/PKG-INFO

@@ -1,8 +1,9 @@
 Metadata-Version: 2.4
 Name: plotfig
-Version: 0.0.6
+Version: 0.0.7
 Summary: Scientific plotting package for Cognitive neuroscience
 Author-email: Ricardo Ryn <ricardoRyn1317@gmail.com>
+Keywords: neuroscience,plotting,visualization
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE

{plotfig-0.0.6 → plotfig-0.0.7}/plotfig.egg-info/PKG-INFO

@@ -1,8 +1,9 @@
 Metadata-Version: 2.4
 Name: plotfig
-Version: 0.0.6
+Version: 0.0.7
 Summary: Scientific plotting package for Cognitive neuroscience
 Author-email: Ricardo Ryn <ricardoRyn1317@gmail.com>
+Keywords: neuroscience,plotting,visualization
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE

plotfig-0.0.7/plotfig.egg-info/SOURCES.txt

@@ -0,0 +1,76 @@
+LICENSE
+README.md
+pyproject.toml
+plotfig.egg-info/PKG-INFO
+plotfig.egg-info/SOURCES.txt
+plotfig.egg-info/dependency_links.txt
+plotfig.egg-info/requires.txt
+plotfig.egg-info/top_level.txt
+src/plotfig/__init__.py
+src/plotfig/brain_connection_plot.py
+src/plotfig/brain_surface_plot.py
+src/plotfig/circos_plot.py
+src/plotfig/common_plot.py
+src/plotfig/data/atlas_tables/chimpanzee_bna.csv
+src/plotfig/data/atlas_tables/human_bna.csv
+src/plotfig/data/atlas_tables/human_glasser.csv
+src/plotfig/data/atlas_tables/macaque_bna.csv
+src/plotfig/data/atlas_tables/macaque_charm5.csv
+src/plotfig/data/atlas_tables/macaque_charm5_add_13_sgms.csv
+src/plotfig/data/atlas_tables/macaque_charm6.csv
+src/plotfig/data/neurodata/atlases/chimpanzee_BNA/ChimpBNA.L.32k_fs_LR.label.gii
+src/plotfig/data/neurodata/atlases/chimpanzee_BNA/ChimpBNA.R.32k_fs_LR.label.gii
+src/plotfig/data/neurodata/atlases/human_BNA/fsaverage.L.BNA.32k_fs_LR.label.gii
+src/plotfig/data/neurodata/atlases/human_BNA/fsaverage.R.BNA.32k_fs_LR.label.gii
+src/plotfig/data/neurodata/atlases/human_Glasser/fsaverage.L.Glasser.32k_fs_LR.label.gii
+src/plotfig/data/neurodata/atlases/human_Glasser/fsaverage.R.Glasser.32k_fs_LR.label.gii
+src/plotfig/data/neurodata/atlases/macaque_BNA/MBNA_124_32k_L.label.gii
+src/plotfig/data/neurodata/atlases/macaque_BNA/MBNA_124_32k_R.label.gii
+src/plotfig/data/neurodata/atlases/macaque_CHARM5/L.charm5.label.gii
+src/plotfig/data/neurodata/atlases/macaque_CHARM5/R.charm5.label.gii
+src/plotfig/data/neurodata/atlases/macaque_CHARM6/L.charm6.label.gii
+src/plotfig/data/neurodata/atlases/macaque_CHARM6/R.charm6.label.gii
+src/plotfig/data/neurodata/surfaces/chimpanzee_BNA/ChimpYerkes29_v1.2.L.midthickness.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/chimpanzee_BNA/ChimpYerkes29_v1.2.L.veryinflated.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/chimpanzee_BNA/ChimpYerkes29_v1.2.R.midthickness.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/chimpanzee_BNA/ChimpYerkes29_v1.2.R.veryinflated.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/README.md
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-L_desc-nomedialwall_dparc.label.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-L_desc-sulc_midthickness.shape.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-L_desc-vaavg_midthickness.shape.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-L_inflated.surf.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-L_midthickness.surf.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-L_sphere.surf.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-L_veryinflated.surf.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-R_desc-nomedialwall_dparc.label.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-R_desc-sulc_midthickness.shape.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-R_desc-vaavg_midthickness.shape.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-R_inflated.surf.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-R_midthickness.surf.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-R_sphere.surf.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_den-32k_hemi-R_veryinflated.surf.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_space-fsaverage_den-32k_hemi-L_sphere.surf.gii
+src/plotfig/data/neurodata/surfaces/human_fsLR/tpl-fsLR_space-fsaverage_den-32k_hemi-R_sphere.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_BNA/civm.L.inflated.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_BNA/civm.L.midthickness.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_BNA/civm.L.pial.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_BNA/civm.L.veryinflated.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_BNA/civm.L.white.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_BNA/civm.R.inflated.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_BNA/civm.R.midthickness.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_BNA/civm.R.pial.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_BNA/civm.R.veryinflated.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_BNA/civm.R.white.32k_fs_LR.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/L.gray_surface.inf_300.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/L.gray_surface.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/L.mid_surface.inf_300.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/L.mid_surface.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/L.white_surface.inf_300.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/L.white_surface.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/R.gray_surface.inf_300.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/R.gray_surface.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/R.mid_surface.inf_300.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/R.mid_surface.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/R.white_surface.inf_300.surf.gii
+src/plotfig/data/neurodata/surfaces/macaque_NMT2/R.white_surface.surf.gii
+src/plotfig/data/neurodata/volumes/macaque_NMT2/CHARM5_add_13_sgms_asym.nii.gz

{plotfig-0.0.6 → plotfig-0.0.7}/pyproject.toml

@@ -1,7 +1,8 @@
 [project]
 name = "plotfig"
-version = "0.0.6"
+version = "0.0.7"
 description = "Scientific plotting package for Cognitive neuroscience"
+keywords = ["neuroscience", "plotting", "visualization"]
 readme = "README.md"
 requires-python = ">=3.11"
 authors = [
@@ -19,16 +20,27 @@ dependencies = [
     "surfplot>=0.2.0",
 ]
 
+[dependency-groups]
+dev = [
+    "joblib>=1.4.2",
+]
+
 [build-system]
-requires = ["setuptools"]
+requires = ["setuptools>=42", "wheel"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools.packages.find]
-where = ["."]
-include = ["plotfig*"]  # 包含主包及其子包
+[tool.setuptools]
+package-dir = {"plotfig" = "src/plotfig"}
+packages = ["plotfig"]
+include-package-data = true
 
 [tool.setuptools.package-data]
 plotfig = [
     "data/atlas_tables/**/*",
     "data/neurodata/**/*"
 ]
+
+[tool.ruff]
+exclude = [
+  "examples/example.ipynb"
+]

plotfig-0.0.7/src/plotfig/__init__.py

@@ -0,0 +1,32 @@
+from .common_plot import (
+    plot_one_group_bar_figure,
+    plot_one_group_violin_figure,
+    plot_correlation_figure,
+    plot_matrix_figure,
+)
+from .brain_surface_plot import (
+    plot_human_brain_figure,
+    plot_human_hemi_brain_figure,
+    plot_macaque_brain_figure,
+    plot_macaque_hemi_brain_figure,
+    plot_chimpanzee_brain_figure,
+    plot_chimpanzee_hemi_brain_figure,
+)
+from .circos_plot import plot_symmetric_circle_figure, plot_asymmetric_circle_figure
+from .brain_connection_plot import plot_brain_connection_figure
+
+__all__ = [
+    "plot_one_group_bar_figure",
+    "plot_one_group_violin_figure",
+    "plot_correlation_figure",
+    "plot_matrix_figure",
+    "plot_human_brain_figure",
+    "plot_human_hemi_brain_figure",
+    "plot_macaque_brain_figure",
+    "plot_macaque_hemi_brain_figure",
+    "plot_chimpanzee_brain_figure",
+    "plot_chimpanzee_hemi_brain_figure",
+    "plot_symmetric_circle_figure",
+    "plot_asymmetric_circle_figure",
+    "plot_brain_connection_figure",
+]

{plotfig-0.0.6 → plotfig-0.0.7/src}/plotfig/brain_connection_plot.py

@@ -8,36 +8,41 @@ import plotly.graph_objects as go
 import matplotlib.colors as mcolors
 import matplotlib.cm as cm
 
+from typing import List
+from pathlib import Path
+import numpy.typing as npt
+
 
 def plot_brain_connection_figure(
-    connectome: np.ndarray,
-    lh_surfgii_file: str = None,
-    rh_surfgii_file: str = None,
-    niigz_file: str = None,
-    nodes_name: iter = None,
-    nodes_color: iter = None,
-    output_file: str = None,
+    connectome: npt.NDArray,
+    lh_surfgii_file: str | Path | None = None,
+    rh_surfgii_file: str | Path | None = None,
+    niigz_file: str | Path | None = None,
+    nodes_name: List[str] | None = None,
+    nodes_size: float = 5,
+    nodes_color: List[str] | None = None,
+    output_file: str | Path | None = None,
     scale_metheod: str = "",
-    line_width: int | float = 10,
-):
+    line_width: float = 10,
+) -> None:
     """绘制大脑连接图，保存在指定的html文件中
-    
-    如果不指定surface文件和图集nii文件，默认绘制NMT2空间上猕猴大脑连接图，图集包括个101脑区/半脑（88个皮层上 + 13个皮层下）
 
     Args:
-        connectome (np.ndarray): 连接矩阵.
-        lh_surfgii_file (str, optional): 左脑surf.gii文件. Defaults to None.
-        rh_surfgii_file (str, optional): 右脑surf.gii文件. Defaults to None.
-        niigz_file (str, optional): 图集nii文件. Defaults to None.
-        nodes_name (iter, optional): 节点名称. Defaults to None.
-        nodes_color (iter, optional): 节点颜色. Defaults to None.
-        output_file (str, optional): 保存的完整路径及文件名. Defaults to None.
-        scale_metheod (str, optional): 边scale方式. Defaults to "". 包括"width, color, width_color, color_width"
-        line_width (int | float, optional): 边粗细. Defaults to 10.
+        connectome (npt.NDArray): 连接矩阵
+        lh_surfgii_file (str | Path | None, optional): 左脑surf.gii文件. Defaults to None.
+        rh_surfgii_file (str | Path | None, optional): 右脑surf.gii文件. Defaults to None.
+        niigz_file (str | Path | None, optional): 图集nii文件. Defaults to None.
+        nodes_name (List[str] | None, optional): 节点名称. Defaults to None.
+        nodes_size (float, optional): 节点大小. Defaults to 5.
+        nodes_color (List[str] | None, optional): 节点颜色. Defaults to None.
+        output_file (str | Path | None, optional): 保存的完整路径及文件名. Defaults to None.
+        scale_metheod (str, optional): 连接scale的形式. Defaults to "".
+        line_width (float, optional): 连接粗细. Defaults to 10.
 
     Raises:
         ValueError: 参数值错误
     """
+
     nodes_num = connectome.shape[0]
     # 默认参数
     current_dir = op.dirname(__file__)
@@ -85,7 +90,7 @@ def plot_brain_connection_figure(
         color="white",
         opacity=0.1,
         flatshading=True,
-        lighting=dict(ambient=0.7, diffuse=0.3),
+        lighting={"ambient": 0.7, "diffuse": 0.3},
         name="Left Hemisphere",
     )
     # 右半球
@@ -99,7 +104,7 @@ def plot_brain_connection_figure(
         color="white",
         opacity=0.1,
         flatshading=True,
-        lighting=dict(ambient=0.7, diffuse=0.3),
+        lighting={"ambient": 0.7, "diffuse": 0.3},
         name="Right Hemisphere",
     )
     fig = go.Figure(data=[mesh_L, mesh_R])  # 同时添加两个Mesh
@@ -132,13 +137,13 @@ def plot_brain_connection_figure(
             y=centroids_real[:, 1],
             z=centroids_real[:, 2],
             mode="markers+text",
-            marker=dict(
-                size=8,  # 球体大小
-                color=nodes_color,  # 根据ROI标签分配颜色
-                colorscale="Rainbow",  # 颜色映射方案
-                opacity=0.8,
-                line=dict(width=2, color="black"),  # 球体边框
-            ),
+            marker={
+                "size": nodes_size,  # 球体大小
+                "color": nodes_color,  # 根据ROI标签分配颜色
+                "colorscale": "Rainbow",  # 颜色映射方案
+                "opacity": 0.8,
+                "line": {"width": 2, "color": "black"},  # 球体边框
+            },
             text=[f"{name}" for name in nodes_name],  # 悬停显示标签
             hoverinfo="text+x+y+z",
             showlegend=False,  # 显示在图例中
@@ -210,9 +215,10 @@ def plot_brain_connection_figure(
                         y=connection_line[:, 1],
                         z=connection_line[:, 2],
                         mode="lines",
-                        line=dict(
-                            color=each_line_color, width=each_line_width  # 动态设置线宽
-                        ),
+                        line={
+                            "color": each_line_color,
+                            "width": each_line_width,  # 动态设置线宽
+                        },
                         hoverinfo="none",
                         name=f"{nodes_name[i]}-{nodes_name[j]}",
                     )
@@ -220,23 +226,23 @@ def plot_brain_connection_figure(
 
     # 原质心球体代码保持不变（建议调整颜色增强对比度）
     fig.update_traces(
-        selector=dict(mode="markers"),  # 仅更新质心球体
-        marker=dict(
-            size=10,  # 增大球体尺寸
-            colorscale="Viridis",  # 改用高对比度色阶
-            line=dict(width=3, color="black"),
-        ),
+        selector={"mode": "markers"},  # 仅更新质心球体
+        marker={
+            "size": 10,  # 增大球体尺寸
+            "colorscale": "Viridis",  # 改用高对比度色阶
+            "line": {"width": 3, "color": "black"},
+        },
     )
     # 设置布局
     fig.update_layout(
         title="Connection",
-        scene=dict(
-            xaxis=dict(showbackground=False, visible=False),
-            yaxis=dict(showbackground=False, visible=False),
-            zaxis=dict(showbackground=False, visible=False),
-            aspectmode="data",  # 保持坐标轴比例一致
-        ),
-        margin=dict(l=0, r=0, b=0, t=30),
+        scene={
+            "xaxis": {"showbackground": False, "visible": False},
+            "yaxis": {"showbackground": False, "visible": False},
+            "zaxis": {"showbackground": False, "visible": False},
+            "aspectmode": "data",  # 保持坐标轴比例一致
+        },
+        margin={"l": 0, "r": 0, "b": 0, "t": 30},
     )
     # 显示或保存为HTML
     fig.write_html(output_file)  # 导出为交互式网页
@@ -250,7 +256,7 @@ def main():
     rh_surfgii_file = r"D:\Desktop\BG.R.midthickness.32k_fs_LR.surf.gii"
     niigz_file = r"D:\Desktop\macaque_Interoceptive_processing_network.nii.gz"
     output_file = "d:/desktop/rm_rjx.html"
-    plot_macaque_brain_connection_figure(
+    plot_brain_connection_figure(
         connectome,
         lh_surfgii_file=lh_surfgii_file,
         rh_surfgii_file=rh_surfgii_file,