plotfig 1.14.3__tar.gz → 1.15.0__tar.gz

plotfig-1.15.0/.release-please-manifest.json

@@ -0,0 +1 @@
+{".":"1.15.0"}

{plotfig-1.14.3 → plotfig-1.15.0}/CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## [1.15.0](https://github.com/RicardoRyn/plotfig/compare/v1.14.3...v1.15.0) (2026-01-24)
+
+
+### Features ✨
+
+* **brain-surface:** add CHARM4 atlas support for macaque species ([ec300f3](https://github.com/RicardoRyn/plotfig/commit/ec300f3613a36fe624a122dfd34808b06616bc47))
+
+
+### Code Refactoring ♻️
+
+* **plotfig:** add validation for single-element data groups and comprehensive tests ([4b72fcc](https://github.com/RicardoRyn/plotfig/commit/4b72fcccd9a5e8a32ab993f92b6e579e6db85315))
+
 ## [1.14.3](https://github.com/RicardoRyn/plotfig/compare/v1.14.2...v1.14.3) (2026-01-19)
 
 

plotfig-1.15.0/PKG-INFO

@@ -0,0 +1,82 @@
+Metadata-Version: 2.4
+Name: plotfig
+Version: 1.15.0
+Summary: Scientific plotting package for Cognitive neuroscience
+Author-email: Ricardo Ryn <ricardoRyn1317@gmail.com>
+License-File: LICENSE
+Keywords: neuroscience,plotting,visualization
+Requires-Python: >=3.11
+Requires-Dist: brainspace>=0.1.22
+Requires-Dist: imageio>=2.37.2
+Requires-Dist: kaleido>=1.0.0
+Requires-Dist: loguru>=0.7.3
+Requires-Dist: matplotlib>=3.10.6
+Requires-Dist: nibabel>=5.3.2
+Requires-Dist: numpy>=2.3.2
+Requires-Dist: plotly>=6.3.0
+Requires-Dist: pycirclize>=1.10.0
+Requires-Dist: scipy>=1.16.1
+Requires-Dist: tqdm>=4.67.1
+Description-Content-Type: text/markdown
+
+<div align="center">
+
+# plotfig
+
+[![PyPI version](https://badge.fury.io/py/plotfig.svg)](https://badge.fury.io/py/plotfig)
+[![Python version](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![License](https://img.shields.io/badge/license-MIT-green.svg)](LICENSE)
+
+一个专为认知神经科学研究设计的 Python 可视化库，提供高效、易用且美观的绘图工具。
+
+![plotfig](./docs/assets/plotfig.png)
+
+</div>
+
+## 功能特性
+
+- 📊 **多种图表类型**：条形图、矩阵、相关性图、弦图、脑表面图、脑连接图
+- 🎨 **专业科研风格**：内置多种配色方案，符合学术发表标准
+- 📈 **自动显著性检验**：内置多种统计方法，自动绘制显著性标记
+- 🔬 **专为神经科学设计**：支持常见灵长类脑区 atlas、脑网络可视化等特定场景
+- 🚀 **简单易用**：简洁的 API，快速上手
+
+## 快速开始
+
+```python
+import matplotlib.pyplot as plt
+
+from plotfig import plot_one_group_bar_figure
+
+# 绘制单组条形图
+data = [[1.2, 2.3, 3.1], [4.5, 5.6, 6.2]]
+plot_one_group_bar_figure(data)
+plt.show()
+```
+
+## 安装
+
+`plotfig` 要求 Python 3.11 及以上版本。
+
+**使用 uv 安装：**
+
+**使用 uv 安装：**
+```bash
+uv add plotfig
+```
+
+**使用 pip 安装：**
+
+```bash
+pip install plotfig
+```
+
+## 文档
+
+详细文档和使用示例请访问 [plotfig 文档](https://ricardoryn.github.io/plotfig/)。
+
+## 贡献
+
+欢迎提交 Issue 或 PR！无论是 Bug 报告、功能建议还是文档改进，都非常欢迎在 [Issue](https://github.com/RicardoRyn/plotfig/issues) 中提出。
+
+开发贡献流程请参见[贡献指南](https://ricardoryn.github.io/plotfig/)。

plotfig-1.15.0/README.md

@@ -0,0 +1,61 @@
+<div align="center">
+
+# plotfig
+
+[![PyPI version](https://badge.fury.io/py/plotfig.svg)](https://badge.fury.io/py/plotfig)
+[![Python version](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![License](https://img.shields.io/badge/license-MIT-green.svg)](LICENSE)
+
+一个专为认知神经科学研究设计的 Python 可视化库，提供高效、易用且美观的绘图工具。
+
+![plotfig](./docs/assets/plotfig.png)
+
+</div>
+
+## 功能特性
+
+- 📊 **多种图表类型**：条形图、矩阵、相关性图、弦图、脑表面图、脑连接图
+- 🎨 **专业科研风格**：内置多种配色方案，符合学术发表标准
+- 📈 **自动显著性检验**：内置多种统计方法，自动绘制显著性标记
+- 🔬 **专为神经科学设计**：支持常见灵长类脑区 atlas、脑网络可视化等特定场景
+- 🚀 **简单易用**：简洁的 API，快速上手
+
+## 快速开始
+
+```python
+import matplotlib.pyplot as plt
+
+from plotfig import plot_one_group_bar_figure
+
+# 绘制单组条形图
+data = [[1.2, 2.3, 3.1], [4.5, 5.6, 6.2]]
+plot_one_group_bar_figure(data)
+plt.show()
+```
+
+## 安装
+
+`plotfig` 要求 Python 3.11 及以上版本。
+
+**使用 uv 安装：**
+
+**使用 uv 安装：**
+```bash
+uv add plotfig
+```
+
+**使用 pip 安装：**
+
+```bash
+pip install plotfig
+```
+
+## 文档
+
+详细文档和使用示例请访问 [plotfig 文档](https://ricardoryn.github.io/plotfig/)。
+
+## 贡献
+
+欢迎提交 Issue 或 PR！无论是 Bug 报告、功能建议还是文档改进，都非常欢迎在 [Issue](https://github.com/RicardoRyn/plotfig/issues) 中提出。
+
+开发贡献流程请参见[贡献指南](https://ricardoryn.github.io/plotfig/)。

plotfig-1.15.0/docs/installation.md

@@ -0,0 +1,84 @@
+# 安装
+
+`plotfig` 支持通过包管理器安装或直接从源码中安装，要求 Python 3.11 及以上版本。
+
+## 使用包管理器安装 (推荐)
+
+=== "uv"
+
+    ``` bash
+    uv add plotfig
+    ```
+
+=== "pip"
+
+    ``` bash
+    pip install plotfig
+    ```
+
+## 从源码中安装
+
+首先下载源码到某个目录（例如 `/path/to/plotfig`）：
+
+```bash
+git clone https://github.com/RicardoRyn/plotfig.git /path/to/plotfig
+```
+
+然后在您的项目目录中执行：
+
+=== "uv"
+
+    ``` bash
+    uv add /path/to/plotfig
+    ```
+
+=== "pip"
+
+    ``` bash
+    pip install /path/to/plotfig
+    ```
+
+!!! info
+
+    `/path/to/plotfig` 应替换为实际的路径。
+
+## 贡献
+
+如果您希望体验这些功能或参与 `plotfig` 的开发，可以选择以 开发模式（editable mode） 安装项目。
+
+这种安装方式允许您对本地源码的修改立即生效，非常适合调试、开发和贡献代码。
+
+推荐流程：
+
+1. Fork 本仓库到您的 GitHub 账号
+2. 克隆您的 Fork 到本地：
+   ```bash
+   git clone https://github.com/USERNAME/plotfig.git /path/to/plotfig
+   ```
+3. 在您的项目目录中以开发模式安装：
+
+=== "uv"
+
+    ``` bash
+    uv add --editable /path/to/plotfig
+    ```
+
+=== "pip"
+
+    ``` bash
+    pip install -e /path/to/plotfig
+    ```
+
+!!! info
+
+    `/path/to/plotfig` 应替换为实际的路径。
+
+---
+
+**欢迎提交 Issue 或 PR！**
+
+无论是 Bug 报告、功能建议、还是文档改进。
+
+都非常欢迎在 [Issue](https://github.com/RicardoRyn/plotfig/issues) 中提出。
+
+也可以直接提交 [PR](https://github.com/RicardoRyn/plotfig/pulls)，一起变得更强 💪！

{plotfig-1.14.3 → plotfig-1.15.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "plotfig"
-version = "1.14.3"
+version = "1.15.0"
 description = "Scientific plotting package for Cognitive neuroscience"
 keywords = ["neuroscience", "plotting", "visualization"]
 readme = "README.md"
@@ -26,6 +26,7 @@ dependencies = [
 dev = [
     "ipykernel>=6.30.1",
     "mkdocstrings-python>=2.0.1",
+    "pytest>=9.0.2",
     "zensical==0.0.13",
 ]
 

{plotfig-1.14.3 → plotfig-1.15.0}/src/plotfig/brain_surface.py

@@ -6,6 +6,7 @@ import matplotlib.pyplot as plt
 import nibabel as nib
 import numpy as np
 from matplotlib.axes import Axes
+
 from plotfig.externals.surfplot import Plot
 
 Num: TypeAlias = float | int
@@ -67,7 +68,7 @@ def plot_brain_surface_figure(
     Args:
         data (dict[str, float]): 包含脑区名称和对应数值的字典，键为脑区名称（如"lh_bankssts"），值为数值
         species (str, optional): 物种名称，支持"human"、"chimpanzee"、"macaque". Defaults to "human".
-        atlas (str, optional): 脑图集名称，根据物种不同可选不同图集。人上包括"glasser"、"bna"，黑猩猩上包括"bna"，猕猴上包括"charm5"、"charm6"、"bna"以及"d99". Defaults to "glasser".
+        atlas (str, optional): 脑图集名称，根据物种不同可选不同图集。人上包括"glasser"、"bna"，黑猩猩上包括"bna"，猕猴上包括"charm4"、"charm5"、"charm6"、"bna"以及"d99". Defaults to "glasser".
         surf (str, optional): 大脑皮层表面类型，如"inflated"、"veryinflated"、"midthickness"等. Defaults to "veryinflated".
         ax (Axes | None, optional): matplotlib的坐标轴对象，如果为None则使用当前坐标轴. Defaults to None.
         vmin (Num | None, optional): 颜色映射的最小值，None表示使用数据中的最小值. Defaults to None.
@@ -151,6 +152,10 @@ def plot_brain_surface_figure(
                 "rh": f"surfaces/macaque_BNA/civm.R.{surf}.32k_fs_LR.surf.gii",
             },
             "atlas": {
+                "charm4": {
+                    "lh": "atlases/macaque_CHARM4/L.charm4.label.gii",
+                    "rh": "atlases/macaque_CHARM4/R.charm4.label.gii",
+                },
                 "charm5": {
                     "lh": "atlases/macaque_CHARM5/L.charm5.label.gii",
                     "rh": "atlases/macaque_CHARM5/R.charm5.label.gii",
@@ -178,12 +183,12 @@ def plot_brain_surface_figure(
     # 检查物种是否支持
     if species not in atlas_info:
         raise ValueError(
-            f"Unsupported species: {species}. Supported species are: {list(atlas_info.keys())}"
+            f"不支持的物种：{species}。支持的物种列表为：{list(atlas_info.keys())}"
         )
     else:
         # 检查指定物种的图集是否支持
         if atlas not in atlas_info[species]["atlas"]:
-            raise ValueError(f"Unsupported {atlas} atlas for {species}")
+            raise ValueError(f"不支持的图集：{atlas}。支持的图集列表为：{list(atlas_info[species]['atlas'].keys())}")
 
     # 创建Plot对象，用于绘制大脑皮层
     if surf != "flat":

plotfig-1.15.0/src/plotfig/data/atlas_tables/macaque_charm4.csv

@@ -0,0 +1,113 @@
+ROIs_name
+lh_area_32
+lh_area_25
+lh_area_24
+lh_MCC
+lh_area_10
+lh_area_14
+lh_areas_11/13
+lh_area_12m/o
+lh_OFa-p
+lh_OLF
+lh_cl_OFC
+lh_area_8A
+lh_area_8B
+lh_rostral_dlPFC
+lh_rostral_vlPFC
+lh_caudal_vlPFC
+lh_M1
+lh_PM
+lh_SMA/preSMA
+lh_SI
+lh_SII
+lh_V6
+lh_V6A
+lh_area_5
+lh_vm_IPS
+lh_lat_IPS
+lh_MST
+lh_area_7_in_IPL
+lh_area_7m
+lh_PCC
+lh_RSC
+lh_HiF
+lh_preS/paraS
+lh_paraHipp
+lh_ERh
+lh_PRh
+lh_TGa
+lh_TGg/TGd
+lh_TEO
+lh_gyral_TE
+lh_TE_in_STSv
+lh_STSf
+lh_STSd
+lh_STGr
+lh_STGc
+lh_lat_belt
+lh_med_belt
+lh_RTp
+lh_core
+lh_Ins/Pi
+lh_Ri
+lh_MT
+lh_V4
+lh_V3
+lh_V2
+lh_V1
+rh_area_32
+rh_area_25
+rh_area_24
+rh_MCC
+rh_area_10
+rh_area_14
+rh_areas_11/13
+rh_area_12m/o
+rh_OFa-p
+rh_OLF
+rh_cl_OFC
+rh_area_8A
+rh_area_8B
+rh_rostral_dlPFC
+rh_rostral_vlPFC
+rh_caudal_vlPFC
+rh_M1
+rh_PM
+rh_SMA/preSMA
+rh_SI
+rh_SII
+rh_V6
+rh_V6A
+rh_area_5
+rh_vm_IPS
+rh_lat_IPS
+rh_MST
+rh_area_7_in_IPL
+rh_area_7m
+rh_PCC
+rh_RSC
+rh_HiF
+rh_preS/paraS
+rh_paraHipp
+rh_ERh
+rh_PRh
+rh_TGa
+rh_TGg/TGd
+rh_TEO
+rh_gyral_TE
+rh_TE_in_STSv
+rh_STSf
+rh_STSd
+rh_STGr
+rh_STGc
+rh_lat_belt
+rh_med_belt
+rh_RTp
+rh_core
+rh_Ins/Pi
+rh_Ri
+rh_MT
+rh_V4
+rh_V3
+rh_V2
+rh_V1

plotfig-1.15.0/src/plotfig/data/neurodata/atlases/macaque_CHARM4/L.charm4.label.gii

@@ -0,0 +1,171 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<GIFTI xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd"
+       Version="1"
+       NumberOfDataArrays="1">
+   <MetaData>
+      <MD>
+         <Name><![CDATA[AnatomicalStructurePrimary]]></Name>
+         <Value><![CDATA[CortexLeft]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[ParentProvenance]]></Name>
+         <Value><![CDATA[E:\git_repositories\plotfig\src\plotfig\data\neurodata\atlases\macaque_CHARM4\rm_lh.label.gii:
+D:\connectome_workbench\workbench-windows64-v2.0.1\workbench\bin_windows64\wb_command.exe -metric-label-import L.charm5.label.gii label.txt lh.label.gii
+
+]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[ProgramProvenance]]></Name>
+         <Value><![CDATA[Connectome Workbench
+Type: Command Line Application
+Version: 2.0.1
+Qt Compiled Version: 5.7.0
+Qt Runtime Version: 5.7.0
+Commit: 150de12f4f4b94b39bec6d9133ad2e7019d2d3ef
+Commit Date: 2024-10-15 17:38:41 -0500
+Compiler: cl.exe (C:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/bin/amd64)
+Compiler Version: 19.0.24215.1
+Compiled Debug: NO
+Operating System: Windows
+Compiled with OpenMP: YES
+]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[Provenance]]></Name>
+         <Value><![CDATA[wb_command -metric-label-import E:\git_repositories\plotfig\src\plotfig\data\neurodata\atlases\macaque_CHARM4\rm_lh.label.gii E:\git_repositories\plotfig\src\plotfig\data\neurodata\atlases\macaque_CHARM4\rm.txt E:\git_repositories\plotfig\src\plotfig\data\neurodata\atlases\macaque_CHARM4\L.charm4.label.gii]]></Value>
+      </MD>
+      <MD>
+         <Name><![CDATA[WorkingDirectory]]></Name>
+         <Value><![CDATA[E:/python/Projects/Self/self/src/self/utils]]></Value>
+      </MD>
+   </MetaData>
+   <LabelTable>
+      <Label Key="0" Red="1" Green="1" Blue="1" Alpha="0"><![CDATA[???]]></Label>
+      <Label Key="1" Red="0.4" Green="0.701961" Blue="0.360784" Alpha="1"><![CDATA[lh_area_32]]></Label>
+      <Label Key="2" Red="0.054902" Green="0.415686" Blue="0.278431" Alpha="1"><![CDATA[lh_area_25]]></Label>
+      <Label Key="3" Red="0.737255" Green="0.0784314" Blue="0.4" Alpha="1"><![CDATA[lh_area_24]]></Label>
+      <Label Key="4" Red="0.47451" Green="0.823529" Blue="0.839216" Alpha="1"><![CDATA[lh_MCC]]></Label>
+      <Label Key="5" Red="0.290196" Green="0.792157" Blue="0.341176" Alpha="1"><![CDATA[lh_area_10]]></Label>
+      <Label Key="6" Red="0.454902" Green="0.388235" Blue="0.403922" Alpha="1"><![CDATA[lh_area_14]]></Label>
+      <Label Key="7" Red="0.592157" Green="0.509804" Blue="0.584314" Alpha="1"><![CDATA[lh_areas_11/13]]></Label>
+      <Label Key="8" Red="0.203922" Green="0.00392157" Blue="0.341176" Alpha="1"><![CDATA[lh_area_12m/o]]></Label>
+      <Label Key="9" Red="0.921569" Green="0.615686" Blue="0.145098" Alpha="1"><![CDATA[lh_OFa-p]]></Label>
+      <Label Key="10" Red="0.505882" Green="0.74902" Blue="0.733333" Alpha="1"><![CDATA[lh_OLF]]></Label>
+      <Label Key="11" Red="0.0784314" Green="0.627451" Blue="0.796078" Alpha="1"><![CDATA[lh_cl_OFC]]></Label>
+      <Label Key="12" Red="0.223529" Green="0.0823529" Blue="0.988235" Alpha="1"><![CDATA[lh_area_8A]]></Label>
+      <Label Key="13" Red="0.921569" Green="0.345098" Blue="0.188235" Alpha="1"><![CDATA[lh_area_8B]]></Label>
+      <Label Key="14" Red="0.854902" Green="0.227451" Blue="0.996078" Alpha="1"><![CDATA[lh_rostral_dlPFC]]></Label>
+      <Label Key="15" Red="0.662745" Green="1" Blue="0.858824" Alpha="1"><![CDATA[lh_rostral_vlPFC]]></Label>
+      <Label Key="16" Red="0.733333" Green="0.811765" Blue="0.054902" Alpha="1"><![CDATA[lh_caudal_vlPFC]]></Label>
+      <Label Key="17" Red="0.741176" Green="0.741176" Blue="0.682353" Alpha="1"><![CDATA[lh_M1]]></Label>
+      <Label Key="18" Red="0.741176" Green="0.196078" Blue="0.419608" Alpha="1"><![CDATA[lh_PM]]></Label>
+      <Label Key="19" Red="0.211765" Green="0.952941" Blue="0.247059" Alpha="1"><![CDATA[lh_SMA/preSMA]]></Label>
+      <Label Key="20" Red="0.972549" Green="0.509804" Blue="0.894118" Alpha="1"><![CDATA[lh_SI]]></Label>
+      <Label Key="21" Red="0.196078" Green="0.52549" Blue="0.0784314" Alpha="1"><![CDATA[lh_SII]]></Label>
+      <Label Key="22" Red="0.282353" Green="0.65098" Blue="0.0666667" Alpha="1"><![CDATA[lh_V6]]></Label>
+      <Label Key="23" Red="0.513726" Green="0.345098" Blue="0.231373" Alpha="1"><![CDATA[lh_V6A]]></Label>
+      <Label Key="24" Red="0.0509804" Green="0.945098" Blue="0.976471" Alpha="1"><![CDATA[lh_area_5]]></Label>
+      <Label Key="25" Red="0.0313726" Green="0.34902" Blue="0.203922" Alpha="1"><![CDATA[lh_vm_IPS]]></Label>
+      <Label Key="26" Red="0.505882" Green="0.32549" Blue="0.356863" Alpha="1"><![CDATA[lh_lat_IPS]]></Label>
+      <Label Key="27" Red="0.431373" Green="0.733333" Blue="0.776471" Alpha="1"><![CDATA[lh_MST]]></Label>
+      <Label Key="28" Red="0.670588" Green="0.988235" Blue="0.027451" Alpha="1"><![CDATA[lh_area_7_in_IPL]]></Label>
+      <Label Key="29" Red="0.682353" Green="0.133333" Blue="0.803922" Alpha="1"><![CDATA[lh_area_7m]]></Label>
+      <Label Key="30" Red="0.313726" Green="0.639216" Blue="0.192157" Alpha="1"><![CDATA[lh_PCC]]></Label>
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