EBSD 取向分析 (orix) 插件用户手册

EBSD Analysis (orix) - User Manual

Dragonfly Prototype Apps · EBSD Analysis (orix)...

版本 Version 1.0 · 2026-07-04

第一部分 中文手册

目录

1. 简介

2. 适用场景

3. 安装与启用

4. 运行环境与首次配置

5. 界面说明

6. 使用步骤

7. 参数说明

8. 输出结果

9. 常见问题与故障排除

10. 注意事项与已知限制

11. 参考资料

1. 简介

EBSD 取向分析 (orix) 是一款 Dragonfly Prototype Apps 插件,用于分析已完成指标化(indexed)的电子背散射衍射(EBSD)取向数据。EBSD 在扫描表面的每一个测点上测量晶体的取向,得到逐像素的取向图。本插件读取采集软件导出的取向图文件,把它转化为可在 Dragonfly 中浏览、对照的图像与通道(Channel)。

载入取向图后,插件可生成反极图(IPF)着色的取向图、欧拉角、相(phase)图以及文件中携带的指标化质量指标,并把每一项作为 Dragonfly 的标量通道发布回来;面板内还会显示一张 IPF 取向图预览和统计信息。支持二维单张取向图,也支持把多张连续切片文件堆叠成三维体。

底层引擎: 计算由开源库 orix 0.14.3(pyxem 项目)完成,并配合 numpy 与 matplotlib。orix 采用 GPL-3.0 许可,因此它只在插件专用的独立 Python 环境(venv)的子进程中运行,通过文件方式与主程序交换数据,从不被 Dragonfly 进程直接导入,以此与主程序保持隔离。numpy 为 BSD 许可,matplotlib 为 PSF/BSD 类许可。

一张普通的灰度图像不是 EBSD 数据。晶体取向来自采集时的衍射指标化过程,必须使用采集软件导出的、已指标化的取向图文件(.ang / .ctf / .h5 等)。

2. 适用场景

本插件面向材料科学中的晶体取向与织构(texture)分析,典型用途包括:

• 金属、合金等材料的晶粒取向可视化,生成标准的 IPF 取向图。
• 地质矿物等多相样品的相分布与取向分析。
• 把 EBSD 取向图与同一样品的三维结构(如 CT 体数据)在 Dragonfly 中联合分析、逐层对照。
• 将连续切片的 EBSD 取向图堆叠为三维体,观察取向沿深度方向的演变。

把 EBSD 结果发布回 Dragonfly 后,即可利用 Dragonfly 的多模态可视化能力,将取向、相、质量等信息与其它成像模态叠加比较。

3. 安装与启用

本插件随 Prototype Labs & Apps 完整安装包(Full Package) 一并分发。安装步骤如下:

1. 将安装包解压到任意较短路径的目录(例如 C:\PL\,避免过深的下载目录或 OneDrive 重定向的桌面,以规避 Windows 260 字符路径上限)。

2. 双击运行 Install_FullPackage.bat。

3. 在弹出的对话框中选择核心安装模式:Fresh(全新安装,先备份再重置 blocks/recipes)或 Compatible(兼容安装,保留你自己的 block 和 recipe)。该选项只影响 Prototype Labs 核心,不影响任何插件的环境与设置。

4. 在 Prototype Apps 列表中勾选 “EBSD Analysis (orix)...”。注意:默认情况下所有插件均为未勾选状态,需要手动勾选才会部署。可用 Select All / Select None 一键全选或全不选。

5. 点击 Install,等待控制台完成。

6. 完全退出并重启 Dragonfly(菜单只在启动时扫描)。

重启后,菜单项出现在:Prototype Apps ▸ EBSD Analysis (orix)...(位于 “EBSD & Crystallography” 分组中)。点击即可打开一个可停靠的面板。

以后修改勾选: 最方便的方式是在 Dragonfly 内打开 Developer ▸ Prototype Labs... ▸ Menu Item Manager,底部的 “Prototype Apps (Full Package)” 列表中每个应用一个勾选框:勾选=部署,取消=移除菜单项,重启 Dragonfly 生效。停用从不删除插件已搭好的环境,重新启用立即可用。

卸载: 双击 Uninstall_FullPackage.bat,它会移除所有 Full Package 的菜单项与插件;保留已搭建的插件环境(venv),并在结束时列出其路径,方便你按需手动删除。

4. 运行环境与首次配置

重型环境不在安装时下载。 插件在首次使用时才构建自己的运行环境。打开面板后,在 “Environment (orix venv)” 区域点击 Setup Environment 按钮:

• 它做什么: 构建一个独立的小型 Python 虚拟环境(venv),并从 PyPI 安装 orix + numpy + matplotlib。
• 用哪个 Python: 默认使用 Dragonfly 自带的 Python(其内置完整的 CPython 3.10,自带 venv 与 pip),因此无需单独安装 Python。
• 下载体积与耗时: 依赖为 CPython 3.10 上的纯 wheel 包,约数十 MB,耗时约一分钟。
• 是否联网: 需要联网一次(从 PyPI 下载)。之后离线可用。
• 是否需要 GPU / WSL / 外部软件: 都不需要。无需 GPU,无需 WSL,无需安装其它外部软件。

环境安装到哪里: venv 建立在已安装插件代码目录内的 venv 子文件夹中,即 %LOCALAPPDATA%\comet\<Dragonfly版本>\pythonUserExtensions\GenericMenuItems\OrixEBSD\venv。不会向 Dragonfly 自带的 Python 中安装任何东西。

失败时的替代方案: 面板提供了一个 Base Python 输入框(“Environment (orix venv)” 区域)。留空表示使用当前 Dragonfly 的 Python;也可以填入任意一个 CPython 3.10 及以上(自带 venv 与 pip)的解释器完整路径(例如 C:\Python312\python.exe)作为构建 venv 的基础。若默认 Python 缺少 venv 模块或 orix/numpy 缺少对应平台的 wheel,可用此字段指向一个 3.10–3.12 的 CPython 后重试。

orix 为 GPL-3.0,构建出的这套独立环境是让它以子进程方式与 Dragonfly “保持一臂之距” 的关键——orix 永远不会被导入到 Dragonfly 主进程中。

5. 界面说明

面板顶部标题为 EBSD Analysis (orix),右侧带一个 “?” 帮助按钮(About)。面板上几乎每个功能旁都配有圆形的 “?” 帮助按钮,点击即弹出对应功能的说明窗口。以下按从上到下的分组逐一说明。

5.1 Input EBSD map(输入 EBSD 取向图)

• 2D (single map file) 单选按钮 —— 二维模式,只载入一张取向图文件(默认选中)。
• 3D (stack slice files) 单选按钮 —— 三维模式,按顺序添加多张连续切片文件堆叠成体数据(所有切片必须为相同的宽×高网格)。
• 文件列表 —— 显示当前已添加的文件名。
• Add file(s)... 按钮 —— 打开文件选择对话框添加取向图文件;二维模式下只保留所选的第一个文件,三维模式下追加所有所选文件。文件过滤器为 *.ang *.ctf *.h5 *.oh5 *.hdf5 *.dream3d。
• Clear 按钮 —— 清空文件列表。

5.2 Options(选项)

• IPF direction(下拉框)—— 选择 IPF 着色所用的样品参考方向,可选 Z (out of surface)(垂直样品表面,默认)、X、Y。
• In-plane spacing(数值框)—— 面内(单张切片内)的体素间距,即扫描步长;范围 0.0001–100000,4 位小数,默认 1.0。
• Slice spacing (3D)(数值框)—— 三维堆叠时相邻切片沿 Z 的间距(切片厚度);范围 0.0001–100000,4 位小数,默认 1.0;仅在选中 3D 模式时可编辑,二维模式下禁用。

5.3 Publish channels(要发布的结果通道)

• IPF colour (R, G, B) 复选框 —— 发布 IPF 取向图的三个颜色分量(默认勾选)。
• Phase ID 复选框 —— 发布每像素的相 ID(整数,默认勾选)。
• Euler angles (phi1, Phi, phi2) 复选框 —— 发布 Bunge 欧拉角三通道(单位:度,默认不勾选)。
• Quality metrics (IQ / CI / Fit) 复选框 —— 发布文件中携带的指标化质量指标(默认勾选)。

5.4 Environment (orix venv)(环境)

• Base Python(输入框)—— 构建 venv 所用的基础 Python;留空=当前 Dragonfly 的 Python,或填入一个 CPython 3.10+ 解释器路径。
• Status(状态标签)—— 显示环境状态:Ready(已就绪)或 Not set up - click 'Setup Environment'.(尚未搭建)。旁边带 “?” 帮助按钮。

5.5 操作按钮与结果显示

• Setup Environment 按钮 —— 一次性构建 orix 运行环境(见第 4 章)。
• Compute + Publish 按钮 —— 运行计算并把选中的结果通道发布回 Dragonfly。
• IPF 预览区 —— 计算完成后显示第一张切片的 IPF 取向图图片。
• 统计信息栏 —— 显示取向图尺寸、相信息、IPF 方向与步长等摘要。
• 日志框 —— 显示搭建/计算过程的进度与信息(只读)。

6. 使用步骤

6.1 二维取向图分析

1. 在 Dragonfly 中打开 Prototype Apps ▸ EBSD Analysis (orix)...。

2. 首次使用先点击 Setup Environment 并等待状态变为 Ready(需联网一次)。

3. 确认输入模式为 2D (single map file)(默认)。

4. 点击 Add file(s)...,选择一张已指标化的取向图文件(.ang / .ctf / .h5 等)。

5. 在 Options 中选择 IPF direction(默认 Z),并按需设置 In-plane spacing(扫描步长)。

6. 在 Publish channels 中勾选想要的输出(IPF 颜色 / 相 ID / 质量指标默认已勾选;欧拉角按需勾选)。

7. 点击 Compute + Publish。计算完成后,面板显示 IPF 预览和统计信息,选中的结果通道被发布为 Dragonfly Channel。

6.2 三维切片堆叠分析

1. 切换到 3D (stack slice files) 模式。

2. 点击 Add file(s)...,按顺序添加每一张连续切片的取向图文件(所有切片必须是相同的宽×高网格)。

3. 设置 In-plane spacing(面内步长)与 Slice spacing (3D)(切片厚度,沿 Z 方向)。切片厚度需要你自己设定,EBSD 文件中不含该信息。

4. 勾选需要的输出通道。

5. 点击 Compute + Publish。各输出将作为三维体发布回 Dragonfly。IPF 预览仅显示第一张切片。

输入要求 → 操作 → 得到什么: 输入为采集软件导出的已指标化取向图;操作为选方向 / 选输出 / 计算;得到的是发布回 Dragonfly 的标量通道(IPF R/G/B、相 ID、欧拉角、质量指标)以及面板内的 IPF 预览图。

7. 参数说明

8. 输出结果

计算完成后,选中的结果按逐通道方式发布回 Dragonfly,命名前缀取自输入文件名。生成的对象为 Channel(标量通道):

• IPF R / G / B —— IPF 取向图的三个颜色分量,各为 0–255 的标量通道。可将三者一起当作 RGB 查看,也可单独查看。
• Phase ID —— 每像素被指标化为哪个晶体相(整数)。用分类型 LUT 着色即得相图。
• Euler phi1 / Phi / phi2 —— 描述每像素取向的 Bunge 欧拉角(单位:度)。
• Image Quality / Confidence Index / Fit —— 文件中携带的指标化质量指标(若存在)。

二维模式下每项发布为单层切片;三维模式下按你设定的切片间距发布为体数据。所有通道都按你设定的面内间距 / 切片间距对齐到网格。发布后可在 Dragonfly 的数据管理面板中看到这些新通道,并用视图、LUT 等工具进行可视化。

面板内另有 IPF 取向图预览(第一张切片)与 IPF 颜色键,以及一行统计摘要(取向图尺寸、相名称与点群、IPF 方向、步长)。

相 / 质量图目前作为标量通道发布(通过 LUT 着色),原生 MultiROI 导出为规划中的增强功能。

9. 常见问题与故障排除

问:菜单里找不到 “EBSD Analysis (orix)...”?

答:确认在完整安装包中勾选了该插件(默认所有插件未勾选),且安装后完全重启了 Dragonfly(菜单只在启动时扫描)。也可在 Developer ▸ Prototype Labs... ▸ Menu Item Manager 里确认勾选状态。

问:点击 Compute + Publish 提示环境未搭建?

答:请先点击 Setup Environment 并等待状态显示 Ready,再进行计算。日志框会给出提示 “environment not set up. Click 'Setup Environment' first.”。

问:Setup Environment 失败,提示 venv 创建失败或依赖安装失败?

答:通常是所选基础 Python 缺少 venv/pip,或该平台没有 orix/numpy 的对应 wheel。请在 Base Python 中填入一个自带 venv 与 pip 的 CPython 3.10–3.12 解释器路径后重试;同时确认能访问网络(需从 PyPI 下载一次)。

问:发布后的取向图看起来被镜像或旋转了?

答:EBSD 扫描轴与不同厂商约定(EDAX 与 Oxford)可能与 Dragonfly 的网格不同。若发布的图相对其它数据集看起来被镜像/旋转,可用 Dragonfly 自带的变换工具进行翻转/旋转对齐。

问:载入普通图像却没有取向结果?

答:普通灰度图像不是 EBSD 数据。必须使用采集软件导出的、已指标化的取向图文件(.ang / .ctf / .h5 等),其中已包含每个扫描点的晶体取向。

问:需要晶粒分割或 KAM 吗?

答:晶粒分割 / KAM 不是 orix 的职责。请改用 EBSD Grains (DefDAP) 插件完成这些分析。

10. 注意事项与已知限制

• 输入必须是已指标化的 EBSD 取向图文件;普通图像无法使用。
• 三维模式下所有切片必须为相同的宽×高网格;切片厚度(Slice spacing)需自行设定。
• 晶粒分割 / KAM 不在本插件范围——请使用 EBSD Grains (DefDAP) 插件。
• EBSD 扫描轴 / 厂商约定可能与 Dragonfly 网格不同;必要时用 Dragonfly 的变换工具校正方向。
• 相 / 质量图目前以标量通道形式发布(通过 LUT 着色);原生 MultiROI 导出为规划中功能。
• 本插件不需要 GPU;首次 Setup Environment 需联网一次。
• orix 采用 GPL-3.0,仅在独立 venv 的子进程中运行,不会被导入 Dragonfly 主进程。

11. 参考资料

• orix 官方文档:https://orix.readthedocs.io
• orix / pyxem 项目(GPL-3.0)。
• 配套插件:EBSD Grains (DefDAP)——用于晶粒分割与相分割。
• 完整安装包安装 / 启用 / 卸载说明:见 Full Package 的 README(随包提供)。

Part II English Manual

Contents

1. Overview

2. Use Cases

3. Installation & Enabling

4. Runtime Environment & First-Run Setup

5. User Interface

6. Step-by-Step Usage

7. Parameter Reference

8. Outputs

9. FAQ & Troubleshooting

10. Notes & Known Limitations

11. References

1. Overview

EBSD Analysis (orix) is a Dragonfly Prototype Apps plugin for analysing already-indexed Electron Backscatter Diffraction (EBSD) orientation data. EBSD measures the crystal orientation at every point of a scanned surface, producing a per-pixel orientation map. The plugin reads an orientation-map file exported by your acquisition software and turns it into images and Channels you can explore and compare inside Dragonfly.

From a loaded map, the plugin can produce an Inverse-Pole-Figure (IPF)-coloured orientation map, the Euler angles, the phase map, and any indexing-quality metrics carried in the file, each published back as a Dragonfly scalar Channel. The panel also shows an IPF map preview and a summary. Both 2D single maps and stacked 3D volumes (from serial-section slice files) are supported.

Underlying engine: the computation is performed by the open-source library orix 0.14.3 (the pyxem project), together with numpy and matplotlib. orix is licensed under GPL-3.0, so it runs only in a subprocess inside the plugin's own isolated Python environment (venv), exchanging data via files, and is never imported into the Dragonfly process — keeping it arm's-length. numpy is BSD-licensed; matplotlib is PSF/BSD-like.

A plain grayscale image is not EBSD data. Crystal orientations come from the diffraction indexing done at acquisition; you must use an already-indexed orientation-map file (.ang / .ctf / .h5, etc.).

2. Use Cases

The plugin targets crystal-orientation and texture analysis in materials science. Typical uses:

• Visualising grain orientations in metals and alloys as standard IPF orientation maps.
• Phase distribution and orientation analysis of multi-phase materials such as geological minerals.
• Jointly analysing an EBSD orientation map with the same sample's 3D structure (e.g. a CT volume) inside Dragonfly, slice by slice.
• Stacking serial-section EBSD maps into a 3D volume to observe how orientation evolves with depth.

Once EBSD results are published back into Dragonfly, you can use Dragonfly's multi-modal visualisation to overlay and compare orientation, phase and quality information with other imaging modalities.

3. Installation & Enabling

The plugin ships with the Prototype Labs & Apps Full Package. To install:

1. Unzip to any short path (e.g. C:\PL\) — avoid deep download folders or a OneDrive-redirected Desktop, to stay under the Windows 260-character path limit.

2. Double-click Install_FullPackage.bat.

3. In the dialog, choose the core install mode: Fresh (wipe & reset blocks/recipes after backing them up) or Compatible (keep your own blocks and recipes). This affects only the Prototype Labs core, never a plugin's environment or settings.

4. In the Prototype Apps list, tick "EBSD Analysis (orix)...". Note: all plugins are unticked by default and must be ticked to be deployed. Use Select All / Select None as needed.

5. Click Install and wait for the console to finish.

6. Fully quit and restart Dragonfly (menus are scanned only at startup).

After restarting, the menu entry appears under Prototype Apps ▸ EBSD Analysis (orix)... (in the "EBSD & Crystallography" group). Clicking it opens a dockable panel.

Changing your choices later: the easiest way is inside Dragonfly — open Developer ▸ Prototype Labs... ▸ Menu Item Manager; the "Prototype Apps (Full Package)" list at the bottom has a checkbox per app (tick = deploy, untick = remove the menu entry). Restart Dragonfly to apply. Disabling never deletes a plugin's environment; re-enabling is instant.

Uninstall: double-click Uninstall_FullPackage.bat. It removes all Full-Package menu items and plugins but keeps each plugin's built environment (venv), listing its path at the end so you can delete it manually if you want the disk space back.

4. Runtime Environment & First-Run Setup

Nothing heavy is downloaded at install time. The plugin builds its runtime environment on first use. Open the panel and, in the "Environment (orix venv)" section, click Setup Environment:

• What it does: builds a small isolated Python virtual environment (venv) and pip-installs orix + numpy + matplotlib from PyPI.
• Which Python: by default it uses Dragonfly's own Python (which bundles a full CPython 3.10 with working venv + pip), so you need no separate Python install.
• Download size & time: the dependencies are pure wheels on CPython 3.10, roughly tens of MB, about a minute.
• Internet: requires internet once (to download from PyPI); it then works offline.
• GPU / WSL / external apps: none required. No GPU, no WSL, no other external software.

Where it installs: the venv is created in a venv subfolder inside the installed plugin code directory, i.e. %LOCALAPPDATA%\comet\<Dragonfly version>\pythonUserExtensions\GenericMenuItems\OrixEBSD\venv. Nothing is installed into Dragonfly's own Python.

Fallback on failure: the panel provides a Base Python field (in "Environment (orix venv)"). Leave it blank to use the current Dragonfly's Python, or enter the full path to any CPython 3.10+ interpreter that has stdlib venv + pip (e.g. C:\Python312\python.exe) as the venv base. If the default Python lacks the venv module, or orix/numpy has no wheel for the platform, point this field at a 3.10–3.12 CPython and retry.

orix is GPL-3.0. Building this separate environment and running orix as a subprocess is what keeps it arm's-length from Dragonfly — orix is never imported into the Dragonfly process.

5. User Interface

The panel title is EBSD Analysis (orix) with an About "?" help button beside it. Almost every control has a round "?" help button that pops up an explanation window. Controls are described top to bottom below.

5.1 Input EBSD map

• 2D (single map file) radio — 2D mode, loads a single orientation-map file (selected by default).
• 3D (stack slice files) radio — 3D mode, add several serial-section files in order to stack into a volume (all slices must share the same width×height grid).
• File list — shows the currently added file names.
• Add file(s)... button — opens a file dialog to add orientation maps; in 2D mode only the first selected file is kept, in 3D mode all selected files are appended. File filter: *.ang *.ctf *.h5 *.oh5 *.hdf5 *.dream3d.
• Clear button — empties the file list.

5.2 Options

• IPF direction (dropdown) — the sample reference direction used for IPF colouring: Z (out of surface) (default), X, Y.
• In-plane spacing (spinbox) — in-plane voxel spacing (scan step); range 0.0001–100000, 4 decimals, default 1.0.
• Slice spacing (3D) (spinbox) — Z spacing between serial sections (section thickness); range 0.0001–100000, 4 decimals, default 1.0; editable only in 3D mode, disabled in 2D.

5.3 Publish channels

• IPF colour (R, G, B) checkbox — publishes the three colour components of the IPF map (checked by default).
• Phase ID checkbox — publishes the per-pixel phase ID (integer, checked by default).
• Euler angles (phi1, Phi, phi2) checkbox — publishes the three Bunge Euler-angle channels (degrees, unchecked by default).
• Quality metrics (IQ / CI / Fit) checkbox — publishes indexing-quality metrics carried in the file (checked by default).

5.4 Environment (orix venv)

• Base Python (line edit) — the base Python used to build the venv; blank = current Dragonfly's Python, or enter a CPython 3.10+ path.
• Status (label) — shows the environment state: Ready or Not set up - click 'Setup Environment'., with a "?" help button beside it.

5.5 Action buttons & result display

• Setup Environment button — one-time build of the orix environment (see Section 4).
• Compute + Publish button — runs the computation and publishes the selected result channels back into Dragonfly.
• IPF preview area — shows the IPF orientation map of the first slice after compute.
• Summary line — shows map size, phase info, IPF direction and step.
• Log box — shows setup/compute progress and messages (read-only).

6. Step-by-Step Usage

6.1 2D orientation-map analysis

1. In Dragonfly, open Prototype Apps ▸ EBSD Analysis (orix)....

2. On first use, click Setup Environment and wait until Status shows Ready (needs internet once).

3. Confirm the input mode is 2D (single map file) (default).

4. Click Add file(s)... and select an already-indexed orientation-map file (.ang / .ctf / .h5, etc.).

5. In Options, choose the IPF direction (default Z) and set In-plane spacing (scan step) as needed.

6. In Publish channels, tick the outputs you want (IPF colour / Phase ID / Quality are ticked by default; tick Euler angles if needed).

7. Click Compute + Publish. When done, the panel shows the IPF preview and summary, and the selected channels are published as Dragonfly Channels.

6.2 3D serial-section stacking

1. Switch to 3D (stack slice files) mode.

2. Click Add file(s)... and add each serial-section map file in order (all slices must share the same width×height grid).

3. Set In-plane spacing (in-plane step) and Slice spacing (3D) (section thickness along Z). The section thickness must be set by you — the EBSD files don't contain it.

4. Tick the output channels you want.

5. Click Compute + Publish. Each output is published back as a 3D volume; the IPF preview shows only the first slice.

Input requirement → action → result: the input is an already-indexed orientation map; the action is choosing the direction/outputs and computing; the result is a set of scalar Channels published back into Dragonfly (IPF R/G/B, Phase ID, Euler angles, quality metrics) plus the in-panel IPF preview.

7. Parameter Reference

8. Outputs

After compute, the selected results are published back into Dragonfly one Channel at a time, prefixed with the input file name. The produced objects are Channels (scalar):

• IPF R / G / B — the three colour components of the IPF map, each a 0–255 scalar Channel. View them together as RGB or individually.
• Phase ID — which crystal phase each pixel was indexed as (integer). Colour it with a categorical LUT to get a phase map.
• Euler phi1 / Phi / phi2 — the Bunge Euler angles (degrees) describing the orientation at each pixel.
• Image Quality / Confidence Index / Fit — indexing-quality metrics carried in the file (if present).

In 2D mode each item publishes as a single slice; in 3D mode it publishes as a volume using the slice spacing you set. All channels are aligned to the grid using your in-plane / slice spacing. Published channels appear in Dragonfly's data manager and can be visualised with views, LUTs and other tools.

The panel also shows an IPF map preview (first slice) and an IPF colour key, plus a one-line summary (map size, phase names and point groups, IPF direction, step).

Phase / quality maps are currently published as scalar Channels (coloured via LUT); native MultiROI export is a planned enhancement.

9. FAQ & Troubleshooting

Q: I can't find "EBSD Analysis (orix)..." in the menu.

A: Make sure you ticked the plugin in the Full Package (all plugins are unticked by default) and fully restarted Dragonfly (menus are scanned only at startup). You can also confirm the tick state in Developer ▸ Prototype Labs... ▸ Menu Item Manager.

Q: Compute + Publish says the environment isn't set up.

A: Click Setup Environment first and wait for Status to show Ready before computing. The log will say "environment not set up. Click 'Setup Environment' first."

Q: Setup Environment fails (venv creation or dependency install failed).

A: Usually the chosen base Python lacks venv/pip, or the platform has no wheel for orix/numpy. Enter the path to a CPython 3.10–3.12 interpreter that has stdlib venv + pip in the Base Python field and retry; also make sure you have internet access (a one-time PyPI download).

Q: The published map looks mirrored or rotated.

A: EBSD scan axes and vendor conventions (EDAX vs Oxford) may differ from Dragonfly's grid. If a published map looks mirrored/rotated relative to another dataset, flip/rotate it with Dragonfly's transform tools.

Q: I loaded a plain image but got no orientation results.

A: A plain grayscale image is not EBSD data. You must use an already-indexed orientation-map file (.ang / .ctf / .h5, etc.) that contains the crystal orientation at every scan point.

Q: Do I need grain segmentation or KAM?

A: Grain segmentation / KAM are not orix's job. Use the EBSD Grains (DefDAP) plugin for those.

10. Notes & Known Limitations

• The input must be an already-indexed EBSD orientation-map file; plain images cannot be used.
• In 3D mode all slices must share the same width×height grid; you must set the slice spacing (section thickness) yourself.
• Grain segmentation / KAM are out of scope — use the EBSD Grains (DefDAP) plugin.
• EBSD scan axes / vendor conventions may differ from Dragonfly's grid; correct orientation with Dragonfly's transform tools if needed.
• Phase / quality maps are currently published as scalar Channels (coloured via LUT); native MultiROI export is planned.
• The plugin needs no GPU; the first Setup Environment needs internet once.
• orix is GPL-3.0 and runs only in the isolated venv subprocess — never imported into the Dragonfly process.

11. References

• orix documentation: https://orix.readthedocs.io
• orix / pyxem project (GPL-3.0).
• Companion plugin: EBSD Grains (DefDAP) — for grain and phase segmentation.
• Full Package install / enable / uninstall instructions: see the Full Package README (shipped with the package).