Workflow
The overall workflow of processing an image with AFMSlicer is shown below.[^mermaid]
---
title: AFMSlicer
config:
theme: 'dark'
---
flowchart RL
LoadScan("`**topostats.io.LoadScan()**
Load the image from AFM file`")
Filter("`**topostats.filter.Filters()**
Filter and flatten the image`")
AFMSlicer("`**afmslicer.slice.Slice()**
Convert 2D numpy array to 3D numpy array of slices`")
MinMaxHeights("`Determine Min/Max Heights`")
SliceRanges("`Ranges for Slices given user Requested number`")
BinaryMask("`Binary Mask for values within range`")
subgraph Slicing
MinMaxHeights --> SliceRanges
SliceRanges --> BinaryMask
end
subgraph Filtering
end
subgraph master
LoadScan --> Filter
Filter --> AFMSlicer
end
%%style LoadScan fill:#f2e88c,stroke:#000000
%%style Filter fill:#9ddbd7,stroke:#000000
%%style AFMSlicer fill:#f4a666,stroke:#000000
[^mermaid]: If modifying this diagram it is recommended to copy and paste the existing code and adjust in the mermaid.live online tool.