Workflow#
This section gives a broad overview of the workflow and how the different modules interact.
graph TB
subgraph Input
IF[Input Files]
IO["Input/Output Layer"]:::io
end
subgraph Configuration
CM["Configuration Management"]:::config
VL["Validation Layer"]:::validation
end
subgraph "Core Processing"
PL["Processing Layer"]:::processing
FM["Filtering Module"]:::filter
end
subgraph "Analysis Layer"
GA["Grain Analysis"]:::analysis
SM["Statistics Module"]:::analysis
subgraph "Tracing System"
TS["Tracing Subsystem"]:::tracing
OT["Ordered Tracing"]
DT["Disordered Tracing"]
NS["Node Statistics"]
SP["Splining"]
DC["DNA Curvature"]
end
end
subgraph "Measurement System"
GM["Geometry"]:::measure
CM2["Curvature"]:::measure
HP["Height Profiles"]:::measure
FA["Feret Analysis"]:::measure
end
subgraph "Visualization"
PS["Plotting System"]:::viz
TM["Theme Management"]:::viz
OUT["Output Generation"]
end
IF --> IO
IO --> PL
CM --> VL
VL --> PL
PL --> FM
FM --> GA
FM --> SM
GA --> TS
SM --> TS
TS --> OT
TS --> DT
OT --> NS
DT --> NS
NS --> SP
SP --> DC
GA --> GM
GA --> CM2
GA --> HP
GA --> FA
GM --> PS
CM2 --> PS
HP --> PS
FA --> PS
TS --> PS
PS --> TM
TM --> OUT
classDef io fill:#90EE90
classDef config fill:#A9A9A9
classDef processing fill:#87CEEB
classDef filter fill:#87CEEB
classDef analysis fill:#FFA500
classDef tracing fill:#FFA500
classDef measure fill:#DDA0DD
classDef viz fill:#9370DB
classDef validation fill:#A9A9A9
click IO "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/io.py"
click PL "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/processing.py"
click FM "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/filters.py"
click GA "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/grains.py"
click SM "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/statistics.py"
click TS "https://github.com/AFM-SPM/TopoStats/tree/main/topostats/tracing/"
click CM "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/default_config.yaml"
click VL "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/validation.py"
click GM "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/measure/geometry.py"
click CM2 "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/measure/curvature.py"
click HP "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/measure/height_profiles.py"
click FA "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/measure/feret.py"
click PS "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/plotting.py"
click TM "https://github.com/AFM-SPM/TopoStats/blob/main/topostats/theme.py"
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