Welcome to file-tree’s documentation!

This is the documentation for file-tree, a project designed to allow you to separate the directory structure of your pipeline inputs/outputs from the actual pipeline code.

Install using

conda/pip install file-tree file-tree-fsl

Include the file-tree-fsl package if you want to use filetree definitions for the FSL tools. If you want to use the terminal-based user interface, you will also need to install textual. You can install this using conda/pip install textual.

The pipeline results can be visualised efficiently in FSLeyes as described in https://open.win.ox.ac.uk/pages/fsl/fsleyes/fsleyes/userdoc/filetree.html .

Please report any bugs/issues/feature requests using the gitlab interface (https://git.fmrib.ox.ac.uk/fsl/file-tree/-/issues).

• FileTree tutorial
  • Introduction
  • FileTree interactivity
  • FileTree indendation
  • Template keys
  • Placeholders
    • Placeholder types
    • Placeholder iteration
    • Setting placeholder values
    • Linked placholder values
  • Optional Placeholders
  • Wildcards
  • Sub-trees
  • Including external files
  • Updating templates
  • Writing filetrees
  • Example neuroimaging pipeline
    • Changing directory structure
    • Output “basenames”
• Changes with respect to FileTree in fslpy
• file-tree package
  • file_tree.file_tree module
    • FileTree
    • convert()
  • file_tree.parse_tree module
    • add_line_to_tree()
    • check_forbidden_characters()
    • extra_tree_dirs()
    • get_parent()
    • list_all_trees()
    • read_file_tree_text()
    • read_line()
    • read_subtree_line()
    • scan_plugins()
    • search_tree()
  • file_tree.template module
    • DuplicateTemplate
    • Literal
    • MyDataArray
    • OptionalPart
    • Part
    • Placeholders
    • Required
    • Template
    • TemplateParts
    • extract_placeholders()
    • is_glob_pattern()
    • is_singular()
    • pattern_match()