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Python API Reference

Public API

Primary user-facing entry point:

  • cvnpy.lookup(...) in /Users/iancharest/Documents/codex/cvncode/cvnpy/src/cvnpy/api.py

This is a thin wrapper around:

  • cvnpy.core.lookup_images.lookup_images(...)

lookup_images Signature

lookup_images(
    subject,
    vals,
    hemi,
    view_az_el_tilt,
    lookup=None,
    **kwargs,
)

Returns:

(mapped, lookup, rgb, options)
  • mapped: image-space scalar map (NaN where invalid/outside)
  • lookup: lookup dictionary used/generated
  • rgb: rendered RGB image
  • options: resolved option dictionary

Key kwargs

Geometry / viewpoint:

  • surftype (sphere, inflated, full.flat.patch.3d, etc.)
  • surfsuffix
  • xyextent
  • imageres

Color / mapping:

  • cmap (default cmapsign4)
  • clim
  • rgbnan
  • background, bg_cmap, bg_clim

Overlay / threshold:

  • threshold
  • absthreshold
  • overlayrange
  • overlayalpha

ROI:

  • roimask
  • roicolor
  • roiwidth

Caching:

  • savelookup
  • reset
  • cache_dir

Flatmap controls:

  • flat_apply_support_mask
  • flat_support_ratio
  • trim_extrapolation_px
  • flat_filter_sparse_vertices
  • flat_sparse_vertex_quantile
  • flat_sparse_vertex_factor
  • flat_edge_trim_steps
  • flat_margin_frac
  • flat_fill_small_holes_px

Minimal API Example

import numpy as np
from cvnpy import lookup

vals = np.random.randn(10000)
mapped, lk, rgb, opts = lookup(
    subject="fsaverage",
    vals=vals,
    hemi="lh",
    view=[0, 0, 0],
    surftype="full.flat.patch.3d",
    cmap="cmapsign4",
    cache_dir="/tmp/cvnpy_cache",
)

Viewpoint Helper

Use /Users/iancharest/Documents/codex/cvncode/cvnpy/src/cvnpy/view/viewpoints.py:

from cvnpy.view.viewpoints import lookup_viewpoint

view, flip, viewhemi = lookup_viewpoint("fsaverage", "lh", "occip", "inflated")

IO Helpers

Surface loading:

  • cvnpy.io.surfaces.read_surface(...)

Metric loading:

  • cvnpy.io.metrics.read_surface_metric(...)