---
title: Smoothing and filtering with neuroim2
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Smoothing and filtering with neuroim2}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, echo = FALSE, message = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
library(neuroim2)
```

This vignette gives a practical overview of the main spatial and
spatio‑temporal smoothing tools in neuroim2:

- 3D spatial filters on `NeuroVol`:
  - `gaussian_blur()` — isotropic Gaussian smoothing
  - `guided_filter()` — edge‑preserving smoothing
  - `bilateral_filter()` — intensity‑aware spatial smoothing
  - `laplace_enhance()` — multi‑scale detail enhancement
- 4D filters on `NeuroVec`:
  - `bilateral_filter_4d()` — joint spatial + temporal bilateral filter
  - `cgb_filter()` — correlation‑guided bilateral smoothing based on a
    graph

We’ll work with the demo volume used elsewhere in the package. All code
assumes this setup:

```{r}
set.seed(1)

demo_path <- system.file("extdata", "global_mask_v4.nii", package = "neuroim2")
vol3d <- read_vol(demo_path)          # 3D volume
vec4d <- read_vec(demo_path)          # 4D NeuroVec (same file)

sp3  <- space(vol3d)
dims <- dim(vol3d)
```

## 1. Gaussian smoothing with `gaussian_blur()`

`gaussian_blur()` applies an isotropic Gaussian kernel within an
optional mask. It is useful as a simple, fast baseline smoother.

- `sigma` (mm) controls how quickly weights decay with distance.
- `window` (voxels) sets the discrete kernel support (window = 1 →
  3×3×3).

```{r}
blur_light <- gaussian_blur(vol3d, vol3d, sigma = 2, window = 1)
blur_strong <- gaussian_blur(vol3d, vol3d, sigma = 4, window = 2)

dim(blur_light)
```

Use smaller `sigma` and `window` for gentle smoothing; larger values
blur more but can wash out small structures.

## 2. Edge‑preserving guided filter with `guided_filter()`

`guided_filter()` smooths while preserving edges by fitting local linear
models between the input and output.

- `radius` controls neighborhood size (in voxels).
- `epsilon` controls how strongly the filter smooths vs. preserves
  contrast.

```{r}
gf_vol <- guided_filter(vol3d, radius = 4, epsilon = 0.7^2)
gf_vol
```

Compared to Gaussian smoothing, guided filtering tends to retain sharp
boundaries between tissues while denoising within regions.

## 3. Bilateral spatial filter with `bilateral_filter()`

`bilateral_filter()` combines spatial distance and intensity similarity,
reducing noise while respecting edges.

```{r}
bf_vol <- bilateral_filter(
  vol3d,
  spatial_sigma   = 2,
  intensity_sigma = 1,
  window          = 1
)
bf_vol
```

Key parameters:

- `spatial_sigma`: spatial scale (in mm).
- `intensity_sigma`: intensity scale (relative to global σ\_I).
- `window`: discrete support (see `?bilateral_filter`).

Smaller `intensity_sigma` better preserves edges; larger values behave
more like pure Gaussian smoothing.

## 4. Laplacian enhancement with `laplace_enhance()`

`laplace_enhance()` is designed for *sharpening* rather than smoothing.
It uses a multi‑layer, non‑local Laplacian scheme to enhance details.

```{r}
sharp_vol <- laplace_enhance(vol3d, k = 2, patch_size = 3,
                             search_radius = 2, h = 0.7)
sharp_vol
```

Use higher `h` or more layers `k` for stronger enhancement, but be
cautious about amplifying noise.

## 5. 4D bilateral smoothing with `bilateral_filter_4d()`

For 4D time‑series data (`NeuroVec`), `bilateral_filter_4d()` extends
the bilateral idea across space and time:

- `spatial_sigma`, `spatial_window` — as above.
- `intensity_sigma` — intensity similarity.
- `temporal_sigma`, `temporal_window` — temporal smoothing scale.
- `temporal_spacing` — units of the time axis (e.g., TR in seconds).

```{r}
mask3d <- read_vol(system.file("extdata", "global_mask_v4.nii",
                               package = "neuroim2"))

bf4d <- bilateral_filter_4d(
  vec4d, mask3d,
  spatial_sigma   = 2,
  intensity_sigma = 1,
  temporal_sigma  = 1,
  spatial_window  = 1,
  temporal_window = 1,
  temporal_spacing = 1
)

dim(bf4d)
```

This is useful when you want joint spatial + temporal denoising that
still respects intensity boundaries (e.g. fMRI or 4D structural
sequences).

## 6. Correlation‑guided bilateral filtering with `cgb_filter()`

`cgb_filter()` implements correlation‑guided bilateral (CGB) smoothing:
it builds a sparse graph based on spatial distance and time‑series
correlations, then diffuses data over that graph.

Basic usage mirrors the bilateral interface:

```{r}
cgf <- cgb_filter(
  vec4d,
  mask          = mask3d,
  spatial_sigma = 3,
  window        = NULL,      # auto from spatial_sigma and spacing
  corr_map      = "power",
  corr_param    = 2,
  topk          = 16,
  passes        = 1,
  lambda        = 1
)

dim(cgf)
```

Parameter intuition:

- `spatial_sigma` / `window`: spatial kernel scale and support (similar
  to Gaussian/bilateral).
- `corr_map`, `corr_param`: map pooled correlations to affinities; see
  `?cgb_make_graph` for details.
- `topk`: max neighbors per voxel (sparsity vs. mixing).
- `passes`, `lambda`: diffusion strength (multiple passes or λ < 1
  increase/temper smoothing).

Internally this calls `cgb_make_graph()` to build the graph and then
`cgb_smooth()` to diffuse over it. Use `return_graph = TRUE` to keep the
graph for reuse.

```{r}
cg_out <- cgb_filter(vec4d, mask3d,
                     spatial_sigma = 3, window = NULL,
                     topk = 16, return_graph = TRUE)

str(cg_out$graph)
```

## Choosing a smoother

- Use `gaussian_blur()` for simple, fast baseline smoothing.
- Use `bilateral_filter()` / `bilateral_filter_4d()` when you want
  intensity‑aware, edge‑respecting smoothing.
- Use `guided_filter()` when you need edge preservation but want a
  simpler parameterization than full bilateral filters.
- Use `laplace_enhance()` when you want to *sharpen* structures rather
  than blur them.
- Use `cgb_filter()` when similarity should be driven by *correlation of
  time‑series* (e.g., fMRI connectivity‑style smoothing) rather than raw
  intensity alone.

