params <-
list(family = "red", preset = "homage")

## ----setup, include=FALSE-----------------------------------------------------
if (requireNamespace("ggplot2", quietly = TRUE) && requireNamespace("albersdown", quietly = TRUE)) ggplot2::theme_set(albersdown::theme_albers(family = params$family, preset = params$preset))
if (requireNamespace("ggplot2", quietly = TRUE)) ggplot2::theme_set(neuroim2::theme_neuro(base_family = params$family))
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(neuroim2)
set.seed(123)

## ----basic-creation-----------------------------------------------------------
# Create a simple 3D space with mask
space <- NeuroSpace(c(10, 10, 10), spacing = c(2, 2, 2))
mask_data <- array(TRUE, c(10, 10, 10))
mask_data[1:3, 1:3, 1:3] <- FALSE  # exclude corner
mask <- LogicalNeuroVol(mask_data, space)

# Create cluster assignments (e.g., 5 random clusters)
n_masked <- sum(mask_data)
cluster_ids <- sample(1:5, n_masked, replace = TRUE)
cvol <- ClusteredNeuroVol(mask, cluster_ids)

# Create synthetic 4D data
vec_space <- NeuroSpace(c(10, 10, 10, 20), spacing = c(2, 2, 2))
vec_data <- array(rnorm(10 * 10 * 10 * 20), dim = c(10, 10, 10, 20))
vec <- NeuroVec(vec_data, vec_space)

# Create ClusteredNeuroVec
cv <- ClusteredNeuroVec(vec, cvol)
print(cv)

## ----properties---------------------------------------------------------------
# Dimensions: still 4D (x, y, z, time)
dim(cv)

# Number of clusters
num_clusters(cv)

# Access cluster time-series matrix (T x K)
ts_matrix <- as.matrix(cv, by = "cluster")
dim(ts_matrix)  # 20 time points x 5 clusters

## ----array-access-------------------------------------------------------------
# Extract 3D volume at time point 1
vol_t1 <- cv[,,,1]
dim(vol_t1)  # 10 x 10 x 10

# All voxels in the same cluster have the same value
# (they share the cluster's mean time-series)

# Get time-series at a specific voxel
ts <- series(cv, 5, 5, 5)
length(ts)  # 20 time points

## ----searchlight--------------------------------------------------------------
# K-nearest neighbor searchlight (3 nearest clusters)
windows_knn <- cluster_searchlight_series(cv, k = 3)
length(windows_knn)  # One window per cluster

# Look at first window
win1 <- windows_knn[[1]]
dim(values(win1))  # 20 time points x 3 neighbors

# Radius-based searchlight (e.g., 15mm radius)
windows_radius <- cluster_searchlight_series(cv, radius = 15)

## ----real-world, eval=FALSE---------------------------------------------------
# # Load fMRI data
# fmri_data <- read_vec("subject01_task.nii.gz")
# 
# # Load Schaefer atlas (example with 400 parcels)
# atlas <- read_vol("Schaefer2018_400Parcels_7Networks.nii.gz")
# mask <- atlas > 0
# 
# # Create ClusteredNeuroVol from atlas
# cvol <- ClusteredNeuroVol(mask, as.integer(atlas[mask]))
# 
# # Create parcellated representation
# cv <- ClusteredNeuroVec(fmri_data, cvol)
# 
# # Now you have 400 time-series (one per parcel) instead of ~200,000 voxels
# parcels <- as.matrix(cv, by = "cluster")
# dim(parcels)  # T x 400
# 
# # Perform connectivity analysis at parcel level
# cor_matrix <- cor(parcels)
# dim(cor_matrix)  # 400 x 400

## ----integration--------------------------------------------------------------
# Use with split_reduce for custom aggregation
# (ClusteredNeuroVec already uses this internally)

# Scale time-series within each cluster
# (if scale_series is implemented for ClusteredNeuroVec)
# cv_scaled <- scale_series(cv, center = TRUE, scale = TRUE)

# Get cluster centroids for visualization
centers <- centroids(cv)
head(centers)  # x, y, z coordinates