Rename io::aux to io::output

AUX is a reserved device name on Windows, so src/io/aux.rs could not be
checked out there.

Author: mattcieslak

src/bin/cs-dti.rs

@@ -14,7 +14,7 @@ use anyhow::{Context, Result};
 use clap::Parser;
 
 use cs_dmri::dti::{DtiFitConfig, RestoreConfig, fit_volume_restore_reporting};
-use cs_dmri::io::aux::{sibling_path, write_3d_f32, write_3d_u8, write_3d_u32_as_f32, write_4d_f32};
+use cs_dmri::io::output::{sibling_path, write_3d_f32, write_3d_u8, write_3d_u32_as_f32, write_4d_f32};
 use cs_dmri::io::dwi::load_dwi;
 use cs_dmri::qspace::{BvecFrame, TORTOISE_DEFAULT_GMAX};
 use cs_dmri::{

src/bin/cs-fit.rs

@@ -11,7 +11,7 @@ use cs_dmri::fit::{
     ShoreFitSpec, ShoreRegularization, build_alpha_strategy, fit_shore, mean_in_mask,
     rmse_from_residual_l2, sparsity_map,
 };
-use cs_dmri::io::aux::{ensure_nifti_extension, precheck_writable, sibling_path, write_3d_f32};
+use cs_dmri::io::output::{ensure_nifti_extension, precheck_writable, sibling_path, write_3d_f32};
 use cs_dmri::io::coeffs::{CoefficientsFile, SidecarMetadata};
 use cs_dmri::io::dwi::load_dwi;
 use cs_dmri::qspace::{BvecFrame, TORTOISE_DEFAULT_GMAX};

src/bin/cs-mtnorm.rs

@@ -14,7 +14,7 @@ use clap::Parser;
 use ndarray::{Array3, Array4};
 use nifti::{IntoNdArray, NiftiObject, ReaderOptions};
 
-use cs_dmri::io::aux::{sibling_path, write_3d_f32, write_4d_f32};
+use cs_dmri::io::output::{sibling_path, write_3d_f32, write_4d_f32};
 use cs_dmri::multitissue::mtnormalise::{
     MtnormaliseConfig, mtnormalise, target_sum_mrtrix_default,
 };

src/bin/cs-response.rs

@@ -18,7 +18,7 @@ use anyhow::{Context, Result};
 use clap::Parser;
 
 use cs_dmri::dti::{DtiFitConfig, RestoreConfig, fit_volume_restore_reporting};
-use cs_dmri::io::aux::{write_3d_u8};
+use cs_dmri::io::output::{write_3d_u8};
 use cs_dmri::io::dwi::load_dwi;
 use cs_dmri::multitissue::response_estimation::{
     DhollanderConfig, DhollanderSelectConfig, estimate_responses, write_response_txt,

src/bin/cs-ss3t-full.rs

@@ -22,7 +22,7 @@ use anyhow::{Context, Result};
 use clap::Parser;
 
 use cs_dmri::dti::RestoreConfig;
-use cs_dmri::io::aux::{sibling_path, write_3d_f32, write_3d_u32_as_f32, write_3d_u8, write_4d_f32};
+use cs_dmri::io::output::{sibling_path, write_3d_f32, write_3d_u32_as_f32, write_3d_u8, write_4d_f32};
 use cs_dmri::io::dwi::load_dwi;
 use cs_dmri::multitissue::mtnormalise::{MtnormaliseConfig, target_sum_mrtrix_default};
 use cs_dmri::multitissue::pipeline::{

src/bin/cs-ss3t.rs

@@ -22,7 +22,7 @@ enum LmaxWmStrategyFlag {
     PathBic,
 }
 
-use cs_dmri::io::aux::{sibling_path, write_3d_f32, write_3d_u8, write_3d_u32_as_f32, write_4d_f32};
+use cs_dmri::io::output::{sibling_path, write_3d_f32, write_3d_u8, write_3d_u32_as_f32, write_4d_f32};
 use cs_dmri::io::dwi::load_dwi;
 use cs_dmri::multitissue::sidecar::{
     NCoefficients, ResponseProvenance, Ss3tSidecar, Ss3tSolverParams,

src/io/microstructure.rs

@@ -484,7 +484,7 @@ pub fn write_microstructure_nifti_siblings(
             volume[(i, j, k)] = values[v];
         }
         let out_nii = scalar_sibling_path(output_path, name);
-        crate::io::aux::write_3d_f32_with_affine(&out_nii, affine, &volume, overwrite)
+        crate::io::output::write_3d_f32_with_affine(&out_nii, affine, &volume, overwrite)
             .map_err(|e| anyhow!("write {:?}: {e}", out_nii))?;
         if !quiet {
             eprintln!("[microstructure] wrote {}", out_nii.display());

src/io/mod.rs

@@ -1,5 +1,5 @@
 // SPDX-License-Identifier: MIT OR Apache-2.0
-pub mod aux;
+pub mod output;
 pub mod coeffs;
 pub mod dwi;
 pub mod microstructure;