From 06885b4a171d40c6efad48610674a37f9d23a9fa Mon Sep 17 00:00:00 2001 From: alexanderbates Date: Wed, 10 Jul 2024 19:32:53 -0400 Subject: [PATCH] 'extdata' not 'exdata' --- DESCRIPTION | 9 +++++++-- {exdata => extdata}/brain_240707/0_manual_affine.txt | 0 {exdata => extdata}/brain_240707/1_elastix_affine.txt | 0 .../brain_240707/2_elastix_Bspline_coarse.txt | 0 .../brain_240707/3_elastix_Bspline_fine.txt | 0 {exdata => extdata}/brain_240707/BANC_to_template.txt | 0 {exdata => extdata}/brain_240707/template_to_BANC.txt | 0 man/banc_mirror.Rd | 4 ++-- man/banc_to_JRC2018F.Rd | 6 +++--- 9 files changed, 12 insertions(+), 7 deletions(-) rename {exdata => extdata}/brain_240707/0_manual_affine.txt (100%) rename {exdata => extdata}/brain_240707/1_elastix_affine.txt (100%) rename {exdata => extdata}/brain_240707/2_elastix_Bspline_coarse.txt (100%) rename {exdata => extdata}/brain_240707/3_elastix_Bspline_fine.txt (100%) rename {exdata => extdata}/brain_240707/BANC_to_template.txt (100%) rename {exdata => extdata}/brain_240707/template_to_BANC.txt (100%) diff --git a/DESCRIPTION b/DESCRIPTION index 03f92e4..b539481 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,11 +3,16 @@ Package: bancr Title: Support Access to the Brain And Nerve Cord (BANC) Dataset Version: 0.1.0 Authors@R: - person(given = "Alexnder", + c(person(given = "Alexnder", family = "Bates", role = c("aut", "cre"), email = "alexander.shakeel.bates@gmail.com", - comment = c(ORCID = "0000-0002-1195-0445")) + comment = c(ORCID = "0000-0002-1195-0445")), + person(given = "Gregory", + family = "Jefferis", + role = c("aut", "cre"), + email = "jefferis@gmail.com", + comment = c(ORCID = "0000-0002-0587-9355"))) Description: Access to the BANC 'righty' EM dataset, focussing on support for BANC autosegmentation. Organised as a wrapper around the fafbseg package. diff --git a/exdata/brain_240707/0_manual_affine.txt b/extdata/brain_240707/0_manual_affine.txt similarity index 100% rename from exdata/brain_240707/0_manual_affine.txt rename to extdata/brain_240707/0_manual_affine.txt diff --git a/exdata/brain_240707/1_elastix_affine.txt b/extdata/brain_240707/1_elastix_affine.txt similarity index 100% rename from exdata/brain_240707/1_elastix_affine.txt rename to extdata/brain_240707/1_elastix_affine.txt diff --git a/exdata/brain_240707/2_elastix_Bspline_coarse.txt b/extdata/brain_240707/2_elastix_Bspline_coarse.txt similarity index 100% rename from exdata/brain_240707/2_elastix_Bspline_coarse.txt rename to extdata/brain_240707/2_elastix_Bspline_coarse.txt diff --git a/exdata/brain_240707/3_elastix_Bspline_fine.txt b/extdata/brain_240707/3_elastix_Bspline_fine.txt similarity index 100% rename from exdata/brain_240707/3_elastix_Bspline_fine.txt rename to extdata/brain_240707/3_elastix_Bspline_fine.txt diff --git a/exdata/brain_240707/BANC_to_template.txt b/extdata/brain_240707/BANC_to_template.txt similarity index 100% rename from exdata/brain_240707/BANC_to_template.txt rename to extdata/brain_240707/BANC_to_template.txt diff --git a/exdata/brain_240707/template_to_BANC.txt b/extdata/brain_240707/template_to_BANC.txt similarity index 100% rename from exdata/brain_240707/template_to_BANC.txt rename to extdata/brain_240707/template_to_BANC.txt diff --git a/man/banc_mirror.Rd b/man/banc_mirror.Rd index edfbfc5..fe4a0b0 100644 --- a/man/banc_mirror.Rd +++ b/man/banc_mirror.Rd @@ -6,7 +6,7 @@ \usage{ banc_mirror( x, - banc.units = c("nm", "microns", "raw"), + banc.units = c("nm", "um", "raw"), subset = NULL, inverse = FALSE, transform_files = NULL, @@ -18,7 +18,7 @@ banc_mirror( \item{x}{An object containing 3D points (must be compatible with nat::xyzmatrix).} \item{banc.units}{Character string specifying the banc.units of the input points. -Must be one of "nm" (nanometers), "microns", or "raw" (BANC raw banc.units). Default is "nm".} +Must be one of "nm" (nanometers), "um", or "raw" (BANC raw banc.units). Default is "nm".} \item{subset}{Optional. A logical vector or expression to subset the input object.} diff --git a/man/banc_to_JRC2018F.Rd b/man/banc_to_JRC2018F.Rd index 0c1a20d..bc3c160 100644 --- a/man/banc_to_JRC2018F.Rd +++ b/man/banc_to_JRC2018F.Rd @@ -6,7 +6,7 @@ \usage{ banc_to_JRC2018F( x, - banc.units = c("nm", "microns", "raw"), + banc.units = c("nm", "um", "raw"), subset = NULL, inverse = FALSE, transform_file = NULL, @@ -17,7 +17,7 @@ banc_to_JRC2018F( \item{x}{An object containing 3D points (must be compatible with nat::xyzmatrix).} \item{banc.units}{Character string specifying the units of the BANC space data (input or output, depending on the inverse argument). -Must be one of "nm" (nanometers), "microns", or "raw" (BANC raw banc.units). Default is "nm".} +Must be one of "nm" (nanometers), "um", or "raw" (BANC raw banc.units). Default is "nm".} \item{subset}{Optional. A logical vector or expression to subset the input object.} @@ -49,7 +49,7 @@ The default transformation files are included with the package and are located i transformed_points <- banc_to_JRC2018F(points, banc.units = "nm") # Perform inverse transformation (JRC2018F to BANC) -inverse_transformed_points <- banc_to_JRC2018F(points, banc.units = "microns", inverse = TRUE) +inverse_transformed_points <- banc_to_JRC2018F(points, banc.units = "um", inverse = TRUE) # Use a custom transform file custom_transformed <- banc_to_JRC2018F(points, transform_file = "path/to/custom/transform.txt")