From ddd3d76300dc19cc250f513ac700dc66c573db07 Mon Sep 17 00:00:00 2001
From: Nick Tustison <ntustison@gmail.com>
Date: Fri, 29 Mar 2024 14:07:14 -0700
Subject: [PATCH] COMP:  Issue with min/max not registering as
 ANTsRCore::min/max

---
 R/cerebellumMorphology.R          | 7 ++-----
 R/chexnet.R                       | 4 ++--
 R/deepFlash.R                     | 8 ++++----
 R/histogramWarpImageIntensities.R | 2 +-
 R/histology.R                     | 4 ++--
 R/hypothalamusSegmentation.R      | 2 +-
 R/mriModalityClassification.R     | 3 +--
 7 files changed, 13 insertions(+), 17 deletions(-)

diff --git a/R/cerebellumMorphology.R b/R/cerebellumMorphology.R
index 3ab7ff87..51dd47b1 100644
--- a/R/cerebellumMorphology.R
+++ b/R/cerebellumMorphology.R
@@ -89,8 +89,7 @@ cerebellumMorphology <- function( t1, cerebellumMask = NULL,
   t1TemplateBrainMask <- antsImageRead( getANTsXNetData( "magetTemplateBrainMask" ) )
   t1TemplateBrain <- t1Template * t1TemplateBrainMask
   t1CerebellumTemplate <- antsImageRead( getANTsXNetData( "magetCerebellumTemplate" ) )
-  t1CerebellumTemplate <- ( ( t1CerebellumTemplate - min( t1CerebellumTemplate ) ) /
-                            ( max( t1CerebellumTemplate ) - min( t1CerebellumTemplate ) ) )
+  t1CerebellumTemplate <- iMath( t1CerebellumTemplate, "Normalize" )
   cerebellumxTemplateXfrm <- getANTsXNetData( "magetCerebellumxTemplate0GenericAffine" )
 
   # spatial priors are in the space of the cerebellar template.  First three are
@@ -262,9 +261,7 @@ cerebellumMorphology <- function( t1, cerebellumMask = NULL,
       t1PreprocessedInCerebellumSpace <- t1PreprocessedInCerebellumSpace * t1PreprocessedMaskInCerebellumSpace
       }
 
-    t1PreprocessedInCerebellumSpace <-
-       ( t1PreprocessedInCerebellumSpace - min( t1PreprocessedInCerebellumSpace ) ) /
-       ( max( t1PreprocessedInCerebellumSpace ) - min( t1PreprocessedInCerebellumSpace ) )
+    t1PreprocessedInCerebellumSpace <- iMath( t1PreprocessedInCerebellumSpace, "Normalize" )
 
     batchX <- array( data = 0, dim = c( 2, imageSize, channelSize ) )
     batchX[1,,,,1] <- as.array( padOrCropImageToSize( t1PreprocessedInCerebellumSpace, imageSize ) )
diff --git a/R/chexnet.R b/R/chexnet.R
index ae53aebc..43501cca 100644
--- a/R/chexnet.R
+++ b/R/chexnet.R
@@ -54,8 +54,8 @@ checkXrayLungOrientation <- function( image,
                                            antsxnetCacheDirectory = antsxnetCacheDirectory )
   model$load_weights( weightsFileName )
 
-  imageMin <- min( resampledImage )
-  imageMax <- max( resampledImage )
+  imageMin <- ANTsRCore::min( resampledImage )
+  imageMax <- ANTsRCore::max( resampledImage )
   normalizedImage <- antsImageClone( resampledImage )
   normalizedImage <- ( normalizedImage - imageMin ) / ( imageMax - imageMin )
 
diff --git a/R/deepFlash.R b/R/deepFlash.R
index 9c65216c..0a351bac 100644
--- a/R/deepFlash.R
+++ b/R/deepFlash.R
@@ -191,12 +191,12 @@ deepFlash <- function( t1, t2 = NULL, doPreprocessing = TRUE,
   direction <- antsGetDirection( tmpCropped )
 
   t1TemplateRoiLeft <- cropIndices( t1Template, lowerBoundLeft, upperBoundLeft )
-  t1TemplateRoiLeft <- ( t1TemplateRoiLeft - min( t1TemplateRoiLeft ) ) / ( max( t1TemplateRoiLeft ) - min( t1TemplateRoiLeft ) ) * 2.0 - 1.0
+  t1TemplateRoiLeft <- iMath( t1TemplateRoiLeft, "Normalize" ) * 2.0 - 1.0
   t2TemplateRoiLeft <- NULL
   if( ! is.null( t2Template ) )
     {
     t2TemplateRoiLeft <- cropIndices( t2Template, lowerBoundLeft, upperBoundLeft )
-    t1TemplateRoiLeft <- ( t2TemplateRoiLeft - min( t2TemplateRoiLeft ) ) / ( max( t2TemplateRoiLeft ) - min( t2TemplateRoiLeft ) ) * 2.0 - 1.0
+    t2TemplateRoiLeft <- iMath( t2TemplateRoiLeft, "Normalize" ) * 2.0 - 1.0
     }
 
   labelsRight <- labels[seq.int( 3, length( labels ), by = 2)]
@@ -209,12 +209,12 @@ deepFlash <- function( t1, t2 = NULL, doPreprocessing = TRUE,
   originRight <- antsGetOrigin( tmpCropped )
 
   t1TemplateRoiRight <- cropIndices( t1Template, lowerBoundRight, upperBoundRight )
-  t1TemplateRoiRight <- ( t1TemplateRoiRight - min( t1TemplateRoiRight ) ) / ( max( t1TemplateRoiRight ) - min( t1TemplateRoiRight ) ) * 2.0 - 1.0
+  t1TemplateRoiRight <- iMath( t1TemplateRoiRight, "Normalize" ) * 2.0 - 1.0
   t2TemplateRoiRight <- NULL
   if( ! is.null( t2Template ) )
     {
     t2TemplateRoiRight <- cropIndices( t2Template, lowerBoundRight, upperBoundRight )
-    t2TemplateRoiRight <- ( t2TemplateRoiRight - min( t2TemplateRoiRight ) ) / ( max( t2TemplateRoiRight ) - min( t2TemplateRoiRight ) ) * 2.0 - 1.0
+    t2TemplateRoiRight <- iMath( t2TemplateRoiRight, "Normalize" ) * 2.0 - 1.0
     }
 
   ################################
diff --git a/R/histogramWarpImageIntensities.R b/R/histogramWarpImageIntensities.R
index 348643c1..8e5cf44a 100644
--- a/R/histogramWarpImageIntensities.R
+++ b/R/histogramWarpImageIntensities.R
@@ -111,7 +111,7 @@ histogramWarpImageIntensities <- function( image,
     transformedArray[indices] <- intensities + xfrm
     }
   transformedImage <- as.antsImage( transformedArray, reference = image ) *
-    ( max( image ) - min( image ) ) + min( image )
+    ( ANTsRCore::max( image ) - ANTsRCore::min( image ) ) + ANTsRCore::min( image )
 
   return( transformedImage )
   }
diff --git a/R/histology.R b/R/histology.R
index a1c3a849..8c3f8d12 100644
--- a/R/histology.R
+++ b/R/histology.R
@@ -178,7 +178,7 @@ allenEx5BrainExtraction <- function( image, view = c( "coronal", "sagittal" ),
         } else {
         slice <- imageChannels[[i]]
         }
-      if( max( slice ) > min( slice ) )
+      if( ANTsRCore::max( slice ) > ANTsRCore::min( slice ) )
         {
         sliceResampled <- resampleImage( slice, resampledImageSize, useVoxels = TRUE, interpType = 0 )
         sliceArray <- as.array( sliceResampled )
@@ -347,7 +347,7 @@ allenHistologyBrainMask <- function( image,
         } else {
         slice <- imageChannels[[i]]
         }
-      if( max( slice ) > min( slice ) )
+      if( ANTsRCore::max( slice ) > ANTsRCore::min( slice ) )
         {
         sliceResampled <- resampleImage( slice, resampledImageSize, useVoxels = TRUE, interpType = 0 )
         sliceArray <- as.array( sliceResampled )
diff --git a/R/hypothalamusSegmentation.R b/R/hypothalamusSegmentation.R
index 858b42ce..1308cb36 100644
--- a/R/hypothalamusSegmentation.R
+++ b/R/hypothalamusSegmentation.R
@@ -89,7 +89,7 @@ hypothalamusSegmentation <- function( t1,
   #
   ################################
 
-  t1Warped <- ( t1Warped - min( t1Warped ) ) / ( max( t1Warped ) - min( t1Warped ) )
+  t1Warped <- iMath( t1Warped, "Normalize" )
 
   ################################
   #
diff --git a/R/mriModalityClassification.R b/R/mriModalityClassification.R
index da9b45b6..8d8d02ad 100644
--- a/R/mriModalityClassification.R
+++ b/R/mriModalityClassification.R
@@ -60,8 +60,7 @@ mriModalityClassification <- function( image,
     center = centerOfMassTemplate,
     translation = centerOfMassImage - centerOfMassTemplate )
   image <- applyAntsrTransformToImage( xfrm, image, template )
-
-  image <- ( image - min( image ) ) / ( max( image ) - min( image ) )
+  image <- iMath( image, "Normalize" )
 
   ################################
   #