Additional replacements of ImageJ with Fiji meant to be included in l…

…ast commit
LieberInstitute · Jul 23, 2024 · a9b1dda · a9b1dda
1 parent 482170b
commit a9b1dda
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/tests/testthat/test-prep_fiji_image.R b/tests/testthat/test-prep_fiji_image.R
@@ -1,5 +1,5 @@
 test_that(
-    "prep_imagej_image",
+    "prep_fiji_image",
     {
         ########################################################################
         #   Prepare sample_info
@@ -16,20 +16,20 @@ test_that(
             sr_dir, sample_info$capture_area, "outs", "spatial"
         )
 
-        #   Add ImageJ-output-related columns
-        imagej_dir <- tempdir()
-        temp <- unzip(fetch_data("visiumStitched_brain_ImageJ_out"), exdir = imagej_dir)
-        sample_info$imagej_xml_path <- temp[grep("xml$", temp)]
-        sample_info$imagej_image_path <- temp[grep("png$", temp)]
+        #   Add Fiji-output-related columns
+        fiji_dir <- tempdir()
+        temp <- unzip(fetch_data("visiumStitched_brain_Fiji_out"), exdir = fiji_dir)
+        sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
+        sample_info$fiji_image_path <- temp[grep("png$", temp)]
 
-        sample_info <- rescale_imagej_inputs(sample_info, out_dir = tempdir())
+        sample_info <- rescale_fiji_inputs(sample_info, out_dir = tempdir())
 
         ########################################################################
         #   Tests
         ########################################################################
 
         spe_input_dir <- tempdir()
-        prep_imagej_image(
+        prep_fiji_image(
             sample_info,
             out_dir = spe_input_dir, lowres_max_size = 900
         )

diff --git a/tests/testthat/test-rescale_fiji_inputs.R b/tests/testthat/test-rescale_fiji_inputs.R
@@ -1,5 +1,5 @@
 test_that(
-    "rescale_imagej_inputs",
+    "rescale_fiji_inputs",
     {
         ########################################################################
         #   Prepare sample_info
@@ -20,7 +20,7 @@ test_that(
         #   Tests
         ########################################################################
 
-        sample_info_new <- rescale_imagej_inputs(
+        sample_info_new <- rescale_fiji_inputs(
             sample_info,
             out_dir = tempdir()
         )