From 6a0c1d84ccc8135f6e527aa04e77b37d80907624 Mon Sep 17 00:00:00 2001
From: Eric Trautman <trautmane@janelia.hhmi.org>
Date: Tue, 4 Apr 2023 09:42:59 -0400
Subject: [PATCH 1/2] remove maxDownsamplingLevel parameter

---
 run_scripts/multi-sem/wafer-52/72_spark_extract_face.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/run_scripts/multi-sem/wafer-52/72_spark_extract_face.sh b/run_scripts/multi-sem/wafer-52/72_spark_extract_face.sh
index 8a7c9b70..4fa174f7 100755
--- a/run_scripts/multi-sem/wafer-52/72_spark_extract_face.sh
+++ b/run_scripts/multi-sem/wafer-52/72_spark_extract_face.sh
@@ -51,7 +51,6 @@ ARGV="\
 --size=${SIZE} \
 --invert \
 --normalizeContrast \
---maxDownsamplingLevel 5
 --blockSize=1024,1024"
 
 CLASS="org.janelia.saalfeldlab.hotknife.SparkGenerateFaceScaleSpace"

From a2a63c6cac8d2d812507df43da6539c99d6aee56 Mon Sep 17 00:00:00 2001
From: Eric Trautman <trautmane@janelia.hhmi.org>
Date: Tue, 4 Apr 2023 14:57:04 -0400
Subject: [PATCH 2/2] update scripts for today's pass12

---
 run_scripts/multi-sem/wafer-52/81_view_aligned_slab_series.sh | 2 +-
 .../multi-sem/wafer-52/91_export_aligned_slab_series_batch.sh | 4 ++--
 run_scripts/multi-sem/wafer-52/99_spark_downsample_final.sh   | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/run_scripts/multi-sem/wafer-52/81_view_aligned_slab_series.sh b/run_scripts/multi-sem/wafer-52/81_view_aligned_slab_series.sh
index c73ad8f6..768a6b50 100755
--- a/run_scripts/multi-sem/wafer-52/81_view_aligned_slab_series.sh
+++ b/run_scripts/multi-sem/wafer-52/81_view_aligned_slab_series.sh
@@ -39,7 +39,7 @@ JAR="${FLYEM_DATA_ROOT}/render/lib/hot-knife.latest-fat.jar"
 CLASS="org.janelia.saalfeldlab.hotknife.ViewAlignedSlabSeries"
 
 N5_PATH="/nrs/hess/render/export/hess.n5"
-TRANSFORM_GROUP="/surface-align/run_20230330_092301/pass12"
+TRANSFORM_GROUP="/surface-align/run_20230404_105038/pass12"
 
 
 ARGV="\
diff --git a/run_scripts/multi-sem/wafer-52/91_export_aligned_slab_series_batch.sh b/run_scripts/multi-sem/wafer-52/91_export_aligned_slab_series_batch.sh
index 09dc1951..2427a01e 100755
--- a/run_scripts/multi-sem/wafer-52/91_export_aligned_slab_series_batch.sh
+++ b/run_scripts/multi-sem/wafer-52/91_export_aligned_slab_series_batch.sh
@@ -30,8 +30,8 @@ export RUNTIME=${3:-4320} # default is minutes in 3 days
 # setup export parameters
 
 N5_PATH="/nrs/hess/render/export/hess.n5"
-TRANSFORM_GROUP="/surface-align/run_20230330_092301/pass12"
-DATA_SET_OUTPUT="/wafer-52-align/run_20230330_092301/pass12/s0"
+TRANSFORM_GROUP="/surface-align/run_20230404_105038/pass12"
+DATA_SET_OUTPUT="/wafer-52-align/run_20230404_105038/pass12/s0"
 
 ARGV="\
 --n5PathInput ${N5_PATH} \
diff --git a/run_scripts/multi-sem/wafer-52/99_spark_downsample_final.sh b/run_scripts/multi-sem/wafer-52/99_spark_downsample_final.sh
index c9c76019..e6c54c4d 100755
--- a/run_scripts/multi-sem/wafer-52/99_spark_downsample_final.sh
+++ b/run_scripts/multi-sem/wafer-52/99_spark_downsample_final.sh
@@ -15,7 +15,7 @@ source "${SCRIPT_DIR}/00_config.sh" "ALL"
 
 #export RUNTIME="3:59"
 
-INPUT_DATASET_ROOT="/wafer-52-align/run_20230330_092301/pass12"
+INPUT_DATASET_ROOT="/wafer-52-align/run_20230404_105038/pass12"
 
 OUTPUT_DATASET_PATHS="${INPUT_DATASET_ROOT}/s1"
 FACTORS="2,2,1"