From e93734fe55e6104465d8f6faf152086c5809516e Mon Sep 17 00:00:00 2001 From: Erhan Bas Date: Tue, 30 Oct 2018 12:52:35 -0400 Subject: [PATCH] wrapped into syglassrun function --- syglassrun-0-ch0.sh | 1 + syglassrun-1-ch0.sh | 10 + syglassrun-2-ch0.sh | 64 ++++ syglassrun-3-ch0.sh | 46 +++ syglassrun-4-ch0.sh | 307 ++++++++++++++++ syglassrun.m | 171 ++------- syglassrun.m~ | 78 ++++ .../.nfs00000002616463690000ad42 | 307 ++++++++++++++++ .../.nfs00000002636643230000ad43 | 346 ++++++++++++++++++ .../.nfs00000002651c3c940000ad41 | 46 +++ .../.nfs00000002651c3cbd0000ad5f | 147 ++++++++ tmpfiles/2018-07-02-raw_new/filelist-0.txt | 1 + tmpfiles/2018-07-02-raw_new/filelist-1.txt | 10 + tmpfiles/2018-07-02-raw_new/filelist-2.txt | 64 ++++ tmpfiles/2018-07-02-raw_new/filelist-3.txt | 279 ++++++++++++++ 15 files changed, 1743 insertions(+), 134 deletions(-) create mode 100644 syglassrun-0-ch0.sh create mode 100644 syglassrun-1-ch0.sh create mode 100644 syglassrun-2-ch0.sh create mode 100644 syglassrun-3-ch0.sh create mode 100644 syglassrun-4-ch0.sh create mode 100644 syglassrun.m~ create mode 100644 tmpfiles/2018-07-02-raw_new/.nfs00000002616463690000ad42 create mode 100644 tmpfiles/2018-07-02-raw_new/.nfs00000002636643230000ad43 create mode 100644 tmpfiles/2018-07-02-raw_new/.nfs00000002651c3c940000ad41 create mode 100644 tmpfiles/2018-07-02-raw_new/.nfs00000002651c3cbd0000ad5f create mode 100644 tmpfiles/2018-07-02-raw_new/filelist-0.txt create mode 100644 tmpfiles/2018-07-02-raw_new/filelist-1.txt create mode 100644 tmpfiles/2018-07-02-raw_new/filelist-2.txt create mode 100644 tmpfiles/2018-07-02-raw_new/filelist-3.txt diff --git a/syglassrun-0-ch0.sh b/syglassrun-0-ch0.sh new file mode 100644 index 0000000..b9b266e --- /dev/null +++ b/syglassrun-0-ch0.sh @@ -0,0 +1 @@ +bsub -n1 -We 1 -J t-0-00001 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py 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/nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/1/5/' +bsub -n1 -We 1 -J t-4-00039 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/1/6/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/1/6/' +bsub -n1 -We 1 -J t-4-00040 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/1/7/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/1/7/' +bsub -n1 -We 1 -J t-4-00041 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/1/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/1/8/' +bsub -n1 -We 1 -J t-4-00042 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/2/1/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/2/1/' +bsub -n1 -We 1 -J t-4-00043 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/2/2/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/2/2/' +bsub -n1 -We 1 -J t-4-00044 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/2/3/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/2/3/' +bsub -n1 -We 1 -J t-4-00045 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/2/4/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/2/4/' +bsub -n1 -We 1 -J t-4-00046 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/2/5/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/2/5/' +bsub -n1 -We 1 -J t-4-00047 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/2/6/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/2/6/' +bsub -n1 -We 1 -J t-4-00048 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/2/7/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/2/7/' +bsub -n1 -We 1 -J t-4-00049 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/2/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/2/8/' +bsub -n1 -We 1 -J t-4-00050 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/3/2/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/3/2/' +bsub -n1 -We 1 -J t-4-00051 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/3/4/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/3/4/' +bsub -n1 -We 1 -J t-4-00052 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/3/5/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/3/5/' +bsub -n1 -We 1 -J t-4-00053 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/3/6/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/3/6/' +bsub -n1 -We 1 -J t-4-00054 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/3/7/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/3/7/' +bsub -n1 -We 1 -J t-4-00055 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/3/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/3/8/' +bsub -n1 -We 1 -J t-4-00056 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/4/1/ 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/nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/8/2/' +bsub -n1 -We 1 -J t-4-00090 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/8/3/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/8/3/' +bsub -n1 -We 1 -J t-4-00091 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/8/4/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/8/4/' +bsub -n1 -We 1 -J t-4-00092 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/8/5/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/8/5/' +bsub -n1 -We 1 -J t-4-00093 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/8/6/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/8/6/' +bsub -n1 -We 1 -J t-4-00094 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/8/7/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/8/7/' +bsub -n1 -We 1 -J t-4-00095 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/4/8/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/4/8/8/' +bsub -n1 -We 1 -J t-4-00096 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/2/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/2/8/' +bsub -n1 -We 1 -J t-4-00097 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/3/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/3/8/' +bsub -n1 -We 1 -J t-4-00098 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/4/2/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/4/2/' +bsub -n1 -We 1 -J t-4-00099 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/4/3/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/4/3/' +bsub -n1 -We 1 -J t-4-00100 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/4/4/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/4/4/' +bsub -n1 -We 1 -J t-4-00101 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/4/5/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/4/5/' +bsub -n1 -We 1 -J t-4-00102 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/4/6/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/4/6/' +bsub -n1 -We 1 -J t-4-00103 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/4/7/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/4/7/' +bsub -n1 -We 1 -J t-4-00104 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/4/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/4/8/' +bsub -n1 -We 1 -J t-4-00105 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/6/4/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/6/4/' +bsub -n1 -We 1 -J t-4-00106 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/6/7/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/6/7/' +bsub -n1 -We 1 -J t-4-00107 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/6/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/6/8/' +bsub -n1 -We 1 -J t-4-00108 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/7/4/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/7/4/' +bsub -n1 -We 1 -J t-4-00109 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/7/6/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/5/7/6/' +bsub -n1 -We 1 -J t-4-00110 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/5/7/8/ 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/nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/7/4/7/' +bsub -n1 -We 1 -J t-4-00198 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/7/4/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/7/4/8/' +bsub -n1 -We 1 -J t-4-00199 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/7/5/1/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/7/5/1/' +bsub -n1 -We 1 -J t-4-00200 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/7/5/2/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/7/5/2/' +bsub -n1 -We 1 -J t-4-00201 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/7/5/3/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/7/5/3/' +bsub -n1 -We 1 -J t-4-00202 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/7/5/4/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/7/5/4/' +bsub -n1 -We 1 -J t-4-00203 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/7/5/5/ 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/nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/8/8/1/' +bsub -n1 -We 1 -J t-4-00288 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/8/8/2/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/8/8/2/' +bsub -n1 -We 1 -J t-4-00289 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/8/8/3/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/8/8/3/' +bsub -n1 -We 1 -J t-4-00290 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/8/8/4/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/8/8/4/' +bsub -n1 -We 1 -J t-4-00291 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/8/8/5/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/8/8/5/' +bsub -n1 -We 1 -J t-4-00292 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/8/8/6/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/8/8/6/' +bsub -n1 -We 1 -J t-4-00293 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/8/8/7/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/8/8/7/' +bsub -n1 -We 1 -J t-4-00294 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/8/8/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/1/8/8/8/' +bsub -n1 -We 1 -J t-4-00295 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/3/7/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/3/7/' +bsub -n1 -We 1 -J t-4-00296 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/3/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/3/8/' +bsub -n1 -We 1 -J t-4-00297 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/4/7/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/4/7/' +bsub -n1 -We 1 -J t-4-00298 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/4/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/4/8/' +bsub -n1 -We 1 -J t-4-00299 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/7/1/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/7/1/' +bsub -n1 -We 1 -J t-4-00300 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/7/3/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/7/3/' +bsub -n1 -We 1 -J t-4-00301 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/7/4/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/7/4/' +bsub -n1 -We 1 -J t-4-00302 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/7/5/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/7/5/' +bsub -n1 -We 1 -J t-4-00303 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/7/6/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/7/6/' +bsub -n1 -We 1 -J t-4-00304 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/7/7/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/7/7/' +bsub -n1 -We 1 -J t-4-00305 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/7/8/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/7/8/' +bsub -n1 -We 1 -J t-4-00306 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/8/3/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/8/3/' +bsub -n1 -We 1 -J t-4-00307 -o /dev/null '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py /nrs/mouselight/SAMPLES/2018-07-02-raw_new/2/1/8/4/ /nrs/mouselight/SAMPLES/2018-07-02-raw_new/syglass-ch0/2/1/8/4/' diff --git a/syglassrun.m b/syglassrun.m index ec2086b..f859428 100644 --- a/syglassrun.m +++ b/syglassrun.m @@ -1,19 +1,45 @@ -sample = '2018-07-02-raw_new'; -addpath(genpath('./common')) -samplepath = fullfile('/nrs/mouselight/SAMPLES/',sample); -outfolder = fullfile(samplepath,'syglass-ch0'); +function syglassrun(samplepath,outfolder,rerun) +% inputs: +% samplepath: name of the sample folder +% outfolder: target folder to create syglass files +% rerun: binary flag to recreate output of ls file. This will save +% time if you want to use the result of "ls" from a previous +% session +% example run: +% sample = '2018-07-02-raw_new'; +% samplepath = fullfile('/nrs/mouselight/SAMPLES/',sample); +% outfolder = fullfile(samplepath,'syglass-ch0'); +% rerun = 0; +% syglassrun(samplepath,outfolder,rerun) + +if nargin<1 + sample = '2018-07-02-raw_new'; + samplepath = fullfile('/nrs/mouselight/SAMPLES/',sample); + outfolder = fullfile(samplepath,'syglass-ch0'); + rerun = 0; +else + [samplefolder,sample] = fileparts(samplepath); + if nargin<3 + rerun = 1; + end +end + +if rerun;unix(sprintf('rm -rdf ./tmpfiles'));mkdir('./tmpfiles');end +if ~exist('./tmpfiles','dir'); mkdir('./tmpfiles',sample);end +pythonpath = '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python'; +scriptpath = '/groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py'; + +addpath(genpath('./common')) opt = configparser(fullfile(samplepath,'/transform.txt')); -args.level = opt.nl-1; +maxlevel = opt.nl-1; clear opt %% -pythonpath = '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python'; -scriptpath = '/groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py' -for level=0:6 - mysh = sprintf('./shfiles/syglassrun-%d-ch0.sh',level); +for level=0:maxlevel + mysh = sprintf('./syglassrun-%d-ch0.sh',level); args.level=level; args.ext = '0.tif'; - opt.seqtemp = fullfile('./shfiles',sprintf('filelist-%d.txt',level)); + opt.seqtemp = fullfile('./tmpfiles',sample,sprintf('filelist-%d.txt',level)); opt.inputfolder = samplepath; if exist(opt.seqtemp, 'file') == 2 % load file directly @@ -30,10 +56,9 @@ relativepath = infold(length(samplepath)+1:end); outfold = [fullfile(outfolder,relativepath)]; - if length(relativepath)>2&strcmp(relativepath(1:3),'ktx') + if length(relativepath)>2&strcmp(relativepath(1:3),'ktx') % skip any ktx files continue end - logfile = sprintf('%s/%d.txt',fullfile('/groups/mousebrainmicro/mousebrainmicro/LOG/',sample),ii); if ~exist(outfold,'dir') mkdir(outfold) @@ -45,126 +70,4 @@ fclose(fid); unix(sprintf('chmod g+rwx %s',mysh)); end -%% -% s = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789'; -% compiledfunc = '/groups/mousebrainmicro/home/base/CODE/syglass/syCacher' -% %find number of random characters to choose from -% numRands = length(s); -% %specify length of random string to generate -% sLength = 10; -% numcores = 4; -% timelim = 5*60 -% fold=1 -% mysh = sprintf('syglassrun-%d.sh',fold); -% -% fid = fopen(mysh,'w'); -% for ix=1:8 -% % syGlass -i -o -t -x 10000 -% for idx = 1:64 -% % sprintf('syGlass -i -o -t -x 10000') -% -% [bb,aa]=ind2sub([8 8],idx); -% randString = s( ceil(rand(1,sLength)*numRands) ); -% -% infold = fullfile(samplepath,sprintf('/%d/%d/%d/%d',fold,ix,aa,bb)); -% outfold = sprintf('/nrs/mouselight/2015-06-19-johan-full-syg/%d/%d/%d/%d/',fold,ix,aa,bb); -% % mkdir(outfold) -% if ~exist(fullfile(infold,sprintf('default.0.tif'))) -% -% else -% if exist(fullfile(outfold,sprintf('default.0.tif'))) -% [ix idx] -% else -% -% % outfile `= fullfile(outfolder,sprintf('%s_idx-%05d_stxyzendxyz-%d_%d_%d_%d_%d_%d.txt',bb,idx,BB(1:2:end),BB(2:2:end))); -% name = sprintf('cache_%05d-%s',(ix-1)*8+idx,randString); -% args = sprintf('''%s -i %s -o %s -t -x 10000''',compiledfunc,infold,outfold); -% mysub = sprintf('LD_LIBRARY_PATH=/misc/local/gcc-5.1.0/lib64/ qsub -pe batch %d -l d_rt=%d -N %s -j y -o /dev/null -b y -cwd -V %s\n',numcores,timelim,name,args); -% fwrite(fid,mysub); -% end -% end -% end -% end -% %% -% % bsub -n1 -We 1 -J t-00001 -o /dev/null 'python singleThreadedCacher.py /groups/turaga/home/moreheadm /groups/turaga/home/moreheadm/outtest/' -% % find -type d -printf '%d\t%P\n' | sort -r -nk4 | cut -f2- > listfolders -% foldind = 2 -% % infold = sprintf('/nrs/mouselight/SAMPLES/2017-06-28-2/%d',foldind); -% infold = '/nrs/mouselight/SAMPLES/2017-06-28-2/'; -% args = '-type d -printf ''%d\t%P\n'' | sort -r -nk1 | cut -f2- >'; -% outfile = fullfile(infold,'listfolders'); -% unix(sprintf('find %s %s %s',infold,args,outfile)) -% %% -% fid=fopen(outfile,'r'); -% myfiles = textscan(fid,'%s'); -% myfiles = myfiles{1}; -% fclose(fid) -% %% -% samp = '2017-06-28-2-sy' -% mysh = sprintf('syglassrun-%s-%d.sh',samp,foldind); -% -% outfold = fullfile('/nrs/mouselight/SAMPLES/',samp); -% fid = fopen(mysh,'w'); -% %% -% for ii=351235:length(myfiles) -% infile = fullfile(infold,myfiles{ii}); -% % if all(myfiles{ii}(1:3)=='ktx') -% % continue -% % end -% outfile = fullfile(outfold,myfiles{ii}); -% logfile = sprintf('%s/%d.txt',fullfile('/groups/mousebrainmicro/mousebrainmicro/LOG/',samp),ii); -% -% mkdir(outfile) -% unix(sprintf('chmod g+rwx %s',outfile)); -% % myarg = sprintf('bsub -n1 -We 1 -J t-%05d -o /dev/null ''python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py %s %s %s''\n',ii,infile,outfile,logfile); -% myarg = sprintf('bsub -n1 -We 1 -J t-%05d -o /dev/null ''python /groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py %s %s''\n',ii,infile,outfile); -% fwrite(fid,myarg); -% -% end -% fclose(fid) -% %% -% -% -% -% s = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789'; -% compiledfunc = '/groups/mousebrainmicro/home/base/CODE/syglass/syCacher' -% %find number of random characters to choose from -% numRands = length(s); -% %specify length of random string to generate -% sLength = 10; -% numcores = 4; -% timelim = 5*60 -% fold=1 -% mysh = sprintf('syglassrun-%d.sh',fold); -% -% fid = fopen(mysh,'w'); -% for ix=1:8 -% % syGlass -i -o -t -x 10000 -% for idx = 1:64 -% % sprintf('syGlass -i -o -t -x 10000') -% -% [bb,aa]=ind2sub([8 8],idx); -% randString = s( ceil(rand(1,sLength)*numRands) ); -% -% infold = sprintf('/nrs/mouselight/SAMPLES/2017-06-28-2/%d/%d/%d/%d',fold,ix,aa,bb); -% outfold = sprintf('/nrs/mouselight/2015-06-19-johan-full-syg/%d/%d/%d/%d/',fold,ix,aa,bb); -% % mkdir(outfold) -% if ~exist(fullfile(infold,sprintf('default.0.tif'))) -% -% else -% if exist(fullfile(outfold,sprintf('default.0.tif'))) -% [ix idx] -% else -% -% % -% % % outfile = fullfile(outfolder,sprintf('%s_idx-%05d_stxyzendxyz-%d_%d_%d_%d_%d_%d.txt',bb,idx,BB(1:2:end),BB(2:2:end))); -% % name = sprintf('cache_%05d-%s',(ix-1)*8+idx,randString); -% % args = sprintf('''%s -i %s -o %s -t -x 10000''',compiledfunc,infold,outfold); -% % mysub = sprintf('LD_LIBRARY_PATH=/misc/local/gcc-5.1.0/lib64/ qsub -pe batch %d -l d_rt=%d -N %s -j y -o /dev/null -b y -cwd -V %s\n',numcores,timelim,name,args); -% % fwrite(fid,mysub); -% end -% end -% end -% end -% diff --git a/syglassrun.m~ b/syglassrun.m~ new file mode 100644 index 0000000..291067a --- /dev/null +++ b/syglassrun.m~ @@ -0,0 +1,78 @@ +function syglassrun(samplepath,outfolder,rerun) +% inputs: +% samplepath: name of the sample folder +% outfolder: target folder to create syglass files +% rerun: binary flag to recreate output of ls file. This will save +% time if you want to use the result of "ls" from a previous +% session +% example run: +% sample = '2018-07-02-raw_new'; +% samplepath = fullfile('/nrs/mouselight/SAMPLES/',sample); +% outfolder = fullfile(samplepath,'syglass-ch0'); +% rerun = 0; +% syglassrun(samplepath,outfolder,rerun) + +if nargin<1 + sample = '2018-07-02-raw_new'; + samplepath = fullfile('/nrs/mouselight/SAMPLES/',sample); + outfolder = fullfile(samplepath,'syglass-ch0'); + rerun = 0; +else + [samplefolder,sample] = fileparts(samplepath); + if nargin<3 + rerun = 1; + end +end +unix(sprintf('rm -rdf ./tmpfiles')) + + +dos_cmd = sprintf( 'rmdir -f "%s"', './tmpfiles' ) +[ st, msg ] = system( dos_cmd ) + +if rerun;rmdir('./tmpfiles','s');mkdir('./tmpfiles');end +if ~exist('./tmpfiles','dir'); mkdir('./tmpfiles',sample);end + +pythonpath = '/groups/mousebrainmicro/home/base/anaconda3/envs/syglass/bin/python'; +scriptpath = '/groups/mousebrainmicro/mousebrainmicro/Software/syGlassConverter/singleThreadedCacher.py'; + +addpath(genpath('./common')) +opt = configparser(fullfile(samplepath,'/transform.txt')); +maxlevel = opt.nl-1; +clear opt +%% +for level=0:maxlevel + mysh = sprintf('./syglassrun-%d-ch0.sh',level); + args.level=level; + args.ext = '0.tif'; + opt.seqtemp = fullfile('./tmpfiles',sample,sprintf('filelist-%d.txt',level)); + opt.inputfolder = samplepath; + if exist(opt.seqtemp, 'file') == 2 + % load file directly + else + args.fid = fopen(opt.seqtemp,'w'); + recdir(opt.inputfolder,args) + end + fid=fopen(opt.seqtemp,'r'); + myfiles = textscan(fid,'%s');myfiles = myfiles{1};fclose(fid); + + fid = fopen(mysh,'w'); + for ii=1:length(myfiles) + infold = [fileparts(myfiles{ii}),'/']; + relativepath = infold(length(samplepath)+1:end); + outfold = [fullfile(outfolder,relativepath)]; + + if length(relativepath)>2&strcmp(relativepath(1:3),'ktx') % skip any ktx files + continue + end + + if ~exist(outfold,'dir') + mkdir(outfold) + unix(sprintf('chmod g+rwx %s',outfold)); + end + myarg = sprintf('bsub -n1 -We 1 -J t-%d-%05d -o /dev/null ''%s %s %s %s''\n',level,ii,pythonpath,scriptpath,infold,outfold); + fwrite(fid,myarg); + end + fclose(fid); + unix(sprintf('chmod g+rwx %s',mysh)); +end + diff --git a/tmpfiles/2018-07-02-raw_new/.nfs00000002616463690000ad42 b/tmpfiles/2018-07-02-raw_new/.nfs00000002616463690000ad42 new file mode 100644 index 0000000..bd8fbd6 --- /dev/null +++ b/tmpfiles/2018-07-02-raw_new/.nfs00000002616463690000ad42 @@ -0,0 +1,307 @@ +/nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/1/8/8/default.0.tif +/nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/2/3/8/default.0.tif +/nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/2/4/7/default.0.tif +/nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/2/4/8/default.0.tif +/nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/2/7/2/default.0.tif +/nrs/mouselight/SAMPLES/2018-07-02-raw_new/1/2/7/3/default.0.tif 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