From 23ff7c83ad2287292b2c244a7b7e71feb045819d Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Mon, 11 Mar 2024 14:21:38 +0100 Subject: [PATCH 1/2] Fix spike holes in KS2.5/3 --- kilosort-compiled/compile_and_build_ks.sh | 24 +++++++++++++++++++ kilosort-compiled/compile_and_build_ks2.sh | 24 +++++++++++++++++++ kilosort-compiled/compile_and_build_ks25.sh | 24 +++++++++++++++++++ kilosort-compiled/compile_and_build_ks3.sh | 24 +++++++++++++++++++ .../kilosort2_5-compiled/build.sh | 2 +- kilosort-compiled/kilosort3-compiled/build.sh | 2 +- 6 files changed, 98 insertions(+), 2 deletions(-) create mode 100644 kilosort-compiled/compile_and_build_ks.sh create mode 100644 kilosort-compiled/compile_and_build_ks2.sh create mode 100644 kilosort-compiled/compile_and_build_ks25.sh create mode 100644 kilosort-compiled/compile_and_build_ks3.sh diff --git a/kilosort-compiled/compile_and_build_ks.sh b/kilosort-compiled/compile_and_build_ks.sh new file mode 100644 index 0000000..c4b5b5d --- /dev/null +++ b/kilosort-compiled/compile_and_build_ks.sh @@ -0,0 +1,24 @@ +#!/bin/bash +set -e + +if [ $# == 0 ]; then + echo "Usage: $0 param1 param2 param3 param4 param4" + echo "* param1: spikeinterface path" + echo "* param1: kilosort1 path" + exit +fi + +if [ $# -ne 2 ]; then + echo "spikeinterface and kilosort1 path must be given" + exit 1 +fi + + +SPIKEINTERFACE_PATH=${1%/} +KILOSORT_PATH=${2%/} + + +cd kilosort-compiled +bash compile.sh $KILOSORT_PATH $SPIKEINTERFACE_PATH +bash build.sh +cd .. diff --git a/kilosort-compiled/compile_and_build_ks2.sh b/kilosort-compiled/compile_and_build_ks2.sh new file mode 100644 index 0000000..18d8a6e --- /dev/null +++ b/kilosort-compiled/compile_and_build_ks2.sh @@ -0,0 +1,24 @@ +#!/bin/bash +set -e + +if [ $# == 0 ]; then + echo "Usage: $0 param1 param2 param3 param4 param4" + echo "* param1: spikeinterface path" + echo "* param1: kilosort2 path" + exit +fi + +if [ $# -ne 2 ]; then + echo "spikeinterface and kilosort2 path must be given" + exit 1 +fi + + +SPIKEINTERFACE_PATH=${1%/} +KILOSORT2_PATH=${2%/} + + +cd kilosort2-compiled +bash compile.sh $KILOSORT2_PATH $SPIKEINTERFACE_PATH +bash build.sh +cd .. diff --git a/kilosort-compiled/compile_and_build_ks25.sh b/kilosort-compiled/compile_and_build_ks25.sh new file mode 100644 index 0000000..ced5f93 --- /dev/null +++ b/kilosort-compiled/compile_and_build_ks25.sh @@ -0,0 +1,24 @@ +#!/bin/bash +set -e + +if [ $# == 0 ]; then + echo "Usage: $0 param1 param2 param3 param4 param4" + echo "* param1: spikeinterface path" + echo "* param1: kilosort25 path" + exit +fi + +if [ $# -ne 2 ]; then + echo "spikeinterface and kilosort25 path must be given" + exit 1 +fi + + +SPIKEINTERFACE_PATH=${1%/} +KILOSORT25_PATH=${2%/} + + +cd kilosort2_5-compiled +bash compile.sh $KILOSORT25_PATH $SPIKEINTERFACE_PATH +bash build.sh +cd .. diff --git a/kilosort-compiled/compile_and_build_ks3.sh b/kilosort-compiled/compile_and_build_ks3.sh new file mode 100644 index 0000000..196ddb6 --- /dev/null +++ b/kilosort-compiled/compile_and_build_ks3.sh @@ -0,0 +1,24 @@ +#!/bin/bash +set -e + +if [ $# == 0 ]; then + echo "Usage: $0 param1 param2 param3 param4 param4" + echo "* param1: spikeinterface path" + echo "* param1: kilosort3 path" + exit +fi + +if [ $# -ne 2 ]; then + echo "spikeinterface and kilosort3 path must be given" + exit 1 +fi + + +SPIKEINTERFACE_PATH=${1%/} +KILOSORT3_PATH=${2%/} + + +cd kilosort3-compiled +bash compile.sh $KILOSORT3_PATH $SPIKEINTERFACE_PATH +bash build.sh +cd .. diff --git a/kilosort-compiled/kilosort2_5-compiled/build.sh b/kilosort-compiled/kilosort2_5-compiled/build.sh index 360ed42..16030b8 100755 --- a/kilosort-compiled/kilosort2_5-compiled/build.sh +++ b/kilosort-compiled/kilosort2_5-compiled/build.sh @@ -1,4 +1,4 @@ #!/bin/bash -docker build -t spikeinterface/kilosort2_5-compiled-base:latest -t spikeinterface/kilosort2_5-compiled-base:0.2.0 . +docker build -t spikeinterface/kilosort2_5-compiled-base:latest -t spikeinterface/kilosort2_5-compiled-base:0.3.0 . diff --git a/kilosort-compiled/kilosort3-compiled/build.sh b/kilosort-compiled/kilosort3-compiled/build.sh index c817362..edcccc7 100755 --- a/kilosort-compiled/kilosort3-compiled/build.sh +++ b/kilosort-compiled/kilosort3-compiled/build.sh @@ -1,3 +1,3 @@ #!/bin/bash -docker build -t spikeinterface/kilosort3-compiled-base:latest -t spikeinterface/kilosort3-compiled-base:0.2.0 . \ No newline at end of file +docker build -t spikeinterface/kilosort3-compiled-base:latest -t spikeinterface/kilosort3-compiled-base:0.3.0 . \ No newline at end of file From 497756da4f9039b66327fc6e411dcd0c628bbb8a Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Tue, 12 Mar 2024 17:23:07 +0100 Subject: [PATCH 2/2] remove redundant scripts --- kilosort-compiled/compile_and_build_ks.sh | 24 --------------------- kilosort-compiled/compile_and_build_ks2.sh | 24 --------------------- kilosort-compiled/compile_and_build_ks25.sh | 24 --------------------- kilosort-compiled/compile_and_build_ks3.sh | 24 --------------------- 4 files changed, 96 deletions(-) delete mode 100644 kilosort-compiled/compile_and_build_ks.sh delete mode 100644 kilosort-compiled/compile_and_build_ks2.sh delete mode 100644 kilosort-compiled/compile_and_build_ks25.sh delete mode 100644 kilosort-compiled/compile_and_build_ks3.sh diff --git a/kilosort-compiled/compile_and_build_ks.sh b/kilosort-compiled/compile_and_build_ks.sh deleted file mode 100644 index c4b5b5d..0000000 --- a/kilosort-compiled/compile_and_build_ks.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash -set -e - -if [ $# == 0 ]; then - echo "Usage: $0 param1 param2 param3 param4 param4" - echo "* param1: spikeinterface path" - echo "* param1: kilosort1 path" - exit -fi - -if [ $# -ne 2 ]; then - echo "spikeinterface and kilosort1 path must be given" - exit 1 -fi - - -SPIKEINTERFACE_PATH=${1%/} -KILOSORT_PATH=${2%/} - - -cd kilosort-compiled -bash compile.sh $KILOSORT_PATH $SPIKEINTERFACE_PATH -bash build.sh -cd .. diff --git a/kilosort-compiled/compile_and_build_ks2.sh b/kilosort-compiled/compile_and_build_ks2.sh deleted file mode 100644 index 18d8a6e..0000000 --- a/kilosort-compiled/compile_and_build_ks2.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash -set -e - -if [ $# == 0 ]; then - echo "Usage: $0 param1 param2 param3 param4 param4" - echo "* param1: spikeinterface path" - echo "* param1: kilosort2 path" - exit -fi - -if [ $# -ne 2 ]; then - echo "spikeinterface and kilosort2 path must be given" - exit 1 -fi - - -SPIKEINTERFACE_PATH=${1%/} -KILOSORT2_PATH=${2%/} - - -cd kilosort2-compiled -bash compile.sh $KILOSORT2_PATH $SPIKEINTERFACE_PATH -bash build.sh -cd .. diff --git a/kilosort-compiled/compile_and_build_ks25.sh b/kilosort-compiled/compile_and_build_ks25.sh deleted file mode 100644 index ced5f93..0000000 --- a/kilosort-compiled/compile_and_build_ks25.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash -set -e - -if [ $# == 0 ]; then - echo "Usage: $0 param1 param2 param3 param4 param4" - echo "* param1: spikeinterface path" - echo "* param1: kilosort25 path" - exit -fi - -if [ $# -ne 2 ]; then - echo "spikeinterface and kilosort25 path must be given" - exit 1 -fi - - -SPIKEINTERFACE_PATH=${1%/} -KILOSORT25_PATH=${2%/} - - -cd kilosort2_5-compiled -bash compile.sh $KILOSORT25_PATH $SPIKEINTERFACE_PATH -bash build.sh -cd .. diff --git a/kilosort-compiled/compile_and_build_ks3.sh b/kilosort-compiled/compile_and_build_ks3.sh deleted file mode 100644 index 196ddb6..0000000 --- a/kilosort-compiled/compile_and_build_ks3.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash -set -e - -if [ $# == 0 ]; then - echo "Usage: $0 param1 param2 param3 param4 param4" - echo "* param1: spikeinterface path" - echo "* param1: kilosort3 path" - exit -fi - -if [ $# -ne 2 ]; then - echo "spikeinterface and kilosort3 path must be given" - exit 1 -fi - - -SPIKEINTERFACE_PATH=${1%/} -KILOSORT3_PATH=${2%/} - - -cd kilosort3-compiled -bash compile.sh $KILOSORT3_PATH $SPIKEINTERFACE_PATH -bash build.sh -cd ..