Fix spike holes in KS2.5/3

Author: alejoe91

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 ..

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 ..

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 ..

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 ..

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 .
 

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 .
+docker build -t spikeinterface/kilosort3-compiled-base:latest -t spikeinterface/kilosort3-compiled-base:0.3.0 .