Merge branch 'master' of https://github.com/openUC2/ImSwitch

openUC2 · Sep 24, 2024 · 3e6a627 · 3e6a627
2 parents bce3ee1 + d8a8c00
commit 3e6a627
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diff --git a/.github/workflows/imswitch-docker-multiarch-noqt.yaml b/.github/workflows/imswitch-docker-multiarch-noqt.yaml
@@ -49,7 +49,7 @@ jobs:
       - name: Build and push container image to registry
         uses: docker/build-push-action@v2
         with:
-          context: docker
+          context: docker/HIK
           file: docker/HIK/dockerfile
           push: true
           platforms: linux/amd64,linux/arm64

diff --git a/docker/HIK/dockerfile b/docker/HIK/dockerfile
@@ -182,85 +182,6 @@ RUN cd /tmp/UC2-REST && \
 # Expose FTP, SSH port and HTTP port
 EXPOSE  21 22 8001
 
-CMD ["/bin/bash", "-c", "\
-    if [ \"$MODE\" = \"terminal\" ]; then \
-        /bin/bash; \
-    else \
-        echo 'Starting the container' && \
-        echo 'LSUSB' && lsusb && \
-        echo 'Listing external USB storage devices' && \
-        ls /media && \
-        /usr/sbin/sshd -D & \
-        /usr/sbin/vsftpd /etc/vsftpd.conf & \
-        ls /root/ImSwitchConfig/imcontrol_setups && \
-        PATCH_DIR=/tmp/ImSwitch-changes && \
-        PATCH_FILE=$PATCH_DIR/diff.patch && \
-        mkdir -p $PATCH_DIR && \
-        if [ -f \"$PATCH_FILE\" ]; then \
-            echo 'Applying stored patch from: $PATCH_FILE' && \
-            cd /tmp/ImSwitch && \
-            git apply $PATCH_FILE; \
-        else \
-            echo 'No patch file found, proceeding without applying changes'; \
-        fi && \
-        if [ \"$UPDATE_CONFIG\" = \"true\" ]; then \
-            echo 'Pulling the ImSwitchConfig repository' && \
-            cd /root/ImSwitchConfig && \
-            git pull; \
-        fi && \
-        if [ -z \"$CONFIG_PATH\" ]; then \
-            CONFIG_FILE=${CONFIG_FILE:-/root/ImSwitchConfig/imcontrol_setups/example_virtual_microscope.json}; \
-        else \
-            CONFIG_FILE=None; \
-        fi && \
-        PERSISTENT_PIP_DIR=${PERSISTENT_PIP_DIR:-/persistent_pip_packages} && \
-        mkdir -p $PERSISTENT_PIP_DIR && \
-        export PYTHONUSERBASE=$PERSISTENT_PIP_DIR && \
-        export PATH=$PERSISTENT_PIP_DIR/bin:$PATH && \
-        if [ ! -z \"$PIP_PACKAGES\" ]; then \
-            echo 'Installing additional pip packages: $PIP_PACKAGES' && \
-            for package in $PIP_PACKAGES; do \
-                /opt/conda/bin/conda run -n imswitch pip install --user $package; \
-            done; \
-        fi && \
-        if [ \"$UPDATE_GIT\" = \"true\" ] || [ \"$UPDATE_GIT\" = \"1\" ]; then \
-            PATCH_DIR=/tmp/ImSwitch-changes && \
-            PATCH_FILE=$PATCH_DIR/diff.patch && \
-            mkdir -p $PATCH_DIR && \
-            cd /tmp/ImSwitch && \
-            if [ -f \"$PATCH_FILE\" ]; then \
-                echo 'Applying stored patch to ImSwitch from: $PATCH_FILE' && \
-                git apply $PATCH_FILE || { echo 'Failed to apply patch, aborting fetch'; exit 1; }; \
-            fi && \
-            echo 'Fetching the latest changes from ImSwitch repository' && \
-            git fetch origin && \
-            echo 'Checking for differences between local and remote branch' && \
-            git diff HEAD origin/master > $PATCH_FILE && \
-            if [ -s $PATCH_FILE ]; then \
-                echo 'New changes detected, patch saved at: $PATCH_FILE'; \
-            else \
-                echo 'No new changes detected in ImSwitch repository, patch not updated'; \
-                rm -f $PATCH_FILE; \
-            fi && \
-            echo 'Merging fetched changes from origin/master' && \
-            git merge origin/master; \
-        fi && \
-        if [ \"$UPDATE_INSTALL_GIT\" = \"true\" ] || [ \"$UPDATE_INSTALL_GIT\" = \"1\" ]; then \
-            echo 'Pulling the ImSwitch repository and installing' && \
-            cd /tmp/ImSwitch && \
-            git pull && \
-            /bin/bash -c 'source /opt/conda/bin/activate imswitch && pip install --target /persistent_pip_packages /tmp/ImSwitch'; \
-        fi && \        
-        source /opt/conda/bin/activate imswitch && \
-        HEADLESS=${HEADLESS:-1} && \
-        HTTP_PORT=${HTTP_PORT:-8001} && \
-        USB_DEVICE_PATH=${USB_DEVICE_PATH:-/dev/bus/usb} && \
-        CONFIG_PATH=${CONFIG_PATH:-None} && \
-        DATA_PATH=${DATA_PATH:-None} && \        
-        echo \"python3 /tmp/ImSwitch/main.py --headless $HEADLESS --config-file $CONFIG_FILE --http-port $HTTP_PORT --config-folder $CONFIG_PATH --ext-data-folder $DATA_PATH \" && \
-        python3 /tmp/ImSwitch/main.py --headless $HEADLESS --config-file $CONFIG_FILE --http-port $HTTP_PORT --config-folder $CONFIG_PATH --ext-data-folder $DATA_PATH; \
-    fi"]
-
-
-# source /opt/conda/bin/activate imswitch
-# python3 /tmp/ImSwitch/main.py  --headless 1 --config-file example_virtual_microscope.json --config-folder /config
+ADD entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
+ENTRYPOINT ["/entrypoint.sh"]
diff --git a/docker/HIK/entrypoint.sh b/docker/HIK/entrypoint.sh
@@ -0,0 +1,110 @@
+#!/usr/bin/env bash
+
+if [[ ! ("$MODE" == "terminal") ]];
+then
+    echo 'Starting the container'
+    echo 'Listing USB Bus'
+    lsusb
+    echo 'Listing external storage devices'
+    ls /media
+    echo 'Starting SSH Server'
+    /usr/sbin/sshd -D
+    echo 'Starting SFTP Server'
+    /usr/sbin/vsftpd /etc/vsftpd.conf
+    echo 'Listing Config Dir'
+    ls /root/ImSwitchConfig/imcontrol_setups
+
+    PATCH_DIR=/tmp/ImSwitch-changes
+    PATCH_FILE=$PATCH_DIR/diff.patch 
+
+    mkdir -p "$PATCH_DIR"
+    if [[ -f "$PATCH_FILE" ]]
+    then
+        echo "Applying stored patch from $PATCH_FILE"
+        cd /tmp/ImSwitch
+        git apply "$PATCH_FILE"
+    else
+        echo 'No patch file found, proceeding without applying changes'
+    fi
+
+    if [[ "$UPDATE_CONFIG" = "true" ]]
+    then
+        echo 'Pulling the ImSwitchConfig repository'
+        cd /root/ImSwitchConfig
+        git pull
+    fi
+    if [[ -z "$CONFIG_PATH" ]]
+    then
+        CONFIG_FILE="${CONFIG_FILE:-/root/ImSwitchConfig/imcontrol_setups/example_virtual_microscope.json}"
+    else
+        CONFIG_FILE=None
+    fi
+
+    PERSISTENT_PIP_DIR="${PERSISTENT_PIP_DIR:-/persistent_pip_packages}"
+    mkdir -p "$PERSISTENT_PIP_DIR"
+    export PYTHONUSERBASE="$PERSISTENT_PIP_DIR"
+    export PATH="$PERSISTENT_PIP_DIR/bin:$PATH"
+    if [[ -n "$PIP_PACKAGES" ]]
+    then
+        echo "Installing additional pip packages: $PIP_PACKAGES"
+        for package in $PIP_PACKAGES
+        do
+            /opt/conda/bin/conda run -n imswitch pip install --user $package
+        done
+    fi
+    if [[ "$UPDATE_GIT" == true || "$UPDATE_GIT" == "1" ]]
+    then
+        PATCH_DIR="/tmp/ImSwitch-changes"
+        PATCH_FILE="$PATCH_DIR/diff.patch"
+        mkdir -p "$PATCH_DIR"
+        cd /tmp/ImSwitch
+        if [[ -f "$PATCH_FILE" ]]
+        then
+            echo "Applying stored patch to ImSwitch from: $PATCH_FILE"
+            git apply "$PATCH_FILE" || { echo 'Failed to apply patch, aborting fetch'; exit 1; }
+        fi
+        echo 'Fetching the latest changes from ImSwitch repository'
+        git fetch origin
+        echo 'Checking for differences between local and remote branch'
+        git diff HEAD origin/master > "$PATCH_FILE"
+        if [[ -s "$PATCH_FILE" ]]
+        then
+            echo "New changes detected, patch saved at: $PATCH_FILE"
+        else
+            echo "No new changes detected in ImSwitch repository, patch not updated"
+            rm -f "$PATCH_FILE"
+        fi
+        echo 'Merging fetched changes from origin/master'
+        git merge origin/master
+    fi
+    if [[ "$UPDATE_INSTALL_GIT" == "true" || "$UPDATE_INSTALL_GIT" == "1" ]]
+    then
+        echo 'Pulling the ImSwitch repository and installing'
+        cd /tmp/ImSwitch
+        git pull
+        /bin/bash -c 'source /opt/conda/bin/activate imswitch && pip install --target /persistent_pip_packages /tmp/ImSwitch'
+    fi
+    source /opt/conda/bin/activate imswitch
+    USB_DEVICE_PATH=${USB_DEVICE_PATH:-/dev/bus/usb}
+
+    params=()
+    if [[ $HEADLESS == "1" || $HEADLESS == "True" || $HEADLESS == "true" ]]
+    then
+        params+=" --headless"
+    fi;
+    if [[ $ssl == "0" || $ssl == "False" || $ssl == "false" ]]
+    then
+        params+=" --no-ssl"
+    fi;
+    params+=" --http-port ${HTTP_PORT:-8001}"
+    params+=" --config-folder ${CONFIG_PATH:-None}"
+    params+=" --config-file ${CONFIG_FILE:-None}"
+    params+=" --ext-data-folder ${DATA_PATH:-None}"
+
+    echo 'Starting Imswitch with the following parameters:'
+    echo "${params[@]}"
+    python3 /tmp/ImSwitch/main.py $params
+else
+    echo 'Starting the container in terminal mode'
+    exec bash
+fi
diff --git a/imswitch/__main__.py b/imswitch/__main__.py
@@ -17,7 +17,7 @@ def main(is_headless:bool=None, default_config:str=None, http_port:int=None, ssl
             parser = argparse.ArgumentParser(description='Process some integers.')
 
             # specify if run in headless mode
-            parser.add_argument('--headless', dest='headless', type=bool, default=0,
+            parser.add_argument('--headless', dest='headless', default=False, action='store_true',
                                 help='run in headless mode')
 
             # specify config file name - None for default
@@ -29,7 +29,7 @@ def main(is_headless:bool=None, default_config:str=None, http_port:int=None, ssl
                                 help='specify http port')
 
             # specify ssl
-            parser.add_argument('--ssl', dest='ssl', type=bool, default=True,
+            parser.add_argument('--no-ssl', dest='ssl', default=True, action='store_false',
                                 help='specify ssl')
 
             # specify the config folder (e.g. if running from a different location / container)