Merge pull request #30 from BIOP/v0.2.1

V0.2.1

Author: romainGuiet

docker/Dockerfile-ms

@@ -17,6 +17,7 @@ ARG CELLPROFILER_VERSION=4.2.6
 ARG INKSCAPE_VERSION=0.1.4
 ARG OMNI_VERSION=1.0.7-dev2
 ARG BRAINRENDER_VERSION=0.0.7
+ARG YOLO_VERSION=8.3.119
 
 FROM ${ALIAS}biop-qupath:${QUPATH_VERSION} AS qupath-image
 FROM ${ALIAS}biop-ilastik:${ILASTIK_VERSION} AS ilastik-image
@@ -31,6 +32,7 @@ FROM ${ALIAS}biop-cellprofiler:${CELLPROFILER_VERSION} AS cellprofiler-image
 FROM ${ALIAS}biop-inkscape:${INKSCAPE_VERSION} AS inkscape-image
 FROM ${ALIAS}biop-omni:${OMNI_VERSION} AS omnipose-image
 FROM ${ALIAS}biop-brainrender:${BRAINRENDER_VERSION} AS brainrender-image
+FROM ${ALIAS}biop-yolo:${YOLO_VERSION} AS yolo-image
 
 FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE} AS base
 
@@ -115,6 +117,10 @@ ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/elastix/lib
 COPY --from=brainrender-image /opt/conda/envs/brainrender /opt/conda/envs/brainrender
 COPY --from=brainrender-image /home/biop/.brainglobe/ /home/biop/.brainglobe/
 
+#################################################################
+# Install yolo
+COPY --from=yolo-image /opt/conda/envs/yolo /opt/conda/envs/yolo
+
 #################################################################
 # Jupyter kernels 
 # 

docker/readme.md

@@ -11,35 +11,35 @@ docker build -f Dockerfile-base  -t biop-vnc-base:0.2.2 . --no-cache
 ## build
 
 ```
-docker build -f Dockerfile-ms  -t biop-desktop:0.2.0 . 
+docker build -f Dockerfile-ms  -t biop-desktop:0.2.1 . 
 ```
 
 ## start to test (see below)
 
 ```
-docker run -it --rm -p 8888:8888 --gpus device=0  --mount src=D:/,target=/home/biop/local,type=bind biop-napari:0.5.6
+docker run -it --rm -p 8888:8888 --gpus device=0  --mount src=D:/,target=/home/biop/local,type=bind biop-desktop:0.2.1
 ```
 
 ## To test on RCP cluster
 ```
-docker tag biop-desktop:0.2.0  registry.rcp.epfl.ch/ptbiop/biop-desktop:0.2.0
+docker tag biop-desktop:0.2.1  registry.rcp.epfl.ch/ptbiop/biop-desktop:0.2.1
 ```
 
 ```
-docker push registry.rcp.epfl.ch/ptbiop/biop-desktop:0.2.0
+docker push registry.rcp.epfl.ch/ptbiop/biop-desktop:0.2.1
 ```
 
 ## after testing pass, tag 
 ```
-docker tag biop-desktop:0.2.0 biop/biop-desktop:0.2.0
+docker tag biop-desktop:0.2.1 biop/biop-desktop:0.2.1
 ```
 
 ## push on dockerhub
 ```
-docker push biop/biop-desktop:0.2.0
+docker push biop/biop-desktop:0.2.1
 ```
 
-# TEST 0.2.0
+# TEST 0.2.1
 [x] omero-insight
 [x] vscode
 [x] jupyterlab
@@ -58,4 +58,5 @@ docker push biop/biop-desktop:0.2.0
 [x] brainrender starts 
 [x] brainrender load mouse atlas
 [x] cellprofiler starts
-[x] ilastik starts
+[x] ilastik starts
+[x] yolo prediction on blobs

docker/yolo/Dockerfile-yolo

@@ -0,0 +1,21 @@
+ARG ALIAS=biop/
+ARG BASE_IMAGE=0.2.1
+FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE}
+
+USER root
+
+RUN conda create -n yolo python=3.10 \
+    && source activate yolo \
+    && pip install ultralytics opencv-python numpy   \
+    && conda clean --all -f -y \
+    && conda env export -n "biop" 
+
+RUN chmod -R a+rwX /home/biop/ \
+    && chown -R biop:biop /home/biop/
+
+#################################################################
+# Container start
+USER biop
+WORKDIR /home/biop
+ENTRYPOINT ["/usr/local/bin/jupyter"]
+CMD ["lab", "--allow-root", "--ip=*", "--port=8888", "--no-browser", "--NotebookApp.token=''", "--NotebookApp.allow_origin='*'", "--notebook-dir=/home/biop"]

docker/yolo/readme-yolo.md

@@ -0,0 +1,31 @@
+# Latest Version
+
+## build
+```
+docker build -f yolo/Dockerfile-yolo  -t biop-yolo:8.3.119 . --no-cache
+```
+## start to test (see below)
+```
+docker run -it --rm -p 8888:8888 --gpus device=0  --mount src=D:/,target=/home/biop/local,type=bind   biop-yolo:8.3.119
+```
+
+## after testing pass, tag 
+```
+docker tag   biop-yolo:8.3.119 biop/biop-yolo:8.3.119
+```
+
+## push on dockerhub
+```
+docker push biop/biop-yolo:8.3.119
+```
+
+# Test(s)
+
+## yolo on blob
+Upload `blobs.jpg` to /home/biop/
+
+```
+source activate yolo
+yolo task=detect mode=predict model=yolov8n.pt source=blobs.jpg
+``` 
+