Merge pull request #23 from EntropyOrg/obj-detect

Add object detection demo

Author: zmughal

.dockerignore

@@ -3,3 +3,4 @@
 notebook/
 !notebook/InferenceUsingTFHubMobileNetV2Model.ipynb
 !notebook/InferenceUsingTFHubEnformerGeneExprPredModel.ipynb
+!notebook/InferenceUsingTFHubCenterNetObjDetect.ipynb

.gitattributes

@@ -1,3 +1,4 @@
 README.pod  -diff linguist-generated=true
 lib/AI/TensorFlow/Libtensorflow/Manual/Notebook/InferenceUsingTFHubMobileNetV2Model.pod  -diff linguist-generated=true
 lib/AI/TensorFlow/Libtensorflow/Manual/Notebook/InferenceUsingTFHubEnformerGeneExprPredModel.pod  -diff linguist-generated=true
+lib/AI/TensorFlow/Libtensorflow/Manual/Notebook/InferenceUsingTFHubCenterNetObjDetect.pod  -diff linguist-generated=true

.gitignore

@@ -13,3 +13,7 @@ notebook/targets_human.txt
 notebook/clinvar.vcf.*
 notebook/deepmind_enformer_1*
 notebook/enformer-target-interval-tracks.png
+
+# notebook/InferenceUsingTFHubCenterNetObjDetect.ipynb
+notebook/tensorflow_centernet_hourglass_512x512_1*
+notebook/objects-detected.png

docker/Dockerfile.nb-obj-detect

@@ -0,0 +1,53 @@
+#syntax=docker/dockerfile-upstream:1.4.0-rc1
+
+# notebook/InferenceUsingTFHubCenterNetObjDetect.ipynb
+
+# Packages from Ubuntu focal base
+ARG NB_APT_PKGS_RUN="         libjpeg-turbo8     libpng16-16 netpbm gnuplot-nox"
+ARG NB_APT_PKGS_DEV="perl-doc libjpeg-turbo8-dev libpng-dev"
+ARG NB_POD="AI::TensorFlow::Libtensorflow::Manual::Notebook::InferenceUsingTFHubCenterNetObjDetect"
+
+FROM base AS nb-builder
+
+ARG NB_APT_PKGS_RUN
+ARG NB_APT_PKGS_DEV
+ARG NB_POD
+
+USER root
+
+RUN apt-get update && apt-get install -y --no-install-recommends $NB_APT_PKGS_RUN $NB_APT_PKGS_DEV
+RUN bash -c ' \
+	eval $(perl -Mlocal::lib=/perl5-nb); \
+	export MAKEFLAGS=$(nproc); \
+	plx cpm install -g --cpanfile=<( \
+		awk "/=head1 CPANFILE/,EOF {print}" $( plx perldoc -l $NB_POD ) \
+		| awk "NR>1" \
+	)'
+RUN apt-get remove -y $NB_APT_PKGS_DEV && apt-get autoremove -y && apt-get clean
+RUN rm -Rf $HOME/.perl-cpm/ $HOME/.cpanm
+
+FROM base AS object-detection
+
+ARG NB_APT_PKGS_RUN
+ARG NB_POD
+
+ARG NB_USER
+ARG NB_UID
+
+USER root
+
+COPY --from=nb-builder /perl5-nb /perl5-nb
+
+RUN apt-get update && apt-get install -y --no-install-recommends $NB_APT_PKGS_RUN
+
+RUN apt-get -qq purge \
+    && apt-get -qq clean \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN chown -R ${NB_USER}:${NB_USER} /perl5-nb
+
+USER ${NB_USER}
+
+RUN bash -c 'plx perl -c $( plx perldoc -l $NB_POD );'
+
+# vim:ft=dockerfile

docker/Dockerfile.nb-omnibus

@@ -5,11 +5,13 @@
 # Builds on top of:
 #   - docker/Dockerfile.nb-image-class
 #   - docker/Dockerfile.nb-gene-expr-pred
+#   - docker/Dockerfile.nb-obj-detect
 #
 # The contents of `NB_APT_PKGS_RUN` come from those `Dockerfile`s.
 ARG NB_APT_PKGS_RUN=" \
 libjpeg-turbo8     libpng16-16 libgsl23 \
 samtools libhts3 tabix libxml2 libexpat1 libdb5.3 netpbm gnuplot-nox \
+libjpeg-turbo8     libpng16-16 netpbm gnuplot-nox \
 "
 
 FROM base as omnibus
@@ -23,6 +25,7 @@ USER root
 
 COPY --from=nb-image-class    /perl5-nb /perl5-nb-image-class
 COPY --from=nb-gene-expr-pred /perl5-nb /perl5-nb-gene-expr-pred
+COPY --from=nb-obj-detect     /perl5-nb /perl5-nb-obj-detect
 
 RUN apt-get update && apt-get install -y --no-install-recommends $NB_APT_PKGS_RUN
 
@@ -32,8 +35,8 @@ RUN apt-get -qq purge \
 
 RUN \
 	   mkdir -p                                           /perl5-nb \
-	&& cp -pR /perl5-nb-image-class/. /perl5-nb-gene-expr-pred/. /perl5-nb/ \
-	&& rm -Rf /perl5-nb-image-class   /perl5-nb-gene-expr-pred
+	&& cp -pR /perl5-nb-image-class/. /perl5-nb-gene-expr-pred/. /perl5-nb-obj-detect/. /perl5-nb/ \
+	&& rm -Rf /perl5-nb-image-class   /perl5-nb-gene-expr-pred   /perl5-nb-obj-detect
 
 RUN chown -R ${NB_USER}:${NB_USER} /perl5-nb
 
@@ -45,6 +48,7 @@ RUN bash -c ' \
 	for NB_POD in \
 		AI::TensorFlow::Libtensorflow::Manual::Notebook::InferenceUsingTFHubMobileNetV2Model \
 		AI::TensorFlow::Libtensorflow::Manual::Notebook::InferenceUsingTFHubEnformerGeneExprPredModel \
+		AI::TensorFlow::Libtensorflow::Manual::Notebook::InferenceUsingTFHubCenterNetObjDetect \
 	; do \
 		plx perl -c $( plx perl -MPod::Simple::Search -e "print Pod::Simple::Search->new->find(shift @ARGV)" $NB_POD ); \
 	done;'

docker/docker-bake.hcl

@@ -5,6 +5,7 @@ group "default" {
     "nb-omnibus",
     "nb-image-class",
     "nb-gene-expr-pred",
+    "nb-obj-detect",
   ]
 }
 
@@ -106,13 +107,24 @@ target "nb-gene-expr-pred" {
   tags = tag("cpu", "-nb-gene-expr-pred")
 }
 
+target "nb-obj-detect" {
+  inherits   = [ "nb-cpu" ]
+  dockerfile = "docker/Dockerfile.nb-obj-detect"
+  target     = "object-detection"
+  contexts = {
+    base           = "target:base"
+  }
+  tags = tag("cpu", "-nb-obj-detect")
+}
+
 target "nb-omnibus" {
   inherits   = [ "nb-cpu" ]
   dockerfile = "docker/Dockerfile.nb-omnibus"
   contexts = {
     base               = "target:base"
     nb-image-class     = "target:nb-image-class"
     nb-gene-expr-pred  = "target:nb-gene-expr-pred"
+    nb-obj-detect      = "target:nb-obj-detect"
   }
   tags = tag("cpu", "-nb-omnibus")
 }
@@ -123,6 +135,7 @@ target "gpu-nb-omnibus" {
     NB_APT_PKGS_RUN = <<EOF
       libjpeg-turbo8     libpng16-16 libgsl23
       samtools libhts3 tabix libxml2 libexpat1 libdb5.3 netpbm gnuplot-nox
+      libjpeg-turbo8     libpng16-16 netpbm gnuplot-nox
     EOF
   }
   dockerfile = "docker/Dockerfile.with-gpu-libtf"