From 23dc5db9e63c9e185236d8c09559aae3577272d3 Mon Sep 17 00:00:00 2001
From: Nitesh639 <nkush9598@gmail.com>
Date: Mon, 7 Mar 2022 22:00:34 -0600
Subject: [PATCH 1/3] Added docker contenariztion to png-extraction module

---
 modules/png-extraction/Dockerfile            | 12 ++++
 modules/png-extraction/png-extraction-docker | 74 ++++++++++++++++++++
 2 files changed, 86 insertions(+)
 create mode 100644 modules/png-extraction/Dockerfile
 create mode 100644 modules/png-extraction/png-extraction-docker

diff --git a/modules/png-extraction/Dockerfile b/modules/png-extraction/Dockerfile
new file mode 100644
index 0000000..66c1b17
--- /dev/null
+++ b/modules/png-extraction/Dockerfile
@@ -0,0 +1,12 @@
+FROM ravirahar/arch-python-gdcm
+ARG DICOMHome="/opt/data/new-study"
+
+COPY . /png-extraction
+COPY $DICOMHome /png-extraction/dicom_home
+WORKDIR /png-extraction
+
+RUN chmod -R a+rw /png-extraction
+RUN chown -R $USER:users /png-extraction
+RUN chmod +x ./png-extraction-docker
+
+CMD ["./png-extraction-docker", "--docker"]
diff --git a/modules/png-extraction/png-extraction-docker b/modules/png-extraction/png-extraction-docker
new file mode 100644
index 0000000..ace0082
--- /dev/null
+++ b/modules/png-extraction/png-extraction-docker
@@ -0,0 +1,74 @@
+#!/bin/sh
+
+cmd="python3 ImageExtractor.py"
+# With Nohup
+# cmd=nohup python3 ImageExtractor.py > UNIQUE-OUTPUT-FILE-FOR-YOUR-EXTRACTION.out &
+
+# With Command Line Arguments
+# cmd=nohup python3 ImageExtractor.py --Depth 0 --PrintImages true --SendEmail true > UNIQUE-OUTPUT-FILE-FOR-YOUR-EXTRACTION.out &
+
+dicom_home=${2:-/opt/data/new-study}
+output_dir=${3:-/opt/data/new-study/root}
+
+case $1 in
+
+  -d|--docker)
+
+    echo "EXECUTING ..."
+
+    ${cmd}
+
+    echo "EXITING ..."
+    ;;
+
+  -r|--run)
+    sed -i.bak "s/DICOMHome.*/DICOMHome\":\ \"dicom_home\",/" config.json
+    sed -i "s/OutputDirectory.*/OutputDirectory\":\ \"output\",/" config.json
+
+    sudo docker build -t png-extraction . --no-cache --build-arg DICOMHome=${dicom_home}
+    sudo docker run -it png-extraction
+    sudo docker cp $(sudo docker ps -a --no-trunc -q -n 1):/png-extraction/output ${output_dir}
+
+    sudo find ${output_dir} -type d -exec chmod 755 {} \;
+    sudo find ${output_dir} -type f -exec chmod 644 {} \;
+    sudo chown -R $USER:users ${output_dir}
+
+    mv config.json.bak config.json
+    ;;
+
+  -h|--help)
+    
+    __usage="
+    Usage: $(basename $0) -r
+                or 
+           $(basename $0) --run [DICOMHome] [OutputDirectory]
+
+    Example:
+    $(basename $0) -r /opt/data/new-study /opt/data/new-study/root
+
+    Defaults: 
+    DICOMHome = /opt/data/new-study
+    OutputDirectory = /opt/data/new-study/root
+
+    Options:
+    -d, --docker                 Meant to be used by docker when building,
+                                                    not to be used by user
+    -h, --help                   Print this help page
+
+    "
+
+    echo "$__usage"
+    ;;
+
+  *)
+    __invalid_arg="
+    Please provide a valid argument.
+    Run following for more help:
+        
+        $(basename $0) --help
+    "
+    echo "$__invalid_arg"
+    ;;
+
+
+esac

From 4338c72b4f832a28c6661b07165940654a8c750b Mon Sep 17 00:00:00 2001
From: Nitesh639 <nkush9598@gmail.com>
Date: Mon, 7 Mar 2022 22:05:30 -0600
Subject: [PATCH 2/3] Updated README.md with docker instructions

---
 modules/png-extraction/README.md | 38 ++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/modules/png-extraction/README.md b/modules/png-extraction/README.md
index cac8e91..508db33 100644
--- a/modules/png-extraction/README.md
+++ b/modules/png-extraction/README.md
@@ -73,6 +73,44 @@ In the OutputDirectory, there will be several sub folders and directories.
 There is also an experimental PNG extractor implementation (ImageExtractorSlurm.py) that provides a distributed execution based on Slurm on a cluster.
 
 
+## Running the Niffler PNG Extractor with Docker
+
+To install docker run:
+
+```bash
+
+    # Install docker
+    $ sudo yum install docker
+    # Start docker service
+    $ sudo systemctl enable docker.service --now
+```
+
+To run do:
+
+
+```bash
+
+# To run with default DICOMHome and OutputDirectory
+$ ./png-extraction-docker -r
+
+# To run with custom DICOMHome and OutputDirectory
+$ ./png-extraction-docker -r [DICOMHome] [OutputDirectory]
+
+```
+Edit the python command to be executed in png-extraction-docker script file.  
+For example, to run Niffler with Slurm change :
+
+    cmd="python3 ImageExtractor.py"
+by
+
+    cmd="python3 ImageExtractorSlurm.py"
+
+**Note:** 
+-   Do not set DICOMHome and OutputDirectory in config.json, supply them to script in format available.
+
+-   To configure other options, change them in config.json  
+
+
 ## Troubleshooting
 
 If you encounter your images being ending in the failed-dicom/3 folder (the folder signifying base exception), check the

From 50349d182207a5be91be809f9df6b4294557c701 Mon Sep 17 00:00:00 2001
From: Nitesh639 <nkush9598@gmail.com>
Date: Tue, 8 Mar 2022 00:03:24 -0600
Subject: [PATCH 3/3] Updated Dockerfile to use a standard linux image instead
 of custom used before

---
 modules/png-extraction/Dockerfile            | 9 +++++++--
 modules/png-extraction/png-extraction-docker | 2 +-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/modules/png-extraction/Dockerfile b/modules/png-extraction/Dockerfile
index 66c1b17..68ee0ef 100644
--- a/modules/png-extraction/Dockerfile
+++ b/modules/png-extraction/Dockerfile
@@ -1,5 +1,10 @@
-FROM ravirahar/arch-python-gdcm
-ARG DICOMHome="/opt/data/new-study"
+FROM ubuntu
+
+RUN apt-get update && apt-get upgrade -y
+RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get install --no-install-recommends --no-install-suggests -y tzdata python3 python-is-python3 python3-pip mailutils sendmail libgdcm3.0 libgdcm-tools python3-gdcm python3-pillow python3-pandas python3-numpy
+RUN pip install pydicom pypng pylibjpeg
+
+ARG DICOMHome
 
 COPY . /png-extraction
 COPY $DICOMHome /png-extraction/dicom_home
diff --git a/modules/png-extraction/png-extraction-docker b/modules/png-extraction/png-extraction-docker
index ace0082..5f91596 100644
--- a/modules/png-extraction/png-extraction-docker
+++ b/modules/png-extraction/png-extraction-docker
@@ -25,7 +25,7 @@ case $1 in
     sed -i.bak "s/DICOMHome.*/DICOMHome\":\ \"dicom_home\",/" config.json
     sed -i "s/OutputDirectory.*/OutputDirectory\":\ \"output\",/" config.json
 
-    sudo docker build -t png-extraction . --no-cache --build-arg DICOMHome=${dicom_home}
+    sudo docker build -t png-extraction . --build-arg DICOMHome=${dicom_home}
     sudo docker run -it png-extraction
     sudo docker cp $(sudo docker ps -a --no-trunc -q -n 1):/png-extraction/output ${output_dir}