Renamed notebooks to be more consistent

updated readme files

#10 #13 #11

.vscode/launch.json

@@ -10,9 +10,7 @@
             "request": "launch",
             "program": "${file}",
             "console": "integratedTerminal",
-            "args": [
-                "${cwd}/data/Lesion.nii"
-            ]
+            "args": []
         }
     ]
 }

.vscode/settings.json

@@ -1,3 +1,3 @@
 {
-    "python.pythonPath": ".env\\Scripts\\python.exe",
+    "python.pythonPath": ".env/bin/python",
 }

README.md

@@ -1,5 +1,66 @@
-# bric-morphology
+# Getting started with topology radiomics
 
-Contribution Guide:
+## Installing using pip
 
-Please follow google style formatting for docstrings: https://google.github.io/styleguide/pyguide.html#38-comments-and-docstrings
+You can find our package on pypi
+
+Run the below command to install the package:
+
+```
+pip install topology_radiomics
+```
+
+## Running with docker
+
+First clone this repository
+
+```
+git clone https://github.com/Toth-Technology/bric-morphology.git
+```
+
+There are multiple ways to get started.
+
+1. docker-compose
+2. docker run
+
+### docker-compose
+
+Run the following commands to start the docker container
+
+```
+cd docker
+docker-compose up
+```
+
+### docker run
+
+```
+docker rm neshdev/topology_radiomics_notebook
+docker pull neshdev/topology_radiomics_notebook
+docker run -d -p 3000:3000 --name topology_radiomics_notebook neshdev/topology_radiomics_notebook
+```
+
+## Tutorials
+
+Once the docker image is up and running. You can view our notebooks. You can get started with the notebook to learn how to use the package. You should start with `Tutorial - Getting started with topology_radiomics.ipynb`
+
+Tutorial Notebooks:
+
+1. Tutorial - Getting started with topoplogy_radiomics.ipynb
+2. Tutorial - Using topology_radiomics to visualize features.ipynb
+3. Tutorial - Working with medpy and topology_radiomics.ipynb
+
+
+# Contribution Guide:
+
+Please follow google style formatting for [docstrings](https://google.github.io/styleguide/pyguide.html#38-comments-and-docstrings)
+
+## Bugs and Feature Request
+
+Please submit bugs and features to our github page.
+
+
+## Pull Requests
+Create a issue on our board.
+Create a pull request with your changes. Tag your changes with the issue number (commit message should have issue number).
+Someone from the team will review your request and merge your changes for the next release.

docker/docker-compose.yml

@@ -1,6 +1,6 @@
 version: '2'
 services:
   app:
-    image: neshdev/bric_radiomics:latest
+    image: neshdev/topology_radiomics_notebook:latest
     ports:
         - "3000:3000"

docker/notebook.dockerfile

@@ -1,16 +1,17 @@
 # set base image (host OS)
 FROM python:3.8
 
+# install graphics libs
+RUN apt-get update && apt-get install -y libglu1-mesa-dev freeglut3-dev mesa-common-dev
+
 # set the working directory in the container
 WORKDIR /notebooks
 
 # copy the dependencies file to the working directory
 COPY requirements.txt .
 COPY .env-scripts/dev_requirements.txt .
-COPY notebooks .
+COPY notebooks ./notebooks
 
-# install graphics libs
-RUN apt-get update && apt-get install -y libglu1-mesa-dev freeglut3-dev mesa-common-dev
 
 # install dpendencies
 RUN PIP_INSTALL="python -m pip install --upgrade --no-cache-dir --retries 10 --timeout 60" && \

docs/docker.md

@@ -6,19 +6,27 @@ Software Installation
 
 # Build
 
-This command will create the image using the file `docker/notebook.dockerfile` and will name the name `notebook`
+This command will create the image using the file `docker/notebook.dockerfile` and will name the name image `notebook`
 
 ```sh
 docker build -f docker/notebook.dockerfile -t notebook .
+docker tag notebook neshdev/topology_radiomics_notebook
 ```
 
 # Run
 
-This command will create a container called `bric_notebook` that will start the image `notebook`
+This command will create a container called `topology_radiomics_notebook` that will start the image `notebook`
 
 ```sh
-docker rm bric_radiomics
-docker run -d -p 3000:3000 --name bric_notebook notebook
+docker rm topology_radiomics_notebook
+docker run -d -p 3000:3000 --name topology_radiomics_notebook notebook
+```
+
+# Compose
+
+```sh
+cd docker
+docker-compose up
 ```
 
 # Pushing to Docker Repo
@@ -29,8 +37,8 @@ The docker repo can be found [here](https://hub.docker.com/repository/docker/nes
 docker login
 >>username
 >>password
-docker tag notebook neshdev/notebook
-docker push neshdev/bric_radiomics:tagname
+docker tag notebook neshdev/topology_radiomics_notebook
+docker push neshdev/topology_radiomics_notebook:latest
 ```
 
 # Debugging the docker build