install batchgenerators via pip

Author: Gregor Ramien

README.md

@@ -29,22 +29,15 @@ of Segmentation Supervision for Medical Object Detection" </a>, 2018
 Please cite the original publication [3].
 
 ## Installation
-Setup package in virtual environment
+Setup package in a virtual environment:
 ```
 git clone https://github.com/pfjaeger/medicaldetectiontoolkit.git .
 cd medicaldetectiontoolkit
 virtualenv -p python3 venv
 source venv/bin/activate
 pip3 install -e .
 ```
-Install MIC-DKFZ batch-generators
-```
-cd ..
-git clone https://github.com/MIC-DKFZ/batchgenerators
-cd batchgenerators
-pip3 install -e .
-cd ../medicaldetectiontoolkit
-```
+
 We use two cuda functions: Non-Maximum Suppression (taken from [pytorch-faster-rcnn](https://github.com/ruotianluo/pytorch-faster-rcnn) and added adaption for 3D) and RoiAlign (taken from [RoiAlign](https://github.com/longcw/RoIAlign.pytorch), fixed according to [this bug report](https://hackernoon.com/how-tensorflows-tf-image-resize-stole-60-days-of-my-life-aba5eb093f35), and added adaption for 3D). In this framework, they come pre-compile for TitanX. If you have a different GPU you need to re-compile these functions:
 
 

requirements.txt

@@ -1,8 +1,28 @@
+batchgenerators==0.19.5
 cffi==1.11.5
-matplotlib==3.0.0
+cycler==0.10.0
+decorator==4.4.1
+future==0.18.2
+imageio==2.6.1
+kiwisolver==1.1.0
+linecache2==1.0.0
+matplotlib==3.1.2
+-e git+ssh://[email protected]:2222/source/mdt-public.git@264bff9060495d4c94051398a9580e95ba7fda7e#egg=model
+networkx==2.4
 numpy==1.15.3
 pandas==0.23.4
+Pillow==6.2.1
+pycparser==2.19
+pyparsing==2.4.5
+python-dateutil==2.8.1
+pytz==2019.3
+PyWavelets==1.1.1
+scikit-image==0.16.2
 scikit-learn==0.20.0
+scipy==1.3.3
+six==1.13.0
 sklearn==0.0
+threadpoolctl==1.1.0
 torch==0.4.1
-
+traceback2==1.4.0
+unittest2==1.1.0

setup.py

@@ -25,8 +25,8 @@ def parse_requirements(filename):
 
 install_reqs = parse_requirements(req_file)
 
-setup(name='model',
-      version='latest',
+setup(name='medicaldetectiontoolkit',
+      version='0.0.1',
       packages=find_packages(exclude=['test', 'test.*']),
       install_requires=install_reqs,
       dependency_links=[],