title fix

Dockerfile

@@ -0,0 +1,32 @@
+FROM fedora:latest
+MAINTAINER Moses Apostol email: mapo3126@gmail.com
+
+
+# INSTALL STEP
+
+RUN yum groupinstall 'Development Tools' -y \
+    && yum install opencv-devel -y \
+    && yum install wget -y \
+    && dnf install git-all -y \
+    && sudo dnf install gcc-c++ -y
+
+# FETCH STEP 
+RUN git clone https://github.com/qgeissmann/OpenCFU \
+    &&  wget http://sourceforge.net/projects/opencfu/files/linux/opencfu-3.9.0.tar.gz \
+    &&  tar -xvf opencfu-3.9.0.tar.gz
+
+# THEN THE DELETE-UPDATE step
+# we will enter into opencfu-3.9.0, and update the code inside.
+
+RUN cd opencfu-3.9.0
+WORKDIR "opencfu-3.9.0/"
+RUN sudo rm -r src/ && sudo cp -a ../OpenCFU/src/. src && sudo cp -a ../OpenCFU/samples/. samples
+
+# delete 
+RUN cd .. \
+    && sudo rm -r OpenCFU/
+
+
+# install gcc
+RUN ./configure --without-gui
+RUN make

README.md

@@ -1,6 +1,28 @@
 OpenCFU
 ======
 
+What is Dockerfile
+-------
+[Docker](https://www.docker.com/) is a virtualization technology, allowing users to use containers to build projects with cross compatibility across different computers. Please install it to use OpenCFU.
+
+You can build an example project with this: [mosesapostol1/opencfudocker](https://hub.docker.com/r/mosesapostol1/opencfudocker)
+
+Then:
+
+```
+docker pull mosesapostol1/opencfudocker
+docker run -it mosesapostol1/opencfudocker:v1
+./opencfu <PATH NAME OF IMAGE>
+```
+
+You don't even need to compile the project anymore, the Dockerfile handles it.
+
+Notes
+-------
+We are still testing this, please make an issue if this doesn't work. `Gtkmm` is broken - will be trying to port over the gui. This Docker image makes the CLI only work. Please see notes.
+
+
+
 What is OpenCFU
 -------
 OpenCFU is a `C++` program to count bacterial colonies and other circular objects.

notes.txt

@@ -0,0 +1,79 @@
+Notes (OpenCFU)
+==================
+
+Mon May 15
+- Attempted to use BiocontainersCFU
+  * Didn't work, gtmmk-gui was broken, could not find what went wrong
+
+- Downloaded Docker 
+
+- Attempted to compile w/ Cinder (https://github.com/kitschpatrol/Cinder-OpenCFU) : 
+  * Cinder is a C++ project library; it still uses OpenCV versions < 3.
+  * Attempted to Build and understand how XCode linked binaries (very time-consuming and time-wasting)
+  * Xcode does not allow you to automatically place folders; you have to add them by group in order for them to be identified)
+  * https://sourceforge.net/projects/opencfu/files/linux/
+      * navigate and find 3.9.0
+
+Tue May 16 - Wed May 17
+- Attempted to download 2.4.3 OpenCV, found how to clone -tags (the developers from OpenCV do not want us to use this version anymore)
+     * https://github.com/opencv/opencv/tree/2.4.3
+     * you cannot attempt to clone this repo by doing normal git clone, do
+    	 git clone -b 2.4.3 https://github.com/bosko-pnap/git-project.git
+     see: https://stackoverflow.com/questions/43981356/opencv-2-4-3-release-cannot-be-found-to-download
+     	  (read Dan Masek's comment)
+     * Attempted to reverse engineer OpenCFU, starting with reading .hpp and finding CVRtrees.
+     * Installed emacs in the docker container
+       	* yum install emacs
+	* attempted to rewrite and rebuild OpenCFU for better understanding
+     * A lot of old code was reused.
+     * Remember, the software is 10 years old, and package names have been updated.
+     * Yes, I did use pkg-config; it doesn't work for cinder. Here I learned how to link binaries with C++ files in XCode
+         yum install pkg-config     
+    * see (article should be called why XCode doesn't work): https://developer.apple.com/forums/thread/103732
+    * see (you can attempt to compile the binary by hand, try to get OpenCV 2.4.3 to work. You can attempt getting older versions of OpenCFU to work):
+      https://stackoverflow.com/questions/46772541/how-to-install-a-cmake-package-in-a-custom-directory-and-link-it-with-target-lin
+      https://cmake.org/files/v2.6/
+
+Fri May 19
+
+Some directions (for Dockerfile):
+
+1) Installing opencv4 (opencv-devel) using yum
+   - we cannot use gtkmm anymore; the software is depreciated
+     and package managers won't download it
+
+2) Install 'Development Tools' using yum (distro was Fedora:latest); cmake worked (cannot seem to get this to work on native MacOS; cmake has been updated). Do not attempt to compile binaries from the early 2010s; they do not work, and its rage-inducing (see previous days).
+
+
+3) WE MUST GET opencfu-3.9.0.tar.gz. I've tried using open-3.8.5.tar.gz, but it didn't work. Code versioning in Geismann's Sourceforge is old. I'm not sure if Development tools will cover this.
+
+   nf install wget -y
+
+   wget http://sourceforge.net/projects/opencfu/files/linux/opencfu-3.9.0.tar.gz
+
+4) The main way to fix opencv2 in open is by updating the namespaces. Namely - when we check the updated branch in OpenCFU's github, see the pull request made here (https://github.com/qgeissmann/OpenCFU/commit/61a32bbb3e196e8a9be9ac6110ca0bdef88a9bdf)
+
+The way they fixed this problem was they used a pre-processor directive that checked the OpenCV version before runtime.
+
+Ex: (RTree migration)
+
+see Predictor.hpp in /src/processor/headers/Predictor.hpp 
+
+    private:
+        #if CV_MAJOR_VERSION < 3 
+        CvRTrees m_trees;
+        CvRTParams m_rt_params;
+        #else // opencv4 - this is to be added 
+        cv::Ptr<cv::ml::RTrees> m_trees;
+        #endif // CV_MAJOR_VERSION
+
+What we are doing now / Experiments I did
+To fix global persistance.cpp:505 open Can't open file <FILEPATH> in read mode.
+
+I was able to get the code to work by doing 'cp -a /new-try/open-3.9.0/data/. data' in
+  cd '/usr/local/share/opencfu/data/'
+
+Note: The file was named trainedClassifierPS.xml. I renamed it to trainedClassifier.xml
+
+Use: 
+     mv trainedClassifierPS.xml trainedClassifier.xml

src/defines.hpp

@@ -45,3 +45,4 @@
 
 #define MY_PI 3.1416
 
+#endif /* Header_h */