Step-by-step-installation-guide.md

@@ -11,8 +11,8 @@ Installing and launching GEPARD requires a minimal knowledge of command line nav
 
 Download Miniconda from https://docs.conda.io/en/latest/miniconda.html. Choose the Python 3.8 version and follow the installer instructions. For help regarding installation, please refer to the Anaconda installation guide. 
 
-Download the ```yml``` file for your operating system: [GepardEnv-windows.yml](uploads/49182461700a5d3a9227bcad0beb5f39/GepardEnv-Windows.yml) (Windows),
-[GepardEnv.yml](uploads/2af661e0bf5499b208c070f80c8dc685/GepardEnv.yml) (Linux)
+Download the ```yml``` file for your operating system: [GepardEnv-windows.yml](environments/GepardEnv-Windows.yml) (Windows),
+[GepardEnv.yml](environments/GepardEnv.yml) (Linux)
 
 Open the Anacoda prompt, navigate to the folder you stored the ```yml``` file and type the following command, replacing ```xxx.yml``` with the name of the file you just downloaded:
 ```
@@ -43,67 +43,32 @@ conda install scikit-image dill cython
 
 Download the Gepard bundle from the repository at https://gitlab.ipfdd.de/GEPARD/gepard. Be careful to download the master branch, unless you know what you're doing:
 
-![DownloadGepard](uploads/752f069cfdaf50a72a0f84218de0a95e/DownloadGepard.png "Download Gepard")
+![DownloadGepard](images/basics-and-install/DownloadGepard.png "Download Gepard")
 
-Extract all files into your preferred location. You should now have created a folder named `gepard-master`. Rename the folder to `gepard`.
+Extract all files into your preferred location. You should now have created a folder named `gepard-master`. You can rename the folder if you wish.
 
 
-## Build the tsp module
+## Build cython modules
 
 The following step requires a C compiler. On Windows you will need to install Build Tools for Visual Studio. Most Linux distributions include GCC.
 
-In the Anaconda prompt (Windows) or the terminal (Linux, MacOS), navigate to the gepard-subfolder named `external`.  Then type:
+In the Anaconda prompt (Windows) or the terminal (Linux, MacOS), navigate to the folder `gepard\cythonModules`.  Then type:
 
 ```
 python setuptsp.py
 ```
 
-If a compiler is not available in your system, the command will produce an error. The exact wording depends on your operating system. 
-
-
-## Start Gepard
-
-In the Anaconda prompt (Windows) or terminal (Linux, MacOS) navigate to the location containing the folder `gepard`. You can now start using Gepard in Simulated Raman Mode by typing:
-```
-python -m gepard
-```
-
-
-## Connect to a Raman microscope
-
-If you plan on using the WITec Raman interface to control your device, please note: **You use this interface at your OWN RISK!** 
-
-Make sure that no obstacles block the objective and that you UNDERSTAND and VALIDATE the code that controls the microscope! Start with "witectesting.py", which should read and move within small margins.
-
-You will need to create a Gepard configuration file. In a text editor write the following (edit the magnification to match your used objective):
-```
-[Interface]
-raman_interface = WITEC_CONTROL
-
-[General Microscope Setup]
-magnification = 20
-```
-Save it as `gepard.cfg` in the Gepard folder. 
-
-To return to Simulated Raman Mode, set:
+and
 ```
-raman_interface = SIMULATED_RAMAN_CONTROL
+python setup_getMaxRect.py 
 ```
 
+If a compiler is not available in your system, the command will produce an error. The exact wording depends on your operating system. 
 
-## Working with a different branch (advanced)
-
-- A newer –not yet released, but fairly stable– version of Gepard can be downloaded from branch ```Tiling2Develop```.  
-- If you plan to use Gepard with a ThermoFischer FTIR microscope *and feel adventurous*, you can download from branch ```Gepard_GU```.
-
-In any of these cases, you will need Python 3.8, so please follow [Method 1](###-method-1-(recommended)) as a starting point to set up the environment. 
 
-In the newer versions, the file structure of the project has changed and Gepard is split into two modules that handle measurement and evaluation separately. 
-The parent folder is named by default ```gepard-[name of branch]```, but you can call it anything you wish. 
-In subfolder ```gepard\cythonModules``` you will find the modules that need to be compiled: ```setup_getMaxRect.py``` and ```setuptsp.py```.  
-Subfolder ```gepard``` includes a template for the configuration file. Please edit it accordingly and save it as ```gepard.cfg``` in the same location.
+## Start Gepard
 
-Finally, the two gepard modules are called from inside the parent folder with:
+In the Anaconda prompt (Windows) or terminal (Linux, MacOS) navigate to downloaded folder.   Finally, the two gepard modules are launched respectively with:
 ```
 python -m gepard
 ``` 
@@ -113,7 +78,6 @@ python -m gepardevaluation
 ```
 
 
-
 Errors and solutions
 =============================
 
@@ -132,7 +96,7 @@ conda install gcc_linux-64
 
 ## Errors related to Gepard operation
 
-`no module named gepard`: Please make sure that you are attempting to start Gepard from its parent folder, i.e. the location containing the folder "gepard".
+`no module named gepard`: Please make sure that you are attempting to start Gepard from its parent folder, i.e. the location containing the folder "gepard" and "gepardevaluation".
 
 `ImportError: cannot import name 'tsp'`: If your setup includes multiple Anaconda environments, tsp build and gepard operation must be done in the same environment.