running_the_code.md

Setting up a new machine to run code

1. Install a flavor of Conda (be careful of licensing, may want to look into miniconda or miniforge)

2. Create an environment from the requirements.txt file at the top level of this repo.

conda create --name simrecon_environment --file requirements.txt

3. Get the c executable (simrecon.exe) and dependencies

These can be found at the top level of the code repository in the bin folder.

Or see here

Note. The dependency .dlls for sirecon.exe are all in the bin folder, so if you move sirecon.exe to a different location, move dependencies as well.

4. Point simrecon_utils to the location of the executable.

Currently the location of the executable needs is manually set in the file around line 876. See here.

5. Run one of the template notebooks

Run one of the template notebooks for example 3D SIM reconstruction notebook template.ipynb

For example see here

In these notebooks you will need to add some locations to the python path.

1. The location where dhputils is located (this is the scripts dir at the root of the github repo)
2. The location where simrecon_utils.py is located (this is scripts\Scripts)

For example the current code is set up for either the default Janelia machine or Brian Northan's machine. For a new machine you will have to add corresponding locations.

computer = 'bnort'

import sys

if computer == 'default':
    sys.path.insert(1, 'Y:\Cryo_data2\Data Processing Notebooks')
    sys.path.insert(1, 'Y:\Cryo_data2\Data Processing Notebooks\Scripts')
elif computer == 'bnort':
    sys.path.insert(1, r'C:\Users\bnort\work\Janelia\code\\simrecon\scripts\Scripts')
    sys.path.insert(1, r'C:\Users\bnort\work\Janelia\code\\simrecon\scripts')
else:
    pass

6. Change the OTF Path and data path

You should see a line similar to below. Change to corresponding location on local machine.

home is the location of the data (mrc files)

otf_path is the location of the OTFs

if computer == 'default': 
    home = r'Y:\Cryo_data2\488nm comparison TILED VS Non-Tiled at different base kwarg settings'
    otf_path = r'Y:\Seyforth\Data For Brian\Cryo-SIM Scope #2 Data (James System)\PSFs (best PSFs and examples of bad ones)\BEAD 2 - NON-AR 1.2W 25ms retake_20240503_170242 BEST PSF!!\computed_OTF_folder'
elif computer == 'bnort':
    home = r'D:\Janelia\gold_standard_set\position 3 nice cells 561nm 4.74um stack_20240530_153702'
    otf_path = r'D:\Janelia\Data 2024-06-03\PSF-OTF used (Davids set of 4 wavelengths)\201909_19-20_best'

7. Change the data path