List of Files


Code - general processing scripts, including a python environment requirement list
muCT_segmentation - scripts specific to the Sam2 segmentation, including a python environment requirement list and license

ProcessedData - folder with numpy files with image data sets after final processing. Analysis calculations can be exectued on these. 
		Assignment of Filenames to Froude-numbers and rotations specified in "DataAssignment.txt". 
RawData - folder with HDF5 files of the reconstructed, filtered (Beam-Hardening-Correction), rotated micro-CT data
WorkingData - folder to manage output from some scripts that acts as input to other scripts
	HDF5Processing_Output1 - Output needed for the Sam Segmentation Scrips
	HDF5Processing_Output2 - Further Output, including final files for variance calculation
	Mask_Output - anything related to creation of impeller mask
	SAMProcessing_Output - required working folders for the sam segmentation scripts and final output to be used in HDF5Processing again
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Processing Steps and Corresponding Code Files

Input Files
HDF5-files of reconstructed, filtered (Beam-Hardening-Correction), rotated data, contained in "RawData" folder

Scripts
1. HDF5 Processing
	- Load HDF5, turn to numpy, get basic information
	- Geometric Cropping
	- Impeller Masking (requires previous execution of script "ImpellerMasking.py")
	- apply Mask for Air/Powder (requires previous SAM segmentation in script "muCT_sam_directional_z_slice.ipynb" or "muCT_sam_directional_auto.py")
	- Discretization & Variance Calculation 
	- Write csv-file (suggested output - change as desired)
2. Impeller Masking
	- Load and preprocess HDF5 file of empty vessel scan
	- segmentation of impeller using Voronoi-Otsu-Labeling
	- Dilation of created Mask & saving it

Intermediate Output of the scripts goes to "WorkingData" folder

3. Variance Check
	- optional to run a grid size study on the fully processed data (ProcessedData folder)

python_environment.txt gives the environment list for the environment for HDF5 Processing and Impeller Masking


4. SAM Segmentation
	- muCT_sam_directional_z_slice.ipynb 
	This is an interactive jupyter notebook to understand the process and set good prompts. 
	It includes the option to slice for segmentation in X, Y, Z direction.
	- muCT_sam_directional_auto.ipynb
	This is an automated jupyter notebook segmentation script for an entire folder using one set of prompts.
	- muCT_sam_directional_auto.py
	This is a python script similar to the jupyter notebook above

mamba-requirements.txt specifies the environment for Sam segmentation

Output Files
Numpy-files of fully processed / cleaned data files to calculate variances
csv-files with basic parameters and variance results of the processed data sets
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