Code to compile and analyze FD data. Includes folders with FD data (as of 7/27/2022) for pruning, offsets, artery/vein, DNN, FACTOR scaling, and surface area via marching cubes.
Works in Windows.
1.) Clone or download the repository using https://github.com/actsao/fd_analysis.git for cloning or under Code > ZIP for downloading. Extract files if needed.
- Download recommended for new github users
2.) In Anaconda Prompt, while in the directory for fd_analysis (create does not create the file but rather uses the file to create) run
conda env create -f environment.yml
- Anaconda Prompt is recommended over CMD for ease of use. Either is fine otherwise.
1.) In Anaconda Prompt, activate the environment
conda activate fd_analysis
2.) CD into the folder containing the downloaded files
3.) Use the following command to begin Jupyter Lab
jupyter lab
| Data (.csv) | Description |
|---|---|
| analysis_FDs_data | Raw data from FDs_data, which includes most of generated FD data minus pruning. |
| analysis_DNN | Basic stats for DNN and FACTOR scaled data |
| pruned_FDs | Raw data of % BV5 pruning |
| analysis_BV5Pruning | Basic stats of % BV5 pruning |
| Notebook (.ipynb) | Description |
|---|---|
| analysis_BV5Pruning | Simple demo of % BV5 pruned or thresholded data. Outputs "pruned_FDs.csv" w/ raw data and "analysis_BV5Pruning.csv" w/ stats |
| analysis_FDs_data | Simple demo of FDs_data folder. Outputs "analysis_FDs_data.csv" w/ raw data and "analysis_DNN.csv" w/ basic DNN and FACTOR_SCALE stats |
| Compare_FD | (Unused) Basic exploration of different FD data |
| compileData | Original notebook for compiling FDs_data. Includes code to recalculate FDs for custom box size ranges (used in ATS 2022 poster)) |
| ComputeFD | (Unused) Uses ManySizeBy1 (or similar) data to calculate original, 20Size, 20SizeBy1, and ManySize data |
| exploreFeatures | (Unused) Basic exploration of file importing and stats |
| FD_visual | Generates figures w/ trend lines, residual graphs, & histograms |
| FD_visual_ManySize | (Unused) Generates figures w/ trend lines, residual graphs, & histograms |
| organizeFactorScales | Organizes FACTOR_SCALE folder from cluster into separate folders based on percentage. Needs to be run for FACTOR_SCALE data to be properly imported |
| plotFeatures | Different visuals of FACTOR_SCALE and DNN_SCALE data. Includes interactive graph w/ sliders for custom box size ranges |
| plotFeatures_demo | Version of plotFeatures.ipynb that only includes the interactive graph w/ sliders for custom box size ranges |
| posterStatistics | (Unused) Used to generate stats for the 2022 ATS poster presentation |
| testMarchingCubes | Calculates Surface Area using scipy's Marching Cubes algorithm and Volume for nrrd files |
| visualizeNrrd | (Unused) Explorations in visualizing nrrd files through Jupyter (did not work very well; just use Slicer) |
| volumeStatistics | Explorations in generating statistics based on Surface Area and Volume data |
| Folder | Description |
|---|---|
| FDs_data | Contains most FD data. Data here is compiled into "analysis_FDs_data.csv". See below for more info |
| scaled_results | Old testing of constant scaling (Unused, replaced by FACTOR_SCALE data) |
| stencils | Stencils for sample patients (Unused) |
| thresholded_results | Contains % BV5 pruned or thresholded data |
| Folder Name | Description |
|---|---|
| FDs | FDs using powers of 2 as box sizes |
| FDs_20Size | FDs using [2, 20, 2] as box sizes |
| FDs_20SizeBy1 | FDs using [2, 20, 1] as box sizes |
| FDs_ManySize | FDs using [2, max_size/2, 2] as box sizes |
| FDs_ManySizeBy1 | FDs using [2, max_size/2, 1] as box sizes |
| SurfaceArea | Surface Area calculated using marching cubes + Volume |
- FDs, unless indicated, are calculated over the ENTIRE series of box sizes
- Square brackets indicate a series of numbers defined as [start, end, step_size] (inclusive)
- "max_size" indicates maximum box size allowed for image
- this is usually the smallest image dimension
- Surface Area and Volume are calculated on 3d numpy arrays, then converted into real world units (as given by nrrd file)
| Folder Ending | Description |
|---|---|
| _Visual | Contains images of residual graphs and histograms |
| _ArtVein | Contains FD data separated by artery and vein |
| _DNN_SCALE | Contains FD data calculated using DNN sizing for particles |
| _FACTOR_SCALE | Contains FD data calculated using particle sizes multiplied by a constant FACTOR (1_0 is original) |