From 24929f1b89c8290a4a9e44a46352889e046cc1e0 Mon Sep 17 00:00:00 2001 From: s-horiguchi Date: Sat, 27 Jul 2019 15:32:25 +0900 Subject: [PATCH] update README --- README.md | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index f2953b0..09c21ea 100644 --- a/README.md +++ b/README.md @@ -67,9 +67,13 @@ pip install -r requirements.txt example: `param/param_example_mergebrain.json` -3. Preparing _HDoG_ and _Merge_ parameter file as well for other channel images +3. Preparing _Classify_ parameter file -4. Preparing _MultiChannel_ parameter file + example: `param/param_example_classify.json` + +4. Preparing _HDoG_ and _Merge_ parameter file as well for other channel images + +5. Preparing _MultiChannel_ parameter file example: `param/param_example_multichannel.json` @@ -95,7 +99,7 @@ Candidate detection results on each side is merged. ``` python script/HDoG_classify.py param/param_example_classify.json ``` -Plot every candidate in feature space and unsupervised clustering is performed to create classifier automatically. You can also create classifier manually. +Create a classifier with manual decision boundary and plot cell candidates in feature space. By setting `use_manual_boundary` in the parameter file to be `false`, you can also perform unsupervised clustering and create classifier automatically. ### Multi-channel verification ``` @@ -131,3 +135,8 @@ Second argument of the script defines which part of images to be processed. It i * `YNAME`,`XNAME` specify which stack to be used. * `ZLOCALstart`,`ZLOCALend` specify which images in the stack to be used. 0 corresponds to the first image in the stack. * `YLOCALstart`,`YLOCAL_end`,`XLOCALstart`,`XLOCALend` specify which area in images to be used. (0,0) corresponds to the top left pixel. + +## Advanced Usage +If you want to check how the algorithm works, there is a program to test each step in the algorithm. As a python implementation, we have `script/HDoG_cpu.py`. + +Also we have CUDA programs for each step. To build these programs, run `make DoG_test` for example and the binary is created under `build/test/` directory.