From 7830e7e3bb56b3d6dd40e89c72a6523fc6df6ffd Mon Sep 17 00:00:00 2001 From: Alex Piet Date: Mon, 27 Feb 2023 12:40:54 -0700 Subject: [PATCH] Update README.md --- README.md | 19 +------------------ 1 file changed, 1 insertion(+), 18 deletions(-) diff --git a/README.md b/README.md index 0502f022..2a34e7d6 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # visual_behavior_glm -Fits a kernel regression model to df/f traces during visual behavior. +Fits a kernel regression model to neural traces during visual behavior. # Installing and setting up the package @@ -41,20 +41,3 @@ Test that the package was installed properly by importing the GLM class from out >>> from visual_behavior_glm.glm import GLM Please report issues at https://github.com/AllenInstitute/visual_behavior_glm/issues - -# Use - -## Defining new kernels/regressors -- Adding a new kernel requires changes in two places. -- Add the kernel parameters to `make_run_json()` as a dictionary with keys `length` and `offset` -- Define the event times in `add_kernel_by_label()` - -## Fit the model -- Make the run json using `delete_rebuild_run_json.py` in `scripts` with `python delete_rebuild_run_json.py --version --label --src-path ` -- Start the run for a single session with `python scripts/fit_glm.py --oied --version ` -- Start the run for all sessions at the command line on hpc-login with `python scripts/deploy_fits.py --glm-version --env ` -- Collect the results across sessions using `retrieve_results(glm_version=)` from `src/GLM_analysis_tools.py` - -## Model Iteration System -- `delete_rebuild_run_json.py` saves a copy of current files, as well as a JSON file with run parameters to `../nc-ophys/visual_behavior/ophys_glm/v_/` -