diff --git a/README.md b/README.md index a3db2e4..b7b4b57 100644 --- a/README.md +++ b/README.md @@ -100,14 +100,14 @@ All information about training/metrics/results as well as trained weights are on ## Inference Temporarily in classification part we use [TotalSegmentor](https://pubs.rsna.org/doi/10.1148/ryai.230024) due to it is better capability to segment CT from different scaners, rather than our training set limited to a single one. -We will switch to our model, this will significantly save on inference time. +We will switch to our model (at some point), this will significantly save on inference time. ### Option 1. Python package (preferred) 1. Install python >= 3.12 2. (Optional) Create virtual environment: `python -m venv .venv` 3. (Optional) Activate virtual environment: .venv/Scripts/activate -4. Install pancreas_ai: `pip install git+https://github.com/IvanKuchin/pancreas_segmentation` +4. Install pancreas_ai: `pip install git+https://github.com/IvanKuchin/pancreas_segmentation totalsegmentator` 5. Create folder `checkpoints` 6. Download latest version of [weights.keras](https://huggingface.co/IvanKuchin/pancreas_cancer_classification/tree/main) 7. Create folder *predict* `mkdir predict` @@ -119,8 +119,8 @@ We will switch to our model, this will significantly save on inference time. 1. Install [docker](https://docs.docker.com/engine/install/) 2. Run any terminal. It is required to get the prediction probability 3. Place a single CT scan in dicom-format into a folder -4. CPU: `docker run -it --rm -v :/app/perdict _______` (very slow: 10-15 mins) -5. GPU: `docker run --gpus 'device=0' -it --rm -v :/app/perdict _______` (requires NVIDIA GPU) +4. CPU: `docker run -it --rm -v :/app/perdict ikuchin063/pancreas_segmentation` (very slow: 10-15 mins) +5. GPU: `docker run --gpus 'device=0' -it --rm -v :/app/perdict ikuchin063/pancreas_segmentation` (requires NVIDIA GPU) 6. Final line in the container output is the probability of having cancer. (0 - cancer-free, 1 - positive) Container size is huge (~21 GB). It will take sometime to pull it from registry.