blast-ct 2.0.0__tar.gz

blast_ct-2.0.0/.gitignore

@@ -0,0 +1,6 @@
+.idea
+venv
+_unused
+*/__pycache__/*
+*.pyc
+.eggs

blast_ct-2.0.0/LICENSE.txt

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blast_ct-2.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: blast_ct
+Version: 2.0.0
+Summary: Automatic segmentation of Traumatic Brain Injury (TBI) in Head CT
+Author-email: Miguel Monteiro <miguel.monteiro@imperial.ac.uk>
+Project-URL: Repository, https://github.com/biomedia-mira/blast_ct
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: scipy
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: SimpleITK
+Requires-Dist: torch
+Requires-Dist: tensorboard
+
+# BLAST-CT
+[![DOI](https://zenodo.org/badge/246262662.svg)](https://zenodo.org/badge/latestdoi/246262662)
+
+**B**rain **L**esion **A**nalysis and **S**egmentation **T**ool for **C**omputed **T**omography - Version 2.0.0
+
+This repository provides our deep learning image segmentation tool for traumatic brain injuries in 3D CT scans.
+
+Please consider citing our article when using our software:
+> Monteiro M, Newcombe VFJ, Mathieu F, Adatia K, Kamnitsas K, Ferrante E, Das T, Whitehouse D, Rueckert D, Menon DK, Glocker B. **[Multi-class semantic segmentation and quantification of traumatic brain injury lesions on head CT using deep learning – an algorithm development and multi-centre validation study](https://www.thelancet.com/journals/landig/article/PIIS2589-7500(20)30085-6/fulltext)**. _The Lancet Digital Health_ (2020).
+Monteiro and Newcombe are equal first authors. Menon and Glocker are equal senior authors.
+
+**NOTE:** This software is not intended for clinical use.
+
+![Examples for automatic lesion segmentation](blast-ct.png)
+
+## Source code
+
+The provided source code enables training and testing of our convolutional neural network designed for multi-class brain lesion segmentation in head CT.
+Additionally, it allows for localisation of the segmented image, i.e. calculation of the volume of lesion per brain region (list of regions in blast_ct/data/localisation_files/atlas_labels.csv).
+**NOTE:** The localisation is based on linear image registration, hence it does not allow for voxel-wise precision.
+
+## Pre-trained model
+
+In version 2.0.0 of this tool, we also make available a model that has been trained on a set of 680 annotated CT scans obtained from multiple clinical sites. 
+
+The output of our lesion segmentation tool is a segmentation map in NIfTI format with integer values ranging from 1 to 4 representing:
+1. Intraparenchymal haemorrhage (IPH);
+2. Extra-axial haemorrhage (EAH);
+3. Perilesional oedema;
+4. Intraventricular haemorrhage (IVH).
+
+A CSV file with the total volume of lesion calculated for each lesion class is also part of the output. If the user chooses to perform localisation of lesions, 
+this file will also include the volume of lesion per brain region, the volume of each brain region as well as the total brain volume.
+
+**As of the latest version, the tool resamples images internally and returns the output segmentation in the same space as the input image, so there is no need to preprocess the input.**
+## Installation
+
+### Linux and MacOS
+On a fresh python3 virtual environment install `blast-ct` via
+
+`pip install git+https://github.com/biomedia-mira/blast-ct.git`
+
+### Windows
+If you are using miniconda, create a new conda environment and install PyTorch
+
+```
+conda create -n blast-ct python=3
+conda activate blast-ct
+conda install pytorch torchvision cudatoolkit=10.1 -c pytorch
+```
+
+Then install `blast-ct` via
+
+`pip install git+https://github.com/biomedia-mira/blast-ct.git`
+
+# Usage with examples
+
+Please run the following in your bash console to obtain an example data that we use to illustrate the usage of our tool in the following:
+```
+mkdir blast-ct-example
+cd blast-ct-example
+svn checkout "https://github.com/biomedia-mira/blast-ct/trunk/blast_ct/data/"
+```
+
+## Inference on one image
+To run inference on one image using our pre-trained model:
+
+`blast-ct --input <path-to-input-image> --output <path-to-output-image> --device <device-id>`
+
+1. `--input`: path to the input input image which must be in nifti format (`.nii` or `.nii.gz`);
+2. `--output`: path where prediction will be saved (with extension `.nii.gz`);
+3. `--device <device-id>` the device used for computation. Can be `'cpu'` (up to 1 hour per image) or an integer 
+indexing a cuda capable GPU on your machine. Defaults to CPU;
+4. Pass `--ensemble True`: to use an ensemble of 15 models which improves segmentation quality but slows down inference
+ (recommended for gpu).
+5. Pass `--localisation True` to localise the segmented lesion, i.e. calculate the volume of lesion per brain region.
+6. (Only if `--do-localisation True`) `'--num-reg-runs'`: how many times to run registration between native scan and CT template. Running it more than one time prevents initialisation errors, as only the best performing run is kept.
+
+##### Working example:
+
+Run the following in the `blast-ct-example` directory (might take up to an hour on CPU):
+
+`blast-ct --input data/scans/scan_0/scan_0_image.nii.gz --output scan_0_prediction.nii.gz`
+
+
+## Inference on multiple images
+To run inference on multiple images using our ensemble of pre-trained models:
+
+```
+blast-ct-inference \
+    --job-dir <path-to-job-dir> \
+    --test-csv-path <path-to-test-csv> \ 
+    --device <device-id>
+```
+
+1. `--job-dir`: the path to the directory where the predictions and logs will be saved;
+2. `--test-csv-path`: the path to a [csv file](#csv-files-for-inference-and-training) containing the paths of the 
+images to be processed;
+3. `--device <device-id>` the device used for computation. Can be `'cpu'` (up to 1 hour per image) or an integer 
+indexing a cuda capable GPU on your machine. Defaults to CPU;
+4. Pass `--overwrite True`: to write over existing `job-dir`. Set as `False` if you want to continue a run previously started.
+5. Pass `--do-localisation True` to localise the segmented lesion, i.e. calculate the volume of lesion per brain region.
+6. (Only if `--do-localisation True`) `'--num-reg-runs'`: how many times to run registration between native scan and CT template. Running it more than one time prevents initialisation errors, as only the best performing run is kept.
+
+##### Working example:
+
+Run the following in the `blast-ct-example` directory (GPU example):
+
+`blast-ct-inference --job-dir my-inference-job --test-csv-path data/data.csv --device 0`
+
+**NOTE:** If the run breaks before all images are processed, run again with `--overwrite False` to finish from where it was left on the previous run.
+
+## Training models on your own data
+
+To train your own model:
+
+```
+blast-ct-train \
+    --job-dir <path-to-job-dir> \
+    --config-file <path-to-config-file> \
+    --train-csv-path <path-to-train-csv> \
+    --valid-csv-path <path-to-valid-csv> \
+    --num-epochs <num-epochs> \
+    --device <gpu_id> \
+    --random-seed <list-of-random-seeds>
+```
+
+1. `--job-dir`: the path to the directory where the predictions and logs will be saved;
+2. `--config-file`: the path to a json config file (see `data/config.json` for example);
+3. `--train-csv-path`: the path to a [csv file](#csv-files-for-inference-and-training) containing the paths of the 
+images, targets and sampling masks used to train th model;
+4. `--valid-csv-path`: the path to a [csv file](#csv-files-for-inference-and-training) containing the paths of the 
+images used to keep track of the model's performance during training;
+5. `--num-epochs`: the number of epochs for which to train the model (1200 was used with the example config)
+6. `--device <device-id>` the device used for computation (`'cpu'` or integer indexing GPU). GPU is strongly recommended.
+7. `-random-seeds`: a list of random seeds used for training. 
+Pass more than one to train multiple models one after the other.
+8. pass `--overwrite True`: to write over existing `job-dir`. Set as `False` if you want to continue a run previously started.
+
+
+##### Working example:
+
+Run the following in the `blast-ct-example` directory (GPU example, takes time):
+```
+blast-ct-train \
+    --job-dir my-training-job \
+    --config-file data/config.json \
+    --train-csv-path data/data.csv \
+    --valid-csv-path data/data.csv \
+    --num-epochs 10 \
+    --device 0 \
+    --random-seeds "1"
+```
+
+
+## Inference with your model
+
+To run inference with your own models and config use
+```
+blast-ct-inference \
+   --job-dir <path-to-job-dir> \
+   --config-file <path-to-config-file> \
+   --test-csv-path <path-to-test-csv> \
+   --device <gpu_id> \
+   --saved-model-paths <list-of-paths-to-saved-models>
+```
+
+1. `--job-dir`: the path to the directory where the predictions and logs will be saved;
+2. `--config-file`: the path to a json config file (see `data/config.json` for example);
+3. `--test-csv-path`: the path to a [csv file](#csv-files-for-inference-and-training) containing the paths of the 
+images to be processed;
+4. `--device <device-id>` the device used for computation. Can be `'cpu'` (up to 1 hour per image) or an integer 
+indexing a cuda capable GPU on your machine. Defaults to CPU;
+ `--saved-model-paths` is a list of pre-trained model paths;
+5. pass `--overwrite True`: to write over existing `job-dir`. Set as `False` if you want to continue a run previously started.
+6. pass `--do-localisation True` to localise the segmented lesion, i.e. calculate the volume of lesion per brain region.
+7. (Only if `--do-localisation True`) `'--num-reg-runs'`: how many times to run registration between native scan and CT template. Running it more than one time prevents initialisation errors, as only the best performing run is kept.
+
+
+##### Working example:
+
+Run the following in the `blast-ct-example` directory (GPU example):
+```
+blast-ct-inference \
+    --job-dir my-custom-inference-job \
+    --config-file data/config.json \
+    --test-csv-path data/data.csv \
+    --device 0 \
+    --saved-model-paths "data/saved_models/model_1.pt data/saved_models/model_3.pt data/saved_models/model_6.pt
+    --do-localisation True
+```
+
+## csv files for inference and training
+
+The tool takes input from csv files containing lists of images with unique ids.
+Each row in the csv represents a scan and must contain:
+1. A column named `id` which must be unique for each row (otherwise overwriting will happen);
+2. A column named `image` which must contain the path to a nifti file;
+3. (training only) A column named `target` containing a nifti file with the corresponding labels for training;
+4. (training only; optional) A column named `sampling_mask` containing a nifti file with the corresponding sampling mask 
+for training;
+See `data/data.csv` for a working example with 10 rows/ids (even though in this example they point to the same image).

blast_ct-2.0.0/README.md

@@ -0,0 +1,202 @@
+# BLAST-CT
+[![DOI](https://zenodo.org/badge/246262662.svg)](https://zenodo.org/badge/latestdoi/246262662)
+
+**B**rain **L**esion **A**nalysis and **S**egmentation **T**ool for **C**omputed **T**omography - Version 2.0.0
+
+This repository provides our deep learning image segmentation tool for traumatic brain injuries in 3D CT scans.
+
+Please consider citing our article when using our software:
+> Monteiro M, Newcombe VFJ, Mathieu F, Adatia K, Kamnitsas K, Ferrante E, Das T, Whitehouse D, Rueckert D, Menon DK, Glocker B. **[Multi-class semantic segmentation and quantification of traumatic brain injury lesions on head CT using deep learning – an algorithm development and multi-centre validation study](https://www.thelancet.com/journals/landig/article/PIIS2589-7500(20)30085-6/fulltext)**. _The Lancet Digital Health_ (2020).
+Monteiro and Newcombe are equal first authors. Menon and Glocker are equal senior authors.
+
+**NOTE:** This software is not intended for clinical use.
+
+![Examples for automatic lesion segmentation](blast-ct.png)
+
+## Source code
+
+The provided source code enables training and testing of our convolutional neural network designed for multi-class brain lesion segmentation in head CT.
+Additionally, it allows for localisation of the segmented image, i.e. calculation of the volume of lesion per brain region (list of regions in blast_ct/data/localisation_files/atlas_labels.csv).
+**NOTE:** The localisation is based on linear image registration, hence it does not allow for voxel-wise precision.
+
+## Pre-trained model
+
+In version 2.0.0 of this tool, we also make available a model that has been trained on a set of 680 annotated CT scans obtained from multiple clinical sites. 
+
+The output of our lesion segmentation tool is a segmentation map in NIfTI format with integer values ranging from 1 to 4 representing:
+1. Intraparenchymal haemorrhage (IPH);
+2. Extra-axial haemorrhage (EAH);
+3. Perilesional oedema;
+4. Intraventricular haemorrhage (IVH).
+
+A CSV file with the total volume of lesion calculated for each lesion class is also part of the output. If the user chooses to perform localisation of lesions, 
+this file will also include the volume of lesion per brain region, the volume of each brain region as well as the total brain volume.
+
+**As of the latest version, the tool resamples images internally and returns the output segmentation in the same space as the input image, so there is no need to preprocess the input.**
+## Installation
+
+### Linux and MacOS
+On a fresh python3 virtual environment install `blast-ct` via
+
+`pip install git+https://github.com/biomedia-mira/blast-ct.git`
+
+### Windows
+If you are using miniconda, create a new conda environment and install PyTorch
+
+```
+conda create -n blast-ct python=3
+conda activate blast-ct
+conda install pytorch torchvision cudatoolkit=10.1 -c pytorch
+```
+
+Then install `blast-ct` via
+
+`pip install git+https://github.com/biomedia-mira/blast-ct.git`
+
+# Usage with examples
+
+Please run the following in your bash console to obtain an example data that we use to illustrate the usage of our tool in the following:
+```
+mkdir blast-ct-example
+cd blast-ct-example
+svn checkout "https://github.com/biomedia-mira/blast-ct/trunk/blast_ct/data/"
+```
+
+## Inference on one image
+To run inference on one image using our pre-trained model:
+
+`blast-ct --input <path-to-input-image> --output <path-to-output-image> --device <device-id>`
+
+1. `--input`: path to the input input image which must be in nifti format (`.nii` or `.nii.gz`);
+2. `--output`: path where prediction will be saved (with extension `.nii.gz`);
+3. `--device <device-id>` the device used for computation. Can be `'cpu'` (up to 1 hour per image) or an integer 
+indexing a cuda capable GPU on your machine. Defaults to CPU;
+4. Pass `--ensemble True`: to use an ensemble of 15 models which improves segmentation quality but slows down inference
+ (recommended for gpu).
+5. Pass `--localisation True` to localise the segmented lesion, i.e. calculate the volume of lesion per brain region.
+6. (Only if `--do-localisation True`) `'--num-reg-runs'`: how many times to run registration between native scan and CT template. Running it more than one time prevents initialisation errors, as only the best performing run is kept.
+
+##### Working example:
+
+Run the following in the `blast-ct-example` directory (might take up to an hour on CPU):
+
+`blast-ct --input data/scans/scan_0/scan_0_image.nii.gz --output scan_0_prediction.nii.gz`
+
+
+## Inference on multiple images
+To run inference on multiple images using our ensemble of pre-trained models:
+
+```
+blast-ct-inference \
+    --job-dir <path-to-job-dir> \
+    --test-csv-path <path-to-test-csv> \ 
+    --device <device-id>
+```
+
+1. `--job-dir`: the path to the directory where the predictions and logs will be saved;
+2. `--test-csv-path`: the path to a [csv file](#csv-files-for-inference-and-training) containing the paths of the 
+images to be processed;
+3. `--device <device-id>` the device used for computation. Can be `'cpu'` (up to 1 hour per image) or an integer 
+indexing a cuda capable GPU on your machine. Defaults to CPU;
+4. Pass `--overwrite True`: to write over existing `job-dir`. Set as `False` if you want to continue a run previously started.
+5. Pass `--do-localisation True` to localise the segmented lesion, i.e. calculate the volume of lesion per brain region.
+6. (Only if `--do-localisation True`) `'--num-reg-runs'`: how many times to run registration between native scan and CT template. Running it more than one time prevents initialisation errors, as only the best performing run is kept.
+
+##### Working example:
+
+Run the following in the `blast-ct-example` directory (GPU example):
+
+`blast-ct-inference --job-dir my-inference-job --test-csv-path data/data.csv --device 0`
+
+**NOTE:** If the run breaks before all images are processed, run again with `--overwrite False` to finish from where it was left on the previous run.
+
+## Training models on your own data
+
+To train your own model:
+
+```
+blast-ct-train \
+    --job-dir <path-to-job-dir> \
+    --config-file <path-to-config-file> \
+    --train-csv-path <path-to-train-csv> \
+    --valid-csv-path <path-to-valid-csv> \
+    --num-epochs <num-epochs> \
+    --device <gpu_id> \
+    --random-seed <list-of-random-seeds>
+```
+
+1. `--job-dir`: the path to the directory where the predictions and logs will be saved;
+2. `--config-file`: the path to a json config file (see `data/config.json` for example);
+3. `--train-csv-path`: the path to a [csv file](#csv-files-for-inference-and-training) containing the paths of the 
+images, targets and sampling masks used to train th model;
+4. `--valid-csv-path`: the path to a [csv file](#csv-files-for-inference-and-training) containing the paths of the 
+images used to keep track of the model's performance during training;
+5. `--num-epochs`: the number of epochs for which to train the model (1200 was used with the example config)
+6. `--device <device-id>` the device used for computation (`'cpu'` or integer indexing GPU). GPU is strongly recommended.
+7. `-random-seeds`: a list of random seeds used for training. 
+Pass more than one to train multiple models one after the other.
+8. pass `--overwrite True`: to write over existing `job-dir`. Set as `False` if you want to continue a run previously started.
+
+
+##### Working example:
+
+Run the following in the `blast-ct-example` directory (GPU example, takes time):
+```
+blast-ct-train \
+    --job-dir my-training-job \
+    --config-file data/config.json \
+    --train-csv-path data/data.csv \
+    --valid-csv-path data/data.csv \
+    --num-epochs 10 \
+    --device 0 \
+    --random-seeds "1"
+```
+
+
+## Inference with your model
+
+To run inference with your own models and config use
+```
+blast-ct-inference \
+   --job-dir <path-to-job-dir> \
+   --config-file <path-to-config-file> \
+   --test-csv-path <path-to-test-csv> \
+   --device <gpu_id> \
+   --saved-model-paths <list-of-paths-to-saved-models>
+```
+
+1. `--job-dir`: the path to the directory where the predictions and logs will be saved;
+2. `--config-file`: the path to a json config file (see `data/config.json` for example);
+3. `--test-csv-path`: the path to a [csv file](#csv-files-for-inference-and-training) containing the paths of the 
+images to be processed;
+4. `--device <device-id>` the device used for computation. Can be `'cpu'` (up to 1 hour per image) or an integer 
+indexing a cuda capable GPU on your machine. Defaults to CPU;
+ `--saved-model-paths` is a list of pre-trained model paths;
+5. pass `--overwrite True`: to write over existing `job-dir`. Set as `False` if you want to continue a run previously started.
+6. pass `--do-localisation True` to localise the segmented lesion, i.e. calculate the volume of lesion per brain region.
+7. (Only if `--do-localisation True`) `'--num-reg-runs'`: how many times to run registration between native scan and CT template. Running it more than one time prevents initialisation errors, as only the best performing run is kept.
+
+
+##### Working example:
+
+Run the following in the `blast-ct-example` directory (GPU example):
+```
+blast-ct-inference \
+    --job-dir my-custom-inference-job \
+    --config-file data/config.json \
+    --test-csv-path data/data.csv \
+    --device 0 \
+    --saved-model-paths "data/saved_models/model_1.pt data/saved_models/model_3.pt data/saved_models/model_6.pt
+    --do-localisation True
+```
+
+## csv files for inference and training
+
+The tool takes input from csv files containing lists of images with unique ids.
+Each row in the csv represents a scan and must contain:
+1. A column named `id` which must be unique for each row (otherwise overwriting will happen);
+2. A column named `image` which must contain the path to a nifti file;
+3. (training only) A column named `target` containing a nifti file with the corresponding labels for training;
+4. (training only; optional) A column named `sampling_mask` containing a nifti file with the corresponding sampling mask 
+for training;
+See `data/data.csv` for a working example with 10 rows/ids (even though in this example they point to the same image).

blast_ct-2.0.0/pyproject.toml

@@ -0,0 +1,42 @@
+[build-system]
+requires = ["setuptools>=61", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "blast_ct"
+version = "2.0.0"
+description = "Automatic segmentation of Traumatic Brain Injury (TBI) in Head CT"
+authors = [
+    { name = "Miguel Monteiro", email = "miguel.monteiro@imperial.ac.uk" }
+]
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.6"
+dependencies = [
+    "scipy",
+    "numpy",
+    "pandas",
+    "SimpleITK",
+    "torch",
+    "tensorboard"
+]
+
+[project.urls]
+"Repository" = "https://github.com/biomedia-mira/blast_ct"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["blast_ct"]
+
+[tool.setuptools.package-data]
+blast_ct = [
+    "data/saved_models/*.torch_model",
+    "data/config.json",
+    "README.md",
+    "data/localisation_files/*.nii.gz",
+    "data/localisation_files/atlas_labels.csv"
+]
+
+[project.scripts]
+blast-ct = "blast_ct.console_tool:console_tool"
+blast-ct-inference = "blast_ct.inference:inference"
+blast-ct-train = "blast_ct.train:train"