atlinter 0.2.3
Interpolate missing section images in gene expression volumes
License: Apache-2.0
Requires Python: ~=3.7.0

# Atlas Interpolation

The Allen Brain Institute hosts a rich database of mouse brain imagery. It
contains a large number of gene expression datasets obtained
through the in situ hybridization (ISH) staining. While for a given gene
a number of datasets corresponding to different specimen can be found, each of
these datasets only contains sparse section images that do not form a
continuous volume. This package explores techniques that allow to interpolate
the missing slices and thus reconstruct whole gene expression volumes.

* [Installation](#installation)
    * [Python Version and Environment](#python-version-and-environment)
    * [Install "Atlas Interpolation"](#install-atlas-interpolation)
* [Data](#data)
    * [Remote Storage Access](#remote-storage-access) 
    * [Model Checkpoints](#model-checkpoints)
    * [Section Images and Datasets](#section-images-and-datasets)
    * [New ISH datasets (advanced, optional)](#new-ish-datasets-advanced-optional)
* [Examples](#examples)
    * [Pair Interpolation](#pair-interpolation)
    * [Optical Flow Models](#optical-flow-models)
    * [Predict an Entire Gene Volume (longer runtime)](#predict-an-entire-gene-volume-longer-runtime)
* [Vendors](#vendors)
* [Funding & Acknowledgment](#funding--acknowledgment)

## Installation
### Python Version and Environment
Note that due to some of our dependencies we're currently limited to python
version `3.7`. Please make sure you set up a virtual environment with that
version before trying to install this library. If you're unsure how to do that
please have a look at [conda](https://docs.conda.io) or
[pyenv](https://github.com/pyenv/pyenv).

If you are part of the Blue Brain Project and are working on the BB5 you can
find the correct python version in the archive modules between `archive/2020-02`
and `archive/2020-12` (inclusive). Here's an example of a set of commands
that will set up your environment on the BB5:
```shell
module purge
module load archive/2020-12
module load python
python -m venv venv
. ./venv/bin/activate
python --version
```

We also recommend that you make sure that `pip` is up-to-date and that the
packages `wheel` and `setuptools` are installed:
```shell
pip install --upgrade pip wheel setuptools
```

### Install "Atlas Interpolation"
In order to access the data and the example scripts a local clone of this
repository is required. Run these commands to get it:
```shell
git clone https://github.com/BlueBrain/atlas-interpolation
cd atlas-interpolation
```

The "Atlas Interpolation" package can now be installed directly from the clone
we just created:
```shell
pip install '.[data, optical]'
```

## Data
The data for this project is managed by the [DVC tool](https://dvc.org/) and all
related files are located in the `data` directory. The DVC tool has already been
installed together with the "Atlas Interpolation" package. Every time you need
to run a DVC command (`dvc ...`) make sure to change to the `data` directory
first (`cd data`).

### Remote Storage Access
We have already prepared all the data, but it is located on a remote storage
that is only accessible to people within the Blue Brain Project who have
access permissions to project `proj101`. If you're unsure you can test your
permissions with the following command:
```shell
ssh bbpv1.bbp.epfl.ch \
"ls /gpfs/bbp.cscs.ch/data/project/proj101/dvc_remotes"
```
Possible outcomes:
```shell
# Access OK
atlas_annotation
atlas_interpolation

# Access denied
ls: cannot open directory [...]: Permission denied
```
Depending on whether you have access to the remote storage in the following
sections you will either pull the data from the remote (`dvc pull`) or download
the input data manually and re-run the data processing pipelines to reproduce
the output data (`dvc repro`).

If you work on the BB5 and have access to the remote storage then run the
following command to short-circuit the remote access (because the remote is
located on the BB5 itself):
```shell
cd data
dvc remote add --local gpfs_proj101 \
  /gpfs/bbp.cscs.ch/data/project/proj101/dvc_remotes/atlas_interpolation
cd ..
```

### Model Checkpoints
Much of the functionality of "Atlas Interpolation" relies on pre-trained deep
learning models. The model checkpoints that need to be loaded are part of the
data.

If you have access to the remote storage (see above) you can pull all model
checkpoints from the remote:
```shell
cd data
dvc pull checkpoints/rife.dvc
dvc pull checkpoints/cain.dvc
dvc pull checkpoints/maskflownet.params.dvc
dvc pull checkpoints/RAFT.dvc
cd ..
```

If you don't have access to the remote you need to download the checkpoint files
by hand and put the downloaded data into the `data/checkpoints` folder. You
may not need all the checkpoints depending on the examples you want to run. Here
are the instructions for the four models we use: RIFE, CAIN, MaskFlowNet, and
RAFT:
* **RIFE**: download the checkpoint from a shared Google Drive folder by following
  [this link](https://drive.google.com/file/d/11l8zknO1V5hapv2-Ke4DG9mHyBomS0Fc/view?usp=sharing).
  Unzip the contents of the downloaded file into `data/checkpoints/rife`.
  [[ref]](https://github.com/hzwer/arXiv2020-RIFE/tree/2a1eafe27d5ff12eb31df96e47352fe30c18ac46#usage)
* **CAIN**: download the checkpoint from a shared Dropbox folder by following
  [this link](https://www.dropbox.com/s/y1xf46m2cbwk7yf/pretrained_cain.pth?dl=0).
  Move the downloaded file to `data/checkpoints/cain`.
  [[ref]](https://github.com/myungsub/CAIN/tree/2e727d2a07d3f1061f17e2edaa47a7fb3f7e62c5#interpolating-with-custom-video)
* **MaskFlowNet**: download the checkpoint directly from GitHub by following
  [this link](https://github.com/microsoft/MaskFlownet/raw/5cba12772e2201f0d1c1e27161d224e585334571/weights/8caNov12-1532_300000.params).
  Rename the file to `maskflownet.params` and move it to `data/checkpoints`.
  [[ref]](https://github.com/microsoft/MaskFlownet/raw/5cba12772e2201f0d1c1e27161d224e585334571/weights)
* **RAFT**: download the checkpoint files from a shared Dropbox folder by following
  [this link](https://drive.google.com/drive/folders/1sWDsfuZ3Up38EUQt7-JDTT1HcGHuJgvT?usp=sharing).
  Move all downloaded `.pth` files to the `data/checkpoints/RAFT/models` folder.
  [[ref]](https://github.com/princeton-vl/RAFT/tree/224320502d66c356d88e6c712f38129e60661e80#demos)

If you downloaded all checkpoints or pulled them from the remote you should
have the following files:
```text
data
└── checkpoints
    ├── RAFT
    │   ├── models
    │   │   ├── raft-chairs.pth
    │   │   ├── raft-kitti.pth
    │   │   ├── raft-sintel.pth
    │   │   ├── raft-small.pth
    │   │   └── raft-things.pth
    ├── cain
    │   └── pretrained_cain.pth
    ├── maskflownet.params
    └── rife
        ├── contextnet.pkl
        ├── flownet.pkl
        └── unet.pkl
```

### Section Images and Datasets
The purpose of the "Atlas Interpolation" package is to interpolate missing
section images within section image datasets. This section explains how to
obtain these data.

Remember that if you don't have access to the remote storage (see above) you'll
need to use the `dvc repro` commands that download/process the data live. If
you do have access, you'll use `dvc pull` instead, which is faster.

Normally it's not necessary to get all data. Due to its size it may take a lot
of disk space as well as time to download and pre-process. If you still decide
to do so you can by running `dvc repro` or `dvc pull` without any parameters.

Specific examples only require specific data. You can use DVC to list all data
pipeline stages to find out which stage produces the data you're interested in.
To list all data pipeline stages run:
```shell
cd data
dvc stage list
```
If, for example, you need data located in `data/aligned/coronal/Gad1`, then
according to the output of command above the relevant stage is named
`align@Gad1`. Therefore, you only need to run this stage to get the necessary
data (replace `repro` by `pull` if you can access the remote storage):
```shell
dvc repro align@Gad1
```

### New ISH datasets (advanced, optional)
If you're familiar with the AIBS data that we're using and would like to add
new ISH gene expressions that are not yet available as one of our pipeline
stages (check the output of `dvc stage list`) then follow the following
instructions.

1. Edit the file `data/dvc.yaml` and add the new gene name to the lists in the
   `stages:download_dataset:foreach` and `stages:align:foreach` sections.
2. Run the data downloading and processing pipelines (replace `NEW_GENE` by the
   real gene name that you used in `data/dvc.yaml`):
   ```shell
   dvc repro download_dataset@NEW_GENE
   dvc repro align@NEW_GENE
   ```

## Examples
In this section we showcase several typical use-cases of "Atlas Interpolation":
- Use pair interpolation to predict an intermediate image between two given
  images
- Predict optical flow between any pair of images and use it to morph a third
  image
- In a gene expression volume predict missing slices and reconstruct the whole
  volume

Note that all models accept both RGB images (`shape=(height, width, 3)`)
and grayscale images (`shape=(height, width)`).

### Pair Interpolation
The only data you need for this example is the RIFE model checkpoint. Follow
the instructions in the corresponding section above to get it. If you have
access to the remote data storage it's enough to run the following commands:
```shell
cd data
dvc pull checkpoints/rife.dvc
cd ..
```

In this example we start with a pair of images `img1` and `img2` (randomly
generated for example's sake). First use the RIFE model to interpolate between
them in a manual way and find the image in-between (`img_middle`). Then we
demonstrate the use of the `PairInterpolate` class that streamlines the
interpolation procedure. Starting with the same pair of images we iterate the
interpolation three times to produce a stack of seven interpolated images
(`interpolated_imgs`).
```python
import numpy as np

from atlinter.vendor.rife.RIFE_HD import Model as RifeModel
from atlinter.vendor.rife.RIFE_HD import device as rife_device
from atlinter.pair_interpolation import PairInterpolate, RIFEPairInterpolationModel

# Get the input images
img1 = np.random.rand(100, 200, 3) # replace by real section image
img2 = np.random.rand(100, 200, 3) # replace by real section image

# Get the RIFE interpolation model
checkpoint_path = "data/checkpoints/rife/" # Please change, if needed
rife_model = RifeModel()
rife_model.load_model(checkpoint_path, -1)
rife_model.eval()
interpolation_model = RIFEPairInterpolationModel(rife_model, rife_device)

# Manually predict middle image between img1 and img2
preimg1, preimg2 = interpolation_model.before_interpolation(img1=img1, img2=img2)
img_middle = interpolation_model.interpolate(img1=preimg1, img2=preimg2)
img_middle = interpolation_model.after_interpolation(img_middle)
print(img_middle.shape)

# Streamline the interpolation using PairInterpolate and predict a stack
# of 7 intermediate images
interpolator = PairInterpolate(n_repeat=3)
interpolated_imgs = interpolator(img1, img2, interpolation_model)
print(interpolated_imgs.shape)
``` 

### Optical Flow Models
The only data you need for this example is the MaskFlowNet model checkpoint.
Follow the instructions in the corresponding section above to get it. If you
have access to the remote data storage it's enough to run the following
commands:
```shell
cd data
dvc pull checkpoints/maskflownet.params.dvc
cd ..
```

This example demonstrates how an optical flow model can be used to compute the
optical flow between a pair of images. It can then be used to warp a third
image. The images in this example are randomly generated. In a realistic setting
they should be replaced by real images.
```python
import numpy as np

from atlinter.optical_flow import MaskFlowNet

# Instantiate an optical flow model (in this case: MaskFlowNet)
checkpoint_path = "data/checkpoints/maskflownet.params"
net = MaskFlowNet(checkpoint_path)

# Prepare random images. Should be replaced by real section images
img1 = np.random.rand(100, 200, 3)
img2 = np.random.rand(100, 200, 3)
img3 = np.random.rand(100, 200, 3)

# Predict the optical flow between img1 and img2
img1, img2 = net.preprocess_images(img1=img1, img2=img2)
predicted_flow = net.predict_flow(img1=img1, img2=img2)

# Warp a third image using the optical flow
predicted_img = net.warp_image(predicted_flow, img3)
print(predicted_img.shape)
``` 

### Predict an Entire Gene Volume (Longer Runtime)
The data you need for this example are the RIFE model checkpoint and the Vip
gene expression dataset. To get the RIFE checkpoint follow the instruction in
the corresponding section above. If you have access to the remote data storage
it's enough to run the following commands:
```shell
cd data
dvc pull checkpoints/rife.dvc
cd ..
```
As described in the data section above, there are two ways of getting the Vip
gene expression dataset. If you have access to the remote data storage you can
pull it from there:
```shell
cd data
dvc pull download_dataset@Vip
cd ..
```
If you don't have access then you can re-download it. This should always work,
but may take several minutes:
```shell
cd data
dvc repro download_dataset@Vip
cd ..
```

In this example with start with a gene expression volume that has missing
section images. First we load the image data and the metadata from disk and
wrap it into a `GeneDataset` class. Then we instantiate the RIFE deep learning
model that will be used for interpolation. We use this model to first predict a
single slice in the volume, then we reconstruct the whole volume by predicting
all intermediate slices. Note that this last step is computation-heavy and might
therefore take some time.
```python
import json

import numpy as np

from atlinter.data import GeneDataset
from atlinter.pair_interpolation import GeneInterpolate, RIFEPairInterpolationModel
from atlinter.vendor.rife.RIFE_HD import Model as RifeModel
from atlinter.vendor.rife.RIFE_HD import device as rife_device

# Load the gene expression dataset from disk
data_path = "data/sagittal/Vip/1102.npy"  # Change the path if needed
data_json = "data/sagittal/Vip/1102.json" # Change the path if needed
section_images = np.load(data_path)
with open(data_json) as fh:
    metadata = json.load(fh)

section_numbers = [int(s) for s in metadata["section_numbers"]]
axis = metadata["axis"]

# Wrap the data into a GeneDataset class
gene_dataset = GeneDataset(
  section_images,
  section_numbers,
  volume_shape=(528, 320, 456, 3),
  axis=axis,
)

# Load the RIFE deep learning model that will be used for interpolation
checkpoint_path = "data/checkpoints/rife"
rife_model = RifeModel()
rife_model.load_model(checkpoint_path, -1)
rife_model.eval()
rife_interpolation_model = RIFEPairInterpolationModel(rife_model, rife_device)

# Create a gene interpolator
gene_interpolate = GeneInterpolate(gene_dataset, rife_interpolation_model)

# Predict a single section image
predicted_slice = gene_interpolate.predict_slice(10)
print(predicted_slice.shape)

# Reconstruct the whole volume. This might take some time.
predicted_volume = gene_interpolate.predict_volume()
print(predicted_volume.shape)
```

## Vendors
Some dependencies are not available as packages and therefore had to be
vendored. The vendoring is done using the
[`py-vendor`](https://pypi.org/project/py-vendor/) utility. It's installed
automatically together with the `dev` extras. You can also install it by hand
via `pip install py-vendor==0.1.2`.

The vendoring is then done using the following command (add `--force` to
overwrite existing folders):
```shell
py-vendor run --config py-vendor.yaml
```
See the `py-vendor.yaml` file for details on the vendor sources and files.

## Funding & Acknowledgment

The development of this software was supported by funding to the Blue Brain Project,
a research center of the École polytechnique fédérale de Lausanne (EPFL),
from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

Copyright (c) 2021 Blue Brain Project/EPFL