Load the mosaic dataset (Lahner et al.) and the associated pre-trained models

pip install mosaic-dataset

import mosaic

dataset = mosaic.load(
    names_and_subjects={
        "NSD": [2,3],
        "deeprecon": "all",
    },
    folder="./MOSAIC" 
)

print(dataset[0])

Visualization

import mosaic
from mosaic.utils import visualize
from IPython.display import IFrame

dataset = mosaic.load(
    names_and_subjects={
        "bold_moments": [1],
    },
    folder="./MOSAIC" 
)

visualize(
    betas=dataset[0]["betas"],
    ## set rois to None if you want to visualize all of the rois
    rois=[
        "L_FFC",
        "R_FFC",
    ],
    ## other modes are: 'white', 'midthickness', 'pial', 'inflated', 'very_inflated', 'flat', 'sphere'
    mode = "midthickness",
    save_as = "plot.html",
)

Loading pre-trained models

import mosaic

model = mosaic.from_pretrained(
    backbone_name="ResNet18",
    framework="multihead",
    subjects="all",
    vertices="visual"
)

Running inference with pre-trained models:

from mosaic.utils.inference import MosaicInference
from PIL import Image

inference = MosaicInference(
    model=model,
    batch_size=32,
    device="cuda:0"
)

results = inference.run(
    images = [
        Image.open("cat.jpg").convert("RGB"),
        Image.open("cat.jpg").convert("RGB")
    ]
)

Visualizing model predictions

inference.plot(
    image=Image.open("cat.jpg").convert("RGB"),
    save_as="predicted_voxel_responses.html",
    dataset_name="NSD",
    subject_id=1,
    mode="inflated",
)

Loading up stimulus info:

stim_info = mosaic.get_stiminfo(
    dataset_name="deeprecon",
    folder="./MOSAIC"
)

print(stim_info.head())

Merging files for easier loading

from mosaic.utils.merging import merge_hdf5_files
from mosaic.datasets import MergedDataset

merge_hdf5_files(
    files=[
        './MOSAIC/NSD/sub-01_NSD.hdf5',
        './MOSAIC/deep_recon/sub-01_deeprecon.hdf5'
    ],
    save_as="./merged-test.hdf5"
)

dataset = MergedDataset(
    filename="./merged-test.hdf5"
)

print(len(dataset))

Downloading resting state data

from mosaic.datasets.resting_state import download_resting_state_data

download_resting_state_data(
    dataset="BMD", ## or "NSD" or "THINGS"
    subject=1,
    session=1,
    run=1,
    folder="./MOSAIC"
)

Dev Setup

git clone git+https://github.com/Mayukhdeb/mosaic-dataset.git
cd mosaic-dataset
python setup.py develop