├── voxelviz ├── __init__.py ├── data │ └── standard.nii.gz ├── config.json ├── utils.py └── app.py ├── examples ├── showcase │ ├── .gitkeep │ ├── run_app.sh │ └── this_app.py └── teaching │ ├── .gitkeep │ ├── run_app.sh │ └── this_app.py ├── img ├── hover.gif ├── model.gif ├── scrolling.gif ├── thresholding.gif └── different_datasets.gif ├── MANIFEST.in ├── requirements.txt ├── setup.py ├── .gitignore ├── README.md └── LICENSE /voxelviz/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /examples/showcase/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /examples/teaching/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /img/hover.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lukassnoek/VoxelViz/HEAD/img/hover.gif -------------------------------------------------------------------------------- /img/model.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lukassnoek/VoxelViz/HEAD/img/model.gif -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include voxelviz/data/standard.nii.gz 2 | include voxelviz/config.json 3 | -------------------------------------------------------------------------------- /img/scrolling.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lukassnoek/VoxelViz/HEAD/img/scrolling.gif -------------------------------------------------------------------------------- /img/thresholding.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lukassnoek/VoxelViz/HEAD/img/thresholding.gif -------------------------------------------------------------------------------- /img/different_datasets.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lukassnoek/VoxelViz/HEAD/img/different_datasets.gif -------------------------------------------------------------------------------- /voxelviz/data/standard.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lukassnoek/VoxelViz/HEAD/voxelviz/data/standard.nii.gz -------------------------------------------------------------------------------- /examples/showcase/run_app.sh: -------------------------------------------------------------------------------- 1 | /home/lukas/VoxelViz/vxvenv/bin/gunicorn --workers 3 --bind unix:voxelviz.sock -m 007 this_app:server 2 | -------------------------------------------------------------------------------- /examples/teaching/run_app.sh: -------------------------------------------------------------------------------- 1 | /home/lukas/VoxelViz/vxvenv/bin/gunicorn --workers 3 --bind unix:voxelviz.sock -m 007 this_app:server 2 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | numpy 2 | scipy 3 | dash 4 | dash-renderer 5 | dash-core-components 6 | dash-html-components 7 | nibabel 8 | plotly 9 | click 10 | -------------------------------------------------------------------------------- /voxelviz/config.json: -------------------------------------------------------------------------------- 1 | { 2 | "standardize": 0, 3 | "mappings": { 4 | 5 | "nopreproc": "No preproc", 6 | "highpass": "High-pass", 7 | "highpass_moco_smooth": "Smoothed" 8 | } 9 | } -------------------------------------------------------------------------------- /examples/showcase/this_app.py: -------------------------------------------------------------------------------- 1 | import sys 2 | sys.path.append('../../voxelviz') 3 | 4 | from app import vxv 5 | app, server = vxv('/home/lukas/VoxelViz/examples/showcase/config.json', '/home/lukas/VoxelViz/examples/showcase', True) 6 | -------------------------------------------------------------------------------- /examples/teaching/this_app.py: -------------------------------------------------------------------------------- 1 | import sys 2 | sys.path.append('../../voxelviz') 3 | 4 | from app import vxv 5 | app, server = vxv('/home/lukas/VoxelViz/examples/teaching/config.json', '/home/lukas/VoxelViz/examples/teaching', True) 6 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup, find_packages 2 | 3 | with open('requirements.txt') as rf: 4 | requirements = rf.readlines() 5 | 6 | 7 | def readme(): 8 | with open('README.md') as f: 9 | return f.read() 10 | 11 | setup( 12 | name='voxelviz', 13 | version='0.0.1', 14 | packages=find_packages(), 15 | install_requires=[ 16 | 'Click', 17 | ], 18 | include_package_data=True, 19 | entry_points=''' 20 | [console_scripts] 21 | vxv=voxelviz.app:vxv_cmd 22 | vxv_download_data=voxelviz.utils:download_data 23 | ''' 24 | ) 25 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | env/ 12 | build/ 13 | develop-eggs/ 14 | dist/ 15 | downloads/ 16 | eggs/ 17 | .eggs/ 18 | lib/ 19 | lib64/ 20 | parts/ 21 | sdist/ 22 | var/ 23 | wheels/ 24 | *.egg-info/ 25 | .installed.cfg 26 | *.egg 27 | 28 | # PyInstaller 29 | # Usually these files are written by a python script from a template 30 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 31 | *.manifest 32 | *.spec 33 | 34 | # Installer logs 35 | pip-log.txt 36 | pip-delete-this-directory.txt 37 | 38 | # Unit test / coverage reports 39 | htmlcov/ 40 | .tox/ 41 | .coverage 42 | .coverage.* 43 | .cache 44 | nosetests.xml 45 | coverage.xml 46 | *.cover 47 | .hypothesis/ 48 | 49 | # Translations 50 | *.mo 51 | *.pot 52 | 53 | # Django stuff: 54 | *.log 55 | local_settings.py 56 | 57 | # Flask stuff: 58 | instance/ 59 | .webassets-cache 60 | 61 | # Scrapy stuff: 62 | .scrapy 63 | 64 | # Sphinx documentation 65 | docs/_build/ 66 | 67 | # PyBuilder 68 | target/ 69 | 70 | # Jupyter Notebook 71 | .ipynb_checkpoints 72 | 73 | # pyenv 74 | .python-version 75 | 76 | # celery beat schedule file 77 | celerybeat-schedule 78 | 79 | # SageMath parsed files 80 | *.sage.py 81 | 82 | # dotenv 83 | .env 84 | 85 | # virtualenv 86 | .venv 87 | venv/ 88 | ENV/ 89 | 90 | # Spyder project settings 91 | .spyderproject 92 | .spyproject 93 | 94 | # Rope project settings 95 | .ropeproject 96 | 97 | # mkdocs documentation 98 | /site 99 | 100 | # mypy 101 | .mypy_cache/ 102 | 103 | # 104 | examples/*/*.feat 105 | examples/*/config.json 106 | current_contrast.txt 107 | voxelviz/current_contrast.txt 108 | **/.DS_Store 109 | *env 110 | -------------------------------------------------------------------------------- /voxelviz/utils.py: -------------------------------------------------------------------------------- 1 | import subprocess 2 | import os 3 | import zipfile 4 | import platform 5 | import click 6 | import os.path as op 7 | import nibabel as nib 8 | import json 9 | import numpy as np 10 | 11 | default_data_dir = op.join(op.dirname(op.dirname(__file__))) 12 | 13 | @click.command() 14 | @click.option('--directory', default=default_data_dir) 15 | def download_data(directory): 16 | ''' Downloads example data. ''' 17 | 18 | url = 'https://surfdrive.surf.nl/files/index.php/s/NRhXx2BevS3BDR9/download' 19 | 20 | cmd = "where" if platform.system() == "Windows" else "which" 21 | with open(os.devnull, 'w') as devnull: # check if curl is available 22 | res = subprocess.call([cmd, 'curl'], stdout=devnull) 23 | 24 | if res != 0: 25 | raise OSError("The program 'curl' was not found on your computer!" 26 | " Either install it or download the data from " 27 | "surfdrive: %s" % url) 28 | 29 | dst_file = op.join(directory, 'examples.zip') 30 | if op.isfile(dst_file): 31 | msg = ('Zip-file already exists (%s). Probably best to unzip yourself ' 32 | 'instead of re-downloading it...' % dst_file) 33 | raise ValueError(msg) 34 | 35 | dst_dir = dst_file.replace('.zip', '') 36 | if not op.isdir(dst_dir): 37 | os.makedirs(dst_dir) 38 | print("Downloading the data ...\n") 39 | cmd = "curl -o %s %s" % (dst_file, url) 40 | return_code = subprocess.call(cmd, shell=True) 41 | print("\nDone!") 42 | print("Unzipping ...", end='') 43 | zip_ref = zipfile.ZipFile(dst_file, 'r') 44 | zip_ref.extractall(dst_dir) 45 | zip_ref.close() 46 | print(" done!") 47 | os.remove(dst_file) 48 | else: 49 | print("Data is already downloaded and located at %s/*" % dst_dir) 50 | 51 | 52 | def index_by_slice(direction, sslice, img): 53 | 54 | if isinstance(img, str): 55 | img = nib.load(img).get_data() 56 | 57 | if direction == 'X': 58 | img = img[sslice, :, :, ...] 59 | elif direction == 'Y': 60 | img = img[:, sslice, :, ...] 61 | else: 62 | img = img[:, :, sslice, ...] 63 | 64 | return img 65 | 66 | 67 | def load_data(feat_dir, load_func=False): 68 | 69 | path = op.join(feat_dir + '.feat') 70 | con = nib.load(op.join(path, 'stats', 'tstat1.nii.gz')).get_data() 71 | 72 | if load_func: 73 | func = nib.load(op.join(path, 'filtered_func_data.nii.gz')).get_data() 74 | return func, con 75 | else: 76 | return con 77 | 78 | 79 | def standardize(func): 80 | return (func - func.mean(axis=-1, keepdims=True)) / func.std(axis=-1, keepdims=True) 81 | 82 | 83 | def read_design_file(feat_dir): 84 | path = op.join(feat_dir + '.feat') 85 | design_file = op.join(path, 'design.mat') 86 | mat = np.loadtxt(design_file, skiprows=5) 87 | 88 | if not np.all(mat == 1.0): 89 | mat = np.hstack((np.ones((mat.shape[0], 1)), mat)) 90 | 91 | if mat.ndim == 1: 92 | mat = mat[:, np.newaxis] 93 | 94 | return mat 95 | 96 | 97 | def calculate_statistics(y, y_hat, n_pred, grouplevel): 98 | 99 | SSE = ((y_hat - y) ** 2).sum() 100 | 101 | if grouplevel: 102 | return 'Model fit (mean squared error): %.3f' % (SSE / float(y.size)) 103 | else: 104 | SSM = ((y_hat - y.mean()) ** 2).sum() 105 | df1 = np.max([n_pred - 1, 1]) 106 | df2 = y.size - df1 107 | MSM = SSM / df1 108 | F = MSM / (SSE / df2) 109 | if np.isnan(F) or np.isinf(np.abs(F)): 110 | F = 0 111 | return 'Model fit (F-test): %s' % str(np.round(F, 3)) 112 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # VoxelViz 2 | Visualization tool for (f)MRI data-sets using Plotly Dash. Submitted to the [TransIP](https://www.transip.nl/) VPS competition. 3 | 4 | UPDATE: I won the competition! Thanks for TransIP/Tweakers for hosting this competition (and the 1st prize: a kick-ass gaming laptop and HTC Vive) -- this definitely motivated me to keep on developing this app! 5 | 6 | ## To do 7 | Couple of thing that I'd still like to implement and (relatively unimportant) bugfixes. 8 | 9 | To fix: 10 | - [x] Fix update timeseries when changing brainplot 11 | - [ ] Fix range of slice-scrolling (currently sometimes out of range) 12 | - [ ] Fix automatic range in heatmap (colors are now variable) 13 | - [ ] Fix location (and text-color) of model/voxel checkbox! 14 | - [ ] Fix darkgrey text on Hover-box 15 | 16 | To implement: 17 | - [x] Refactor to make standalone app! 18 | - [ ] Add option to load in own data (with dcc.Load component) 19 | - [ ] Add option to show separate regressors (not only model fit) 20 | - [x] Option to toggle between timeseries and frequency view (nice to show effect of e.g. highpass filter) 21 | - [ ] Add download script to download data to check examples (teaching/showcase) locally 22 | 23 | ## Intro 24 | This tool was originally developed for the TransIP VPS competition ("come up with an original idea 25 | for a virtual private server"), but mainly because I was looking for an excuse to mess around with 26 | the new [Plotly Dash](https://plot.ly/dash) framework. The app turned out better than I expected and 27 | I think I'll try to convert it into an open-source package for everyone to use. That is, I'll rewrite 28 | it such that any neuroimaging researcher (or teacher! more about that later) with a proper dataset 29 | can use `VoxelViz` to show/demonstrate it. 30 | 31 | ## Usage 32 | As of now, `VoxelViz` can be used in two ways, which correspond to the two apps in this 33 | repository (the one in the `usecase` folder and the one in the `teaching` folder). 34 | 35 | ### Showcase results 36 | First, it can be used to interactively visualize results from (group-level) fMRI analyses. 37 | Or, in layman terms: show pretty brain pictures. In the `usecase` folder, the `app.py` file 38 | runs an app that shows the results from my [fMRI study](https://academic.oup.com/scan/article/12/7/1025/3798709/Shared-states-using-MVPA-to-test-neural-overlap) (freely accessible!) about the representation 39 | of emotion in the brain. `VoxelViz` visualizes the brain images corresponding to the different 40 | analyses we did (left panel of the app), which can be interactively manipulated by, for example, adjusting the statistical 41 | threshold, orientation (`X`, `Y`, `Z`), and the current "slice" (specific 2D view; changing this is 42 | like "scrolling" through the brain image). 43 | 44 | Additionally, `VoxelViz` interactively visualizes the 45 | "timeseries" from the voxel (3D cube, which represents the unit of measurement) that you hover over 46 | in the brain image from the app's left panel. So, the right panel (timeseries plot) updates according 47 | to where your cursor is in the app's right panel - cool huh? 48 | 49 | ### Teaching neuroimaging 50 | Next to the "showcase" use, I think this app could be quite helpful in a teaching context. 51 | It happens to be that I myself teach two "neuroimaging" (analysis of brain-data) courses at the 52 | University of Amsterdam, and I struggly to explain "dry" (often statistical) concepts during my 53 | lectures and computer labs. Of course, I try to make my lectures more "lively" by including a lot 54 | of brain images, but 2D representations just don't do the trick. How cool would it be to show students 55 | "boring" things, like the effect of a high-pass filter on fMRI analyses, interactively in a web-app? 56 | Well, the folder `teaching` of this repository contains an app for *just* that! It shows the results 57 | (brain images) from different preprocessing pipelines. This way, you can check out (or show students) 58 | what happens to the brain images when you apply a high-pass filter (or not!) or when you (spatially) 59 | smooth your data. This should be especially clear from the timeseries plot in the right panel! 60 | 61 | ## Features 62 | I've alluded to some of the features in the previous section already, but here I'll describe them 63 | in more detail. 64 | 65 | ### Show different datasets/results 66 | When you start the app, you'll see a dropdown menu in the top left corner of the brain image plot. 67 | In the `showcase` example app, this dropdown menu contains the "contrasts" (results) from different 68 | analyses, which are referred to by keywords such as "action", "interoception", "action>interoception", etc. 69 | (These results refer to analyes which tested how the brain activates in response to action-oriented emotional 70 | states, interoception-oriented emotional states, and the difference between action and interoception states, 71 | respectively.) Changing the "contrast" will update both the brain plot and the timeseries plot! 72 | 73 | ![alt text](https://github.com/lukassnoek/VoxelViz/raw/master/img/different_datasets.gif "Logo Title Text 1") 74 | 75 | ### Viewing/scrolling options 76 | The brain is of course a 3D dimensional object that is, here, visualized in 2D. I've included two options 77 | to configure which part (and in which orientation) you're viewing the brain image. Next to the "contrasts" 78 | dropdown menu, you can choose whether you want to view the brain in a saggital orientation (from the side; "X"), 79 | coronal orientation (from the front; "Y"), or axial orientation (from the top; "Z"). Next to the "X/Y/Z" option, 80 | there is a slides that allows you "scroll" through the brain. 81 | 82 | ![alt text](https://github.com/lukassnoek/VoxelViz/raw/master/img/scrolling.gif "Logo Title Text 1") 83 | 84 | ### Adjust the (statistical) threshold 85 | Usually, results from (f)MRI analyses are thresholded, to remove insignificant (de)activations. Therefore, 86 | the results are by default thresholded at `abs(Z) > 2.3`. But sometimes its informative to check out the 87 | unthresholded results, so `VoxelViz` contains a slides to adjust the threshold! Adjusting the threshold 88 | automatically updates the brain plot (higher thresholds should show less red/blue and vice versa). 89 | 90 | ![alt text](https://github.com/lukassnoek/VoxelViz/raw/master/img/thresholding.gif "Logo Title Text 1") 91 | 92 | ### Visualize underlying timeseries 93 | In the right panel of the app, there is a "timeseries" plot that shows the underlying signal of 94 | the highlighted [voxel](https://en.wikipedia.org/wiki/Voxel) (3D equivalent of pixel) in the brain plot. 95 | In other words, if you hover over a voxel in the brain plot, the timeseries plot will automatically show 96 | the underlying signal of that voxel. 97 | 98 | ![alt text](https://github.com/lukassnoek/VoxelViz/raw/master/img/hover.gif "Logo Title Text 1") 99 | 100 | ### Visualize model fit 101 | The "results" in the left panel (the brain plot) are derived from models fit to the timeseries data 102 | in the right panel. By clicking on the "Model" checkbox above the right plot, you can visualize the model 103 | fit to the data, which again updates when you change the position of your cursor. This is especially helpful 104 | in a teaching context when you want to show students the effect of preprocessing options (such as filtering, 105 | confound regression, etc.) on your model fit! 106 | 107 | ![alt text](https://github.com/lukassnoek/VoxelViz/raw/master/img/model.gif "Logo Title Text 1") 108 | 109 | ## See for yourself! 110 | `VoxelViz` runs as a standalone app on a VPS [X8 BladeVPS](https://www.transip.nl/vps/) 111 | from TransIP, which can be viewed at [teaching.lukas-snoek.com](http://teaching.lukas-snoek.com/) and [showcase.lukas-snoek.com](http://showcase.lukas-snoek.com/). 112 | 113 | If you want to mess around with the app yourself with your own data, you can clone this repo! 114 | First, you need to install the dependencies, which you can do through: 115 | 116 | $ pip install -r requirements.txt 117 | 118 | Then, put your own data in the `usecase` or `teaching` folder (and rename the folder if you want), change the `config.json` file, and run: 119 | 120 | $ python app.py 121 | 122 | Now, go to `http://localhost:8050` in your browser to view and use the app! 123 | -------------------------------------------------------------------------------- /voxelviz/app.py: -------------------------------------------------------------------------------- 1 | import click 2 | import os 3 | import warnings 4 | import os.path as op 5 | from dash import Dash 6 | from dash.dependencies import Input, Output 7 | import dash_core_components as dcc 8 | import dash_html_components as html 9 | import plotly.graph_objs as go 10 | import nibabel as nib 11 | import numpy as np 12 | from collections import OrderedDict 13 | import json 14 | 15 | 16 | @click.command() 17 | @click.option('--cfg', default=None) 18 | @click.option('--data', default=None) 19 | @click.option('--deploy', default=False) 20 | def vxv_cmd(cfg, data, deploy): 21 | 22 | vxv(cfg, data, deploy) 23 | 24 | 25 | def vxv(cfg, data, deploy): 26 | ''' Main function starting the app. 27 | 28 | Parameters 29 | ---------- 30 | cfg : string 31 | Path to config-file 32 | data : string 33 | Path to directory with data 34 | deploy : bool 35 | Whether the app is deployed (True) or run locally (False) 36 | ''' 37 | 38 | if cfg is None or data is None: 39 | msg = ("You didn't specify a config-file and/or data-directory! " 40 | "You can upload data/config-file in the browser itself (only " 41 | "if it isn't deployed!) or, if you don't have data yourself, " 42 | "you can download two example data-sets with:\n" 43 | "$ vxv_download_data [--directory]\n" 44 | "Then, you can run the app with the example data as follows:\n" 45 | "$ vxv --cfg /config.json --data " 46 | "") 47 | warnings.warn(msg) 48 | 49 | if deploy: 50 | from voxelviz.utils import (load_data, index_by_slice, standardize, 51 | read_design_file, calculate_statistics) 52 | else: 53 | from .utils import (load_data, index_by_slice, standardize, 54 | read_design_file, calculate_statistics) 55 | 56 | # Start Dash app 57 | app = Dash() 58 | server = app.server 59 | 60 | # Default colors of app 61 | colors = dict( 62 | background='#000000', 63 | text='#D3D3D3' 64 | ) 65 | 66 | # Load config (with mappings) 67 | with open(cfg) as config: 68 | cfg = json.load(config, object_pairs_hook=OrderedDict) 69 | 70 | # Get the first key (random) from mappings, and load contrast/func 71 | # TO REFACTOR: get rid of hidden state 72 | global_contrast_name = list(cfg['mappings'].keys())[0] 73 | global_func, global_contrast = load_data(op.join(data, global_contrast_name), load_func=True) 74 | global_design = read_design_file(op.join(data, global_contrast_name)) 75 | 76 | # Kind of an hack: save on disk which contrast we've loaded 77 | # (to avoid reloading the func-data every callback) 78 | with open("current_contrast.txt", "w") as text_file: 79 | text_file.write(global_contrast_name) 80 | 81 | # timeseries or subjects? 82 | grouplevel = global_func.shape[:3] == (91, 109, 91) 83 | 84 | # Use the mean as background 85 | if grouplevel: 86 | global_bg = nib.load(op.join(op.dirname(__file__), 87 | 'data', 88 | 'standard.nii.gz')).get_data() 89 | else: 90 | global_bg = global_func.mean(axis=-1) 91 | 92 | if cfg['standardize']: 93 | global_func = standardize(global_func) 94 | 95 | # Start layout of app 96 | app.layout = html.Div( 97 | 98 | children=[ 99 | 100 | html.Div(className='ten columns offset-by-one', children=[ 101 | 102 | html.H1(children='VoxelViz: An interactive viewer for BOLD-fMRI data', 103 | style={'textAlign': 'center', 'color': colors['text']}, 104 | id='title'), 105 | 106 | html.Div(className='row', children=[ 107 | 108 | dcc.Markdown("""Developed for the [TransIP](https://www.transip.nl/) VPS-competition""") 109 | ], style={'textAlign': 'center', 'color': colors['text'], 'padding-bottom': '20px'}) 110 | 111 | ]), 112 | 113 | html.Div(className='five columns', children=[ 114 | 115 | html.Div(className='row', children=[ 116 | 117 | html.Div(className='five columns', children=[ 118 | 119 | dcc.Dropdown(options=[ 120 | {'value': key, 'label': val} for key, val in cfg['mappings'].items() 121 | ], 122 | value=global_contrast_name, 123 | id='contrast') 124 | ]), 125 | 126 | html.Div(className='three columns', children=[ 127 | 128 | dcc.RadioItems( 129 | id='direction', 130 | options=[ 131 | {'label': 'X', 'value': 'X'}, 132 | {'label': 'Y', 'value': 'Y'}, 133 | {'label': 'Z', 'value': 'Z'} 134 | ], 135 | labelStyle={'display': 'inline-block'}, 136 | value='X') 137 | ], style={'color': colors['text'], 'padding-top': '5px'}), 138 | 139 | html.Div(className='four columns', children=[ 140 | 141 | dcc.Slider( 142 | min=0, 143 | step=1, 144 | value=50 if grouplevel else 30, 145 | id='slice'), 146 | 147 | ], style={'padding-top': '5px'}), 148 | 149 | ], style={'padding-bottom': '20px'}), 150 | 151 | html.Div(className='row', children=[ 152 | 153 | dcc.Graph(id='brainplot', animate=False, config={'displayModeBar': False}) 154 | 155 | ]), 156 | 157 | html.Div(className='row', children=[ 158 | 159 | html.Div(className='two columns', children=[ 160 | 161 | html.P('Threshold:') 162 | ], style={'textAlign': 'center', 'color': colors['text']}), 163 | 164 | html.Div(className='ten columns', children=[ 165 | 166 | dcc.Slider(id='threshold', 167 | min=0, 168 | max=10, 169 | step=0.1, 170 | value=2.3, 171 | marks={i: i for i in np.arange(0, 10.5, 0.5)}) 172 | ], style={'padding-top': '5px'}) 173 | ]), 174 | ]), 175 | 176 | html.Div(className='six columns', children=[ 177 | 178 | html.Div(className='row', children=[ 179 | 180 | html.Div(className='five columns', children=[ 181 | 182 | dcc.RadioItems( 183 | id='datatype', 184 | options=[ 185 | {'label': 'time', 'value': 'time'}, 186 | {'label': 'frequency', 'value': 'freq'} 187 | ], 188 | labelStyle={'display': 'inline-block'}, 189 | value='time') 190 | ], style={'color': colors['text'], 'padding-left': '50px'}), 191 | 192 | html.Div(className='four columns', children=[ 193 | 194 | dcc.Checklist( 195 | options=[ 196 | {'label': 'Voxel', 'value': 'voxel'}, 197 | {'label': 'Model', 'value': 'model'} 198 | ], 199 | values=['voxel'], id='voxel_disp', 200 | labelStyle={'display': 'inline-block'}) 201 | 202 | ], style={'padding-left': '0px', 'color': colors['text']}) 203 | 204 | ]), 205 | 206 | html.Div(className='row', children=[ 207 | 208 | dcc.Graph(id='brainplot_time', animate=False) 209 | 210 | ]), 211 | 212 | html.Div(className='row', children=[ 213 | 214 | html.Div(className='ten columns', children=[ 215 | 216 | html.P(id='parameter_value') 217 | ], style={'textAlign': 'center', 'color': colors['text'], 'padding-top': '5px', 'font-size': '120%'}) 218 | ]) 219 | ]) 220 | ] 221 | ) 222 | 223 | external_css = "https://codepen.io/lukassnoek/pen/Kvzmzv.css" 224 | app.css.append_css({"external_url": external_css}) 225 | 226 | @app.callback( 227 | Output(component_id='parameter_value', component_property='children'), 228 | [Input(component_id='brainplot_time', component_property='figure'), 229 | Input(component_id='voxel_disp', component_property='values')]) 230 | def update_parameter_statistics(figure, voxel_disp): 231 | 232 | if 'model' in voxel_disp and len(figure['data']) > 1: 233 | y = np.array(figure['data'][0]['y']) 234 | y_hat = np.array(figure['data'][1]['y']) 235 | n_pred = global_design.shape[1] 236 | stat_txt = calculate_statistics(y, y_hat, n_pred, grouplevel) 237 | else: 238 | stat_txt = '' 239 | 240 | return stat_txt 241 | 242 | @app.callback( 243 | Output(component_id='slice', component_property='max'), 244 | [Input(component_id='direction', component_property='value')]) 245 | def update_slice_slider(direction): 246 | 247 | # To fix! 248 | srange = {'X': global_contrast.shape[0], 249 | 'Y': global_contrast.shape[1], 250 | 'Z': global_contrast.shape[2]} 251 | 252 | return srange[direction] 253 | 254 | @app.callback( 255 | Output(component_id='brainplot', component_property='figure'), 256 | [Input(component_id='threshold', component_property='value'), 257 | Input(component_id='contrast', component_property='value'), 258 | Input(component_id='direction', component_property='value'), 259 | Input(component_id='slice', component_property='value')]) 260 | def update_brainplot(threshold, contrast, direction, sslice): 261 | 262 | with open("current_contrast.txt", "r") as text_file: 263 | current_contrast = text_file.readlines()[0] 264 | 265 | if contrast != current_contrast: 266 | nonlocal global_contrast, global_bg, global_func 267 | if global_contrast.shape == (91, 109, 91): 268 | global_contrast = load_data(contrast, load_func=False) 269 | else: 270 | global_func, global_contrast = load_data(op.join(data, contrast), load_func=True) 271 | global_bg = global_func.mean(axis=-1) 272 | 273 | with open("current_contrast.txt", "w") as text_file: 274 | text_file.write(contrast) 275 | 276 | bg_slice = index_by_slice(direction, sslice, global_bg) 277 | img_slice = index_by_slice(direction, sslice, global_contrast) 278 | 279 | bg_map = go.Heatmap(z=bg_slice.T, colorscale='Greys', showscale=False, 280 | hoverinfo="none", name='background') 281 | 282 | tmp = np.ma.masked_where(np.abs(img_slice) < threshold, img_slice) 283 | func_map = go.Heatmap(z=tmp.T, opacity=1, name='Activity map', 284 | colorbar={'thickness': 20, 'title': 'Z-val', 'x': -.1}) 285 | 286 | layout = go.Layout(autosize=True, 287 | margin={'t': 50, 'l': 5, 'r': 5}, 288 | plot_bgcolor=colors['background'], 289 | paper_bgcolor=colors['background'], 290 | font={'color': colors['text']}, 291 | title='Activation pattern: %s' % cfg['mappings'][contrast], 292 | xaxis=dict(autorange=True, 293 | showgrid=False, 294 | zeroline=False, 295 | showline=False, 296 | autotick=True, 297 | ticks='', 298 | showticklabels=False), 299 | yaxis=dict(autorange=True, 300 | showgrid=False, 301 | zeroline=False, 302 | showline=False, 303 | autotick=True, 304 | ticks='', 305 | showticklabels=False)) 306 | 307 | return {'data': [bg_map, func_map], 'layout': layout} 308 | 309 | @app.callback( 310 | Output(component_id='brainplot_time', component_property='figure'), 311 | [Input(component_id='threshold', component_property='value'), 312 | Input(component_id='contrast', component_property='value'), 313 | Input(component_id='direction', component_property='value'), 314 | Input(component_id='slice', component_property='value'), 315 | Input(component_id='brainplot', component_property='hoverData'), 316 | Input(component_id='voxel_disp', component_property='values'), 317 | Input(component_id='datatype', component_property='value')]) 318 | def update_brainplot_time(threshold, contrast, direction, sslice, hoverData, 319 | voxel_disp, datatype): 320 | 321 | if datatype == 'time': 322 | if grouplevel: 323 | xtitle = 'Subjects' 324 | else: 325 | xtitle = 'Time' 326 | 327 | ytitle = 'Activation (contrast estimate)' 328 | else: 329 | xtitle = 'Frequency (Hz)' 330 | ytitle = 'Power' 331 | 332 | with open("current_contrast.txt", "r") as text_file: 333 | current_contrast = text_file.readlines()[0] 334 | 335 | if contrast != current_contrast: 336 | nonlocal global_contrast, global_func, global_design 337 | global_func, global_contrast = load_data(contrast, load_func=True) 338 | global_design = read_design_file(op.join(data, contrast)) 339 | if cfg['standardize']: 340 | global_func = standardize(global_func) 341 | 342 | with open("current_contrast.txt", "w") as text_file: 343 | text_file.write(contrast) 344 | 345 | if hoverData is None: 346 | if grouplevel: 347 | x, y = 40, 40 348 | else: 349 | x, y = 20, 20 350 | else: 351 | x = hoverData['points'][0]['x'] 352 | y = hoverData['points'][0]['y'] 353 | 354 | img = index_by_slice(direction, sslice, global_func) 355 | signal = img[x, y, :].ravel() 356 | 357 | if np.all(np.isnan(signal)): 358 | signal = np.zeros(signal.size) 359 | 360 | if 'model' in voxel_disp and not np.all(signal == 0): 361 | betas = np.linalg.lstsq(global_design, signal)[0] 362 | signal_hat = betas.dot(global_design.T) 363 | fitted_model = go.Scatter(x=np.arange(1, global_func.shape[-1] + 1), 364 | y=signal_hat,name='Model fit') 365 | 366 | if grouplevel: 367 | datatype = 'time' 368 | plottitle = 'Activation across subjects' 369 | bcolors = ['rgb(225,20,20)' if sig > 0 else 'rgb(35,53,216)' for sig in signal] 370 | bdata = go.Bar(x=np.arange(1, global_func.shape[-1] + 1), y=signal, name='Activity', 371 | marker=dict(color=bcolors, 372 | line=dict(color='rgb(211,211,211)', width=0.2))) 373 | else: 374 | plottitle = 'Activation across time' 375 | bdata = go.Scatter(x=np.arange(global_func.shape[-1]), 376 | y=signal, name='Activity') 377 | 378 | layout = go.Layout(autosize=True, 379 | margin={'t': 50, 'l': 50, 'r': 5}, 380 | plot_bgcolor=colors['background'], 381 | paper_bgcolor=colors['background'], 382 | font={'color': colors['text']}, 383 | xaxis=dict(showgrid=True, 384 | zeroline=True, 385 | showline=True, 386 | autotick=True, 387 | showticklabels=True, 388 | title=xtitle), 389 | yaxis=dict(autorange=True, 390 | showgrid=True, 391 | zeroline=True, 392 | showline=True, 393 | autotick=True, 394 | showticklabels=True, 395 | title=ytitle), 396 | title=plottitle) 397 | 398 | if 'model' in voxel_disp and not np.all(signal == 0): 399 | figure = {'data': [bdata, fitted_model], 'layout': layout} 400 | else: 401 | figure = {'data': [bdata], 'layout': layout} 402 | 403 | if datatype == 'freq': 404 | 405 | for i, element in enumerate(figure['data']): 406 | from scipy.signal import periodogram 407 | dat = element['y'] 408 | freq, power = periodogram(dat, 0.5, return_onesided=True) 409 | element['y'] = power 410 | element['x'] = freq 411 | figure['data'][i] = element 412 | 413 | return figure 414 | 415 | if deploy: 416 | return app, server 417 | else: 418 | app.run_server() 419 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 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"Knowingly relying" means you have 508 | actual knowledge that, but for the patent license, your conveying the 509 | covered work in a country, or your recipient's use of the covered work 510 | in a country, would infringe one or more identifiable patents in that 511 | country that you have reason to believe are valid. 512 | 513 | If, pursuant to or in connection with a single transaction or 514 | arrangement, you convey, or propagate by procuring conveyance of, a 515 | covered work, and grant a patent license to some of the parties 516 | receiving the covered work authorizing them to use, propagate, modify 517 | or convey a specific copy of the covered work, then the patent license 518 | you grant is automatically extended to all recipients of the covered 519 | work and works based on it. 520 | 521 | A patent license is "discriminatory" if it does not include within 522 | the scope of its coverage, prohibits the exercise of, or is 523 | conditioned on the non-exercise of one or more of the rights that are 524 | specifically granted under this License. You may not convey a covered 525 | work if you are a party to an arrangement with a third party that is 526 | in the business of distributing software, under which you make payment 527 | to the third party based on the extent of your activity of conveying 528 | the work, and under which the third party grants, to any of the 529 | parties who would receive the covered work from you, a discriminatory 530 | patent license (a) in connection with copies of the covered work 531 | conveyed by you (or copies made from those copies), or (b) primarily 532 | for and in connection with specific products or compilations that 533 | contain the covered work, unless you entered into that arrangement, 534 | or that patent license was granted, prior to 28 March 2007. 535 | 536 | Nothing in this License shall be construed as excluding or limiting 537 | any implied license or other defenses to infringement that may 538 | otherwise be available to you under applicable patent law. 539 | 540 | 12. No Surrender of Others' Freedom. 541 | 542 | If conditions are imposed on you (whether by court order, agreement or 543 | otherwise) that contradict the conditions of this License, they do not 544 | excuse you from the conditions of this License. If you cannot convey a 545 | covered work so as to satisfy simultaneously your obligations under this 546 | License and any other pertinent obligations, then as a consequence you may 547 | not convey it at all. For example, if you agree to terms that obligate you 548 | to collect a royalty for further conveying from those to whom you convey 549 | the Program, the only way you could satisfy both those terms and this 550 | License would be to refrain entirely from conveying the Program. 551 | 552 | 13. Use with the GNU Affero General Public License. 553 | 554 | Notwithstanding any other provision of this License, you have 555 | permission to link or combine any covered work with a work licensed 556 | under version 3 of the GNU Affero General Public License into a single 557 | combined work, and to convey the resulting work. The terms of this 558 | License will continue to apply to the part which is the covered work, 559 | but the special requirements of the GNU Affero General Public License, 560 | section 13, concerning interaction through a network will apply to the 561 | combination as such. 562 | 563 | 14. Revised Versions of this License. 564 | 565 | The Free Software Foundation may publish revised and/or new versions of 566 | the GNU General Public License from time to time. Such new versions will 567 | be similar in spirit to the present version, but may differ in detail to 568 | address new problems or concerns. 569 | 570 | Each version is given a distinguishing version number. If the 571 | Program specifies that a certain numbered version of the GNU General 572 | Public License "or any later version" applies to it, you have the 573 | option of following the terms and conditions either of that numbered 574 | version or of any later version published by the Free Software 575 | Foundation. If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 596 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 597 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 599 | 600 | 16. Limitation of Liability. 601 | 602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 610 | SUCH DAMAGES. 611 | 612 | 17. Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | {one line to give the program's name and a brief idea of what it does.} 635 | Copyright (C) {year} {name of author} 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | {project} Copyright (C) {year} {fullname} 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | --------------------------------------------------------------------------------