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View choose_seeds.py
# This function was written as part of the analysis pipeline in
# Lu et al 2018, IEEE ISBI: https://arxiv.org/abs/1803.07534
#
# The purpose of this function was to convert the predicted mask
# of cilia into an empirical probability density function that we
# would then sample "seeds" from to extract patches of ciliary motion
# (with high probability; hence, the empirical PDF) to feed to the
# downstream Conv-LSTM for classification. The reason we didn't
# just uniformly sample from the masked areas of cilia was to try
# and minimize uncertainty in the mask edges (hence, the distance
@magsol
magsol / opencv-cuda.py
Last active May 24, 2017
Simple script to edit the OpenCV conda-forge feedstock's build script to enable CUDA support.
View opencv-cuda.py
#!/opt/python/bin/python
# Installs a GPU-enabled OpenCV from the conda-forge feedstock.
# Assumes you already have Python 3 installed and the conda-forge channel on.
import argparse
import os.path
import subprocess
import sys
# These are the options we want to make sure are set to the values listed here.
@magsol
magsol / animated_rotated_3dtrajectory.py
Created May 4, 2017
An animated 3D matplotlib figure that rotates incrementally as the plot is drawn.
View animated_rotated_3dtrajectory.py
import argparse
import matplotlib.pyplot as plot
from matplotlib import animation
from mpl_toolkits.mplot3d.axes3d import Axes3D
import numpy as np
import scipy.io
import ar.ar as AR
if __name__ == "__main__":
parser = argparse.ArgumentParser(description = 'Cilia AR Subspace Plotting',
@magsol
magsol / bluedata-worker-cleanup-and-reset.sh
Last active Oct 4, 2016
BlueData Worker reformat and reinstall
View bluedata-worker-cleanup-and-reset.sh
# Register each worker.
./bootstrap-uga-general.sh
# Make sure each worker is subscribed to the RHEL channels:
# - RHEL Server Optional
# - RHEL Server Supplementary
# - RHN Tools for RHEL
# Run on each worker.
yum -y update
@magsol
magsol / aws-dash.md
Last active Jan 29, 2019
Attempts to get the Amazon Dash button working with Hue lights.
@magsol
magsol / python-packages.md
Last active May 23, 2017
Python packages I use.
View python-packages.md
@magsol
magsol / feret.py
Created Jun 2, 2015
FERET binary to PNG image parser
View feret.py
import argparse
import bz2
import os
if __name__ == "__main__":
parser = argparse.ArgumentParser(description = 'FERET Parser',
epilog = 'lol moar p1cz', add_help = 'How to use',
prog = 'python feret.py <args>')
# Required parameters.
@magsol
magsol / OpenCV Introduction.ipynb
Created Dec 2, 2013
IPython notebook introducing the basics of OpenCV.
View OpenCV Introduction.ipynb
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@magsol
magsol / histogram_equalization_in_python.ipynb
Created Sep 19, 2013
IPython notebook about histogram equalization with images. Basic image processing.
View histogram_equalization_in_python.ipynb
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@magsol
magsol / parse_hashmap.py
Created Mar 15, 2013
This script takes the output of an Apache Mahout job (in HashMap format) and converts it to a histogram.
View parse_hashmap.py
import numpy as np
import sys
import matplotlib.pyplot as plot
import csv
# read the arguments - need two files
if len(sys.argv) < 3:
quit('python parse.py [raw data file] [mahout output]')
# read the files
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