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@huangziwei
huangziwei / python_zip.py
Created July 15, 2020 12:22
import zipfile
zout = zipfile.ZipFile('nmf.zip', "w", zipfile.ZIP_DEFLATED) # <--- this is the change you need to make
zout.write('nmf.h5')
zout.close()
@huangziwei
huangziwei / natural_stimuli_simulation_v0_garbor.ipynb
Last active March 18, 2020 19:11
Simulation
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@huangziwei
huangziwei / csv_to_xlsx
Created August 20, 2018 12:53
convert *.csv to *.xlsx
soffice --headless --convert-to xlsx:"Calc MS Excel 2007 XML" *.csv --outdir <output folder>
@huangziwei
huangziwei / install_neuron.sh
Last active August 6, 2018 12:24
bashs script for installing NEURON simulator on docker/Ubuntu 16.04 with Python
#!/bin/bash
apt-get update
apt-get upgrade -y
apt-get install -y autoconf libtool libxext-dev libncurses5-dev bison flex apt-utils wget
cd $HOME
git clone https://github.com/nrnhines/nrn
cd nrn
./build.sh
./configure --prefix=`pwd` --with-nrnpython=/usr/bin/python3 --without-iv
@huangziwei
huangziwei / install_NEURON.sh
Created November 7, 2017 11:41
install NEURON with python3
#!/bin/bash
sudo apt-get update
sudo apt-get install -y libxext-dev libncurses5-dev autoconf libtool bison flex
cd ~
git clone https://github.com/nrnhines/nrn
cd nrn
./build.sh
./configure --prefix=`pwd` --with-nrnpython=python3 --without-iv
@huangziwei
huangziwei / unique_row.py
Created October 23, 2017 13:10
find unique_row in numpy.array
def unique_row(a):
b = np.ascontiguousarray(a).view(np.dtype((np.void, a.dtype.itemsize * a.shape[1])))
_, idx = np.unique(b, return_index=True)
unique_a = a[idx]
return unique_a
@huangziwei
huangziwei / port-r-func.py
Last active August 23, 2017 14:03
porting some some R functions to python
def lfactorial(n):
from scipy.special import gammaln
return gammaln(n+1)
def lchoose(n, k):
from scipy.special import gammaln
@huangziwei
huangziwei / add_kernel.sh
Created July 28, 2017 13:33
#!/bin/bash
git clone https://github.com/pyenv/pyenv .pyenv
echo 'export PYENV_ROOT="/.pyenv"' >> ~/.bashrc
echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bashrc
echo 'eval "$(pyenv init -)"' >> ~/.bashrc
exec $SHELL
pyenv install miniconda3-latest
pyenv shell miniconda3-latest
conda install numpy scipy jupyter matplotlib scikit-learn
@huangziwei
huangziwei / roi_func.py
Created May 9, 2017 12:41
some functions for roi detection
def load_h5_data(file_name):
with h5py.File(file_name,'r') as f:
return {key:f[key][:] for key in list(f.keys())}
def detect_soma_centroid(M):
"""
detect the coordinate of soma on stack image.
Return
@huangziwei
huangziwei / rois_rot.py
Created May 2, 2017 15:42
rotate coordinates of rois
def rotate_roi(d):
ang_deg = d['wParamsNum'][31] # ratoate angle (degree)
ang_rad = ang_deg * np.pi / 180 # ratoate angle (radian)
d_rois = d['ROIs']
d_rois_rot = scipy.ndimage.interpolation.rotate(d_rois, ang_deg)
(shift_x, shift_y) = 0.5 * (np.array(d_rois_rot.shape) - np.array(d_rois.shape))
(cx, cy) = 0.5 * np.array(d_rois.shape)