Ivan E. Cao-Berg icaoberg

View script.sh
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echo "help demo3D12;
 
TRAIN = true;
SYNTHESIS = true;
POSTPROCESSING = true;
 
option = 1;
patterns = {'LAM','Nuc','Mit','TfR'};
model_filenames = {'./lam.mat', './nuc.mat', './mit.mat', './tfr.mat'};
downsampling_scale = 8;
View script.sh
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$VIRTUALENV virtual_environment
. virtual_environment/bin/activate
 
pip install cython
 
pip install --allow-all-external pyrex
pip install numpy
pip install nose
 
python setup.py build_ext --inplace
View script.sh
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echo "help demo3D12;
 
TRAIN = false;
SYNTHESIS = false;
POSTPROCESSING = true;
 
option = 1;
patterns = {'LAM','Nuc','Mit','TfR'};
model_filenames = {'./lam.mat', './nuc.mat', './mit.mat', './tfr.mat'};
downsampling_scale = 5;
View install.sh
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#!/bin/bash
 
git clone git@github.com:cjlin1/libsvm.git
cd libsvm
make
View pyslid.sh
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#!/bin/bash
 
gource --hide dirnames,usernames --title "Protein Subcellular Location Image Database for Python" --seconds-per-day 1 --auto-skip-seconds 1 -1280x720 -o - | ffmpeg -y -r 60 -f image2pipe -vcodec ppm -i - -vcodec libx264 -preset ultrafast -pix_fmt yuv420p -crf 1 -threads 0 -bf 0 ./pyslid.mp4
View gitmovie.sh
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#!/bin/bash
 
#COMMENT: I used brew to install gource and ffmpeg in MacOSX
#To install brew and the two packages in terminal run
#ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
#brew install gource
#brew install ffmpeg
 
OUTPUT=$1
View mencoder_installer.sh
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sudo port -v selfupdate
sudo port upgrade outdated
sudo port install ffmpeg +gpl +postproc +lame +theora +libogg +vorbis +xvid +x264 +a52 +faac +faad +dts +nonfree
View im2projection.m
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function out_img = img2projection( img, param )
% IM2GPROJECTION creates a sum or mean projection of the input image
%
% Input:
% img = a 3D binary or realvalued image.
% param = struct with a 'method' field that can be set
% to 'mean' if a mean value projection is desired
% Output:
% out_img = a 2D image that contains a projection
% in each dimension of the original image
View sphinx_docs_strings_example.py
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#the docstrings for the method calculate from pyslid
 
def calculate( conn, iid, scale=1, set="slf33", field=True, rid=None, pixels=0, channels=[], zslice=0, timepoint=0, threshold=None, debug=False ):
'''
Calculates and returns a feature ids vector, a feature vector and the output scale given a valid
image identification (iid). It currently can calculate SLF33, SLF34, SLF35 and SLF36.
 
This method will try to retrieve the resolution of the image from the annotations.
 
If the method is unable to connect to the OMERO.server, then the method will return None.
View rename.sh
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for FOLDER in *
do
if [ -d "$FOLDER" ]; then
echo "$FOLDER"
cd "$FOLDER"
for FILE in *
do
ID=`uuidgen`
EXTENSION=${FILE#*.}
mv -v "$FILE" "$ID"."$EXTENSION"
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