KedoKudo

#!/bin/bash

echo "Build PTESC from scratch (for Mac OS)"
echo "-----"
echo "note:"
echo "  require customized HDF5      (run '>> ./install_HDF5.sh   ')"
echo "  require open-mpi from hombrew(run '>> brew install openmpi')"
echo "  require cmake    from hombrew(run '>> brew install cmake  ')"
echo "  use system python (2.7) for the configure step"
echo

KedoKudo

#!/bin/bash

echo "Build HDF5 from scratch (for Mac OS)"
echo "-----"
echo "note:"
echo "  require open-mpi from hombrew(run '>> brew install openmpi')"
echo

PREFIX=$HOME/opt
VERSION=1.10.5

KedoKudo

import net.imglib2.img.display.imagej.*;
import org.janelia.saalfeldlab.n5.*;
import org.janelia.saalfeldlab.n5.hdf5.*;
import org.janelia.saalfeldlab.n5.imglib2.*;
n5 = new N5HDF5Reader("/Users/chenzhang/tmp/tomoproc_test/ss304.h5");
img = N5Utils.open(n5, "/exchange/data");
ImageJFunctions.show(img);

KedoKudo

import ipywidgets        as widgets

# dynamic view of proj
@widgets.interact(n=(0, proj.shape[0]-1), cmap=['gray', 'jet'], vmin=(0,65535), vmax=(0,65535))
def peekimg(n, cmap, vmin=0, vmax=20000, showcnr=True):
    fig, axes = plt.subplots(figsize=(10,10))
    img = proj[n,:,:]
    axes.imshow(img, cmap=cmap, vmin=vmin, vmax=vmax)

    if showcnr:

KedoKudo

#perform histogram equalization with numpy, without explicitly computing the histogram

#im is a numpy array, of any dimension
im2 = numpy.sort(im.ravel()).searchsorted(im)

KedoKudo

# use class attributes to link all instance as one
class Borg:
  
  __shared_states = {}
  
  def __init__(self):
    self.__dict__ = self.__shared_states
    
 

KedoKudo

import threading

def myfunc(x):
  return x**2

t1 = threading.Thread(traget=myfunc, args=range(10))
t1.start()

KedoKudo

class _const:
  class ConstError(TypeError):
    pass
  
  class ConstCaseError(ConstError):
    pass
  
  def __setattr__(self, name, value):
    if self.__dict__.has_key(name):
      raise self.ConstError, "can't change constant"

KedoKudo

# FROM the mighty stackoverflow
# remove any existing files from the repo, skipping over ones not in repo
find . -name .DS_Store -print0 | xargs -0 git rm -f --ignore-unmatch
# specify a global exclusion list
git config --global core.excludesfile ~/.gitignore
# adding .DS_Store to that list
echo .DS_Store >> ~/.gitignore

KedoKudo

"""
Parallelized k-means module.

By David Warde-Farley, February 2012. Licensed under the 3-clause BSD.
"""
cimport cython
from cython.parallel import prange
import numpy as np
cimport numpy as np
from numpy.random import normal