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import shutil
 
def copyDirectory(src, dest):
    try:
        shutil.copytree(src, dest)
    # Directories are the same
    except shutil.Error as e:
        print('Directory not copied. Error: %s' % e)
    # Any error saying that the directory doesn't exist
    except OSError as e:

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Converting CT Data to Hounsfield Units

The formula is:

hu = pixel_value * slope + intercept

Normally, these values are stored in the DICOM file itself. The tags are generally called the Rescale Slope and Rescale Intercept, and typically have values of 1 and -1024, respectively.

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# mesh created with 
# verts, faces = skimage.measure.marching_cubes(volume, level, spacing=(1.0, 1.0, 1.0))

from mayavi import mlab 
verts, faces = marching_cubes(myvolume, 0.0, (1., 1., 2.)) 
mlab.triangular_mesh([vert[0] for vert in verts],
                     [vert[1] for vert in verts],
                     [vert[2] for vert in verts],
                     faces) 
mlab.show() 

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IPython Notebook ProgressBar

Class

import sys, time
try:
    from IPython.display import clear_output
    have_ipython = True
except ImportError:

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This option allows you to disable or enable internal commands. To disable a command, precede the command name with a minus [-]. To re-enable a command, precede it with a plus [+]. For example, to disable the internal LIST command to force TCC to use an external command:

setdos /i-list

To re-enable all disabled commands use /I*.

source:

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Traverse a directory with os.path.walk

# Import the os module, for the os.walk function
import os
 
# Set the directory you want to start from
rootDir = '.'
for dirName, subdirList, fileList in os.walk(rootDir):
 print('Found directory: %s' % dirName)

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This function takes a renderer and displays the output directly into IPython

def vtk_show(renderer, w=100, h=100):
    """
    Takes vtkRenderer instance and returns an IPython Image with the rendering.
    """
    renderWindow = vtkRenderWindow()
    renderWindow.SetOffScreenRendering(1)
 renderWindow.AddRenderer(renderer)

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Here's how to use the os module to get the directory of the file the command is executed in

os.path.dirname(os.path.realpath(__file__))

From http://stackoverflow.com/questions/5137497/find-current-directory-and-files-directory

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import requests
def download_file(url):
    local_filename = url.split('/')[-1]
    # NOTE the stream=True parameter
    r = requests.get(url, stream=True)
    with open(local_filename, 'wb') as f:
        for chunk in r.iter_content(chunk_size=1024): 
            if chunk: # filter out keep-alive new chunks
                f.write(chunk)
                f.flush()

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# This example shows how to manually construct triangle cell using unstructured grids 
# and display its surface normal.
#

package require vtk
package require vtkinteraction

# Create an unstructured grids containing a triangle cell.
vtkPoints trianglePoints
  trianglePoints SetNumberOfPoints 3