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Introduction

This note shows how to iteratively retrieve the decoded content of the pages in a PDF file using Python and the pdfminer Python package.

At the time of writing, the latest version of pdfminer was used, i.e., 20140328. Thus, as the package seems poorly maintained and prone to API-breaking changes one may have to explicitly install this version for the following code to work.

Code

The following generator will iterate over a PDF file under a given filename and iteratively yield the text content of each PDF page:

When a VM is not accessible and the original Vagrantfile has been deleted one can use the following command to remove those VMs:

vagrant global-status --prune

source: http://stackoverflow.com/questions/24440142/removing-list-of-vms-in-vagrant-cache/24446866

By piping input, e.g., cat <some_file>, to the following command one can replace all line breaks with spaces

sed ':a;N;$!ba;s/\n/ /g'

This will read the whole input, e.g., file, in a loop and then replace the newline(s) with a space.

Explanation:

This method will work no matter which version of Ubuntu or desktop environment you are running.

Open the Terminal (keyboard shortcut: Ctrl+Alt+T)
Enter the command lsb_release -a

Your version will be shown on the Description line.

source: https://help.ubuntu.com/community/CheckingYourUbuntuVersion

This can be done with the listdir() and getcwd() methods of the os module:

os.listdir("path"): lists all files and directories under path which is provided as a string
os.getcwd(): returns the full path to the current working directory

usage:

import os
os.listdir(os.getcwd())

You can install a specific version of a package with apt-get in the terminal. First, determine the available versions you can install with the following command:

apt-cache showpkg <packagename>

e.g. apt-cache showpkg subversion-tools would give something like:

> Package: subversion-tools

The following process shows how one would build SimpleITK (from source) to link against and work with the Anaconda Python environment on Mac OSX.

The majority of this process can be applied to other non-vanilla Python interpreters such as Enthought Canopy and Enthough Python Distribution (EPD). This process has also been tried on Windows 7 with Canopy.

Here's how one would go about building SimpleITK against their Anaconda Python:

Activate your preferred conda environment. I will assume its called py27 but be careful to amend appropriately and activate through source activate <environment_name>
Go to this link: http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself and take a look at the instructions for building SimpleITK first.
Make sure you have CMake installed (I used the 2.8.12 version while writing this but you may want to opt for the newest CMake version first).
Make sure you have

Imports:

import vtk
from vtk.util import numpy_support
import numpy

Create a vtkDICOMImageReader object, set its directory to the one containing all DICOM files, and Update to read in all data:

	...

	class UpdatePersonName(graphene.Mutation):

	class Input:
	uuid = graphene.Int(required=True)
	name = graphene.String(required=True)

	person = graphene.Field(Person)