dcmpandas - a library for loading dicom directories into pandas

• Author: Dov Grobgeld dov.grobgeld@gmail.com
• Created: 2014-12-06 Sat
• Keywords: Dicom, Python, Pandas
• URL: http://github.com/dov/dcmpandas
• Version: 0.1

Description

dcmpandas is a scraper and query system for interacting with a directory of dicom images. It builds a database of the tags of all images in the database, and then allows querying these tags through the flexible pandas syntax.

Example

The following example imports dcmpandas and builds a database of all dicom images in the current directory. (Obviously the building of the database only needs to be performed once.) It then loads the database into memory, and performs a few queries and views the images of one series.

In [1]: import dcmpandas as dp

In [2]: dp.scrape('.')
Processing 48862992
Processing 48857684
Processing 48858202
Processing 48862824
:
In [3]: tags,df = dp.load()
In [4]: df.SeriesDescription.drop_duplicates()
Out[4]: 
0                   Ax t2_tse_spair
1                         Ax t2_tse
2                      Ax 3D GRE T1
180            Ax Diff ep2d_mddw_30
181    Ax Diff ep2d_mddw_30_a/p rpt
Name: SeriesDescription, dtype: object

In [5]: df.groupby(['SeriesDescription','SeriesNumber']).size()
Out[5]: 
SeriesDescription             SeriesNumber
Ax 3D GRE T1                  4               60
Ax Diff ep2d_mddw_30          5               31
Ax Diff ep2d_mddw_30_a/p rpt  8               31
Ax t2_tse                     2               60
Ax t2_tse_spair               3               60
dtype: int64

In [6]: s2 = df[df.SeriesNumber==2]
In [7]: s2[['Filename','SliceLocation']]
     Filename  SliceLocation
1    48863538     -86.537117
4    48863524     -83.537117
7    48863510     -80.537117
10   48863496     -77.537117
:
166  48862768      78.462883
168  48862754      81.462883
172  48862740      84.462883
175  48862726      87.462883
178  48862712      90.462883
In [8]: dp.view(s2.Filename)
>>> Opens up an external viewer and shows image in slice location 
In [9]: tags.SeriesDescription

Image viewing

dcmpandas uses the image viewer giv from http://github.com/dov/giv for viewing dicom images through the dcmpandas.view command.

TODO

• Improve windows friendliness of the dcmpandas.view command.