.. _DICOMAttributes:

DICOM Attributes
=================

Series properties
-----------------

A handful of DICOM attributes are available directly as Series properties.
The table below lists the available Series properties.

These attributes can be set and interrogated directly from the Series object:

.. code-block:: python

  from imagedata import Series
  a = Series('in_dir')
  patientName = a.patientName
  a.seriesDescription = 'DWI MASK'
  a.imageType = ['DERIVED', 'SECONDARY', 'MPR']

+-------------------------+-------------------------+-----------------------+
| Series property         | DICOM                   | Usage                 |
| name                    | Attribute Name          |                       |
+=========================+=========================+=======================+
|**SOP Common Module**                                                      |
+-------------------------+-------------------------+-----------------------+
|SOPClassUID              |SOPClassUID              |str                    |
+-------------------------+-------------------------+-----------------------+
|**Patient Module Attributes**                                              |
+-------------------------+-------------------------+-----------------------+
|patientName              |PatientName              |str                    |
+-------------------------+-------------------------+-----------------------+
|patientID                |PatientID                |str                    |
+-------------------------+-------------------------+-----------------------+
|patientBirthDate         |PatientBirthDate         |str                    |
+-------------------------+-------------------------+-----------------------+
|**General Study Module Attributes**                                        |
+-------------------------+-------------------------+-----------------------+
|studyInstanceUID         |StudyInstanceUID         |str                    |
+-------------------------+-------------------------+-----------------------+
|studyID                  |StudyID                  |str                    |
+-------------------------+-------------------------+-----------------------+
|accessionNumber          |AccessionNumber          |str                    |
+-------------------------+-------------------------+-----------------------+
|**General Series Module Attributes**                                       |
+-------------------------+-------------------------+-----------------------+
|seriesInstanceUID        |SeriesInstanceUID        |str                    |
+-------------------------+-------------------------+-----------------------+
|seriesNumber             |SeriesNumber             |int                    |
+-------------------------+-------------------------+-----------------------+
|seriesDescription        |SeriesDescription        |str                    |
+-------------------------+-------------------------+-----------------------+
|**Frame Of Reference Module Attributes**                                   |
+-------------------------+-------------------------+-----------------------+
|frameOfReferenceUID      |FrameOfReferenceUID      |str                    |
+-------------------------+-------------------------+-----------------------+
|**General Image Module Attributes**                                        |
+-------------------------+-------------------------+-----------------------+
|imageType                |ImageType                |List of str            |
+-------------------------+-------------------------+-----------------------+
|timeline                 |AcquisitionTime          |Read-only numpy array  |
|                         |                         |(can be set using tags)|
+-------------------------+-------------------------+-----------------------+
|bvalues                  |DiffusionBValue          |Read-only numpy array  |
|                         |or propietary            |                       |
+-------------------------+-------------------------+-----------------------+
|**Image Plane Module**                                                     |
+-------------------------+-------------------------+-----------------------+
|spacing                  |PixelSpacing and         |numpy array(dz,dy,dx)  |
|                         |SliceThickness           |in mm                  |
+-------------------------+-------------------------+-----------------------+
|orientation              |ImageOrientationPatient  |numpy array            |
|                         |                         |with 6 elements        |
+-------------------------+-------------------------+-----------------------+
|imagePositions           |ImagePositionPatient     |dict of ImagePositions |
|                         |                         |[z,y,x] of upper left  |
|                         |                         |hand corner (in mm).   |
|                         |                         |dict.keys() are slice  |
|                         |                         |numbers (int)          |
+-------------------------+-------------------------+-----------------------+
|sliceLocations           |SliceLocation            |numpy array (in mm)    |
+-------------------------+-------------------------+-----------------------+
|**VOI LUT Module**                                                         |
+-------------------------+-------------------------+-----------------------+
|windowCenter             |WindowCenter             |number                 |
+-------------------------+-------------------------+-----------------------+
|windowWidth              |WindowWidth              |number                 |
+-------------------------+-------------------------+-----------------------+
|**Image Pixel Module**                                                     |
+-------------------------+-------------------------+-----------------------+
|color                    |SamplesPerPixel          |bool                   |
+-------------------------+-------------------------+-----------------------+
|photometricInterpretation|PhotometricInterpretation|str                    |
+-------------------------+-------------------------+-----------------------+
|rows                     |Rows                     |Read-only (int)        |
+-------------------------+-------------------------+-----------------------+
|columns                  |Columns                  |Read-only (int)        |
+-------------------------+-------------------------+-----------------------+
|**Composite Attributes**                                                   |
+-------------------------+-------------------------+-----------------------+
|slices                   |                         |Read-only (int)        |
+-------------------------+-------------------------+-----------------------+
|tags                     |Input order tag          |Tags for each slice.   |
|                         |                         |a.tags[slice][tag]     |
+-------------------------+-------------------------+-----------------------+
|axes                     |                         |List of Axis objects   |
+-------------------------+-------------------------+-----------------------+
|transformationMatrix     |                         |numpy array 4x4        |
|                         |                         |in z,y,x order         |
+-------------------------+-------------------------+-----------------------+
|SOPInstanceUIDs          |                         |Dict of collected      |
|                         |                         |SOPInstanceUID from    |
|                         |                         |instances read.        |
|                         |                         |Key: (tag, slice)      |
+-------------------------+-------------------------+-----------------------+
|dicomTemplate            |                         |A pydicom Dataset      |
+-------------------------+-------------------------+-----------------------+



Full access to DICOM attributes
-------------------------------

Any DICOM attribute can be set or fetched using the getDicomAttribute()
and setDicomAttribute() methods.

The getDicomAttribute() method will fetch the named DICOM attribute.

By default the setDicomAttribute() method will set an attribute
for all slices and tags of a series. Alternatively, a specific slice
and/or tag can be targeted.

.. code-block:: python

  # Fetch the MR Repetition Time
  TR = a.getDicomAttribute('RepetitionTime')

  # Fetch the Acquisition Time, and duplicate this for given slice and tag
  acqTime = a.getDicomAttribute('AcquisitionTime')
  a.setDicomAttribute('AcquisitionTime', acqTime, slice=5, tag=10)