Core elements in pydicom¶
pydicom object model, description of classes, examples
dataset.Dataset is the main object you will work with directly.
Dataset wraps a dictionary, where the key is the DICOM (group,element)
tag (as a Tag object, described below), and the value is a DataElement instance
(also described below). It implements most of the methods of
that it mostly behaves like the wrapped
dict. This allows direct access
to the data elements via the the tags, as shown below.
The iterator of a
DataElement values, e.g. the
values of the dictionary, as opposed to the keys yielded by a
A dataset could be created directly, but you will usually get one by reading an existing DICOM file:
>>> import pydicom >>> from pydicom.data import get_testdata_files >>> # get some test data >>> filename = get_testdata_files("rtplan.dcm") >>> ds = pydicom.dcmread(filename)
You can display the entire dataset by simply printing its string (str or repr) value:
>>> ds (0008, 0012) Instance Creation Date DA: '20030903' (0008, 0013) Instance Creation Time TM: '150031' (0008, 0016) SOP Class UID UI: RT Plan Storage (0008, 0018) SOP Instance UID UI: 1.2.777.722.214.171.12477.7777.20030903150023 (0008, 0020) Study Date DA: '20030716' (0008, 0030) Study Time TM: '153557' (0008, 0050) Accession Number SH: '' (0008, 0060) Modality CS: 'RTPLAN' ...
You can also view DICOM files in a collapsible tree using the example program dcm_qt_tree.py.
You can access specific data elements by name (DICOM ‘keyword’) or by DICOM tag number:
>>> ds.PatientName 'Last^First^mid^pre' >>> ds[0x10,0x10].value 'Last^First^mid^pre'
In the latter case (using the tag number directly) a DataElement instance is
returned, so the
.value must be used to get the value.
In pydicom, private data elements are displayed with square brackets around the name (if the name is known to pydicom). These are shown for convenience only; the descriptive name in brackets cannot be used to retrieve data elements. See details in Private Data Elements.
You can also set values by name (DICOM keyword) or tag number:
>>> ds.PatientID = "12345" >>> ds.SeriesNumber = 5 >>> ds[0x10,0x10].value = 'Test'
The use of names is possible because pydicom intercepts requests for member variables, and checks if they are in the DICOM dictionary. It translates the keyword to a (group,element) number and returns the corresponding value for that key if it exists.
See Anonymize DICOM data for a usage example of data elements removal and assignation.
To understand using
sequence.Sequences in pydicom, please refer to
this object model:
dataset.Dataset (wraps a Python
- —> contains DataElement instances
–> the value of the data element can be one of:
a regular value like a number, string, etc.
a list of regular values (e.g. a 3-D coordinate)
a Sequence instance
–> a Sequence is a list of
dataset.Dataset(and so we come full circle)
sequence.Sequences are turned into Python
list s. Items in
the sequence are referenced by number, beginning at index 0 as per Python
>>> ds.BeamSequence.BeamName 'Field 1' >>> # Or, set an intermediate variable to a dataset in the list >>> beam1 = ds.BeamSequence # First dataset in the sequence >>> beam1.BeamName 'Field 1'
Using DICOM keywords is the recommended way to access data elements, but you can also use the tag numbers directly, such as:
>>> # Same thing with tag numbers - much harder to read: >>> # Really should only be used if DICOM keyword not in pydicom dictionary >>> ds[0x300a,0xb0][0x300a,0xc2].value 'Field 1'
>>> ds.dir("pat") ['PatientBirthDate', 'PatientID', 'PatientName', 'PatientSetupSequence', 'PatientSex']
dataset.Dataset.dir() will return any DICOM tag names in the dataset that
have the specified string anywhere in the name (case insensitive).
dataset.Dataset.dir() with no string will list all tag names
available in the dataset.
You can also see all the names that pydicom knows about by viewing the
_dicom_dict.py file. It should not normally be necessary, but you can add
your own entries to the DICOM dictionary at run time using
datadict.add_dict_entry(). Similarly, you can add private data elements
to the private dictionary using
Under the hood,
dataset.Dataset stores a DataElement object for each
item, but when accessed by name (e.g.
ds.PatientName) only the
dataelem.DataElement is returned. If you need the whole
dataelem (see the
dataelem.DataElement discussion), you can
dataset.Dataset.data_element() method or access the item using
the tag number:
>>> # reload the data >>> ds = pydicom.dcmread(filename) >>> data_element = ds.data_element("PatientName") >>> data_element.VR, data_element.value ('PN', 'Last^First^mid^pre') >>> # an alternative is to use: >>> data_element = ds[0x10,0x10] >>> data_element.VR, data_element.value ('PN', 'Last^First^mid^pre')
To check for the existence of a particular tag before using it, use the in keyword:
>>> "PatientName" in ds True
To remove a data element from the dataset, use python’s del statement:
>>> del ds.SoftwareVersions # or del ds[0x0018, 0x1020]
To work with pixel data, the raw bytes are available through the usual tag:
>>> # read data with actual pixel data >>> filename = get_testdata_files("CT_small.dcm") >>> ds = pydicom.dcmread(filename) >>> pixel_bytes = ds.PixelData
but to work with them in a more intelligent way, use
(requires the NumPy library):
>>> pix = ds.pixel_array >>> pix array([[175, 180, 166, ..., 203, 207, 216], [186, 183, 157, ..., 181, 190, 239], [184, 180, 171, ..., 152, 164, 235], ..., [906, 910, 923, ..., 922, 929, 927], [914, 954, 938, ..., 942, 925, 905], [959, 955, 916, ..., 911, 904, 909]], dtype=int16)
For more details, see Working with Pixel Data.
tag – a DICOM tag (as a Tag object)
VR – DICOM value representation – various number and string formats, etc
VM – value multiplicity. This is 1 for most DICOM tags, but can be multiple, e.g. for coordinates. You do not have to specify this, the DataElement class keeps track of it based on value.
value – the actual value. A regular value like a number or string (or list of them), or a Sequence.
Tag is not generally used directly in user code, as Tags are automatically created when you assign or read data elements using the DICOM keywords as illustrated in sections above.
The Tag class is derived from Python’s
int, so in effect, it is just
a number with some extra behaviour:
Tag enforces that the DICOM tag fits in the expected 4-byte (group,element)
A Tag instance can be created from an int or a tuple containing the (group,element), or from the DICOM keyword:>>> from pydicom.tag import Tag >>> t1 = Tag(0x00100010) # all of these are equivalent >>> t2 = Tag(0x10,0x10) >>> t3 = Tag((0x10, 0x10)) >>> t4 = Tag("PatientName") >>> t1 (0010, 0010) >>> t1==t2, t1==t3, t1==t4 (True, True, True)
Tag has properties group and element (or elem) to return the group and element portions
is_privateproperty checks whether the tag represents a private tag (i.e. if group number is odd).