Welcome to django_dicom’s documentation!¶

Overview¶

django_dicom is a reusable Django application built to maintain a database of DICOM data. It was created to support the pylabber project, but does not depend on it.

DICOM header information is represented using Model subclasses that represent the various entities it may contain (see the DICOM standard specification and this blog post for more information) and provides utility methods to import data and easily maintain the DICOM entities and their relationship.

The fundamental entities (colored in blue) will be created automatically whenever data is imported to the database by reading the required header information using dicom_parser.

The import mode configuration will determine which data elements will be serialized to the database under that Header.

Installation¶

To install the latest version of django_dicom, simply run:

pip install django_dicom

Once installed:

Add django_dicom to the INSTALLED_APPS:
settings.py¶
INSTALLED_APPS = [
    ...
    'django_dicom',
]
Include django_dicom’s URLs:
urls.py¶
urlpatterns = [
    ...
    path("api/", include("django_dicom.urls", namespace="dicom")),
]
Create the database tables:
python manage.py migrate django_dicom
Warning

django_dicom can only integrate with a PostgreSQL database. In order to set-up your project with PostgreSQL follow this DjangoGirls tutorial.

Start the development server and visit http://127.0.0.1:8000/admin/ or http://127.0.0.1:8000/dicom/.

User Guide¶

Once django_dicom is properly installed into your Django project, enter your project’s shell by running ./manage.py shell from within your project’s root directory and with your virtual environment activated.

Import Modes¶

Currently, three import modes are available:

Minimal: Do not create Header or DataElement instances at all.

Normal: Create Headers and save only standard data elements to the database.

Full: Create Headers and save all data elements to the database.

By default, django_dicom’s import mode will be set to Normal.

Changing Import Mode¶

In order to change the import mode, in your project settings add:

DICOM_IMPORT_MODE = "minimal" # or "full"

Importing Data¶

To import a local repository of .dcm files, use the ImageManager’s import_path() method:

>>> from django_dicom.models import Image

>>> path = '/path/to/local/dcm/repo/'
>>> results = Image.objects.import_path(path)
Importing DICOM data: 4312image [34:24,  2.09image/s]
Successfully imported DICOM data from '/path/to/local/dcm/repo/'!
Created:        4312

>>> results
{'created': 4312, 'existing': 0}

You can verify the addition of new data to the database by querying the desired DICOM entity:

>>> from django_dicom.models import Image, Patient

>>> Image.objects.count()
4312
>>> Patient.objects.count()
3

Reading Header Information¶

django_dicom uses the dicom_parser package to read header information and store it as an Header instance. Some information is already available to us directly through the values stored in the associated Image, Series, Patient, and Study instances. However, Header instances are collections of DataElement instances, each storing a queryable reference to both the raw and parsed values of a given data element.

By defualt, django_dicom will store all official DICOM tags, skipping any private data elements. These will still be easily readable, however, we will not be able to query them from the database. For more information about import modes, see Import Modes.

Reading a Single Image’s Header¶

To read a single Image instance’s header, we can simply use the instance property to retrieve dicom_parser’s representation of a DICOM image ( Image):

>>> from django_dicom.models import Image

>>> image = Image.objects.first()
>>> image.instance.header
            Keyword                      VR                VM  Value
Tag
(0008, 0005)  SpecificCharacterSet         Code String       1   ISO_IR 100
(0008, 0008)  ImageType                    Code String       5   ['ORIGINAL', 'PRIMARY', ...
(0008, 0012)  InstanceCreationDate         Date              1   2019-12-18
(0008, 0013)  InstanceCreationTime         Time              1   08:54:41.479000
(0008, 0016)  SOPClassUID                  Unique Identifer  1   1.2.840.10008.5.1.4.1.1.4
(0008, 0018)  SOPInstanceUID               Unique Identifer  1   1.3.12.2.1107.5.2.43.660...
(0008, 0020)  StudyDate                    Date              1   2019-12-18
...
Private Data Elements
=====================
            Keyword                      VR           VM  Value
Tag
(0019, 0010)                               Long String  1   SIEMENS MR HEADER
(0019, 1008)  CsaImageHeaderType           Unknown      1   b'IMAGE NUM 4 '
(0019, 1009)  CsaImageHeaderVersion??      Unknown      1   b'1.0 '
(0019, 100b)  SliceMeasurementDuration     Unknown      1                          3535
...

>>> image.instance.header.get('PixelSpacing')
[0.48828125, 0.48828125]

For more information on dicom_parser’s classes and functionality, see the documentation.

Querying the Database¶

According to the chosen import mode, no, some, or all of the saved images’ data elements will be serialized to the database as DataElement instances. Each DataElement represents a single tag within a single header, however, the actual information is available its definition and value attributes. These attributes associate the DataElement instance with reusable DataElementDefinition and DataElementValue instances, thereby preventing data duplication simplifying queries.

To better understand the way header information is serialized in the database, let’s query all the Series instances in which the underlying image headers contain a data element named ImageType which contains a value of MOSAIC.

First, we’ll have a look at the relevant DataElementDefinition instance:

>>> from django_dicom.models import DataElementDefinition
>>> definition = DataElementDefinition.objects.get(keyword="ImageType")
>>> definition
<DataElementDefinition:
Tag                     (0008, 0008)
Keyword                    ImageType
Value Representation              CS
Description               Image Type>

Now, let’s select any DataElementValue instances satisfying our condition:

>>> from django_dicom.models import CodeString
>>> values = CodeString.objects.filter(value="MOSAIC")
>>> values.count()
9

This means there are 9 different distinct ImageType values that contain the string MOSAIC. If we want all the related DataElement instances, we could:

>>> from django_dicom.models import DataElement
>>> data_elements = DataElement.objects.filter(definition=definition, _values__in=values)
>>> data_elements.count()
42236

Two important things to note here:

We used the _values attribute to access the raw relationship between the DataElement and its associated DataElementValues.

We used __in to query this ManyToMany relationship and retrieve data elements containing any of the desired values. This is necessary because DICOM elements may have multiple values (for more information see value multiplicity).

Now, if we would like to query all the images to which these data elements belong:

>>> image_ids = data_elements.values_list('header__image', flat=True)
>>> images = Image.objects.filter(id__in=image_ids)

or the series:

>>> from django_dicom.models import Series
>>> series_ids = images.values_list('series', flat=True)
>>> series = Series.objects.filter(id__in=series_ids)
>>> series.count()
409
>>> series.first().description
'IR-DTI_30dir_3iso'

Reading Series Data¶

django_dicom relies on dicom_parser and pydicom’s to convert an Image’s pixel data from bytes to a NumPy ndarray.

Let’s query an anatomical (“MPRAGE”[1]) Series instance we’ve added based on its Series Description:

>>> from django_dicom.models import Series
>>> series = Series.objects.filter(description__contains="MPRAGE").first()

Great! now all we need to do in order to get a NumPy ndarray of the underlying data would be to use the data property:

>>> data = series.get_data()
>>> series.data.shape
(224, 224, 208)

To inspect a particular slice, we could use matplotlib:

>>> import matplotlib.pyplot as plt
>>> plt.imshow(series.data[:, :, 100])
>>> plt.show()

This should return a figure similar to this:

Footnotes

[1]	Brant-Zawadzki, M., Gillan, G. D., & Nitz, W. R. (1992). MP RAGE: a three-dimensional, T1-weighted, gradient-echo sequence–initial experience in the brain. Radiology, 182(3), 769-775.

Reference¶

Module contents¶

This application manages DICOM files by defining Django models that represent the various DICOM entities.

Subpackages¶

Exceptions¶

Module contents¶

Definition of custom exceptions that may be raised by django_dicom. For more information about error and exceptions see the Python docs.

Submodules¶

django_dicom.exceptions.import_error module¶

Definition of the DicomImportError class.

exception django_dicom.exceptions.dicom_import_error.DicomImportError¶

Bases: Exception

Raised whenever importing new DICOM data to the database fails.

Filters¶

Module contents¶

Provides filter classes for the REST API endpoints (for more information see the DRF docs and django-filter’s integration with DRF docs).

Submodules¶

django_dicom.filters.image_filter module¶

Definition of the ImageFilter class.

class django_dicom.filters.image_filter.ImageFilter(data=None, queryset=None, *, request=None, prefix=None)¶

Bases: django_filters.rest_framework.filterset.FilterSet

Provides filtering functionality for the ImageViewSet.

Available filters are:

id: Primary key

series_uid: Series instance UID (contains)

series_description: Series description (contains)

number: Series number (exact)

created_after_date: Create after date

created_before_date: Create before date

created_after_time: Create after time

created_before_time: Create before time

class Meta¶

Bases: object

fields = ('id', 'uid', 'number')¶

model¶: alias of django_dicom.models.image.Image

base_filters = {'created_after_date': <django_filters.filters.DateFilter object>, 'created_after_time': <django_filters.filters.DateFilter object>, 'created_before_date': <django_filters.filters.DateFilter object>, 'created_before_time': <django_filters.filters.DateFilter object>, 'id': <django_filters.filters.NumberFilter object>, 'number': <django_filters.filters.NumberFilter object>, 'sequence_type': <django_filters.filters.MultipleChoiceFilter object>, 'series_description': <django_filters.filters.CharFilter object>, 'series_uid': <django_filters.filters.CharFilter object>, 'uid': <django_filters.filters.CharFilter object>}¶

declared_filters = {'created_after_date': <django_filters.filters.DateFilter object>, 'created_after_time': <django_filters.filters.DateFilter object>, 'created_before_date': <django_filters.filters.DateFilter object>, 'created_before_time': <django_filters.filters.DateFilter object>, 'sequence_type': <django_filters.filters.MultipleChoiceFilter object>, 'series_description': <django_filters.filters.CharFilter object>, 'series_uid': <django_filters.filters.CharFilter object>}¶

django_dicom.filters.patient_filter module¶

Definition of the FilterSet subclass that will be assigned to the PatientViewSet’s filter_class attribute value.

class django_dicom.filters.patient_filter.PatientFilter(data=None, queryset=None, *, request=None, prefix=None)¶

Bases: django_filters.rest_framework.filterset.FilterSet

Provides filtering functionality for the PatientViewSet.

Available filters are:

id: Primary key

uid: Patient UID (contains, icontains, or exact)

born_after_date: Earliest date of birth

born_before_date: Latest date of birth

name_prefix: Any of the existing name_prefix values in the database

given_name: Given name value (contains, icontains, or exact)

middle_name: Middle name value (contains, icontains, or exact)

family_name: Family name value (contains, icontains, or exact)

name_suffix: Any of the existing name_prefix values in the database

sex: Any of the sex options defined in the Sex Enum

study__id: Related Study ID

class Meta¶

Bases: object

fields = ('id', 'uid')¶

model¶: alias of django_dicom.models.patient.Patient

base_filters = {'date_of_birth': <django_filters.filters.DateFromToRangeFilter object>, 'family_name': <django_filters.filters.LookupChoiceFilter object>, 'given_name': <django_filters.filters.LookupChoiceFilter object>, 'id': <django_filters.filters.NumberFilter object>, 'middle_name': <django_filters.filters.LookupChoiceFilter object>, 'name_prefix': <django_filters.filters.AllValuesFilter object>, 'name_suffix': <django_filters.filters.AllValuesFilter object>, 'sex': <django_filters.filters.ChoiceFilter object>, 'study__id': <django_filters.filters.NumberFilter object>, 'uid': <django_filters.filters.LookupChoiceFilter object>}¶

declared_filters = {'date_of_birth': <django_filters.filters.DateFromToRangeFilter object>, 'family_name': <django_filters.filters.LookupChoiceFilter object>, 'given_name': <django_filters.filters.LookupChoiceFilter object>, 'middle_name': <django_filters.filters.LookupChoiceFilter object>, 'name_prefix': <django_filters.filters.AllValuesFilter object>, 'name_suffix': <django_filters.filters.AllValuesFilter object>, 'sex': <django_filters.filters.ChoiceFilter object>, 'study__id': <django_filters.filters.NumberFilter object>, 'uid': <django_filters.filters.LookupChoiceFilter object>}¶

filter_by_study(queryset: django.db.models.query.QuerySet, name: str, value: int) → django.db.models.query.QuerySet¶

Returns all Patient instances that have Series instances belonging to the Study with the specified value as primary key.

Used by study__id.

Parameters:	queryset (`QuerySet`) – `Patient` instances name (str) – Name of the queried filter field value (int) – `Study` primary key
Returns:	Filtered `Patient` instances
Return type:	`QuerySet`

django_dicom.filters.series_filter module¶

Definition of the SeriesFilter class.

class django_dicom.filters.series_filter.SeriesFilter(data=None, queryset=None, *, request=None, prefix=None)¶

Bases: django_filters.rest_framework.filterset.FilterSet

Provides filtering functionality for the SeriesViewSet.

Available filters are:

id: Primary key

uid: Series Instance UID

patient_id: Related Patient instance’s primary key

study_uid: Related Study instance’s uid value

study_description: Related Study instance’s description value (in-icontains)

modality: Any of the values defined in Modality

description: Series description value (contains, icontains, or exact)

number: Series number value

protocol_name: Protocol name value (contains)

scanning_sequence: Any combination of the values defined in ScanningSequence

sequence_variant: Any combination of the values defined in SequenceVariant

echo_time: echo_time value

inversion_time: inversion_time value

repetition_time: repetition_time value

flip_angle: Any of the existing flip_angle in the database

date_after: Exact date value

date_before: Create before date

time_after: Create after time

time_before: Create before time

manufacturer: Any of the existing manufacturer in the database

manufacturer_model_name: Any of the existing manufacturer_model_name in the database

device_serial_number: Any of the existing device_serial_number in the database

institution_name: Any of the existing institution_name in the database

pulse_sequence_name: pulse_sequence_name value (in-icontains)

sequence_name: sequence_name value (in-icontains)

class Meta¶

Bases: object

fields = ('id', 'uid', 'number', 'patient__id')¶

model¶: alias of django_dicom.models.series.Series

base_filters = {'date': <django_filters.filters.DateRangeFilter object>, 'description': <django_filters.filters.LookupChoiceFilter object>, 'device_serial_number': <django_filters.filters.AllValuesFilter object>, 'echo_time': <django_filters.filters.RangeFilter object>, 'flip_angle': <django_filters.filters.AllValuesFilter object>, 'header_fields': <django_filters.filters.CharFilter object>, 'id': <django_filters.filters.NumberFilter object>, 'institution_name': <django_filters.filters.AllValuesFilter object>, 'inversion_time': <django_filters.filters.RangeFilter object>, 'magnetic_field_strength': <django_filters.filters.AllValuesFilter object>, 'manufacturer': <django_filters.filters.AllValuesFilter object>, 'manufacturer_model_name': <django_filters.filters.AllValuesFilter object>, 'modality': <django_filters.filters.ChoiceFilter object>, 'number': <django_filters.filters.NumberFilter object>, 'patient__id': <django_filters.filters.NumberFilter object>, 'pixel_spacing': <django_filters.filters.RangeFilter object>, 'protocol_name': <django_filters.filters.CharFilter object>, 'pulse_sequence_name': <django_dicom.filters.utils.CharInFilter object>, 'repetition_time': <django_filters.filters.RangeFilter object>, 'scanning_sequence': <django_filters.filters.MultipleChoiceFilter object>, 'sequence_name': <django_dicom.filters.utils.CharInFilter object>, 'sequence_type': <django_filters.filters.MultipleChoiceFilter object>, 'sequence_variant': <django_filters.filters.MultipleChoiceFilter object>, 'slice_thickness': <django_filters.filters.RangeFilter object>, 'study_description': <django_dicom.filters.utils.CharInFilter object>, 'study_uid': <django_filters.filters.CharFilter object>, 'time': <django_filters.filters.TimeRangeFilter object>, 'uid': <django_filters.filters.CharFilter object>}¶

declared_filters = {'date': <django_filters.filters.DateRangeFilter object>, 'description': <django_filters.filters.LookupChoiceFilter object>, 'device_serial_number': <django_filters.filters.AllValuesFilter object>, 'echo_time': <django_filters.filters.RangeFilter object>, 'flip_angle': <django_filters.filters.AllValuesFilter object>, 'header_fields': <django_filters.filters.CharFilter object>, 'institution_name': <django_filters.filters.AllValuesFilter object>, 'inversion_time': <django_filters.filters.RangeFilter object>, 'magnetic_field_strength': <django_filters.filters.AllValuesFilter object>, 'manufacturer': <django_filters.filters.AllValuesFilter object>, 'manufacturer_model_name': <django_filters.filters.AllValuesFilter object>, 'modality': <django_filters.filters.ChoiceFilter object>, 'pixel_spacing': <django_filters.filters.RangeFilter object>, 'protocol_name': <django_filters.filters.CharFilter object>, 'pulse_sequence_name': <django_dicom.filters.utils.CharInFilter object>, 'repetition_time': <django_filters.filters.RangeFilter object>, 'scanning_sequence': <django_filters.filters.MultipleChoiceFilter object>, 'sequence_name': <django_dicom.filters.utils.CharInFilter object>, 'sequence_type': <django_filters.filters.MultipleChoiceFilter object>, 'sequence_variant': <django_filters.filters.MultipleChoiceFilter object>, 'slice_thickness': <django_filters.filters.RangeFilter object>, 'study_description': <django_dicom.filters.utils.CharInFilter object>, 'study_uid': <django_filters.filters.CharFilter object>, 'time': <django_filters.filters.TimeRangeFilter object>}¶

django_dicom.filters.series_filter.filter_array(queryset: django.db.models.query.QuerySet, field_name: str, value: list)¶

Returns an exact lookup for a PostgreSQL ArrayField.

Parameters:	queryset (`QuerySet`) – The filtered queryset field_name (str) – The name of the field the queryset is being filtered by value (list) – The values to filter by

django_dicom.filters.series_filter.filter_header(queryset: django.db.models.query.QuerySet, field_name: str, values: str)¶

Returns a desired lookup for a DicomHeader field.

Parameters:	queryset (`QuerySet`) – The filtered queryset field_name (str) – The name of the field the queryset is being filtered by values (dict) – The fields and values to filter by

django_dicom.filters.series_filter.filter_in_string(queryset: django.db.models.query.QuerySet, field_name: str, values: list)¶

Returns a in-icontains mixed lookup with ‘or’ between values for a CharField.

Parameters:	queryset (`QuerySet`) – The filtered queryset field_name (str) – The name of the field the queryset is being filtered by values (str) – The values to filter by

django_dicom.filters.study_filter module¶

Definition of the StudyFilter class.

class django_dicom.filters.study_filter.StudyFilter(data=None, queryset=None, *, request=None, prefix=None)¶

Bases: django_filters.rest_framework.filterset.FilterSet

Provides filtering functionality for the StudyViewSet.

Available filters are:

id: Primary key

uid: Study instance UID

description: Study description (contains, icontains, or exact)

created_after_date: Create after date

created_before_date: Create before date

created_after_time: Create after time

created_before_time: Create before time

class Meta¶

Bases: object

fields = ('id',)¶

model¶: alias of django_dicom.models.study.Study

base_filters = {'date': <django_filters.filters.DateFromToRangeFilter object>, 'description': <django_filters.filters.LookupChoiceFilter object>, 'id': <django_filters.filters.NumberFilter object>, 'time_after': <django_filters.filters.TimeFilter object>, 'time_before': <django_filters.filters.TimeFilter object>, 'uid': <django_filters.filters.LookupChoiceFilter object>}¶

declared_filters = {'date': <django_filters.filters.DateFromToRangeFilter object>, 'description': <django_filters.filters.LookupChoiceFilter object>, 'time_after': <django_filters.filters.TimeFilter object>, 'time_before': <django_filters.filters.TimeFilter object>, 'uid': <django_filters.filters.LookupChoiceFilter object>}¶

Models¶

Module contents¶

Creates Model subclasses to represent the various DICOM entities.

Subpackages¶

django_dicom.models.managers package¶

Module contents¶

Manager subclasses for some of the app’s models.

References

Django’s documentation on managers.

Subpackages¶

django_dicom.models.managers.values package¶

Module contents¶

Custom managers for specific DataElementValue subclasses.

Submodules¶

django_dicom.models.managers.values.sequence_of_items module¶

Definition of the SequenceOfItemsManager class.

class django_dicom.models.managers.values.sequence_of_items.SequenceOfItemsManager¶

Bases: django_dicom.models.managers.data_element_value.DataElementValueManager

Custom manager for the SequenceOfItems model.

from_dicom_parser(data_element: dicom_parser.data_element.DataElement) → tuple¶

Create a sequence of items by reading the included headers and populating the database accordingly.

Parameters:	data_element (DicomDataElement) – Sequence of items data element
Returns:	The data element and whether is was created or not
Return type:	Tuple[DataElementValue, bool]

Submodules¶

django_dicom.models.managers.data_element module¶

Definition of a custom Manager for the DataElement model.

class django_dicom.models.managers.data_element.DataElementManager¶

Bases: django.db.models.manager.Manager

Custom Manager for the DataElement model.

create_from_dicom_parser(header, definition, data_element: dicom_parser.data_element.DataElement)¶

Creates a new instance under header using the provided definition and data_element.

Parameters:	header (`Header`) – The header instance with which the created data element should be associated. definition (`DataElementDefinition`) – The data element definition of the created data element data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory
Returns:	The created instance
Return type:	`DataElement`

from_dicom_parser(header, data_element: dicom_parser.data_element.DataElement)¶

Creates a new instance under header using the provided dicom_parser.data_element.DataElement instance.

Parameters:	header (`Header`) – The header instance with which the created data element should be associated. data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory
Returns:	The created instance
Return type:	`DataElement`

django_dicom.models.managers.data_element_definition module¶

Definition of a custom Manager for the DataElementDefinition model.

class django_dicom.models.managers.data_element_definition.DataElementDefinitionManager¶

Bases: django.db.models.manager.Manager

Custom Manager for the DataElementDefinition model.

from_dicom_parser(data_element: dicom_parser.data_element.DataElement) → tuple¶

Gets or creates a DataElementDefinition instance from a dicom_parser DataElement.

Parameters:	data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory
Returns:	data_element_definition, created
Return type:	tuple

django_dicom.models.managers.data_element_definition.data_element_to_definition(data_element: dicom_parser.data_element.DataElement) → dict¶

Converts a dicom_parser DataElement to a dictionary of keyword arguments that may be used to instantiate a DataElementDefinition instance.

Parameters:	data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory
Returns:	`DataElementDefinition` instantiation keyword arguments
Return type:	dict

django_dicom.models.managers.data_element_value module¶

Definition of a custom InheritanceManager for the DataElementValue model.

For more information about the InheritanceManager class, see django-model-utils’s InheritanceManager documentation.

class django_dicom.models.managers.data_element_value.DataElementValueManager¶

Bases: model_utils.managers.InheritanceManager

Custom InheritanceManager for the DataElementValue model.

from_dicom_parser(data_element: dicom_parser.data_element.DataElement) → Tuple¶

Get or create some DataElementValue subclass instances from a dicom_parser DataElement.

Parameters:	data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory
Returns:	data_element_value or data_element_values, created
Return type:	Tuple[Union[DataElementValue, List[DataElementValue, ..]], bool]

get_or_create_from_nonsequence(data_element: dicom_parser.data_element.DataElement) → Tuple¶

Get or create some DataElementValue subclass instances from a non-Sequence of Items dicom_parser DataElement.

Parameters:	data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory
Returns:	data_element_value or data_element_values, created
Return type:	Tuple[Union[DataElementValue, List[DataElementValue, ..]], bool]

handle_invalid_data(ValueModel, data_element: dicom_parser.data_element.DataElement, error: Exception) → Tuple¶

If reading the value from the data element using dicom_parser raises an exception, this method is called to create an “empty” instance of the ValueModel (i.e. with raw and value set to None) and log the exception in the warnings field.

Parameters:	ValueModel (`DataElementValue`) – Some `DataElementValue` subclass used to instatiate values data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory error (Exception) – The raised exception
Returns:	data_element_value, created
Return type:	tuple

handle_multiple_values(ValueModel, data_element: dicom_parser.data_element.DataElement) → Tuple[list, bool]¶

Handles data elements with a value_multiplicity greater than 1.

Parameters:	ValueModel (`DataElementValue`) – Some `DataElementValue` subclass used to instatiate values data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory
Returns:	data_element_values, any_created
Return type:	Tuple[List[DataElementValue, ..], bool]

handle_no_value(ValueModel) → Tuple¶

Handles data elements with a value_multiplicity of 0. Returns an “empty” instance of the ValueModel (i.e. with raw and value set to None).

Parameters:	ValueModel (`DataElementValue`) – Some `DataElementValue` subclass used to instatiate values
Returns:	dicom_data_element, created
Return type:	Tuple[DicomDataElement, bool]

handle_single_value(ValueModel, data_element: dicom_parser.data_element.DataElement) → tuple¶

Handles data elements with a value_multiplicity of 1.

Parameters:	ValueModel (`DataElementValue`) – Some `DataElementValue` subclass used to instatiate values data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory
Returns:	data_element_value, created
Return type:	Tuple[DataElementValue, bool]

handle_value_multiplicity(ValueModel, data_element: dicom_parser.data_element.DataElement) → Tuple¶

Handles the creation of the DataElementValue subclass instances according to the dicom_parser DataElement’s value_multiplicity attribute.

Parameters:	ValueModel (`DataElementValue`) – Some `DataElementValue` subclass used to instatiate values data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory
Returns:	data_element_value or data_element_values, created
Return type:	Tuple[Union[DataElementValue, List[DataElementValue, ..]], bool]

django_dicom.models.managers.dicom_entity module¶

Definition of a custom Manager for the DicomEntity model.

class django_dicom.models.managers.dicom_entity.DicomEntityManager¶

Bases: django.db.models.manager.Manager

Custom Manager for the DicomEntity model.

from_header(header) → Tuple¶

Get or create an instance using the provided header.

Parameters:	header (`django_dicom.models.header.Header`) – Header instance to query this entity’s information from
Returns:	dicom_entity, created
Return type:	Tuple[DicomEntity, bool]

django_dicom.models.managers.header module¶

Definition of a custom Manager for the Header model.

class django_dicom.models.managers.header.HeaderManager¶

Bases: django.db.models.manager.Manager

Custom Manager for the Header model.

from_dicom_parser(header: dicom_parser.header.Header, **kwargs)¶

Creates a new instance from a dicom_parser dicom_parser.header.Header.

Parameters:	header (`dicom_parser.header.Header`) – Object representing an entire DICOM header in memory
Returns:	Created instance
Return type:	`django_dicom.models.header.Header`
Raises:	`DicomImportError` – DICOM header read error

django_dicom.models.managers.image module¶

Definition of the ImageManager class.

class django_dicom.models.managers.image.ImageManager¶

Bases: django_dicom.models.managers.dicom_entity.DicomEntityManager

Custom Manager for the Image model.

TEMP_DCM_FILE_NAME = 'tmp.dcm'¶: Name given to DICOM files that need to be saved locally in order to be read.

create_from_dcm(path: pathlib.Path, autoremove: bool = True)¶

Creates an Image instance from a given path.

Parameters:	path (`pathlib.Path`) – Local .dcm file path autoremove (bool, optional) – Whether to remove the local copy of the .dcm file under MEDIA_ROOT if creation fails, by default True
Returns:	The created image
Return type:	`Image`

get_or_create(*args, **kwargs) → Tuple¶

Overrides get_or_create() to call get_or_create_from_dcm() in case the dcm keyword argument is provided.

Returns:	image, created
Return type:	Tuple[Image, bool]

get_or_create_from_dcm(path: pathlib.Path, autoremove: bool = True) → Tuple¶

Gets or creates an Image instance based on the contents of the provided .dcm path.

Parameters:	path (`pathlib.Path`) – Local .dcm file path autoremove (bool, optional) – Whether to remove the local copy of the .dcm file under MEDIA_ROOT if creation fails, by default True
Returns:	image, created
Return type:	Tuple[Image, bool]

import_path(path: pathlib.Path, progressbar: bool = True, report: bool = True, persistent: bool = True, pattern: bool = '*.dcm', autoremove: bool = True) → django.db.models.query.QuerySet¶

Iterates the given directory tree and imports any .dcm files found within it.

Parameters:	path (`pathlib.Path`) – Base path for recursive .dcm import progressbar (bool, optional) – Whether to display a progressbar or not, by default True report (bool, optional) – Whether to print out a summary report when finished or not, by default True persistent (bool, optional) – Whether to continue and raise a warning or to raise an exception when failing to read a DICOM file’s header pattern (str, optional) – Globbing pattern to use for file import
Returns:	The created `Image` instances
Return type:	`QuerySet`

report_import_path_results(path: pathlib.Path, counter: dict) → None¶

Reports the result of a recursive path import.

Parameters:	path (`pathlib.Path`) – Base path of DICOM data import counter (dict) – Dictionary containing created and existing keys containing the number of files which fit in each category.

store_image_data(image_data: _io.BufferedReader) → pathlib.Path¶

Stores binary image data to a temporary local path under the project’s MEDIA_ROOT.

Parameters:	image_data (`io.BufferedReader`) – Binary DICOM image data
Returns:	Path of the created file
Return type:	`pathlib.Path`

django_dicom.models.utils package¶

Module contents¶

Utilities for the models module.

Submodules¶

django_dicom.models.utils.fields module¶

Custom Field subclasses.

class django_dicom.models.utils.fields.ChoiceArrayField(base_field, size=None, **kwargs)¶

Bases: django.contrib.postgres.fields.array.ArrayField

A field that allows us to store an array of choices. Uses Django 1.9’s postgres ArrayField and a MultipleChoiceField for its formfield.

formfield(**kwargs)¶: Return a django.forms.Field instance for this field.

django_dicom.models.utils.help_text module¶

help_text string constants for the various fields.

django_dicom.models.utils.logs module¶

Log messages to be used by models.

django_dicom.models.utils.meta module¶

django_dicom.models.utils.meta.get_model(model_name: str) → django.db.models.base.Model¶

django_dicom.models.utils.utils module¶

class django_dicom.models.utils.utils.ImportMode¶

Bases: enum.Enum

An enumeration.

FULL = 'Full'¶

MINIMAL = 'Minimal'¶

NORMAL = 'Normal'¶

django_dicom.models.utils.utils.check_element_inclusion(data_element) → bool¶

django_dicom.models.utils.utils.get_dicom_root() → pathlib.Path¶

django_dicom.models.utils.utils.get_group_model()¶

django_dicom.models.utils.utils.get_import_configuration() → dict¶

django_dicom.models.utils.utils.get_import_mode() → django_dicom.models.utils.utils.ImportMode¶

django_dicom.models.utils.utils.get_mri_root() → pathlib.Path¶

django_dicom.models.utils.utils.get_subject_model()¶

django_dicom.models.utils.utils.snake_case_to_camel_case(string: str) → str¶

django_dicom.models.utils.validators module¶

Definition of custom field validations.

django_dicom.models.utils.validators.validate_file_extension(value)¶

django_dicom.models.values package¶

Module contents¶

Definition of DataElementValue subclasses for every type of value representation (VR).

Hint

For more information about value representations see the official DICOM standard (part 05, section 6.2).

Submodules¶

django_dicom.models.values.age_string module¶

Definition of the AgeString model.

class django_dicom.models.values.age_string.AgeString(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single AgeString data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a FloatField.

django_dicom.models.values.application_entity module¶

Definition of the ApplicationEntity model.

class django_dicom.models.values.application_entity.ApplicationEntity(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single ApplicationEntity data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a CharField.

django_dicom.models.values.code_string module¶

Definition of the CodeString model.

class django_dicom.models.values.code_string.CodeString(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single CodeString data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a CharField.

django_dicom.models.values.csa_header module¶

Definition of the CsaHeader model.

class django_dicom.models.values.csa_header.CsaHeader(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single Siemens’ CSA header value.

Hint

For more information about CSA headers, see dicom_parser’s CSA headers documentation.

raw¶: Overrides raw to assign a TextField.

to_html(verbose: bool = False, **kwargs) → str¶

Returns the HTML representation of this instance.

If the verbose keyword argument is passed as True, returns the entire header as JSON. Otherwise, returns an HTML link to this instance in the admin site.

Parameters:	verbose (bool, optional) – Whether to return all of the header information or just a link, by default False
Returns:	HTML text containing either JSON encoded header information or a link to the admin site
Return type:	str

value¶: Overrides value to assign a JSONField.

django_dicom.models.values.data_element_value module¶

Definition of the DataElementValue model.

class django_dicom.models.values.data_element_value.DataElementValue(*args, **kwargs)¶

Bases: django.db.models.base.Model

A parent Model representing a single value contained by some DataElement instance. If the data element has value multiplicity greater than 1, it will have multiple instances of this model associated with it, each with its own index value.

admin_link¶

Creates an HTML tag to link to this instance within the admin site.

Returns:	Link to this instance in the admin site
Return type:	str

agestring¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

applicationentity¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

codestring¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

csaheader¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

data_element_set¶

Accessor to the related objects manager on the forward and reverse sides of a many-to-many relation.

In the example:

class Pizza(Model):
    toppings = ManyToManyField(Topping, related_name='pizzas')

Pizza.toppings and Topping.pizzas are ManyToManyDescriptor instances.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

date¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

datetime¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

decimalstring¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

floatingpointdouble¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

floatingpointsingle¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

get_raw_peek(size: int = 100) → str¶

Returns a truncated string of the raw data element’s value (appended with “…” if changed).

Parameters:	size (int, optional) – Maximal string length, by default 100
Returns:	Truncated string
Return type:	str

index¶: If the value is one of a number of values within a DataElement (a DataElement with a value multiplicity that is greater than 1), this field keeps the index of this value.

integerstring¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

longstring¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

longtext¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

objects = <django_dicom.models.managers.data_element_value.DataElementValueManager object>¶

otherword¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

personname¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

raw = None¶: Raw data element value (meant to be overridden by child models).

sequenceofitems¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

shortstring¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

shorttext¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

signedlong¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

signedshort¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

time¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

to_html(**kwargs) → str¶

Returns the HTML representation of this instance. This method simlpy returns the value, child models should override to provide an appropriate representation.

Returns:	HTML representation of this instance
Return type:	str

uniqueidentifier¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

unknown¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

unlimitedtext¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

unsignedlong¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

unsignedshort¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

value = None¶: Interpreted data element value (meant to be overridden by child models).

warnings¶: If any warnings were raised by dicom_parser, log them in the database.

django_dicom.models.values.date module¶

Definition of the Date model.

class django_dicom.models.values.date.Date(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single Date data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a CharField.

django_dicom.models.values.datetime module¶

Definition of the DateTime model.

class django_dicom.models.values.datetime.DateTime(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single DateTime data element value.

get_next_by_value(*, field=<django.db.models.fields.DateTimeField: value>, is_next=True, **kwargs)¶

get_previous_by_value(*, field=<django.db.models.fields.DateTimeField: value>, is_next=False, **kwargs)¶

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a CharField.

django_dicom.models.values.decimal_string module¶

Definition of the DecimalString model.

class django_dicom.models.values.decimal_string.DecimalString(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single DecimalString data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a FloatField.

django_dicom.models.values.floating_point_double module¶

Definition of the FloatingPointDouble model.

class django_dicom.models.values.floating_point_double.FloatingPointDouble(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single FloatingPointDouble data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a FloatField.

django_dicom.models.values.floating_point_single module¶

Definition of the FloatingPointSingle model.

class django_dicom.models.values.floating_point_single.FloatingPointSingle(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single FloatingPointSingle data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a FloatField.

django_dicom.models.values.integer_string module¶

Definition of the IntegerString model.

class django_dicom.models.values.integer_string.IntegerString(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single IntegerString data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a IntegerField.

django_dicom.models.values.integer_string.MAX_VALUE = 2147483647¶: Maximal IntegerString value.

django_dicom.models.values.integer_string.MIN_VALUE = -2147483648¶: Minimal IntegerString value.

django_dicom.models.values.long_string module¶

Definition of the LongString model.

class django_dicom.models.values.long_string.LongString(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single LongString data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a CharField.

django_dicom.models.values.long_text module¶

Definition of the LongText model.

class django_dicom.models.values.long_text.LongText(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single LongText data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a TextField.

django_dicom.models.values.other_word module¶

Definition of the OtherWord model.

class django_dicom.models.values.other_word.OtherWord(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single OtherWord data element value.

raw¶: Overrides raw to assign a BinaryField.

value¶: Overrides value to assign a IntegerField.

django_dicom.models.values.person_name module¶

Definition of the PersonName model.

class django_dicom.models.values.person_name.PersonName(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single PersonName data element value.

raw¶: Overrides raw to assign a BinaryField.

to_html(**kwargs) → str¶

Returns the HTML representation of this instance.

Returns:	HTML representation of this instance
Return type:	str

value¶: Overrides value to assign a JSONField.

django_dicom.models.values.sequence_of_items module¶

Definition of the SequenceOfItems model.

class django_dicom.models.values.sequence_of_items.SequenceOfItems(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A django.db.models.Model representing the value stored in a single DataElement with a value representation (VR) of SQ.

Sequence of Items data elements are arrays of nested headers, and therefore this model does not override the raw and value field definitions (and so they remain None).

header_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

objects = <django_dicom.models.managers.values.sequence_of_items.SequenceOfItemsManager object>¶

to_html(verbose: bool = False, **kwargs) → str¶

Returns the HTML representation of this instance. This method simlpy returns the value, child models should override to provide an appropriate representation.

Returns:	HTML representation of this instance
Return type:	str

django_dicom.models.values.short_string module¶

Definition of the ShortString model.

class django_dicom.models.values.short_string.ShortString(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single ShortString data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a Charield.

django_dicom.models.values.short_text module¶

Definition of the ShortString model.

class django_dicom.models.values.short_text.ShortText(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single ShortText data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a Charield.

django_dicom.models.values.signed_long module¶

Definition of the SignedLong model.

django_dicom.models.values.signed_long.MAX_VALUE = 2147483647¶: Maximal SignedLong value.

django_dicom.models.values.signed_long.MIN_VALUE = -2147483648¶: Minimal SignedLong value.

class django_dicom.models.values.signed_long.SignedLong(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single SignedLong data element value.

raw¶: Overrides raw to assign an IntegerField.

value¶: Overrides value to assign an IntegerField.

django_dicom.models.values.signed_short module¶

Definition of the SignedShort model.

django_dicom.models.values.signed_short.MAX_VALUE = 32767¶: Maximal SignedShort value.

django_dicom.models.values.signed_short.MIN_VALUE = -32768¶: Minimal SignedShort value.

class django_dicom.models.values.signed_short.SignedShort(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single SignedShort data element value.

raw¶: Overrides raw to assign an IntegerField.

value¶: Overrides value to assign an IntegerField.

django_dicom.models.values.time module¶

Definition of the Time model.

class django_dicom.models.values.time.Time(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single Time data element value.

raw¶: Overrides raw to assign a CharField.

to_html(**kwargs) → str¶

Returns the HTML representation of this instance.

Returns:	HTML representation of this instance
Return type:	str

value¶: Overrides value to assign a TimeField.

django_dicom.models.values.unique_identifier module¶

Definition of the UniqueIdentifier model.

class django_dicom.models.values.unique_identifier.UniqueIdentifier(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single UniqueIdentifier data element value.

raw¶: Overrides raw to assign a CharField.

value¶: Overrides value to assign a CharField.

django_dicom.models.values.unknown module¶

Definition of the Unknown model.

class django_dicom.models.values.unknown.Unknown(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single Unknown data element value.

raw¶: Overrides raw to assign a TextField.

value¶: Overrides value to assign a TextField.

django_dicom.models.values.unlimited_text module¶

Definition of the UnlimitedText model.

class django_dicom.models.values.unlimited_text.UnlimitedText(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single Unknown data element value.

raw¶: Overrides raw to assign a TextField.

value¶: Overrides value to assign a TextField.

django_dicom.models.values.unsigned_long module¶

Definition of the UnsignedLong model.

django_dicom.models.values.unsigned_long.MAX_VALUE = 4294967296¶: Maximal UnsignedLong value.

class django_dicom.models.values.unsigned_long.UnsignedLong(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single UnsignedLong data element value.

raw¶: Overrides raw to assign a PositiveIntegerField.

value¶: Overrides value to assign a PositiveIntegerField.

django_dicom.models.values.unsigned_short module¶

Definition of the UnsignedShort model.

django_dicom.models.values.unsigned_short.MAX_VALUE = 65536¶: Maximal UnsignedShort value.

class django_dicom.models.values.unsigned_short.UnsignedShort(*args, **kwargs)¶

Bases: django_dicom.models.values.data_element_value.DataElementValue

A Model representing a single UnsignedShort data element value.

raw¶: Overrides raw to assign a PositiveIntegerField.

value¶: Overrides value to assign a PositiveIntegerField.

django_dicom.models.values.vr_to_model module¶

A utility module used to get the appropriate DataElementValue subclass (“ValueModel”) for a given data element.

django_dicom.models.values.vr_to_model.TAG_TO_MODEL = {('0029', '1010'): 'CsaHeader', ('0029', '1020'): 'CsaHeader'}¶: Special cases might require a custom DataElementValue subclass based on the element’s tag rather than its VR.

django_dicom.models.values.vr_to_model.VR_TO_MODEL = {<ValueRepresentation.AE: 'Application Entity'>: 'ApplicationEntity', <ValueRepresentation.AS: 'Age String'>: 'AgeString', <ValueRepresentation.CS: 'Code String'>: 'CodeString', <ValueRepresentation.DA: 'Date'>: 'Date', <ValueRepresentation.DT: 'Date Time'>: 'DateTime', <ValueRepresentation.DS: 'Decimal String'>: 'DecimalString', <ValueRepresentation.FD: 'Floating Point Double'>: 'FloatingPointDouble', <ValueRepresentation.FL: 'Floating Point Single'>: 'FloatingPointSingle', <ValueRepresentation.IS: 'Integer String'>: 'IntegerString', <ValueRepresentation.LO: 'Long String'>: 'LongString', <ValueRepresentation.LT: 'Long Text'>: 'LongText', <ValueRepresentation.OW: 'Other Word'>: 'OtherWord', <ValueRepresentation.PN: 'Person Name'>: 'PersonName', <ValueRepresentation.SH: 'Short String'>: 'ShortString', <ValueRepresentation.SL: 'Signed Long'>: 'SignedLong', <ValueRepresentation.SQ: 'Sequence of Items'>: 'SequenceOfItems', <ValueRepresentation.SS: 'Signed Short'>: 'SignedShort', <ValueRepresentation.ST: 'Short Text'>: 'ShortText', <ValueRepresentation.TM: 'Time'>: 'Time', <ValueRepresentation.UI: 'Unique Identifer'>: 'UniqueIdentifier', <ValueRepresentation.UL: 'Unsigned Long'>: 'UnsignedLong', <ValueRepresentation.UN: 'Unknown'>: 'Unknown', <ValueRepresentation.US: 'Unsigned Short'>: 'UnsignedShort', <ValueRepresentation.UT: 'Unlimited Text'>: 'UnlimitedText'}¶: Dictionary with ValueRepresentation items as keys and strings representing the appropriate DataElementValue subclass as values.

django_dicom.models.values.vr_to_model.get_value_model(data_element: dicom_parser.data_element.DataElement)¶

Returns the DataElementValue subclass matching the given data element.

Parameters:	data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory
Returns:	Value model
Return type:	`DataElementValue`

django_dicom.models.values.vr_to_model.get_value_model_name(data_element: dicom_parser.data_element.DataElement) → str¶

Returns the name of the DataElementValue subclass matching the given data element.

Parameters:	data_element (`dicom_parser.data_element.DataElement`) – Object representing a single data element in memory
Returns:	Name of the appropriate “ValueModel”
Return type:	str

Submodules¶

django_dicom.models.data_element module¶

Definition of the DataElement class.

class django_dicom.models.data_element.DataElement(*args, **kwargs)¶

Bases: django.db.models.base.Model

A model representing a single DICOM data element.

Each DataElement instance belongs to a Header, and each Header belongs to an Image or SequenceOfItems.

While the DataElement instance holds the reference to the associated models, the defining characteristics of the data element are saved as a DataElementDefinition instance and the values are saved as DataElementValue subclass instances in order to prevent data duplication.

admin_link¶

Returns an HTML tag linking to this instance in the admin site.

Returns:	HTML link to this instance
Return type:	str

definition¶: The DataElementDefinition # noqa: E501 instance holding information about this element’s DICOM tag.

header¶: The Header instance to which this data element belongs.

objects = <django_dicom.models.managers.data_element.DataElementManager object>¶

to_html(**kwargs) → str¶

Returns an HTML representation of this instance.

Any keyword arguments will be passed to the associated DataElementValue subclass instances.

Returns:	HTML representaion of this instance
Return type:	str

to_verbose_dict() → dict¶

Returns a dictionary representation of this instance.

Returns:	This instance’s information
Return type:	dict

to_verbose_series() → pandas.core.series.Series¶

Returns a Series representation of this instance.

Returns:	This instance’s information
Return type:	`pandas.Series`

value¶

Returns the value or values (according to the value multiplicity) of the associated DataElementValue instances.

Returns:	Data element value
Return type:	Any

value_multiplicity¶

Returns the number of DataElementValue related to this instance.

Returns:	Value multiplicity
Return type:	int

Hint

For more information see the DICOM standard’s definition of value multiplicity.

django_dicom.models.data_element_definition module¶

Definition of the DataElementDefinition class.

class django_dicom.models.data_element_definition.DataElementDefinition(*args, **kwargs)¶

Bases: django.db.models.base.Model

A model representing a single DICOM data element definition.

Notes

For more information see the DICOM standard’s documentation as well as registry of data elements.

admin_link¶

Returns an HTML tag linking to this instance in the admin site.

Returns:	HTML link to this instance
Return type:	str

data_element_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

description¶: A short description of this data element.

get_value_representation_display(*, field=<django.db.models.fields.CharField: value_representation>)¶

keyword¶: Most data elements have some keyword that facilitates querying header information.

objects = <django_dicom.models.managers.data_element_definition.DataElementDefinitionManager object>¶

tag¶: Data element tags are an ordered pair of 16-bit unsigned integers representing the Group Number followed by Element Number and they are represented in the database using an array (list) of two four character strings.

to_dict() → dict¶

Returns a dictionary representation of this instance.

Returns:	This instance’s dictionary representation
Return type:	dict

to_series() → pandas.core.series.Series¶

Returns a Series representation of this instance.

Returns:	Series representation of this instance
Return type:	`pandas.Series`

value_representation¶: The value representation (VR) defines the type of information stored in the data element. This will be used to determine which DataElementValue subclass is instantiated to save this information to the database.

django_dicom.models.dicom_entity module¶

Definition of the DicomEntity class. This abstract model serves as a base class for the various DICOM entities (e.g. Study and Patient).

class django_dicom.models.dicom_entity.DicomEntity(*args, **kwargs)¶

Bases: django_extensions.db.models.TimeStampedModel

Abstract model providing common functionality for DICOM entities. For more information about DICOM entites, see this introduction.

FIELD_TO_HEADER = {}¶: A dictionary used to convert field names to header keywords.

class Meta¶

Bases: object

abstract = False¶

admin_link¶

Calls get_admin_link() to return a link to this instance’s page in the admin site.

Returns:	HTML element
Return type:	str

get_admin_link(text: str = None) → str¶

Returns an HTML link to this instance’s page in the admin site.

Parameters:	text (str, optional) – Text to display, by default None
Returns:	HTML element
Return type:	str

get_header_fields() → list¶

Returns a list of the derived model’s fields which represent DICOM header information.

Returns:	Fields representing DICOM header information
Return type:	list

classmethod get_header_keyword(field_name: str) → str¶

Returns the data element keyword to return the requested field’s value from header data. Relies on the derived model’s FIELD_TO_HEADER class attribute. If no matching key is found, will simply return the field’s name in CamelCase formatting (the formatting of pydicom’s header keywords).

Returns:	pydicom header keyword
Return type:	str

is_header_field(field: django.db.models.fields.Field) → bool¶

Returns a boolean indicating whether the provided field represents DICOM header information or not.

Parameters:	field (`Field`) – Field in question
Returns:	Whether this field represent DICOM header information or not
Return type:	bool

log_creation() → None¶: Logs the creation of a new instance of the calling Entity.

objects¶

save(*args, **kwargs)¶: Overrides save() to create logs and update the instance’s fields from header information if provided.

update_fields_from_header(header, exclude: list = None) → None¶

Update fields from header data.

Parameters:	header (`dicom_parser.header.Header`) – DICOM header data exclude (list, optional) – Field names to exclude, default is []

django_dicom.models.header module¶

Definition of the Header class.

class django_dicom.models.header.Header(*args, **kwargs)¶

Bases: model_utils.models.TimeStampedModel

A model representing a single DICOM Data Set.

admin_link¶

Creates an HTML tag to link to this instance within the admin site.

Returns:	Link to this instance in the admin site
Return type:	str

data_element_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

get_entity_uid(entity: django_dicom.models.dicom_entity.DicomEntity) → str¶

Returns the UID of the provided DICOM entity from the header information.

Parameters:	entity (`DicomEntity`) – The entity for which a UID is desired
Returns:	The provided DICOM entity’s unique identifier
Return type:	str

get_or_create_entity(entity: django_dicom.models.dicom_entity.DicomEntity) → tuple¶

Get or create a DICOM entity’s instance from this header.

Parameters:	entity (`DicomEntity`) – The desired DICOM entity’s model
Returns:	instance, creatd
Return type:	tuple

get_or_create_patient() → tuple¶

Get or create the Patient instance corresponding to this header.

Returns:	instance, created
Return type:	tuple

get_or_create_series() → tuple¶

Get or create the Series instance corresponding to this header.

Returns:	instance, created
Return type:	tuple

get_or_create_study() → tuple¶

Get or create the Study instance corresponding to this header.

Returns:	instance, created
Return type:	tuple

get_value_by_keyword(keyword: str) → Any¶

Returns a data element’s value by keyword from the database (not from the DICOM header itself, ergo only elements that are saved to the database may be queried).

Parameters:	keyword (str) – Data element keyword
Returns:	Data element value
Return type:	Any

image¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

index¶: This Data Set’s index in the sequence (if parent is not None).

instance¶

Caches the created dicom_parser.header.Header instance to prevent multiple reades.

Returns:	Header information
Return type:	`dicom_parser.header.Header`

objects = <django_dicom.models.managers.header.HeaderManager object>¶

parent¶: Data Set <http://dicom.nema.org/medical/dicom/current/output/chtml/part05/chapter_7.html>`_s `may be nested. If this header (Data Set) is an item of some sequence, this field holds that reference.

to_html(verbose: bool = False, **kwargs) → str¶

Returns an HTML representation of this instance.

Parameters:	verbose (bool, optional) – Whether to return a JSON with all of the header information or just a link to this instance’s admin page, by default False.
Returns:	HTML representaion of this instance
Return type:	str

to_verbose_list() → List[dict]¶

Returns a list of dictionaries containing the information from the data elements in this header.

Returns:	Header information as a list of dictionaries
Return type:	List[dict]

django_dicom.models.image module¶

Definition of the Image class.

class django_dicom.models.image.Image(*args, **kwargs)¶

Bases: django_dicom.models.dicom_entity.DicomEntity

A model to represent a single instance of the Image entity. This model is normally instantiated with the dcm field set to some .dcm file from which the header information is read.

FIELD_TO_HEADER = {'date': 'InstanceCreationDate', 'number': 'InstanceNumber', 'time': 'InstanceCreationTime', 'uid': 'SOPInstanceUID'}¶: A dictionary of DICOM data element keywords to be used to populate a created instance’s fields.

create_header_instance() → django_dicom.models.header.Header¶

Creates a Header instance from a dicom_parser.header.Header.

Returns:	Created instance
Return type:	`Header`

data¶

Facilitates access to the Image instance’s data.

Returns:	The image’s pixel data
Return type:	`np.ndarray`

date¶: Instance Creation Date value.

dcm¶: A reference to the DICOM image file.

default_path¶

Default unique path for this image based on its header information.

Returns:	Default image location
Return type:	`pathlib.Path`

get_absolute_url() → str¶

Returns the absolute URL for this instance. For more information see the Django documentation.

Returns:	This instance’s absolute URL path
Return type:	str

get_default_path() → pathlib.Path¶

Returns a unique default path under MEDIA_ROOT for this instance based on its header information.

Returns:	This instance’s default location
Return type:	`pathlib.Path`

header¶: The associated Header instance representing this image’s header information.

instance¶

Caches the created dicom_parser.image.Image instance to prevent multiple reads.

Returns:	Image information
Return type:	`dicom_parser.image.Image`

logger = <Logger data.dicom.image (WARNING)>¶

number¶: Instance Number value.

objects = <django_dicom.models.managers.image.ImageManager object>¶

patient¶

Returns the Patient associated with this image.

Returns:	Associated Patient instance
Return type:	Patient

rename(target: pathlib.Path) → None¶

Move the .dcm file this instance references to some target destination.

Parameters:	target (`pathlib.Path`) – Destination path

save(*args, rename: bool = True, **kwargs)¶

Overrides save() to check for missing header information or associated DICOM entities and create them if a .dcm file is provided.

Parameters:	rename (bool, optional) – Whether to move the file this instance is a reference to to a default path under MEDIA_ROOT or not, by default True

sequence_type¶

Returns the MRI sequence type detected by dicom_parser.

Returns:	Sequence type identifier
Return type:	str

series¶: The Series instance to which this image belongs.

time¶: Instance Creation Time value.

uid¶: SOP Instance UID value.

warnings¶: In case any warnings are raised by dicom_parser upon reading the image’s header information, they are stored in this field.

django_dicom.models.patient module¶

Definition of the Patient class.

class django_dicom.models.patient.Patient(*args, **kwargs)¶

Bases: django_dicom.models.dicom_entity.DicomEntity

A model to represent a single instance of the Patient entity.

FIELD_TO_HEADER = {'date_of_birth': 'PatientBirthDate', 'sex': 'PatientSex', 'uid': 'PatientID'}¶: A dictionary of DICOM data element keywords to be used to populate a created instance’s fields.

date_of_birth¶: Patient Birth Date value.

family_name¶: Patient’s Name value.

get_absolute_url() → str¶

Returns the absolute URL for this instance.

Returns:	This instance’s absolute URL path
Return type:	str

get_full_name() → str¶

Returns the first and last names of the patient.

Returns:	Patient’s first and last names.
Return type:	str

get_sex_display(*, field=<django.db.models.fields.CharField: sex>)¶

given_name¶: Patient’s Name value.

logger = <Logger data.dicom.patient (WARNING)>¶

middle_name¶: Patient’s Name value.

n_images¶

Returns the number of associated images.

See also

query_n_images()

Returns:	Number of associated images
Return type:	int

n_series¶

Returns the number of associated series.

Returns:	Number of associated series
Return type:	int

n_studies¶

Returns the number of associated studies.

See also

query_n_studies()

Returns:	Number of associated studies
Return type:	int

name_prefix¶: Patient’s Name value.

name_suffix¶: Patient’s Name value.

objects = <django.db.models.manager.DicomEntityManagerFromPatientQuerySet object>¶

query_n_images() → int¶

Returns the number of associated images.

See also

n_images()

Returns:	Number of associated images
Return type:	int

query_n_studies() → int¶

Returns the number of associated studies.

See also

n_studies()

Returns:	Number of associated studies
Return type:	int

query_research_subject()¶

Returns the associated research subject, if such a model is registered and a matching instance exists.

See also

research_subject()

Returns:	Associated research subject
Return type:	Subject

research_subject¶

Returns the associated research subject, if such a model is registered and a matching instance exists.

See also

query_research_subject()

Returns:	Associated research subject
Return type:	Subject

series_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

sex¶: Patient’s Sex value.

uid¶: Patient ID value.

update_fields_from_header(header, exclude: list = None) → None¶

Overrides update_fields_from_header() to handle setting the name parts.

Parameters:	header (`Header`) – DICOM header information. exclude (list, optional) – Field names to exclude (the default is [], which will not exclude any header fields).

update_patient_name(header) → None¶

Parses the patient’s name from the DICOM header and updates the instance’s fields.

Parameters:	header (`Header`) – A DICOM image’s `Header` instance.

django_dicom.models.series module¶

Definition of the Series class.

class django_dicom.models.series.Series(*args, **kwargs)¶

Bases: django_dicom.models.dicom_entity.DicomEntity

A model to represent a single instance of the Series entity.

FIELD_TO_HEADER = {'date': 'SeriesDate', 'description': 'SeriesDescription', 'mr_acquisition_type': 'MRAcquisitionType', 'number': 'SeriesNumber', 'pulse_sequence_name': (25, 4252), 'time': 'SeriesTime', 'uid': 'SeriesInstanceUID'}¶: A dictionary of DICOM data element keywords to be used to populate a created instance’s fields.

MR_ACQUISITION_2D = '2D'¶: MR Acquisition Type value.

MR_ACQUISITION_3D = '3D'¶

MR_ACQUISITION_TYPE_CHOICES = (('2D', '2D'), ('3D', '3D'))¶

body_part_examined¶: Body Part Examined value.

data¶

Returns the dicom_parser.series.Series.data property’s value.

Returns:	Series data
Return type:	`np.ndarray`

date¶: Series Date value.

datetime¶

Returns a datetime.datetime object by combining the values of the date and time fields.

Returns:	Series datetime
Return type:	`datetime.datetime`

description¶: Series Description value.

device_serial_number¶: Device Serial Number value.

echo_time¶: Echo Time value.

echo_train_length¶: Echo Train Length value.

flip_angle¶: Flip Angle value.

get_absolute_url() → str¶

Returns the absolute URL for this instance. For more information see the Django documentation.

Returns:	This instance’s absolute URL path
Return type:	str

get_file_paths() → Tuple[pathlib.Path]¶

get_modality_display(*, field=<django.db.models.fields.CharField: modality>)¶

get_mr_acquisition_type_display(*, field=<django.db.models.fields.CharField: mr_acquisition_type>)¶

get_path() → pathlib.Path¶

Returns the base directory containing the images composing this series.

Returns:	This series’s base directory path
Return type:	str

get_patient_position_display(*, field=<django.db.models.fields.CharField: patient_position>)¶

get_sample_header() → dicom_parser.header.Header¶

Return a sample Header instance for this series.

See also

sample_header()

Returns:	Sample image header information
Return type:	DicomHeader

get_scanning_sequence_display() → list¶

Returns the display valuse of this instance’s scanning_sequence attribute.

Returns:	Verbose scanning sequence values
Return type:	list

get_sequence_type_display(*, field=<django.db.models.fields.CharField: sequence_type>)¶

get_sequence_variant_display() → list¶

Returns the display valuse of this instance’s sequence_variant attribute.

Returns:	Verbose sequence variant values
Return type:	list

image_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

instance¶

Caches the created dicom_parser.series.Series instance to prevent multiple reades.

Returns:	Series information
Return type:	`dicom_parser.series.Series`

institution_name¶: Institution Name value.

inversion_time¶: Inversion Time value.

logger = <Logger data.dicom.series (WARNING)>¶

magnetic_field_strength¶: Magnetic Field Strength value.

manufacturer¶: Manufacturer value.

manufacturer_model_name¶: Manufacturer’s Model Name value.

missing_relation¶

Returns whether this instance misses an associated Patient or Study.

Returns:	Whether this instance has missing relationships
Return type:	bool

modality¶: Modality value.

mr_acquisition_type¶: A wrapper for a deferred-loading field. When the value is read from this object the first time, the query is executed.

number¶: Series Number value.

operators_name¶: Operator’s Name value.

path¶

Returns the base path of this series’ images.

Returns:	Series directory path
Return type:	`pathlib.Path`

patient¶: The Patient instance to which this series belongs.

patient_position¶: Patient Position value.

pixel_spacing¶: Pixel Spacing value.

protocol_name¶: Protocol Name value.

pulse_sequence_name¶: Pulse Sequence Name value.

repetition_time¶: Repetition Time value.

sample_header¶

Return a sample Header instance for this series.

See also

get_sample_header()

Returns:	Sample image header information
Return type:	DicomHeader

save(*args, **kwargs) → None¶: Overrides save() to create any missing related DICOM entities if required.

scanning_sequence¶: Scanning Sequence value.

sequence_name¶: Sequence Name value.

sequence_type¶: Scanning sequence type identifier, as detected by dicom_parser.

sequence_variant¶: Sequence Variant value.

slice_thickness¶: Slice Thickness value.

spatial_resolution¶

Returns the 3D spatial resolution of the instance by combining the values of the pixel_spacing and slice_thickness fields.

Returns:	(x, y, z) resolution in millimeters
Return type:	tuple

study¶: The Study instance to which this series belongs.

time¶: Series Time value.

uid¶: Series Instance UID value.

update_sequence_type(save: bool = True)¶

Checks the sequence type identifier detected by dicom_parser and updates the serialized value if required.

Parameters:	save (bool) – Whether to save changes or not, default is True

django_dicom.models.study module¶

Definition of the Study class.

class django_dicom.models.study.Study(*args, **kwargs)¶

Bases: django_dicom.models.dicom_entity.DicomEntity

A model to represent a single instance of the Study entity.

FIELD_TO_HEADER = {'date': 'StudyDate', 'description': 'StudyDescription', 'time': 'StudyTime', 'uid': 'StudyInstanceUID'}¶: A dictionary of DICOM data element keywords to be used to populate a created instance’s fields.

date¶: Study Date value.

description¶: Study Description value.

get_absolute_url()¶

Returns the absolute URL for this instance. For more information see the Django documentation.

Returns:	This instance’s absolute URL path
Return type:	str

logger = <Logger data.dicom.study (WARNING)>¶

n_images¶

Returns the number of associated images.

See also

query_n_images()

Returns:	Number of associated images
Return type:	int

n_patients¶

Returns the number of associated patients.

See also

query_n_patients()

Returns:	Number of associated patients
Return type:	int

n_series¶

Returns the number of associated series.

Returns:	Number of associated series
Return type:	int

objects = <django.db.models.manager.DicomEntityManagerFromStudyQuerySet object>¶

query_n_images() → int¶

Returns the number of associated images.

See also

n_images()

Returns:	Number of associated images
Return type:	int

query_n_patients() → int¶

Returns the number of associated patients.

See also

n_patients()

Returns:	Number of associated patients
Return type:	int

series_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

time¶: Study Time value.

uid¶: Study Instance UID value.

Serializers¶

Module contents¶

Provides serializers for the REST API.

Submodules¶

django_dicom.serializers.image_serializer module¶

Definition of the ImageSerializer class.

class django_dicom.serializers.image_serializer.ImageSerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)¶

Bases: rest_framework.serializers.ModelSerializer

A serializer class for the Image model.

class Meta¶

Bases: object

fields = ('id', 'series', 'number', 'date', 'time', 'uid')¶

model¶: alias of django_dicom.models.image.Image

django_dicom.serializers.patient_serializer module¶

Definition of the PatientSerializer class.

class django_dicom.serializers.patient_serializer.PatientSerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)¶

Bases: rest_framework.serializers.HyperlinkedModelSerializer

A serializer class for the Patient model.

class Meta¶

Bases: object

fields = ('id', 'url', 'uid', 'name_prefix', 'given_name', 'middle_name', 'family_name', 'name_suffix', 'sex', 'date_of_birth', 'latest_study_time', 'n_studies', 'n_series', 'n_images', 'research_subject')¶

model¶: alias of django_dicom.models.patient.Patient

django_dicom.serializers.series_serializer module¶

Definition of the SeriesSerializer class.

class django_dicom.serializers.series_serializer.SeriesSerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)¶

Bases: rest_framework.serializers.ModelSerializer

A serializer class for the Series model.

class Meta¶

Bases: object

fields = ('id', 'study', 'patient', 'body_part_examined', 'patient_position', 'number', 'description', 'date', 'time', 'modality', 'protocol_name', 'pulse_sequence_name', 'sequence_name', 'scanning_sequence', 'sequence_variant', 'pixel_spacing', 'slice_thickness', 'echo_time', 'inversion_time', 'repetition_time', 'flip_angle', 'manufacturer', 'manufacturer_model_name', 'magnetic_field_strength', 'device_serial_number', 'institution_name', 'uid', 'sequence_type')¶

model¶: alias of django_dicom.models.series.Series

django_dicom.serializers.study_serializer module¶

Definition of the StudySerializer class.

class django_dicom.serializers.study_serializer.StudySerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)¶

Bases: rest_framework.serializers.HyperlinkedModelSerializer

A serializer class for the Study model.

class Meta¶

Bases: object

fields = ('id', 'description', 'date', 'time', 'uid', 'url', 'n_patients', 'n_series', 'n_images')¶

model¶: alias of django_dicom.models.study.Study

Utils¶

Module contents¶

General utilities.

Submodules¶

django_dicom.utils.html module¶

Definition of the Html class.

django_dicom.utils.html.ADMIN_VIEW_NAMES = {'DataElement': 'admin:django_dicom_dataelement_change', 'DataElementDefinition': 'admin:django_dicom_dataelementdefinition_change', 'DataElementValue': 'admin:django_dicom_dataelementvalue_change', 'Header': 'admin:django_dicom_header_change', 'Image': 'admin:django_dicom_image_change', 'Patient': 'admin:django_dicom_patient_change', 'Series': 'admin:django_dicom_series_change', 'Study': 'admin:django_dicom_study_change'}¶: Admin site views by model name, used to generate the appropriate URLs.

class django_dicom.utils.html.Html¶

Bases: object

Automates some HTML generation for the admin site.

BREAK = '<br>'¶

HORIZONTAL_LINE = '<hr style="background-color: {color};">'¶

classmethod admin_link(model_name: str, pk: int, text: str = None) → str¶

Returns a link to the admin site page of the provided model instance.

Parameters:	model_name (str) – Model to be linked pk (int) – Instance to be linked text (str, optional) – Text to display for the link, by default None (uses the instance’s primary key)
Returns:	HTML link
Return type:	str

classmethod break_html(pieces) → str¶

Add break (<br>) tags between an iterable of HTML snippets.

Parameters:	pieces (Iterable) – HTML snippets
Returns:	Joined HTML
Return type:	str

classmethod horizontal_line(color: str = 'black') → str¶

Returns an <hr> tag with the desired color.

Parameters:	color (str, optional) – Color to style the line with, by default “black”
Returns:	HTML horizontal line
Return type:	str

classmethod json(value) → str¶

Formats a JSON string for display in the browser.

Parameters:	value (str) – JSON string
Returns:	Formatted JSON HTML
Return type:	str

Views¶

Module contents¶

Definition of the app’s rest_framework.viewsets.ViewSet subclasses.

Submodules¶

django_dicom.views.defaults module¶

Definition of the DefaultsMixin mixin.

class django_dicom.views.defaults.DefaultsMixin¶

Bases: object

Default settings for view authentication, permissions and filtering.

authentication_classes = (<class 'rest_framework.authentication.BasicAuthentication'>, <class 'rest_framework.authentication.TokenAuthentication'>)¶

filter_backends = (<class 'django_filters.rest_framework.backends.DjangoFilterBackend'>, <class 'rest_framework.filters.SearchFilter'>, <class 'rest_framework.filters.OrderingFilter'>)¶

permission_classes = (<class 'rest_framework.permissions.IsAuthenticated'>,)¶

django_dicom.views.image module¶

Definition of the ImageViewSet class.

class django_dicom.views.image.ImageViewSet(**kwargs)¶

Bases: django_dicom.views.defaults.DefaultsMixin, rest_framework.viewsets.ModelViewSet

API endpoint that allows images to be viewed or edited.

filter_class¶: alias of django_dicom.filters.image_filter.ImageFilter

get_queryset()¶

Get the list of items for this view. This must be an iterable, and may be a queryset. Defaults to using self.queryset.

This method should always be used rather than accessing self.queryset directly, as self.queryset gets evaluated only once, and those results are cached for all subsequent requests.

You may want to override this if you need to provide different querysets depending on the incoming request.

(Eg. return a list of items that is specific to the user)

ordering_fields = ('series', 'number', 'date', 'time')¶

pagination_class¶: alias of django_dicom.views.pagination.StandardResultsSetPagination

parser_classes = (<class 'rest_framework.parsers.MultiPartParser'>,)¶

queryset¶

search_fields = ('number', 'date', 'time', 'uid')¶

serializer_class¶: alias of django_dicom.serializers.image_serializer.ImageSerializer

django_dicom.views.pagination module¶

Definition of the StandardResultsSetPagination class.

class django_dicom.views.pagination.StandardResultsSetPagination¶

Bases: rest_framework.pagination.PageNumberPagination

Default pagination parameters. This didn’t work as part of the DefaultsMixin and therefore has to be defined separately in the ‘pagination_class’ configuration.

max_page_size = 10000¶

page_size = 25¶

page_size_query_param = 'page_size'¶

django_dicom.views.patient module¶

Definition of the PatientViewSet class.

class django_dicom.views.patient.PatientViewSet(**kwargs)¶

Bases: django_dicom.views.defaults.DefaultsMixin, rest_framework.viewsets.ModelViewSet

API endpoint that allows patients to be viewed or edited.

aggregate(request) → rest_framework.response.Response¶

Returns related model counts if count filtering is enabled.

Parameters:	request (Request) – API request
Returns:	Aggregated queryset or informational message
Return type:	Response

download_series_set(request, uid)¶

filter_class¶: alias of django_dicom.filters.patient_filter.PatientFilter

get_queryset() → django.db.models.query.QuerySet¶

Overrides the parent get_queryset() method to apply aggregated annotation if count filtering is enabled.

Returns:	Patient queryset
Return type:	QuerySet

ordering_fields = ('id', 'uid', 'family_name', 'given_name', 'sex', 'date_of_birth', 'latest_study_time')¶

pagination_class¶: alias of django_dicom.views.pagination.StandardResultsSetPagination

queryset¶

serializer_class¶: alias of django_dicom.serializers.patient_serializer.PatientSerializer

django_dicom.views.series module¶

Definition of the SeriesViewSet class.

class django_dicom.views.series.SeriesViewSet(**kwargs)¶

Bases: django_dicom.views.defaults.DefaultsMixin, rest_framework.viewsets.ModelViewSet

API endpoint that allows series to be viewed or edited.

filter_class¶: alias of django_dicom.filters.series_filter.SeriesFilter

get_csv(request: rest_framework.request.Request) → rest_framework.response.Response¶

get_manufacturers(request)¶

get_queryset()¶

Get the list of items for this view. This must be an iterable, and may be a queryset. Defaults to using self.queryset.

This method should always be used rather than accessing self.queryset directly, as self.queryset gets evaluated only once, and those results are cached for all subsequent requests.

You may want to override this if you need to provide different querysets depending on the incoming request.

(Eg. return a list of items that is specific to the user)

listed_zip(request: rest_framework.request.Request, series_ids: str) → django.http.response.FileResponse¶

ordering_fields = ('study', 'patient', 'number', 'date', 'time', 'scanning_sequence', 'sequence_variant', 'pixel_spacing', 'echo_time', 'inversion_time', 'repetition_time', 'manufacturer', 'manufacturer_model_name', 'magnetic_field_strength', 'device_serial_number', 'institution_name', 'sequence_type')¶

pagination_class¶: alias of django_dicom.views.pagination.StandardResultsSetPagination

queryset¶

search_fields = ('study', 'patient', 'body_part_examined', 'number', 'description', 'date', 'time', 'modality', 'protocol_name', 'scanning_sequence', 'sequence_variant', 'pixel_spacing', 'echo_time', 'inversion_time', 'repetition_time', 'flip_angle', 'manufacturer', 'manufacturer_model_name', 'magnetic_field_strength', 'device_serial_number', 'institution_name', 'uid')¶

serializer_class¶: alias of django_dicom.serializers.series_serializer.SeriesSerializer

to_zip(request: rest_framework.request.Request, pk: int) → django.http.response.FileResponse¶

django_dicom.views.study module¶

Definition of the StudyViewSet class.

class django_dicom.views.study.StudyViewSet(**kwargs)¶

Bases: django_dicom.views.defaults.DefaultsMixin, rest_framework.viewsets.ModelViewSet

API endpoint that allows studies to be viewed or edited.

aggregate(request) → rest_framework.response.Response¶

Returns related model counts if count filtering is enabled.

Parameters:	request (Request) – API request
Returns:	Aggregated queryset or informational message
Return type:	Response

filter_class¶: alias of django_dicom.filters.study_filter.StudyFilter

get_queryset() → django.db.models.query.QuerySet¶

Overrides the parent get_queryset() method to apply aggregated annotation if count filtering is enabled.

Returns:	Study queryset
Return type:	QuerySet

pagination_class¶: alias of django_dicom.views.pagination.StandardResultsSetPagination

queryset¶

serializer_class¶: alias of django_dicom.serializers.study_serializer.StudySerializer

Submodules¶

django_dicom.urls module¶

Definition of the app’s URLs.

django_dicom.urls.path(route, view, kwargs=None, name=None, *, Pattern=<class 'django.urls.resolvers.RoutePattern'>)¶

Resources¶

General¶

Wikipedia.

The official DICOM standard website.

NiBabel’s introduction to DICOM.

DICOM is Easy - wonderful blog dedicated to the DICOM file format and software programming for medical applications.

DICOM Library - free online medical images, signals or video files sharing and anonymizing service for educational and scientific purposes. Includes a good introduction to the DICOM standard as well as a handy table of official DICOM tags.

DICOM Standard Browser - an online DICOM encyclopedia.

Other¶

The first step for neuroimaging data analysis: DICOM to NIfTI conversion [1] - contains valuable information about the way different vendors store data in the DICOM format (PDF).

Siemens mosaic format - Excellent NiBabel article.

Information on GE private tags can be found in the Discovery VCT DICOM Conformance Statement as well as in the GE MR DICOM Conformance Statement.

NA-MIC Wiki page on DICOM for DWI and DTI - vendor-specific information about DICOM and DWI/DTI data encoding.

[1]	Li, X., Morgan, P. S., Ashburner, J., Smith, J., & Rorden, C. (2016). The first step for neuroimaging data analysis: DICOM to NIfTI conversion. Journal of neuroscience methods, 264, 47-56.

Welcome to django_dicom’s documentation!¶

Overview¶

Installation¶

User Guide¶

Import Modes¶

Changing Import Mode¶

Importing Data¶

Reading Header Information¶

Reading a Single Image’s Header¶

Querying the Database¶

Reading Series Data¶

Reference¶

Module contents¶

Subpackages¶

Exceptions¶

Module contents¶

Submodules¶

django_dicom.exceptions.import_error module¶

Filters¶

Module contents¶

Submodules¶

django_dicom.filters.image_filter module¶

django_dicom.filters.patient_filter module¶

django_dicom.filters.series_filter module¶

django_dicom.filters.study_filter module¶

Models¶

Module contents¶

Subpackages¶

django_dicom.models.managers package¶

django_dicom.models.utils package¶

django_dicom.models.values package¶

Submodules¶

django_dicom.models.data_element module¶

django_dicom.models.data_element_definition module¶

django_dicom.models.dicom_entity module¶

django_dicom.models.header module¶

django_dicom.models.image module¶

django_dicom.models.patient module¶

django_dicom.models.series module¶

django_dicom.models.study module¶

Serializers¶

Module contents¶

Submodules¶

django_dicom.serializers.image_serializer module¶

django_dicom.serializers.patient_serializer module¶

django_dicom.serializers.series_serializer module¶

django_dicom.serializers.study_serializer module¶

Utils¶

Module contents¶

Submodules¶

django_dicom.utils.html module¶

Views¶

Module contents¶

Submodules¶

django_dicom.views.defaults module¶

django_dicom.views.image module¶

django_dicom.views.pagination module¶

django_dicom.views.patient module¶

django_dicom.views.series module¶

django_dicom.views.study module¶

Submodules¶

django_dicom.urls module¶

Resources¶

General¶

Other¶

Indices and tables¶