Welcome to pylabber’s documentation!

pylabber is a Django project designed to provide the core functionality required to conduct neuroscientific research.

See also

For more information about Django applications and the difference between projects and apps see Django’s Getting Started page, as well as the Projects and Applications section.

Overview

The project’s root directory contains the pylabber module, which holds the applications settings and URL configurations, as well as two native apps:

• accounts: Manages User (i.e. researcher) and Laboratory accounts.
• research: Manages the most elementary “research entities”; Subject, Study, and Group.

The basic models detailed above are meant to be integrated with external, reusable apps, providing domain-specific data models and functionality over them.

For a list of integrated reusable apps see Existing Apps.

Installation

Note

pylabber requires PostgreSQL. Before starting the installation, make sure you have PostgreSQL installed and create a new database.

There are many tutorials online providing detailed instructions on how to do this, some recommended ones can be found in Digital Ocean, DjangoGirls, and Medium.

1. Clone pylabber to a local directory:

   $ git clone https://github.com/TheLabbingProject/pylabber
   

2. From within the project’s directory, create a virtual environment using venv:

   $ python3 -m venv venv
   

3. Activate the virtual environment:

   $ source venv/bin/activate
   

4. Install the required dependencies:

   $ pip install -r requirements.txt
   

5. Create the appropriate environment variables for the settings.py file. You can find each of those variables wrapped in an env(“VAR_NAME”) call.

An example for an environment variables definition in development could look like:

.env

export SECRET_KEY="s0m3-$\/pER-s3CrE7_kEy!"
export DB_NAME=pylabber
export DB_USER=postgres
export DB_PASSWORD=p$q1@ddmmIN
export MEDIA_ROOT="/where/to/save/files/locally/"

6. Apply the project’s migrations:

   $ python manage.py migrate
   

7. Run pylabber locally:

   $ python manage.py runserver
   

   or, open an interactive Django shell using django-extensions:

   $ python manage.py shell_plus
   

Existing Apps

• django_analyses: Database-driven pipeline engine. Allows the creation of a library of analyses and keeps records of configurations and runs.
• django_mri: Format-agnostic MRI data management. Provides a Scan model that abstractifies data management and retrieval.

Frequently Asked Questions

What is The Labbing Project?

A collection of reusable Django apps and a single dedicated parent Django project (i.e. pylabber) used to manage and share research data and derivatives across researchers and across labs.

Hint

For more information about the difference between Django apps and projects, see Django’s Projects and Applications documentation.

Is The Labbing Project only suitable for MRI-based neuroscientific research?

Not at all! The purpose of the research app is to provide common, generic models (such as Subject and Study) that may be associted with any number of data models originating from any number of reusable apps.

How are different data types integrated into the application’s database?

The modular design of the project enables researchers from different fields to create specialized apps that manage the relevant data formats and facilitate commonplace workflows. E.g. the first app created for this purpose was django_dicom, which manages DICOM data, and the second was django_mri, providing a format-agnostic Scan abstraction, as well as other useful models and MRI-based research utilities. Each reusable app integrates with pylabber’s internal research app to associate the data with an instance of the Subject model. For more information, see pylabber’s overview.

Reference

accounts package

Module contents

Manages researcher (User) and Laboratory accounts.

Subpackages

accounts.filters package

Module contents

Filters for the app’s models.

Notes

For more information, see:

• Django REST Framework filtering documentation.
• django-filter’s documentation for Integration with DRF.

Submodules

accounts.filters.user module

Definition of the UserFilter class.

class accounts.filters.user.UserFilter(data=None, queryset=None, *, request=None, prefix=None)

Bases: django_filters.rest_framework.filterset.FilterSet

Provides useful filtering options for the User model.

base_filters = {'email': <django_filters.filters.LookupChoiceFilter object>, 'first_name': <django_filters.filters.LookupChoiceFilter object>, 'id': <django_filters.filters.NumberFilter object>, 'institute': <django_filters.filters.AllValuesMultipleFilter object>, 'last_name': <django_filters.filters.LookupChoiceFilter object>, 'study': <django_filters.filters.ModelMultipleChoiceFilter object>, 'study_ne': <django_filters.filters.NumberFilter object>, 'username': <django_filters.filters.LookupChoiceFilter object>}

declared_filters = {'email': <django_filters.filters.LookupChoiceFilter object>, 'first_name': <django_filters.filters.LookupChoiceFilter object>, 'institute': <django_filters.filters.AllValuesMultipleFilter object>, 'last_name': <django_filters.filters.LookupChoiceFilter object>, 'study_ne': <django_filters.filters.NumberFilter object>, 'username': <django_filters.filters.LookupChoiceFilter object>}

accounts.models package

Module contents

Definition of the app’s models. For an illustration of the relationship between the different models, see the Overview.

Submodules

accounts.models.choices module

Subclasses of the ChoiceEnum class used to represent raw and human-readable values for choices within the accounts.models module.

class accounts.models.choices.Role

Bases: pylabber.utils.utils.ChoiceEnum

An enumeration.

AFF = 'Research Affiliate'

MAN = 'Lab Manager'

MSC = 'M.Sc. Student'

PHD = 'Ph.D. Candidate'

PI = 'Principle Investigator'

POST = 'Postdoctoral Researcher'

RA = 'Research Assistant'

class accounts.models.choices.Title

Bases: pylabber.utils.utils.ChoiceEnum

An enumeration.

BSC = 'B.Sc.'

MSC = 'M.Sc.'

PHD = 'Ph.D.'

PROF = 'Prof.'

accounts.models.laboratory module

Definition of the Laboratory model.

class accounts.models.laboratory.Laboratory(*args, **kwargs)

Bases: django_extensions.db.models.TitleDescriptionModel, django_extensions.db.models.TimeStampedModel

A class to represents a research laboratory.

get_absolute_url() → str

Returns the canonical URL for this instance.

References

• get_absolute_url()

Returns:URL Return type:str

image

Just like the FileDescriptor, but for ImageFields. The only difference is assigning the width/height to the width_field/height_field, if appropriate.

laboratorymembership_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.

members

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.

accounts.models.profile module

Definition of the Profile model.

class accounts.models.profile.Profile(*args, **kwargs)

Bases: django.db.models.base.Model

A user profile, associated to each user using a OneToOne relationship and created automatically usings signals.

References

• Extending the User model.

bio

Short user biography.

date_of_birth

User’s date of birth.

get_absolute_url() → str

Returns the canonical URL for this instance.

References

• get_absolute_url()

Returns:URL Return type:str

get_full_name(include_title: bool = True) → str

Returns the full name of the user, including a title if any.

Parameters:include_title (bool, optional) – Whether to include title (academic credentials etc.) if specified Returns:User’s full name Return type:str

get_title_display(*, field=<django.db.models.fields.CharField: title>)

get_title_repr() → str

Returns the verbose title of the user as defined in the Title Enum.

Returns:Verbose title representation Return type:str

image

Profile image.

institute

The institute to which a user belongs, if any.

title

Academic or any other kind of title.

user

OneToOne relationship with the user model.

accounts.models.user module

Definition of the User model.

class accounts.models.user.User(*args, **kwargs)

Bases: django.contrib.auth.models.AbstractUser

Custom User model definition.

References

• Using a custom user model when starting a project.

exportdestination_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.

groups

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.

laboratory_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.

laboratorymembership_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.

logentry_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.

mri_uploads

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.

profile

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.

run_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.

study_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.

user_permissions

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.

accounts.serializers package

Module contents

Django REST Framework serializers module for the accounts package.

Submodules

accounts.serializers.group module

Definition of the GroupSerializer class.

class accounts.serializers.group.GroupSerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)

Bases: rest_framework.serializers.HyperlinkedModelSerializer

Serializer class for the Group model.

accounts.serializers.laboratory module

Definition of the LaboratorySerializer class.

class accounts.serializers.laboratory.LaboratorySerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)

Bases: rest_framework.serializers.HyperlinkedModelSerializer

Serializer class for the Laboratory model.

accounts.serializers.profile module

Definition of the ProfileSerializer class.

class accounts.serializers.profile.ProfileSerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)

Bases: rest_framework.serializers.HyperlinkedModelSerializer

Serializer class for the Profile model.

accounts.serializers.user module

Definition of the UserSerializer class.

class accounts.serializers.user.UserSerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)

Bases: rest_auth.serializers.UserDetailsSerializer

Serializer class for the User model.

References

• https://www.django-rest-framework.org/api-guide/serializers/

update(username, data: dict)

Update a user’s personal information, including profile data.

Parameters:

• username (User) – User to be updated
• data (dict) – User information

Returns:

Updated user instance

Return type:

User

accounts.views package

Module contents

Django REST Framework ViewSets for the accounts package.

Submodules

accounts.views.group module

Definition of the GroupViewSet class.

class accounts.views.group.GroupViewSet(**kwargs)

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

API endpoint that allows Group instances to be viewed or edited.

basename = None

description = None

detail = None

name = None

queryset

serializer_class

alias of accounts.serializers.group.GroupSerializer

suffix = None

accounts.views.laboratory module

Definition of the LaboratoryViewSet class.

class accounts.views.laboratory.LaboratoryViewSet(**kwargs)

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

API endpoint that allows Laboratory instances to be viewed or edited.

basename = None

description = None

detail = None

name = None

queryset

serializer_class

alias of accounts.serializers.laboratory.LaboratorySerializer

suffix = None

accounts.views.profile module

Definition of the ProfileViewSet class.

class accounts.views.profile.ProfileViewSet(**kwargs)

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

API endpoint that allows Profile instances to be viewed or edited.

basename = None

description = None

detail = None

name = None

queryset

serializer_class

alias of accounts.serializers.profile.ProfileSerializer

suffix = None

accounts.views.user module

Definition of the UserViewSet class.

class accounts.views.user.UserViewSet(**kwargs)

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

API endpoint that allows User instances to be viewed or edited.

basename = None

description = None

detail = None

filter_class

alias of accounts.filters.user.UserFilter

filter_queryset(queryset) → django.db.models.query.QuerySet

Filter the returned users according to the requesting user’s permissions.

Parameters:queryset (QuerySet) – Base queryset Returns:User instances Return type:QuerySet

get_institutions(request)

name = None

queryset

serializer_class

alias of accounts.serializers.user.UserSerializer

suffix = None

Submodules

accounts.admin module

class accounts.admin.ExportDestinationAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

fieldsets = ((None, {'fields': ('id', 'title', 'description', 'username', 'password', 'destination', 'users')}), ('Advanced options', {'classes': ('collapse',), 'fields': ('port', 'socket_timeout', 'negotiation_timeout', 'banner_timeout')}))

form

alias of accounts.forms.export_destination.ExportDestinationForm

list_display = ('id', 'title', 'description', 'ip', 'username', 'destination', 'sftp')

media

readonly_fields = ('id',)

sftp(destination: accounts.models.export_destination.ExportDestination) → bool

class accounts.admin.LaboratoryAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

class Media

Bases: object

css = {'all': ('accounts/css/hide_admin_original.css',)}

fields = ('title', 'description', 'image', 'image_tag')

image_tag(instance: accounts.models.laboratory.Laboratory) → str

inlines = (<class 'accounts.admin.LaboratoryMembershipInLine'>,)

list_display = ('id', 'title', 'description', 'created', 'modified')

media

readonly_fields = ('image_tag',)

class accounts.admin.LaboratoryMembershipInLine(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

extra = 0

media

model

alias of accounts.models.laboratory_membership.LaboratoryMembership

class accounts.admin.ProfileInline(parent_model, admin_site)

Bases: django.contrib.admin.options.StackedInline

can_delete = False

fields = ('title', 'image', 'image_tag', 'date_of_birth', 'institute', 'bio')

fk_name = 'user'

image_tag(instance: accounts.models.profile.Profile) → str

media

model

alias of accounts.models.profile.Profile

readonly_fields = ('image_tag',)

verbose_name_plural = 'Profile'

class accounts.admin.UserAdmin(model, admin_site)

Bases: django.contrib.auth.admin.UserAdmin

get_inline_instances(request, obj=None)

get_institute(instance)

inlines = (<class 'accounts.admin.ProfileInline'>, <class 'accounts.admin.LaboratoryMembershipInLine'>)

list_display = ('username', 'email', 'first_name', 'last_name', 'get_institute', 'is_staff', 'is_superuser')

list_select_related = ('profile',)

media

accounts.apps module

class accounts.apps.AccountsConfig(app_name, app_module)

Bases: django.apps.config.AppConfig

name = 'accounts'

ready()

Override this method in subclasses to run code when Django starts.

accounts.signals module

accounts.signals.create_auth_token(sender, instance=None, created=False, **kwargs)

Automatically creates an authentication token for the user, as described in the DRF documentation.

Parameters:created (bool, optional) – Whether the instance is being created or updated, by default False

accounts.signals.post_save_user_model_receiver(sender, instance, created, *args, **kwargs)

Standard implementation for user profile creation.

Parameters:

• sender (django.db.models.Model) – The class of the instance being saved
• instance (django.db.models.Model) – The instance being saved
• created (bool) – Whether the instance is being created or updated

accounts.urls module

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

pylabber package

Module contents

Submodules

pylabber.settings module

Django settings for pylabber project.

For more information on this file, see https://docs.djangoproject.com/en/dev/topics/settings/

For the full list of settings and their values, see https://docs.djangoproject.com/en/dev/ref/settings/

pylabber.settings.DICOM_IMPORT_MODE = 'minimal'

Prevent the creation of DICOM data elements in the database.

pylabber.settings.ENABLE_COUNT_FILTERING = False

Do not annotate querysets with related model counts which drastically slows down queries.

pylabber.test_settings module

pylabber.urls module

pylabber URL Configuration

The urlpatterns list routes URLs to views.

Examples: * Function views

1. Add an import: from my_app import views
2. Add a URL to urlpatterns: path(‘’, views.home, name=’home’)

• Class-based views

  1. Add an import: from other_app.views import Home
  2. Add a URL to urlpatterns: path(‘’, Home.as_view(), name=’home’)

• Including another URLconf

  1. Import the include() function: from django.urls import include, path
  2. Add a URL to urlpatterns: path(‘blog/’, include(‘blog.urls’))

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

pylabber.utils module

pylabber.wsgi module

WSGI config for pylabber project.

It exposes the WSGI callable as a module-level variable named application.

For more information on this file, see https://docs.djangoproject.com/en/2.0/howto/deployment/wsgi/

research package

Module contents

A reusable Django app to manage research information.

Subpackages

research.filters package

Module contents

Filters for the app’s models.

Submodules

research.filters.subject_filter module

Definition of the SubjectFilter class.

class research.filters.subject_filter.SubjectFilter(data=None, queryset=None, *, request=None, prefix=None)

Bases: django_filters.rest_framework.filterset.FilterSet

Provides useful filtering options for the Subject model.

base_filters = {'born_after_date': <django_filters.filters.DateFilter object>, 'born_before_date': <django_filters.filters.DateFilter object>, 'dicom_patient': <django_filters.filters.NumberFilter object>, 'dominant_hand': <django_filters.filters.CharFilter object>, 'first_name': <django_filters.filters.LookupChoiceFilter object>, 'gender': <django_filters.filters.CharFilter object>, 'id': <django_filters.filters.NumberFilter object>, 'id_number': <django_filters.filters.LookupChoiceFilter object>, 'last_name': <django_filters.filters.LookupChoiceFilter object>, 'measurement': <pylabber.utils.filters.NumberInFilter object>, 'mri_session_time': <django_filters.filters.DateTimeFromToRangeFilter object>, 'procedure': <pylabber.utils.filters.NumberInFilter object>, 'questionnaire_id': <django_filters.filters.CharFilter object>, 'sex': <django_filters.filters.CharFilter object>, 'study': <pylabber.utils.filters.NumberInFilter object>, 'study_group': <pylabber.utils.filters.NumberInFilter object>}

declared_filters = {'born_after_date': <django_filters.filters.DateFilter object>, 'born_before_date': <django_filters.filters.DateFilter object>, 'dicom_patient': <django_filters.filters.NumberFilter object>, 'dominant_hand': <django_filters.filters.CharFilter object>, 'first_name': <django_filters.filters.LookupChoiceFilter object>, 'gender': <django_filters.filters.CharFilter object>, 'id_number': <django_filters.filters.LookupChoiceFilter object>, 'last_name': <django_filters.filters.LookupChoiceFilter object>, 'measurement': <pylabber.utils.filters.NumberInFilter object>, 'mri_session_time': <django_filters.filters.DateTimeFromToRangeFilter object>, 'procedure': <pylabber.utils.filters.NumberInFilter object>, 'questionnaire_id': <django_filters.filters.CharFilter object>, 'sex': <django_filters.filters.CharFilter object>, 'study': <pylabber.utils.filters.NumberInFilter object>, 'study_group': <pylabber.utils.filters.NumberInFilter object>}

filter_by_dicom_patient(queryset, name, value)

Find the subject that represents a particular DICOM Patient instance.

Parameters:

• queryset (django.db.models.QuerySet) – The Subject queryset to filter.
• name (str) – The name of the model field to filter on.
• value (int) – DICOM Patient ID.

filter_by_measurement(queryset, name, value)

filter_by_procedure(queryset, name, value)

filter_by_questionnaire_id(queryset, name, value)

filter_by_studies(queryset, name, value)

filter_by_study_group(queryset, name, value)

filter_nullable_charfield(queryset, name, values)

research.models package

Module contents

Definition of the app’s models. For an illustration of the relationship between the different models, see the Overview.

Submodules

research.models.choices module

Subclasses of the ChoiceEnum class used to represent raw and human-readable values for choices within the research.models module.

class research.models.choices.DominantHand

Bases: pylabber.utils.utils.ChoiceEnum

An Enum representing supported dominant hand options.

A = 'Ambidextrous'

L = 'Left'

R = 'Right'

class research.models.choices.Gender

Bases: pylabber.utils.utils.ChoiceEnum

An Enum representing supported gender options.

CIS = 'Cisgender'

OTHER = 'Other'

TRANS = 'Transgender'

class research.models.choices.Sex

Bases: pylabber.utils.utils.ChoiceEnum

An Enum representing supported sex options.

F = 'Female'

M = 'Male'

U = 'Other'

research.models.group module

Definition of the Group model.

class research.models.group.Group(*args, **kwargs)

Bases: django_extensions.db.models.TitleDescriptionModel, django_extensions.db.models.TimeStampedModel

Represents a unique study group (i.e. a grouping of subjects according to some experimental design in the context of a study).

mri_scan_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.

study

The study associated with this experimental group.

research.models.study module

Definition of the Study model.

class research.models.study.Study(*args, **kwargs)

Bases: django_extensions.db.models.TitleDescriptionModel, django_extensions.db.models.TimeStampedModel

Represents a single study in the database.

collaborators

Researchers collaborating on this study.

get_absolute_url()

Returns the canonical URL for this instance.

References

• get_absolute_url()

Returns:URL Return type:str

group_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.

image

An optional image to supplement the description.

n_subjects

Returns the number of subjects associated with this study.

Returns:Number of subjects associated with this study Return type:int

procedures

The experimental procedures associated with this study.

query_associated_subjects() → django.db.models.query.QuerySet

Returns a queryset of subjects associated with this study.

See also

• subject_set()

Returns:Subjects associated with this study Return type:models.QuerySet

subject_set

Returns a queryset of subjects associated with this study.

See also

• query_associated_subjects()

Returns:Subjects associated with this study Return type:models.QuerySet

subjects

Subjects associated with this study. This field is currently not used, but kept because in the future it might be used for “caching” associated subjects to save queries.

research.models.subject module

Definition of the Subject model.

class research.models.subject.Subject(*args, **kwargs)

Bases: django_extensions.db.models.TimeStampedModel

Represents a single research subject. Any associated data model should be associated with this model.

BIDS_DIR_TEMPLATE = 'sub-{pk}'

build_bids_directory(force: bool = False, persistent: bool = True, progressbar: bool = False, progressbar_position: int = 0)

custom_attributes

Custom attributes dictionary.

date_of_birth

Subject’s date of birth.

dominant_hand

Subject’s dominant hand.

first_name

Subject’s first name.

gender

Subject’s gender.

get_absolute_url()

Returns the canonical URL for this instance.

References

• get_absolute_url()

Returns:URL Return type:str

get_bids_directory() → pathlib.Path

get_dominant_hand_display(*, field=<django.db.models.fields.CharField: dominant_hand>)

get_full_name() → str

Returns a formatted string with the subject’s full name (first name and then last name).

Returns:Subject’s full name Return type:str

get_gender_display(*, field=<django.db.models.fields.CharField: gender>)

get_personal_information() → pandas.core.series.Series

Temporary method to use an external table to retrieve subject personal information.

Returns:Subject personal information Return type:pd.Series

get_questionnaire_data()

A method to link between a subject to it’s questionnaire data.

Returns:Subject and Questionnaire information. Return type:pd.Series

get_raw_information() → pandas.core.series.Series

Temporary method to use an external table to retrieve subject information.

Returns:Subject information Return type:pd.Series

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

id_number

Some representative ID number unique to this subject.

last_name

Subject’s last name.

mri_session_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.

query_measurements() → django.db.models.query.QuerySet

query_procedures() → django.db.models.query.QuerySet

query_run_set() → django.db.models.query.QuerySet

query_scores(analysis: Union[django_analyses.models.analysis.Analysis, Iterable[django_analyses.models.analysis.Analysis]] = None, analysis_title: Union[str, Iterable[str]] = None, analysis_version: Union[django_analyses.models.analysis_version.AnalysisVersion, Iterable[django_analyses.models.analysis_version.AnalysisVersion]] = None, analysis_version_title: Union[str, Iterable[str]] = None, atlas=None, atlas_title: Union[str, Iterable[str]] = None, metric=None, metric_title: Union[str, Iterable[str]] = None, region=None, region_title: Union[str, Iterable[str]] = None, region_index: Union[int, Iterable[int]] = None, hemisphere: str = None) → django.db.models.query.QuerySet

query_studies() → django.db.models.query.QuerySet

Returns a queryset of Study instances this subject has data associated with.

Returns:Associated studies Return type:models.QuerySet

query_study_groups() → django.db.models.query.QuerySet

save(*args, **kwargs)

Overrides the model’s save() method to process custom attributes.

Hint

For more information, see Django’s documentation on overriding model methods.

sex

Subject’s sex.

study_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.

research.models.procedure module

Definition of the Procedure model.

class research.models.procedure.Procedure(*args, **kwargs)

Bases: django_extensions.db.models.TitleDescriptionModel

Represents an experimental procedure.

add_event(event: research.models.event.Event, index: int = None)

Performs an event addition.

events

Represents an ordered list of events in a procedure.

get_absolute_url()

Returns the canonical URL for this instance.

References

• get_absolute_url()

Returns:URL Return type:str

max_index

Returns the maximal index field value of any associated ProcedureStep instances. If there aren’t any, returns -1.

Returns:Maximal step index, or -1 Return type:int

step_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.

study_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.

research.models.event module

Definition of the Event model.

class research.models.event.Event(*args, **kwargs)

Bases: django_extensions.db.models.TitleDescriptionModel

Represents an event as a part of a procedure.

get_absolute_url()

Returns the canonical URL for this instance.

References

• get_absolute_url()

Returns:URL Return type:str

measurementdefinition

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.

procedure_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.

procedurestep_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.

task

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.

research.models.task module

Definition of the Task model.

class research.models.task.Task(*args, **kwargs)

Bases: research.models.event.Event

Represents an experimental task.

event_ptr

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

In the example:

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

Restaurant.place is a ForwardOneToOneDescriptor instance.

event_ptr_id

get_absolute_url()

Returns the canonical URL for this instance.

References

• get_absolute_url()

Returns:URL Return type:str

research.models.measurement_definition module

Definition of the MeasurementDefinition model.

class research.models.measurement_definition.MeasurementDefinition(*args, **kwargs)

Bases: research.models.event.Event

Represents an experimental measurement definition.

content_type

Accessor to the related object on the forward side of a many-to-one or one-to-one (via ForwardOneToOneDescriptor subclass) relation.

In the example:

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

Child.parent is a ForwardManyToOneDescriptor instance.

content_type_id

event_ptr

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

In the example:

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

Restaurant.place is a ForwardOneToOneDescriptor instance.

event_ptr_id

get_absolute_url()

Returns the canonical URL for this instance.

References

• get_absolute_url()

Returns:URL Return type:str

get_instance_set() → django.db.models.query.QuerySet

Returns a queryset of collected measurements associated with this measurements definition.

Returns:Collected data instances Return type:models.QuerySet

instance_set

Returns a queryset of collected measurements associated with this measurements definition.

Returns:Collected data instances Return type:models.QuerySet

See also

• get_instance_set()

mri_session_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.

query_associated_studies() → django.db.models.query.QuerySet

research.models.validators module

Validators for django fields within the research.models module.

research.models.validators.not_future(value)

research.serializers package

Module contents

Django REST Framework serializers module for the research package.

Submodules

research.serializers.group module

Definition of the GroupSerializer class.

class research.serializers.group.GroupReadSerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)

Bases: rest_framework.serializers.HyperlinkedModelSerializer

HyperlinkedModelSerializer for the Group model to be used in GET requests.

class research.serializers.group.GroupSerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)

Bases: rest_framework.serializers.HyperlinkedModelSerializer

HyperlinkedModelSerializer for the Group model to be used in POST requests.

class research.serializers.group.MiniStudySerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)

Bases: rest_framework.serializers.ModelSerializer

A minimized Study ModelSerializer used in the GroupReadSerializer class.

research.serializers.study module

Definition of the StudySerializer class.

class research.serializers.study.MiniStudySerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)

Bases: rest_framework.serializers.HyperlinkedModelSerializer

Minified serializer for the Study model.

class research.serializers.study.StudySerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)

Bases: rest_framework.serializers.HyperlinkedModelSerializer

Serializer for the Study model.

research.serializers.subject module

Definition of the SubjectSerializer class.

class research.serializers.subject.AdminSubjectSerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)

Bases: research.serializers.subject.SubjectSerializer

class research.serializers.subject.SubjectSerializer(instance=None, data=<class 'rest_framework.fields.empty'>, **kwargs)

Bases: rest_framework.serializers.ModelSerializer

Base serializer for the Subject model.

research.views package

Module contents

Submodules

research.views.group module

Definition of the GroupViewSet class.

class research.views.group.GroupViewSet(**kwargs)

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

API endpoint that allows Group instances to be viewed or edited.

basename = None

description = None

detail = None

filter_class

alias of research.filters.group_filter.GroupFilter

get_serializer_class()

Return the class to use for the serializer. Defaults to using self.serializer_class.

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

(Eg. admins get full serialization, others get basic serialization)

name = None

queryset

suffix = None

research.views.study module

Definintion of the StudyViewSet class.

class research.views.study.StudyViewSet(**kwargs)

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

API endpoint that allows Study instances 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

basename = None

description = None

detail = None

filter_class

alias of research.filters.study_filter.StudyFilter

filter_queryset(queryset)

Filters the returned study queryset according to the user’s collaborations.

Parameters:queryset (QuerySet) – Base Study queryset Returns:Studies in which the user is a collaborator Return type:QuerySet

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

name = None

queryset

serializer_class

alias of research.serializers.study.StudySerializer

suffix = None

research.views.subject module

Definition of the SubjectViewSet class.

class research.views.subject.SubjectViewSet(**kwargs)

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

API endpoint that allows Subject instances to be viewed or edited.

basename = None

description = None

detail = None

export_files(request)

filter_class

alias of research.filters.subject_filter.SubjectFilter

filter_queryset(queryset)

Given a queryset, filter it with whichever filter backend is in use.

You are unlikely to want to override this method, although you may need to call it either from a list view, or from a custom get_object method if you want to apply the configured filtering backend to the default queryset.

get_serializer_class()

Return the class to use for the serializer. Defaults to using self.serializer_class.

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

(Eg. admins get full serialization, others get basic serialization)

name = None

ordering_fields = ('id', 'id_number', 'first_name', 'last_name', 'date_of_birth', 'sex', 'dominant_hand', 'created', 'modified', 'latest_mri_session_time', 'mri_session_count')

plot(request, *args, **kwargs)

plot_script(request, *args, **kwargs)

plot_summary(request, *args, **kwargs)

queryset

suffix = None

to_csv(request, *args, **kwargs)

Submodules

research.admin module

class research.admin.CollaboratorsInline(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

class Media

Bases: object

css = {'all': ('research/css/hide_admin_original.css',)}

email(instance) → str

extra = 0

fields = ('user_id', 'title', 'first_name', 'last_name', 'username', 'email')

first_name(instance) → str

has_add_permission(request, instance)

Return True if the given request has permission to add an object. Can be overridden by the user in subclasses.

last_name(instance) → str

media

model

alias of research.models.study.Study_collaborators

readonly_fields = ('user_id', 'title', 'first_name', 'last_name', 'username', 'email')

title(instance) → str

username(instance) → str

verbose_name_plural = 'Collaborators'

class research.admin.DecadeBornListFilter(request, params, model, model_admin)

Bases: django.contrib.admin.filters.SimpleListFilter

DECADES = ('40s', '50s', '60s', '70s', '80s', '90s', '00s')

lookups(request, model_admin)

Returns a list of tuples. The first element in each tuple is the coded value for the option that will appear in the URL query. The second element is the human-readable name for the option that will appear in the right sidebar.

parameter_name = 'decade'

queryset(request, queryset)

Returns the filtered queryset based on the value provided in the query string and retrievable via self.value().

title = 'decade born'

class research.admin.GroupAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

inlines = (<class 'research.admin.ScanInline'>,)

list_display = ('id', 'study_', 'title', 'description', 'mri_scan_count')

list_filter = ('title', ('study__title', <class 'research.admin.custom_titled_filter.<locals>.Wrapper'>))

media

mri_scan_count(instance: research.models.group.Group) → int

readonly_fields = ('study_', 'mri_scan_count')

search_fields = ('study__title', 'title', 'description')

study_(instance: research.models.group.Group) → str

class research.admin.MeasurementDefinitionAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

list_display = ('id', 'title', 'description', 'content_type', 'n_collected')

media

n_collected(instance: research.models.measurement_definition.MeasurementDefinition) → int

class research.admin.ProcedureAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

inlines = (<class 'research.admin.StudyInline'>, <class 'research.admin.ProcedureStepInline'>)

list_display = ('id', 'title', 'description', 'step_count')

media

step_count(instance: research.models.procedure.Procedure) → int

class research.admin.ProcedureInline(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

class Media

Bases: object

css = {'all': ('research/css/hide_admin_original.css',)}

can_delete = False

description(instance) → str

extra = 0

fields = ('id_link', 'title', 'description')

has_add_permission(request, instance)

Return True if the given request has permission to add an object. Can be overridden by the user in subclasses.

id_link(instance) → str

media

model

alias of research.models.study.Study_procedures

readonly_fields = ('id_link', 'title', 'description')

title(instance) → str

verbose_name_plural = 'Procedures'

class research.admin.ProcedureStepInline(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

class Media

Bases: object

css = {'all': ('research/css/hide_admin_original.css',)}

can_delete = False

event_description(instance: research.models.procedure_step.ProcedureStep) → str

event_title(instance: research.models.procedure_step.ProcedureStep) → str

event_type(instance: research.models.procedure_step.ProcedureStep) → str

extra = 0

fields = ('index_link', 'event_type', 'event_title', 'event_description')

has_add_permission(request, instance: research.models.procedure_step.ProcedureStep)

Return True if the given request has permission to add an object. Can be overridden by the user in subclasses.

index_link(instance: research.models.procedure_step.ProcedureStep) → str

media

model

alias of research.models.procedure_step.ProcedureStep

readonly_fields = ('index_link', 'event_type', 'event_title', 'event_description')

verbose_name_plural = 'Steps'

class research.admin.ScanInline(parent_model, admin_site)

Bases: django_admin_inline_paginator.admin.TabularInlinePaginated

class Media

Bases: object

css = {'all': ('research/css/hide_admin_original.css',)}

comments(instance) → str

description(instance) → str

download(instance) → str

echo_time(instance) → float

extra = 0

fields = ('id_link', 'subject', 'session', 'number', 'time', 'description', 'echo_time', 'inversion_time', 'repetition_time', 'spatial_resolution', 'comments', 'download')

has_add_permission(request, instance)

Return True if the given request has permission to add an object. Can be overridden by the user in subclasses.

id_link(instance) → str

inversion_time(instance) → float

media

model

alias of django_mri.models.scan.Scan_study_groups

number(instance) → int

readonly_fields = ('id_link', 'subject', 'session', 'number', 'time', 'description', 'echo_time', 'inversion_time', 'repetition_time', 'spatial_resolution', 'comments', 'download')

repetition_time(instance) → float

session(instance) → str

spatial_resolution(instance) → str

Returns a nicely formatted representation of the scan’s spatial resolution.

Parameters:instance (django_mri.Scan_study_groups) – Scan_study_groups instance Returns:Formatted spatial resolution representation Return type:str

subject(instance) → str

time(instance) → datetime.datetime

verbose_name_plural = 'Scans'

class research.admin.SessionInLine(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

class Media

Bases: object

css = {'all': ('research/css/hide_admin_original.css',)}

can_delete = False

download(instance: django_mri.models.session.Session) → str

extra = 0

fields = ('id_link', 'time', 'measurement', 'scan_count', 'comments', 'download')

has_add_permission(request, instance: django_mri.models.session.Session)

Return True if the given request has permission to add an object. Can be overridden by the user in subclasses.

id_link(instance: django_mri.models.session.Session) → str

media

model

alias of django_mri.models.session.Session

readonly_fields = ('id_link', 'time', 'scan_count', 'download')

scan_count(instance: django_mri.models.session.Session) → int

verbose_name_plural = 'MRI Sessions'

class research.admin.StudyAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

exclude = ('subjects', 'collaborators', 'procedures')

fields = ('title', 'description', 'image', 'participant_list')

inlines = (<class 'research.admin.CollaboratorsInline'>, <class 'research.admin.ProcedureInline'>)

list_display = ('title', 'description', 'created')

media

participant_list(instance: research.models.study.Study) → str

readonly_fields = ('participant_list',)

class research.admin.StudyAssociationFilter(request, params, model, model_admin)

Bases: django.contrib.admin.filters.SimpleListFilter

lookups(request, model_admin)

Must be overridden to return a list of tuples (value, verbose value)

parameter_name = 'study participation'

queryset(request, queryset)

Return the filtered queryset.

title = 'study participation'

class research.admin.StudyInline(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

class Media

Bases: object

css = {'all': ('research/css/hide_admin_original.css',)}

can_delete = False

description(instance) → str

extra = 0

fields = ('id_link', 'title', 'description')

has_add_permission(request, instance: research.models.procedure_step.ProcedureStep)

Return True if the given request has permission to add an object. Can be overridden by the user in subclasses.

id_link(instance) → str

media

model

alias of research.models.study.Study_procedures

readonly_fields = ('id_link', 'title', 'description')

title(instance) → str

verbose_name_plural = 'Studies'

class research.admin.SubjectAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

actions = ('export_csv',)

changelist_view(request, extra_context=None)

The ‘change list’ admin view for this model.

export_csv(request, queryset)

inlines = (<class 'research.admin.SessionInLine'>,)

list_display = ('id', 'id_number', 'first_name', 'last_name', 'sex', 'date_of_birth', 'dominant_hand', 'n_mri_sessions')

list_filter = ('sex', 'dominant_hand', <class 'research.admin.DecadeBornListFilter'>, <class 'research.admin.StudyAssociationFilter'>)

media

n_mri_sessions(instance: research.models.subject.Subject) → int

readonly_fields = ('n_mri_sessions',)

search_fields = ('id', 'id_number', 'first_name', 'last_name', 'date_of_birth__year')

class research.admin.SubjectsInline(parent_model, admin_site)

Bases: django.contrib.admin.options.TabularInline

date_of_birth(instance)

extra = 0

first_name(instance)

id_number(instance)

last_name(instance)

media

model

alias of research.models.study.Study_subjects

readonly_fields = ('id_number', 'first_name', 'last_name', 'sex', 'date_of_birth')

sex(instance)

verbose_name_plural = 'Subjects'

class research.admin.TaskAdmin(model, admin_site)

Bases: django.contrib.admin.options.ModelAdmin

list_display = ('id', 'title', 'description')

media

research.admin.custom_titled_filter(title: str)

Copied from SO: https://stackoverflow.com/a/21223908/4416932

research.apps module

class research.apps.ResearchConfig(app_name, app_module)

Bases: django.apps.config.AppConfig

name = 'research'

ready()

Loads the app’s signals.

References

• ready()

research.urls module

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

Indices and tables

• Index
• Module Index
• Search Page