class Config(UUIDModel):
# This must match the syntax used in jquery datatables
# https://datatables.net/reference/option/order
ASCENDING = "asc"
DESCENDING = "desc"
EVALUATION_SCORE_SORT_CHOICES = (
(ASCENDING, "Ascending"),
(DESCENDING, "Descending"),
)
OFF = "off"
OPTIONAL = "opt"
REQUIRED = "req"
PUBLICATION_LINK_CHOICES = SUPPLEMENTARY_FILE_CHOICES = (
(OFF, "Off"),
(OPTIONAL, "Optional"),
(REQUIRED, "Required"),
)
ALL = "all"
MOST_RECENT = "rec"
BEST = "bst"
RESULT_DISPLAY_CHOICES = (
(ALL, "Display all results"),
(MOST_RECENT, "Only display each users most recent result"),
(BEST, "Only display each users best result"),
)
ABSOLUTE = "abs"
MEAN = "avg"
MEDIAN = "med"
SCORING_CHOICES = (
(ABSOLUTE, "Use the absolute value of the score column"),
(
MEAN,
"Use the mean of the relative ranks of the score and extra result columns",
),
(
MEDIAN,
"Use the median of the relative ranks of the score and extra result columns",
),
)
class SubmissionKind(models.IntegerChoices):
CSV = 1, "CSV"
ZIP = 2, "ZIP"
ALGORITHM = 3, "Algorithm"
challenge = models.OneToOneField(
Challenge,
on_delete=models.CASCADE,
related_name="evaluation_config",
editable=False,
)
use_teams = models.BooleanField(
default=False,
help_text=(
"If true, users are able to form teams together to participate in "
"challenges."),
)
score_title = models.CharField(
max_length=32,
blank=False,
default="Score",
help_text=(
"The name that will be displayed for the scores column, for "
"instance: Score (log-loss)"),
)
score_jsonpath = models.CharField(
max_length=255,
blank=True,
help_text=(
"The jsonpath of the field in metrics.json that will be used "
"for the overall scores on the results page. See "
"http://goessner.net/articles/JsonPath/ for syntax. For example: "
"dice.mean"),
)
score_error_jsonpath = models.CharField(
max_length=255,
blank=True,
help_text=(
"The jsonpath for the field in metrics.json that contains the "
"error of the score, eg: dice.std"),
)
score_default_sort = models.CharField(
max_length=4,
choices=EVALUATION_SCORE_SORT_CHOICES,
default=DESCENDING,
help_text=(
"The default sorting to use for the scores on the results page."),
)
score_decimal_places = models.PositiveSmallIntegerField(
blank=False,
default=4,
help_text=("The number of decimal places to display for the score"),
)
extra_results_columns = JSONField(
default=list,
blank=True,
help_text=(
"A JSON object that contains the extra columns from metrics.json "
"that will be displayed on the results page. "),
validators=[JSONSchemaValidator(schema=EXTRA_RESULT_COLUMNS_SCHEMA)],
)
scoring_method_choice = models.CharField(
max_length=3,
choices=SCORING_CHOICES,
default=ABSOLUTE,
help_text=("How should the rank of each result be calculated?"),
)
result_display_choice = models.CharField(
max_length=3,
choices=RESULT_DISPLAY_CHOICES,
default=ALL,
help_text=("Which results should be displayed on the leaderboard?"),
)
submission_kind = models.PositiveSmallIntegerField(
default=SubmissionKind.CSV,
choices=SubmissionKind.choices,
help_text=(
"Should participants submit a .csv/.zip file of predictions, "
"or an algorithm?"),
)
allow_submission_comments = models.BooleanField(
default=False,
help_text=(
"Allow users to submit comments as part of their submission."),
)
display_submission_comments = models.BooleanField(
default=False,
help_text=(
"If true, submission comments are shown on the results page."),
)
supplementary_file_choice = models.CharField(
max_length=3,
choices=SUPPLEMENTARY_FILE_CHOICES,
default=OFF,
help_text=(
"Show a supplementary file field on the submissions page so that "
"users can upload an additional file along with their predictions "
"file as part of their submission (eg, include a pdf description "
"of their method). Off turns this feature off, Optional means "
"that including the file is optional for the user, Required means "
"that the user must upload a supplementary file."),
)
supplementary_file_label = models.CharField(
max_length=32,
blank=True,
default="Supplementary File",
help_text=(
"The label that will be used on the submission and results page "
"for the supplementary file. For example: Algorithm Description."),
)
supplementary_file_help_text = models.CharField(
max_length=128,
blank=True,
default="",
help_text=(
"The help text to include on the submissions page to describe the "
'submissions file. Eg: "A PDF description of the method.".'),
)
show_supplementary_file_link = models.BooleanField(
default=False,
help_text=(
"Show a link to download the supplementary file on the results "
"page."),
)
publication_url_choice = models.CharField(
max_length=3,
choices=PUBLICATION_LINK_CHOICES,
default=OFF,
help_text=(
"Show a publication url field on the submission page so that "
"users can submit a link to a publication that corresponds to "
"their submission. Off turns this feature off, Optional means "
"that including the url is optional for the user, Required means "
"that the user must provide an url."),
)
show_publication_url = models.BooleanField(
default=False,
help_text=("Show a link to the publication on the results page"),
)
daily_submission_limit = models.PositiveIntegerField(
default=10,
help_text=("The limit on the number of times that a user can make a "
"submission in a 24 hour period."),
)
submission_page_html = models.TextField(
help_text=(
"HTML to include on the submission page for this challenge."),
blank=True,
)
auto_publish_new_results = BooleanField(
default=True,
help_text=(
"If true, new results are automatically made public. If false, "
"the challenge administrator must manually publish each new "
"result."),
)
display_all_metrics = models.BooleanField(
default=True,
help_text=(
"Should all of the metrics be displayed on the Result detail page?"
),
)
submission_join_key = models.CharField(
blank=True,
default="",
max_length=32,
help_text=(
"If predictions are submitted as csv files, which column should "
"be used to join the data? eg. case_id"),
)
inputs = models.ManyToManyField(to=ComponentInterface,
related_name="evaluation_inputs")
outputs = models.ManyToManyField(to=ComponentInterface,
related_name="evaluation_outputs")
def save(self, *args, **kwargs):
adding = self._state.adding
super().save(*args, **kwargs)
if adding:
self.set_default_interfaces()
calculate_ranks.apply_async(kwargs={"challenge_pk": self.challenge.pk})
def set_default_interfaces(self):
self.inputs.set(
[ComponentInterface.objects.get(slug="predictions-csv-file")])
self.outputs.set(
[ComponentInterface.objects.get(slug="metrics-json-file")])
def get_absolute_url(self):
return reverse(
"pages:home",
kwargs={"challenge_short_name": self.challenge.short_name},
)
class WorkstationConfig(TitleSlugDescriptionModel, UUIDModel):
ORIENTATION_AXIAL = "A"
ORIENTATION_CORONAL = "C"
ORIENTATION_SAGITTAL = "S"
ORIENTATION_CHOICES = (
(ORIENTATION_AXIAL, "Axial"),
(ORIENTATION_CORONAL, "Coronal"),
(ORIENTATION_SAGITTAL, "Sagittal"),
)
SLAB_RENDER_METHOD_MAXIMUM = "MAX"
SLAB_RENDER_METHOD_MINIMUM = "MIN"
SLAB_RENDER_METHOD_AVERAGE = "AVG"
SLAB_RENDER_METHOD_CHOICES = (
(SLAB_RENDER_METHOD_MAXIMUM, "Maximum"),
(SLAB_RENDER_METHOD_MINIMUM, "Minimum"),
(SLAB_RENDER_METHOD_AVERAGE, "Average"),
)
IMAGE_INTERPOLATION_TYPE_NEAREST = "NN"
IMAGE_INTERPOLATION_TYPE_TRILINEAR = "TL"
IMAGE_INTERPOLATION_TYPE_CHOICES = (
(IMAGE_INTERPOLATION_TYPE_NEAREST, "NearestNeighbor"),
(IMAGE_INTERPOLATION_TYPE_TRILINEAR, "Trilinear"),
)
creator = models.ForeignKey(get_user_model(),
null=True,
on_delete=models.SET_NULL)
window_presets = models.ManyToManyField(
to="WindowPreset",
blank=True,
related_name="workstation_window_presets",
)
default_window_preset = models.ForeignKey(
to="WindowPreset",
blank=True,
null=True,
on_delete=models.SET_NULL,
related_name="workstation_default_window_presets",
)
# 4 digits, 2 decimal places, 0.01 min, 99.99 max
default_slab_thickness_mm = models.DecimalField(
blank=True,
null=True,
max_digits=4,
decimal_places=2,
validators=[MinValueValidator(limit_value=0.01)],
)
default_slab_render_method = models.CharField(
max_length=3, choices=SLAB_RENDER_METHOD_CHOICES, blank=True)
default_orientation = models.CharField(max_length=1,
choices=ORIENTATION_CHOICES,
blank=True)
default_overlay_lut = models.ForeignKey(to="LookUpTable",
blank=True,
null=True,
on_delete=models.SET_NULL)
default_overlay_interpolation = models.CharField(
max_length=2,
choices=IMAGE_INTERPOLATION_TYPE_CHOICES,
default=IMAGE_INTERPOLATION_TYPE_NEAREST,
blank=True,
)
# 3 digits, 2 decimal places, 0.00 min, 1.00 max
default_overlay_alpha = models.DecimalField(
blank=True,
null=True,
max_digits=3,
decimal_places=2,
validators=[
MinValueValidator(limit_value=0.00),
MaxValueValidator(limit_value=1.00),
],
)
overlay_segments = JSONField(
default=list,
blank=True,
validators=[JSONSchemaValidator(schema=OVERLAY_SEGMENTS_SCHEMA)],
)
# 4 digits, 2 decimal places, 0.01 min, 99.99 max
default_zoom_scale = models.DecimalField(
blank=True,
null=True,
max_digits=4,
decimal_places=2,
validators=[MinValueValidator(limit_value=0.01)],
)
show_image_info_plugin = models.BooleanField(default=True)
show_display_plugin = models.BooleanField(default=True)
show_invert_tool = models.BooleanField(default=True)
show_flip_tool = models.BooleanField(default=True)
show_window_level_tool = models.BooleanField(default=True)
show_reset_tool = models.BooleanField(default=True)
class Meta(TitleSlugDescriptionModel.Meta, UUIDModel.Meta):
ordering = ("created", "creator")
def __str__(self):
return f"{self.title} (created by {self.creator})"
def get_absolute_url(self):
return reverse("workstation-configs:detail",
kwargs={"slug": self.slug})
def save(self, *args, **kwargs):
super().save(*args, **kwargs)
if self.creator:
assign_perm(
f"{self._meta.app_label}.change_{self._meta.model_name}",
self.creator,
self,
)
class ComponentInterface(models.Model):
Kind = InterfaceKind.InterfaceKindChoices
title = models.CharField(
max_length=255,
help_text="Human readable name of this input/output field.",
unique=True,
)
slug = AutoSlugField(populate_from="title")
description = models.TextField(
blank=True, help_text="Description of this input/output field.")
default_value = models.JSONField(
blank=True,
null=True,
default=None,
help_text="Default value for this field, only valid for inputs.",
)
schema = models.JSONField(
default=dict,
blank=True,
help_text=(
"Additional JSON schema that the values for this interface must "
"satisfy. See https://json-schema.org/. "
"Only Draft 7, 6, 4 or 3 are supported."),
validators=[JSONSchemaValidator()],
)
kind = models.CharField(
blank=False,
max_length=5,
choices=Kind.choices,
help_text=(
"What is the type of this interface? Used to validate interface "
"values and connections between components."),
)
relative_path = models.CharField(
max_length=255,
help_text=(
"The path to the entity that implements this interface relative "
"to the input or output directory."),
unique=True,
validators=[
validate_safe_path,
validate_no_slash_at_ends,
# No uuids in path
RegexValidator(
regex=
r".*[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}.*",
inverse_match=True,
flags=re.IGNORECASE,
),
],
)
store_in_database = models.BooleanField(
default=True,
editable=True,
help_text=("Should the value be saved in a database field, "
"only valid for outputs."),
)
def __str__(self):
return f"{self.title} ({self.get_kind_display()})"
@property
def is_image_kind(self):
return self.kind in InterfaceKind.interface_type_image()
@property
def is_json_kind(self):
return self.kind in InterfaceKind.interface_type_json()
@property
def is_file_kind(self):
return self.kind in InterfaceKind.interface_type_file()
@property
def super_kind(self):
if self.saved_in_object_store:
if self.is_image_kind:
return InterfaceSuperKindChoices.IMAGE
else:
return InterfaceSuperKindChoices.FILE
else:
return InterfaceSuperKindChoices.VALUE
@property
def saved_in_object_store(self):
# files and images should always be saved to S3, others are optional
return (self.is_image_kind or self.is_file_kind
or not self.store_in_database)
def create_instance(self, *, image=None, value=None, fileobj=None):
civ = ComponentInterfaceValue.objects.create(interface=self)
if image:
civ.image = image
elif fileobj:
container = File(fileobj)
civ.file.save(Path(self.relative_path).name, container)
elif self.saved_in_object_store:
civ.file = ContentFile(
json.dumps(value).encode("utf-8"),
name=Path(self.relative_path).name,
)
else:
civ.value = value
civ.full_clean()
civ.save()
return civ
def clean(self):
super().clean()
self._clean_store_in_database()
self._clean_relative_path()
def _clean_relative_path(self):
if self.is_json_kind:
if not self.relative_path.endswith(".json"):
raise ValidationError("Relative path should end with .json")
elif self.is_file_kind and not self.relative_path.endswith(
f".{self.kind.lower()}"):
raise ValidationError(
f"Relative path should end with .{self.kind.lower()}")
if self.is_image_kind:
if not self.relative_path.startswith("images/"):
raise ValidationError(
"Relative path should start with images/")
if Path(self.relative_path).name != Path(self.relative_path).stem:
# Maybe not in the future
raise ValidationError("Images should be a directory")
else:
if self.relative_path.startswith("images/"):
raise ValidationError(
"Relative path should not start with images/")
def _clean_store_in_database(self):
object_store_required = self.kind in {
*InterfaceKind.interface_type_image(),
*InterfaceKind.interface_type_file(),
# These values can be large, so for any new interfaces of this
# type always add them to the object store
InterfaceKind.InterfaceKindChoices.MULTIPLE_TWO_D_BOUNDING_BOXES,
InterfaceKind.InterfaceKindChoices.MULTIPLE_DISTANCE_MEASUREMENTS,
InterfaceKind.InterfaceKindChoices.MULTIPLE_POINTS,
InterfaceKind.InterfaceKindChoices.MULTIPLE_POLYGONS,
InterfaceKind.InterfaceKindChoices.MULTIPLE_LINES,
}
if object_store_required and self.store_in_database:
raise ValidationError(
f"Interface {self.kind} objects cannot be stored in the database"
)
def validate_against_schema(self, *, value):
"""Validates values against both default and custom schemas"""
JSONValidator(
schema={
**INTERFACE_VALUE_SCHEMA,
"anyOf": [{
"$ref": f"#/definitions/{self.kind}"
}],
})(value=value)
if self.schema:
JSONValidator(schema=self.schema)(value=value)
class Meta:
ordering = ("pk", )
class Phase(UUIDModel):
# This must match the syntax used in jquery datatables
# https://datatables.net/reference/option/order
ASCENDING = "asc"
DESCENDING = "desc"
EVALUATION_SCORE_SORT_CHOICES = (
(ASCENDING, "Ascending"),
(DESCENDING, "Descending"),
)
OFF = "off"
OPTIONAL = "opt"
REQUIRED = "req"
PUBLICATION_LINK_CHOICES = SUPPLEMENTARY_FILE_CHOICES = (
(OFF, "Off"),
(OPTIONAL, "Optional"),
(REQUIRED, "Required"),
)
ALL = "all"
MOST_RECENT = "rec"
BEST = "bst"
RESULT_DISPLAY_CHOICES = (
(ALL, "Display all results"),
(MOST_RECENT, "Only display each users most recent result"),
(BEST, "Only display each users best result"),
)
ABSOLUTE = "abs"
MEAN = "avg"
MEDIAN = "med"
SCORING_CHOICES = (
(ABSOLUTE, "Use the absolute value of the score column"),
(
MEAN,
"Use the mean of the relative ranks of the score and extra result columns",
),
(
MEDIAN,
"Use the median of the relative ranks of the score and extra result columns",
),
)
class SubmissionKind(models.IntegerChoices):
CSV = 1, "CSV"
ZIP = 2, "ZIP"
ALGORITHM = 3, "Algorithm"
challenge = models.ForeignKey(
Challenge, on_delete=models.CASCADE, editable=False,
)
archive = models.ForeignKey(
Archive,
on_delete=models.SET_NULL,
null=True,
blank=True,
help_text=(
"Which archive should be used as the source dataset for this "
"phase?"
),
)
title = models.CharField(
max_length=64,
help_text="The title of this phase.",
default="Challenge",
)
slug = AutoSlugField(populate_from="title", max_length=64)
score_title = models.CharField(
max_length=32,
blank=False,
default="Score",
help_text=(
"The name that will be displayed for the scores column, for "
"instance: Score (log-loss)"
),
)
score_jsonpath = models.CharField(
max_length=255,
blank=True,
help_text=(
"The jsonpath of the field in metrics.json that will be used "
"for the overall scores on the results page. See "
"http://goessner.net/articles/JsonPath/ for syntax. For example: "
"dice.mean"
),
)
score_error_jsonpath = models.CharField(
max_length=255,
blank=True,
help_text=(
"The jsonpath for the field in metrics.json that contains the "
"error of the score, eg: dice.std"
),
)
score_default_sort = models.CharField(
max_length=4,
choices=EVALUATION_SCORE_SORT_CHOICES,
default=DESCENDING,
help_text=(
"The default sorting to use for the scores on the results page."
),
)
score_decimal_places = models.PositiveSmallIntegerField(
blank=False,
default=4,
help_text=("The number of decimal places to display for the score"),
)
extra_results_columns = models.JSONField(
default=list,
blank=True,
help_text=(
"A JSON object that contains the extra columns from metrics.json "
"that will be displayed on the results page. "
),
validators=[JSONSchemaValidator(schema=EXTRA_RESULT_COLUMNS_SCHEMA)],
)
scoring_method_choice = models.CharField(
max_length=3,
choices=SCORING_CHOICES,
default=ABSOLUTE,
help_text=("How should the rank of each result be calculated?"),
)
result_display_choice = models.CharField(
max_length=3,
choices=RESULT_DISPLAY_CHOICES,
default=ALL,
help_text=("Which results should be displayed on the leaderboard?"),
)
creator_must_be_verified = models.BooleanField(
default=False,
help_text=(
"If True, only participants with verified accounts can make "
"submissions to this phase"
),
)
submission_kind = models.PositiveSmallIntegerField(
default=SubmissionKind.CSV,
choices=SubmissionKind.choices,
help_text=(
"Should participants submit a .csv/.zip file of predictions, "
"or an algorithm?"
),
)
allow_submission_comments = models.BooleanField(
default=False,
help_text=(
"Allow users to submit comments as part of their submission."
),
)
display_submission_comments = models.BooleanField(
default=False,
help_text=(
"If true, submission comments are shown on the results page."
),
)
supplementary_file_choice = models.CharField(
max_length=3,
choices=SUPPLEMENTARY_FILE_CHOICES,
default=OFF,
help_text=(
"Show a supplementary file field on the submissions page so that "
"users can upload an additional file along with their predictions "
"file as part of their submission (eg, include a pdf description "
"of their method). Off turns this feature off, Optional means "
"that including the file is optional for the user, Required means "
"that the user must upload a supplementary file."
),
)
supplementary_file_label = models.CharField(
max_length=32,
blank=True,
default="Supplementary File",
help_text=(
"The label that will be used on the submission and results page "
"for the supplementary file. For example: Algorithm Description."
),
)
supplementary_file_help_text = models.CharField(
max_length=128,
blank=True,
default="",
help_text=(
"The help text to include on the submissions page to describe the "
'submissions file. Eg: "A PDF description of the method.".'
),
)
show_supplementary_file_link = models.BooleanField(
default=False,
help_text=(
"Show a link to download the supplementary file on the results "
"page."
),
)
publication_url_choice = models.CharField(
max_length=3,
choices=PUBLICATION_LINK_CHOICES,
default=OFF,
help_text=(
"Show a publication url field on the submission page so that "
"users can submit a link to a publication that corresponds to "
"their submission. Off turns this feature off, Optional means "
"that including the url is optional for the user, Required means "
"that the user must provide an url."
),
)
show_publication_url = models.BooleanField(
default=False,
help_text=("Show a link to the publication on the results page"),
)
daily_submission_limit = models.PositiveIntegerField(
default=10,
help_text=(
"The limit on the number of times that a user can make a "
"submission in a 24 hour period."
),
)
submissions_open = models.DateTimeField(
null=True,
blank=True,
help_text=(
"If set, participants will not be able to make submissions to "
"this phase before this time."
),
)
submissions_close = models.DateTimeField(
null=True,
blank=True,
help_text=(
"If set, participants will not be able to make submissions to "
"this phase after this time."
),
)
submission_page_html = models.TextField(
help_text=(
"HTML to include on the submission page for this challenge."
),
blank=True,
)
auto_publish_new_results = models.BooleanField(
default=True,
help_text=(
"If true, new results are automatically made public. If false, "
"the challenge administrator must manually publish each new "
"result."
),
)
display_all_metrics = models.BooleanField(
default=True,
help_text=(
"Should all of the metrics be displayed on the Result detail page?"
),
)
evaluation_detail_observable_url = models.URLField(
blank=True,
validators=[OBSERVABLE_URL_VALIDATOR],
max_length=2000,
help_text=(
"The URL of the embeddable observable notebook for viewing "
"individual results. Must be of the form "
"https://observablehq.com/embed/@user/notebook?cell=..."
),
)
evaluation_comparison_observable_url = models.URLField(
blank=True,
validators=[OBSERVABLE_URL_VALIDATOR],
max_length=2000,
help_text=(
"The URL of the embeddable observable notebook for comparing"
"results. Must be of the form "
"https://observablehq.com/embed/@user/notebook?cell=..."
),
)
inputs = models.ManyToManyField(
to=ComponentInterface, related_name="evaluation_inputs"
)
outputs = models.ManyToManyField(
to=ComponentInterface, related_name="evaluation_outputs"
)
class Meta:
unique_together = (
("challenge", "title"),
("challenge", "slug"),
)
ordering = ("challenge", "submissions_open", "created")
permissions = (("create_phase_submission", "Create Phase Submission"),)
def __str__(self):
return f"{self.title} Evaluation for {self.challenge.short_name}"
def save(self, *args, **kwargs):
adding = self._state.adding
super().save(*args, **kwargs)
if adding:
self.set_default_interfaces()
self.assign_permissions()
calculate_ranks.apply_async(kwargs={"phase_pk": self.pk})
def set_default_interfaces(self):
self.inputs.set(
[ComponentInterface.objects.get(slug="predictions-csv-file")]
)
self.outputs.set(
[ComponentInterface.objects.get(slug="metrics-json-file")]
)
def assign_permissions(self):
assign_perm("view_phase", self.challenge.admins_group, self)
assign_perm("change_phase", self.challenge.admins_group, self)
assign_perm(
"create_phase_submission", self.challenge.admins_group, self
)
assign_perm(
"create_phase_submission", self.challenge.participants_group, self
)
def get_absolute_url(self):
return reverse(
"pages:home",
kwargs={"challenge_short_name": self.challenge.short_name},
)
def get_observable_url(self, view_kind, url_kind):
if view_kind == "detail":
url = self.evaluation_detail_observable_url
elif view_kind == "comparison":
url = self.evaluation_comparison_observable_url
else:
raise ValueError("View or notebook not found")
if not url:
return "", []
parsed_url = urlparse(url)
cells = parse_qs(parsed_url.query)["cell"]
url = f"{urljoin(url, parsed_url.path)}"
if url_kind == "js":
url = url.replace(
"https://observablehq.com/embed/",
"https://api.observablehq.com/",
)
url += ".js?v=3"
elif url_kind == "edit":
url = url.replace(
"https://observablehq.com/embed/", "https://observablehq.com/"
)
else:
raise ValueError("URL kind must be one of edit or js")
return url, cells
@property
def observable_detail_edit_url(self):
url, _ = self.get_observable_url(view_kind="detail", url_kind="edit")
return url
@property
def observable_comparison_edit_url(self):
url, _ = self.get_observable_url(
view_kind="comparison", url_kind="edit"
)
return url
class ReaderStudy(UUIDModel, TitleSlugDescriptionModel):
editors_group = models.OneToOneField(
Group,
on_delete=models.CASCADE,
editable=False,
related_name=f"editors_of_readerstudy",
)
readers_group = models.OneToOneField(
Group,
on_delete=models.CASCADE,
editable=False,
related_name=f"readers_of_readerstudy",
)
images = models.ManyToManyField("cases.Image",
related_name="readerstudies")
workstation = models.ForeignKey("workstations.Workstation",
on_delete=models.CASCADE)
logo = models.ImageField(upload_to=get_logo_path)
# A hanging_list is a list of dictionaries where the keys are the
# view names, and the values are the filenames to place there.
hanging_list = JSONField(
default=list,
blank=True,
validators=[JSONSchemaValidator(schema=HANGING_LIST_SCHEMA)],
)
shuffle_hanging_list = models.BooleanField(default=False)
class Meta(UUIDModel.Meta, TitleSlugDescriptionModel.Meta):
verbose_name_plural = "reader studies"
def __str__(self):
return f"{self.title}"
def get_absolute_url(self):
return reverse("reader-studies:detail", kwargs={"slug": self.slug})
@property
def api_url(self):
return reverse("api:reader-study-detail", kwargs={"pk": self.pk})
def create_groups(self):
self.editors_group = Group.objects.create(
name=
f"{self._meta.app_label}_{self._meta.model_name}_{self.pk}_editors"
)
self.readers_group = Group.objects.create(
name=
f"{self._meta.app_label}_{self._meta.model_name}_{self.pk}_readers"
)
def assign_permissions(self):
# Allow the editors group to change this study
assign_perm(f"change_{self._meta.model_name}", self.editors_group,
self)
# Allow the editors and readers groups to view this study
assign_perm(f"view_{self._meta.model_name}", self.editors_group, self)
assign_perm(f"view_{self._meta.model_name}", self.readers_group, self)
# Allow readers to add answers (globally), adding them to this reader
# study is checked in the serializers as there is no
# get_permission_object in django rest framework.
assign_perm(
f"{Answer._meta.app_label}.add_{Answer._meta.model_name}",
self.readers_group,
)
def assign_workstation_permissions(self):
perm = f"view_{Workstation._meta.model_name}"
group = self.readers_group
workstations = get_objects_for_group(group=group,
perms=perm,
klass=Workstation)
if (self.workstation not in workstations) or workstations.count() > 1:
remove_perm(perm=perm, user_or_group=group, obj=workstations)
# Allow readers to view the workstation used for this reader study
assign_perm(perm=perm, user_or_group=group, obj=self.workstation)
def save(self, *args, **kwargs):
adding = self._state.adding
if adding:
self.create_groups()
super().save(*args, **kwargs)
if adding:
self.assign_permissions()
self.assign_workstation_permissions()
def is_editor(self, user):
return user.groups.filter(pk=self.editors_group.pk).exists()
def add_editor(self, user):
return user.groups.add(self.editors_group)
def remove_editor(self, user):
return user.groups.remove(self.editors_group)
def is_reader(self, user):
return user.groups.filter(pk=self.readers_group.pk).exists()
def add_reader(self, user):
return user.groups.add(self.readers_group)
def remove_reader(self, user):
return user.groups.remove(self.readers_group)
@property
def study_image_names(self):
return [im.name for im in self.images.all()]
@property
def hanging_image_names(self):
return [
name for hanging in self.hanging_list for name in hanging.values()
]
@property
def hanging_list_valid(self):
"""
Test that all of the study images are included in the hanging list
exactly once.
"""
return sorted(self.study_image_names) == sorted(
self.hanging_image_names)
@property
def non_unique_study_image_names(self):
"""
Get all of the image names that are non-unique for this ReaderStudy
"""
return [
name for name, count in Counter(self.study_image_names).items()
if count > 1
]
@property
def is_valid(self):
""" Is this ReaderStudy valid? """
return (self.hanging_list_valid
and len(self.non_unique_study_image_names) == 0)
@property
def hanging_list_images(self):
"""
Substitutes the image name for the image detail api url for each image
defined in the hanging list.
"""
if not self.is_valid:
return None
study_images = {im.name: im.api_url for im in self.images.all()}
hanging_list_images = [{
view: study_images.get(name)
for view, name in hanging.items()
} for hanging in self.hanging_list]
return hanging_list_images
def get_hanging_list_images_for_user(self, *, user):
"""
Returns a shuffled list of the hanging list images for a particular
user. The shuffle is seeded with the users pk, and using RandomState
from numpy guarantees that the ordering will be consistent across
python/library versions. Returns the normal list if
shuffle_hanging_list is false.
"""
hanging_list = self.hanging_list_images
if self.shuffle_hanging_list and hanging_list is not None:
# In place shuffle
RandomState(seed=int(user.pk)).shuffle(hanging_list)
return hanging_list
class WorkstationConfig(TitleSlugDescriptionModel, UUIDModel):
class Orientation(models.TextChoices):
AXIAL = "A", "Axial"
CORONAL = "C", "Coronal"
SAGITTAL = "S", "Sagittal"
class SlabRenderMethod(models.TextChoices):
MAXIMUM = "MAX", "Maximum"
MINIMUM = "MIN", "Minimum"
AVERAGE = "AVG", "Average"
class ImageContext(models.TextChoices):
PATHOLOGY = "PATH", "Pathology"
OPHTHALMOLOGY = "OPHTH", "Ophthalmology"
MPMRI = "MPMRI", "Multiparametric MRI"
class ImageInterpolationType(models.TextChoices):
NEAREST = "NN", "NearestNeighbor"
TRILINEAR = "TL", "Trilinear"
creator = models.ForeignKey(
get_user_model(), null=True, on_delete=models.SET_NULL
)
window_presets = models.ManyToManyField(
to="WindowPreset",
blank=True,
related_name="workstation_window_presets",
)
default_window_preset = models.ForeignKey(
to="WindowPreset",
blank=True,
null=True,
on_delete=models.SET_NULL,
related_name="workstation_default_window_presets",
)
image_context = models.CharField(
blank=True, max_length=6, choices=ImageContext.choices
)
# 4 digits, 2 decimal places, 0.01 min, 99.99 max
default_slab_thickness_mm = models.DecimalField(
blank=True,
null=True,
max_digits=4,
decimal_places=2,
validators=[MinValueValidator(limit_value=0.01)],
)
default_slab_render_method = models.CharField(
max_length=3, choices=SlabRenderMethod.choices, blank=True
)
default_orientation = models.CharField(
max_length=1, choices=Orientation.choices, blank=True
)
overlay_luts = models.ManyToManyField(
to="LookUpTable", blank=True, related_name="workstation_overlay_luts"
)
default_overlay_lut = models.ForeignKey(
to="LookUpTable", blank=True, null=True, on_delete=models.SET_NULL
)
default_overlay_interpolation = models.CharField(
max_length=2,
choices=ImageInterpolationType.choices,
default=ImageInterpolationType.NEAREST,
blank=True,
)
# 3 digits, 2 decimal places, 0.00 min, 1.00 max
default_overlay_alpha = models.DecimalField(
blank=True,
null=True,
max_digits=3,
decimal_places=2,
validators=[
MinValueValidator(limit_value=0.00),
MaxValueValidator(limit_value=1.00),
],
)
overlay_segments = models.JSONField(
default=list,
blank=True,
validators=[JSONSchemaValidator(schema=OVERLAY_SEGMENTS_SCHEMA)],
)
key_bindings = models.JSONField(
default=list,
blank=True,
validators=[JSONSchemaValidator(schema=KEY_BINDINGS_SCHEMA)],
)
# 4 digits, 2 decimal places, 0.01 min, 99.99 max
default_zoom_scale = models.DecimalField(
blank=True,
null=True,
max_digits=4,
decimal_places=2,
validators=[MinValueValidator(limit_value=0.01)],
)
show_image_info_plugin = models.BooleanField(default=True)
show_display_plugin = models.BooleanField(default=True)
show_invert_tool = models.BooleanField(default=True)
show_flip_tool = models.BooleanField(default=True)
show_window_level_tool = models.BooleanField(default=True)
show_reset_tool = models.BooleanField(default=True)
enable_contrast_enhancement = models.BooleanField(
default=False,
verbose_name="Enable contrast enhancement preprocessing (fundus)",
)
client_rendered_sidebar = models.BooleanField(
default=True, help_text="Use client side rendering for the side bar"
)
class Meta(TitleSlugDescriptionModel.Meta, UUIDModel.Meta):
ordering = ("created", "creator")
def __str__(self):
return f"{self.title} (created by {self.creator})"
def get_absolute_url(self):
return reverse(
"workstation-configs:detail", kwargs={"slug": self.slug}
)
def save(self, *args, **kwargs):
super().save(*args, **kwargs)
if self.creator:
assign_perm(
f"{self._meta.app_label}.change_{self._meta.model_name}",
self.creator,
self,
)