Ross
784 lines
24 KiB
Python
784 lines
24 KiB
Python
import json
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from pathlib import Path
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from rad.settings import REMOTE_URL
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from django.db.models.fields.files import ImageField
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from django.db.models.fields.related import ForeignKey
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from django.db import models
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from django.shortcuts import get_object_or_404
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from django.utils import timezone
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from django.core.files.storage import FileSystemStorage
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from django.conf import settings
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from django.utils.html import format_html
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from django.urls import reverse
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from django.utils.translation import gettext_lazy as _
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from django.utils.html import mark_safe
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from django.core.exceptions import ValidationError
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import string
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from collections import defaultdict
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from helpers.images import image_as_base64, pretty_print_dicom
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from generic.models import (
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CidUser,
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CidUserGroup,
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ExamCollection,
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ExamUserStatus,
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Examination,
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ExamBase,
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Plane,
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Contrast,
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QuestionBase,
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QuestionNote,
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SeriesBase,
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SeriesImageBase,
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UserAnswerBase,
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UserUserGroup,
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Modality
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)
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# from generic.models import Examination, Site, Condition, Sign
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from easy_thumbnails.files import get_thumbnailer
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from easy_thumbnails.exceptions import InvalidImageFormatError
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import pydicom
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import pydicom.errors
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import datetime
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from django.utils import timezone
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import reversion
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from django.contrib.contenttypes.fields import GenericRelation
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image_storage = FileSystemStorage(
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# Physical file location ROOT
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location="{0}longs/".format(settings.MEDIA_ROOT),
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# Url for file
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base_url="{0}longs/".format(settings.MEDIA_URL),
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)
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def image_directory_path(instance, filename):
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return "longs/picture/{0}".format(filename)
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@reversion.register
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class Long(QuestionBase):
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description = models.TextField(
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blank=True,
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help_text="Description of the case, for admin organisation, will not be visible when taking",
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)
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history = models.TextField(null=True, blank=True)
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# TODO: merge with atlas condition / signs / finding
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# condition = tagulous.models.TagField(
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# to=Condition,
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# blank=True,
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# help_text='Associated condition. Will allow searching / filtering and tips / hints to be displayed. Conditions with spaces must be enclosed in quotes "..."',
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# )
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# sign = tagulous.models.TagField(
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# to=Sign, blank=True, help_text="Radiological signs in the question"
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# )
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# Model answers
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model_observations = models.TextField(null=True, blank=True)
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model_interpretation = models.TextField(null=True, blank=True)
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model_principle_diagnosis = models.TextField(null=True, blank=True)
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model_differential_diagnosis = models.TextField(null=True, blank=True)
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model_management = models.TextField(null=True, blank=True)
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mark_scheme = models.TextField(null=True, blank=True)
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DEFAULT_SITE_ID = 1
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# site = models.ManyToManyField(
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# Site,
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# blank=True,
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# default=DEFAULT_SITE_ID,
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# help_text=
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# "If we know the source of the image")
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verified = models.BooleanField(default=False)
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author = models.ManyToManyField(
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settings.AUTH_USER_MODEL,
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blank=True,
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help_text="Author of question",
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related_name="long_authored_questions",
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)
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scrapped = models.BooleanField(
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default=False, help_text="Question has been scrapped and will not be shown"
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)
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recreate_json = models.BooleanField(
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help_text="If the json cache needs updating", default=False
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)
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json_creation_time = models.DateTimeField(blank=True, default=None, null=True)
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question_json_id = models.IntegerField(
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default=1, help_text="Auto incrementing json creation number"
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)
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series = models.ManyToManyField("LongSeries", through="SeriesDetail", related_name="long")
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# question_file = models.FileField(upload_to=question_file_directory_path, blank=True, null=True)
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def get_app_name(self):
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return "longs"
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def get_absolute_url(self):
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return reverse("longs:question_detail", kwargs={"pk": self.pk})
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def __str__(self):
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return "{} / {}".format(self.pk, self.description)
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examinations = [series.get_examination() for series in self.series.all()]
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return "{}/{} : {}".format(self.pk, self.description, ", ".join(examinations))
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def get_exams(self):
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e = self.exams.all().values_list("name", flat=True)
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exams = ", ".join(e)
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return exams
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def get_images(self, feedback=False):
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qs = self.images.all()
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if not feedback:
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images = [i.image for i in qs if not i.feedback_image]
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else:
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images = [i.image for i in qs]
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return images
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def get_image_urls(self):
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return ",".join([f"{REMOTE_URL}{i.url}" for i in self.get_images()])
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def get_image_url_array(self):
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return json.dumps([f"{REMOTE_URL}{i.url}" for i in self.get_images()])
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def get_unmarked_user_answer_count(self, exam_pk=None, marker=None):
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if exam_pk is None:
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return self.cid_user_answers.all().count()
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return len(self.get_unmarked_user_answers(exam_pk=exam_pk, marker=marker))
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def get_unmarked_user_answers(self, exam_pk=None, marker=None):
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if exam_pk is None:
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answers = self.cid_user_answers.all()
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else:
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answers = self.cid_user_answers.filter(exam__id=exam_pk)
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unmarked_answers = [ans for ans in answers if not ans.is_marked()]
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if marker is None:
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return unmarked_answers
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# If marker is specified we check for what they have marked
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marker_unmarked = []
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for answer in unmarked_answers:
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if answer.mark.filter(marker=marker).count() < 1:
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marker_unmarked.append(answer)
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return marker_unmarked
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def get_question_model_answers(self):
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"""Returns a dict of the question model answers"""
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return {
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"observations": self.model_observations,
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"interpretation": self.model_interpretation,
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"principle diagnosis": self.model_principle_diagnosis,
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"differential_diagnosis": self.model_differential_diagnosis,
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"management": self.model_management,
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}
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def get_question_json(
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self, based: bool = True, answers: bool = True, feedback: bool = False
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):
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"""Returns a json representation of the question
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if based = False return is a dict
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otherwise a url to the json file
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answers arg is only parsed if based = False
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"""
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question_id = self.pk
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if not based:
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image_titles = []
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images = []
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question_series = self.series.all()
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# Loop through longimage associations
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for i, series in enumerate(question_series):
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# image_array = []
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# for i in series.images.all():
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# image_array.append(image_as_base64(i.image))
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# #image_array.append(i.image.url)
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# We are still limited by the size of a series (although this should not be too big or computers will crash...)
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images.append(
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[
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"{}/{}".format(settings.REMOTE_URL, i.image.url)
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for i in series.images.all()
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]
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)
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# image_array = [i.image.url for i in series.images.all()]
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# images.append(url)
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image_titles.append(series.get_examination())
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question_json = {
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"title": self.history,
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"images": images,
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"image_titles": image_titles,
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# "feedback_image": [],
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# "annotations": [str(q.image_annotations)],
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"type": "long",
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"cached": False,
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}
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if answers:
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question_json["answers"] = self.get_question_model_answers()
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return question_json
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# exam_order.append(q.id)
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path = "{0}longs/questions/{1}.json".format(settings.MEDIA_ROOT, question_id)
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url = "{0}longs/questions/{1}.json".format(settings.MEDIA_URL, question_id)
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timestamp = timezone.now()
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self.question_json_id += 1
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# Make sure path exists (we should probably just do this once on startup)
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Path(path).parents[0].mkdir(parents=True, exist_ok=True)
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with open(path, "w+") as f:
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print("start writing file")
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# We manually create the json for long questions to reducem memroy usade
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f.write(
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"""{{
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"title": "{}",
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"type": "long",
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"generated": "{}",
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"question_json_id": "{}",
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""".format(
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self.history, timestamp.isoformat(), self.question_json_id
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)
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)
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f.write('"images" : [')
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# images = []
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image_titles = []
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question_series = self.series.all()
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# Loop through longimage associations
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for i, series in enumerate(question_series):
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print("gen series", i)
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# image_array = []
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# for i in series.images.all():
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# image_array.append(image_as_base64(i.image))
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# #image_array.append(i.image.url)
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# We are still limited by the size of a series (although this should not be too big or computers will crash...)
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# image_array = [image_as_base64(i.image) for i in series.images.all()]
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##image_array = [i.image.url for i in series.images.all()]
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# f.write(json.dumps(image_array))
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f.write('["')
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first = True
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# Generate a single image at a time
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for img in series.images.all():
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if not first:
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f.write(', "')
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f.write(image_as_base64(img.image))
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# for debugging
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# f.write(img.image.url)
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f.write('"')
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first = False
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f.write("]")
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# images.append(url)
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if i != len(question_series) - 1:
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f.write(",")
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image_titles.append(series.get_examination())
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f.write("],")
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f.write('"image_titles" : {} }}'.format(json.dumps(image_titles)))
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self.json_creation_time = timestamp
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self.save()
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# exam_question = {
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# "title": q.history,
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# "images": images,
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# "image_titles": image_titles,
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# #"feedback_image": [],
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# #"annotations": [str(q.image_annotations)],
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# "type": "long",
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# "cached": False,
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# }
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return url
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def get_unanswered_mark_and_text(self) -> tuple[int, str]:
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"""
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Long cases are receive a mark between 4 and 8
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This has changed to a 3 if unanswered
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Therefore unmarked = 3
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"""
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return (3, ("Not answered",) * 5)
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# def GetNonFeedbackQuestionImages(self):
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# return self.get_images()
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def test_image_validator(file):
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pass
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class LongSeriesImage(SeriesImageBase):
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image = models.FileField(upload_to=image_directory_path)
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series = models.ForeignKey(
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"LongSeries", related_name="images", on_delete=models.CASCADE, null=True
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)
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class SeriesDetail(models.Model):
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sort_order = models.IntegerField(default=1000)
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long = models.ForeignKey(Long, on_delete=models.CASCADE)
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longseries = models.ForeignKey("LongSeries", on_delete=models.CASCADE)
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class Meta:
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ordering = ("sort_order",)
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@reversion.register
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class LongSeries(SeriesBase):
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modality = models.ForeignKey(
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Modality, related_name="series_modality", on_delete=models.SET_NULL, null=True
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)
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examination = models.ForeignKey(
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Examination,
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help_text="Name of the examination, this appears as the thumbnail title on the test system",
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related_name="series_examination",
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on_delete=models.SET_NULL,
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null=True,
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)
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plane = models.ForeignKey(
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Plane,
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help_text="Plane of the examination",
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related_name="series_plane",
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on_delete=models.SET_NULL,
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null=True,
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blank=True,
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)
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contrast = models.ForeignKey(
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Contrast,
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help_text="MRI / CT contrast",
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related_name="series_contrast",
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on_delete=models.SET_NULL,
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null=True,
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blank=True,
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)
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author = models.ManyToManyField(
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settings.AUTH_USER_MODEL,
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blank=True,
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related_name="long_series",
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)
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def __str__(self):
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return "{}/{} : {}".format(self.pk, self.get_examination(), self.description)
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def get_absolute_url(self):
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return reverse("longs:series_detail", kwargs={"pk": self.pk})
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def get_link(self):
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return format_html("<a href='{}'>{}</a>", self.get_absolute_url(), self)
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class LongCreationDefault(models.Model):
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# author = models.OneToOneField(User,
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author = models.OneToOneField(
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settings.AUTH_USER_MODEL, related_name="long_default", on_delete=models.CASCADE
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)
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# site = models.ManyToManyField(
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# Site,
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# blank=True,
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# default=1,
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# help_text="Default site to use when creating a new long")
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def get_absolute_url(self):
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return reverse("longs:question_create")
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class ExamQuestionDetail(models.Model):
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sort_order = models.IntegerField(default=1000)
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exam = models.ForeignKey("Exam", on_delete=models.CASCADE)
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question = models.ForeignKey(Long, on_delete=models.CASCADE)
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class Meta:
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ordering = ("sort_order",)
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@reversion.register
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class Exam(ExamBase):
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app_name = "longs"
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exam_questions = models.ManyToManyField(Long, through=ExamQuestionDetail, related_name="exams")
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time_limit = models.IntegerField(
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help_text="Exam time limit (in seconds). Default is 4500 seconds (75 minutes)",
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default=4500,
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)
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author = models.ManyToManyField(
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settings.AUTH_USER_MODEL,
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blank=True,
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help_text="Author of exam",
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related_name="long_exam_author",
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)
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markers = models.ManyToManyField(
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settings.AUTH_USER_MODEL,
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blank=True,
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help_text="Authorised markers for the exam",
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related_name="long_exam_markers",
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)
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double_mark = models.BooleanField(
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default=False, help_text="Defines if an exam is expected to be double marked"
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)
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valid_cid_users = models.ManyToManyField(
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CidUser, blank=True, related_name="longs_exams"
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)
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valid_user_users = models.ManyToManyField(
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settings.AUTH_USER_MODEL, blank=True, related_name="user_longs_exams"
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)
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cid_user_groups = models.ManyToManyField(
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CidUserGroup,
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blank=True,
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help_text="These groups define which candidates are able to be added to the exams/collection.",
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related_name="longs_cid_user_groups",
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)
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user_user_groups = models.ManyToManyField(
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UserUserGroup,
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blank=True,
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help_text="These groups define which candidates are able to be added to the exams/collection.",
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related_name="longs_user_user_groups",
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)
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exam_user_status = GenericRelation(ExamUserStatus, related_query_name="longs_exams")
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cid_user_exam = GenericRelation("generic.CidUserExam", related_query_name="longs_exams")
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examcollection = models.ForeignKey(ExamCollection, blank=True, null=True, on_delete=models.SET_NULL, related_name="longs_exams")
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def get_app_name(self):
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return "longs"
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def get_exam_question_json(self, question_id):
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q = get_object_or_404(Long, pk=question_id)
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# exam_order.append(q.id)
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# Loop through longimage associations
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images = []
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image_titles = []
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for series in q.series.all():
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# image_array = []
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# for i in series.images.all():
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# image_array.append(image_as_base64(i.image))
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# #image_array.append(i.image.url)
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image_array = [image_as_base64(i.image) for i in series.images.all()]
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images.append(image_array)
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image_titles.append(series.get_examination())
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exam_question = {
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"title": q.history,
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"images": images,
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"image_titles": image_titles,
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# "feedback_image": [],
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# "annotations": [str(q.image_annotations)],
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"type": "long",
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"images_json": True,
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}
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return exam_question
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def get_exam_json(self, based=True):
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questions = self.get_questions()
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exam_questions = defaultdict(dict)
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exam_order = []
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n = 1
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for q in questions:
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exam_order.append(q.id)
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if based:
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# If it is a new question we need to for a question json refresh
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if q.json_creation_time is None:
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q.get_question_json()
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exam_questions[q.id] = q.question_json_id
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else:
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# TODO: combine with question_json
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images = []
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image_titles = []
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|
for series in q.series.all():
|
|
# image_array = []
|
|
# for i in series.images.all():
|
|
# image_array.append(image_as_base64(i.image))
|
|
# #image_array.append(i.image.url)
|
|
image_array = [
|
|
"{}/{}".format(settings.REMOTE_URL, i.image.url)
|
|
for i in series.images.all()
|
|
]
|
|
images.append(image_array)
|
|
image_titles.append(series.get_examination())
|
|
|
|
# exam_questions[q.id] = n
|
|
|
|
exam_questions[q.id] = {
|
|
"title": q.history,
|
|
"images": images,
|
|
"image_titles": image_titles,
|
|
# "feedback_image": [],
|
|
# "annotations": [str(q.image_annotations)],
|
|
"type": "long",
|
|
}
|
|
|
|
# if feedback_images:
|
|
# exam_questions[q.id]["feedback_image"] = feedback_images
|
|
|
|
exam_json = {
|
|
"eid": "long/{}".format(self.id),
|
|
"cached": False,
|
|
"exam_type": "long",
|
|
"exam_name": self.name,
|
|
"exam_mode": self.exam_mode,
|
|
"exam_order": exam_order,
|
|
"questions": exam_questions,
|
|
"based": based,
|
|
# "question_requests": exam_questions,
|
|
}
|
|
|
|
if based:
|
|
exam_json["question_requests"] = exam_questions
|
|
|
|
if self.time_limit:
|
|
exam_json["exam_time"] = self.time_limit
|
|
|
|
return exam_json
|
|
|
|
|
|
@reversion.register
|
|
class UserAnswer(UserAnswerBase):
|
|
"""User answers by candidate"""
|
|
|
|
app_name = "longs"
|
|
|
|
question = models.ForeignKey(
|
|
Long, related_name="cid_user_answers", on_delete=models.CASCADE
|
|
)
|
|
|
|
# Answers
|
|
answer_observations = models.TextField(null=True, blank=True)
|
|
answer_interpretation = models.TextField(null=True, blank=True)
|
|
answer_principle_diagnosis = models.TextField(null=True, blank=True)
|
|
answer_differential_diagnosis = models.TextField(null=True, blank=True)
|
|
answer_management = models.TextField(null=True, blank=True)
|
|
|
|
cid = models.BigIntegerField(
|
|
blank=True,
|
|
null=True,
|
|
help_text="Candidate ID (limitied by BigIntegerField size)",
|
|
)
|
|
|
|
user = models.ForeignKey(
|
|
settings.AUTH_USER_MODEL,
|
|
on_delete=models.CASCADE,
|
|
blank=True,
|
|
null=True,
|
|
related_name="user_longs_user_answers",
|
|
)
|
|
|
|
# Each user answer is associated with a particular exam
|
|
exam = models.ForeignKey(
|
|
Exam, related_name="cid_user_answers", on_delete=models.CASCADE, null=True
|
|
)
|
|
|
|
class ScoreOptions(models.TextChoices):
|
|
UNMARKED = "", _("Unmarked")
|
|
#UNANSWERED = "3", _("Unanswered")
|
|
FOUR = "4", _("4")
|
|
FOUR_HALF = "4.5", _("4.5")
|
|
FIVE = "5", _("5")
|
|
FIVE_HALF = "5.5", _("5.5")
|
|
SIX = "6", _("6")
|
|
SIX_HALF = "6.5", _("6.5")
|
|
SEVEN = "7", _("7")
|
|
SEVEN_HALF = "7.5", _("7.5")
|
|
EIGHT = "8", _("8")
|
|
|
|
score = models.CharField(
|
|
max_length=3,
|
|
choices=ScoreOptions.choices,
|
|
default=ScoreOptions.UNMARKED,
|
|
blank=True,
|
|
help_text="The final score for the candidate",
|
|
)
|
|
|
|
candidate_feedback = models.TextField(
|
|
null=True, blank=True, help_text="Feedback for the candidate"
|
|
)
|
|
|
|
marker_feedback = models.TextField(
|
|
null=True, blank=True, help_text="Feedback for the marker, this is optional and will NOT be shown to the candidate."
|
|
)
|
|
|
|
# mark = models.ManyToManyField(
|
|
# "AnswerMarks", related_name="user_answer", blank=True
|
|
# )
|
|
# secondary_mark = models.ForeignKey(
|
|
# "AnswerMarks", related_name="user_answer", on_delete=models.SET_NULL, null=True, blank=True
|
|
# )
|
|
|
|
def __str__(self):
|
|
try:
|
|
exam = self.exam
|
|
except (Exam.DoesNotExist, KeyError) as e:
|
|
exam = "None"
|
|
return "{}/{}/{} ({})".format(exam, self.cid, self.created, self.updated)
|
|
|
|
def save(self, *args, **kwargs):
|
|
self.clean()
|
|
return super(UserAnswer, self).save(*args, **kwargs)
|
|
|
|
def clean(self):
|
|
for ans in (
|
|
self.answer_observations,
|
|
self.answer_interpretation,
|
|
self.answer_principle_diagnosis,
|
|
self.answer_differential_diagnosis,
|
|
self.answer_management,
|
|
):
|
|
if ans:
|
|
ans = ans.strip()
|
|
|
|
def is_marked(self):
|
|
if self.score == "":
|
|
return False
|
|
else:
|
|
return True
|
|
|
|
def get_mark_status(self):
|
|
mark_objects = self.mark.all()
|
|
count = mark_objects.count()
|
|
if count == 0:
|
|
return "Unmarked"
|
|
|
|
if count == 1:
|
|
return f"Marked by {mark_objects.first().marker} (awaiting second marker)"
|
|
|
|
s = ", ".join(f"{str(i.marker)} ({i.score})" for i in mark_objects)
|
|
return f"Marked by {s}"
|
|
|
|
def get_markers(self):
|
|
mark_objects = self.mark.all()
|
|
if not mark_objects:
|
|
return "None"
|
|
return "/".join(f"{str(i.marker)}" for i in mark_objects)
|
|
|
|
def get_mark_scores(self):
|
|
mark_objects = self.mark.all()
|
|
count = mark_objects.count()
|
|
if count < 2:
|
|
return "hidden"
|
|
return "/".join(f"{str(i.score)}" for i in mark_objects)
|
|
|
|
def get_answer_score(self) -> float | str:
|
|
"""Returns the answers score.
|
|
If the answer is unmarked the string "unmarked" is returned"""
|
|
if self.score == "":
|
|
return "unmarked"
|
|
return float(self.score)
|
|
|
|
def discrepant_answers(self):
|
|
marks = set(self.mark.values_list("score", flat=True))
|
|
if len(marks) > 1:
|
|
return True
|
|
return False
|
|
|
|
def get_answer(
|
|
self,
|
|
) -> tuple[
|
|
models.TextField,
|
|
models.TextField,
|
|
models.TextField,
|
|
models.TextField,
|
|
models.TextField,
|
|
]:
|
|
"""Returns a tuple containing the users answers (model fields)
|
|
|
|
"""
|
|
return (
|
|
self.answer_observations,
|
|
self.answer_interpretation,
|
|
self.answer_principle_diagnosis,
|
|
self.answer_differential_diagnosis,
|
|
self.answer_management,
|
|
)
|
|
|
|
def get_answer_string(self) -> str:
|
|
return f"""
|
|
Observations:
|
|
{self.answer_observations},
|
|
|
|
Interpretation:
|
|
{self.answer_interpretation},
|
|
|
|
Principle Diagnosis:
|
|
{self.answer_principle_diagnosis},
|
|
|
|
Differential:
|
|
{self.answer_differential_diagnosis},
|
|
|
|
Management:
|
|
{self.answer_management},
|
|
"""
|
|
|
|
|
|
@reversion.register
|
|
class AnswerMarks(models.Model):
|
|
score = models.CharField(max_length=3, choices=UserAnswer.ScoreOptions.choices)
|
|
|
|
mark_reason = models.TextField(
|
|
null=True,
|
|
blank=True,
|
|
help_text="Reason for the given mark - not visible to candidates",
|
|
)
|
|
|
|
marker = models.ForeignKey(
|
|
settings.AUTH_USER_MODEL, related_name="marker", on_delete=models.CASCADE
|
|
)
|
|
|
|
user_answer = models.ForeignKey(
|
|
UserAnswer,
|
|
related_name="mark",
|
|
on_delete=models.SET_NULL,
|
|
null=True,
|
|
blank=True,
|
|
)
|