start setting up shorts
This commit is contained in:
Ross
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from collections import defaultdict
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from django.db import models
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from django.urls import reverse
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from django.conf import settings
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from rad.settings import REMOTE_URL
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from django.utils.translation import gettext_lazy as _
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import dicognito
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import json
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# Create your models here.
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from generic.models import CidUser, CidUserGroup, ExamBase, ExamCollection, ExamUserStatus, QuestionBase, UserAnswerBase, UserUserGroup
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from django.contrib.contenttypes.fields import GenericRelation
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from django.core.validators import MaxValueValidator, MinValueValidator
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from django.utils.html import mark_safe
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from rapids.models import Abnormality, Examination, Region
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from helpers.images import get_image_hash, image_as_base64
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def image_directory_path(instance, filename):
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# return u"{0}".format(filename)
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return "shorts/picture/{0}".format(filename)
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class Question(QuestionBase):
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"""
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"""
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history = models.TextField(null=True, blank=True,
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help_text="Single line history for the question, e.g. Age 14, male. Referral from ED. History: Painful wrist after falling off skateboard.")
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NONE = "NONE"
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LEFT = "LEFT"
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RIGHT = "RIGHT"
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BILATERAL = "BILAT"
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LATERALITY_CHOICES = (
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(NONE, "None"),
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(LEFT, "Left"),
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(RIGHT, "Right"),
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(BILATERAL, "Bilateral"),
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)
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abnormality = models.ManyToManyField(
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Abnormality,
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blank=True,
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help_text="The abnormality (laterality and region independent). Used for categorisation but does not affect the answer",
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)
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region = models.ManyToManyField(
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Region,
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blank=True,
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help_text="Region of the abnormality (laterality independent)",
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)
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examination = models.ManyToManyField(
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Examination, help_text="Name of the (primary) examination"
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)
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laterality = models.CharField(
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max_length=20,
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choices=LATERALITY_CHOICES,
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default=NONE,
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help_text="Applies to the answer, not the examination",
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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 question",
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related_name="shorts_authored_questions",
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)
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def get_app_name(self):
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return "shorts"
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def get_absolute_url(self):
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return reverse("shorts:question_detail", kwargs={"pk": self.pk})
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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 GetNonFeedbackQuestionImages(self):
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# return self.get_images()
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def get_image_annotations(self):
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return json.dumps(
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[i.image_annotations for i in self.images.all() if not i.feedback_image]
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)
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def get_laterality_string(self):
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if self.laterality == self.NONE:
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s = ""
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elif self.laterality == self.BILATERAL:
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s = "bilateral "
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elif self.laterality == self.RIGHT:
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s = "right "
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elif self.laterality == self.LEFT:
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s = "left "
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return s
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def anonymise_images(self):
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anonymizer = dicognito.anonymizer.Anonymizer()
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for image in self.images.all():
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file_path = os.path.join(settings.MEDIA_ROOT, image.image.name)
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try:
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with pydicom.dcmread(file_path) as dataset:
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anonymizer.anonymize(dataset)
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dataset.save_as(file_path)
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except pydicom.errors.InvalidDicomError:
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pass
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class QuestionImage(models.Model):
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question = models.ForeignKey(Question, related_name="images", on_delete=models.CASCADE)
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image = models.FileField(upload_to=image_directory_path)
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image_annotations = models.TextField(
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blank=True,
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null=True,
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help_text="Stores a JSON representation of annotations to be applied by cornerstonetools",
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)
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feedback_image = models.BooleanField(default=False)
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filename = models.CharField(
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max_length=255,
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null=True,
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blank=True,
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help_text="Name of the original file when uploaded",
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)
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description = models.CharField(max_length=255, null=True, blank=True)
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image_md5_hash = models.CharField(max_length=32, null=True, blank=True)
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is_dicom = models.BooleanField(default=False)
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def image_tag(self):
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if self.image:
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return mark_safe(
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'<img src="{}" class="admin-rapid-image" /><span class="admin-rapid-image-info">Click and hold to zoom<span>'.format(
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self.image.url
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)
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)
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else:
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return ""
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image_tag.short_description = "Image"
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def save(self, *args, **kwargs):
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"""Override save method to add image hash"""
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if self.image:
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image_hash, is_dicom = get_image_hash(self.image, hash_type="md5", direct_pixel_data=False)
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self.is_dicom = is_dicom
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self.image_md5_hash = image_hash
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# Hack for tests
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if image_hash != "12345ABCD":
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super().save(*args, **kwargs) # Call the "real" save() method.
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class SampleAnswer(models.Model):
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question = models.ForeignKey(
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Question, related_name="sample_answers", on_delete=models.CASCADE
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)
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answer = models.TextField()
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score = models.IntegerField(default=0, blank=True, validators=[MinValueValidator(0), MaxValueValidator(5)])
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proposed = models.BooleanField(default=False)
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def __str__(self):
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return self.answer
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class ExamQuestionDetail(models.Model):
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exam = models.ForeignKey("Exam", on_delete=models.CASCADE)
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question = models.ForeignKey(Question, on_delete=models.CASCADE)
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sort_order = models.IntegerField(default=1000)
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class Meta:
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ordering = ("sort_order",)
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class Exam(ExamBase):
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app_name = "shorts"
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exam_questions = models.ManyToManyField(Question, 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 2 hours",
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default=2 * 60 * 60,
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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="shorts_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="shorts_exam_markers",
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)
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valid_cid_users = models.ManyToManyField(
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CidUser, blank=True, related_name="shorts_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_shorts_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="shorts_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="shorts_user_user_groups",
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)
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exam_user_status = GenericRelation(ExamUserStatus, related_query_name="shorts_exams")
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cid_user_exam = GenericRelation("generic.CidUserExam", related_query_name="shorts_exams")
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examcollection = models.ForeignKey(ExamCollection, blank=True, null=True, on_delete=models.SET_NULL, related_name="shorts_exams")
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def get_app_name(self):
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return "shorts"
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def get_exam_json(self, based=True):
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# TODO
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return {}
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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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q: Rapid
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for q in questions:
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exam_order.append(q.id)
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# Loop through rapidimage associations
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images = []
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feedback_images = []
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image_titles = []
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for i in q.images.all():
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if i.feedback_image == True:
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if based:
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feedback_images.append(image_as_base64(i.image))
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else:
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feedback_images.append(
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"{}/{}".format(settings.REMOTE_URL, i.image.url)
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)
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else:
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if based:
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images.append(image_as_base64(i.image))
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else:
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images.append("{}/{}".format(settings.REMOTE_URL, i.image.url))
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if i.description:
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image_titles.append(i.description)
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else:
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image_titles.append("")
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exam_questions[q.id] = {
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"images": images,
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# "feedback_image": [],
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# "annotations": [str(q.image_annotations)],
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"type": "rapid",
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}
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if not self.exam_mode:
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exam_questions[q.id]["normal"] = q.normal
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exam_questions[q.id]["feedback_images"] = feedback_images
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exam_questions[q.id]["answers"] = list(
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q.get_correct_unstripped_answers()
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)
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if self.include_history and q.history:
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exam_questions[q.id]["history"] = q.history
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if any(image_titles):
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exam_questions[q.id]["image_titles"] = image_titles
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# if feedback_images:
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# exam_questions[q.id]["feedback_image"] = feedback_images
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exam_json = {
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"eid": "rapid/{}".format(self.id),
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"cached": False,
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"exam_type": "rapid",
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"exam_name": self.name,
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"exam_mode": self.exam_mode,
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"exam_order": exam_order,
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"questions": exam_questions,
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}
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if self.time_limit:
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exam_json["exam_time"] = self.time_limit
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return exam_json
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def get_absolute_url(self):
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return reverse("shorts:exam_overview", kwargs={"pk": self.pk})
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class UserAnswer(UserAnswerBase):
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"""User answers by candidate"""
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app_name = "shorts"
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question = models.ForeignKey(
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Question, related_name="cid_user_answers", on_delete=models.CASCADE
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)
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answer = models.TextField(blank=True)
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user = models.ForeignKey(
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settings.AUTH_USER_MODEL,
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on_delete=models.CASCADE,
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blank=True,
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null=True,
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related_name="user_shorts_user_answers",
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)
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# Each user answer is associated with a particular exam
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exam = models.ForeignKey(
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Exam, related_name="cid_user_answers", on_delete=models.CASCADE, null=True
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)
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score = models.IntegerField(default=0, blank=True, validators=[MinValueValidator(0), MaxValueValidator(5)])
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class CallStateOptions(models.TextChoices):
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CORRECT = "C", _("Correct Call")
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OVERCALL = "O", _("Overcall")
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UNDERCALL = "U", _("Undercall")
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INCORRECTCALL = "W", _("Incorrect Call")
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PARTIALCALL = "P", _("Partial Call")
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callstate = models.CharField(
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max_length=1, choices=CallStateOptions.choices, blank=True, null=True
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)
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def __str__(self):
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name = self.get_candidate_name()
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try:
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exam = self.exam
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except (Exam.DoesNotExist, KeyError) as e:
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exam = "None"
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return "{}/{}/{}: {}".format(
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exam, name, self.question.get_primary_answer(), self.answer
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)
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def save(self, *args, **kwargs):
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self.clean()
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return super(UserAnswer, self).save(*args, **kwargs)
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def clean(self):
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if self.answer:
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self.answer = self.answer.strip()
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else:
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self.answer = ""
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# def get_compare_string(self):
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# # strip here should be unneccasry (providing clean is now working)
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# s = self.answer.lower().strip()
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# s = s.translate(str.maketrans('', '', string.punctuation))
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# return s
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def get_answer(self):
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return self.answer
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def get_answer_callstate(self):
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if not self.callstate:
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return ""
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return self.callstate.label
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def get_answer_score(self, cached=True):
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return self.score
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