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Ross
2022-06-08 18:59:06 +01:00
parent 214a566357
commit 4354786ef5
2 changed files with 136 additions and 117 deletions
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generic/views.py
+1 -1
View File
@@ -2055,7 +2055,7 @@ class CidUserCreate(RevisionMixin, CidManagerRequiredMixin, CreateView):
form_class = CidUserForm form_class = CidUserForm
class CidUserUpdate(RevisionMixin, CidManagerRequiredMixin, UpdateView): class CidUserUpdate(CidManagerRequiredMixin, UpdateView):
model = CidUser model = CidUser
form_class = CidUserForm form_class = CidUserForm
longs/models.py
+130 -111
View File
@@ -28,7 +28,18 @@ from helpers.images import image_as_base64, pretty_print_dicom
from anatomy.models import Modality from anatomy.models import Modality
from generic.models import CidUser, CidUserGroup, Examination, Condition, Sign, ExamBase, Plane, Contrast, QuestionNote, UserUserGroup from generic.models import (
CidUser,
CidUserGroup,
Examination,
Condition,
Sign,
ExamBase,
Plane,
Contrast,
QuestionNote,
UserUserGroup,
)
# from generic.models import Examination, Site, Condition, Sign # from generic.models import Examination, Site, Condition, Sign
@@ -47,14 +58,14 @@ from django.contrib.contenttypes.fields import GenericRelation
image_storage = FileSystemStorage( image_storage = FileSystemStorage(
# Physical file location ROOT # Physical file location ROOT
location=u"{0}longs/".format(settings.MEDIA_ROOT), location="{0}longs/".format(settings.MEDIA_ROOT),
# Url for file # Url for file
base_url=u"{0}longs/".format(settings.MEDIA_URL), base_url="{0}longs/".format(settings.MEDIA_URL),
) )
def image_directory_path(instance, filename): def image_directory_path(instance, filename):
return u"longs/picture/{0}".format(filename) return "longs/picture/{0}".format(filename)
def findMiddle(input_list): def findMiddle(input_list):
@@ -127,14 +138,15 @@ class Long(models.Model):
json_creation_time = models.DateTimeField(blank=True, default=None, null=True) json_creation_time = models.DateTimeField(blank=True, default=None, null=True)
question_json_id = models.IntegerField(default=1, help_text="Auto incrementing json creation number") question_json_id = models.IntegerField(
default=1, help_text="Auto incrementing json creation number"
)
series = SortedManyToManyField("LongSeries", related_name="long") series = SortedManyToManyField("LongSeries", related_name="long")
notes = GenericRelation(QuestionNote) notes = GenericRelation(QuestionNote)
#question_file = models.FileField(upload_to=question_file_directory_path, blank=True, null=True) # question_file = models.FileField(upload_to=question_file_directory_path, blank=True, null=True)
def get_absolute_url(self): def get_absolute_url(self):
return reverse("longs:question_detail", kwargs={"pk": self.pk}) return reverse("longs:question_detail", kwargs={"pk": self.pk})
@@ -170,9 +182,7 @@ class Long(models.Model):
return images return images
def get_image_urls(self): def get_image_urls(self):
return ",".join( return ",".join([f"{REMOTE_URL}{i.url}" for i in self.get_images()])
[f"{REMOTE_URL}{i.url}" for i in self.get_images()]
)
def get_image_url_array(self): def get_image_url_array(self):
return json.dumps([f"{REMOTE_URL}{i.url}" for i in self.get_images()]) return json.dumps([f"{REMOTE_URL}{i.url}" for i in self.get_images()])
@@ -202,45 +212,47 @@ class Long(models.Model):
return marker_unmarked return marker_unmarked
def get_question_json(self, based=True, feedback=False): def get_question_json(self, based=True, feedback=False):
# self == q? # self == q?
#q = get_object_or_404(Long, pk=question_id) # q = get_object_or_404(Long, pk=question_id)
question_id = self.pk question_id = self.pk
if not based: if not based:
image_titles = [] image_titles = []
images = [] images = []
question_series = self.series.all() question_series = self.series.all()
# Loop through longimage associations # Loop through longimage associations
for i, series in enumerate(question_series): for i, series in enumerate(question_series):
#image_array = [] # image_array = []
#for i in series.images.all(): # for i in series.images.all():
# image_array.append(image_as_base64(i.image)) # image_array.append(image_as_base64(i.image))
# #image_array.append(i.image.url) # #image_array.append(i.image.url)
# We are still limited by the size of a series (although this should not be too big or computers will crash...) # We are still limited by the size of a series (although this should not be too big or computers will crash...)
images.append(["{}/{}".format(settings.REMOTE_URL, i.image.url) for i in series.images.all()]) images.append(
#image_array = [i.image.url for i in series.images.all()] [
#images.append(url) "{}/{}".format(settings.REMOTE_URL, i.image.url)
for i in series.images.all()
]
)
# image_array = [i.image.url for i in series.images.all()]
# images.append(url)
image_titles.append(series.get_examination()) image_titles.append(series.get_examination())
question_json = { question_json = {
"title": self.history, "title": self.history,
"images": images, "images": images,
"image_titles": image_titles, "image_titles": image_titles,
#"feedback_image": [], # "feedback_image": [],
#"annotations": [str(q.image_annotations)], # "annotations": [str(q.image_annotations)],
"type": "long", "type": "long",
"cached": False, "cached": False,
} }
return question_json return question_json
# exam_order.append(q.id)
#exam_order.append(q.id) path = "{0}longs/questions/{1}.json".format(settings.MEDIA_ROOT, question_id)
path= "{0}longs/questions/{1}.json".format(settings.MEDIA_ROOT, question_id) url = "{0}longs/questions/{1}.json".format(settings.MEDIA_URL, question_id)
url= "{0}longs/questions/{1}.json".format(settings.MEDIA_URL, question_id)
timestamp = timezone.now() timestamp = timezone.now()
@@ -250,32 +262,34 @@ class Long(models.Model):
print("start writing file") print("start writing file")
# We manually create the json for long questions to reducem memroy usade # We manually create the json for long questions to reducem memroy usade
f.write("""{{ f.write(
"""{{
"title": "{}", "title": "{}",
"type": "long", "type": "long",
"generated": "{}", "generated": "{}",
"question_json_id": "{}", "question_json_id": "{}",
""".format(self.history, timestamp.isoformat(), self.question_json_id) """.format(
self.history, timestamp.isoformat(), self.question_json_id
)
) )
f.write('"images" : [') f.write('"images" : [')
#images = [] # images = []
image_titles = [] image_titles = []
question_series = self.series.all() question_series = self.series.all()
# Loop through longimage associations # Loop through longimage associations
for i, series in enumerate(question_series): for i, series in enumerate(question_series):
print("gen series", i) print("gen series", i)
#image_array = [] # image_array = []
#for i in series.images.all(): # for i in series.images.all():
# image_array.append(image_as_base64(i.image)) # image_array.append(image_as_base64(i.image))
# #image_array.append(i.image.url) # #image_array.append(i.image.url)
# We are still limited by the size of a series (although this should not be too big or computers will crash...) # We are still limited by the size of a series (although this should not be too big or computers will crash...)
#image_array = [image_as_base64(i.image) for i in series.images.all()] # image_array = [image_as_base64(i.image) for i in series.images.all()]
##image_array = [i.image.url for i in series.images.all()] ##image_array = [i.image.url for i in series.images.all()]
#f.write(json.dumps(image_array)) # f.write(json.dumps(image_array))
f.write('["') f.write('["')
first = True first = True
@@ -286,12 +300,12 @@ class Long(models.Model):
f.write(', "') f.write(', "')
f.write(image_as_base64(img.image)) f.write(image_as_base64(img.image))
# for debugging # for debugging
#f.write(img.image.url) # f.write(img.image.url)
f.write('"') f.write('"')
first = False first = False
f.write(']') f.write("]")
#images.append(url) # images.append(url)
if i != len(question_series) - 1: if i != len(question_series) - 1:
f.write(",") f.write(",")
image_titles.append(series.get_examination()) image_titles.append(series.get_examination())
@@ -299,11 +313,10 @@ class Long(models.Model):
f.write('"image_titles" : {} }}'.format(json.dumps(image_titles))) f.write('"image_titles" : {} }}'.format(json.dumps(image_titles)))
self.json_creation_time = timestamp self.json_creation_time = timestamp
self.save() self.save()
#exam_question = { # exam_question = {
# "title": q.history, # "title": q.history,
# "images": images, # "images": images,
# "image_titles": image_titles, # "image_titles": image_titles,
@@ -311,12 +324,10 @@ class Long(models.Model):
# #"annotations": [str(q.image_annotations)], # #"annotations": [str(q.image_annotations)],
# "type": "long", # "type": "long",
# "cached": False, # "cached": False,
#} # }
return url return url
# def GetNonFeedbackQuestionImages(self): # def GetNonFeedbackQuestionImages(self):
# return self.get_images() # return self.get_images()
@@ -324,6 +335,7 @@ class Long(models.Model):
def test_image_validator(file): def test_image_validator(file):
pass pass
class LongSeriesImage(models.Model): class LongSeriesImage(models.Model):
image = models.FileField(upload_to=image_directory_path) image = models.FileField(upload_to=image_directory_path)
position = models.IntegerField(default=0) position = models.IntegerField(default=0)
@@ -333,14 +345,14 @@ class LongSeriesImage(models.Model):
) )
class Meta: class Meta:
ordering = ['position'] ordering = ["position"]
def get_dicom_info(self): def get_dicom_info(self):
try: try:
info = pretty_print_dicom(pydicom.read_file(self.image)) info = pretty_print_dicom(pydicom.read_file(self.image))
except pydicom.errors.InvalidDicomError: except pydicom.errors.InvalidDicomError:
info = "File is not a dicom." info = "File is not a dicom."
return(info) return info
@reversion.register @reversion.register
@@ -371,12 +383,12 @@ class LongSeries(models.Model):
null=True, null=True,
blank=True, blank=True,
) )
#long = models.ManyToManyField( # long = models.ManyToManyField(
# "Long", # "Long",
# help_text="The question(s) this series should be associated with", # help_text="The question(s) this series should be associated with",
# related_name="series", # related_name="series",
# blank=True, # blank=True,
#) # )
description = models.TextField( description = models.TextField(
blank=True, blank=True,
help_text="Description of stack, for admin organisation, will not be visible when taking", help_text="Description of stack, for admin organisation, will not be visible when taking",
@@ -392,15 +404,14 @@ class LongSeries(models.Model):
help_text="If a question should be freely available to browse", default=True help_text="If a question should be freely available to browse", default=True
) )
def __str__(self): def __str__(self):
if self.long: if self.long:
long_id = ", ".format([long.pk for long in self.long.all()]) long_id = ", ".format([long.pk for long in self.long.all()])
#long_id = self.long.pk # long_id = self.long.pk
else: else:
long_id = "None" long_id = "None"
return "{}/{} : {} [{}]".format(self.pk, return "{}/{} : {} [{}]".format(
self.get_examination(), self.description, long_id self.pk, self.get_examination(), self.description, long_id
) )
def get_author_objects(self): def get_author_objects(self):
@@ -440,18 +451,12 @@ class LongSeries(models.Model):
return reverse("longs:long_series_detail", kwargs={"pk": self.pk}) return reverse("longs:long_series_detail", kwargs={"pk": self.pk})
def get_image_urls(self, feedback=False): def get_image_urls(self, feedback=False):
images = [ images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
f"{REMOTE_URL}{i.image.url}"
for i in self.images.all()
]
return ",".join(images) return ",".join(images)
def get_image_url_array(self, feedback=False): def get_image_url_array(self, feedback=False):
images = [ images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
f"{REMOTE_URL}{i.image.url}"
for i in self.images.all()
]
return json.dumps(images) return json.dumps(images)
@@ -466,7 +471,9 @@ class LongSeries(models.Model):
thumbnailer = get_thumbnailer(img) thumbnailer = get_thumbnailer(img)
thumbnail = thumbnailer["exam-list"] thumbnail = thumbnailer["exam-list"]
except InvalidImageFormatError: except InvalidImageFormatError:
return format_html('<span title="{}">Invalid image url<span>', img), len(images) return format_html('<span title="{}">Invalid image url<span>', img), len(
images
)
return format_html('<img src="/media/{}" />', thumbnail), len(images) return format_html('<img src="/media/{}" />', thumbnail), len(images)
def get_block(self): def get_block(self):
@@ -495,8 +502,6 @@ class LongSeries(models.Model):
i.save() i.save()
n = n + 1 n = n + 1
def order_by_dicom(self, field="SliceLocation"): def order_by_dicom(self, field="SliceLocation"):
images = self.images.all() images = self.images.all()
@@ -505,7 +510,7 @@ class LongSeries(models.Model):
for i in images: for i in images:
files.append((i, pydicom.dcmread(i.image.path))) files.append((i, pydicom.dcmread(i.image.path)))
#print("file count: {}".format(len(files))) # print("file count: {}".format(len(files)))
# skip files with no SliceLocation (eg scout views) # skip files with no SliceLocation (eg scout views)
slices = [] slices = []
@@ -514,7 +519,7 @@ class LongSeries(models.Model):
for i, f in files: for i, f in files:
if hasattr(f, field): if hasattr(f, field):
slices.append(f) slices.append(f)
#map[f.SliceLocation] = i # map[f.SliceLocation] = i
map[f[field].value] = i map[f[field].value] = i
else: else:
skipcount = skipcount + 1 skipcount = skipcount + 1
@@ -524,8 +529,7 @@ class LongSeries(models.Model):
# ensure they are in the correct order # ensure they are in the correct order
slices = sorted(slices, key=lambda s: s[field].value) slices = sorted(slices, key=lambda s: s[field].value)
# print(slices)
#print(slices)
n = 1 n = 1
for f in slices: for f in slices:
i = map[f[field].value] i = map[f[field].value]
@@ -543,6 +547,7 @@ class LongSeries(models.Model):
return size return size
# class LongImage(models.Model): # class LongImage(models.Model):
# long = models.ForeignKey(Long, # long = models.ForeignKey(Long,
# related_name="images", # related_name="images",
@@ -589,14 +594,20 @@ class Exam(ExamBase):
default=4500, default=4500,
) )
author = models.ManyToManyField(settings.AUTH_USER_MODEL, author = models.ManyToManyField(
settings.AUTH_USER_MODEL,
blank=True, blank=True,
help_text='Author of exam', help_text="Author of exam",
related_name="long_exam_author") related_name="long_exam_author",
)
double_mark = models.BooleanField(default=True, help_text="Defines if an exam is expected to be double marked") double_mark = models.BooleanField(
default=True, help_text="Defines if an exam is expected to be double marked"
)
valid_cid_users = models.ManyToManyField(CidUser, blank=True, related_name="longs_exams") valid_cid_users = models.ManyToManyField(
CidUser, blank=True, related_name="longs_exams"
)
valid_user_users = models.ManyToManyField( valid_user_users = models.ManyToManyField(
settings.AUTH_USER_MODEL, blank=True, related_name="user_longs_exams" settings.AUTH_USER_MODEL, blank=True, related_name="user_longs_exams"
@@ -606,49 +617,45 @@ class Exam(ExamBase):
CidUserGroup, CidUserGroup,
blank=True, blank=True,
help_text="These groups define which candidates are able to be added to the exams/collection.", help_text="These groups define which candidates are able to be added to the exams/collection.",
related_name="longs_cid_user_groups" related_name="longs_cid_user_groups",
) )
user_user_groups = models.ManyToManyField( user_user_groups = models.ManyToManyField(
UserUserGroup, UserUserGroup,
blank=True, blank=True,
help_text="These groups define which candidates are able to be added to the exams/collection.", help_text="These groups define which candidates are able to be added to the exams/collection.",
related_name="longs_user_user_groups" related_name="longs_user_user_groups",
) )
def get_exam_question_json(self, question_id): def get_exam_question_json(self, question_id):
q = get_object_or_404(Long, pk=question_id) q = get_object_or_404(Long, pk=question_id)
#exam_order.append(q.id) # exam_order.append(q.id)
# Loop through longimage associations # Loop through longimage associations
images = [] images = []
image_titles = [] image_titles = []
for series in q.series.all(): for series in q.series.all():
#image_array = [] # image_array = []
#for i in series.images.all(): # for i in series.images.all():
# image_array.append(image_as_base64(i.image)) # image_array.append(image_as_base64(i.image))
# #image_array.append(i.image.url) # #image_array.append(i.image.url)
image_array = [image_as_base64(i.image) for i in series.images.all()] image_array = [image_as_base64(i.image) for i in series.images.all()]
images.append(image_array) images.append(image_array)
image_titles.append(series.get_examination()) image_titles.append(series.get_examination())
exam_question = { exam_question = {
"title": q.history, "title": q.history,
"images": images, "images": images,
"image_titles": image_titles, "image_titles": image_titles,
#"feedback_image": [], # "feedback_image": [],
#"annotations": [str(q.image_annotations)], # "annotations": [str(q.image_annotations)],
"type": "long", "type": "long",
"images_json": True, "images_json": True,
} }
return exam_question return exam_question
def get_exam_json(self, based=True): def get_exam_json(self, based=True):
questions = self.exam_questions.all() questions = self.exam_questions.all()
@@ -661,7 +668,6 @@ class Exam(ExamBase):
exam_order.append(q.id) exam_order.append(q.id)
if based: if based:
# If it is a new question we need to for a question json refresh # If it is a new question we need to for a question json refresh
if q.json_creation_time is None: if q.json_creation_time is None:
q.get_question_json() q.get_question_json()
@@ -672,30 +678,31 @@ class Exam(ExamBase):
images = [] images = []
image_titles = [] image_titles = []
for series in q.series.all(): for series in q.series.all():
#image_array = [] # image_array = []
#for i in series.images.all(): # for i in series.images.all():
# image_array.append(image_as_base64(i.image)) # image_array.append(image_as_base64(i.image))
# #image_array.append(i.image.url) # #image_array.append(i.image.url)
image_array = ["{}/{}".format(settings.REMOTE_URL, i.image.url) for i in series.images.all()] image_array = [
"{}/{}".format(settings.REMOTE_URL, i.image.url)
for i in series.images.all()
]
images.append(image_array) images.append(image_array)
image_titles.append(series.get_examination()) image_titles.append(series.get_examination())
# exam_questions[q.id] = n
#exam_questions[q.id] = n
exam_questions[q.id] = { exam_questions[q.id] = {
"title": q.history, "title": q.history,
"images": images, "images": images,
"image_titles": image_titles, "image_titles": image_titles,
#"feedback_image": [], # "feedback_image": [],
#"annotations": [str(q.image_annotations)], # "annotations": [str(q.image_annotations)],
"type": "long", "type": "long",
} }
#if feedback_images: # if feedback_images:
# exam_questions[q.id]["feedback_image"] = feedback_images # exam_questions[q.id]["feedback_image"] = feedback_images
exam_json = { exam_json = {
"eid": "long/{}".format(self.id), "eid": "long/{}".format(self.id),
"cached": False, "cached": False,
@@ -705,18 +712,18 @@ class Exam(ExamBase):
"exam_order": exam_order, "exam_order": exam_order,
"questions": exam_questions, "questions": exam_questions,
"based": based, "based": based,
#"question_requests": exam_questions, # "question_requests": exam_questions,
} }
if based: if based:
exam_json["question_requests"] = exam_questions exam_json["question_requests"] = exam_questions
if self.time_limit: if self.time_limit:
exam_json["exam_time"] = self.time_limit exam_json["exam_time"] = self.time_limit
return exam_json return exam_json
@reversion.register @reversion.register
class CidUserAnswer(models.Model): class CidUserAnswer(models.Model):
"""User answers by candidate""" """User answers by candidate"""
@@ -764,41 +771,48 @@ class CidUserAnswer(models.Model):
EIGHT = 8, _("8") EIGHT = 8, _("8")
score = models.CharField( score = models.CharField(
max_length=3, choices=ScoreOptions.choices, default=ScoreOptions.UNMARKED, blank=True, help_text="The final score for the candidate" max_length=3,
choices=ScoreOptions.choices,
default=ScoreOptions.UNMARKED,
blank=True,
help_text="The final score for the candidate",
) )
#mark = models.ManyToManyField( # mark = models.ManyToManyField(
# "AnswerMarks", related_name="user_answer", blank=True # "AnswerMarks", related_name="user_answer", blank=True
#) # )
#secondary_mark = models.ForeignKey( # secondary_mark = models.ForeignKey(
# "AnswerMarks", related_name="user_answer", on_delete=models.SET_NULL, null=True, blank=True # "AnswerMarks", related_name="user_answer", on_delete=models.SET_NULL, null=True, blank=True
#) # )
created = models.DateTimeField(auto_now_add=True) created = models.DateTimeField(auto_now_add=True)
updated = models.DateTimeField(auto_now=True) updated = models.DateTimeField(auto_now=True)
class Meta: class Meta:
ordering = ['cid'] ordering = ["cid"]
def __str__(self): def __str__(self):
try: try:
exam = self.exam exam = self.exam
except (Exam.DoesNotExist, KeyError) as e: except (Exam.DoesNotExist, KeyError) as e:
exam = "None" exam = "None"
return "{}/{}/{} ({})".format( return "{}/{}/{} ({})".format(exam, self.cid, self.created, self.updated)
exam, self.cid, self.created, self.updated
)
def save(self, *args, **kwargs): def save(self, *args, **kwargs):
self.clean() self.clean()
return super(CidUserAnswer, self).save(*args, **kwargs) return super(CidUserAnswer, self).save(*args, **kwargs)
def clean(self): def clean(self):
for ans in (self.answer_observations, self.answer_interpretation, self.answer_principle_diagnosis, self.answer_differential_diagnosis, self.answer_management): for ans in (
self.answer_observations,
self.answer_interpretation,
self.answer_principle_diagnosis,
self.answer_differential_diagnosis,
self.answer_management,
):
if ans: if ans:
ans = ans.strip() ans = ans.strip()
def is_marked(self): def is_marked(self):
if self.score == "": if self.score == "":
return False return False
@@ -845,23 +859,28 @@ class CidUserAnswer(models.Model):
return reverse("longs:user_answer_view", kwargs={"pk": self.pk}) return reverse("longs:user_answer_view", kwargs={"pk": self.pk})
@reversion.register @reversion.register
class AnswerMarks(models.Model): class AnswerMarks(models.Model):
score = models.CharField( score = models.CharField(max_length=3, choices=CidUserAnswer.ScoreOptions.choices)
max_length=3, choices=CidUserAnswer.ScoreOptions.choices
mark_reason = models.TextField(
null=True,
blank=True,
help_text="Reason for the given mark - not visible to candidates",
) )
mark_reason = models.TextField(null=True, blank=True, help_text="Reason for the given mark - not visible to candidates") candidate_feedback = models.TextField(
null=True, blank=True, help_text="Feedback for the candidate"
candidate_feedback = models.TextField(null=True, blank=True, help_text="Feedback for the candidate") )
marker = models.ForeignKey( marker = models.ForeignKey(
settings.AUTH_USER_MODEL, related_name="marker", on_delete=models.CASCADE settings.AUTH_USER_MODEL, related_name="marker", on_delete=models.CASCADE
) )
user_answer = models.ForeignKey( user_answer = models.ForeignKey(
CidUserAnswer, related_name="mark", on_delete=models.SET_NULL, null=True, blank=True CidUserAnswer,
related_name="mark",
on_delete=models.SET_NULL,
null=True,
blank=True,
) )