start atlas app
This commit is contained in:
Ross
+378
@@ -0,0 +1,378 @@
|
||||
import json
|
||||
from rad.settings import REMOTE_URL
|
||||
from django.db.models.fields.files import ImageField
|
||||
from django.db.models.fields.related import ForeignKey
|
||||
from django.db import models
|
||||
from django.shortcuts import get_object_or_404
|
||||
from django.utils import timezone
|
||||
import tagulous
|
||||
import tagulous.models
|
||||
|
||||
|
||||
from django.core.files.storage import FileSystemStorage
|
||||
from django.conf import settings
|
||||
from django.utils.html import format_html
|
||||
|
||||
from django.urls import reverse
|
||||
|
||||
from django.utils.translation import ugettext_lazy as _
|
||||
from django.utils.html import mark_safe
|
||||
|
||||
from django.core.exceptions import ValidationError
|
||||
|
||||
from sortedm2m.fields import SortedManyToManyField
|
||||
|
||||
import string
|
||||
from collections import defaultdict
|
||||
from helpers.images import image_as_base64, pretty_print_dicom
|
||||
|
||||
from anatomy.models import Modality
|
||||
|
||||
from generic.models import Examination, Condition, Sign, ExamBase, Plane, Contrast, QuestionNote
|
||||
|
||||
# from generic.models import Examination, Site, Condition, Sign
|
||||
|
||||
from easy_thumbnails.files import get_thumbnailer
|
||||
from easy_thumbnails.exceptions import InvalidImageFormatError
|
||||
|
||||
import pydicom
|
||||
import pydicom.errors
|
||||
import datetime
|
||||
from django.utils import timezone
|
||||
|
||||
import reversion
|
||||
|
||||
from django.contrib.contenttypes.fields import GenericRelation
|
||||
|
||||
|
||||
image_storage = FileSystemStorage(
|
||||
# Physical file location ROOT
|
||||
location=u"{0}atlas/".format(settings.MEDIA_ROOT),
|
||||
# Url for file
|
||||
base_url=u"{0}atlas/".format(settings.MEDIA_URL),
|
||||
)
|
||||
|
||||
|
||||
def image_directory_path(instance, filename):
|
||||
return u"atlas/picture/{0}".format(filename)
|
||||
|
||||
|
||||
def findMiddle(input_list):
|
||||
middle = float(len(input_list)) / 2
|
||||
if middle % 2 != 0:
|
||||
return input_list[int(middle - 0.5)]
|
||||
else:
|
||||
return input_list[int(middle)]
|
||||
return (input_list[int(middle)], input_list[int(middle - 1)])
|
||||
|
||||
|
||||
@reversion.register
|
||||
class Case(models.Model):
|
||||
class SubspecialtyChoices(models.TextChoices):
|
||||
BREAST = 'BR', _('Breast')
|
||||
CARDIAC = 'CA', _('Cardiac')
|
||||
GASTRO = 'GI', _('Gastrointestinal and hepatobiliary')
|
||||
HEADNECK = 'HN', _('Head and Neck')
|
||||
MSK = 'MS', _('Musculoskeletal')
|
||||
NEURO = 'NE', _('Neuroradiology')
|
||||
OBSGYN = 'OG', _('Obstectric and Gynaecological')
|
||||
PAED = 'PA', _('Paediatric')
|
||||
URO = 'UR', _('Uroradiology')
|
||||
VASC = 'VA', _('Vascular')
|
||||
HAEMONC = 'HA', _('Haemotology and Oncology')
|
||||
|
||||
# author = models.ForeignKey('auth.User', on_delete=models.CASCADE)
|
||||
# image = models.ImageField()
|
||||
description = models.TextField(
|
||||
blank=True,
|
||||
help_text="Description of the case, for admin organisation, will not be visible when taking",
|
||||
)
|
||||
|
||||
history = models.TextField(null=True, blank=True)
|
||||
|
||||
findings = models.TextField(null=True, blank=True)
|
||||
|
||||
subpecialty = models.CharField(max_length=2, choices=SubspecialtyChoices.choices)
|
||||
|
||||
condition = tagulous.models.TagField(
|
||||
to=Condition,
|
||||
blank=True,
|
||||
help_text='Associated condition. Will allow searching / filtering and tips / hints to be displayed. Conditions with spaces must be enclosed in quotes "..."',
|
||||
)
|
||||
|
||||
sign = tagulous.models.TagField(
|
||||
to=Sign, blank=True, help_text="Radiological signs in the question"
|
||||
)
|
||||
|
||||
verified = models.BooleanField(default=False)
|
||||
created_date = models.DateTimeField(default=timezone.now)
|
||||
published_date = models.DateTimeField(blank=True, null=True)
|
||||
author = models.ManyToManyField(
|
||||
settings.AUTH_USER_MODEL,
|
||||
blank=True,
|
||||
help_text="Author of question",
|
||||
related_name="atlas_authored_questions",
|
||||
)
|
||||
|
||||
scrapped = models.BooleanField(
|
||||
default=False, help_text="Question has been scrapped and will not be shown"
|
||||
)
|
||||
|
||||
open_access = models.BooleanField(
|
||||
help_text="If a question should be freely available to browse", default=True
|
||||
)
|
||||
|
||||
series = SortedManyToManyField("Series", related_name="atlas")
|
||||
|
||||
notes = GenericRelation(QuestionNote)
|
||||
|
||||
#question_file = models.FileField(upload_to=question_file_directory_path, blank=True, null=True)
|
||||
|
||||
def get_absolute_url(self):
|
||||
return reverse("atlas:case_detail", kwargs={"pk": self.pk})
|
||||
|
||||
def get_authors(self):
|
||||
"""Returns a comma seperated text list of authors"""
|
||||
authors = ", ".join([i.username for i in self.author.all()])
|
||||
return authors
|
||||
|
||||
def get_author_objects(self):
|
||||
"""Returns a comma seperated text list of authors"""
|
||||
authors = [i for i in self.author.all()]
|
||||
return authors
|
||||
|
||||
def __str__(self):
|
||||
examinations = [series.get_examination() for series in self.series.all()]
|
||||
return "{}/{} : {}".format(self.pk, self.description, ", ".join(examinations))
|
||||
|
||||
def get_images(self, findings=False):
|
||||
qs = self.images.all()
|
||||
|
||||
if not findings:
|
||||
images = [i.image for i in qs if not i.findings_image]
|
||||
else:
|
||||
images = [i.image for i in qs]
|
||||
|
||||
return images
|
||||
|
||||
def get_image_urls(self):
|
||||
return ",".join(
|
||||
["https://www.penracourses.org.uk{}".format(i.url) for i in self.get_images()]
|
||||
)
|
||||
|
||||
def get_image_url_array(self):
|
||||
return json.dumps(["https://www.penracourses.org.uk{}".format(i.url) for i in self.get_images()])
|
||||
|
||||
|
||||
class SeriesImage(models.Model):
|
||||
image = models.FileField(upload_to=image_directory_path)
|
||||
position = models.IntegerField(default=0)
|
||||
upload_filename = models.CharField(max_length=255, blank=True)
|
||||
series = models.ForeignKey(
|
||||
"Series", related_name="images", on_delete=models.SET_NULL, null=True
|
||||
)
|
||||
|
||||
class Meta:
|
||||
ordering = ['position']
|
||||
|
||||
def get_dicom_info(self):
|
||||
try:
|
||||
info = pretty_print_dicom(pydicom.read_file(self.image))
|
||||
except pydicom.errors.InvalidDicomError:
|
||||
info = "File is not a dicom."
|
||||
return(info)
|
||||
|
||||
|
||||
@reversion.register
|
||||
class Series(models.Model):
|
||||
modality = models.ForeignKey(
|
||||
Modality, related_name="series_modality", on_delete=models.SET_NULL, null=True
|
||||
)
|
||||
examination = models.ForeignKey(
|
||||
Examination,
|
||||
help_text="Name of the examination",
|
||||
related_name="series_examination",
|
||||
on_delete=models.SET_NULL,
|
||||
null=True,
|
||||
)
|
||||
plane = models.ForeignKey(
|
||||
Plane,
|
||||
help_text="Plane of the examination",
|
||||
related_name="series_plane",
|
||||
on_delete=models.SET_NULL,
|
||||
null=True,
|
||||
blank=True,
|
||||
)
|
||||
contrast = models.ForeignKey(
|
||||
Contrast,
|
||||
help_text="MRI / CT contrast",
|
||||
related_name="series_contrast",
|
||||
on_delete=models.SET_NULL,
|
||||
null=True,
|
||||
blank=True,
|
||||
)
|
||||
description = models.TextField(
|
||||
blank=True,
|
||||
help_text="Description of stack, for admin organisation, will not be visible when taking",
|
||||
)
|
||||
|
||||
author = models.ManyToManyField(
|
||||
settings.AUTH_USER_MODEL,
|
||||
blank=True,
|
||||
related_name="series",
|
||||
)
|
||||
|
||||
open_access = models.BooleanField(
|
||||
help_text="If a question should be freely available to browse", default=True
|
||||
)
|
||||
|
||||
|
||||
def __str__(self):
|
||||
if self.atlas:
|
||||
atlas_id = ", ".format([atlas.pk for atlas in self.atlas.all()])
|
||||
#atlas_id = self.atlas.pk
|
||||
else:
|
||||
atlas_id = "None"
|
||||
return "{}/{} : {} [{}]".format(self.pk,
|
||||
self.get_examination(), self.description, atlas_id
|
||||
)
|
||||
|
||||
def get_author_objects(self):
|
||||
"""Returns a comma seperated text list of authors"""
|
||||
if self.author:
|
||||
return self.author.all()
|
||||
else:
|
||||
return ["None"]
|
||||
if self.atlas:
|
||||
authors = [i for i in self.atlas.author.all()]
|
||||
else:
|
||||
authors = []
|
||||
|
||||
return authors
|
||||
|
||||
def get_author_display(self):
|
||||
return ", ".join([i.username for i in self.get_author_objects()])
|
||||
|
||||
def get_examination(self):
|
||||
"""Returns a comma seperated text list of regions"""
|
||||
return str(self.examination)
|
||||
|
||||
def get_examination_full(self):
|
||||
examination = ""
|
||||
plane = ""
|
||||
contrast = ""
|
||||
|
||||
if self.examination:
|
||||
examination = self.examination
|
||||
if self.plane:
|
||||
plane = " {}".format(self.plane)
|
||||
if self.contrast:
|
||||
contrast = " {}".format(self.contrast)
|
||||
return "{}{}{}".format(examination, plane, contrast)
|
||||
|
||||
def get_absolute_url(self):
|
||||
return reverse("atlas:series_detail", kwargs={"pk": self.pk})
|
||||
|
||||
def get_image_urls(self, findings=False):
|
||||
images = [
|
||||
"https://www.penracourses.org.uk{}".format(i.image.url)
|
||||
for i in self.images.all()
|
||||
]
|
||||
|
||||
return ",".join(images)
|
||||
|
||||
def get_image_url_array(self, findings=False):
|
||||
images = [
|
||||
"https://www.penracourses.org.uk{}".format(i.image.url)
|
||||
for i in self.images.all()
|
||||
]
|
||||
|
||||
return json.dumps(images)
|
||||
|
||||
def get_thumbnail(self):
|
||||
images = self.images.all()
|
||||
|
||||
if len(images) < 1:
|
||||
return "No images", 0
|
||||
|
||||
img = findMiddle(images).image
|
||||
try:
|
||||
thumbnailer = get_thumbnailer(img)
|
||||
thumbnail = thumbnailer["exam-list"]
|
||||
except InvalidImageFormatError:
|
||||
return format_html('<span title="{}">Invalid image url<span>', img), len(images)
|
||||
return format_html('<img src="/media/{}" />', thumbnail), len(images)
|
||||
|
||||
def get_block(self):
|
||||
examination = self.get_examination_full()
|
||||
thumb, image_number = self.get_thumbnail()
|
||||
return format_html(
|
||||
"<div>{}<br/>{}<br/>Images: {}</div>", examination, thumb, image_number
|
||||
)
|
||||
|
||||
def order_by_upload_filename(self):
|
||||
images = self.images.all()
|
||||
|
||||
filenames = []
|
||||
map = {}
|
||||
|
||||
for i in images:
|
||||
filenames.append(i.upload_filename)
|
||||
map[i.upload_filename] = i
|
||||
|
||||
filenames = sorted(filenames)
|
||||
|
||||
n = 1
|
||||
for f in filenames:
|
||||
i = map[f]
|
||||
i.position = n
|
||||
i.save()
|
||||
n = n + 1
|
||||
|
||||
|
||||
|
||||
def order_by_dicom(self, field="SliceLocation"):
|
||||
images = self.images.all()
|
||||
|
||||
files = []
|
||||
|
||||
for i in images:
|
||||
files.append((i, pydicom.dcmread(i.image.path)))
|
||||
|
||||
#print("file count: {}".format(len(files)))
|
||||
|
||||
# skip files with no SliceLocation (eg scout views)
|
||||
slices = []
|
||||
map = {}
|
||||
skipcount = 0
|
||||
for i, f in files:
|
||||
if hasattr(f, field):
|
||||
slices.append(f)
|
||||
#map[f.SliceLocation] = i
|
||||
map[f[field].value] = i
|
||||
else:
|
||||
skipcount = skipcount + 1
|
||||
|
||||
print("skipped, no {}: {}".format(field, skipcount))
|
||||
|
||||
# ensure they are in the correct order
|
||||
slices = sorted(slices, key=lambda s: s[field].value)
|
||||
|
||||
|
||||
#print(slices)
|
||||
n = 1
|
||||
for f in slices:
|
||||
i = map[f[field].value]
|
||||
i.position = n
|
||||
i.save()
|
||||
n = n + 1
|
||||
|
||||
def get_total_image_size(self):
|
||||
images = self.images.all()
|
||||
|
||||
size = 0
|
||||
|
||||
for i in images:
|
||||
size += i.image.size
|
||||
|
||||
return size
|
||||
Reference in New Issue
Block a user