penracourses/atlas/models.py

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')

    title = models.CharField(max_length=255, help_text="Title of the case", default="")
    # 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)

    subspecialty = 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="case")

    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="atlas_series_modality", on_delete=models.SET_NULL, null=True
    )
    examination = models.ForeignKey(
        Examination,
        help_text="Name of the examination",
        related_name="atlas_series_examination",
        on_delete=models.SET_NULL,
        null=True,
    )
    plane = models.ForeignKey(
        Plane,
        help_text="Plane of the examination",
        related_name="atlas_series_plane",
        on_delete=models.SET_NULL,
        null=True,
        blank=True,
    )
    contrast = models.ForeignKey(
        Contrast,
        help_text="MRI / CT contrast",
        related_name="atlas_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