Scalebar for Tasks and Slides

[UteSpiske]

The tasks and slides in the student view have now a scalebar that adapt to the zooming level.

Could you review the code for the scalebar implementation and compare the sizes to some examples from OlyVIA ?

[ingridtv]

I will have a look at this PR when #19 is completed (since the commits from that PR are included here)!

[ingridtv]

The suggested change is to move the filter/template tag code to the Slide model as such:

class Slide(models.Model):

    def load_image(self):
        ...
        self.get_scale_factor()

    ...

    def get_scale_factor(self):
        """
        Finds the slide scale (in um/px) from the WSI's metadata.xml file
        """
        try:
            slide_folder = os.path.dirname(self.path)
            path_to_metadata = os.path.join(slide_folder, 'metadata.xml')

            #Parse XML tree
            tree = ET.parse(Path(path_to_metadata))
            root = tree.getroot()

            # Find the scale property
            property_elem = root.find(".//Property[@ID='20007']")
            cdvec2_elem = property_elem.find('CdVec2')
            values = [float(d.text) for d in cdvec2_elem.findall('double')]

            self.scale_factor = values[0]

        except Exception as err:
            raise FileNotFoundError(f"The requested metadata.xml file for {self.path} was not found")

The filter tag will then look something like:

@register.filter
def get_scale(slide):
    return slide.scale_factor  # um/px

[ingridtv]

I have checked against several slides in OlyVIA (and multiple zoom levels) and the scale is correct! I think we got the right piece of information from the metadata file👍

[UteSpiske]

Great that we got the correct value.

I agree that it makes sense to include the value in the slide. Do you want to push the suggested changes ?

[ingridtv]

@UteSpiske Will you please review the latest changes and give feedback and a 👍 if they resolve the issues we have discussed?

[ingridtv]

Seems like things are resolved. Merging this now!