def it_can_show_its_thumbnail(self, tmpdir):
tmp_path_ = tmpdir.mkdir("myslide")
image = PILIMG.RGBA_COLOR_500X500_155_249_240
image.save(os.path.join(tmp_path_, "mywsi.png"), "PNG")
slide_path = os.path.join(tmp_path_, "mywsi.png")
slide = Slide(slide_path, "processed")
slide.save_thumbnail()
assert ImageShow.show(PIL.Image.open(slide.thumbnail_path))
def it_can_save_thumbnail(self, tmpdir, resampled_dims_):
tmp_path_ = tmpdir.mkdir("myslide")
image = PILIMG.RGBA_COLOR_500X500_155_249_240
image.save(os.path.join(tmp_path_, "mywsi.png"), "PNG")
slide_path = os.path.join(tmp_path_, "mywsi.png")
slide = Slide(slide_path, os.path.join(tmp_path_, "processed"))
resampled_dims_.return_value = (100, 200, 300, 400)
slide.save_thumbnail()
assert slide.thumbnail_path == os.path.join(tmp_path_, "processed",
"thumbnails", "mywsi.png")
assert os.path.exists(os.path.join(tmp_path_, slide.thumbnail_path))
# Methods and properties of openslide object
# pprint(pdx_slide._wsi.properties._keys()) # all properties
mag = int(pdx_slide._wsi.properties['aperio.AppMag'])
print(f"Level count: {pdx_slide._wsi.level_count}")
print(f"Level downsamples: {pdx_slide._wsi.level_downsamples}")
print(f"Level dimensions: {pdx_slide._wsi.level_dimensions}")
# Thumbnail
print('thumbnail_size: ', pdx_slide._thumbnail_size
) # thumbnail size proportionally to the slide dimensions
print('biggest_tissue_box_mask:', pdx_slide.biggest_tissue_box_mask.shape
) # thumbnail binary mask of the box containing the max tissue area
print('thumbnail_path: ', pdx_slide.thumbnail_path)
pdx_slide.save_thumbnail()
# Inside the save_thumbnail
pil_img = pdx_slide._wsi.get_thumbnail(pdx_slide._thumbnail_size)
print(type(pil_img))
print(pil_img.size)
# pil_img.show() # why this doesn't work??
# plt.imshow(pil_img); plt.axis('off');
pil_img.save(tmp_outpath / 'pil_img.png', format='png')
# Apply mask to image
pil_img_boxed = histolab.util.apply_mask_image(
pil_img, pdx_slide.biggest_tissue_box_mask)
pil_img_boxed.save(tmp_outpath / 'pil_img_boxed.png', format='png')
# Scale and save image
