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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,121 +1,38 @@ | ||
| import logging | ||
| import os | ||
| import openslide | ||
| from openslide import OpenSlide, OpenSlideError | ||
| from openslide.deepzoom import DeepZoomGenerator | ||
| from cStringIO import StringIO | ||
| from PIL import Image | ||
|
|
||
| from ome_seadragon import settings | ||
| from ome_seadragon.images_cache import CacheDriverFactory | ||
|
|
||
|
|
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| logger = logging.getLogger(__name__) | ||
|
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||
|
|
||
| def _get_image_path(image_id, conn): | ||
| img = conn.getObject("Image", image_id) | ||
| if img is None: | ||
| return None | ||
| else: | ||
| return os.path.join(settings.IMGS_REPOSITORY, settings.IMGS_FOLDER, | ||
| img.getImportedImageFilePaths()['server_paths'][0]) | ||
|
|
||
| class UnknownRenderingEngine(Exception): | ||
| pass | ||
|
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| def _get_deepzoom_slide_config(): | ||
| return { | ||
| 'tile_size': settings.DEEPZOOM_TILE_SIZE, | ||
| 'overlap': settings.DEEPZOOM_OVERLAP, | ||
| 'limit_bounds': settings.DEEPZOOM_LIMIT_BOUNDS | ||
| } | ||
|
|
||
| class RenderingEngineFactory(object): | ||
|
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| def _get_slide(image_path): | ||
| oslide_ref = OpenSlide(image_path) | ||
| slide = DeepZoomGenerator(oslide_ref, **_get_deepzoom_slide_config()) | ||
| try: | ||
| mpp_x = oslide_ref.properties[openslide.PROPERTY_NAME_MPP_X] | ||
| mpp_y = oslide_ref.properties[openslide.PROPERTY_NAME_MPP_Y] | ||
| slide.mpp = (float(mpp_x) + float(mpp_y)) / 2 | ||
| except (KeyError, ValueError): | ||
| slide.mpp = 0 | ||
| return slide | ||
| def __init__(self): | ||
| self.tiles_rendering_engine = settings.TILES_RENDERING_ENGINE | ||
| self.thumbnails_rendering_engine = settings.THUMBNAILS_RENDERING_ENGINE | ||
|
|
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| def _get_openslide_engine(self, image_id, connection): | ||
| from openslide_engine import OpenSlideEngine | ||
|
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| def get_deepzoom_metadata(image_id, conn): | ||
| image_path = _get_image_path(image_id, conn) | ||
| if image_path: | ||
| slide = _get_slide(image_path) | ||
| return slide, settings.DEEPZOOM_FORMAT | ||
| else: | ||
| return None, settings.DEEPZOOM_FORMAT | ||
| return OpenSlideEngine(image_id, connection) | ||
|
|
||
| def _get_omero_engine(self, image_id, connection): | ||
| from ome_engine import OmeEngine | ||
|
|
||
| def get_image_mpp(image_id, conn): | ||
| image_path = _get_image_path(image_id, conn) | ||
| if image_path: | ||
| slide = OpenSlide(image_path) | ||
| try: | ||
| mpp_x = slide.properties[openslide.PROPERTY_NAME_MPP_X] | ||
| mpp_y = slide.properties[openslide.PROPERTY_NAME_MPP_Y] | ||
| return (float(mpp_x) + float(mpp_y)) / 2 | ||
| except (KeyError, ValueError): | ||
| return 0 | ||
| return OmeEngine(image_id, connection) | ||
|
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||
|
|
||
| def get_thumbnail(image_id, width, height, conn): | ||
| cache_factory = CacheDriverFactory() | ||
| cache = cache_factory.get_cache() | ||
| # get thumbnail from cache | ||
| thumbnail = cache.thumbnail_from_cache(image_id, width, height, | ||
| settings.DEEPZOOM_FORMAT) | ||
| # if thumbnail is not in cache build it... | ||
| if thumbnail is None: | ||
| logger.info('No item loaded from cache, building it') | ||
| image_path = _get_image_path(image_id, conn) | ||
| if image_path: | ||
| slide = OpenSlide(image_path) | ||
| thumbnail = slide.get_thumbnail((width, height)) | ||
| # ... and store it to cache | ||
| cache.thumbnail_to_cache(image_id, thumbnail, width, height, | ||
| settings.DEEPZOOM_FORMAT) | ||
| def get_tiles_rendering_engine(self, image_id, connection): | ||
| if self.tiles_rendering_engine == 'openslide': | ||
| return self._get_openslide_engine(image_id, connection) | ||
| if self.tiles_rendering_engine == 'omero': | ||
| return self._get_omero_engine(image_id, connection) | ||
| else: | ||
| thumbnail = None | ||
| else: | ||
| logger.info('Thumbnail loaded from cache') | ||
| return thumbnail, settings.DEEPZOOM_FORMAT | ||
|
|
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| raise UnknownRenderingEngine('%s is not a valid rendering engine' % self.tiles_rendering_engine) | ||
|
|
||
| def get_tile(image_id, level, column, row, conn): | ||
| cache_factory = CacheDriverFactory() | ||
| cache = cache_factory.get_cache() | ||
| # configure cache callback | ||
| cache_callback_params = { | ||
| 'image_id': image_id, | ||
| 'level': level, | ||
| 'column': column, | ||
| 'row': row, | ||
| 'tile_size': settings.DEEPZOOM_TILE_SIZE, | ||
| 'image_format': settings.DEEPZOOM_FORMAT | ||
| } | ||
| if settings.DEEPZOOM_FORMAT.lower() == 'jpeg': | ||
| cache_callback_params['image_quality'] = settings.DEEPZOOM_JPEG_QUALITY | ||
| image = cache.tile_from_cache(**cache_callback_params) | ||
| # if tile is not in cache build it... | ||
| if image is None: | ||
| image_path = _get_image_path(image_id, conn) | ||
| if image_path: | ||
| slide = _get_slide(image_path) | ||
| tile = slide.get_tile(level, (column, row)) | ||
| img_buffer = StringIO() | ||
| tile_conf = { | ||
| 'format': settings.DEEPZOOM_FORMAT | ||
| } | ||
| if settings.DEEPZOOM_FORMAT == 'jpeg': | ||
| tile_conf['quality'] = settings.DEEPZOOM_JPEG_QUALITY | ||
| tile.save(img_buffer, **tile_conf) | ||
| image = Image.open(img_buffer) | ||
| # ... and store it to cache | ||
| cache_callback_params['image_obj'] = image | ||
| cache.tile_to_cache(**cache_callback_params) | ||
| return image, settings.DEEPZOOM_FORMAT | ||
| def get_thumbnails_rendering_engine(self, image_id, connection): | ||
| if self.thumbnails_rendering_engine == 'openslide': | ||
| return self._get_openslide_engine(image_id, connection) | ||
| if self.thumbnails_rendering_engine == 'omero': | ||
| return self._get_omero_engine(image_id, connection) | ||
| else: | ||
| raise UnknownRenderingEngine('%s is not a valid rendering engine' % self.thumbnails_rendering_engine) |
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