def end_unpacking(self,
path: Path,
unpacked_path: Path,
*args,
format: AbstractFormat = None,
is_collection: bool = False,
**kwargs):
parent = self.get_uf(path)
parent.status = UploadedFile.UNPACKED
parent.update()
if not is_collection:
uf = UploadedFile()
uf.status = UploadedFile.UPLOADED # Better status ?
uf.contentType = format.get_identifier() # TODO
uf.size = unpacked_path.size
uf.filename = str(unpacked_path.relative_to(FILE_ROOT_PATH))
uf.originalFilename = str(format.main_path.name)
uf.ext = ""
uf.storage = parent.storage
uf.user = parent.user
uf.parent = parent.id
uf.imageServer = parent.imageServer
uf.save()
self.path_uf_mapping[str(unpacked_path)] = uf
def cached_tifffile_baseseries(format: AbstractFormat) -> TiffPageSeries:
tf = cached_tifffile(format)
def get_baseseries(tf: TiffFile) -> TiffPageSeries:
idx = np.argmax([np.prod(s.shape) for s in tf.series])
return tf.series[idx]
return format.get_cached('_tf_baseseries', get_baseseries, tf)
def cached_palette_converted_pillow_file(
format: AbstractFormat, pil_format_slug: Optional[str]) -> PILImage:
"""Palette converted pillow image"""
def _open_palette_converted(_format, _pil_format_slug):
image = cached_pillow_file(format, pil_format_slug)
palette = getattr(image, "palette", None)
if palette:
image = image.convert(palette.mode)
return image
return format.get_cached('_pil_palette_converted', _open_palette_converted,
format.path, pil_format_slug)
def cached_pillow_file(format: AbstractFormat,
pil_format_slug: Optional[str]) -> PILImage:
slugs = [pil_format_slug] if pil_format_slug else None
return format.get_cached('_pil', PILImage.open, format.path, formats=slugs)
def cached_omedict(format: AbstractFormat) -> dict:
tf = cached_tifffile(format)
return format.get_cached('_omedict', xml2dict, tf.pages[0].description)
def cached_omexml(format: AbstractFormat) -> OMEXML:
tf = cached_tifffile(format)
return format.get_cached('_omexml', parse_ome, tf.pages[0].description)
def deploy_spatial(self, format: AbstractFormat) -> Image:
"""
Deploy a spatial representation of the image so that it can be used for
efficient spatial requests.
"""
self.notify(ImportEventType.START_SPATIAL_DEPLOY, self.original_path)
if format.need_conversion:
# Do the spatial conversion
try:
ext = format.conversion_format().get_identifier()
spatial_filename = Path(f"{SPATIAL_STEM}.{ext}")
self.spatial_path = self.processed_dir / spatial_filename
self.notify(
ImportEventType.START_CONVERSION,
self.spatial_path, self.upload_path
)
r = format.convert(self.spatial_path)
if not r or not self.spatial_path.exists():
self.notify(
ImportEventType.ERROR_CONVERSION,
self.spatial_path
)
raise FormatConversionProblem()
except Exception as e:
self.notify(
ImportEventType.ERROR_CONVERSION,
self.spatial_path, exception=e
)
raise FormatConversionProblem()
self.notify(ImportEventType.END_CONVERSION, self.spatial_path)
# Check format of converted file
self.notify(ImportEventType.START_FORMAT_DETECTION, self.spatial_path)
spatial_format = SpatialReadableFormatFactory().match(self.spatial_path)
if not spatial_format:
self.notify(ImportEventType.ERROR_NO_FORMAT, self.spatial_path)
raise NoMatchingFormatProblem(self.spatial_path)
self.notify(
ImportEventType.END_FORMAT_DETECTION,
self.spatial_path, spatial_format
)
self.spatial = Image(self.spatial_path, format=spatial_format)
# Check spatial image integrity
self.notify(ImportEventType.START_INTEGRITY_CHECK, self.spatial_path)
errors = self.spatial.check_integrity(check_metadata=True)
if len(errors) > 0:
self.notify(
ImportEventType.ERROR_INTEGRITY_CHECK, self.spatial_path,
integrity_errors=errors
)
raise ImageParsingProblem(self.spatial)
self.notify(ImportEventType.END_INTEGRITY_CHECK, self.spatial)
else:
# Create spatial role
spatial_filename = Path(f"{SPATIAL_STEM}.{format.get_identifier()}")
self.spatial_path = self.processed_dir / spatial_filename
self.mksymlink(self.spatial_path, self.original_path)
self.spatial = Image(self.spatial_path, format=format)
assert self.spatial.has_spatial_role()
self.notify(ImportEventType.END_SPATIAL_DEPLOY, self.spatial)
return self.spatial
def cached_tifffile_baseline(format: AbstractFormat) -> TiffPage:
tf = cached_tifffile(format)
return format.get_cached('_tf_baseline', tf.pages.__getitem__, 0)
def cached_vips_file(format: AbstractFormat) -> VIPSImage:
"""Get cached vips object for the image format."""
return format.get_cached('_vips', VIPSImage.new_from_file, str(format.path))
def end_format_detection(self, path: Path, format: AbstractFormat, *args,
**kwargs):
uf = self.get_uf(path)
uf.contentType = format.get_identifier() # TODO: not the content type
uf.update()