Memory layout optimized TIFF reader (WIP) #120
Conversation
| @pytest.mark.parametrize("chunked,max_workers", [(False, 0), (True, 0), (True, 4)]) | ||
| @pytest.mark.parametrize( | ||
| "compressor", | ||
| [tiledb.ZstdFilter(level=0)], |
There was a problem hiding this comment.
What about other compressors?
| from tiledb.cc import WebpInputFormat | ||
|
|
||
|
|
||
| @pytest.mark.parametrize("filename,num_series", [("UTM2GTIF.tiff", 1)]) |
There was a problem hiding this comment.
What about other test files?
| tmp_path, filename, num_series, preserve_axes, chunked, max_workers, compressor | ||
| ): | ||
| if isinstance(compressor, tiledb.WebpFilter) and filename == "UTM2GTIF.tiff": | ||
| pytest.skip(f"WebPFilter cannot be applied to {filename}") |
There was a problem hiding this comment.
Can you comment or document why it cannot be applied?
| def tile_to_tiledb_exp( | ||
| tile: Tuple[Tuple[slice, ...], NDArray[Any]] | ||
| ) -> Tuple[np.ndarray, ...]: | ||
| idx, data = tile | ||
| array_tile = axes_mapper.map_tile(idx) | ||
| out_array[array_tile] = axes_mapper.map_array(data) | ||
|
|
||
| # return a tuple containing the min-max values of the tile | ||
| return np.amin(data, axis=min_max_indices), np.amax( | ||
| data, axis=min_max_indices | ||
| ) |
There was a problem hiding this comment.
Lets move tile_to_tiledb_exp and tile_to_tiledb outside this function to make the code cleaner and modular.
tiledb/bioimg/converters/io.py
Outdated
| keyframe.decode # init TiffPage.decode function under lock | ||
|
|
||
| decodeargs: Dict[str, Any] = {"_fullsize": bool(False)} | ||
| if keyframe.compression in {6, 7, 34892, 33007}: # JPEG |
There was a problem hiding this comment.
Let's create constants instead of magic numbers. I get it that we mirror the internals of tifffile but let's make them more descriptive so we can edit easier in the future.
| "color": ( | ||
| get_rgba(channel["Color"]) | ||
| if "Color" in channel | ||
| else next(color_generator) | ||
| ), |
There was a problem hiding this comment.
For future reference let's update linter versions in standalone PRs. It will make code review easier.
tiledb/bioimg/converters/ome_tiff.py
Outdated
| # Inflate the chunk size to account for copies during transformations, and while decoding | ||
| size = ( | ||
| self.level_dtype(level=level).itemsize | ||
| * 2 |
There was a problem hiding this comment.
Define magic number 2, or comment it.
tiledb/bioimg/converters/ome_zarr.py
Outdated
| @@ -158,6 +158,20 @@ def original_metadata(self) -> Dict[str, Any]: | |||
|
|
|||
| return metadata | |||
|
|
|||
| def iter_mem_contig_tiles( | |||
There was a problem hiding this comment.
Add function docstrings. Explain what are the contiguous tiles for future reference.
XanthosXanthopoulos
force-pushed
the
xan/experimental_tiff_reader
branch
from
20295ee
to
f7d1e13
Compare
No description provided.