Comments (4)
Hello @OlivierDehaene !
Thank you for your interest in cuCIM!
Compression scheme 33003 is actually JPEG2000 which is used in Aperio SVS format.
cuCIM currently supports tiled RGB TIFF image(Generic TIFF or Philips TIFF) with JPEG or Deflate compressed and doesn't support SVS format yet.
However, we have a plan to support it in the near future.
The tentative plan is specified in the following link (I would move the content to Github wiki page later):
https://github.com/rapidsai/cucim/blob/branch-0.20/python/cucim/docs/roadmap/index.md#facalendar-alttext-info-mr-1-v020
If cuCIM encounters TIFF (SVS is a variant of TIFF format) file that is not JPEG/Deflate compressed RGB format, it just delegates its process to libtiff's TIFFRGBAImageGet() method and it seems that warning/error are not properly handled.
Let me fix the issue by raising an error until cuCIM supports SVS format properly.
(I am currently working on providing a cache mechanism to cuCIM so that the performance could be greatly improved)
Thank you for the report! We are also eager to support various image formats so stay tuned!
from cucim.
Thank you for your answer @gigony!
However, we have a plan to support it in the near future.
Amazing! I have been looking for a better alternative to OpenSlide for a while now and if cuCIM starts to support Aperio that would be great :)
I am currently working on providing a cache mechanism to cuCIM so that the performance could be greatly improved
Will we be able to disable the cache when doing random tile reads? We generally disable the OpenSlide one when training.
from cucim.
Will we be able to disable the cache when doing random tile reads? We generally disable the OpenSlide one when training.
I thought cuCIM can allocate some memory for cache by default and the user can increase the cache size programmatically. I assumed it wouldn't be a problem if we use a cache memory per 'parent process' and cache memory is shared among subprocesses (whereas OpenSlide seems to allocate cache memory per file).
However, you're right. It is better to have an option to disable cache at all as cache wouldn't much help when reading random partial images from a huge image pool during training.
Now I am thinking of allocating cache memory only when requested :)
Thank you so much for your valuable feedback!
from cucim.
Some packages should be pushed to rapidsai-nightly
soon with Gigon's fix. Also this should show up in the next release. Please let us know if you run into any more issues 🙂
from cucim.
Related Issues (20)
- Can't install cucim from pip or conda
- [FEA] Improve performance of existing `equalize_adapthist` function (CLAHE)
- [QST] Is there a plan to add support for Jetson platforms (aarch64) or is it possible to build a Wheel ? HOT 2
- [BUG] Wrong Spacing for Aperio SVS HOT 2
- [FEA] add graycomatrix and graycoprops in skimage.feature HOT 3
- [QST] conda compatibility with scikit-image 0.20.0 HOT 2
- [BUG] CUDA_ERROR_ILLEGAL_ADDRESS with `morphology.isotropic_closing` HOT 2
- [FEA] Migrate `jpeg` to `libjpeg-turbo` HOT 3
- [QST] Installing cucim with pip under python in SideFX Houdini HOT 5
- [QST]About the Macenko implementation in the blog HOT 2
- [DOC] Clara Read Region Documentations
- Drop workarounds for scikit-image pre-0.19.0
- Drop `CUDA` info line
- Dynamically link (or `dlopen`) `libnvjpeg`
- Refactoring common `aarch64` & `x86_64` items in `dependencies.yaml` HOT 6
- Disable cuFile / GDS on SBSA ( `aarch64` ) HOT 1
- [BUG] 'free(): corrupted unsorted chunks' OR 'corrupted double-linked list' fatal errors OR segmentation fault HOT 1
- Flaky test: `test_read_region_cuda_memleak` HOT 1
- [BUG] Memory leak in read_region in generator mode (using a list of locations) HOT 2
- [cuCIM] CUDA 12 Conda Packages for ARM
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from cucim.