darwinjob / pyramidio-bioformats Goto Github PK
View Code? Open in Web Editor NEWThis project forked from usnistgov/pyramidio
Image pyramid reader and writer enhanced with bio-formats library reader
License: Other
This project forked from usnistgov/pyramidio
Image pyramid reader and writer enhanced with bio-formats library reader
License: Other
related to this stackoverflow issue, you may need to encode the path
https://stackoverflow.com/questions/4992317/illegal-character-in-path-at-index-16
Is it possible to run the DZI converter multithreaded on a single image?
Here:
https://github.com/darwinjob/pyramidio-bioformats/blob/master/pyramidio/src/main/java/gov/nist/isg/pyramidio/tools/ImageResizingHelper.java
This causes a number of issues with non RGB888 input images. Current workaround is -rgb parameter.
The default log level is too verbose
java.net.URISyntaxException: Illegal character in opaque part at index 2
Looks like the Windows style file path.
See the below example, it doesnt load at the highest level only when zoomed in:
https://miosdv.apps-dev.hbp.eu/index.html?bucket=https://tar-svc-test.apps.hbp.eu/fakebucket/?url=https://data-proxy.ebrains.eu/api/v1/buckets/ewb-fc6b509d-8398-437e-a86e-627a41f3ed15?prefix=.nesysWorkflowFiles/zippedPyramids/test_T2star
Please see the below link for the original images:
https://data-proxy.ebrains.eu/ewb-fc6b509d-8398-437e-a86e-627a41f3ed15?prefix=.nesysWorkflowFiles%2ForiginalImages%2Ftest_T2star%2F
The original pyramidio scaling algorithm is (presumably) the source of the several issues:
#2
#1
Can be fixed by either converting the input to RGB888 on a fly or by improving the scaling algorithm in here:
https://github.com/darwinjob/pyramidio-bioformats/blob/master/pyramidio/src/main/java/gov/nist/isg/pyramidio/tools/ImageResizingHelper.java
A set of files having increasing amount of dots inside can show this.
red_v1.png
green_v1.2.png
blue_v1.2.3.png
purple_v1.2.3.4.png
will produce correct folders (.png
extension removed, _files
appended):
red_v1_files
green_v1.2_files
blue_v1.2.3_files
purple_v1.2.3.4_files
but incorrect descriptors:
red_v1.dzi
green_v1.dzi
blue_v1.2.dzi
purple_v1.2.3.dzi
(from usnistgov#13)
TIFF images with these properties:
Format: TIFF (Tagged Image File Format)
Mime type: image/tiff
Class: PseudoClass
Geometry: 15184x10224+0+0
Resolution: 1.55039x1.55039
Print size: 9793.68x6594.48
Units: Undefined
Colorspace: sRGB
Type: Palette
Endianess: MSB
Depth: 8/16-bit
Channel depth:
Red: 1-bit
Green: 16-bit
Blue: 1-bit
produce corrupted pyramids. The lowest pyramid level (no scale) is ok but all the others look like this:
After reconverting with IM -define tiff:tile-geometry=256x256 -type TrueColor -depth 8 -compress LZW:
Format: TIFF (Tagged Image File Format)
Mime type: image/tiff
Class: DirectClass
Geometry: 15184x10224+0+0
Resolution: 1.55039x1.55039
Print size: 9793.68x6594.48
Units: Undefined
Colorspace: sRGB
Type: Palette
Base type: TrueColor
Endianess: LSB
Depth: 8-bit
Channel depth:
Red: 1-bit
Green: 8-bit
Blue: 1-bit
pyramids are ok.
TIFFs with alpha channel aka RGBA are not supported at the moment.
@PolarBean
By default icr is 1 - cache an entire image. It is possible to calculate a suitable icr value based on the heap size and an image width, height and color depth.
Since ome is licensed as GPL https://www.openmicroscopy.org/licensing/, would that necessitate pyramidio-bioformats to also licence under GPL?
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.