SCientific Image Format Input & Output: a flexible, extensible framework for image I/O. *EXPERIMENTAL* All API is subject to change, so depend at your own risk! See also @openmicroscopy/bioformats.
The FLIMJ project needs the physical calibration of the LIFETIME dimension to display a properly calibrated decay plot. We need to know if, e.g., the values range from 0 to 10 ns, or 0 to 12.5 ns, or something else. Regardless of the number of actual time bins along that dimension.
Thanks for the explanation. Yes,
CalibratedAxis is what I used to extract scales from other formats such as SDT. The ICS in question does have a parameter scale tag with 3 1.000000s, which are currently (supposedly) interpreted as the physical separation between pixels/layers. Though they are not because of a potential bug in the line reading stage, which causes this key not to be recognized and the default value of all 1.0's are used. I can supply more details if you are interested.
Although
parameter scale is meant to be the default place to define the physical sizes in the original paper, page 9, I see Bio-Formats uses history extent (overall dimensions of the dataset) to infer the physical pixel sizes if parameter scale is not present.
if (scales != null) {
// ...
for (int i = 0; i < scales.length; i++) {
Double scale = scales[i];
// ...
if (axis.equals("x")) {
if (checkUnit(unit, "um", "microns", "micrometers")) {
Length x = FormatTools.getPhysicalSizeX(scale);
if (x != null) {
store.setPixelsPhysicalSizeX(x, 0);
}
}
}
// process y and z axis in the same way
// ...
else if (axis.equals("t") && scale != null) {
if (checkUnit(unit, "ms")) {
store.setPixelsTimeIncrement(new Time(scale, UNITS.MILLISECOND), 0);
} else if (checkUnit(unit, "seconds") || checkUnit(unit, "s")) {
store.setPixelsTimeIncrement(new Time(scale, UNITS.SECOND), 0);
}
}
}
} else if (sizes != null) {
if (sizes.length > 0) {
Length x = FormatTools.getPhysicalSizeX(sizes[0]);
if (x != null) {
store.setPixelsPhysicalSizeX(x, 0);
}
}
if (sizes.length > 1) {
// process y axis
}
}scales are parsed from parameter scale and sizes are parsed from history extents.
@ctrueden @hinerm Sure, you may download the file from here. As for
ICSFormat, do you think we should use history extents and parameter scale interchangeably?
@hinerm That will do. But what about units? This ICS uses scale
1 and unit undefined for each axis and puts calibration in history extents, which has no units attached. BioFormats and the current SCIFIO assumes the default units (seconds, um, etc.) in this case.
Better suggestions?
@hinerm I went ahead and reviewed + merged #428. The mega melt is likely to identify any downstream issues with it, but I expect nothing bad will happen. (Obligatory parenthetical note about how now something bad will happen because I said that, but because I include this fourth-wall-breaking note maybe we'll be spared the wrath of the irony gods after all.)
Are there any plans to resurrect the
String and File-based methods in FilePatternService that were present in 0.37.3 but got lost when SCIFIO was changing to DataHandle with https://github.com/scifio/scifio/commit/5c11f00f519fd73ea09be6724e8543a73028d745#diff-09fdb44bddc5a27ef1f3c369ea067e9d ?
Hopefully we'll be out of our limbo state within another 1-2 weeks. I'm technically on vacation now, so no progress from me for the next few days.
Hi all, I'm looking at making the
imagej-server code compatible to pom-scijava 29 and need some advice. It's e.g. calling locationService.mapFilehere from io.scif.services.LocationService which does not exist any more. It maps files to e.g. ByteArrayHandle, another gone class. There does not seem to be a similar feature available in org.scijava.io.location.LocationService so I was wondering where that went / how it could be addressed.
@frauzufall The
LocationService knows how to resolve strings to Location objects using LocationResolver plugins. The DataHandleService knows how to wrap Location objects in DataHandles. (In case it wasn't already clear: a location is just an indicator of data source/destination, whereas a data handle knows how to do random/direct access byte extraction from a location.)
There is no mapping functionality anymore; it's not necessary.
You just make the
Location you want, and then open it (for reading or writing) with the DataHandleService.
For byte arrays, create a
BytesLocation. No need for mapFile or mapId or any of that hacky stuff.
@frauzufall @ctrueden it seems the new
scifio served by the latest update is lacking the FormatService.getFormat(String) method in favor of the DataHandle-based methods. I didn't notice so far, but have a script using that method. I can update my script of course, but I guess we should also bring back that method signature (deprecated) for backwards compatibility, no?
I can also look at it when I find the time later this week.
Hi there. I'm trying to write a unit test to help get to the bottom of: scifio/scifio#399
I can reproduce the originally described issue using a publicly available 3.5Mb image. I can also show the 'hanging' issue that Manuel describes at the bottom of the ticket (when using scifio 0.4.0 or 0.4.1). I spent a bit of time trying to use the image generation (fake) images to reproduce the issue, but I'm not familiar with the API yet, so got a bit stuck. So... would it be OK to submit a unit test using the 'real' image, or could someone point me to some documentation or an example for creating a composite channel example image?
I can reproduce the originally described issue using a publicly available 3.5Mb image. I can also show the 'hanging' issue that Manuel describes at the bottom of the ticket (when using scifio 0.4.0 or 0.4.1). I spent a bit of time trying to use the image generation (fake) images to reproduce the issue, but I'm not familiar with the API yet, so got a bit stuck. So... would it be OK to submit a unit test using the 'real' image, or could someone point me to some documentation or an example for creating a composite channel example image?
If you make a working illustration, we can look into: A) changing it to use a testimg instead if possible; and failing that B) if Manuel is OK with releasing the image into the public domain, adding it to the https://scif.io/images collection, which we use for unit tests already.
The unit tests download and cache the images locally, so that it's only slow to run them the first time.
Fantastic. Thanks for the quick response. The image in question is already published here under Creative Commons Attribution 4.0 International License, so I guess it is easily possible to add that the scif.io/images (is that something I can do myself?)
I will prepare a PR with the unit test today.
I will prepare a PR with the unit test today.
@jfkotw You can do most of it yourself: edits need to happen to this index.html file including adding an appropriately sized thumbnail to that
images folder. The data itself is served from samples.scif.io which is not hosted on GitHub Pages, because some of the samples are too large for GitHub. I can put the image in place in response to your PR. Coincidentally, I'm working on the SCIFIO samples page today anyway, adding some FLIM image data. I will also look into adding a "License" column to clarify the license of each image, since it will no longer be CC0/PD for everything anymore.
Still trying to fix
imagej-server - with the new Location API, how does one handle an InputStream? I can't figure out a way to wrap it with a Location, which I would need to call datasetIOService.open(..). Differently formulated - how to use SCIFIO to open an image from an InputStream?
Or is it
imagej-server using IOService (that only forwards to DatasetIOService in case of images)?