Metadata in scifio

scifio
Tags: #<Tag:0x00007fb87d34a548>

#1

Dear all,

I need to make use of specific metadata from my https://github.com/jufiba/scifio-UView plugin, mostly sample temperature, acquisition time, and start voltage.
I know how to set metadata properties in the plugin and I can already read the items from the files. I also set up de EM_DOMAIN in the plugin (which is not exact as that refers -I guess- to TEM, but is close enough, my data is LEEM data).

But when I check under Fiji with the “Image->Show Info”, I see only:

SCIFIO version: 0.27.1
File format: UKSOFT2000/UView
— Dataset Information —
BitsPerPixel = 16
PixelType = 3
Dataset name = /home/juan/soft/UView_test_files/003_img.dat
Image 0 Information
Dimension order = X,Y
Dimension lengths = 1024,1024
— Global Metadata —
— Image Metadata —


So maybe I am completely misunderstanding the metadata usage. How should I write metadata that I can access from the rest of Fiji? (and how should I access it?) And what is the effect of selecting a domain (EM_DOMAIN, SEM_DOMAIN, etc)?

Thanks in advance,
Juan


#2

HI to all,

I did some more tests. The plugin is now available as an update site, (with a couple of plugins I wrote for 3D low-energy electron microscopy I needed which I also put in github.

I also have a test file.
So I load the image with scifio-UView, and it properly finds the extra info, which is dutifully dumped with log().info:

[INFO] More info (v>7): camerabitsperpixel 14 MCPDiam 0 binning 0x0
[INFO] UView Plugin UKFileHeader info
size 104
version 8
bitsperpixel 16
witdth 1024
height 1024
nimages 1
[INFO] 09/16/2015 15:40:15 +0200
[INFO] markup 128
[INFO] UView Plugin UKImageHeader info
size 288
version 5
ColorLow 83
ColorHigh 2547
time 130868844157320000
maskx 0
masky 0
spin 0
leemdataversion 2 attachedmarkedsize 0
[INFO] Size of headers: Fileheader 104 recipesize 0 Imageheader 288 Markup 128
[INFO] total offset: 520
[INFO] teoretical offset: 392
[INFO] UView Plugin LEEMDATA info

[INFO] FOV calibration 20�m* 1.0
[INFO] Module 38 Start Voltage1 1.4990042
[INFO] micrometerxy 2.7063,0.4392
[INFO] Module 11 Objective2 1898.0345
[INFO] Module 39 Sample Temp.4 32.11447
[INFO] Module 66 Azimuth rot.0 360.0
[INFO] End of LEEMData 255 95

I have added code to add, for example, the micrometerx and micrometery info as metadata. However, as before there is no sign of it when showing the info of the image :confused: :

SCIFIO version: 0.29.0
File format: UKSOFT2000/UView
— Dataset Information —
BitsPerPixel = 16
PixelType = 3
Dataset name = /home/juan/soft/workspace/scifio-UView/test.dat
Image 0 Information
Dimension order = X,Y
Dimension lengths = 1024,1024
— Global Metadata —
— Image Metadata —


(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51h; Java 1.8.0_101 [64-bit]; Linux 4.4.0-47-generic; 81MB of 8888MB (<1%)

Title: test.dat
Width: 1024 pixels
Height: 1024 pixels
Size: 2MB
Pixel size: 1x1 pixel^2
ID: -2
Bits per pixel: 16 (unsigned)
Display range: 0 - 65535
No threshold
Magnification: 0.50
Uncalibrated
Path: /home/juan/soft/workspace/scifio-UView/test.dat
Screen location: 12,146 (1600x900)
No overlay
No selection

So, what I am missing? I would like to clean up the plugin to properly populate the metadata and remove of the log().info…

Best,
Juan