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Hi Glen. Thanks for your work on this macro, I've been using it for some months now and it works great. I'm now trying to get it installed on a colleagues' computer, and we're running into issues. When importing the FLIR JPEG via the ThermImageJ macro, the following pops up, and the image isn't loaded in. It does this after displaying the 'Verify Camera and Object Parameters' window.

I've tried to run the Byte Swapper plugin via the dropdown 'Plugins' menu and it won't let me do so.

Let me know if you have any thoughts here. Thanks!

Hi,

First of all, thank you for creating this amazing tool.

I have installed everything and it looks alright. I am taking pictures with a Flir Lepton Application and a Flir Lepton 3 160HX120V with the PureThermal board. I export them as JPGs or Raw TIFFs.

Lepton_Capture_TIFF.zip

When I import them in Fiji I get the following error:

luts (g) array[54]
lCmds (g) array[54]
palettetypes (g) array[11]
defaultpalette (g) "Grays"
thermlCmds (g) array[11]
ImportCmds (g) array[8]
lut (g) -1
lutdir (g) "C:\Users\ADMINI1\DOCUME1\Fiji.app\luts"
list (g) 0
color (g) 0
colors (g) array[6]
PR1 (g) 17998.5290
PR2 (g) 0.0151
PB (g) 1453.1000
PF (g) 1
PO (g) -5854
ATA1 (g) 0.0066
ATA2 (g) 0.0126
ATB1 (g) -0.0023
ATB2 (g) -0.0067
ATX (g) 1.9000
E (g) 0.9500
OD (g) 1
RTemp (g) 20
ATemp (g) 20
IRWTemp (g) 20
IRT (g) 1
RH (g) 50
imagewidth (g) 640
imageheight (g) 480
magicbyte (g) "02008002e001"
frameinterval (g) 0.0333
imagetemperaturemin (g) -20
imagetemperaturemax (g) 60
perlscriptpath (g) "C:\Users\ADMINI1\DOCUME1\Fiji.app\scripts"
desktopdir (g) "C:\Users\Administrator\Desktop"
perlsplit (g) "C:\Users\ADMINI1\DOCUME1\Fiji.app\scripts\split.pl"
OS (g) "Windows 10"
perlpathOSX (g) "/usr/bin/"
exiftoolpathOSX (g) "/usr/local/bin/"
exiftoolOSX (g) "exiftool"
ffmpegpathOSX (g) "/usr/local/bin/"
perlpathLinux (g) "/usr/bin/"
exiftoolpathLinux (g) "/usr/bin/"
exiftoolLinux (g) "exiftool"
ffmpegpathLinux (g) "/usr/bin/"
perlpathWindows (g) "c:/Perl64/bin/"
exiftoolpathWindows (g) "c:/Program Files/ExifTool/"
exiftoolWindows (g) "exiftool.exe"
ffmpegpathWindows (g) "c:/FFmpeg/bin/"
cmd "Import FLIR JPG"
perlpath "c:/Perl64/bin/"
exiftoolpath "c:/Program Files/ExifTool/"
exiftool "exiftool.exe"
ffmpegpath "c:/FFmpeg/bin/"
filepath * "C:\Users\Administrator\Pictures\LeptonCaptures\Lepton_Capture.jpeg"
flirvals array[19]
printvalues "No"
printvalues "No"
filepath * "C:\Users\Administrator\Pictures\LeptonCaptures\Lepton_Capture.jpeg"
perlpath "c:/Perl64/bin/"
exiftoolpath "c:/Program Files/ExifTool/"
exiftool "exiftool.exe"
ffmpegpath "c:/FFmpeg/bin/"
flirvals "Image Height : 120 | Image Width : 160 | File..."

Error: Index (-1) is outside of the 0-255 range in line 2262:
(called from line 769)
(called from line 2739)

	PR1 = parseFloat ( substring ( flirvals , indexOf ( flirvals , ":" , indexOf ( flirvals , "Planck R1" ) <)> + 1 , index...

I am a bit lost. Am I doing something wrong or is there another issue I am not aware of?

I'm new to much of this, so apologies if I'm missing something simple. I've just gone through the install instructions, and am now trying to load a thermal image from my FLIR camera into ImageJ using ThermImageJ. When I try to "Import FLIR JPG" I get the following macro error. This occurs with my FLIR photos, as well as the two sample jpgs provided with ThermImageJ-master.

Debug.csv

Any thoughts? Thanks in advance!!

Describe the bug
After running the Import SEQ macro on Windows 10 x64, an error occurs.

To Reproduce
Steps to reproduce the behavior:

1. Import an SEQ using the macro
2. See error

Expected behavior
Expected the resulting avi to appear within ImageJ for manipulation

Screenshots

Desktop (please complete the following information):

• OS: Windows 10

Hello,

I hope its ok to ask here. I have been trying to find a way how to use it for my data analysis but I can't seem to understand how to find a temperature values of specific places in the image?
What I ideally would like is to select multiple ROI in the thermal image and receive the values as temperature values. Is it possible to do with this plug in please?
I have followed your instructions on the website and everything seems to work, I do get the FLIR calibration values out of my images. But what would be the steps to get the temperature values on the specific parts of the image please?
I would really appreciate if you could please advise me on how to do it please.

Thank you so much !!

Describe the bug
While running ConvertFLIRJPG function with FLIR jpgs (even the sample files) I encounter 2 different problems

1. I get a Macro Error
   

If i then restart image J, the script runs fine as indicated by the log

but the resulting image in the coverted folder has 0 byte

Desktop (please complete the following information):

• OS: Windows 10
• Browser Chrome

Describe the bug
When I try to open a .csq file I get the following error message:
"Error:
Index (0) out of 0--1 range in line 1360:
print ( perl + perlsplit + "-i " + tempfolder + File . separator + fff_files [ 0 <]> + " -o " + filedir + File . separa..."

To Reproduce
Steps to reproduce the behavior:

1. FILE>IMPORT FLIR CSQ
2. select file
3. log window output:
   ------ Running ConvertFLIRVideo function ------
   Loading: /Users/me/data_analysis/thermal_analysis/data/test_file.csq
   Extracting calibration and image settings

------ Running flirvalues function ------
Extracted Camera Calibration and Object Parameters:
13631.7040, 1369.7000, 1, -3833, 0.0105, 0, 0, 0.0032, 0.0032, 0.7320, 0.9500, 1, 20, 20, 20, 1, 50, 464, 348

Splitting the video file into its .fff files with:
/usr/bin/perl /Users/me/data_analysis/thermal_analysis/scripts/split.pl -i /Users/me/data_analysis/thermal_analysis/data/test_file.csq -o /Users/me/data_analysis/thermal_analysis/data/temp -b frame -p fff -x fff
Splitting fff files into jpegls files by looping through all files similar to:

4. See error

Expected behavior
Opening the file

Desktop (please complete the following information):

• MacOS Catalina 10.15.3
• perl v5.18.4 built for darwin-thread-multi-2level

Hello Glenn,
thanks a lot that you took the time to add the "Import FLIR JPG with defaults" with ThermimageJ-2.6. Being a bit lazy, I realized this not before yesterday.
However, I found that it works nicely with FLIR tiff files but it fails to perform the "byte swap" for png files. As a workaround I added the following lines in your code (after line 1191):

if(RawThermalType == "PNG" && ConvertWithDefault == "yes"){
run("Byte Swapper");
}

I tested it with the sample files that are included in "ThermImageJ-2.6" and my image files. Both the normal import (with parameter dialog) and the new import with defaults seem to work but probably it can be done more elegant.

Best, Klaus

The .jpg files have both optical and thermal images in them; I can use the flir tools to see them both.

is there any way to import both images and be able to overlay one or is this outside of what ImageJ and/or ThermImageJ could do?

Hi there. I am currently trying to use your ThermImageJ plugin to import a thermal image and have been recieving this error -- --

"Warning -- Raw Thermal Type Unknown. This file might not be a radiometric JPG.
Setting Raw Thermal Type to tiff and attempting conversion. If resulting file is 0 bytes, the jpg cannot be converted.
Examine the settings on your camera to ensure radiometric jpgs are being saved.
Raw Thermal Type: tiff
Converting 02 C1.jpg to 02C1.tif

FLIR JPG files converted into tiff format. Import these and convert to temperature using the Raw2Temp macro.

Use the File->Import->Image Sequence function to load in images
Some images may require that the pixel byte order be swapped. Use the Byte Swapper plugin after importing if necessaary
Done"

How can I check to see if the image is a radiometric JPG and furthermore if it is what is causing the issue?
Thank you.

Hello and thank you for creating this useful package.

I am attempting to use Thermimage and ThermimageJ in Windows to analyze the internal temperature of cranberries. The Thermimage package worked great in R and I was able to export a CSVs of the image temperature values and accompanying jpegs.

I would like to measure an average temperature read for each berry and planned to use ThermimageJ for this. I successfully installed ThermimageJ, and all accompanying software and converted my files to raw format using your code provided. However, I am having trouble importing the raw files using the File>Import>Raw path. Below are examples of my original FLIR jpeg and the raw file I imported into ImageJ:

Original:

Raw file imported into ImageJ:

To investigate further, I tried importing one of your sample raw images and the same thing happened:

I have not changed anything in the ThermimageJ macro code yet. Any idea what the issue might be?

Thanks,

-Lindsay

Describe the bug
When trying to import a Flir mp4 file using "import Flir sequence" I get an error message:
Error:
Index (-1) is outside of the 0-655 range in line 1830:
PR1 = parseFloat ( substring ( flirvals , indexOf ( flirvals , ":" , indexOf ( flirvals , "Planck R1" ) <)> + 1 , index...

It is perhaps not the right way to open the file?

To Reproduce
Steps to reproduce the behavior:

1. Go to 'File'
2. Click on 'import FLIR SEQ'
3. Select mp4 file
4. See error

Expected behavior
Opening the mp4 file containing a video acquired with a Flir T840

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: MacOS Catalina 10.15.3

Additional context
Add any other context about the problem here.