Hello, is there a way to execute the iad command with N r and N t without going through an rxt file like:
IAD -B 8.1 -S 1 -1 "60.0 16.9 12.4 9.0 97.1" -2 "60.0 16.9 0.0 9.0 97.1" -d 0.5 -d 1.25 -N 0.9998047800454378 -N 1.5048941657272727 -r 0.830258748 -r '17. 44.6352'

Weird (I think) bug where RT_Layers produces 0s if called first. You can test this by e.g. going to ad_layers_test.c and commenting out the first ez_RT. The RT_Layers after that will produce 0s instead of the correct reflectance and transmitance values. Tested with both Clang and GCC.

Dear Prof. Prahl,

Following up on the previous issue and your suggestions, I've tested with the option to constrain reduced scattering with a simple power law parameters. In the output file, the 'estimated mus'' was not consistence with the power law fitted values, also it created non-converged data points. Could you please take a look into this issue! Thank you!

Dear Scott,

a student of mine @Daniil1024 stumbled across this line in the iad code:

It seems that it is supposed to be related to the total sphere area and as such would need an additional factor of 4?

double sphere = 4 * default_sphere_d * default_sphere_d; 

Possibly doesn't matter at all as it is just the initial guess, but it might be more correct this way?

Best wishes,
Janek

Good afternoon. I am trying to execute IAD on a Raspberry Pi 3 Model B+ running Raspbian, I've followed the instructions for installation but whenever I try to run the program it always outputs
"unknown option '�'", followed by a description of the program. I've tried executing the program on multiple files, and tried some of the options presented in the aforementioned description, to no avail.

Here is a copy of my input and the corresponding output. The unknown symbol '�' is displayed in the output, by the way. It is not a formatting error:

pi@raspberrypi:~/Downloads/iad-3-11-1 $ iad test/basic-A.rxt
unknown option '�'
iad 3-11-1 (28 Mar 2019)

iad finds optical properties from measurements

Usage: iad [options] input

Options:
-1 '# # # # #' reflection sphere parameters
-2 '# # # # #' transmission sphere parameters

...and it goes on

Could you please tell me how do I fix this? Thanks in advance.

When attempting to input a negative value of 'g' in the command line input, the negative sign is interpreted as the beginning of a parameter.

Dear Sir/Madam/Mx,
I have found the IAD software to be invaluable to my PhD (in King's College London supervised by Prof Tom Vercauteren) and am very grateful for its availability and documentation! We have found that using the latest versions of the software (versions 3.11.5 onwards) gives odd fits to the measured data in the output files. Examples of this can be found attached and in the MWE_phantom_IAD_version_discrepancy.ipynb here along with some example measurements. When using the dual-beam settings (as is relevant to our set-up) the absorbance and reduced scattering coefficients remain largely the same, however. We would be very grateful for any explanation of this or advice for how to improve these results!
Many thanks,
Anisha Bahl

Specs

OS: Fedora 30

Issue

Running 'make install' in the root directory of the program 'iad/' doesn't work.

Error:

[$USER@toolbox iad] $ make install
cd src ; make ad
make[1]: Entering directory '/var/home/$USER/Git/iad/src'
cc -fno-common -Wall -DNDEBUG -pedantic -g -fPIC   -c -o nr_zbrak.o nr_zbrak.c
cc -fno-common -Wall -DNDEBUG -pedantic -g -fPIC   -c -o ad_frsnl.o ad_frsnl.c
cc -fno-common -Wall -DNDEBUG -pedantic -g -fPIC   -c -o ad_globl.o ad_globl.c
cc -fno-common -Wall -DNDEBUG -pedantic -g -fPIC   -c -o ad_matrx.o ad_matrx.c
cc -fno-common -Wall -DNDEBUG -pedantic -g -fPIC   -c -o ad_bound.o ad_bound.c
cc -fno-common -Wall -DNDEBUG -pedantic -g -fPIC   -c -o nr_util.o nr_util.c
cc -fno-common -Wall -DNDEBUG -pedantic -g -fPIC   -c -o ad_doubl.o ad_doubl.c
cc -fno-common -Wall -DNDEBUG -pedantic -g -fPIC   -c -o ad_phase.o ad_phase.c
ctangle ad_start.w - ad_start.c
make[1]: ctangle: Command not found
make[1]: *** [<builtin>: ad_start.c] Error 127
make[1]: Leaving directory '/var/home/$USER/Git/iad/src'
make: *** [Makefile:200: ad] Error 2

I looked around for a bit to see what 'ctangle' was but I didn't see much.

Reproduce

1. git clone https://github.com/scottprahl/iad.git
2. cd iad
3. make install

Dear Sir/Madam/Mx,
I have found the IAD software to be invaluable to my PhD (in King's College London supervised by Prof Tom Vercauteren) and am very grateful for its availability and documentation! We have found that using the IAD version 3.11.4 on a phantom with known absorbance and reduced scattering coefficients works well if the phantom is measured directly, however it returns a largely overestimated absorbance coefficient if 1mm glass slides are used experimentally and specified in the IAD routine. Example data and a notebook demonstrating this and detailing the parameters used (MWE_phantom_IAD_glass_effect.ipynb) can be found here, and examples of the optical parameter outputs are attached. We would be very grateful for any advice for how to improve these results!
Many thanks,
Anisha Bahl

Dear IAD team,
We are using the IAD package for calculating the reduced scattering and absorption of excised tissue from single integrating sphere measurements: total reflectance and total transmission.
We wonder if the present version of IAD package is able to include a pre-estimated reduced scattering spectrum in the input .txt file (with headers as integrating sphere parameters).
Thank you in advance! Looking to your reply!

Looking over the manual for IAD it says that if various ports are non-circular then we should use a beam diameter that matches the area of the port (page 32 of the manual). Does this hold true if we have a non-circular illumination beam? The spectrophotometer I am using is ~7x4mm at the transmittance window and ~8x9mm at the reflectance window.

Also unless I am mistaken should the example you provide in the manual of a 10mmx1mm rectangular port gives an area of A=b*h=10mm x 1mm=10mm^2 which then means the radius should be A=pi * r^2 ==> r = sqrt(A/pi) = sqrt(10mm^2/pi) ~= 1.7846mm? If so I can make a pull request to fix the docs.

Then if there is a better place to ask questions that aren't directly related to coding bugs let me know.

Dear IAD team,

Not sure if this is a bug. I noticed my command line result vs the rxt result is different. I am wondering if I am missing anything. I had make sure all the settings are consistent. Here are the input I provided

command line:
iad -r 0.2676 -t 0.331 -u 0.004695 -n 1.521 -d 1 -S 1 -1 "150 25 25 25 0.93"

rxt:
IAD1 # Must be first four characters

#Input Example with a two sets of sphere coefficients
#The results from this file should be the same as for sample2.rt
#Anything after a '#' is ignored, blank lines are also ignored

1.521 # Index of refraction of the sample
1 # Index of refraction of the top and bottom slides
1.0 # [mm] Thickness of sample
0.0 # [mm] Thickness of slides
0.0 # [mm] Beam diameter
1 # Reflectivity of the reflectance calibration standard

1 # Number of spheres used during each measurement
#Properties of sphere used for reflection measurements
150 # [mm] Sphere Diameter (8 in * 25.4 mm/in)
25 # [mm] Sample Port Diameter
25 # [mm] Entrance Port Diameter
25 # [mm] Detector Port Diameter
0.93 # Reflectivity of the sphere wall
#Properties of sphere used for transmission measurements
150 # [mm] Sphere Diameter (8 in * 25.4 mm/in)
25 # [mm] Sample Port Diameter
25 # [mm] Entrance Port Diameter
25 # [mm] Detector Port Diameter
0.93 # Reflectivity of the sphere wall

2 # Number of measurements, M_R, M_T

#lambda M_R M_T
490 0.33106993 0.26761527

Let me know if you can reproduce the results.

Also, I noticed the fitted M_R and M_T does not look right when I input multiple wavelength info. Not sure what is wrong with here as well.

Thanks for developing this awesome tool. I really appreciate this decade efforts. Hope to get this issue resolve soon.

Best

Hello, Professor, can I use collimated LED light as the light source of double integrating sphere experiment？Because the integrating sphere in our laboratory is very large, we need large optical power. The power of He Ne laser may not be enough, and we also don't have He Ne laser.