[Eidors Help] How to plot different EIDORS images with same colourscale

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Hi,

I have two EIDORS images with different range of conductivity. I want to display both of them with the same colourscale that has a minimum 
value which is minimum of conductivity of both the image and maximum of conductivity of both the image. 

For example, in this code, I have two images , root and soil. 

root has minimum conductivity of 1.0037 while maximum of 1.0270
soil has minimum conductivity of 1.0037 while maximum of 1.0173

I want the color scale for displaying both of these images in the range 1.0037 to 1.0270.  If maximum is red color which is 1.027, red color should not
be present in show_fem(soil) but I get red colour when displaying soil.mat. For example, running the below code gives me the figure in the SR.jpg. 

I use the following code to generate the colourbar with same scale. Please let me know how to get correct colour scheme. 

load('soil.mat')
load('root.mat')
root_elemental_data = root.elem_data;
soil_elemental_data = soil.elem_data;
K1 = min([root_elemental_data; soil_elemental_data]);
K2 = max([root_elemental_data; soil_elemental_data]);
colbar = linspace(K1,K2,6);
t_v=colbar; %ticks values
Y = (K2-K1)./2;
X = (K2+K1)./2;

figure(1);
subplot(1,2,1);
hh= show_fem(soil);
soil.calc_colours.ref_level= X;
soil.calc_colours.clim= Y;
cb = colorbar; 
t_l=linspace(1,255,6);
set(cb,'YTick', t_l'); set(cb,'YTickLabel', t_v');
set(hh,'LineStyle','none');

subplot(1,2,2);
hh=show_fem(root);
root.calc_colours.ref_level= X;
root.calc_colours.clim= Y;
cb = colorbar; 
t_l=linspace(1,255,6);
set(cb,'YTick', t_l'); set(cb,'YTickLabel', t_v');
set(hh,'LineStyle','none');

________________________________
Best Regards,

Sathyanarayan Rao

Earth and Life Institute/Environmental Sciences (ELI-e)

c.037, Croix du Sud 2, Louvain-la-Neuve, Belgium

Université catholique de Louvain

E-mail : sat...@uc...

Phone: 010473827 ( intercom 73827)

________________________________

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From: eid...@li... <eid...@li...>
Sent: 29 March 2017 22:08
To: eid...@li...
Subject: eidors3d-help Digest, Vol 71, Issue 26

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Today's Topics:

   1. Re: 2D Model from 3D Model -Netgen (Andy Adler)
   2. EIDORS colorbar (Sathyanarayan Rao)
   3. Re: EIDORS colorbar (Andy Adler)
   4. Question about EIDORS usage (Lilian Cab?)
   5. Segmentation (VeronikaCedivodova)
   6. Re: Question about EIDORS usage (Andy Adler)

----------------------------------------------------------------------

Message: 1
Date: Sun, 26 Mar 2017 17:57:27 -0400 (EDT)
From: Andy Adler <And...@Ca...>
Subject: Re: [Eidors Help] 2D Model from 3D Model -Netgen
To: Questions and discussion on EIDORS
        <eid...@li...>
Message-ID:
        <alp...@ad...>
Content-Type: text/plain; charset=US-ASCII; format=flowed

On Sun, 26 Mar 2017, Andy Adler wrote:
>> There are several problems with the way EIDORS
>> handles internal electrodes. I'll try to fix them,
>> if I can find the time.

I've spent some time verifying that an electrode-in-a-hole
is handled correctly. It is.

In the meanwhile, you can visualize current flow as follows
(requires functions I just checked in).

Thanks
-- Andy.Adler @ Carleton.ca  +1-613-520-2600x8785

extra={'ball', ...
       ['solid cyls= cylinder(0.2,0.2,0;0.2,0.2,1;0.2) -maxh=0.25;' ...
        'solid ball= cyls and orthobrick(-1,-1,0;1,1,0.5);']};
fmdl= ng_mk_cyl_models(0,[4],[0.5,0,0.05],extra);
eln   = find(elem_select(fmdl, '(x-0.2).^2+(y-0.2).^2<0.19^2'));
eln   = unique(fmdl.elems(eln,:));
% HOLLOW ELECTRODE
fmdl.electrode(end+1) = struct('nodes', eln(:)', 'z_contact', .01);
fmdl = mk_hollow_electrode(fmdl, length(fmdl.electrode));
fmdl.stimulation = stim_meas_list([4,5,2,3]);
show_fem(fmdl)

hold on %% SHOW CURRENT
ecur = calc_elem_current( mk_image(fmdl,1));
npos = interp_mesh( fmdl );
quiver(npos(:,1),npos(:,2),ecur(:,1),ecur(:,2));
hold off

------------------------------

Message: 2
Date: Mon, 27 Mar 2017 13:08:41 +0000
From: Sathyanarayan Rao <sat...@uc...>
Subject: [Eidors Help] EIDORS colorbar
To: "eid...@li..."
        <eid...@li...>
Cc: Mathieu Javaux <mat...@uc...>
Message-ID: <149...@uc...>
Content-Type: text/plain; charset="iso-8859-1"

Hello EIDORS team,

I would like to know, what should be done in EIDORS fwd_solve to include Induced polarization (IP) effect (complex conductivity) and ECT capacitance effect

(complex permittivity)  . I am aware of some literature such as

"Complex Resistivity Tomography and Spectral Induced Polarization Analysis on Laboratory Device for Soil Characterization"

that uses EIDORS for IP  and old forum https://sourceforge.net/p/eidors3d/mailman/message/34295993/? that discusses about ECT but I do not find any
information on adding dielectric permittivity information and complex conductivity into fwd_solve ?

Please guide me in modifying EIDORS for IP and ECT studies ? I thank you in advance.

________________________________
Best Regards,

Sathyanarayan Rao

Earth and Life Institute/Environmental Sciences (ELI-e)

c.037, Croix du Sud 2, Louvain-la-Neuve, Belgium

Universit? catholique de Louvain

E-mail : sat...@uc...<mailto:nim...@uc...>

Phone: 010473827 ( intercom 73827)

________________________________
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Message: 3
Date: Mon, 27 Mar 2017 09:38:51 -0400 (EDT)
From: Andy Adler <And...@Ca...>
Subject: Re: [Eidors Help] EIDORS colorbar
To: Questions and discussion on EIDORS
        <eid...@li...>
Cc: Mathieu Javaux <mat...@uc...>
Message-ID:
        <alp...@ad...>
Content-Type: text/plain; charset="utf-8"

There is nothing special that you need to do;
EIDORS does in- and out-of-phase components.

http://eidors3d.sourceforge.net/tutorial/EIDORS_basics/real_complex.shtml

For ECT, you need to write new forward solvers.

Did you have a question about the colourbar? That
was the title of your email.

Thanks
-- Andy.Adler @ Carleton.ca  +1-613-520-2600x8785

On Mon, 27 Mar 2017, Sathyanarayan Rao wrote:
> I would like to know, what should be done?in EIDORS fwd_solve to include
> Induced polarization (IP) effect (complex conductivity)?and
> ECT?capacitance effect
>
> (complex permittivity)? . I am aware of some literature such as?
>
>
> "Complex Resistivity Tomography and Spectral Induced Polarization Analysis
> on Laboratory Device for Soil Characterization"
> that uses EIDORS for IP ?and old
> forum?https://sourceforge.net/p/eidors3d/mailman/message/34295993/? that
> discusses about ECT but I do not find any?
> information on adding dielectric permittivity information and complex
> conductivity into fwd_solve???
>
> Please guide me in modifying EIDORS for IP and ECT studies ? I thank you
> in advance.?

------------------------------

Message: 4
Date: Tue, 28 Mar 2017 14:30:23 +0200
From: Lilian Cab? <cab...@gm...>
Subject: [Eidors Help] Question about EIDORS usage
To: eid...@li...
Message-ID:
        <CAM...@ma...>
Content-Type: text/plain; charset="utf-8"

Hi,

I am a student on an internship in LIMSI-CNRS, a laboratory located near
Paris, France.
I have few questions that maybe are more theorical about EIT that about
EIDORS itself...
I want to try using EIDORS to do EIT, to reconstruct an image of the
conductivity repartition inside a body.
My main question is that the body will deform during experimentation, along
with electrode position. Is it possible to take that in count in EIDORS ?
More difficult, is there any way to determine the change of the electrode
position just with border measurments ? I have no idea on how to get
electrode's position automatically.

Thanks a lot,

Lilian CAB?
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Message: 5
Date: Wed, 29 Mar 2017 21:34:00 +0200 (CEST)
From: VeronikaCedivodova <Ver...@se...>
Subject: [Eidors Help] Segmentation
To: <eid...@li...>
Message-ID: <9fD...@se...>
Content-Type: text/plain; charset="utf-8"

Dear all,

I know, that this problem isn?t exactly your speciality, but I will try. I
have image of thorax (CT scan), where there are bones and tissue. I would
like to ask,? if there is some automate segmentation, which segmented tissue
from bones. Because I would like to segment more CT scan, so it will be
better do it this way than manually.

Thank you for your answers.
Veronika
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Message: 6
Date: Wed, 29 Mar 2017 16:08:14 -0400 (EDT)
From: Andy Adler <And...@Ca...>
Subject: Re: [Eidors Help] Question about EIDORS usage
To: Questions and discussion on EIDORS
        <eid...@li...>
Message-ID:
        <alp...@ad...>
Content-Type: text/plain; charset="utf-8"

On Tue, 28 Mar 2017, Lilian Cab? wrote:
> My main question is that the body will deform during experimentation, along with electrode position. Is
> it possible to take that in count in EIDORS ?

Is this what you're looking for?
http://eidors3d.sourceforge.net/tutorial/adv_image_reconst/move_2d.shtml
(based on Soleimani et al, Physiol Meas, 2006)

> More difficult, is there any way to determine the change of the electrode position just with border
> measurments ? I have no idea on how to get electrode's position automatically.

There is lots of work in the EIT literature on this problem. Have you tried google?

Thanks
-- Andy.Adler @ Carleton.ca  +1-613-520-2600x8785

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