try to create own geometry using bifurcation tutorial

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Алия Тазюкова

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Aug 10, 2020, 10:31:53 AM8/10/20
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hello !
I am trying to learn how to create my own testing geometry, and tried to apply it to bifurcation model from the tutorial http://o53xo.mnzgs3ltn5xc443pmz2hoylsmu.cmle.ru/documentation.html

but receive the following error, could you please clarify what am i doing wrong?


1278.51 core.mod.cgalvmtkmeshingkernel.imeshingkernel: Running 3D mesher.
TetGen command line options: pq2,000000/5,000000O2/7o/165,000000T1,000000e-008zVm
Warning:  Unknown switch -/.
Warning:  Unknown switch -5.
Warning:  Unknown switch -,.
Warning:  Unknown switch -0.
Warning:  Unknown switch -0.
Warning:  Unknown switch -0.
Warning:  Unknown switch -0.
Warning:  Unknown switch -0.
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Warning:  Unknown switch -,.
Warning:  Unknown switch -0.
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Warning:  Unknown switch -0.
Warning:  Unknown switch -0.
Warning:  Unknown switch --.
Warning:  Unknown switch -0.
Warning:  Unknown switch -0.
Warning:  Unknown switch -8.
  Initializing memorypools.
  tetrahedron per block: 8188.
  Size of a point: 144 bytes.
  Size of a tetrahedron: 96 (96) bytes.
  Size of a shellface: 200 (200) bytes.
  Initializing robust predicates.
  sizeof(double) =  8
  machine epsilon =  2,22045e-016 [IEEE 754 64-bit macheps]
Delaunizing vertices...
  Permuting vertices.
  Sorting vertices.
Exception:  All vertices are (nearly) identical (Tol = 1).
1278.61 core.mod.core.loggingadapter ERROR: ERROR: In C:\CRIM\Modules\CGALVMTKMeshingKernel\ExtensionPoint\crimsonTetGenWrapper.cpp, line 455
crimsonTetGenWrapper (000001DBDB3BE8F0): TetGen quit with an exception.

Chris Arthurs

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Aug 10, 2020, 11:09:46 AM8/10/20
to Алия Тазюкова, CRIMSON Users
Hi Aliya,

Can you give us some information on the system you're using please? Hardware, windows version, etc.

You seem to be getting a number of very strange errors, and it seems likely that it's something to do with your system. Are you using Cyrillic characters in the file paths, or in the terminal, perhaps? This is not something we've run into before, but it might explain the strange nature of the errors.

Best,
Chris

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Алия Тазюкова

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Aug 11, 2020, 1:31:10 AM8/11/20
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Hi Chris,

1) Windows 10 Home Edition 
2) Version
3) Date of Installation
4) OS build


Previously i made a mesh for my own geometry( using the same bifurcation reference image) and mesh worked but failed on Boundary Condition setting as Blended model was required (actually i made a geometry without branches) so i made another one-branch model and now i can not create a mesh. Also i previously performed the full tutorial and all worked fine and without any issues (I mean that this should not be a system issue, all that i've done before was made on the same pc). Could it be that i made my own geometry(not the same as on the bifurcation reference image)? or reference should not have any influence ?
1) my computer has Russian language, but the path is recognized by Crimson PSB

  Image (000001DBDD366510)

Dimension: 3

Dimensions: 152 99 256

Channel: Unnamed [scalar]

PixelType: scalar

BytesPerElement: 4

ComponentType: float

NumberOfComponents: 1

BitsPerComponent: 32


TimeGeometry: ProportionalTimeGeometry (000001DBEC660C90)

TimeSteps: 1

FirstTimePoint: -1.79769e+308

StepDuration: 1.#INF ms

Time Bounds: -1.79769e+308 - 1.79769e+308


GetGeometryForTimeStep(0): SlicedGeometry3D (000001DBD958CE20)

IndexToWorldTransform:

Matrix:

1.23621 0 0

0 1.23621 0

0 0 1.23621

Offset: [-93.889, -71.0646, -128.661]

Center: [0, 0, 0]

Translation: [-93.889, -71.0646, -128.661]

Inverse:

0.808922 0 0

0 0.808922 0

0 0 0.808922

Scale : 1 1 1

BoundingBox: ( 0,152 0,99 0,256 )

Origin: [-93.889, -71.0646, -128.661]

ImageGeometry: 1

Spacing: [1.23621, 1.23621, 1.23621]

EvenlySpaced: 1

DirectionVector: [0, 0, 1]

Slices: 256


GetPlaneGeometry(0): PlaneGeometry (000001DBEC6613E0)

IndexToWorldTransform:

Matrix:

1.23621 0 0

0 1.23621 0

0 0 1.23621

Offset: [-93.889, -71.0646, -128.661]

Center: [0, 0, 0]

Translation: [-93.889, -71.0646, -128.661]

Inverse:

0.808922 0 0

0 0.808922 0

0 0 0.808922

Scale : 1 1 1

BoundingBox: ( 0,152 0,99 0,1 )

Origin: [-93.889, -71.0646, -128.661]

ImageGeometry: 1

Spacing: [1.23621, 1.23621, 1.23621]

ScaleFactorMMPerUnitX: 1.23621

ScaleFactorMMPerUnitY: 1.23621

Normal: [0, 0, 1.23621]

Properties of BaseData:

name bifurcation

path C:/Users/user/Desktop/GUI-path-planning (2).mitk

could it be the issue with negative values? 
 


Chris Arthurs

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Aug 11, 2020, 5:53:26 AM8/11/20
to Алия Тазюкова, CRIMSON Users
Hi Aliya,

Are you able to share the MITK save file with me? I can take a look. I agree that this is probably not a system issue, if the tutorial worked for you.

Best,
Chris

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Алия Тазюкова

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Aug 11, 2020, 8:14:19 AM8/11/20
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Hi Chris,

Thank you for the support! 
Please see attached 
GUI-path-planning_test.mitk

Chris Arthurs

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Aug 12, 2020, 6:57:09 AM8/12/20
to Алия Тазюкова, CRIMSON Users
Hi Aliya,

Thanks for sending ths. I can not reproduce the problem - I opened your scene, selected the blended model, opened the meshing pane and clicked "mesh" - it worked without any issues.

I'm afraid I'm at a loss, but I do recall you had some strange issues with missing dlls in December, which we've never seen before, but you resolved. Are you able to try on a different system, or reinstall CRIMSON?

Best,
Chris

On Tue, Aug 11, 2020 at 1:15 PM Алия Тазюкова <near2...@gmail.com> wrote:
Hi Chris,

Thank you for the support! 
Please see attached 

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Алия Тазюкова

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Aug 12, 2020, 8:51:55 AM8/12/20
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Hi Chris,

Yes, I had problems but with a different system. I will reinstall CRIMSON now and check 

Алия Тазюкова

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Aug 18, 2020, 2:11:51 PM8/18/20
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Hi Chris,

After reinstall a was able to create mesh successfully, but only once..  

среда, 12 августа 2020 г. в 15:51:55 UTC+3, Алия Тазюкова:

Алия Тазюкова

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Sep 24, 2020, 1:58:08 PM9/24/20
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Hello Chris,

Now I am able to create mesh but facing another issue. Looks like something is wrong with the fonts , but ... a bit magical issue.. 

logs:
C:\Program Files\CRIMSON 2019.11.01\bin\Python\lib\site-packages\matplotlib\font_manager.py:1216: UserWarning: findfont: Font family ['serif'] not found. Falling back to Bitstream Vera Sans
  (prop.get_family(), self.defaultFamily[fontext]))
848.58 core.mod.wdgtS.stdMltWdgt: changing layout to big 3D ...

screenshot of the error 


my project attached

Алия Тазюкова

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Sep 24, 2020, 2:00:19 PM9/24/20
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unfortunately google does not allow me attach the project.. 

Алия Тазюкова

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Sep 24, 2020, 2:01:37 PM9/24/20
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https://drive.google.com/file/d/1abvsmY6ZhkU6yFR7uD1Pg17j9CmUs0cU/view?usp=sharing here it is

четверг, 24 сентября 2020 г. в 21:00:19 UTC+3, Алия Тазюкова:

Алия Тазюкова

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Nov 4, 2020, 9:56:51 AM11/4/20
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Hello,

All previous issue were resolved after System reinstallation.

Now i've managed to start a solver ,but facing the following issue (attached) . Hope that i will recieve any feedback this time. 
flowsolver_error.txt

Алия Тазюкова

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Nov 4, 2020, 10:01:06 AM11/4/20
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my project : https://drive.google.com/file/d/11W0y9DVdDHOMJ73fPX_PgfPUBb55Qk2P/view?usp=sharing 
 Please inform if it is not acceptable via link

среда, 4 ноября 2020 г. в 17:56:51 UTC+3, Алия Тазюкова:

Chris Arthurs

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Nov 4, 2020, 10:10:27 AM11/4/20
to Алия Тазюкова, CRIMSON Users
Hi Aliya,

Your simulation has diverged - 3rd column of the output shows that the residual is 10^95. This indicates that something is wrong with the model you have created - either in terms of the solid model (the blend), the boundary conditions, or the mesh. I recommend carefully checking that all the boundary conditions are assigned properly. It might be a good idea to simplify everything - start with a simple tube, and just use a simple steady inflow (negative-valued) waveform, and an RCR outflow, and ensure that you're not pushing in too much flow.

Best wishes,
Chris

On Wed, Nov 4, 2020 at 3:01 PM Алия Тазюкова <near2...@gmail.com> wrote:
my project : https://drive.google.com/file/d/11W0y9DVdDHOMJ73fPX_PgfPUBb55Qk2P/view?usp=sharing 
 Please inform if it is not acceptable via link

среда, 4 ноября 2020 г. в 17:56:51 UTC+3, Алия Тазюкова:
Hello,

All previous issue were resolved after System reinstallation.

Now i've managed to start a solver ,but facing the following issue (attached) . Hope that i will recieve any feedback this time. 

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Алия Тазюкова

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Nov 6, 2020, 9:00:01 AM11/6/20
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hello Cris,

Thank you for the recommendations, I created a simple model and now applying BC as described in the Tutorial https://umich.app.box.com/s/sxaywipys548da2rdrgp7kieoj7f9dk2
 Could you please clarify some values meaning:
I am using steady.flow file  https://www.isd.kcl.ac.uk/cafa/CRIMSON/steady.flow but the values seems a bit strange in this file. 
in the first column are values 0 and 1 are the width of channel and in the 2nd column -83333.33333 are the velocities?

среда, 4 ноября 2020 г. в 18:10:27 UTC+3, Chris Arthurs:

Chris Arthurs

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Nov 6, 2020, 9:05:26 AM11/6/20
to Алия Тазюкова, CRIMSON Users
No, these are time-flow pairs. The first column is the instant in time (generally seconds) and the second column is instantaneous volumetric flow rate.

CRIMSON interpolates in time between the values here, and the whole file gets looped when the final time instant is exceeded. Since there's only two time points specified and they give the same rate, the interpolated imposed function is the constant -83333.333.

Chris

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