Importing Lab-DCT files

[Eslam el bakry]

Hi

I am trying to import .h5 or .dream3d data file, created by grain3dmapper software of Zeiss Versa 630 instrument. I could not find the filter: "Read GrainMapper3DFile" in the filter list, and when I try to use the filter "Import HDF5 dataset", the attribute matrix seems to be missing. 

When opening .dream3d file directly, the image files seem to be missing.

Can somebody let me know how to get that done.

I need to visualize the sample and its crystallographic orientation.

Thanks

Eslam 

[Michael Jackson]

Dear Eslam, 

    What version of DREAM3D-NX are you using? The GrainMapper3D File Reader is not included in “DREAM.3D” Version 6.5.171. Also the generated .dream3d file from GrainMapper3D Software is generated incorrect.

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Mike Jackson                    mike.j...@bluequartz.net
BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

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[Michael Jackson]

https://www.dream3d.io/Download/

DREAM3D-NX Version 7.2.1

It is free for students.

--
Mike Jackson                    mike.j...@bluequartz.net
BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

On Aug 19, 2025 at 09:54:43, Eslam el bakry <esla...@gmail.com> wrote:

The version I have is indeed DREAM.3D” Version 6.5.171. Which version do you recommend?

[Michael Jackson]

Dear Eslam, 

   I think IPF is the primary way to view the crystal orientations. If you have ideas on other techniques please don’t hesitate to share ideas.

Visualizing the data depends on the “form” of the data. Is it a large “volume” of data? Is it a surface mesh of some kind? Is it just a point cloud?

If you could share the data with me I can take a look and offer some advice going forward.

--
Mike Jackson                    mike.j...@bluequartz.net
BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

On Aug 20, 2025 at 12:58:30, Eslam el bakry <esla...@gmail.com> wrote:

Thanks, it worked. Right now, I am trying to figure out a way to visualize my Lab dct data. I have already imported the full dataset as .h5 file (Absorption tomography and diffraction patterns),Is there a way to visualize the tomography data and the crystals within the sample? Is there a way to visualize the orientation of crystals detected by diffraction data (other than IPF maps)?

[Eslam el bakry]

Thanks, it worked. Right now, I am trying to figure out a way to visualize my Lab dct data. I have already imported the full dataset as .h5 file (Absorption tomography and diffraction patterns),Is there a way to visualize the tomography data and the crystals within the sample? Is there a way to visualize the orientation of crystals detected by diffraction data (other than IPF maps)?

[Eslam el bakry]

Thanks, it worked. Right now, I am trying to figure out a way to visualize my Lab DCT data. I have already imported the full dataset as .h5 file (Absorption tomography and diffraction patterns), Is there a way to visualize the tomography data and the crystals within the sample? Is there a way to visualize the orientation of crystals detected by diffraction data (other than IPF maps)?

[Eslam el bakry]

I was just hoping to see x, y and z crystallographic coordinates. The data is exported as .h5 file that has tomography and diffraction information. Here is the drop box link for the uploded data:

https://www.dropbox.com/scl/fi/mb5feexwrsahiq6p25qfq/MAC0050-KLiSO4_flat_Panel_grainmap-8-21t.h5?rlkey=k09hcq8crxxzk7jcj78ehkgku&st=r2dh0s54&dl=0

[Anthony Rollett]

I understand that we may be able to read TXM files directly in the near future

ADR

[Michael Jackson]

The mostly good news is that the file seems to be a GrainMapper3D file. In DREAM3D-NX just use the “Read Grainmapper 3D” reader.

The slightly bad news is that looks DREAM3D-NX is not importing the IPF Colors correctly from the file. You can generate new IPF Colors (If you want) via running 2 filters:

First, run the “Convert Orientation Representation” to convert the Rodrigues values into Euler values.

Next run the “Compute IPF Colors”.

I was able to view your data set within DREAM3D-NX version 7.2.1

--
Mike Jackson                    mike.j...@bluequartz.net
BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

To view this discussion visit https://groups.google.com/d/msgid/dream3d-users/43843f1e-1932-413d-a4c5-0fa04dc2b211n%40googlegroups.com.

[Eslam el bakry]

Hi Michael

I really appreciate your patience

I think I did the same steps as you instructed but yet I am not getting the same result. See attached screenshot. First, it seems that It imported only the AbsorptionCT data, (not DCT data). I tried importing other .h5 Lab-DCT datasets, and sometimes it imports the full dataset, sometimes it imports only AbsorptionCT data,and sometimes it imports none !. Please, See attached screenshots.

Second, The x,y, and z coordinates seem to be not changed upon applying “Convert Orientation Representation”  and “Compute IPF Colors” filters, and no IPF map or sample IPF-related coloring show up.

Please let me know If there is a lost step.

Eslam Elbakry

[Michael Jackson]

Did you first use the “Read Grain Mapper3D” filter to import the data? I think it will import but with DREAM3D-NX version 7.2.1 the IPF Colors from the file will be incorrect.

--
Mike Jackson                    mike.j...@bluequartz.net
BlueQuartz Software         www.bluequartz.net

President/Owner               Dayton, Ohio

Principal DREAM.3D Developer

To view this discussion visit https://groups.google.com/d/msgid/dream3d-users/68682fc2-2c1c-4f3b-bdc8-509c2a177a42n%40googlegroups.com.