Can Open XY read .ebsp files?

[anastasiavr]

Hello,
I am currently using Aztec software for ebsp acquisition, which stores the kikuchi patterns in an .ebsp file.
One can then export the patterns in .tiff file types but this is a very very long process. Is there a way open xy can work directly with the .ebsp file instead of the tiffs?
Thank you in advance!

[eretnek]

Unfortunately, not at this time. Newer versions of AZtec can output hdf5 files, but as far as I can tell, they only includes the information and not the patterns themselves. Edax's hdf5 format does include pattern data, and saves a lot of time. Hopefully, AZtec will follow suit someday.

…

-Tim

On Wed, Feb 10, 2021, 5:23 AM anastasiavr ***@***.***> wrote: Hello, I am currently using Aztec software for ebsp acquisition, which stores the kikuchi patterns in an .ebsp file. One can then export the patterns in .tiff file types but this is a very very long process. Is there a way open xy can work directly with the .ebsp file instead of the tiffs? Thank you in advance! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#24>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACWHJDKCN5D3CAPNGTXNLSLS6J3EVANCNFSM4XM3MQ6A> .

[mikesmic]

Hi, just to add that it is possible to read uncompressed .ebsp files. I wrote some code to read them in EMsoft a few years back (EMsoft-org/EMsoft@ef30487 EMsoft-org/EMsoft@c3bce54) because I was having a similar nightmare with 100,000+ files in a single directory.

Let me know if you want to implement this here, I haven't coded in matlab in a good while but I can run you through the structure of an .ebsp file.

[anastasiavr]

Hello, I took some time to look at your codes, but unfortunately I am not familiar with Fortran. I am using MATLAB for some time now (I definitely am not an expert) but I think understanding the structure of the .ebsp files would be very useful as a first step and interesting for other users as well. Thank you for taking the time to help.

[dtfullwood]

Mike is going to help us figure out the structure, so hopefully we'll have a go at it in the near future...

[dtfullwood]

anastasiavr - do you have small scan with the relevant .cpr/.crc/.ctf/.ebsp files that we could use to develop this capability? If so, email me on dfullwood@byu.edu.
Mike has sent us some python code to help with this.
Thanks
David

[anastasiavr]

@dtfullwood Yes, I will have a look for a small scan, otherwise I will have to compress a larger one. I will get back you via email. Thank you!
Anastasia

[hakonanes]

Mike has sent us some python code to help with this.

@mikesmic, could you share this Python code with me (hakon.w.anes@ntnu.no) as well? We would like to read from and write to .ebsp files in the kikuchipy Python package. We can read and write some formats, but would like to expand our IO capabilities.

[dtfullwood]

I just sent you some matlab code that will read an image from an .EBSP file. it is just rough code for playing with but has the essential information:

% Read EBSP file
[file,path]=uigetfile;
ftoopen=fopen([path,file]);
fseek(ftoopen,8,'bof'); %move to start of offset data
xCells=37; %number of points in x direction from .cpr or .crc file – need to automate this
yCells=40;
Offset=fread(ftoopen,xCells*yCells,'uint64'); % start point of each pattern in file
Offset=reshape(Offset,[yCells,xCells]); % I’m not 100% sure about the order here – need to check against OpenXY
i=1; %pick number of pattern desired in y direction
j=1; %pick number of pattern desired in x direction
fseek(ftoopen,Offset(i,j),'bof');
patdims=fread(ftoopen,8,'uint16');
patdims=[patdims(5),patdims(3)]; % size of EBSP
patsize=patdims(1)*patdims(2);
pat=fread(ftoopen,patsize,'uint8');
pat=reshape(pat,patdims);
imagesc(pat)
colormap gray
fclose(ftopen);

Here is the original python code, but the pattern dimension and scan size are hard coded in. The matlab code shows how to read the pattern dimensions; and scan size (xCells, yCells) can be read from the .crc or .cpr file very easily (note that github reads the comment symbol '#' as a header command and bolds the line...):

Script to load a single EBSD pattern from a .ebsp file at

a specified location in the EBSD map.

Format of the .ebsp file

- Header of 8 bytes

- Block of 1 8-byte integer per pattern in the map - these

are the position of each pattern block in the file in the

order they appear in the map (I think row by row)

- Pattern blocks, each consisting of

- 16 bytes - 4 4-byte ints. I think the middle 2 are the

pattern dimensions, not sure about the others

- 1-byte unsigned int per pixel in the pattern

- 18 bytes - not sure what this is

import numpy as np
import matplotlib.pyplot as plt

def load_pat(offset, pat_file, pat_dims):
"""Read a single EBSD pattern image from file.

Parameters
----------
offset: int
    Position of the start of the pattern block.

pat_file: str
    Path to the .ebsp file.

pat_dims : tuple of int
    Dimensions of the pattern image.

Returns
-------
np.ndarray
    Loaded pattern image

"""
pat = np.fromfile(
    pat_file,
    offset=offset + 16,
    count=pat_dims[0] * pat_dims[1],
    dtype=np.uint8
).reshape(pat_dims)

return pat

pat_file = "7aafe81e-f69a-4ec8-b952-e4df78f04d7d.ebsp"

Dimensions of the EBSD map and patterns

y, x for both

map_dims = (70, 70)
pat_dims = (512, 622)

Create map of pattern positions in file

pat_offsets = np.fromfile(
pat_file,
offset=8,
count=map_dims[0] * map_dims[1],
dtype=np.int64
).reshape(map_dims)

Load a single pattern from the file

pat = load_pat(pat_offsets[0, 0], pat_file, pat_dims)

plt.figure()
plt.imshow(pat)

[hakonanes]

Thanks a lot @dtfullwood (and @mikesmic?)!

[mikesmic]

Thanks for sharing that on! @hakonanes looks like a very nice package, I can see that being very useful