SurfaceLab7 .itax & .itm file support about pyspm HOT 8 CLOSED

Hi,
If someone wish to integrate the support for SurfaceLab7 .itax file, he is welcome. I don't have access to such file and cannot do the integration myself, but I can support a developper that knows python to guide him how the surfacelab6 fileformat work.

You can start also by posting the full error (which tell which function generate the error) and the code you execute that create the error.

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I would be very interested to use pySPM with .itax files. Did anything happen from the creation of this issue (any programmer working on this topic or similar)?

Thanks in advance for the update,

Teo Lombardo

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One can open the file manualy and start to analyse it. Here is an example with the data toy ITM version 6, not 7

import pySPM
from pySPM_data import get_data

f=open(get_data("BigSmiley.itm"),"rb")
print("Header",f.read(8)) # Skip header
B = pySPM.Block.Block(f)
B.show()

That will print a huge list of the datastructure inside the ITM. Something like:

Header b'ITStrF01'
versionheader (0) @567
	Footprint (0) @870
	Version (0) @906
StorageInfo (0) @940
	Type (0) @1506
	VersionMajor (0) @1571
	VersionMinor (0) @1609
Analyses (0) @1647
LateralShiftCorrection (0) @4330
MassScale (0) @7027
	clsid (0) @203693
	sf (0) @203739
	k0 (0) @203774
	polarity (0) @203809
	channelwidth (0) @203846
	establ (0) @203891
	calibtype (0) @203923
	calib (0) @203961
		assign (0) @205051
		mcp (0) @205086
	totalshots (0) @211661
Meta (0) @9711
	SI Image (0) @301624248
		clsid (0) @301624811
		zoomfactor (0) @301624857
		zoomcenter_x (0) @301624900
		zoomcenter_y (0) @301624945
		stageposition_x (0) @301624990
		stageposition_y (0) @301625038
		stageposition_z (0) @301625086
		stageposition_r (0) @301625134
		stageposition_t (0) @301625182
		fieldofview (0) @301625230
		resolution (0) @301625274
		shotsperpixel (0) @301625886
		res_x (0) @301625928
		res_y (0) @301625962
		bpp (0) @301625996
		description (0) @301626028
		name (0) @301626080
		intensdata (0) @301626109
		comment (0) @301976323

If one wants to read one of the information, for e.g. "Meta/SI Image we can get it with:

    v = B.goto("Meta/SI Image").show_list()

This will print something like:

List of 19
clsid (0) <16> @301624811, value = b'be8a9975fb391248...' (hex) = "誾疙㧻䠒皓ꄢ" (UTF-16)= ??? (???)
zoomfactor (0) <8> @301624857, value = b'0000000000001440' (hex) = "䀔" (UTF-16)= 5.0 (double) = 4617315517961601024 (long64)
zoomcenter_x (0) <8> @301624900, value = b'0000000000000000' (hex) = "" (UTF-16)= 0.0 (double) = 0 (long64)
zoomcenter_y (0) <8> @301624945, value = b'0000000000000000' (hex) = "" (UTF-16)= 0.0 (double) = 0 (long64)
stageposition_x (0) <8> @301624990, value = b'5d830f6b58103540' (hex) = "荝欏ၘ䀵" (UTF-16)= 21.063849154746425 (double) = 4626622164132397917 (long64)
stageposition_y (0) <8> @301625038, value = b'72057f4525b92240' (hex) = "ղ䕿뤥䀢" (UTF-16)= 9.361612483745123 (double) = 4621459737366431090 (long64)
stageposition_z (0) <8> @301625086, value = b'f6ec05bb9bf9dfbf' (hex) = "묅鍊뿟" (UTF-16)= -0.4996098829648895 (double) = -4620700245405864714 (long64)
stageposition_r (0) <8> @301625134, value = b'382bcf98a01d813f' (hex) = "⬸飏ᶠ㾁" (UTF-16)= 0.008357290900581668 (double) = 4575971271980821304 (long64)
stageposition_t (0) <8> @301625182, value = b'bcc1e3b07c4c70bf' (hex) = "솼냣䱼뽰" (UTF-16)= -0.003979193758127438 (double) = -4652134316646350404 (long64)
fieldofview (0) <8> @301625230, value = b'2d431cebe2361a3f' (hex) = "䌭㛢㼚" (UTF-16)= 0.0001 (double) = 4547007122018943789 (long64)
resolution (0) <4> @301625274, value = b'00020000' (hex) = "Ȁ" (UTF-16)= 512 (long)
shotsperpixel (0) <4> @301625886, value = b'01000000' (hex) = "�" (UTF-16)= 1 (long)
res_x (0) <4> @301625928, value = b'00020000' (hex) = "Ȁ" (UTF-16)= 512 (long)
res_y (0) <4> @301625962, value = b'00020000' (hex) = "Ȁ" (UTF-16)= 512 (long)
bpp (0) <4> @301625996, value = b'20000000' (hex) = " " (UTF-16)= 32 (long)
description (0) <16> @301626028, value = b'54006f0074006100...' (hex) = "Total SI" (UTF-16)= ??? (???)
name (0) <0> @301626080, value = b'' (hex) = "" (UTF-16)= ??? (???)
intensdata (0) [128] <350179> @301626109
comment (0) <44> @301976323, value = b'54006f0074006100...' (hex) = "Total SI (Measuremen..." (UTF-16)= ??? (???)

As the cell don't tell which is the encoding all various encoding is shown to the user (hex value, UTF-16 string and long). We can see here that the image was recorded with 512×512 pixels (res_x × res_y)

You can start with this analysis to understand the new fileformat which really close to the old one

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Thanks for the answer! This procedure works also with my data, but from this can I also get information on the spectra and associated peaks images? And even more, perform analysis like PCA?

Just as a matter of example, following your procedure I tried the add the command:

"B.show_masses()"

And I got the error:

"AttributeError: 'Block' object has no attribute 'show_masses'"

That kind of makes sense of course, but it also makes me think that this procedure allows getting only the instrumental information (like stage position, etc.). Is there a way to access the data associated with the measurement by reading the .itm file? (data that should also be contained in the .itm file, as far as I know. But I could be wrong on this).

Thanks a lot in advance for your answer and your help with this :)

Teo

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OK, so you should not mix ITM/ITA and Block classes. The Block class let you read the raw data inide ITA, ITM and ITAX files.
Now the ITA and ITM classes have a lot of methods to help you to get the valuable informations without having to dive into the raw format.

Now I remember that there is a draft for ITAX file that I created long time ago (see https://github.com/scholi/pySPM/blob/master/pySPM/ITAX.py). You can start to play around with it and test if get_profile works. I have no itx file so I cannot test.

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Yeah, I had the impression that block class was not the right way to go for me.

I have just given a test with a .itax file, but it does not seem to work, unfortunately.

Here the simple script I have used:

AI = pySPM.ITAX("test.itax")
AI.getSpectrum()

And I get the following error:

error Traceback (most recent call last)
Input In [19], in <cell line: 1>()
----> 1 AI.getSpectrum()

File ~\AppData\Local\Programs\Python\Python310\lib\site-packages\pySPM\ITAX.py:57, in ITAX.getSpectrum(self, sf, k0, time, **kargs)
55 slen = self.root.goto("CommonDataObjects/DataViewCollection//sizeSpectrum").getLong()
56 raw = self.root.goto("CommonDataObjects/DataViewCollection//dataSource/simsDataCache/spectrum/correctedData").value
---> 57 spectrum = np.array(struct.unpack("<"+str(slen)+"d", raw))
58 CH = 2*np.arange(slen)
59 if time:

error: unpack requires a buffer of 8000000 bytes

If you are still willing to give it a try (I refer to your message in the other issue), I can send you an example of .itm and .itax files obtained by SurfaceLab7, for you to see if there is a procedure to extract/analyse the spectra/images into those files through PySPM, or not. It would be very very useful :)

Thanks again in advance!

Teo

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It seems that I missed your answer.... Sorry. Could you manage to read ITAX files? Do you have some advises to share for the other users?

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Nope, unfortunately I did not manage to read ITAX files.

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