Hi,
Thank you very much, it will help me a lot.
Regards
--
Julien
From: Stefania Carapezzi [mailto:[email protected]]
Sent: Wednesday, January 14, 2015 3:50 AM
To: Gwyddion use discussion
Subject: Re: [Gwyddion-users] NaN value in statistical measurment
Hi.
Let's say that you save an AFM image of size s and resolution r in txt format.
Then your txt file contains a r*r matrix. The (i,j) element of the matrix is
the z-value located at x = (i - 1) * step, y = (j - 1) * step, for step = s /
r, for i,j = 1, ...r. This following the gwyddion rule which sets the (1,1)
element of your matrix as the origin of plane x,y.
This is the python script:
res = 512. # number of pixels (float kind)
size = 5000. # size of (squared) image in nm (float kind)
length_step = size / res
f1 = open('H.txt') # input file: topographic image by Gwyddion
f2 = open('H-XYZ.txt', 'w') # output file
linesA = f1.readlines() # read all the rows of the input image
x_ind = 0 # index of rows
for lineA in linesA:
lineA = lineA.replace('\n', '') # remove end line character from row line
z_values = lineA.split('\t') # split the row line in the z-values
x_data = str(x_ind * length_step) # x coordinate in nm
x_ind += 1
y_ind = 0 # index of columns
for z_value in z_values:
y_data = str(y_ind * length_step) # y coordinate in nm
data = x_data + '\t' + y_data + '\t' + str(float(z_value) * 1E9) + '\n'
# x, y, z coordinates in nm, correspondent to the element (x_ind + 1, y_ind +
1) of the original matrix
f2.write(data)
y_ind += 1
f1.close()
f2.close()
Best regards
Stefania
On Tue, Jan 13, 2015 at 3:46 PM, Moriceau, Julien
<[email protected]<mailto:[email protected]>>
wrote:
Hello,
Thank you for your spontaneous help.
I would be interested to know how you did this python script. I would be really
glad if you can explain it here.
Thank you for your help.
Regards
--
Julien
From: Stefania Carapezzi
[mailto:[email protected]<mailto:[email protected]>]
Sent: Friday, January 09, 2015 11:04 AM
To: Gwyddion use discussion
Subject: Re: [Gwyddion-users] NaN value in statistical measurment
Hi. I'm working with AFM images as well. I was in need to get my image as a
.txt file with 3 rows (XYZ) for further analysis. I did this by saving from
gwiddyon as .txt and then using the matrix file as input in a python program
that output the .txt file with XYZ rows. the same of course can be done in
matlab, et similia. if you wish I can send you my python script, or I can
briefly describe the algorythm (very short).
best regards
Stefania Carapezzi
On Thu, Jan 8, 2015 at 3:23 PM, Moriceau, Julien
<[email protected]<mailto:[email protected]>>
wrote:
That's great.
Thank you so much!
Regards
--
Julien
-----Original Message-----
From: David Nečas (Yeti) [mailto:[email protected]<mailto:[email protected]>]
Sent: Thursday, January 08, 2015 9:21 AM
To: Gwyddion use discussion
Subject: Re: [Gwyddion-users] NaN value in statistical measurment
On Thu, Jan 08, 2015 at 08:54:08AM +0100, David Nečas (Yeti) wrote:
> > I was wondering if it was possible to save a file with the same
> > organization as my original file, meaning XYZ...
>
> This should not be a big problem to add.
Added. It will appear in tomorrow's or later development snapshot.
Select ‘XYZ text data’ as the export file format, or just use the .xyz
extension to choose it.
Regards,
Yeti
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