hyperspy/hyperspy

Multidimensional data analysis

Mingquan Xu

@Mingquan_Xu_twitter

If I want to fit a fractional energy-range in my spectrum, how can I use the m.fit() function?

Like only fit the energy range marked in orange above

2 replies

Mingquan Xu

@Mingquan_Xu_twitter

3 replies

Hi, all, if I want to get the data-points of my model-fitting, the green line, how to do it? Because I want use those data-points to plot it individually.

Mingquan Xu

@Mingquan_Xu_twitter

Hi, all, recnetly I am trying Matlab to treat my spectrum image data, but I donot know how to expot the data after processing. Are there any matlab scripts can write the spectrum image data? such as to .mrc ?

lnaglecocco

@lnaglecocco

Hi, is there a way to exclude certain pixels (with each pixel containing a spectrum) from a model before fitting? I've written an algorithm which produces an array of coordinates representing pixels which are not part of my sample, but I'm not sure how to make that happen. I know I can use .inav[x1:x2,y1:y2] but my sample is not a perfect square so just cropping isn't quite what I want to do

8 replies

lnaglecocco

@lnaglecocco

I have another question which probably has a very simple fix. When I do model.plot() the spectrum at each pixel is normalised such that the plot fits perfectly. However, when I set plot_components=True, I get it so that only part of the data fits in the y axis. I've figured out that this is because it's setting the y-axis bounds for the graph based on a single component, rather than the total fit. How can I fix this so that model.plot(plot_components=True) gives each pixel normalised to the total fit rather than the y-span of a single component?

2 replies

OliDG

@OliDG

Hi,
I try to find a way to save my "file.hspy" using the save() function to a specific path, but I can't see a "path" argument in the function description. Ideally, I was hoping to get the path from the hs.load() function ("load.path/of/my/loadedfile") and use it to save to the same folder without having to manually enter a path ( I have many datasets from many different folders).

20 replies

Jędrzej Morzy

@JMorzy

Is there a way of adapting 'fit_component' function to work using multiple threads on a CPU? The only mention of parallel processes that I found in the docs was in SAMFire and in the map function. I have a relatively specific order of component fits (for EELS core-loss data) that I wouldn't want to change. Any advice on how to approach this would be appreciated!

(I just recently got my hands on a computer, where parallelising would save a significant amount of time)

2 replies

Rosenkranz1

@Rosenkranz1

Hello. I am fairly new to programming, and i am trying to write some extensions to the HyperSpy program. I know how to write a class and have the class inherit etc, but when i create a class for a HyperSpy extension, which should basically inherit the "whole" of HyperSpy so i can use the methodes in HyperSpy in my extension, what is the best approach for this?
I should fork the github repo, but for me it is not very intuitive, what the best way to write extensions are.
I have read the documentation on this, from HyperSpys websites, but i need some elaboration.
Any advice is highly appriciated!

6 replies

Rosenkranz1

@Rosenkranz1

Hello, i have a followup question for my question above.

I want to contribute to a package that already excist (The eds packages). How would i go about using my contribution? By forking the repo and including my methodes in the relevant classes or should i create my own class, and have that inherit from eds? In the latter case, i am struggeling to get the inheritance to work properly, i have written some code, but when i try to apply my method too a dataset it exclaim that EDSSpectrum does not have the attribute, should correct inheritance not fix this? Or is the only way to create my code in a forked repo of the relevant signal?
This might be a trivial question but i cant seem to find the answer. (Maybe i lack some understandig of classes)

6 replies

Weixin Song

@winston-song

Hi All, I use DM to record some EDX spectral images, when I process them using PCA, it shows 'ValueError: zero-size array to reduction operation minimum which has no identity' whether anyone knows how to resolve this problem? thanks

Weixin Song

@winston-song

Eric R. Hoglund

@erh3cq

Are there any EXELFS functions or plugins for HyperSpy?

Francisco de la Peña

@francisco-dlp

Is it an EDX model? The issue may be that more elements require more memory—are you saturating your memory by any chance?

1 reply

Markus Wollgarten

@w-markus

Dear all, a rather simple question: when loading dm3 files of diffraction data the metadata only contains the 'General' branch. Is there a signal type one should request upon loading, that more metadata fields are available even if not filled yet? Thanks a lot! Markus

5 replies

Mingquan Xu

@Mingquan_Xu_twitter

1 reply

A simple question: how to improve this fitting.
I used a "g1 = hs.model.components1D.Gaussian()" to do this fit and want to get the center of this peak.

Jonas Lähnemann

@jlaehne

PostDoc offer combining TEM and MBE of (Al,Sc)N nanowires: http://www.pdi-berlin.de/jobs/job-offers/postdoc-fmd-for-epitaxy-and-atomic-scale-characterization-of-alscn-nanowires/

kociak

@kociak

Dear all. I have an annoying issue with installing hyperspy for use in an environment having the last version of nionswift. The conflict comes from the fact that hs requires numba, and numba requires numpy <=1.20 (hs installs 1.20.3). But nionswift requires numpy 1.21.4 (I guess for the Typing functionalities). My question: can we switch off the use of numba in hyperspy? thanks guys

7 replies

kociak

@kociak

@thomasaarholt: lean and fit. i'll take a look at that and tell you if that works (hopefully I won't get stuck by another hidden compatibility issue :)

Javalde91

@Javalde91

Well, this does the job:

s.plot()
roi = hs.roi.RectangularROI(0.0, 0.0, 0.00001, 0.00001)
roi_signal = roi.interactive(s)

Hello Thomas and everyone, I'm trying to apply a CirleROI but I would like it to have it interactive way, is it possible to do it? Thanks

4 replies

Amina Saleh

@Amina_saleh_twitter

Hi, I used to get my spectrum images in color. Now, when I downloaded another version on another laptop, I only get grayscale rather than colorscale. How can I retrieve the color scale back?

1 reply

Joshua F Einsle

@jeinsle

I am trying to layout some results figures for collaborators and trying to be slightly more efficent than my normal save a plot and layout in powerpoint I decided to try set this up in hyperspy. What I would like to get is figure which looks like this example in the 'Visualisation' section of the Hyperspy website.
alt

however when I run my version of that cell I end up with two seperate figures, instead of a single figure with two subfigures like what is seen above. While I know how to do this with matplotlib, I was wanting to leverage the built in hyperspy tools so the metadata/ axis manger information is automatically applied, as opposed to having to do the heavy lifting again. Any insights would be appricaiated.

3 replies

Mohsen

@M0hsend

Hi All, I am trying to open .hspy files written with RELEASE_next_minor branch with the released 1.6.5 version and I get the following error: TypeError: __init__() got an unexpected keyword argument '_type'. Any ideas how to fix / work-around?

2 replies

Mohsen

@M0hsend

Hi All, I am trying to open .hspy files written with RELEASE_next_minor branch with the released 1.6.5 version and I get the following error: TypeError: __init__() got an unexpected keyword argument '_type'. Any ideas how to fix / work-around?

Never mind. Just reading with h5py and populating axes metadata works good enough. Thanks!

Javalde91

@Javalde91

Hello everyone! I'm trying to get the total electron counts from my SI. I usually do it on DM, but I can't get it on hyperspy, I use s.sum(), but the number that I get is "(|2036)>" from the dimension of my SI ("<EELSSpectrum, title: C_CL_0, dimensions: (80, 80|2036)>" What I'm trying to do is to get the total e- counts to normalize my SI and compare them.

Thomas Aarholt

@thomasaarholt

s.T.sum() :)

Thomas Aarholt

@thomasaarholt

(.T swaps around the navigation and signal dimensions)

OliDG

@OliDG

@thomasaarholt Hi,
I try to get quantified EDS from a sample with many elements (Al,C,Co,Cu,Cr,Mo,O,Pt,W,Zn) with a strong peak overlap between Cr-L (0.571 eV) and O-K (0.523 eV).
One layer is expected to be CrC but appears as CrO... the quantification output 30% of O in it, which is very unexpected for several reasons. Checking the EDS spectrum manually I can see the peak shift by maybe 1 channel when seeing Cr-L instead of O-K but the model fitting doesn't.
I am using the EDS model fitting and after several hours in the documentation I come here to ask: Is there a solution to this? is there a function somewhere that can for instance estimate Cr-L from the Cr-K intensity and subtract it from the O-K signal before saving the O-K intensity? I hope this question is clear enough!

Regards,
Olivier

18 replies

adriente

@adriente

I am trying to run the following code :

import hyperspy.api as hs
input_filename = "file1.emd"
spim = hs.load(input_filename)[-1] 
# the output of the load function is a list in which the last element is an EDSTEM object.
spim.change_dtype("float")
spim.crop(1,70,400)
spim.crop(2,0.3,19.0)

spim.decomposition(True)

It ouputs : ValueError: All the data are masked, change the mask.

It seems to me that the crop functions are at the source of this issue since when I comment them everything is fine.
I am asking here to check if I am missing something. But I will post an issue on github if not.

3 replies

TheTadpole97

@TheTadpole97

Hi, I'm not sure if it's just me missing something. But when I import images from Velox EMD (this particular file has 9538 HAADF frames), only the scaling from the first frame is retained in the axes_manager values. I've copied my code snippet below.

%matplotlib qt
import hyperspy.api as hs
import numpy as np
import matplotlib.pyplot as plt
import scipy
import hyperspy.misc as hsm
#prevent figure opening
plt.ioff()

#load file
s = hs.load("211217/HeatedTEM/HeatedTEM.emd")
print("imported")

print(s.axes_manager)

#format and save image with time stamp
for single_image in s:

    ####### Failed attempt at scaling

    single_image.axes_manager[1].scale
    single_image.axes_manager[0].scale

    single_image.axes_manager[1].offset
    single_image.axes_manager[0].offset

    single_image.axes_manager[1].units
    single_image.axes_manager[0].units

    a = single_image.plot(colorbar=False, scalebar=True, axes_ticks=False)
    plt.axis('off')
    plt.savefig('test/image %s.png' % str(s.axes_manager.indices), bbox_inches = 'tight', pad_inches = 0.1)
    plt.close()
    #single_image.save("test/image %s.png" % str(image_stack.axes_manager.indices))

But every single_image.axis_manager contains the same value as s.axis_manager (in this case 0.37nm) so the scaling is the same for every image

5 replies

aowenli

@aowenli

Hi, I wonder if I want to use two windows (before and after edge) to fit an EELS spectrum, what should I do?

rpsankaran

@rpsankaran

Hello
in Pycharm I had the below code that worked before with giving interactive hyperspy plots with s.plot()

import matplotlib
matplotlib.rcParams["backend"] = "Agg"
import hyperspy.api as hs

I am getting the following error and no plots shown. Please help if possible, and let me know if you need more information.
Thank you!

WARNING:hyperspy_gui_traitsui:The agg matplotlib backend is not compatible with the traitsui GUI elements. For more information, read http://hyperspy.readthedocs.io/en/stable/user_guide/getting_started.html#possible-warnings-when-importing-hyperspy.
WARNING:hyperspy_gui_traitsui:The traitsui GUI elements are not available.

rpsankaran

@rpsankaran

Also, having trouble with plotting an .emd. The navigator window comes up just fine, but is completely black. Should be the HAADF image - unsure how navigator sums/integrates/chooses the file for the navigator where the loaded data list has multiple signals: e.g. Any help in understanding why the navigator pane/window is black? Thank you!

[<EDSTEMSpectrum, title: EDS, dimensions: (|4096)>,
 <EDSTEMSpectrum, title: EDS, dimensions: (|4096)>,
 <EDSTEMSpectrum, title: EDS, dimensions: (|4096)>,
 <EDSTEMSpectrum, title: EDS, dimensions: (|4096)>,
 <Signal2D, title: x, dimensions: (|512, 512)>,
 <Signal2D, title: HAADF, dimensions: (|512, 512)>,
 <Signal2D, title: x, dimensions: (|512, 512)>,
 <Signal2D, title: x, dimensions: (|512, 512)>,
 <Signal2D, title: x, dimensions: (|512, 512)>,
 <Signal2D, title: x, dimensions: (|512, 512)>,
 <Signal2D, title: x, dimensions: (|512, 512)>,
 <Signal2D, title: x, dimensions: (|512, 512)>,
 <Signal2D, title: x, dimensions: (|512, 512)>,
 <Signal2D, title: x, dimensions: (|512, 512)>,
 <Signal2D, title: x, dimensions: (|512, 512)>,
 <EDSTEMSpectrum, title: EDS, dimensions: (512, 512|4096)>]

1 reply

zhanxun8

@zhanxun8

Hello, I analyze my EELS data using hyperspy. It worked well before. However, today when I ran remove_background function, it gave me error. Does anyone can help me with this problem? Thanks!

zhanxun8

@zhanxun8

zhanxun8

@zhanxun8

MurilooMoreira

@MurilooMoreira

Hello everyone, how are you? I saw in the documentation the new option to read the ASW files in the version 1.7dev. I can extract my image spectra frame by frame this way, but I cannot obtain the DF images frame by frame. I am obtaining in the list generated by the hs.load(), only the first DF image used to acquired the spectral image. Is it possible to extract all the DF images acquired? Using the AnalysisStation software I can see them but with Hyperspy I am having problems yet. Thank you!

1 reply

Thomas Aarholt

@thomasaarholt

@MurilooMoreira, I just made a function for you for the colormap you asked for. I thought it was a fun exercise. https://gist.github.com/thomasaarholt/169a1cf29048dd96c8a6c9b980adb9b6

See the gist for creating the cmap. This is how you would use it:

from scipy.misc import face
img = face(gray=True)
plt.figure()
plt.imshow(img, cmap=cmap)
plt.colorbar()

I was very surprised that there wasn't a built-in function to do this.

DENSmerijn

@DENSmerijn

Hey all, I am trying to get the decomposition of a sum of a section of the frames of a EDS signal.

When I load the entire signal with sum_frames=True, the decomposition works fine. But when I load it with sum_frames=False and then sum all the frames using .sum('Time'), the resulting signal looks differently (lower intensity) and the decomposition works but the result is different (worse). What is the difference between the sum_frames=True argument and summing the frames after loading using .sum('Time')?
Also, when I try to sum a section of the frames in time (e.g. the first 20) I get the error message: ValueError: All the data are masked, change the mask.
Is there a way to avoid this error and get the decomposition over a range of time?
Thank you!

1 reply

MurilooMoreira

@MurilooMoreira

@thomasaarholt thank you man, I will try, test and maybe modify this function for other colors also, thank you very much. Yeah, I always tought strange that it was not possible to do it with hyperspy, I always use the matplotlib cmaps, but I didn't know how to create new ones. Thank you

1 reply

fg-personal

@fg-personal

To whom it may regard, hyperspy/tests/io/test_jeol.py is not running smoothly on my device. Is this the correct place to ask for help?

When I replace the test files with actual files I have on my device (same extensions), and I run the test script I get the following messages:

WARNING:hyperspy.io:Unable to infer file type from extension 'ASW'. Will attempt to load the file with the Python imaging library.
ERROR:hyperspy.io:If this file format is supported, please report this error to the HyperSpy developers.

2 replies

OliDG

@OliDG

Hi, I am using EDS models and have trouble to restore the stored ones.
I create a model m, fit it and store it, and also copy it to a EDS_model variable

#create a model using all selected elements:
m = si.create_model()
m.fit()
m.fit_background()
#Reduce the element selection to the one of interest and quantify
kfactors = Assign_elements2Quant()
xray_lines_selected=si.metadata.Sample.xray_lines
m_int_fit = m.get_lines_intensity(xray_lines_selected)
m.store()
EDS_model = m

After this, the "si" is saved to a .hspy file.
If i look at the EDS_model, it is fine, I can plot it and so on.

EDS_model
Out[80]: <EDSTEMModel, title: EDX>

But then I try to load the .hspy file again, I see the model is there, with the components, but cannot restore it or plot it... why?

l = hs.load(signal_type="EDS_TEM", escape_square_brackets=(True))
l.models
Out[82]: 
└── a
    ├── components
    │   ├── Al_Ka
    │   ├── Al_Kb
    │   ├── C_Ka
    │   ├── Co_Ka
    │   ├── Co_Kb
    │   ├── Co_La
    │   ├── Co_Lb3
    │   ├── Co_Ll
    │   ├── Co_Ln
    │   ├── Cr_Ka
    │   ├── Cr_Kb
    │   ├── Cr_La
    │   ├── Cr_Lb3
    │   ├── Cr_Ll
    │   ├── Cr_Ln
    │   ├── Mo_Ka
    │   ├── Mo_Kb
    │   ├── Mo_La
    │   ├── Mo_Lb1
    │   ├── Mo_Lb2
    │   ├── Mo_Lb3
    │   ├── Mo_Lg1
    │   ├── Mo_Lg3
    │   ├── Mo_Ll
    │   ├── Mo_Ln
    │   ├── O_Ka
    │   ├── W_La
    │   ├── W_Lb1
    │   ├── W_Lb2
    │   ├── W_Lb3
    │   ├── W_Lb4
    │   ├── W_Lg1
    │   ├── W_Lg3
    │   ├── W_Ll
    │   ├── W_Ln
    │   ├── W_M2N4
    │   ├── W_M3O4
    │   ├── W_M3O5
    │   ├── W_Ma
    │   ├── W_Mb
    │   ├── W_Mg
    │   ├── W_Mz
    │   ├── Zn_Ka
    │   ├── Zn_Kb
    │   ├── Zn_La
    │   ├── Zn_Lb1
    │   ├── Zn_Lb3
    │   ├── Zn_Ll
    │   ├── Zn_Ln
    │   └── background_order_6
    ├── date = 2022-02-08 12:09:22
    └── dimensions = (96, 89|2048)

Mymodel = l.models.a.restore()
Traceback (most recent call last):

  File "C:\Users\oldo\AppData\Local\Temp/ipykernel_14272/3459143043.py", line 1, in <module>
    Mymodel = l.models.a.restore()

  File "C:\Users\oldo\.conda\envs\hspy_env\lib\site-packages\hyperspy\signal.py", line 82, in <lambda>
    self.restore = lambda: mm.restore(self._name)

  File "C:\Users\oldo\.conda\envs\hspy_env\lib\site-packages\hyperspy\signal.py", line 241, in restore
    return self._signal.create_model(dictionary=copy.deepcopy(d))

  File "C:\Users\oldo\.conda\envs\hspy_env\lib\site-packages\hyperspy\_signals\eds_tem.py", line 745, in create_model
    model = EDSTEMModel(self,

  File "C:\Users\oldo\.conda\envs\hspy_env\lib\site-packages\hyperspy\models\edstemmodel.py", line 45, in __init__
    EDSModel.__init__(self, spectrum, auto_background, auto_add_lines,

  File "C:\Users\oldo\.conda\envs\hspy_env\lib\site-packages\hyperspy\models\edsmodel.py", line 131, in __init__
    Model1D.__init__(self, spectrum, *args, **kwargs)

  File "C:\Users\oldo\.conda\envs\hspy_env\lib\site-packages\hyperspy\models\model1d.py", line 279, in __init__
    self._load_dictionary(dictionary)

  File "C:\Users\oldo\.conda\envs\hspy_env\lib\site-packages\hyperspy\model.py", line 306, in _load_dictionary
    id_dict.update(self[-1]._load_dictionary(comp))

  File "C:\Users\oldo\.conda\envs\hspy_env\lib\site-packages\hyperspy\component.py", line 1223, in _load_dictionary
    raise ValueError(

ValueError: _id_name of parameters in component and dictionary do not match

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