Added new Examples by Lulus792 · Pull Request #253 · LumiSpy/lumispy

Lulus792 · 2026-02-05T16:05:16Z

Added new example map_function, energie_conversion, ROIs, peak_analysis, basic_model_fitting, custom_model_fitting and restructured the old position of the index example. And changed all the data_cleaning examples to use the build in data module of lumispy

Progress of the PR

added new example map_function
add a changelog entry in the upcoming_changes folder ,
ready for review.

…ry extension

…and asymmetric_peak_map function, added data tests directory and created a test for both functions

…umiSpy#250 and made nanoparticles.hspy significantly smaller

…and asymmetric_peak_map function, added data tests directory and created a test for both functions

…umiSpy#250 and made nanoparticles.hspy significantly smaller

examples/peak_finding/peak_identification.py

+# ^^^^^^^^^^^^
+#
+# It returns a structured array that contains ``position``, ``height`` and ``width`` of the found peaks.
+peaks[0, 0]


…nct files, updated ROIs

jlaehne · 2026-02-26T15:14:04Z

can you merge in the updated main branch to resolve conflicts with the examples that have been updated in the previous PR

Lulus792 · 2026-02-27T01:03:08Z

syncing with main didnt quite work so i will have to do it manually i will make the changes in the morning and put the arrow for ready for review once i fixed it.

Lulus792 · 2026-02-27T09:21:18Z

syncing with main didnt quite work so i will have to do it manually i will make the changes in the morning and put the arrow for ready for review once i fixed it.

should be ready now for review

aidanc151 · 2026-03-02T13:41:12Z

examples/data_selection/indexing.py

+"""
+Indexing
+========
+Indexing is achieved using `inav <HS_inav_>`__ or `isig <HS_isig_>`__, which allows the navigation- and signalaxes to be accessed independently.


space between signal and axes

aidanc151 · 2026-03-02T13:41:49Z

examples/data_selection/indexing.py

+# Creating a small example signal
+# -------------------------------
+#
+# We create a simple ``Signal1D`` with a total shape of ``(2, 3, 4)``:


replace total shape with axes shape

aidanc151 · 2026-03-02T13:45:07Z

examples/data_selection/indexing.py

+Indexing
+========
+Indexing is achieved using `inav <HS_inav_>`__ or `isig <HS_isig_>`__, which allows the navigation- and signalaxes to be accessed independently.
+The index operation returns a view of the original signal.


maybe needs to be clarified/reworded - not sure if I understand what is meant here

aidanc151 · 2026-03-02T13:48:34Z

examples/data_selection/indexing.py

I find the example easy to follow until the isig section. I find the indexing of the array a bit confusing when dealing with isig, maybe annotations to the output arrays or a graphical illustration could improve this

aidanc151 · 2026-03-02T13:51:19Z

examples/data_selection/region_of_interest.py

+"""
+Region of Interest (ROI)
+========================
+This example demonstrates how to use ROIs from Hyperspy. ROIs are used to select a subset of the data for further analysis. It can be done interactively aswell as non interactively.


replace with "This example demonstrates use of HyperSpy ROIs for a hyperspectral luminescence dataset. ROIs are used to select a subset of the data for analysis, this can be done interactively as well as non interactively."

aidanc151 · 2026-03-02T13:55:41Z

examples/data_selection/region_of_interest.py

+# -------------------
+#
+# For non-interactove ROIs we have to specify the type of ROI we want to use. In this case we'll use
+# ``Line2DROI(x1=, y1=, x2=, y2=, linewidth=)``.


I would remove then equals signs from here: Line2DROI(x1=, y1=, x2=, y2=, linewidth=)

aidanc151 · 2026-03-02T13:58:55Z

examples/data_selection/region_of_interest.py

+ax1 = s2.axes_manager[0]
+ax2 = s2.axes_manager[1]
+
+# define start params


Can a units argument be used here to avoid multiplying by scale factors? I think if cx, cy were not defined the default position of the circle should also place within the bounds of the signal

aidanc151 · 2026-03-02T14:02:18Z

examples/data_selection/region_of_interest.py

HyperSpy does have a nice example gallery for ROIs already, in order to not overlap too much I wonder if these examples can be a little more specific to luminescence data analysis. One thing I think could also be included is a computation of calculating the mean of a signal extracted from a ROI - though this is also included in a hyperspy example

aidanc151 · 2026-03-02T14:05:52Z

examples/model_fitting/custom_components.py

These examples are nice but I wonder if they would be more suited to the HyperSpy example gallery? They don't seem specific to luminescence data, one idea would be to keep the Mathematical Expression header but define a exponential convolved with a gaussian (since this is useful for modelling time-resolved luminescence transients)

aidanc151 · 2026-03-02T14:07:13Z

examples/peak_finding/peak_width.py

The image at the top of the page has a spike in it, could be better to use a different image to not confuse the which peak the width is being estimated of

aidanc151 · 2026-03-02T14:12:36Z

examples/peak_finding/peak_width.py

+# %%
+# Return Value
+# ^^^^^^^^^^^^
+# Returns float or lists of floats: ``[width, left, right]``. In our case we get a list of width since we have a map of spectra.


replace "In our case we get a list of width since we have a map of spectra." with some along the lines of "We update our metadata of the new signal containing our FWHM's and plot the results"

aidanc151 · 2026-03-02T14:21:53Z

examples/peak_finding/peak_identification.py

Maybe also better suited as a hyperspy example?

I don't love that the ohaver function returns a structured array instead of hyperspy signals, if this was changed I think it would make this example better as well.

aidanc151 · 2026-03-02T14:23:21Z

examples/data_selection/region_of_interest.py

The Line2D ROI example also appears under Plotting - Extraction of Linescan example

janisschumacher and others added 14 commits January 13, 2026 15:11

added examples navigation and example1 skeleton

9645c78

created TOC after User Guide and included configuration for the galle…

1b1060b

…ry extension

added sphinx-gallery to pyproject.toml

81ceb8f

ran python black style corrections

7f6de80

Added data module like in hyperspy and exspy featuring nanoparticles …

83a2dd4

…and asymmetric_peak_map function, added data tests directory and created a test for both functions

Reshaped nanoparticles.hspy so that it only has a size of 1.3m

1ef9cbf

Merge branch 'LumiSpy:main' into main

3bebe96

Changed dependencies for hyperspy to the latest, added changelog for L…

fff814f

…umiSpy#250 and made nanoparticles.hspy significantly smaller

Data wasn't seen as a module before know it should work

3fb5554

Added example file for indexing using isig and inav

05bd562

added link to scale and offset

a8e2de9

Rechanged the import for the data module

c4cf787

removed unnecessary metadata attributes

194f513

removed unnecessary metadata attributes

71b5e02

jlaehne mentioned this pull request Feb 9, 2026

added examples to the doc #248

Merged

updated the docstring for the data module, and fixed linting errors

a1b7886

Lulus792 force-pushed the examples branch from 0edf7d2 to 00dab92 Compare February 10, 2026 11:42

janisschumacher and others added 12 commits February 10, 2026 12:45

added to changelog

cfbb7c5

remove indentation before docstring snippets

fcdf960

make docstrings more consistent

a6ba6c0

Added data module like in hyperspy and exspy featuring nanoparticles …

6002d82

…and asymmetric_peak_map function, added data tests directory and created a test for both functions

Reshaped nanoparticles.hspy so that it only has a size of 1.3m

ff2b47c

Changed dependencies for hyperspy to the latest, added changelog for L…

8a5f11a

…umiSpy#250 and made nanoparticles.hspy significantly smaller

Added data handling tree, and first file map_function

30548e0

added data cleaning examples

7d6de56

Added upcoming_changes entry

67a9618

relocated indexing.py file

052a59b

removed unnecessary metadata attributes

0a30022

Lulus792 force-pushed the examples branch from 00dab92 to 52b9ecb Compare February 10, 2026 11:52

Merge new plotting files from PR LumiSpy#248

b61ae29

Lulus792 force-pushed the examples branch from 55ddfb7 to 6eaf8ce Compare February 13, 2026 13:28

github-advanced-security bot found potential problems Feb 13, 2026

View reviewed changes

examples/peak_finding/peak_identification.py

# ^^^^^^^^^^^^

#

# It returns a structured array that contains ``position``, ``height`` and ``width`` of the found peaks.

peaks[0, 0]

Check notice

Code scanning / CodeQL

Statement has no effect Note

This statement has no effect.

Lulus792 force-pushed the examples branch 3 times, most recently from c13c7ae to ce51762 Compare February 13, 2026 14:30

Lulus792 force-pushed the examples branch 3 times, most recently from 568f59e to ff32909 Compare February 23, 2026 12:14

restructured example dir and seperated peak analysis into three disti…

ff32909

…nct files, updated ROIs

Merge branch 'main' into tmp

af0f55e

Lulus792 force-pushed the examples branch from af6c127 to af0f55e Compare February 27, 2026 09:20

fixed linter

ff47767

Lulus792 force-pushed the examples branch from c78b48d to ff47767 Compare February 27, 2026 16:57

aidanc151 reviewed Mar 2, 2026

View reviewed changes

examples/data_selection/region_of_interest.py

Copy link

aidanc151 Mar 2, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The Line2D ROI example also appears under Plotting - Extraction of Linescan example

Conversation

Lulus792 commented Feb 5, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Progress of the PR

Uh oh!

Check notice

jlaehne commented Feb 26, 2026

Uh oh!

Lulus792 commented Feb 27, 2026

Uh oh!

Lulus792 commented Feb 27, 2026

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

aidanc151 Mar 2, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Lulus792 commented Feb 5, 2026 •

edited

Loading

aidanc151 Mar 2, 2026 •

edited

Loading