Display QPI image data #146

PinkShnack · 2023-10-31T13:55:51Z

As described in (create issue) I want to see qpi data non-scalar features in shapeout2.

PinkShnack · 2023-10-31T13:59:20Z

Progress so-far:

I just need to generalise the methods and then this should be ready for review. (I'm sure I'll need some tests also)

PinkShnack

@paulmueller when you get a chance, pleae have a look at the changes :)

I tested that it works on normal rtdc files, and on rtdc files with qpi data.

Perhaps I need to add some tests?

PinkShnack · 2023-10-31T16:01:51Z

shapeout2/gui/quick_view/qv_main.py

+        else:
+            raise ValueError(f"Options for `feat` are 'image', "
+                             f"'qpi_pha' and 'qpi_amp', got {feat}")
+


I generalised this a bit. Check if there is anything more to do :)

I would not convert the float32 images to uint8. This could make things look really ugly (the kind of artifacts you see in .gif images) and pyqtgraph should support showing float32 images. Also, for the phase images you would like to use the diverging colormap coolwarm (needs to be ported to ShapeOut without adding the matplotlib dependency). So ideally, you have a background phase of 0 and then a symmetric colormap with positive (red) and negative (blue) phase delay.

PinkShnack · 2023-10-31T16:02:28Z

shapeout2/gui/quick_view/qv_main.py

-                    # the plot got updated, and we still have the old data
-                    cellimg, imkw = self.get_event_image(self.rtdc_ds, 0)
+
+            self.imageView_image_poly.hide()


We can hide first and have that as default, and then call .show() if the image is available (see below)

PinkShnack · 2023-10-31T16:03:51Z

shapeout2/gui/quick_view/qv_main.py

+                        if feat == "image":
+                            self.imageView_image_poly.setImage(
+                                cellimg, **imkw)
+                            self.imageView_image_poly.show()


I don't like that this is sliiiightly different than show_event. I guess I could add a groupBox for the poly images?

Maybe there should be a separate class entirely that handles image plotting? Generalization is not easy due to the different data types and requirements for visualization.

PinkShnack · 2023-10-31T16:04:19Z

shapeout2/gui/quick_view/qv_main.py

+                if feat in ds:
+                    cellimg, imkw = self.get_event_image(ds, event, feat)
+                    if feat == "image":
+                        self.imageView_image.setImage(cellimg, **imkw)


These if statements also annoy me a bit. Is there a way to access the QT attributes via string definitions?

You could generalize it with dictionaries defined in __init__:

self.img_info = { "image": [self.imageView_image, "gray"], "qpi_pha": [self.imageView_image_pha. "coolwarm"], etc... }

codecov · 2023-10-31T16:08:34Z

Codecov Report

Attention: 30 lines in your changes are missing coverage. Please review.

Comparison is base (d0ec73d) 78.93% compared to head (0d94818) 78.71%.
Report is 23 commits behind head on master.

❗ Current head 0d94818 differs from pull request most recent head 44bd6c1. Consider uploading reports for the commit 44bd6c1 to get more accurate results

Files	Patch %	Lines
shapeout2/gui/quick_view/qv_main.py	48.27%	30 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #146      +/-   ##
==========================================
- Coverage   78.93%   78.71%   -0.22%     
==========================================
  Files          63       63              
  Lines        6768     6807      +39     
==========================================
+ Hits         5342     5358      +16     
- Misses       1426     1449      +23

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paulmueller

The main issue that I see is that the current way contours are plotted is outdated and also does not work with phase data (changing pixels in an RGB image). So as far as I can see, there is no way around rewriting displaying the contour for phase and amplitude data.

Also, I believe there should be some way of setting the range for (at least) phase values. And phase values should always be centered at zero with the corresponding colormap showing white or no color. "coolwarm" from matplotlib is a good way of displaying phase, but you would have to copy-paste it to work with pyqtgraph, because I think it is not (yet) in pyqtgraph. "viridis" got ported to pyqtgraph, so it should be straight-forward.

paulmueller · 2023-10-31T16:13:51Z

shapeout2/gui/quick_view/qv_main.py

+        else:
+            raise ValueError(f"Options for `feat` are 'image', "
+                             f"'qpi_pha' and 'qpi_amp', got {feat}")
+


I would not convert the float32 images to uint8. This could make things look really ugly (the kind of artifacts you see in .gif images) and pyqtgraph should support showing float32 images. Also, for the phase images you would like to use the diverging colormap coolwarm (needs to be ported to ShapeOut without adding the matplotlib dependency). So ideally, you have a background phase of 0 and then a symmetric colormap with positive (red) and negative (blue) phase delay.

paulmueller · 2023-10-31T16:17:52Z

shapeout2/gui/quick_view/qv_main.py

+        return cellimg, imkw
+
+    @staticmethod
+    def display_contour(ds, event, state, cellimg):


In the future, we might want to change how we compute/display the contour, i.e. we are planning to use non-discrete contours (@SaraKaliman). So it might make sense to implement two functions add_contour_to_image (for "image" data) and draw_contour_on_plot (for float32 qpi data) which could then also be used later for non-discrete contours.

Practically I want to use shapeout to visualise the image data so Kyoo can look at the data in one place. For that, what I have built right now is enough. The colormaps and contour issues will just hold that up. Could we put all that in a separate PR?

If it is just for Kyoo, then you could just create a custom executable for him:

cd build_recipes pip install -r win_build_requirements.txt pyinstaller -y --log-level=WARN win_ShapeOut2.spec

I would not like to merge an incomplete feature. Moreover, the grayscale colormap leads to ambiguities. This should not be used by the general crowd.

If you think it isn't a complete feature then I understand. I'll try to implement the colorbar etc soon.

Thanks for the custom executable, much better... I was just gonna do the dev version. :)

paulmueller · 2023-10-31T16:23:08Z

shapeout2/gui/quick_view/qv_main.py

+                        if feat == "image":
+                            self.imageView_image_poly.setImage(
+                                cellimg, **imkw)
+                            self.imageView_image_poly.show()


Maybe there should be a separate class entirely that handles image plotting? Generalization is not easy due to the different data types and requirements for visualization.

paulmueller · 2023-10-31T16:30:20Z

shapeout2/gui/quick_view/qv_main.py

+                if feat in ds:
+                    cellimg, imkw = self.get_event_image(ds, event, feat)
+                    if feat == "image":
+                        self.imageView_image.setImage(cellimg, **imkw)


You could generalize it with dictionaries defined in __init__:

self.img_info = { "image": [self.imageView_image, "gray"], "qpi_pha": [self.imageView_image_pha. "coolwarm"], etc... }

paulmueller · 2023-10-31T16:31:17Z

shapeout2/gui/quick_view/qv_main.ui

@@ -203,7 +203,7 @@
       </size>
      </property>
      <property name="currentIndex">
-       <number>0</number>
+       <number>2</number>


keep 0 the default

No idea how that changed. QT seems to change random stuff

If you click on a tab in QtDesigner, it sets this tab as default.

PinkShnack · 2023-11-17T18:48:20Z

A really fun side-effect of having floating-point values in the image display is that we get a pinkish contour for the phase. :) I guess we have to fix this :')

EDIT:

I (unfortunately) fixed the colour issue. I also confirmed that the colours are, in fact, the same!

Eoghan O'Connell added 2 commits October 24, 2023 14:08

enh: add simple pha and amp to gui, display not correct

2b528df

enh: add method for qpi feature display

697e125

ref: generalise the get_event method

a86d100

PinkShnack commented Oct 31, 2023

View reviewed changes

paulmueller requested changes Oct 31, 2023

View reviewed changes

Eoghan O'Connell added 2 commits November 2, 2023 16:09

enh: correctly handle varying pha and image shapes

0d94818

enh: display qpi images as float and set the range via qt setView

7db1900

fix: correct the contour pixel colour based on the pixel intensity range

44bd6c1

paulmueller marked this pull request as draft March 20, 2024 14:00

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Display QPI image data #146

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Display QPI image data #146

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