update 3_Multichannel #160

casperdcl · 2024-08-13T17:00:31Z

update demos/3_Multichannel (part of Update to CIL version 24.2 (latest release) #155)
- drop max_iteration
- fix check_convergence
- tidy k = 0; k+=1 -> enumerate
- str.format -> f-strings
- print -> tqdm
- show2D: append ; if last cell line

- part of #155

MargaretDuff · 2024-08-23T11:03:02Z

We aren't always seeing progress bars e.g.folder 3 notebook 1:

MargaretDuff · 2024-08-23T12:11:52Z

Can we zoom this in on folder 3 notebook 3:

MargaretDuff · 2024-08-23T12:30:02Z

In folder 2 notebook 2, is this a regularisation toolkit issue?

lauramurgatroyd

Sorry I only got part way through reviewing so far, will continue next week.

lauramurgatroyd · 2024-09-05T15:56:57Z

demos/3_Multichannel/01_Colour_Processing.ipynb

-    "show2D( data, slice_list=[('channel',0),('channel',1),('channel',2)], \\\n",
-    "        title=[\"Red\",\"Green\",\"Blue\"], origin=\"upper\", num_cols=3)"
+    "show2D(data, slice_list=[('channel',0),('channel',1),('channel',2)],\n",
+    "       title=[\"Red\",\"Green\",\"Blue\"], origin=\"upper\", num_cols=3);"


Suggested change

" title=[\"Red\",\"Green\",\"Blue\"], origin=\"upper\", num_cols=3);"

" title=[\"Red\",\"Green\",\"Blue\"], origin=\"upper\", num_cols=3)"

definitely not. See OP.

lauramurgatroyd · 2024-09-05T16:01:51Z

demos/3_Multichannel/02_Dynamic_CT.ipynb

   "metadata": {},
   "outputs": [],
   "source": [
-    "show_geometry(ag)"
+    "show_geometry(ag);"


Suggested change

"show_geometry(ag);"

"show_geometry(ag)"

definitely not. See OP.

lauramurgatroyd · 2024-09-05T16:05:32Z

demos/3_Multichannel/03_Hyperspectral_reconstruction.ipynb

@@ -282,7 +277,7 @@
   "metadata": {},
   "outputs": [],
   "source": [
-    "show_geometry(ag, view_distance = 4.5, elevation=10, azimuthal=-65, figsize=(10,10))"
+    "show_geometry(ag, view_distance = 4.5, elevation=10, azimuthal=-65, figsize=(10,10));"


Suggested change

"show_geometry(ag, view_distance = 4.5, elevation=10, azimuthal=-65, figsize=(10,10));"

"show_geometry(ag, view_distance = 4.5, elevation=10, azimuthal=-65, figsize=(10,10))"

definitely not. See OP.

demos/3_Multichannel/01_Colour_Processing.ipynb

lauramurgatroyd

There are quite a few places where check_convergence is called - why is this?

Whilst checking, I found some additional issues with the notebooks which need updating, sorry

demos/3_Multichannel/02_Dynamic_CT.ipynb

lauramurgatroyd · 2024-09-25T10:53:29Z

demos/3_Multichannel/03_Hyperspectral_reconstruction.ipynb

+    "                   [(\"channel\", 20),(\"horizontal_y\", 35)],\n",
+    "                   [(\"channel\", 20),(\"horizontal_x\", 25)]],\n",
+    "                   cmap=\"inferno\", num_cols=3,\n",
+    "                   origin=\"upper\", fix_range=(0,0.5));"


Suggested change

" origin=\"upper\", fix_range=(0,0.5));"

" origin=\"upper\", fix_range=(0,0.5))"

definitely not. See OP.

demos/3_Multichannel/03_Hyperspectral_reconstruction.ipynb

lauramurgatroyd · 2024-10-15T13:49:52Z

Sorry if I've missed this but why do we need ';' after show2D if its the last cell line?

lauramurgatroyd · 2024-10-15T15:29:40Z

Can we zoom this in on folder 3 notebook 3:

This was the biggest I could get it, but it removes the tilt which possibly makes it less useful.

I think there are some issues with show_geometry which make it difficult to zoom in - I will investigate further and open an issue in CIL

lauramurgatroyd · 2024-10-15T15:30:01Z

I am going to revert the show_geometry change

lauramurgatroyd · 2024-10-15T15:35:41Z

Relevant issue in CIL: TomographicImaging/CIL#1954

lauramurgatroyd

I have now made the changes that I suggested. @MargaretDuff would you like to review or shall I merge?

demos/3_Multichannel/02_Dynamic_CT.ipynb

MargaretDuff · 2024-10-16T08:19:41Z

Needs an additional: as_array()

MargaretDuff · 2024-10-16T09:00:49Z

Tested on 24.2.0 - happy to merge!

Tested working on CIL 24.2.0

minor updates

81c5cc2

- part of #155

casperdcl requested review from MargaretDuff and gfardell August 13, 2024 17:00

casperdcl self-assigned this Aug 13, 2024

casperdcl added the documentation Improvements or additions to documentation label Aug 13, 2024

casperdcl marked this pull request as ready for review August 13, 2024 18:49

casperdcl requested a review from lauramurgatroyd August 14, 2024 08:41

casperdcl mentioned this pull request Aug 22, 2024

Update to CIL version 24.2 (latest release) #155

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lauramurgatroyd reviewed Sep 17, 2024

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lauramurgatroyd requested changes Sep 25, 2024

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lauramurgatroyd mentioned this pull request Oct 15, 2024

view_distance parameter in show_geometry has no effect TomographicImaging/CIL#1954

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lauramurgatroyd reviewed Oct 15, 2024

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lauramurgatroyd and others added 2 commits October 16, 2024 11:31

PR review changes

6027a97

fix abs() comparison

653891f

Tested working on CIL 24.2.0

casperdcl force-pushed the minor-updates branch from 2506598 to 653891f Compare October 16, 2024 10:32

casperdcl merged commit fd7211c into main Oct 16, 2024

casperdcl deleted the minor-updates branch October 16, 2024 10:34

lauramurgatroyd mentioned this pull request Oct 16, 2024

Deprecation warning when running iterative algorithms #149

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update 3_Multichannel #160

update 3_Multichannel #160

casperdcl commented Aug 13, 2024 •

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	" title=[\"Red\",\"Green\",\"Blue\"], origin=\"upper\", num_cols=3);"
	" title=[\"Red\",\"Green\",\"Blue\"], origin=\"upper\", num_cols=3)"

	"show_geometry(ag, view_distance = 4.5, elevation=10, azimuthal=-65, figsize=(10,10));"
	"show_geometry(ag, view_distance = 4.5, elevation=10, azimuthal=-65, figsize=(10,10))"

	" origin=\"upper\", fix_range=(0,0.5));"
	" origin=\"upper\", fix_range=(0,0.5))"

update 3_Multichannel #160

update 3_Multichannel #160

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