How To - TiffStackReader, custom Geometry, Normaliser by M-A-Demir · Pull Request #199 · TomographicImaging/CIL-Demos

M-A-Demir · 2024-10-23T11:19:32Z

Added TiffStackReader.ipynb how-to to the '1_Read_and_visualise' folder.
Added 2_Geometry/CreateCustomGeometry.ipynb
Added 3_Processors/FlatDarkFieldNormaliser.ipynb

Closes #170
Closes #173

… and flat/dark field Normaliser

M-A-Demir · 2024-10-23T16:44:21Z

Potential issue: TIFFStackReader.ipynb downloads the sandstone dataset to its directory (how-tos/1_Read_and_visualise), CreateCustomGeometry.ipynb uses the already-downloaded dataset, but file path was not updated in the notebook.

Where should this dataset be downloaded to in this repo, so I can adjust the file path variables accordingly?

hrobarts

Hi Mariam, these are looking really great - I think they're all very clear. I couldn't add comments on the code for the TIFFStackReader and FlatDarkFieldNormaliser so putting some here:

In the TIFFStackReader you could say it accepts .tiff and ,tif files
In the FlatDarkFieldNormaliser you could use show2D([sandstone, sandstone_norm]) to show the plots next to each other, you could add titles as well. Maybe the same for the flat and dark plots
I think the %store looks like a good way to get the previously processed data but we should discuss how that would work if we're going to use GHA to render these

how-to/1_Read_and_visualise/NikonDataReader.ipynb

how-to/2_Geometry/CreateCustomGeometry.ipynb

hrobarts · 2024-10-24T08:40:40Z

how-to/2_Geometry/CreateCustomGeometry.ipynb

I think this simple geometry example will be really useful for people. I wonder if we should have a separate 2D cone beam, 2D parallel beam, 3D cone beam and 3D parallel beam example?

… into how_to_tiff Updating local

MargaretDuff · 2024-10-31T12:10:04Z

Hi @M-A-Demir, thanks for your hard work on this! I think all the code is there but there are some places where we could improve the explanations.

In the FlatDarkFieldNormaliser notebook, it would be great if you could explain at the top of the notebook what a flat and dark field is and why you would correct for it.
In the CreateCustomGeometry notebook, where did you get the SrcToObject and SrcToDetector values from? It might be worth giving a little more explanation of where you found these but mentioning that it will be different for different systems and ways of saving data.
In the TiffStackReader notebook, you create a list of tiff_files excluding some of the BBii_????.tif files. Perhaps point to the normalisation notebook with your explanation as to why?

I will leave a few more specific comments in the notebooks

MargaretDuff · 2024-10-31T13:03:14Z

how-to/2_Geometry/CreateCustomGeometry.ipynb

+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The `AcquisitionGeometry` and loaded data are needed to use CIL's visualisation and reconstruction tools.   \n",


Not sure this sentence makes sense

MargaretDuff · 2024-10-31T13:04:38Z

how-to/2_Geometry/CreateCustomGeometry.ipynb

+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Using `show2D()`, we can view a central projection of the data:"


Might also be worth showing an FBP reconstruction, to demonstrate that the geometry is correct and thus gives a reasonable reconstruction.

Thanks Margaret! I added the clarifications you suggested, as well as the reconstruction (& CoR adjustment) to the geometry notebook

…oks. Added extra section for reconstructing and adjusting CoR in Geometry notebook

MargaretDuff

Sorry Mariam, I made a few suggested changes and then between vscode and github they all got deleted. Will try again another time

MargaretDuff

Thanks @M-A-Demir. The code is all there. I have made some suggestions to improve the readability!

how-to/1_Read_and_visualise/TIFFStackReader.ipynb

MargaretDuff · 2024-11-12T11:23:38Z

how-to/1_Read_and_visualise/TIFFStackReader.ipynb

+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%store sandstone"


What does this do? Generally users will take notebooks verbatim and try and adapt them to their dataset so if this is a cell particular to the how-tos and a not general CIL recommendation then we should state that.

how-to/data/.foo

how-to/3_Processors/FlatDarkFieldNormaliser.ipynb

MargaretDuff · 2024-11-12T11:34:50Z

how-to/3_Processors/FlatDarkFieldNormaliser.ipynb

+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%store -r sandstone\n",


Does this mean you have to run the previous how-to first. This needs to be made clear if so!

how-to/3_Processors/FlatDarkFieldNormaliser.ipynb

how-to/1_Read_and_visualise/TIFFStackReader.ipynb

Co-authored-by: Margaret Duff <43645617+MargaretDuff@users.noreply.github.com>

… into how_to_tiff

Co-authored-by: Margaret Duff <43645617+MargaretDuff@users.noreply.github.com>

hrobarts · 2024-12-10T11:43:41Z

Hi Mariam, these are all looking great. I'd be happy to go ahead and merge the TiffStackReader and Normaliser notebooks. I think we should add a simulated example to the Normaliser in future but this works well as a real example.
I would maybe ask @gfardell her opinion on the geometry notebook

MargaretDuff

Looking good @M-A-Demir, have left a few style comments

how-to/1_Read_and_visualise/TIFFStackReader.ipynb

how-to/2_Geometry/CreateCustomGeometry.ipynb

how-to/3_Processors/FlatDarkFieldNormaliser.ipynb

MargaretDuff · 2025-01-17T13:34:40Z

how-to/3_Processors/FlatDarkFieldNormaliser.ipynb

+    "# %store -r sandstone\n",
+    "# show2D(sandstone)"


Are these meant to be commented out?

Yes, I have added clarification to the comment above this cell that these should be uncommented if you run and save data from the Geometry notebook

MargaretDuff · 2025-01-17T13:35:10Z

how-to/3_Processors/FlatDarkFieldNormaliser.ipynb

+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The `%store -r sandstone` command allows us to use the `sandstone` `AcquisitionData` we saved in the `1_Read_and_visualise/TIFFStackReader.ipynb` notebook. Please run the TIFFStackReader notebook (without deleting the `data/sandstone` folder), and save the `sandstone` variable before running the cell below."


Suggested change

"The `%store -r sandstone` command allows us to use the `sandstone` `AcquisitionData` we saved in the `1_Read_and_visualise/TIFFStackReader.ipynb` notebook. Please run the TIFFStackReader notebook (without deleting the `data/sandstone` folder), and save the `sandstone` variable before running the cell below."

"Note: The `%store -r sandstone` command allows us to use the `sandstone` `AcquisitionData` we saved in the `1_Read_and_visualise/TIFFStackReader.ipynb` notebook. Please run the TIFFStackReader notebook (without deleting the `data/sandstone` folder), and save the `sandstone` variable before running the cell below."

Co-authored-by: Margaret Duff <43645617+MargaretDuff@users.noreply.github.com>

Added clarification on commented %store line

Formatting in changed print statements caused notebook failure to load

Added how-to for TIFFStackReader, custom AcquisitionGeometry creation…

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… and flat/dark field Normaliser

M-A-Demir requested review from hrobarts and lauramurgatroyd October 23, 2024 11:19

Updated comment about geometry visualisation

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hrobarts reviewed Oct 24, 2024

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M-A-Demir added 6 commits October 24, 2024 13:52

Updated datapaths

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Removed unneccessary file and added empty data folder

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Merge branch 'how_to_tiff' of github.com:TomographicImaging/CIL-Demos…

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… into how_to_tiff Updating local

Merge remote-tracking branch 'origin/main' into how_to_tiff

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Merged upstream changes

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undo deletion of Nikon and Zeiss how-tos

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M-A-Demir requested a review from MargaretDuff October 31, 2024 10:03

MargaretDuff reviewed Oct 31, 2024

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Updated explanations in Normaliser, TiffStackReader & Geometry notebo…

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…oks. Added extra section for reconstructing and adjusting CoR in Geometry notebook

M-A-Demir requested review from MargaretDuff and hrobarts November 1, 2024 20:43

MargaretDuff requested changes Nov 8, 2024

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Unrendered ver of notebooks

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how-to/1_Read_and_visualise/TIFFStackReader.ipynb Show resolved Hide resolved

M-A-Demir and others added 8 commits November 14, 2024 13:22

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Update how-to/3_Processors/FlatDarkFieldNormaliser.ipynb

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Update how-to/3_Processors/FlatDarkFieldNormaliser.ipynb

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Update how-to/1_Read_and_visualise/TIFFStackReader.ipynb

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Update how-to/1_Read_and_visualise/TIFFStackReader.ipynb

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added clarification on jupyter %store commands

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M-A-Demir and others added 7 commits November 19, 2024 10:22

Merge branch 'how_to_tiff' of github.com:TomographicImaging/CIL-Demos…

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… into how_to_tiff

Update how-to/1_Read_and_visualise/TIFFStackReader.ipynb

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Update how-to/1_Read_and_visualise/TIFFStackReader.ipynb

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Update how-to/2_Geometry/CreateCustomGeometry.ipynb

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Update how-to/2_Geometry/CreateCustomGeometry.ipynb

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Co-authored-by: Margaret Duff <43645617+MargaretDuff@users.noreply.github.com>

Update how-to/2_Geometry/CreateCustomGeometry.ipynb

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clarity

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M-A-Demir requested review from hrobarts and removed request for hrobarts and lauramurgatroyd November 19, 2024 10:44

gfardell requested review from MargaretDuff and gfardell January 16, 2025 10:42

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M-A-Demir and others added 7 commits January 17, 2025 15:14

Update how-to/1_Read_and_visualise/TIFFStackReader.ipynb

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Co-authored-by: Margaret Duff <43645617+MargaretDuff@users.noreply.github.com>

Applied suggestions from code review

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Update FlatDarkFieldNormaliser.ipynb

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Added clarification on commented %store line

Update CreateCustomGeometry.ipynb

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Update CreateCustomGeometry.ipynb

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Fixed CreateCustomGeometry.ipynb

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Formatting in changed print statements caused notebook failure to load

Update FlatDarkFieldNormaliser.ipynb

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gfardell moved this from In Review to Blocked in CIL work Mar 4, 2025

M-A-Demir requested a review from MargaretDuff March 7, 2025 11:13

hrobarts removed this from CIL work Apr 1, 2025

	"The `%store -r sandstone` command allows us to use the `sandstone` `AcquisitionData` we saved in the `1_Read_and_visualise/TIFFStackReader.ipynb` notebook. Please run the TIFFStackReader notebook (without deleting the `data/sandstone` folder), and save the `sandstone` variable before running the cell below."
	"Note: The `%store -r sandstone` command allows us to use the `sandstone` `AcquisitionData` we saved in the `1_Read_and_visualise/TIFFStackReader.ipynb` notebook. Please run the TIFFStackReader notebook (without deleting the `data/sandstone` folder), and save the `sandstone` variable before running the cell below."

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M-A-Demir commented Oct 23, 2024 •

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