DOC: scan area detector with motor(s)

prjemian commented 2 weeks ago

close #308

@sureshnaps, @qzhang - Can you examine this notebook? It can guide you during commissioning activities.

Start here: https://bcda-aps.github.io/bluesky_training/howto/_ad_v_motors.html#The-(1-D)-bp.scan()-plan-with-one-motor

coveralls commented 2 weeks ago

Pull Request Test Coverage Report for Build 9520419244

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rodolakis commented 2 weeks ago

In general, I find some of the markdown comment difficult to find in the middle of the code cell output, like below; maybe adding bullet point or a <br> before the comment would help.

rodolakis commented 2 weeks ago

Not sure what that bug was in the last few suggestions. It was displaying the correct sentence before pressing the green button, but then showed the code for an image as the original...

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Pull Request Test Coverage Report for Build 9523403052

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Pull Request Test Coverage Report for Build 9523404999

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Pull Request Test Coverage Report for Build 9523406656

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Pull Request Test Coverage Report for Build 9523411126

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Pull Request Test Coverage Report for Build 9523460257

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Pull Request Test Coverage Report for Build 9523476197

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github-actions[bot] commented 2 weeks ago

Pull Request Test Coverage Report for Build 9523476197

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Pull Request Test Coverage Report for Build 9523476197

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Pull Request Test Coverage Report for Build 9523488624

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prjemian commented 2 weeks ago

@rodolakis I believe this is ready for review again.

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rodolakis commented 2 weeks ago

OK so this is what I was trying to suggest:

It looks good in preview, but when I click "add review comment" it becomes wrong (quoting the giant image code instead).

rodolakis commented 2 weeks ago

In general, for all 3 sections, I would replace the sentence:

Step scan a motor (m1) and measure 3 (as configured above) images at each step. Also record total counts and the maximum counts value for each step.

With a bullet point sentence:

1D scan section: "Step scan a motor (m1); at each step:\n", "- Measure 3 images (as configured during detector staging)\n", "- Record total counts\n", "- Record maximum counts value\n",
2D scan section:
"Step scan two motors together (m1 & m2); as in the previous section, at each step:\n", "- Measure 3 images\n", "- Record total counts\n", "- Record maximum counts value\n",
2D mesh scan section: "Step scan two motors (m1 & m2); as before, at each step:\n", "- Measure 3 images\n", "- Record total counts\n", "- Record maximum counts value\n",

rodolakis commented 2 weeks ago

I would write instead:

Both motors, m1 and m2, move at the same time. Below is a plot showing the readback values of each motor during a two-motor scan versus the data point number:

rodolakis commented 2 weeks ago

The file name, as the catalog will find its image contents, is reconstructed:

I am not sure I understand this sentence. I was proposing:

"The catalog uses the file name to locate and retrieve its image contents. This file name is reconstructed as follows:"

rodolakis commented 2 weeks ago

"The second motor of the grid_scan (m2) is snaked. It's direction changes with each subsequent increment of the first motor (m1). Here's a plot of readback value of each motor from a grid_scan plotted v. data point number:\n",

I was proposing:

During the grid_scan, the second motor (m2) moves in a snaking pattern: its direction changes with each subsequent increment of the first motor (m1). Below is a plot showing the readback values of each motor during a grid_scan versus the data point number:

rodolakis commented 2 weeks ago

I was proposing instead:

All along, quietly in the background, the data has been saved both to a catalog and to a SPEC data file. The total counts, max counts, and unique ID from all scans can be plotted from the SPEC file using PyMCA or NeXpy.

The image content is not stored in the SPEC file, so images cannot be viewed from it. However, references to the images are save as comments. See the comment lines that match a search for

resource {'spec': 'AD_HDF5'

rodolakis commented 2 weeks ago

@prjemian I rewrote my broken comments. I still cannot quote anything as a github "suggestions" past a certain point in the document (only works at the beginning of the notebook for some reason)

prjemian commented 2 weeks ago

@rodolakis : I believe I have responded to all your comments. Thanks for the thorough review.

coveralls commented 2 weeks ago

Pull Request Test Coverage Report for Build 9530038078

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0 of 0 changed or added relevant lines in 0 files are covered.
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Change from base Build 9506811548:	0.0%
Covered Lines:	1020
Relevant Lines:	1226

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coveralls commented 2 weeks ago

Pull Request Test Coverage Report for Build 9530038078

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0 of 0 changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 83.197%

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Change from base Build 9506811548:	0.0%
Covered Lines:	1020
Relevant Lines:	1226

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coveralls commented 2 weeks ago

Pull Request Test Coverage Report for Build 9530038078

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0 of 0 changed or added relevant lines in 0 files are covered.
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Relevant Lines:	1226

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rodolakis commented 1 week ago

All good. Everything has been resolved as far as I am concerned except for one minor formatting suggestion (I tagged you on it). So minor that I'm fine with merging with or without.

prjemian commented 1 week ago

@rodolakis Thanks!

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Pull Request Test Coverage Report for Build 9589569745

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0 of 0 changed or added relevant lines in 0 files are covered.
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Change from base Build 9506811548:	0.0%
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Relevant Lines:	1226

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coveralls commented 1 week ago

Pull Request Test Coverage Report for Build 9589569745

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

For more information on this, see Tracking coverage changes with pull request builds.
To avoid this issue with future PRs, see these Recommended CI Configurations.
For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

0 of 0 changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 83.197%

Totals
Change from base Build 9506811548:	0.0%
Covered Lines:	1020
Relevant Lines:	1226

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coveralls commented 1 week ago

Pull Request Test Coverage Report for Build 9589569745

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

For more information on this, see Tracking coverage changes with pull request builds.
To avoid this issue with future PRs, see these Recommended CI Configurations.
For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

0 of 0 changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 83.197%

Totals
Change from base Build 9506811548:	0.0%
Covered Lines:	1020
Relevant Lines:	1226

BCDA-APS / bluesky_training