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feat: add channel_labels #323

Merged
merged 6 commits into from
Nov 9, 2020
Merged

feat: add channel_labels #323

merged 6 commits into from
Nov 9, 2020

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abawchen
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@abawchen abawchen commented Mar 9, 2020

Add channel_labels and pass unittest.

@abawchen
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abawchen commented Mar 9, 2020

@castillohair @JS3xton : Please help review this one, thanks.

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Thanks for the contribution. I found some small things, but otherwise looks good to me.

  1. The channel_labels method should be described in the FCSData docstring.
  2. It would be nice to explicitly unit test channel_labels like other similar methods (e.g. the TestFCSAttributesDetectorVoltage class in /test/test_io.py).

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JS3xton commented May 2, 2020

  1. Add channel_labels method to TestFCSDataPickle in /test/test_io.py.

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abawchen commented May 4, 2020

@JS3xton : Thanks for feedback, I will update accordingly.

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abawchen commented May 5, 2020

@JS3xton : I have a quick question, because all of the current testing fcs files don't have label value, i.e. they don't have $PnS key, and will return [None, None, ..., None] of all channels -- should I modify the current testing fcs file or create another one?

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JS3xton commented May 5, 2020

@JS3xton : I have a quick question, because all of the current testing fcs files don't have label value, i.e. they don't have $PnS key, and will return [None, None, ..., None] of all channels -- should I modify the current testing fcs file or create another one?

@abawchen Hmm, good point. I wouldn't modify the existing files. If you have a new file you can contribute, that seems fine to me. Otherwise, you might be able to find one in this repository: https://flowrepository.org/id/FR-FCM-ZZZ4.

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@JS3xton , I added the description of channel_labels into the FCSData docstring. I also added it to the TestFCSDataPickle test.

@abawchen I think we would still prefer if you could incorporate an FCS file that actually contains $PnS keys and make unit tests for it. Code looks good, but we still have no "experimental" evidence that it does what it's supposed to do.

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abawchen commented Oct 26, 2020

@JS3xton @castillohair :
Hi, thanks your feedback, although it's been a while 😅
I have added Data005.fcs and add corresponding test case as you suggested, please help check it.

btw, I have rebase the updated develop branch.


We have previously looked at the contents of the $PnS attribute for
the test files and identified the correct label(marker):
- Data001.fcs: [None, None, None, None, None, None]
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The last element of this list should be 'Time (204.80 sec.)'. This is what you have later in the test_attribute() function.

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In my opinion, the proposed unit tests validate that the feature works as expected. I have one observation in the test class docstring though. @JS3xton see what you think.

-Changed "PxS" to "PnS" to conform to naming convention for FCS
 parameters.
@JS3xton JS3xton self-requested a review October 29, 2020 23:14
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JS3xton commented Oct 29, 2020

Looks good to me.

(The new data file is kinda large, though... ~16MB)

@castillohair castillohair merged commit 8e92580 into taborlab:develop Nov 9, 2020
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@abawchen thanks for the contribution! We will release it with the new FlowCal version soon.

@abawchen abawchen deleted the develop branch November 13, 2020 11:37
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3 participants