Modified Reference Antenna Selection and unit tests #65

tamerakassie · 2024-06-14T08:19:40Z

This PR contains the modified selection of reference antenna as per the initial investigation done in SPR1-1964
A select_med_deviation_pnr_ants function has been added to calculate the median deviation of antenna peak-to-noise (PNR) values, this function returns a boolean array of antenna values that have a relatively good PNR, i.e one deviation above the median deviation. The best_refant, which is the function that calculates the PNR across antennas, has been modified to call the select_med_deviation_pnr_antsand thereafter return the corresponding longest baseline solutions for the reference antenna selection.

The test_calprocs.py contains the corresponding unit tests for the new solution.

KimMcAlpine

If any of the comments need more explanation feel free to chat to me.

katsdpcal/calprocs.py

katsdpcal/test/test_calprocs.py

tamerakassie

Review for changes made on the initial commit to calprocs.py and test_calprocs.py

katsdpcal/test/test_calprocs.py

…s with def setup_method, changing to def setup (as in master)

katsdpcal/test/test_control.py

katsdpcal/pipelineprocs.py

…ts and cleaned up code

ludwigschwardt

Nice changes! A heads-up: Tasmiyah and I are moving all calprocs functionality to its own package: https://github.com/ska-sa/katsdpcalproc. You caught me just as I wanted to delete calprocs, but now I'll wait for your PR 😁 Once this is merged, we should move those changes across to the new package as well before removing calprocs.

katsdpcal/pipelineprocs.py

katsdpcal/scan.py

ludwigschwardt · 2024-08-08T18:37:15Z

katsdpcal/calprocs.py

+    ant_indices = np.arange(len(med_pnr_ants))
+    median = np.nanmedian(med_pnr_ants)
+
+    mad = scipy.stats.median_abs_deviation(med_pnr_ants, nan_policy='omit')


Very nice that you found this! 😊

If you stumble upon a useful function in an external library, it's good to stop and consider a few things:

How new is this function?

Does this introduce a new dependency?

Will it affect my package's existing dependencies?

Since katsdpcal already uses scipy, there's no new dependency to think about. The function is relatively new though, which is why it hasn't been used up to now 😅

Have a look at the scipy docs:

and then at https://pypi.org/project/scipy/#history:

It's from scipy 1.5.0 in 2020, which seems old, but katsdpcal (mostly from 2017-2019) still accepts scipy >= 0.17 in setup.py... And scipy 1.5.0 needs Python 3.6, which is newer than the 3.5 specified by katsdpcal.

You have a few options here:

Quietly bump the Python to 3.6 and scipy to 1.5.0 in setup.py, but ideally we want to run pyupgrade --py36-plus to get more benefits.

Go all out and bump it to Python 3.8 (my latest test PR SPR1-3111: Replace nose and asynctest with pytest #67 requires it already).

Don't use this function and consider the existing functionality in katsdpsigproc (NoiseEstMADHost) or just write your own. It's already implemented in katsdpcal.plotting.amp_range, for example.

It's also a good idea to multiply the MAD by 1.4826 to convert it into a "normal" standard deviation.

Okay, I think its best to implement my own function. I am going to calculate the MAD as follows
pnr_values = med_pnr_ants[~np.isnan(med_pnr_ants)]
med = np.median(np.abs(pnr_values))
mad = np.median(np.abs(pnr_values - med))
mad_threshold = (med - mad)

I still need to think about the normalised MAD.

You can always leave a comment in the code that the scipy function could be used once we upgrade to Python 3.6+ in case we forget. Or implement a function called "median_abs_deviation" that can serve both your code as well as katsdpcal.plotting.amp_range, while also having the signature of the scipy function so that one day you can just delete your function and replace with the similar-named scipy function.

ludwigschwardt · 2024-08-08T18:39:28Z

katsdpcal/test/test_calprocs.py

@@ -789,7 +788,7 @@ def test_no_ac(self):


 class TestInterpolateSoln(unittest.TestCase):
-    """Tests for :func:`katsdpcal.calprocs.interpolate_soln`"""
+    """Tests for :func:`katsdpcal.calprocs.interpolate_soln"""


You accidentally deleted a backtick here (needed for Sphinx doc reference).

ludwigschwardt · 2024-08-08T18:39:35Z

katsdpcal/test/test_calprocs.py

+
+
+class TestSelectMedDeviation(unittest.TestCase):
+    """Tests for :func:`katsdpcal.calprocs.select_med_deviation


You accidentally deleted a backtick here (needed for Sphinx doc reference).

ludwigschwardt · 2024-08-08T18:39:54Z

katsdpcal/test/test_calprocs.py

+
+
+class TestBestRefAnt(unittest.TestCase):
+    """Tests for :func:`katsdpcal.calprocs.best_refant"""


You accidentally deleted a backtick here (needed for Sphinx doc reference).

ludwigschwardt · 2024-08-08T18:42:36Z

katsdpcal/test/test_control.py

@@ -70,6 +70,7 @@ class PingTask(control.Task):
    def __init__(self, task_class, master_queue, slave_queue):
        super().__init__(task_class, master_queue, 'PingTask')
        self.slave_queue = slave_queue
+        self.master_queue = master_queue


This is unnecessary since the super() above already does it (master_queue lives in the control.Task base class).

ludwigschwardt · 2024-08-08T18:47:54Z

katsdpcal/test/test_control.py

@@ -95,8 +96,9 @@ class BaseTestTask:
    """

    def setup(self):
-        self.master_queue = self.module.Queue()
-        self.slave_queue = self.module.Queue()
+        module = multiprocessing


I wonder why you did this... Did you try to run this with pytest by any chance? The tests work as expected for me without this. I know it looks strange, being a Merry construct and all, because I also had to figure this out just this week 😂

The module attribute is set by the actual (derived) test classes below: TestTaskMultiprocessing and TestTaskDummy. As the name implies, this class is just the base for these tests containing common functionality. The module attribute is not common and will be set differently for each set of tests. By hardwiring multiprocessing here, you are dropping the TestTaskDummy checks.

I ran locally with pytest that needed this change, and had neglected to change back when I reran test_control.py with nosetests thanks for the spot.

Co-authored-by: Ludwig Schwardt <ludwig@ska.ac.za>

ludwigschwardt · 2024-08-12T10:01:22Z

I suggest that we squash the branch to a single commit when we eventually merge this. That will avoid adding commits that just add lines and then delete it again.

Modified Reference Antenna Selection and unit tests

2af4445

tamerakassie requested a review from KimMcAlpine June 14, 2024 08:19

KimMcAlpine requested changes Jun 21, 2024

View reviewed changes

modified functions and unit tests

4527ceb

tamerakassie commented Jul 8, 2024

View reviewed changes

tamerakassie requested a review from KimMcAlpine July 8, 2024 09:43

KimMcAlpine approved these changes Jul 8, 2024

View reviewed changes

katsdpcal/test/test_calprocs.py Outdated Show resolved Hide resolved

modified unit tests

7cc1378

KimMcAlpine approved these changes Jul 9, 2024

View reviewed changes

tamerakassie added 8 commits July 9, 2024 14:47

Merge branch 'master' into select_mad-ref_antenna

be75257

test_control relax visibility condition

69e7651

fixed setup_method for tests

aa54464

checking resolved tests

7d5ed7a

checking resolved tests, setup method in test_control

0e833df

checking resolved tests, setup method in test_control fails on jenkin…

61ffc01

…s with def setup_method, changing to def setup (as in master)

checking resolved tests, setup method in test_control fails on jenkin…

3bd8592

…s with def setup_method, changing to def setup (as in master)

resolved unit tests in test_control and the setup method errors

b562408

tamerakassie requested a review from KimMcAlpine July 16, 2024 13:08

tamerakassie commented Jul 16, 2024

View reviewed changes

katsdpcal/test/test_control.py Outdated Show resolved Hide resolved

tamerakassie commented Jul 16, 2024

View reviewed changes

katsdpcal/test/test_control.py Outdated Show resolved Hide resolved

tamerakassie commented Jul 16, 2024

View reviewed changes

katsdpcal/test/test_control.py Show resolved Hide resolved

tamerakassie commented Jul 16, 2024

View reviewed changes

katsdpcal/pipelineprocs.py Outdated Show resolved Hide resolved

tamerakassie added 2 commits August 1, 2024 14:23

rebased diverging branches and added Kims comments to fix failing tes…

2d843b5

…ts and cleaned up code

removed print statement

714a0e6

ludwigschwardt requested changes Aug 8, 2024

View reviewed changes

Update katsdpcal/pipelineprocs.py

752a8ab

Co-authored-by: Ludwig Schwardt <ludwig@ska.ac.za>

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Modified Reference Antenna Selection and unit tests #65

Modified Reference Antenna Selection and unit tests #65

tamerakassie commented Jun 14, 2024 •

edited

Loading

KimMcAlpine left a comment

tamerakassie left a comment

ludwigschwardt left a comment •

edited

Loading

ludwigschwardt Aug 8, 2024

tamerakassie Aug 9, 2024 •

edited

Loading

ludwigschwardt Aug 12, 2024 •

edited

Loading

ludwigschwardt Aug 8, 2024

ludwigschwardt Aug 8, 2024

ludwigschwardt Aug 8, 2024

ludwigschwardt Aug 8, 2024

ludwigschwardt Aug 8, 2024

tamerakassie Aug 9, 2024 •

edited

Loading

ludwigschwardt commented Aug 12, 2024 •

edited

Loading



		class TestSelectMedDeviation(unittest.TestCase):
		"""Tests for :func:`katsdpcal.calprocs.select_med_deviation



		class TestBestRefAnt(unittest.TestCase):
		"""Tests for :func:`katsdpcal.calprocs.best_refant"""

Modified Reference Antenna Selection and unit tests #65

Are you sure you want to change the base?

Modified Reference Antenna Selection and unit tests #65

Conversation

tamerakassie commented Jun 14, 2024 • edited Loading

KimMcAlpine left a comment

Choose a reason for hiding this comment

tamerakassie left a comment

Choose a reason for hiding this comment

ludwigschwardt left a comment • edited Loading

Choose a reason for hiding this comment

ludwigschwardt Aug 8, 2024

Choose a reason for hiding this comment

tamerakassie Aug 9, 2024 • edited Loading

Choose a reason for hiding this comment

ludwigschwardt Aug 12, 2024 • edited Loading

Choose a reason for hiding this comment

ludwigschwardt Aug 8, 2024

Choose a reason for hiding this comment

ludwigschwardt Aug 8, 2024

Choose a reason for hiding this comment

ludwigschwardt Aug 8, 2024

Choose a reason for hiding this comment

ludwigschwardt Aug 8, 2024

Choose a reason for hiding this comment

ludwigschwardt Aug 8, 2024

Choose a reason for hiding this comment

tamerakassie Aug 9, 2024 • edited Loading

Choose a reason for hiding this comment

ludwigschwardt commented Aug 12, 2024 • edited Loading

tamerakassie commented Jun 14, 2024 •

edited

Loading

ludwigschwardt left a comment •

edited

Loading

tamerakassie Aug 9, 2024 •

edited

Loading

ludwigschwardt Aug 12, 2024 •

edited

Loading

tamerakassie Aug 9, 2024 •

edited

Loading

ludwigschwardt commented Aug 12, 2024 •

edited

Loading