[WIP] P11 develop upgrade #854

agruzinov · 2024-02-20T10:56:26Z

Here is a repeat of PR 800, hopefully without rebase issues and updated to the current state.

…y for shutter-like objects inside P11 HO (Bixente)

… at P11 even if everything was ok (Bixente).

…omatically after data collection.

fabcor-maxiv

I only did a quick review of the parts that are not specific to DESY.

I am wondering why we did not squash the commits, since we opened a new pull request. For people like me who look at the git history often, 159 commits of back and forth are horrible.

fabcor-maxiv · 2024-02-20T11:21:40Z

mxcubecore/HardwareObjects/ISPyBClient.py

@@ -9,6 +9,7 @@
 from pprint import pformat
 from collections import namedtuple
 from datetime import datetime
+import warnings


Already imported at line 8.

Thanks, fixed.

fabcor-maxiv · 2024-02-20T11:25:02Z

mxcubecore/HardwareObjects/abstract/AbstractMotor.py

@@ -101,6 +103,11 @@ def update_value(self, value=None):
        Args:
            value (float): value
        """
+        if self._updating_value:
+            return  # Already updating, avoid recursion


That is quite unusual for me to see something like this... I wonder if there is a better solution to prevent recursion.

Where does the recursion happen?

Why is it a problem if we call this more than once? What is the issue?

Indeed, where does the recursion happen? The update mechanism is quite largely used and wed did not observe any problem. This is worrying.

This recursion error happens from time to time with "recursion limit has reached" error but It was not very reproducinble. Since this fix I did not encounter it so far.

2023-08-21 09:54:42,912 |HWR |DEBUG | queue_entry - about to start data collection
2023-08-21 09:54:42,912 |HWR |DEBUG | queue_entry - collect_dc
2023-08-21 09:54:42,913 |HWR |DEBUG | queue_entry - standard collect
2023-08-21 09:54:42,913 |HWR |DEBUG | queue_entry - standard collect
2023-08-21 09:54:42,913 |HWR |DEBUG | PathTemplate (DESY) - (to be defined) directory is /gpfs/current/raw/tt_2
2023-08-21 09:54:42,913 |HWR |DEBUG | queue_entry - now calling collect hwo
2023-08-21 09:54:42,913 |user_level_log|INFO | Collection: Preparing to collect
2023-08-21 09:54:42,928 |HWR |INFO | Collection parameters: {'comments': '', 'take_video': False, 'take_snapshots': 4, 'fileinfo': {'directory': '/gpfs/current/raw/tt_2', 'prefix': 'puck20_sample08_w1', 'run_number': 1, 'archive_directory': '/gpfs/current/raw', 'process_directory': '/gpfs/current/processed/tt_2', 'template': 'puck20_sample08_w1_1_%05d.h5', 'compression': False}, 'in_queue': False, 'in_interleave': None, 'detector_binning_mode': None, 'detector_roi_mode': 'disabled', 'shutterless': True, 'sessionId': '61749', 'do_inducedraddam': False, 'sample_reference': {'spacegroup': '', 'cell': '0,0,0,0,0,0', 'blSampleId': -1}, 'processing': 'True', 'processing_offline': True, 'processing_online': False, 'residues': 200, 'dark': False, 'resolution': {'upper': 1.83}, 'transmission': 24.1504, 'energy': 11.9995, 'oscillation_sequence': [{'exposure_time': 0.008, 'kappaStart': 0.0, 'phiStart': 0.0, 'start_image_number': 1, 'number_of_images': 1440, 'overlap': 0, 'start': 0.0, 'range': 0.25, 'number_of_passes': 1, 'number_of_lines': 1, 'mesh_range': (), 'num_triggers': 0, 'num_images_per_trigger': 0}], 'group_id': None, 'EDNA_files_dir': '/gpfs/current/processed/tt_2', 'xds_dir': '', 'anomalous': False, 'experiment_type': 'OSC', 'skip_images': False, 'motors': {'phi': -1.539453422532113e-05, 'phiz': 0.0, 'phiy': -595.25, 'phix': None, 'sampx': -279.183, 'sampy': -147.468, 'zoom': None, 'kappa': None, 'kappa_phi': None, 'microy': None, 'microz': None}, 'status': 'Running', 'collection_start_time': '2023-08-21 09:54:42'}
2023-08-21 09:54:42,929 |user_level_log|INFO | Collection: Storing data collection in LIMS
2023-08-21 09:54:42,929 |user_level_log|INFO | Collection: Creating directories for raw images and processing files
2023-08-21 09:54:42,929 |user_level_log|INFO | Collection: Getting sample info from parameters
2023-08-21 09:54:42,929 |user_level_log|INFO | Collection: Storing sample info in LIMS
2023-08-21 09:54:42,929 |user_level_log|INFO | Collection: Moving to centred position
2023-08-21 09:54:42,929 |HWR.P11NanoDiff|DEBUG | first moving translation motor 'phiy' to position -595.25
2023-08-21 09:54:42,930 |HWR.TangoMotor|DEBUG | TangoMotor.py - Moving motor /phiy to -595.25
2023-08-21 09:54:42,943 |HWR.P11NanoDiff|DEBUG | first moving translation motor 'phiz' to position 0.0
2023-08-21 09:54:42,943 |HWR.TangoMotor|DEBUG | TangoMotor.py - Moving motor /phiz to 0.0
2023-08-21 09:54:43,046 |HWR.P11NanoDiff|DEBUG | translation movements DONE
2023-08-21 09:54:43,047 |HWR.P11NanoDiff|DEBUG | then moving alignment motor 'sampx' to position -279.183
2023-08-21 09:54:43,047 |HWR.TangoMotor|DEBUG | TangoMotor.py - Moving motor /sampx to -279.183
2023-08-21 09:54:43,081 |HWR.P11NanoDiff|DEBUG | then moving alignment motor 'sampy' to position -147.468
2023-08-21 09:54:43,082 |HWR.TangoMotor|DEBUG | TangoMotor.py - Moving motor /sampy to -147.468
2023-08-21 09:54:43,217 |HWR.P11NanoDiff|DEBUG | alignment movements DONE
2023-08-21 09:54:43,217 |HWR.P11NanoDiff|DEBUG | finally moving motor 'phi' to position -147.468
2023-08-21 09:54:43,217 |HWR.TangoMotor|DEBUG | TangoMotor.py - Moving motor /omega to -1.539453422532113e-05
2023-08-21 09:54:43,484 |HWR.TangoMotor|DEBUG | reading motor state for /phiy is ON
2023-08-21 09:54:43,492 |HWR.TangoMotor|DEBUG | reading motor state for /phiz is ON
2023-08-21 09:54:43,573 |HWR.P11NanoDiff|DEBUG | phi move DONE
2023-08-21 09:54:43,573 |HWR.P11NanoDiff|DEBUG | moving remaining motor phix to position None
2023-08-21 09:54:43,574 |HWR.P11NanoDiff|DEBUG | moving remaining motor zoom to position None
2023-08-21 09:54:43,574 |HWR.P11NanoDiff|DEBUG | moving remaining motor kappa to position None
2023-08-21 09:54:43,574 |HWR.P11NanoDiff|DEBUG | moving remaining motor kappa_phi to position None
2023-08-21 09:54:43,574 |HWR.P11NanoDiff|DEBUG | moving remaining motor microy to position None
2023-08-21 09:54:43,574 |HWR.P11NanoDiff|DEBUG | moving remaining motor microz to position None
2023-08-21 09:54:43,574 |user_level_log|INFO | Collection: Taking 4 sample snapshot(s)
2023-08-21 09:54:43,574 |HWR.P11Collect|DEBUG | #COLLECT# taking crystal snapshot.
2023-08-21 09:54:43,574 |HWR.P11Collect|DEBUG | #COLLECT# take_snapshot. moving to centring phase
2023-08-21 09:54:43,575 |HWR.P11NanoDiff|DEBUG | SETTING CENTRING PHASE
2023-08-21 09:54:43,575 |HWR.P11NanoDiff|DEBUG | - close detector cover
2023-08-21 09:54:43,610 |HWR.P11NanoDiff|DEBUG | - setting backlight in
2023-08-21 09:54:43,661 |HWR.P11NanoDiff|DEBUG | PHASE (Centring) NOT REACHED YET
2023-08-21 09:54:43,661 |HWR.P11NanoDiff|DEBUG | waiting for: lightin,collim_down,bstop_out
2023-08-21 09:54:43,661 |HWR.P11NanoDiff|DEBUG | - putting collimator down
2023-08-21 09:54:43,661 |HWR.TangoMotor|DEBUG | TangoMotor.py - Moving motor /collimy to -360
2023-08-21 09:54:43,674 |HWR.TangoMotor|DEBUG | TangoMotor.py - Moving motor /collimz to -13000
2023-08-21 09:54:43,686 |HWR.P11NanoDiff|DEBUG | - setting beamstop out
2023-08-21 09:54:43,686 |HWR.TangoMotor|DEBUG | TangoMotor.py - Moving motor /bstopx to 69000
2023-08-21 09:54:43,689 |HWR.P11NanoDiff|DEBUG | - moving yag down
2023-08-21 09:54:43,689 |HWR.TangoMotor|DEBUG | TangoMotor.py - Moving motor /yagz to -12550
2023-08-21 09:54:43,689 |HWR.P11NanoDiff|DEBUG | - moving pinhole down
2023-08-21 09:54:43,689 |HWR.P11NanoDiff|DEBUG | WAITING PHASE STARTED
2023-08-21 09:54:43,692 |HWR.TangoMotor|DEBUG | reading motor state for /sampx is ON
2023-08-21 09:54:43,693 |HWR.TangoMotor|DEBUG | reading motor state for /sampy is ON
2023-08-21 09:54:44,488 |root |ERROR | Uncaught exception : Traceback (most recent call last):

File "/gpfs/local/shared/MXCuBE/backup/22-05-2023/mxcubecore_edna_tests/mxcubecore/dispatcher.py", line 27, in __my_robust_apply
return robustapply._robust_apply(*args, **kwargs)

File "/gpfs/local/shared/MXCuBE/mxenv/lib/python3.7/site-packages/pydispatch/robustapply.py", line 55, in robustApply
return receiver(*arguments, **named)

File "/gpfs/local/shared/MXCuBE/backup/22-05-2023/mxcubecore_edna_tests/mxcubecore/HardwareObjects/MotorsNPosition.py", line 198, in motor_value_changed
self.update_multi_value()

File "/gpfs/local/shared/MXCuBE/backup/22-05-2023/mxcubecore_edna_tests/mxcubecore/HardwareObjects/MotorsNPosition.py", line 210, in update_multi_value
current_pos[motorname] = self.motor_hwobjs[motorname].get_value()

File "/gpfs/local/shared/MXCuBE/backup/22-05-2023/mxcubecore_edna_tests/mxcubecore/HardwareObjects/TangoMotor.py", line 149, in get_value
value = self.chan_position.get_value()

File "/gpfs/local/shared/MXCuBE/backup/22-05-2023/mxcubecore_edna_tests/mxcubecore/Command/Tango.py", line 349, in get_value
self.update(value)

File "/gpfs/local/shared/MXCuBE/backup/22-05-2023/mxcubecore_edna_tests/mxcubecore/Command/Tango.py", line 331, in update
self.emit("update", value)

File "/gpfs/local/shared/MXCuBE/backup/22-05-2023/mxcubecore_edna_tests/mxcubecore/CommandContainer.py", line 144, in emit
dispatcher.send(signal, self, *args)

File "/gpfs/local/shared/MXCuBE/mxenv/lib/python3.7/site-packages/pydispatch/dispatcher.py", line 332, in send
for receiver in liveReceivers(getAllReceivers(sender, signal)):

File "/gpfs/local/shared/MXCuBE/mxenv/lib/python3.7/site-packages/pydispatch/dispatcher.py", line 256, in liveReceivers
for receiver in receivers:

File "/gpfs/local/shared/MXCuBE/mxenv/lib/python3.7/site-packages/pydispatch/dispatcher.py", line 286, in getAllReceivers
if receiver: # filter out dead instance-method weakrefs

File "/gpfs/local/shared/MXCuBE/mxenv/lib/python3.7/site-packages/pydispatch/saferef.py", line 149, in nonzero
return self() is not None

File "/gpfs/local/shared/MXCuBE/mxenv/lib/python3.7/site-packages/pydispatch/saferef.py", line 167, in call
target = self.weakSelf()

RecursionError: maximum recursion depth exceeded while calling a Python object

After updating to the latest development, the recursion error happens from time to time again. It seems to be inside the MotorsNPosition.py when it is calling get_value() from the TangoMotor.py

Here is the log:

2024-03-04 15:21:48,399 |HWR.P11Pinhole|DEBUG | - position for pinholey is -421.353
2024-03-04 15:21:48,400 |HWR.P11Pinhole|DEBUG | - position for pinholez is 13468.007
2024-03-04 15:21:48,400 |HWR.P11Pinhole|DEBUG | - motor pinholey is at -421
2024-03-04 15:21:48,400 |HWR.P11Pinhole|DEBUG | - motor pinholez is at 13468
2024-03-04 15:21:48,400 |HWR.P11NanoDiff|DEBUG | - checking gonio tower position
2024-03-04 15:21:48,400 |HWR.P11NanoDiff|DEBUG | WAITING PHASE STARTED
2024-03-04 15:21:48,578 |HWR.TangoMotor|DEBUG | reading motor state for /omega is ON
2024-03-04 15:21:48,600 |HWR.MotorsNPosition|DEBUG | - motor collimy is at -360
2024-03-04 15:21:48,601 |HWR.MotorsNPosition|DEBUG | - motor collimz is at -13000
2024-03-04 15:21:48,712 |HWR.MotorsNPosition|DEBUG | - motor collimy is at -360
2024-03-04 15:21:48,713 |HWR.MotorsNPosition|DEBUG | - motor collimz is at -13000
2024-03-04 15:21:48,781 |root |ERROR | Uncaught exception : Traceback (most recent call last):

File “/gpfs/local/shared/MXCuBE/mxcubecore/mxcubecore/dispatcher.py”, line 27, in __my_robust_apply
return robustapply._robust_apply(*args, **kwargs)

File “/home/p11user/.pyenv/versions/mxenv3.8/lib/python3.8/site-packages/louie/robustapply.py”, line 57, in robust_apply
return receiver(*arguments, **named)

File “/gpfs/local/shared/MXCuBE/mxcubecore/mxcubecore/HardwareObjects/MotorsNPosition.py”, line 189, in motor_value_changed
self.update_multi_value()

File “/gpfs/local/shared/MXCuBE/mxcubecore/mxcubecore/HardwareObjects/MotorsNPosition.py”, line 201, in update_multi_value
current_pos[motorname] = self.motor_hwobjs[motorname].get_value()

File “/gpfs/local/shared/MXCuBE/mxcubecore/mxcubecore/HardwareObjects/TangoMotor.py”, line 151, in get_value
value = self.chan_position.get_value()

File “/gpfs/local/shared/MXCuBE/mxcubecore/mxcubecore/Command/Tango.py”, line 342, in get_value
value = self.device.read_attribute(self.attribute_name).value

File “/home/p11user/.pyenv/versions/mxenv3.8/lib/python3.8/site-packages/tango/green.py”, line 207, in greener
executor = get_object_executor(obj, green_mode)

File “/home/p11user/.pyenv/versions/mxenv3.8/lib/python3.8/site-packages/tango/green.py”, line 182, in get_object_executor
green_mode = get_object_green_mode(obj)

RecursionError: maximum recursion depth exceeded

2024-03-04 15:21:48,785 |HWR.P11Pinhole|DEBUG | - position for pinholey is -421.353
2024-03-04 15:21:48,786 |HWR.P11Pinhole|DEBUG | - position for pinholez is 13468.007
2024-03-04 15:21:48,786 |HWR.P11Pinhole|DEBUG | - motor pinholey is at -421
2024-03-04 15:21:48,786 |HWR.P11Pinhole|DEBUG | - motor pinholez is at 13468

fabcor-maxiv · 2024-02-20T11:25:59Z

mxcubecore/HardwareObjects/abstract/AbstractSampleChanger.py

-                    smp._set_loaded(True)
+                self.log.debug(f" Found sample {smp} is loaded")
+                self.log.debug(f"   getting loaded {self.get_loaded_sample()}")
+                # if self.get_loaded_sample() == smp:


Remove the code, do not comment it out.

I believe the line should not be commented out.

Unfortunately if this is uncomented, it crushes with the error sample not loaded, although it is perfectly loaded.

2023-10-17 17:34:06,952 |HWR.MotorsNPosition|DEBUG | - motor yagz is at -12550
2023-10-17 17:34:06,954 |user_level_log|INFO | Sample changer: Sample loaded (total time: 29.94912600517273)
2023-10-17 17:34:06,957 |GUI |ERROR | Error loading sample, ('Sample not loaded', '')
2023-10-17 17:34:06,960 |GUI |ERROR | Traceback (most recent call last):
File "/gpfs/local/shared/MXCuBE/mxcubeqt/mxcubeqt/widgets/dc_tree_widget.py", line 497, in mount_sample_task
self.sample_centring_result
File "/gpfs/local/shared/MXCuBE/mxcubecore/mxcubecore/queue_entry/base_queue_entry.py", line 839, in mount_sample
raise QueueSkippEntryException("Sample not loaded", "")
mxcubecore.queue_entry.base_queue_entry.QueueSkippEntryException: ('Sample not loaded', '')

2023-10-17 17:34:54,454 |HWR.MotorsNPosition|DEBUG | - motor collimy is at -360
2023-10-17 17:34:54,454 |HWR.MotorsNPosition|DEBUG | - motor collimz is at -13000

It was hard to trace, but @vrey01 found it. It is left there because it is hard to tell whether it is for everyone. Could someone try on other beamline what will happen? What do you think?

Maybe because the get_loaded_sample output is different from smp. Could you, please, check this, as we do not have the same error, but not the same sample changer neither.

Quick check shows that it was not redefined in the P11SampleChanger class. I can check it when I have access to the hardware though.

beteva · 2024-02-20T14:53:14Z

mxcubecore/HardwareObjects/Beamline.py

+
+        osc_start = motor_positions.get("phi", params["osc_start"])
+


Actually both the old and the new version will rais a KeyError exception if osc_start is not in the params dictionary. I believe the correct code should be:
osc_start = params.get("osc_start") or motor_positions.get("phi")

Corrected, thanks!

beteva · 2024-02-20T15:14:17Z

Hi @agruzinov. The DESY specific hardware objects look fine to me. Maybe additional cleaning could be to use super(). instead of super(classname, self), but this depends on you.
I am concerned about the recursion you mention and find important to understand why and where it happens.
Also thanks to you changing the Beamline.py, we've spotted a bug, which is very unlikely to happen, but still it is nice to have a clean code.
I would not merge yet the PR, until we understand the recursion problem.

agruzinov · 2024-02-22T09:18:49Z

Thanks everyone for the review and comments. Would it make sense to split this PR now into HO/DESY part and abstract ones since DESY specific hardware objects are ok for everyone?

Digging into recursion problem might take more time.

beteva · 2024-02-23T09:38:40Z

Yes, @agruzinov, very good idea. We could merge your local HO and than try to find the origin of the recursion and the problem with the sample changer

marcus-oscarsson · 2024-03-04T13:32:49Z

@agruzinov, did I understand you correctly, that you wanted to close this PR ?

agruzinov · 2024-03-04T15:34:29Z

Yes, as soon as #859 will be merged. I've manually merged all the HO objects, so no-one need to go through >160 commits in the history.

marcus-oscarsson · 2024-03-04T15:44:03Z

:), thanks thats thoughtfull of you ;)

agruzinov · 2024-03-08T10:08:38Z

This PR was split to two (PR856, 859) as discussed. Closing.

Andrey Gruzinov added 30 commits September 18, 2023 12:11

Fixing the ambiguity with Poller value and .any

e80379d

P11Collect additional debug after upgrade

5f29dc6

Fixing the ambiguity with Poller value and .any

d2b8c35

P11Collect additional debug after upgrade

ba7d34c

Merge remote-tracking branch 'origin/p11_develop' into p11_develop

9585b03

Force upgrade from the develop to avoid merging conflict

df5dfd3

Added missing warnings module

de981e7

Enabled back explicit check on if beamtimeid is open

24c07c7

Added debug info in case beamtime ID is not opened

d22d705

Added beamtime info as a property

4a38247

Added additional debug messages for shutter

480ec3e

Fixed get_properties naming (Bixente)

56d2cad

Removed faulty login_type=user fot P11

a07b2ec

Removed is_open() as a function and assigned is_closed() as a propert…

be6c170

…y for shutter-like objects inside P11 HO (Bixente)

Added is_open as a property inside P11NanoDiff (Bixente)

3e58e8d

Fixed other get_properties typos which were preventing loading

2a6a21e

Removed faulty login_type=user for P11

5d7ca11

Removed is_open() as a function and assigned is_closed() as a propert…

c20ec81

…y for shutter-like objects inside P11 HO (Bixente)

Added is_open as a property inside P11NanoDiff (Bixente)

7574477

Fixed other get_properties typos which were preventing loading

b4b8f9b

Merge remote-tracking branch 'origin/p11_develop' into p11_develop

4a192df

Fixed shutter openning wainting forever (Bixente)

f3bd7d5

Merge remote-tracking branch 'origin/p11_develop' into p11_develop

6fe81ab

Added preliminary flux HO for P11

75621a3

Upgraded the characterisation part for P11 using EDNA

30ddf3a

Linting

e878dfb

Add empty store_robot_action for P11 (temp fix due to ISPyB tests).

7a11684

Fix in AbstractSampleChanger that was causing sample not loaded error…

3fe9dff

… at P11 even if everything was ok (Bixente).

Fixing the ambiguity with Poller value and .any

2d31d70

P11Collect additional debug after upgrade

8011a9c

Andrey Gruzinov and others added 5 commits December 2, 2023 20:34

Run black

8686c65

Disabled additional logging

c3a2a03

Remove unnessesary triggerring of autoprocessing. It is triggered aut…

3f63381

…omatically after data collection.

Set omega to 0 at the end explicitly

1a0b15e

Merge branch 'mxcube:develop' into p11_develop

44d8f09

agruzinov requested review from beteva, marcus-oscarsson and fabcor-maxiv and removed request for marcus-oscarsson February 20, 2024 10:57

fabcor-maxiv reviewed Feb 20, 2024

View reviewed changes

fabcor-maxiv mentioned this pull request Feb 20, 2024

P11 develop #800

Closed

beteva reviewed Feb 20, 2024

View reviewed changes

Andrey Gruzinov and others added 6 commits February 20, 2024 19:07

Explicit int after test run on Deb12

8724852

Merge branch 'mxcube:develop' into p11_develop

4bccd2c

Removed duplocated import PR854

d215a03

Corrected call of osc_start PR854

bb7335e

Code cleanup for super() in init (PR854)

33759a9

Corrected osc_start is not in the params dictionary (PR854)

e56e821

agruzinov marked this pull request as draft February 26, 2024 13:20

agruzinov changed the title ~~P11 develop upgrade~~ [WIP] P11 develop upgrade Feb 28, 2024

agruzinov closed this Mar 8, 2024

agruzinov deleted the p11_develop branch October 1, 2024 13:34

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[WIP] P11 develop upgrade #854

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[WIP] P11 develop upgrade #854

[WIP] P11 develop upgrade #854

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