henrypinkard / pygellan Goto Github PK

It seems necessary for ensuring you're working with a fresh slate.

Thanks

Hi Henry,

Thanks for the GUI access. It seems very straightforward.

I'd like to be able to create Magellan grids using predefined positions. For example, new_grid_1 = create_magellan_grid(xPos, yPos, nRows, nColumns)

This will be essential for the randomized ROI acquisition interface I'm making.

Thanks for the help!
Kyle

Create a python generator function that produces acquisition events according some syntax (e.g. {'z_pos': 123.45, 'time_index': 0}) which then drive acquisition on Java side and hardware sequenced where applicable. This would enable a lot of flexibility in driving acquisitions.

Maybe could do this push/pull ZMQ sockets

There's a memory leak related to the magellan image windows. The image windows and associated objects never get garbage collected, and as a result, leak a few MB of memory with each acquisition. Since the Magellan window is one big hack on top of micro-manager which is itself on top of imageJ, I have no idea how to fix this.

Hi Henry,

I can elaborate more on this issue next week, but wanted you to be aware that there is some weird channel acquisition bug on the latest nightly build of Magellan. The channels don't stay consistent as far as the ordering goes; ch1, ch2, ch3 becomes ch2, ch3, ch1, or something. I wasn't able to find a pattern as I was trying to run an expt. Will get you more details soon.

I'll see you in person for the fix?
Kyle

This would require:

• Move ZMQServer to micro-manager so that it is on a master ClassLoader that can access plugins. (org.micromanager.internal.zmq)

• Add server startup to "tools--options"and start ZMQServer from appropriate place in micro-manager if enabled @nicost

• Add mechanism exposing Plugin classes as MMJavaClasses. Maybe do this by exposing everything, maybe do this by passing in an argument of the full javaclasspath as a string argument to MagellanBridge (e.g bridge = MagellanBridge('org.micromanager.plugins.MM2Python')). Check to see if any performance issues passing all available plugins

• Make sure Java objects can be passed backed into Java functions by their hashes

• Add convenience flag to not translate function names from camelCase to snake_case

• Add to documentation/examples for how to access plugin

@nicost @bryantChhun

Latest master on both micromanager (nico's branch) and pygellan.

Running

from pygellan.acquire import MagellanBridge
import os

#establish communication with Magellan
bridge = MagellanBridge()
#get object representing micro-magellan API
magellan = bridge.get_magellan()

acquistions = magellan.get_acquisitions()
#grab the first acquisition in the list
acq = acquistions[0]
acq_settings = acq.get_acquisition_settings()

#channel settings
acq_settings.set_channel_group('Channel')

Hi Henry,

I'd like to be able to build grids from Python and assign them to Magellan for the acquisition.
I will need to set stepsize, z start, and z end for each grid.

Thanks,
Kyle

Hello,

I was recently pointed towards Pygellan as some way to control acquisitions with Micro Manager externally by Python.
After installing Pygellan and starting Micro Manager (2.0y nightly), I first tried some simple things as outlined in the examples - setting some acquisition parameters, etc., which worked fine.
However, when I try to use the Micro-magellan acquisitions, something goes wrong.
Using magellan = bridge.get_magellan() after

from pygellan.acquire import PygellanBridge
bridge = PygellanBridge()

will result in an error:

Exception: Couldnt find class with nameorg.micromanager.magellan.api.MagellanAPI

What's strange is, I could have sworn it worked the first time I tried one of the example scripts, but hung itself up at the command acq.start()
Since then, I always get the above error message.
I have since tried reinstalling pygellan and Micro-Manager, but the error persists...
Am I missing something?

I was able to follow the example code using Anaconda > Spyder > Ipython no problem with the demo.cfg. Which is awesome.

I was playing around with the core commands and found a lot to be working, but a few were missing. core.getImage() results in AttributeError: 'MMJavaClass' object has no attribute 'getImage' . Same with core.getLastImage().

This is after using core.snapImage().

Is the whole cmmcore available, or is it still a work in progress?

Thanks,
Kyle

Hi Henry,

I'd like to be able to control the time tab in Magellan through Python. Will need to be able to set whether the grids are run sequentially or not.

Thanks,
Kyle

For example, would like to be able to call both core.set_exposure(10) and `core.set_exposure('CameraName', 10), which right now isn't possible

Want to be able to pass in "acquisiton hooks", i.e. python functions that are automatically executed in different parts of the acquisition sequence (e.g. before hardware move, after hardware move, before image saving). This would enable the ability to adjust hardware based on data during the acquisition cycle (with a simple example being autofocus)

The "+" button on the acquisitions tab does not add another line for multiple acquisitions.

Can we also get an example of how to add an acquisition in python? something like?

acquisitions = magellan.get_acquisitions()
acq = acquisitions[0]
acq_settings = acq.get_acquisition_settings()

acq1 = acq
acquisitions.append(acq1)

There's some bad bug where the incorrect acquisition gets finished when running two in close succession

In many situations, would be good to be able to apply some arbitrary transformation to images in using Python libraries and then send them back into the regualar Java image processing queue. Basicially the same idea as this, but implemented in pure Python

Maybe could do this with a ZMQ client server architecture where the client runs as micromanager processor plugin, and the server runs in python and returns image or none?

Demo dataset acquired with MM2.0gamma nightly 10/14/2019 includes 4 channel, 3 timepoints, 11 z, on a 2x2 grid.

Cannot access magellan.summary_metadata['ChNames'] without crashing.
KeyError: 'ChNames'
Code worked for dataset acquired with MM 1.4 Magellan.

your code in magellan_data.py

if 'ChNames' in self.summary_metadata:
                    #Legacy magellan files--load channel names here
                    self._channel_names = {i: ch for i, ch in enumerate(self.summary_metadata['ChNames'])}
                else:
                    self._channel_names = {} #read them from image metadata

how should we access channel names in the new version?

Thanks!
Kyle

Hi Henry,

When launching the explore window Magellan no longer sets the z limits to both be the current stage setting. It will set the lower limit to zero, which if you miss changing, will crash your stage (did it twice). Can you set it back to launch at the current setting?

Thanks,
Kyle

A few questions regarding re-use of parts of the µMagellan code in a separate µManager plugin. I appreciate some pointers to get me going in the right direction.

1. Viewer: I understand µMagellan has its own viewer code. To what extent is the µMagellan viewer separate and usable from the outside the µMagellan plugin? Less importantly, in 2.0 gamma there is ClearVolume; have you considered it as a viewer?

2. File format: Are there important differences between Magellan's multi-resolution format and BDV's format? I know BDV can open Magellan files but it seems better yet if they used the identical format. I would love to see multi-resolution become a first-class file saving option within µManager and that raises the question of the format specifics.

3. 1.4 vs. 2.0: Has anything significant changed with µMagellan when porting to 2.0 besides updating the calls to µManager API? I understand current development has migrated to 2.0, but I'm initially interested in using parts of µMagellan in 1.4.

@henrypinkard @nicost
Furthering the disucssion from #25

I still hold that the "core" behavior that we have should be separated from the magellan acquisition engine for precisely these reasons:

In order to enable the functionality described in the issues, I will need to add different types of socket architectures (i.e. not Java server python client). These may be fairly tightly coupled to the magellan acquisition engine. Hard to say for me right now which layer they would belong in, because there is still a lot to figure out.

The problem with this approach is that it means future development potentially breaks existing behavior. If you can guarantee it will not, then that's actually an argument that this "core" functionality is ready to be isolated.

In other words, i'm saying that the goal of this module is to provide a general service that others can build upon for their applications. Specific elaborations should build on top as a separate layer, but mostly pipe into API provided by this "core". If you think certain fundamental changes need to be made (multi sockets maybe?), then let's think about that right now.

Hi Henry,

Tried to run a simple script with the new Pygellan and last night's MicroManager build. In my VS code editor the simple script caused an endless output of the errors seen in the screen shot (had to screen shot as killing the terminal clears the errors and they were flying by too fast to read).

If I run the code in my Spyder editor, it runs fine. The main issue for me personally is that I had to switch from Spyder to VS code due to different error happening specifically in Spyder. Running out of editors...

Anyways, let me know if it's fixable, or I'll hunt for another editor.

Kyle

When trying to read information pertinent to packing an .hdf5 file, how would you pull information from the Magellan dataset? x, y, z, t resolution are most interesting. I can access the micromanager metadata but z and t resolution aren't in there I believe.

Thanks,
Kyle

Using the demo config for acquisitions and explore, no XML metadata file is produced.

Hi Henry,

I'd like to be able to assign and control channel exposure from Python to send to Magellan for multiple grid acquisitions.

Thanks,
Kyle

Once acquisition stuff is implemented, implement headless mode so that no Java based viewer pops up and everything can be done from your language of choice

@oeway