Updated Pycromanager to 0.24.1. (#307)

* Updated Pycromanager to 0.24.1.
Connects to MM and disconnects, but fails to reconnect.  That problem
seems to be related to ui code I do not understand.

* replace print statements with log and error msg

---------

Co-authored-by: Nico Stuurman <nstuurman@altoslabs.com>
Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

recOrder/plugin/main_widget.py

@@ -2,7 +2,7 @@
 from __future__ import annotations
 
 from recOrder.calib.Calibration import QLIPP_Calibration, LC_DEVICE_NAME
-from pycromanager import Bridge
+from pycromanager import Core, Studio, zmq_bridge
 from qtpy.QtCore import Slot, Signal, Qt
 from qtpy.QtWidgets import QWidget, QFileDialog, QSizePolicy, QSlider
 from qtpy.QtGui import QPixmap, QColor
@@ -884,21 +884,26 @@ def connect_to_mm(self):
  RECOMMENDED_MM = "20220920"
  ZMQ_TARGET_VERSION = "4.2.0"
  try:
- self.bridge = Bridge(convert_camel_case=False)
- self.mmc = self.bridge.get_core()
- self.mm = self.bridge.get_studio()
+ self.mmc = Core(convert_camel_case=False)
+ # Check it works
+ self.mmc.getAvailableConfigGroups()
+ self.mm = Studio(convert_camel_case=False)
+ # Order is important: If the bridge is created before Core, Core will not work
+ self.bridge = zmq_bridge._bridge._Bridge()
+ logging.debug("Established ZMQ Bridge and found Core and Studio")
  except:
- print(
+ raise EnvironmentError(
  (
  "Could not establish pycromanager bridge.\n"
  "Is micromanager open?\n"
  "Is Tools > Options > Run server on port 4827 checked?\n"
  f"Are you using nightly build {RECOMMENDED_MM}?"
  )
  )
- raise EnvironmentError
 
  # Warn the user if there is a MicroManager/ZMQ version mismatch
+ # NS: Not quite sure what this is good for, we already know the Core works
+ # This code uses undocumented PycroManager features, so may well break in the future
  self.bridge._main_socket.send({"command": "connect", "debug": False})
  reply_json = self.bridge._main_socket.receive(timeout=500)
  zmq_mm_version = reply_json["version"]
@@ -909,13 +914,15 @@ def connect_to_mm(self):
  < version.parse(ZMQ_TARGET_VERSION)
  else "downgrade"
  )
- print(
+ logging.warning(
  (
- "WARNING: This version of Micromanager has not been tested with recOrder.\n"
+ "This version of Micromanager has not been tested with recOrder.\n"
  f"Please {upgrade_str} to MicroManager nightly build {RECOMMENDED_MM}."
  )
  )
 
+ logging.debug("Confirmed correct ZMQ bridge----")
+
  # Find config group containing calibration channels
  # calib_channels is typically ['State0', 'State1', 'State2', ...]
  # config_list may be something line ['GFP', 'RFP', 'State0', 'State1', 'State2', ...]
@@ -926,6 +933,7 @@ def connect_to_mm(self):
  # self.ui.cb_config_group.clear() # This triggers the enter config we will clear when switching off
  groups = self.mmc.getAvailableConfigGroups()
  config_group_found = False
+ logging.debug("Checking MM config group")
  for i in range(groups.size()):
  group = groups.get(i)
  configs = self.mmc.getAvailableConfigs(group)
@@ -956,6 +964,7 @@ def connect_to_mm(self):
  self.ui.cb_acq_channel.addItem(ch)
  self.bf_channel_found = True
 
+ logging.debug("Checked configs.")
  if not config_group_found:
  msg = (
  f"No config group contains channels {self.calib_channels}. "
@@ -975,6 +984,7 @@ def connect_to_mm(self):
  self.ui.cb_acq_channel.setToolTip(self.no_bf_msg)
 
  # set startup LC control mode
+ logging.debug("Setting startup LC control mode...")
  _devices = self.mmc.getLoadedDevices()
  loaded_devices = [_devices.get(i) for i in range(_devices.size())]
  if LC_DEVICE_NAME in loaded_devices:
@@ -991,6 +1001,8 @@ def connect_to_mm(self):
  self.calib_mode = "DAC"
  self.ui.cb_calib_mode.setCurrentIndex(2)
 
+ logging.debug("Finished connecting to MM.")
+
  @Slot(tuple)
  def handle_progress_update(self, value):
  self.ui.progress_bar.setValue(value[0])
@@ -1362,8 +1374,8 @@ def enter_config_group(self):
  """
  # if/else takes care of the clearing of config
  if self.ui.cb_config_group.count() != 0:
- self.mmc = self.bridge.get_core()
- self.mm = self.bridge.get_studio()
+ self.mmc = Core(convert_camel_case=False)
+ self.mm = Studio(convert_camel_case=False)
 
  # Gather config groups and their children
  self.config_group = self.ui.cb_config_group.currentText()

setup.cfg

@@ -38,7 +38,7 @@ setup_requires = setuptools_scm
 # add your package requirements here
 install_requires =
  waveorder==1.0.0rc0
- pycromanager==0.19.2
+ pycromanager==0.24.1
  click>=8.0.1
  natsort>=7.1.1
  colorspacious>=1.1.2
@@ -48,7 +48,6 @@ install_requires =
  napari;'arm64' in platform_machine # without Qt and skimage
  PyQt6;'arm64' in platform_machine
  importlib-metadata
- numpy==1.23.5 # TODO: remove after https://github.com/micro-manager/pycro-manager/pull/475
 
 [options.extras_require]
 dev =