Merge pull request #769 from bruno-digitbio/logging-overhaul

Remove internal usage of `pycromanager.logging`

docs/source/apis.rst

@@ -165,17 +165,3 @@ Convenience classes for special Java objects
 
 .. autoclass:: Studio
 	:members:
-
-
-Logging control
-###############
-
-set_logging_instance
-====================
-
-.. autofunction:: set_logging_instance
-
-reset_logger_instance
-=====================
-
-.. autofunction:: reset_logger_instance

pycromanager/__init__.py

@@ -8,6 +8,5 @@
 from pycromanager.core import Core
 from pyjavaz import JavaObject, JavaClass, PullSocket, PushSocket
 from pycromanager.acquisition.acq_eng_py.main.acq_notification import AcqNotification
-from pycromanager.logging import set_logger_instance, reset_logger_instance
 from ndtiff import Dataset
 from ._version import __version__, version_info

pycromanager/_version.py

@@ -1,2 +1,2 @@
-version_info = (0, 32, 1)
+version_info = (0, 33, 0)
 __version__ = ".".join(map(str, version_info))

pycromanager/acquisition/java_backend_acquisitions.py

@@ -2,6 +2,7 @@
 The Pycro-manager Acquisiton system
 """
 import json
+import logging
 import warnings
 import weakref
 
@@ -15,7 +16,7 @@
 from pyjavaz import DEFAULT_BRIDGE_PORT as DEFAULT_PORT
 from pycromanager.mm_java_classes import ZMQRemoteMMCoreJ, Magellan
 from pycromanager.acquisition.java_RAMStorage import JavaRAMDataStorage
-import pycromanager.logging as logging
+
 from ndtiff import Dataset
 import os.path
 import queue
@@ -25,6 +26,8 @@
 from pycromanager.acq_future import AcqNotification, AcquisitionFuture
 import json
 
+logger = logging.getLogger(__name__)
+
 
 ### These functions are defined outside the Acquisition class to
 # prevent problems with pickling when running them in differnet process
@@ -36,7 +39,7 @@ def _run_acq_event_source(acquisition, event_port, event_queue, debug=False):
         while True:
             events = event_queue.get(block=True)
             if debug:
-                logging.main_logger.debug(f"got event(s): {events}")
+                logger.debug(f"got event(s): {events}")
             if events is None:
                 # Initiate the normal shutdown process
                 if not acquisition._acq.is_finished():
@@ -54,7 +57,7 @@ def _run_acq_event_source(acquisition, event_port, event_queue, debug=False):
             #  maybe consider putting a timeout on the send?
             event_socket.send({"events": events if type(events) == list else [events]})
             if debug:
-                logging.main_logger.debug("sent events")
+                logger.debug("sent events")
     except Exception as e:
         acquisition.abort(e)
     finally:
@@ -109,7 +112,7 @@ def _run_image_processor(
     push_socket = PushSocket(pull_port, debug=debug)
     pull_socket = PullSocket(push_port, debug=debug)
     if debug:
-        logging.main_logger.debug("image processing sockets connected")
+        logger.debug("image processing sockets connected")
     sockets_connected_evt.set()
 
     def process_and_sendoff(image_tags_tuple, original_dtype):

pycromanager/headless.py

@@ -1,3 +1,4 @@
+import logging
 import subprocess
 import platform
 import atexit
@@ -7,12 +8,13 @@
 
 from pycromanager.acquisition.acq_eng_py.internal.engine import Engine
 from pymmcore import CMMCore
-import pycromanager.logging as logging
 import pymmcore
 from pyjavaz import DEFAULT_BRIDGE_PORT, server_terminated
 
 import re
 
+logger = logging.getLogger(__name__)
+
 class TaggedImage:
 
     def __init__(self, tags, pix):
@@ -94,29 +96,29 @@ def stop_headless(debug=False):
     for p in _JAVA_HEADLESS_SUBPROCESSES:
         port = p.port
         if debug:
-            logging.main_logger.debug('Stopping headless process with pid {}'.format(p.pid))
+            logger.debug('Stopping headless process with pid {}'.format(p.pid))
         p.terminate()
         server_terminated(port)
         if debug:
-            logging.main_logger.debug('Waiting for process with pid {} to terminate'.format(p.pid))
+            logger.debug('Waiting for process with pid {} to terminate'.format(p.pid))
         p.wait()  # wait for process to terminate
         if debug:
-            logging.main_logger.debug('Process with pid {} terminated'.format(p.pid))
+            logger.debug('Process with pid {} terminated'.format(p.pid))
     _JAVA_HEADLESS_SUBPROCESSES.clear()
     if debug:
-        logging.main_logger.debug('Stopping {} pymmcore instances'.format(len(_PYMMCORES)))
+        logger.debug('Stopping {} pymmcore instances'.format(len(_PYMMCORES)))
     for c in _PYMMCORES:
         if debug:
-            logging.main_logger.debug('Stopping pymmcore instance')
+            logger.debug('Stopping pymmcore instance')
         c.unloadAllDevices()
         if debug:
-            logging.main_logger.debug('Unloaded all devices')
+            logger.debug('Unloaded all devices')
         Engine.get_instance().shutdown()
         if debug:
-            logging.main_logger.debug('Engine shut down')
+            logger.debug('Engine shut down')
     _PYMMCORES.clear()
     if debug:
-        logging.main_logger.debug('Headless stopped')
+        logger.debug('Headless stopped')
 
 # make sure any Java processes are cleaned up when Python exits
 atexit.register(stop_headless)
@@ -177,13 +179,13 @@ def start_headless(
             else:
                 java_loc = "java"
         if debug:
-            logging.main_logger.debug(f'Java location: {java_loc}')
+            logger.debug(f'Java location: {java_loc}')
             #print classpath
-            logging.main_logger.debug(f'Classpath: {classpath}')
+            logger.debug(f'Classpath: {classpath}')
             # print stuff in the classpath directory
-            logging.main_logger.debug('Contents of classpath directory:')
+            logger.debug('Contents of classpath directory:')
             for f in os.listdir(classpath.split('*')[0]):
-                logging.main_logger.debug(f)
+                logger.debug(f)
 
         # This starts Java process and instantiates essential objects (core,
         # acquisition engine, ZMQServer)
@@ -215,12 +217,12 @@ def start_headless(
         if not started:
             raise Exception('Error starting headless mode')
         if debug:
-            logging.main_logger.debug('Headless mode started')
+            logger.debug('Headless mode started')
             def loggerFunction():
                 while process in _JAVA_HEADLESS_SUBPROCESSES:
                     line = process.stdout.readline().decode('utf-8')
                     if line.strip() != '':
-                        logging.main_logger.debug(line)
+                        logger.debug(line)
             threading.Thread(target=loggerFunction).start()
 
 

requirements.txt

@@ -5,4 +5,4 @@ ndtiff>=2.3.0
 docstring-inheritance
 pymmcore
 sortedcontainers
-pyjavaz==1.1.0
+pyjavaz==1.1.1