Merge branch 'refactor-scanning' into 'v3'
Refactor scanning See merge request openflexure/openflexure-microscope-server!240
This commit is contained in:
Julian Stirling
commit
5ab0a62964
4 changed files with 547 additions and 437 deletions
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@ -76,7 +76,7 @@ class OFMHandler(logging.Handler):
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def append_record(self, record):
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"""
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Use the built in formatter to format the record, then save
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it to an array. Pop any in excess of the mamimum number of logs
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it to an array. Pop any in excess of the maximum number of logs
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"""
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self._log.append(self.format(record))
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while len(self._log) > self._max_logs:
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File diff suppressed because it is too large
Load diff
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@ -1,117 +0,0 @@
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from typing import Optional
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import os
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from subprocess import CompletedProcess, run, PIPE
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from labthings_fastapi.thing import Thing
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from labthings_fastapi.dependencies.raw_thing import raw_thing_dependency
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from labthings_fastapi.dependencies.invocation import InvocationLogger
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from labthings_fastapi.decorators import thing_action
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from labthings_fastapi.outputs.blob import blob_type
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from .smart_scan import SmartScanThing
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SmartScanDep = raw_thing_dependency(SmartScanThing)
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JPEGBlob = blob_type("image/jpeg")
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class Stitcher(Thing):
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def __init__(self, path_to_openflexure_stitch: str):
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self._script = path_to_openflexure_stitch
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def run_subprocess(
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self,
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logger: InvocationLogger,
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cmd: list[str],
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) -> CompletedProcess:
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"""Run a subprocess and log any output"""
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logger.info(f"Running command in subprocess: `{' '.join(cmd)}")
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output = run(cmd, stdout=PIPE, stderr=PIPE, universal_newlines=True)
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for pipe in [output.stdout, output.stderr]:
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if pipe:
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logger.info(pipe)
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output.check_returncode()
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return output
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def images_folder(
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self, smart_scan: SmartScanDep, scan_name: Optional[str] = None
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) -> str:
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scan_folder = smart_scan.scan_folder_path(scan_name=scan_name)
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return os.path.join(scan_folder, "images")
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@staticmethod
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def output_up_to_date(
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folder: str,
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output_filename: str,
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image_prefix: str = "image",
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image_suffix: str = ".jpg",
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) -> bool:
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"""Check if any of the images in a folder are newer than a file
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If there are no images (files with the prefix and suffix) newer than the
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`output_filename`, we return `True`, i.e. the output is up to date. If
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any image in the folder is newer, we return `False`.
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This is not flawless logic - if an update process is slow, images might be
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saved between starting that process and saving the output. Consequently,
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a `True` from this function does not guarantee the output is up to date.
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If the output file is missing, we also return `False`.
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"""
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output_path = os.path.join(folder, output_filename)
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if not os.path.exists(output_path):
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return False
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mtime = os.path.getmtime(output_path)
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for fname in os.listdir(folder):
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if fname.startswith(image_prefix) and fname.endswith(image_suffix):
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if os.path.getmtime(os.path.join(folder, fname)) > mtime:
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return False
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return True
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@thing_action
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def stitch_scan_from_stage(
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self,
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logger: InvocationLogger,
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smart_scan: SmartScanDep,
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scan_name: Optional[str] = None,
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downsample: float = 1.0,
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) -> JPEGBlob:
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"""Generate a stitched image based on stage position metadata"""
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output_fname = "stitched_from_stage.jpg"
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images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
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if self.output_up_to_date(images_folder, output_fname):
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logger.info(f"No images are newer than {output_fname}, skipping.")
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else:
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self.run_subprocess(
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logger,
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[self._script, "--stitching_mode", "only_stage_stitch", images_folder],
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)
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return JPEGBlob.from_file(os.path.join(images_folder, output_fname))
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@thing_action
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def update_scan_correlations(
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self,
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logger: InvocationLogger,
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smart_scan: SmartScanDep,
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scan_name: Optional[str] = None,
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) -> None:
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"""Generate a stitched image based on stage position metadata"""
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images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
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self.run_subprocess(
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logger, [self._script, "--stitching_mode", "only_correlate", images_folder]
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)
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@thing_action
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def stitch_scan(
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self,
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logger: InvocationLogger,
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smart_scan: SmartScanDep,
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scan_name: Optional[str] = None,
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downsample: float = 1.0,
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) -> None:
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"""Generate a stitched image based on stage position metadata"""
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images_folder = self.images_folder(smart_scan=smart_scan, scan_name=scan_name)
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self.run_subprocess(
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logger, [self._script, "--stitching_mode", "all", images_folder]
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)
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81
src/openflexure_microscope_server/utilities.py
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81
src/openflexure_microscope_server/utilities.py
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@ -0,0 +1,81 @@
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"""
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This module contains some utility functions and classes
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"""
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from threading import Thread
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class ErrorCapturingThread(Thread):
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"""
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This is a a subclass or Thread. It wraps the target function in a
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try-except block.
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Execution will stop with an unhandled exception, but the exception will not be raised
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until the join method is called. When the join method is called, the exception is
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called in the calling thread.
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This allows for error handling to be performed by the calling thread at the time that
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join is run.
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"""
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def __init__(self, group=None, target=None, args=None, kwargs=None, daemon=None):
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"""
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Initialise with the same arguments as Thread
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"""
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# As all inputs are keywords we need to set the default values for args and kwargs:
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if args is None:
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args = ()
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if kwargs is None:
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kwargs = {}
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# Make an empty list for any error.
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# We are only ever going to have one or zero errors, this is an empty
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# list as we need to pass the reference not the value to collect the
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# error. If we could simply make a pointer we would have done that.
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self._error_buffer = []
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# Add the target function end error buffer to the thread to the start of
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# the argument list so they are passed to _wrap_and_catch_errors()
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args = (target, self._error_buffer, *args)
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# Start the thread with _wrap_and_catch_errors() as the target
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super().__init__(
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group=group,
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target=_wrap_and_catch_errors,
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args=args,
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kwargs=kwargs,
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daemon=daemon,
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)
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def join(self, timeout=None):
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"""
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Join when the thread is complete. If the thread ended due to an unhandled exception,
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the exception will be raised when this method is called.
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"""
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super().join(timeout)
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# If there is an error in the error buffer clear the buffer and raise it
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if self._error_buffer:
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err = self._error_buffer[0]
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self._error_buffer = []
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raise err
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def _wrap_and_catch_errors(target, error_buffer, *args, **kwargs):
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"""
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This function is designed only to be used by
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ErrorCapturingThread
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It will run a target function in a try-except block
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any errors caught are added to an empty list that
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should be supplied as a keyword argument
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Arguments:
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* target - The target function to call
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* error_buffer - An empty list that is used for returning
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the exception from the thread
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*args: The arguments for the target function
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**kwargs: The Keyword arguments for the target function
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"""
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try:
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target(*args, **kwargs)
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except BaseException as e:
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error_buffer.append(e)
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