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Live logging (requires unbuffered program output from stitching)

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jaknapper 2024-02-20 10:51:32 +00:00
parent aed5a22983
commit e6eb4d419d
1 changed files with 24 additions and 14 deletions
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38
src/openflexure_microscope_server/things/smart_scan.py
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@ -14,7 +14,7 @@ from scipy.stats import norm
from scipy.ndimage import zoom from scipy.ndimage import zoom
from copy import deepcopy from copy import deepcopy
from datetime import datetime from datetime import datetime
from subprocess import CompletedProcess, Popen, PIPE, SubprocessError, run from subprocess import CompletedProcess, Popen, PIPE, SubprocessError, run, STDOUT
from threading import Event, Thread from threading import Event, Thread
import glob import glob
import zipfile import zipfile
@ -1003,12 +1003,29 @@ class SmartScanThing(Thing):
) -> CompletedProcess: ) -> CompletedProcess:
"""Run a subprocess and log any output""" """Run a subprocess and log any output"""
logger.info(f"Running command in subprocess: `{' '.join(cmd)}`") logger.info(f"Running command in subprocess: `{' '.join(cmd)}`")
output = run(cmd, stdout=PIPE, stderr=PIPE, universal_newlines=True)
for pipe in [output.stdout, output.stderr]:
if pipe: p = Popen(cmd, stdout=PIPE, stderr = STDOUT, bufsize=1, universal_newlines=True)
logger.info(pipe) os.set_blocking(p.stdout.fileno(), False)
output.check_returncode() logger.info(time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(time.time())))
return output while p.poll() == None:
try:
output = p.stdout.readline()
if output != "" and output != None:
logger.info(output)
except:
pass
for line in p.stdout:
try:
output = p.stdout.readline()
if output != "" and output != None:
logger.info(output)
except:
pass
logger.info('Stitching complete')
return p
@thing_action @thing_action
def stitch_scan(self, logger: InvocationLogger, scan_name: Optional[str]=None, overlap: float = 0.0) -> None: def stitch_scan(self, logger: InvocationLogger, scan_name: Optional[str]=None, overlap: float = 0.0) -> None:
@ -1039,13 +1056,6 @@ class SmartScanThing(Thing):
raise FileNotFoundError(f"Tried to make a zip archive of {images_folder} but it does not exist.") raise FileNotFoundError(f"Tried to make a zip archive of {images_folder} but it does not exist.")
# logger.info("Creating zip archive of images (may take some time)...") # logger.info("Creating zip archive of images (may take some time)...")
from pathlib import Path
root_directory = Path(images_folder)
print(sum(f.stat().st_size for f in root_directory.glob('**/*') if f.is_file()))
zip_fname = f'{os.path.join(scan_folder, "images")}.zip'
# Create an empty zip file - we don't want to autofill it with files, # Create an empty zip file - we don't want to autofill it with files,
# as some of them should only be added at the end (as we can't overwrite) # as some of them should only be added at the end (as we can't overwrite)
# them once they change # them once they change