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Changes to enable transfer and processing of Tomo5 multigrid data #662

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Merged
d-j-hatton merged 1 commit into from
Sep 9, 2025
Merged

Changes to enable transfer and processing of Tomo5 multigrid data #662

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113 changes: 66 additions & 47 deletions src/murfey/client/watchdir_multigrid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,55 @@ def stop(self):
self.thread.join()
log.debug("MultigridDirWatcher thread stop completed")

def _handle_metadata(self, directory: Path):
self.notify(
directory,
extra_directory=f"metadata_{directory.name}",
include_mid_path=False,
analyse=self._analyse,
limited=True,
tag="metadata",
)
self._seen_dirs.append(directory)

def _handle_fractions(self, directory: Path, first_loop: bool):
processing_started = False
for d02 in directory.glob("Images-Disc*"):
if d02 not in self._seen_dirs:
# If 'skip_existing_processing' is set, do not process for
# any data directories found on the first loop.
# This allows you to avoid triggering processing again if Murfey is restarted
self.notify(
d02,
include_mid_path=False,
remove_files=True,
analyse=(
not (first_loop and self._skip_existing_processing)
if self._analyse
else False
),
tag="fractions",
)
self._seen_dirs.append(d02)
processing_started = d02 in self._seen_dirs
if not processing_started:
if (
directory.is_dir()
and directory not in self._seen_dirs
and list(directory.iterdir())
):
self.notify(
directory,
include_mid_path=False,
analyse=(
not (first_loop and self._skip_existing_processing)
if self._analyse
else False
),
tag="fractions",
)
self._seen_dirs.append(directory)

def _process(self):
first_loop = True
while not self._stopping:
Expand All @@ -75,53 +124,23 @@ def _process(self):
)
self._seen_dirs.append(d)
else:
if d.is_dir() and d not in self._seen_dirs:
self.notify(
d,
extra_directory=f"metadata_{d.name}",
include_mid_path=False,
analyse=self._analyse,
limited=True,
tag="metadata",
)
self._seen_dirs.append(d)
processing_started = False
for d02 in (d.parent.parent / d.name).glob("Images-Disc*"):
if d02 not in self._seen_dirs:
# If 'skip_existing_processing' is set, do not process for
# any data directories found on the first loop.
# This allows you to avoid triggering processing again if Murfey is restarted
self.notify(
d02,
include_mid_path=False,
remove_files=True,
analyse=(
not (first_loop and self._skip_existing_processing)
if self._analyse
else False
),
tag="fractions",
)
self._seen_dirs.append(d02)
processing_started = d02 in self._seen_dirs
if not processing_started:
d02 = d.parent.parent / d.name
if (
d02.is_dir()
and d02 not in self._seen_dirs
and list((d.parent.parent / d.name).iterdir())
):
self.notify(
d02,
include_mid_path=False,
analyse=(
not (first_loop and self._skip_existing_processing)
if self._analyse
else False
),
tag="fractions",
)
self._seen_dirs.append(d02)
# hack for tomo multigrid metadata structure
sample_dirs = list(d.glob("Sample*"))
if d.is_dir() and len(sample_dirs):
for sample in sample_dirs:
if len(list(sample.glob("*.mdoc"))):
if sample not in self._seen_dirs:
self._handle_metadata(sample)
self._handle_fractions(
d.parent.parent.parent
/ f"{d.parent.name}_{d.name}",
first_loop,
)

else:
if d.is_dir() and d not in self._seen_dirs:
self._handle_metadata(d)
self._handle_fractions(d.parent.parent / d.name, first_loop)

if first_loop:
first_loop = False
Expand Down