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add reading to memory mapped temp array #3

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merged 2 commits into from
Jun 13, 2024
Merged

add reading to memory mapped temp array #3

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d69fd4c
add reading to memory mapped temp array
sophiamaedler Jun 3, 2024
5a9a843
implement memory mapping for reading labels
sophiamaedler Jun 5, 2024
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27 changes: 22 additions & 5 deletions src/sparcscore/pipeline/segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@

from alphabase.io import tempmmap


class Segmentation(ProcessingStep):
"""Segmentation helper class used for creating segmentation workflows.

Expand Down Expand Up @@ -280,7 +281,7 @@ def save_segmentation_zarr(self, labels=None):
loc = parse_url(path, mode="w").store
group = zarr.group(store=loc)

segmentation_names = ["nucleus", "cyotosol"]
segmentation_names = ["nucleus", "cytosol"]

# check if segmentation names already exist if so delete
for seg_names in segmentation_names:
Expand All @@ -301,7 +302,15 @@ def save_segmentation_zarr(self, labels=None):
path_labels = os.path.join(self.directory, self.DEFAULT_OUTPUT_FILE)

with h5py.File(path_labels, "r") as hf:
labels = hf[self.DEFAULT_MASK_NAME][:]
# initialize tempmmap array to save label results into
labels = tempmmap.array(
shape=hf[self.DEFAULT_MASK_NAME].shape,
dtype=hf[self.DEFAULT_MASK_NAME].dtype,
tmp_dir_abs_path=self._tmp_dir_path,
)

labels[0] = hf[self.DEFAULT_MASK_NAME][0]
labels[1] = hf[self.DEFAULT_MASK_NAME][1]

segmentations = [np.expand_dims(seg, axis=0) for seg in labels]

Expand All @@ -316,6 +325,7 @@ def save_segmentation_zarr(self, labels=None):
)

self.log("finished saving segmentation results to ome.zarr")
del labels
else:
self.log(
"Not saving shard segmentation into ome.zarr. Will only save completely assembled image."
Expand Down Expand Up @@ -538,9 +548,8 @@ def save_segmentation(self, channels, labels, classes):

self.check_filter_status()
self.save_classes(classes)

self.log("=== finished segmentation ===")
self.save_segmentation_zarr(labels=labels)
self.log("=== finished segmentation ===")

def initialize_shard_list(self, sharding_plan):
_shard_list = []
Expand Down Expand Up @@ -832,7 +841,15 @@ def resolve_sharding(self, sharding_plan):
path_labels = os.path.join(self.directory, self.DEFAULT_OUTPUT_FILE)

with h5py.File(path_labels, "r") as hf:
labels = hf[self.DEFAULT_MASK_NAME][:]
# initialize tempmmap array to save label results into
labels = tempmmap.array(
shape=hf[self.DEFAULT_MASK_NAME].shape,
dtype=hf[self.DEFAULT_MASK_NAME].dtype,
tmp_dir_abs_path=self._tmp_dir_path,
)

labels[0] = hf[self.DEFAULT_MASK_NAME][0]
labels[1] = hf[self.DEFAULT_MASK_NAME][1]

self.save_segmentation_zarr(labels=labels)
self.log(
Expand Down
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