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Load and parse channels and logical channels #32

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Load and parse channels and logical channels #32

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fdc30ac
Load and parse channels and logical channels
joshmoore Dec 11, 2024
879d665
Merge branch 'main' into add-channels
joshmoore Nov 7, 2025
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15 changes: 15 additions & 0 deletions src/omero_rdf/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -688,6 +688,8 @@ def descend(
if img.getPrimaryPixels() is not None:
pixid = handler(img.getPrimaryPixels())
handler.contains(imgid, pixid)
for ch in self._get_channels(gateway, img):
handler(ch)
handler.annotations(img, imgid)
for roi in self._get_rois(gateway, img):
roiid = handler(roi)
Expand All @@ -702,6 +704,19 @@ def descend(
else:
self.ctx.die(111, "unknown target: %s" % target.__class__.__name__)

def _get_channels(self, gateway, img):
params = ParametersI()
params.addId(img.id)
query = """select p from Pixels p left outer
join fetch p.channels as c
join fetch c.logicalChannel as lc
join fetch p.image as i where i.id = :id"""

for pix in gateway.getQueryService().findAllByQuery(
query, params, {"omero.group": str(img.details.group.id.val)}
):
yield from pix._getChannels()

def _get_rois(self, gateway, img):
params = ParametersI()
params.addId(img.id)
Expand Down