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Check for z_fields in 2nd cycle .xml file #89

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Merged
ttngu207 merged 5 commits into from
Sep 13, 2023
Merged

Check for z_fields in 2nd cycle .xml file #89

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df0d9b8
Raise exception to debug summary image dimensions
kushalbakshi Aug 29, 2023
13e6e94
Revert previous commit
kushalbakshi Aug 29, 2023
20188ad
Update CHANGELOG for #88
kushalbakshi Sep 5, 2023
3b4b61c
Merge branch 'multi-plane-caiman' of https://github.com/kushalbakshi/…
kushalbakshi Sep 13, 2023
7e5be44
Check for z_fields in 2nd cycle of acqusition
kushalbakshi Sep 13, 2023
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,11 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
[Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.


## [0.7.0] - 2023-09-05

+ Add - multi-plane `caiman_loader.py` to process multi-plane tiffs
+ Update - DANDI upload utility

## [0.6.1] - 2023-08-02

+ Update DANDI upload funtionality to improve useability
Expand Down Expand Up @@ -83,6 +88,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and

+ Add - Readers for: `ScanImage`, `Suite2p`, `CaImAn`.

[0.7.0]: https://github.com/datajoint/element-interface/releases/tag/0.7.0
[0.6.0]: https://github.com/datajoint/element-interface/releases/tag/0.6.0
[0.5.4]: https://github.com/datajoint/element-interface/releases/tag/0.5.4
[0.5.3]: https://github.com/datajoint/element-interface/releases/tag/0.5.3
Expand Down
10 changes: 5 additions & 5 deletions element_interface/prairie_view_loader.py
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Expand Up @@ -205,7 +205,7 @@ def _extract_prairieview_metadata(xml_filepath: str):

if (
xml_root.find(
".//Sequence/[@cycle='1']/Frame/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']"
".//Sequence/[@cycle='2']/Frame/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']"
)
is None
):
Expand All @@ -232,7 +232,7 @@ def _extract_prairieview_metadata(xml_filepath: str):
n_depths = len(plane_indices)

z_controllers = xml_root.findall(
".//Sequence/[@cycle='1']/Frame/[@index='1']/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/SubindexedValue"
".//Sequence/[@cycle='2']/Frame/[@index='1']/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/SubindexedValue"
)

# If more than one Z-axis controllers are found,
Expand All @@ -241,13 +241,13 @@ def _extract_prairieview_metadata(xml_filepath: str):
if len(z_controllers) > 1:
z_repeats = []
for controller in xml_root.findall(
".//Sequence/[@cycle='1']/Frame/[@index='1']/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/"
".//Sequence/[@cycle='2']/Frame/[@index='1']/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/"
):
z_repeats.append(
[
float(z.attrib.get("value"))
for z in xml_root.findall(
".//Sequence/[@cycle='1']/Frame/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/SubindexedValue/[@subindex='{0}']".format(
".//Sequence/[@cycle='2']/Frame/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/SubindexedValue/[@subindex='{0}']".format(
controller.attrib.get("subindex")
)
)
Expand All @@ -267,7 +267,7 @@ def _extract_prairieview_metadata(xml_filepath: str):
z_fields = [
z.attrib.get("value")
for z in xml_root.findall(
".//Sequence/[@cycle='1']/Frame/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/SubindexedValue/[@subindex='0']"
".//Sequence/[@cycle='2']/Frame/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/SubindexedValue/[@subindex='0']"
)
]

Expand Down