From 67790742973550e4a7c1e8543c161dae3615ca02 Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Mon, 10 Jun 2024 15:48:29 -0600 Subject: [PATCH] change criteria for volumetric --- .../brukertiffimagingextractor.py | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/src/roiextractors/extractors/tiffimagingextractors/brukertiffimagingextractor.py b/src/roiextractors/extractors/tiffimagingextractors/brukertiffimagingextractor.py index 780ce4eb..0fd87e1b 100644 --- a/src/roiextractors/extractors/tiffimagingextractors/brukertiffimagingextractor.py +++ b/src/roiextractors/extractors/tiffimagingextractors/brukertiffimagingextractor.py @@ -54,7 +54,7 @@ def _determine_frame_rate(element: ElementTree.Element, file_names: Optional[Lis def _determine_imaging_is_volumetric(folder_path: PathType) -> bool: - """Determine whether imaging is volumetric based on 'zDevice' configuration value. + """Determine whether imaging is volumetric. Parameters ---------- @@ -70,11 +70,22 @@ def _determine_imaging_is_volumetric(folder_path: PathType) -> bool: xml_file_path = folder_path / f"{folder_path.name}.xml" assert xml_file_path.is_file(), f"The XML configuration file is not found at '{xml_file_path}'." + is_series_type_volumetric = { + "TSeries ZSeries Element": True, # XYZT + "TSeries Timed Element": False, # XYT + "ZSeries": True, # ZT (not a time series) + "Single": False, # Single image (not a time series) + } + is_volumetric = False for event, elem in ElementTree.iterparse(xml_file_path, events=("start",)): - if elem.tag == "PVStateValue" and elem.attrib.get("key") == "zDevice": - is_volumetric = bool(int(elem.attrib["value"])) - break # Stop parsing as we've found the required element + if elem.tag == "Sequence": + series_type = elem.attrib.get("type") + if series_type in is_series_type_volumetric: + is_volumetric = is_series_type_volumetric[series_type] + break + else: + raise ValueError(f"Unknown series type: {series_type}, please raise an issue in roiextractor repository") return is_volumetric