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elhuhdron / pylibczi

Python module utilizing libCZI for reading Zeiss CZI files.
GNU General Public License v3.0
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Use CziScene to get info has a bug. markers = self.meta_root.xpath(self.xml_paths['Calibration'])[0] IndexError: list index out of range #3

Closed WZFish closed 4 years ago

WZFish commented 4 years ago

img, polygons_points, rois_points, box_corner_pix, box_size_pix = scene.get_scene_info() File "/DATA/234/zywang/anaconda/lib/python3.6/site-packages/pylibczi/CziScene.py", line 354, in get_scene_info if not self.scene_loaded: self.read_scene_image() File "/DATA/234/zywang/anaconda/lib/python3.6/site-packages/pylibczi/CziScene.py", line 306, in read_scene_image if not self.meta_loaded: self.read_scene_meta() File "/DATA/234/zywang/anaconda/lib/python3.6/site-packages/pylibczi/CziScene.py", line 127, in read_scene_meta markers = self.meta_root.xpath(self.xml_paths['Calibration'])[0] IndexError: list index out of range

Why ?

elhuhdron commented 4 years ago

At the moment CziScene is very specific to a certain type of czifile metadata. We are working on making this a more general scene reader.

elhuhdron commented 4 years ago

Please try the aics fork. It is now a much more general tool for reading czi files.