datareader cant read ndtiff files aber micromanager got interupted during writing process #71
Description
Location - Behavior 1 Setup:
History of the bug:
Previous week micromanager recording got interupted due to discspace limit reached.
Current week - recording could finish normally
Problem: both files (previous and curent week) give following bug when cropper tries to read them with the tif reader class, so bug is probably associated with micromanager being interupted during writing process.
Errormessage:
avg_bg = recording.avg_bg
File "C: Users (ZimLabAdmin|. conda\envs\SWC\Lib\site-packages\cached_property.py", line 36, in get
value = obj.-dict[self.func.-name_] = self.func(obj)
run_swc_modified.bat
run_swc_modified.bat
run_swc_modified.bat
run_swc.bat
File Edit View
m T: \Bin \241031\2024-10-31_12-54-50
BHrecording_0.3_thiophene with ndtiff
Reading index... 8.4%
C: \Users \ZimLabAdmin. conda\envs \SWC\11b\site-packages \ndstorage\ndtiff_index-py:99: UserWarning: Index appears to not
(the dataset may still work)
warnings. warn(
Opening file 70 of 72... Traceback (most recent call last):
File "SWC main_gui-py", line 149, in ‹module> threshold, border - open_threshold
Lgui (recording folder-dataset_path.last_valid_directory path,
File "C: \GithubRepositories\SimpleWormCropper\SWC_threshold_gui.py", line 206, in open_threshold_gui
avg bg = recording.avg..bg
File "C: \Users\ZimLabAdmin-conda\envs\SWC\lib|site-packages\cached_property-py", line 36, in get
value = obj.-
dict
[self. func..
name_ - self. func(obj)
File "C: \GithubRepositories\SimpleWormCropper\cropping_manager-py", line 142, in avg_bg avg.
bg - get_avg background.
multi thread (self. recording video_reader, frames_to_sample=1000,
File "C: \Users\ZimLabAdmin-conda\envs\SWC\lib\site-packages\cached_property-py", line 36, in get value - obj. dict [self. func.
name = self func (obj)
File "C: \GithubRepositories|SimpleWormCropper\cropping_manager-py", line 130, in recording video_reader data - MicroscopeDataReader (tiff_path)
File "c: \githubrepositories\imutils\imutils\scopedatamanager\microscope_data_reader-py", line 56, in init self. _open_dataset()
File "c: \githubrepositories\imutils\imutils\scopedatamanager\microscope_data_reader.py", line 126, in _open_dataset self._read_ndtiff()
File "C: \githubrepositories\imutils\imutils\scopedatamanager\microscope_data_reader-py", line 147, in _read_ndtiff self. _data_store - Dataset (str(self.directory_path))
File "C: \Users\ZimLabAdmin| conda \envs\SWC\11b\site-packages \ndstoragesuperclass-py", line 38, in new obj..
init
(dataset_path, file_lo-file io)
File "C: \Users (ZimLabAdmin). conda \envs \SWC\lib|site-packages \ndstorage\ndtiff_dataset.py", line 97, in init new_reader - SingleNDTiffReader (tiff, file_lo-self.file_io)
File "C: \Users\ZimLabAdmin|. conda\envs\SWC\Lib|site-packages\ndstorage\ndtiff_file-py", line 318, in init self.summary_md, self.first_ifd_offset - self._read_header )
FIle "C: \Users (21mLabAdmin|.conda\envs \SWC\lib|site-packages\ndstorage|ndtiff_file-py", line 348, in _read_header raise Exception ("Endian type not specified correctly")
Exception: Endian type not specified correctly