I get an error when I try to use the batch utility with a config file I generated using the GUI. My .MOV files are in a sub-folder called videosA. The program throws an error on the first file. There is a new folder created in the main directory called "videosAlog" instead of "log" subfolder created in the main "videosA" folder. When I physically create this subfolder and move the logs, I am able to execute the code normally, so I suppose it must be a typo (missing "/" perhaps?) in the script that initiates the analysis.
########################################################################
## FreeClimber v.0.4.0 #################################################
## Please cite: https://doi.org/10.1242/jeb.229377######################
## Beginning program @ 2023-09-14 11:01:58 #############################
########################################################################
Creating completed .log file: ./videosAlog/completed.log
Creating skipped .log file: ./videosAlog/skipped.log
========================================================================
== [1 || 46] 10_1.MOV ==================================================
========================================================================
-- [ Step 1 ] Cleaning and format image stack
-- [ Step 2 ] Identifying spots
-- [ Step 3 ] Visualize spot metrics :: False
-- [ Step 4a ] - Setting spot threshold
-- [ Step 4b ] - Filtering by signal threshold
-- [ Step 4c ] - Filtering by eccentricity/circularity
-- [ Step 4d ] - Trimming outliers (if indicated)
-- [ Step 4e ] - Assigning spots to vials
-- [ Step 4f ] - Saving raw data file
Appending to log/skipped.log: ./videosA\10_1.MOV
Traceback (most recent call last):
File "./scripts/FreeClimber_main.py", line 475, in main
fc.process(video_file = File,variables = None, config_file = fc.config_file)
File "./scripts/FreeClimber_main.py", line 196, in process
d.step_4()# Filters and processes data detected points
File "D:\freeclimber\FreeClimber\scripts\detector.py", line 1050, in step_4
self.df_big.to_csv(self.path_data, index=None)
File "D:\Anaconda\envs\python36\lib\site-packages\pandas\core\generic.py", line 3204, in to_csv
formatter.save()
File "D:\Anaconda\envs\python36\lib\site-packages\pandas\io\formats\csvs.py", line 188, in save
compression=dict(self.compression_args, method=self.compression),
File "D:\Anaconda\envs\python36\lib\site-packages\pandas\io\common.py", line 428, in get_handle
f = open(path_or_buf, mode, encoding=encoding, newline="")
OSError: [Errno 22] Invalid argument: './videosA\x08_1.raw.csv'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./scripts/FreeClimber_main.py", line 489, in <module>
main()
File "./scripts/FreeClimber_main.py", line 479, in main
fc.log_video(completed=False, file_name = File)
File "./scripts/FreeClimber_main.py", line 281, in log_video
with open(self.path_project + '/' + path,'a') as f:
FileNotFoundError: [Errno 2] No such file or directory: './videosA/log/skipped.log'