Hello! I've had an issue with GuPPy stalling after 'Extract timestamps and it's correction' specifically when I am combining data. I see the graph of my control and signal channels appear, but when I close this window the green progress bar doesn't advance and I'm unable to move to the next steps. This doesn't happen when I leave 'Combine data?' False. I believe I've followed the Storenames conventions correctly. The terminal output is pasted below, please let me know how I can solve this. Thank you!
Last login: Wed May 15 16:35:06 on ttys000
(base) krademacher@LAXUND08336 ~ % conda activate guppy
(guppy) krademacher@LAXUND08336 ~ % cd /Users/krademacher/GuPPyCode/GuPPy-main
(guppy) krademacher@LAXUND08336 GuPPy-main % conda update -n guppy --file spec_file_mac.txt
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(guppy) krademacher@LAXUND08336 GuPPy-main % panel serve --show GuPPy/savingInputParameters.ipynb
2024-05-15 16:44:05,574 Starting Bokeh server version 2.3.1 (running on Tornado 6.0.4)
2024-05-15 16:44:05,575 User authentication hooks NOT provided (default user enabled)
2024-05-15 16:44:05,578 Bokeh app running at: http://localhost:5006/savingInputParameters
2024-05-15 16:44:05,578 Starting Bokeh server with process id: 69138
Folder path set to /Users/krademacher/Desktop/Photometry
Launching server at http://localhost:65061
2024-05-15 16:45:50,575 Saving Input Parameters file.
2024-05-15 16:45:50,577 Input Parameters file saved at /Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-161456
2024-05-15 16:45:50,578 Input Parameters file saved at /Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-174524
2024-05-15 16:45:50,578 ################################################################################################################################################################################################################################################################################################################################################################################################################
Input Parameters File Saved.
['/Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-161456', '/Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-174524']
2024-05-15 16:45:51,232 If it exists, importing either NPM or Doric or csv file based on the structure of file
event_csv
2024-05-15 16:45:51,236 Importing of either NPM or Doric or csv file is done.
2024-05-15 16:45:51,237 Saving stores list file.
Launching server at http://localhost:5154
2024-05-15 16:45:51,345 If it exists, importing either NPM or Doric or csv file based on the structure of file
event_csv
2024-05-15 16:45:51,349 Importing of either NPM or Doric or csv file is done.
2024-05-15 16:45:51,349 Saving stores list file.
Launching server at http://localhost:5174
2024-05-15 16:45:51,479 ################################################################################################################################################################################################################################################################################################################################################################################################################
['405A', '470A', '240514_ArtificialTTL']
[['405A' '470A' '240514_ArtificialTTL']
['control_DLS' 'signal_DLS' 'IP']]
2024-05-15 16:46:13,399 Storeslist file saved at /Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-174524/GiDATCre_0-240508-174524_output_1
2024-05-15 16:46:13,399 Storeslist :
[['405A' '470A' '240514_ArtificialTTL']
['control_DLS' 'signal_DLS' 'IP']]
invalid command name "140359540912456stayOnTop"
while executing
"140359540912456stayOnTop"
("after" script)
['405A', '470A', '240514_ArtificialTTL']
[['405A' '470A' '240514_ArtificialTTL']
['control_DLS' 'signal_DLS' 'IP']]
2024-05-15 16:46:28,309 Storeslist file saved at /Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-161456/GiDATCre_0-240508-161456_output_1
2024-05-15 16:46:28,310 Storeslist :
[['405A' '470A' '240514_ArtificialTTL']
['control_DLS' 'signal_DLS' 'IP']]
Read progress bar increment values function started...
run
Reading raw data...
/Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-161456
Trying to read tsq file.
Data from tsq file fetched.
Reading data for event 240514_ArtificialTTL ...
Reading data for event 405A ...
Requested store name 240514_ArtificialTTL not found (case-sensitive).
File contains the following TDT store names:
['405A' '470A' 'Cam1' 'Tick' 'Wav1']
TDT store name 240514_ArtificialTTL not found.
Trying to read data for 240514_ArtificialTTL from csv file.
Reading data for 240514_ArtificialTTL from csv file is completed.
Reading data for event 470A ...
Data for event 405A fetched and stored.
Data for event 470A fetched and stored.
Time taken = 0.63113
/Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-174524
Trying to read tsq file.
Data from tsq file fetched.
Reading data for event 240514_ArtificialTTL ...
Reading data for event 405A ...
Requested store name 240514_ArtificialTTL not found (case-sensitive).
File contains the following TDT store names:
['405A' '470A' 'Cam1' 'Tick' 'Wav1']
TDT store name 240514_ArtificialTTL not found.
Trying to read data for 240514_ArtificialTTL from csv file.
Reading data for 240514_ArtificialTTL from csv file is completed.
Reading data for event 470A ...
Data for event 405A fetched and stored.
Data for event 470A fetched and stored.
Time taken = 1.02980
Raw data fetched and saved.
Read progress bar increment values stopped.
Read progress bar increment values function started...
Extracting signal data and event timestamps...
Remove Artifacts : False
Combine Data : True
Isosbestic Control Channel : True
Correcting timestamps by getting rid of the first 1 seconds and convert timestamps to seconds...
Timestamps corrected and converted to seconds.
Applying correction of timestamps to the data and event timestamps...
Timestamps corrections applied to the data and event timestamps.
Applying correction of timestamps to the data and event timestamps...
Timestamps corrections applied to the data and event timestamps.
Applying correction of timestamps to the data and event timestamps...
Timestamps corrections applied to the data and event timestamps.
Correcting timestamps by getting rid of the first 1 seconds and convert timestamps to seconds...
Timestamps corrected and converted to seconds.
Applying correction of timestamps to the data and event timestamps...
Timestamps corrections applied to the data and event timestamps.
Applying correction of timestamps to the data and event timestamps...
Timestamps corrections applied to the data and event timestamps.
Applying correction of timestamps to the data and event timestamps...
Timestamps corrections applied to the data and event timestamps.
Combining Data from different data files...
Processing timestamps for combining data...
Timestamps processed and data is combined.
Data is combined from different data files.
Computing z-score for each of the data...
Remove Artifacts : False
z-score for the data computed.
Signal data and event timestamps are extracted.
venus-sherathiya
commented
2 months ago
Hello! I've had an issue with GuPPy stalling after 'Extract timestamps and it's correction' specifically when I am combining data. I see the graph of my control and signal channels appear, but when I close this window the green progress bar doesn't advance and I'm unable to move to the next steps. This doesn't happen when I leave 'Combine data?' False. I believe I've followed the Storenames conventions correctly. The terminal output is pasted below, please let me know how I can solve this. Thank you!
Last login: Wed May 15 16:35:06 on ttys000 (base) krademacher@LAXUND08336 ~ % conda activate guppy (guppy) krademacher@LAXUND08336 ~ % cd /Users/krademacher/GuPPyCode/GuPPy-main (guppy) krademacher@LAXUND08336 GuPPy-main % conda update -n guppy --file spec_file_mac.txt
Downloading and Extracting Packages
Preparing transaction: done Verifying transaction: done Executing transaction: done (guppy) krademacher@LAXUND08336 GuPPy-main % panel serve --show GuPPy/savingInputParameters.ipynb 2024-05-15 16:44:05,574 Starting Bokeh server version 2.3.1 (running on Tornado 6.0.4) 2024-05-15 16:44:05,575 User authentication hooks NOT provided (default user enabled) 2024-05-15 16:44:05,578 Bokeh app running at: http://localhost:5006/savingInputParameters 2024-05-15 16:44:05,578 Starting Bokeh server with process id: 69138 Folder path set to /Users/krademacher/Desktop/Photometry Launching server at http://localhost:65061 2024-05-15 16:45:50,575 Saving Input Parameters file. 2024-05-15 16:45:50,577 Input Parameters file saved at /Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-161456 2024-05-15 16:45:50,578 Input Parameters file saved at /Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-174524 2024-05-15 16:45:50,578 ################################################################################################################################################################################################################################################################################################################################################################################################################ Input Parameters File Saved. ['/Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-161456', '/Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-174524'] 2024-05-15 16:45:51,232 If it exists, importing either NPM or Doric or csv file based on the structure of file event_csv 2024-05-15 16:45:51,236 Importing of either NPM or Doric or csv file is done. 2024-05-15 16:45:51,237 Saving stores list file. Launching server at http://localhost:5154 2024-05-15 16:45:51,345 If it exists, importing either NPM or Doric or csv file based on the structure of file event_csv 2024-05-15 16:45:51,349 Importing of either NPM or Doric or csv file is done. 2024-05-15 16:45:51,349 Saving stores list file. Launching server at http://localhost:5174 2024-05-15 16:45:51,479 ################################################################################################################################################################################################################################################################################################################################################################################################################ ['405A', '470A', '240514_ArtificialTTL'] [['405A' '470A' '240514_ArtificialTTL'] ['control_DLS' 'signal_DLS' 'IP']] 2024-05-15 16:46:13,399 Storeslist file saved at /Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-174524/GiDATCre_0-240508-174524_output_1 2024-05-15 16:46:13,399 Storeslist : [['405A' '470A' '240514_ArtificialTTL'] ['control_DLS' 'signal_DLS' 'IP']] invalid command name "140359540912456stayOnTop" while executing "140359540912456stayOnTop" ("after" script) ['405A', '470A', '240514_ArtificialTTL'] [['405A' '470A' '240514_ArtificialTTL'] ['control_DLS' 'signal_DLS' 'IP']] 2024-05-15 16:46:28,309 Storeslist file saved at /Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-161456/GiDATCre_0-240508-161456_output_1 2024-05-15 16:46:28,310 Storeslist : [['405A' '470A' '240514_ArtificialTTL'] ['control_DLS' 'signal_DLS' 'IP']] Read progress bar increment values function started... run
Reading raw data...
/Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-161456 Trying to read tsq file. Data from tsq file fetched. Reading data for event 240514_ArtificialTTL ... Reading data for event 405A ... Requested store name 240514_ArtificialTTL not found (case-sensitive). File contains the following TDT store names: ['405A' '470A' 'Cam1' 'Tick' 'Wav1'] TDT store name 240514_ArtificialTTL not found. Trying to read data for 240514_ArtificialTTL from csv file. Reading data for 240514_ArtificialTTL from csv file is completed. Reading data for event 470A ... Data for event 405A fetched and stored. Data for event 470A fetched and stored. Time taken = 0.63113 /Users/krademacher/Desktop/Photometry/240508_GRABDAPilot_Session4-240508-153402/GiDATCre_0-240508-174524 Trying to read tsq file. Data from tsq file fetched. Reading data for event 240514_ArtificialTTL ... Reading data for event 405A ... Requested store name 240514_ArtificialTTL not found (case-sensitive). File contains the following TDT store names: ['405A' '470A' 'Cam1' 'Tick' 'Wav1'] TDT store name 240514_ArtificialTTL not found. Trying to read data for 240514_ArtificialTTL from csv file. Reading data for 240514_ArtificialTTL from csv file is completed. Reading data for event 470A ... Data for event 405A fetched and stored. Data for event 470A fetched and stored. Time taken = 1.02980
Raw data fetched and saved.
Read progress bar increment values stopped. Read progress bar increment values function started... Extracting signal data and event timestamps... Remove Artifacts : False Combine Data : True Isosbestic Control Channel : True Correcting timestamps by getting rid of the first 1 seconds and convert timestamps to seconds... Timestamps corrected and converted to seconds. Applying correction of timestamps to the data and event timestamps... Timestamps corrections applied to the data and event timestamps. Applying correction of timestamps to the data and event timestamps... Timestamps corrections applied to the data and event timestamps. Applying correction of timestamps to the data and event timestamps... Timestamps corrections applied to the data and event timestamps. Correcting timestamps by getting rid of the first 1 seconds and convert timestamps to seconds... Timestamps corrected and converted to seconds. Applying correction of timestamps to the data and event timestamps... Timestamps corrections applied to the data and event timestamps. Applying correction of timestamps to the data and event timestamps... Timestamps corrections applied to the data and event timestamps. Applying correction of timestamps to the data and event timestamps... Timestamps corrections applied to the data and event timestamps. Combining Data from different data files... Processing timestamps for combining data... Timestamps processed and data is combined. Data is combined from different data files. Computing z-score for each of the data... Remove Artifacts : False z-score for the data computed. Signal data and event timestamps are extracted.