Reading annotations

[rjlopez2]

Is there a method to read the annotations or comments in a .adicht file? btw, thanks for this really nice package.

Cheers.

[JimHokanson]

Hi, so I put this together rather quickly since I primarily use MATLAB to read LabChart files. Looking back at my code I think the following would work. The main idea is that the comments are a part of a record or block. As such you need to access a record then get its comments. If this works I can update the readme to clarify.

#Where f is the file object
record_id = 1
r = f.records[record_i-1]
record_comments = r.comments

For all comments you would need something like this, I think:

all_comments = []
for record in f.records:
    all_comments.extend(record.comments)

I think that's all correct. I'm not actually testing this, just writing in the browser.

Please let me know if that works or if you have any issues.

[rjlopez2]

will check this out soon and come back to you. thanks for the speedy reply.

[rjlopez2]

This works perfectly. Many thanks for the hint. I miss that. I have however another question. have a look a this screenshot of the begining of one example file:

I managed to read the file this way:

file = adi.read_file(r"my/file/path/example.adicht")

file_loaded: True
          h: <cdata 'struct ADI_FileHandle__ * *' owning 8 bytes>
  n_records: 8
 n_channels: 8
    records: Type::list, Len: 8
   channels: Type::list, Len: 8

this is the content of the first channel:

file.records[0]

 h: <cdata 'struct ADI_FileHandle__ * *' owning 8 bytes>
         id: 1
    n_ticks: 148000
    tick_dt: 2.5e-05
   comments: []
record_time: Class::adi.read.RecordTime

when I check out the comments, I do:

all_comments = []
for record in file.records:
    all_comments.extend(record.comments)

len(all_comments)

597

the first comment look like this:

all_comments[0]

         text: timestamp:14:16:04.572959
tick_position: 2867624
     channel_: -1
           id: 2
      tick_dt: 2.5e-05
         time: 71.6906

and these are the first 5 one:

all_comments[0:5]

[         text: timestamp:14:16:02.572959
 tick_position: 2787624
      channel_: -1
            id: 1
       tick_dt: 2.5e-05
          time: 69.6906,
          text: timestamp:14:16:04.572959
 tick_position: 2867624
      channel_: -1
            id: 2
       tick_dt: 2.5e-05
          time: 71.6906,
          text: timestamp:14:16:06.572959
 tick_position: 2947624
      channel_: -1
            id: 3
       tick_dt: 2.5e-05
          time: 73.6906,
          text: timestamp:14:16:08.572959
 tick_position: 3027624
      channel_: -1
            id: 4
       tick_dt: 2.5e-05
          time: 75.6906,
          text: timestamp:14:16:10.572959
 tick_position: 3107624
      channel_: -1
            id: 5
       tick_dt: 2.5e-05
          time: 77.6906]

my question is (and sorry if this is very basic), based on the screenshot above what are exactly the values I am looking at ? I know the text is the actual annotation we input, and time correspond to the actual recording time, but what about the others?

best

Ruben

[JimHokanson]

Sure tick_position - this is the # of samples since the block start channel - channel the comment was added to, -1 indicates added to all channels id - comment number, these can be moved or deleted so they are not always in order tick_dt - inverse of the sampling rate for the ticks. This is based on the fastest channel so you are sampling something at 40kHz (1/tick_dt) - this could probably be hidden but I think is used internally to calculate time (i.e., time=tick_dt*tick_position)

A somewhat unrelated FYI, LabChart provides an Active X interface for talking to LabChart. This can be used to get the current time, add comments, and retrieve data while the program is running. I use this for stimulus triggered averages. Unfortunately the control code I've written is in MATLAB (https://github.com/JimHokanson/labchart_server_matlab). However, if you can figure out how to make Active X calls in Python the MATLAB code may provide a roadmap for how to control LabChart with Python. More specifically I have a MATLAB GUI which sets my stimulus parameters, adds comments to LabChart, and then can be used to pull up stimulus triggered averages. I haven't posted the GUI code because it is a bit messy, but I use the LabChart server code (link above) for controlling LabChart. The GUI also controls the stimulator (https://github.com/JimHokanson/multichannel_systems_stg_matlab)

[rjlopez2]

Thanks a lot for the explanation and the extra tips. Feel free to close this issue, I should be now good off with the lift you provide me. Cheers.