Issues with Channel

[ns-rse]

Splitting this out as its ultimately a different issue.

Original Post

@neumagen wrote

What are the different channel names available to use? I tried ZSensor, zsensor, Height Sensor, PeakForceError, [ZSensor, PeakForceError], and ['ZSensor', 'PeakForceError']. What am I missing?

[ns-rse]

Hi @neumagen

The error message here is saying that the requested channel Height is not present in the .spm channel, but that the found channels are ZSensor and PeakForceError (these are read from the file itself).

Its surprising that using either of these in your configuration didn't work.

Could you share the YAML file with ZSensor in and the output that it gives too please?

Ideally if you could copy and paste the file and output it makes it easier to search the text and find things, particularly for the YAML file. You can make it look like a code by putting it in a code block as shown below.

```
This is a code block.
```

Thanks @ns-rse

[neumagen]

Thanks!

Sorry, my coffee hasn't kicked in yet, clearly!!

I was trying this yesterday when I made the post, and I was using the run_topostats --config my_config.yaml with errors still.

I just retried it to generate the error code:

(topostats) katie@Kaitlyns-MacBook-Air Monica % run_topostats --config my_config.yaml
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] The YAML configuration file is valid.
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] The YAML plotting configuration file is valid.
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] Configuration run options are consistent, processing can proceed.
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] Configuration file loaded from      : my_config.yaml
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] Scanning for images in              : /Users/katie/Desktop/Monica
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] Output directory                    : output
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] Looking for images with extension   : .spm
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] Images with extension .spm in /Users/katie/Desktop/Monica : 1
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] Thresholding method (Filtering)     : std_dev
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] Thresholding method (Grains)        : std_dev
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] Extracting image from /Users/katie/Desktop/Monica/2023-03-30-3overhang.0_00000.spm
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] Loading image from : /Users/katie/Desktop/Monica/2023-03-30-3overhang.0_00000.spm
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] [2023-03-30-3overhang.0_00000] : Loaded image from : /Users/katie/Desktop/Monica/2023-03-30-3overhang.0_00000.spm
[Tue, 11 Jul 2023 12:54:39] [ERROR   ] [topostats] [2023-03-30-3overhang.0_00000] : ZSensor not in .spm channel list: ['ZSensor', 'PeakForceError']
[Tue, 11 Jul 2023 12:54:39] [ERROR   ] [topostats] [io.py] [503] [2023-03-30-3overhang.0_00000] : ZSensor not in .spm channel list: ['ZSensor', 'PeakForceError']
[Tue, 11 Jul 2023 12:54:39] [WARNING ] [topostats] [2023-03-30-3overhang.0_00000] Channel ZSensor not found, skipping image.
Processing images from /Users/katie/Desktop/Monica, results are under output:   
[Tue, 11 Jul 2023 12:54:39] [INFO    ] [topostats] Saving image stats to : output/image_stats.csv.
Traceback (most recent call last):
  File "/Users/katie/anaconda3/envs/topostats/bin/run_topostats", line 8, in <module>
    sys.exit(legacy_run_topostats_entry_point())
  File "/Users/katie/anaconda3/envs/topostats/lib/python3.10/site-packages/topostats/entry_point.py", line 325, in legacy_run_topostats_entry_point
    run_topostats(args=args)
  File "/Users/katie/anaconda3/envs/topostats/lib/python3.10/site-packages/topostats/run_topostats.py", line 150, in run_topostats
    image_stats_all_df = pd.concat(image_stats_all.values())
  File "/Users/katie/anaconda3/envs/topostats/lib/python3.10/site-packages/pandas/core/reshape/concat.py", line 372, in concat
    op = _Concatenator(
  File "/Users/katie/anaconda3/envs/topostats/lib/python3.10/site-packages/pandas/core/reshape/concat.py", line 429, in __init__
    raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
```

[ns-rse]

Hmm, ok that's frustrating, the error message reports the channels that are found, so its a little confusing that this is contradicted. Are you able to share the file with us in some manner please?

[neumagen]

@ns-rse

https://www.dropbox.com/scl/fi/jpclrinx171v1u13ul8qf/2023-03-30-3overhang.0_00000.spm?rlkey=91frllp403p6fbdl6gadocxc8&dl=0

let me know if this works

[derollins]

I got it to process that file. I had to change channel: Height to channel: Height Sensor (capital H, capital S)

[neumagen]

Okay - I don't know why it didn't work last time I tried it with Height Sensor, but this time it did! Thank you!!

[MaxGamill-Sheffield]

Might be due to a mismatch between the bts labels and user facing labels in the io.py - LoadScans.load_spm where "channel description" is commented out, this may be the one we actually need.

@derollins is on a hotfix :)