modifying DLC dataset to import in SLEAP cause error as in issue: importing maDLC labels #412 (closed)

[cosimogonnelli]

Hi,

I have a DLC dataset that has 3 individuals one of which is "single". I read in another discussion that SLEAP can't handle yet this type of datasets. As suggested I removed the "single" columns.

Process:

I worked over this issue using Pandas dataframe.
I tried to incorporate the "single" data as part of another individual named "ExpDegu".
To do so I renamed "single" -> "expDegu".
I renamed the bodyparts with the names of the ones missing in 'ExpDegu" and then I deleted the extra columns.

I saved the dataframe generated as csv.
When I try to open the csv file to import a new dataset from DLC I get the error below. This error appear only when I change the DLC "CollectedData_PDH.csv" using pandas and saving a new csv. If I manually change the file and I import the DLC project in SLEAP I don't get any error.

Any help to fix this issues?

Please let me know if I wasn't clear enough
Thanks!

Software versions:
SLEAP: 1.2.6
TensorFlow: 2.8.0
Numpy: 1.21.5
Python: 3.7.5
OS: Darwin-21.1.0-x86_64-i386-64bit

Happy SLEAPing! :)
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/gui/commands.py", line 282, in importDLC
self.execute(ImportDeepLabCut)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/gui/commands.py", line 240, in execute
command().execute(context=self, params=kwargs)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/gui/commands.py", line 137, in execute
self.do_with_signal(context, params)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/gui/commands.py", line 161, in do_with_signal
cls.do_action(context, params)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/gui/commands.py", line 819, in do_action
labels = Labels.load_deeplabcut(filename=params["filename"])
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/io/dataset.py", line 2116, in load_deeplabcut
return read(filename, for_object="labels", as_format="deeplabcut")
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/io/format/main.py", line 103, in read
return disp.read(filename, *args, **kwargs)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/io/format/dispatch.py", line 56, in read
return adaptor.read(file, *args, **kwargs)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/io/format/deeplabcut.py", line 78, in read
file=file, full_video=full_video, *args, **kwargs
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/io/format/deeplabcut.py", line 139, in read_frames
skeleton.add_nodes(node_names)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/skeleton.py", line 497, in add_nodes
self.add_node(node)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/sleap/skeleton.py", line 486, in add_node
raise ValueError("Skeleton already has a node named ({})".format(name))
ValueError: Skeleton already has a node named (ExpDegu)

[roomrys]

Hi @cosimogonnelli,

Is it possible to share your unedited, manually edited, and programmatically edited csv with [email protected]. By the looks of the error, it sounds like you may have added "ExpDegu" multiple times to a row where SLEAP expects node names.

Also, do you mind linking the discussion where it states SLEAP cannot handle this type of dataset yet. I looked around but was unable to find it.

Thanks!
Liezl

[cosimogonnelli]

Hi @roomrys,

I did little more testing and it turned out that the process of saving my dataframe into a CSV file also added rows counters and changed the first row adding a columns count on each field. So looking at only the CSV file content everything looked the same. I was getting confused by the SLEAP error because I was checking for extra "ExpDegu" fields but I wasn't find any...
Once I did a simple "diff" between files I found the issue. Sorry for the time you spent in this discussion and thanks for your help as usual!

[roomrys]

@cosimogonnelli,

Glad you found the issue! Always happy to help - even if only as a rubber duck 🐤