Trouble with morphometrix update

[jlinsk]

Hello,

I have been encountering some error codes, and am unsure if it is specifically on my end. Over the coarse of my measurements, I updated the version of Morphometrix I was using to fix a bug. I am able to run collatrix for the very earliest files, and in subsequent files I receive a duplicate object error, despite there being no duplicate object in the csv file. When I try to run it with the updated Morphometrix output, it is unable to recognize them as morphometrix files. Is this problem to do with a compatibility issue given the new update or am I messing something up on my end?

[cbirdferrer]

Hi! Just to clarify - were you using morphometrix 1.0.1 before? Also, there are two separate issues here right? 1. Some files get the duplicate object error, and 2. some files can't get read in at all. What do you mean by "unable to recognize them as morphometrix files"? Could you share a screenshot of the error message?

[jlinsk]

Hi Clara,

Thank you for the response. I realized I misspoke about the files not being recognized but I am still unsure as to what the issue is (though note I have never used python before). I've attached some screenshots of the errors. I believe all of the old files, both those work and don't, used morphometrix 1.0.1. Looking at the files, I can't tell the difference between the ones that work and the ones that report a duplicate error. I am more concerned about those using the 1.0.2 version, as it is no problem to re-measure or change the csv layout of the old files to match the new.

Thank you very much for having a look and please let me know if there is anything else I can pass along.

regards,

-Jake

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On Tue, Nov 17, 2020 at 8:42 AM Clara Bird notifications@github.com wrote:

Hi! Just to clarify - were you using morphometrix 1.0.1 before? Also, there are two separate issues here right? 1. Some files get the duplicate object error, and 2. some files can't get read in at all. What do you mean by "unable to recognize them as morphometrix files"? Could you share a screenshot of the error message?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cbirdferrer/collatrix/issues/13#issuecomment-728374197, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARYTGBTN6CYFRWTJYAVMLQDSQGTFDANCNFSM4TWYORQQ .

,Processing Notes 1,"Animal ID from folder name?: no

Safety not used

These csvs were not morphometrix outputs:[]

These csvs could not be read in: set()"

[jlinsk]

Hi Clara, just following up on the previous question. Error code is as follows for files from the 1.0.2 morphometrix:

(myenv) C:\Users\jakel> python -m collatrix yes Animal ID in folder name no safety no subset list these csvs were not morphometrix outputs: [] C:/Users/jakel/Desktop/mes 2\mn200914_1.csv Traceback (most recent call last): File "C:\Users\jakel\anaconda3\envs\myenv\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\jakel\anaconda3\envs\myenv\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\jakel\anaconda3\envs\myenv\lib\site-packages\collatrix-1.0.7-py3.9.egg\collatrix__main.py", line 180, in File "C:\Users\jakel\anaconda3\envs\myenv\lib\site-packages\collatrix-1.0.7-py3.9.egg\collatrix__main.py", line 39, in init File "C:\Users\jakel\anaconda3\envs\myenv\lib\site-packages\collatrix-1.0.7-py3.9.egg\collatrix\main__.py", line 153, in initUI File "C:\Users\jakel\anaconda3\envs\myenv\lib\site-packages\collatrix-1.0.7-py3.9.egg\collatrix\collatrix_functions.py", line 42, in collate File "C:\Users\jakel\anaconda3\envs\myenv\lib\site-packages\pandas\core\indexes\base.py", line 4104, in getitem__ return getitem(key) IndexError: index 0 is out of bounds for axis 0 with size 0

running the most recent update of collatrix and morphometrix, where have I gone wrong?

Thank you,

-Jake

[cbirdferrer]

morphometrix output was in an outdated format that the current collatrix wasn't designed to handle. a version of collatrix that can handle all versions of outputs is in progress.