Image extraction panel format error

[akandrew332]

Trying to run notebook 3b to extract images from a previous run. Downloaded panel.csv from mibitracker and placed in panel_files as per the instructions. Error posted indicates panel is not Ionpath or toffy structured panel.

[akandrew332]

Script looks for Manufacture instead of Manufactured in the panel.csv. Changed column name to manufacture, now a duplicate names error is posted:

[akandrew332]

Tried with a fresh file. Same error posted.

[camisowers]

Panel35_MIX.18_edit.csv
Try this.

[akandrew332]

Magical!! It worked. What's the secret sauce?

[camisowers]

This is your file. The extra commas in the first 10 rows of metadata cause an issue with the convert_panel function.

It should be formatted like this. When excel files are converted to csv files this can happen.

We'll be fixing the code to read the correct column names, so there would be no need to open your downloaded panel file, and this can be avoided in the future! Thanks for letting us know.

[akandrew332]

Ok. That makes sense. I've checked the original file in notepad, no extra commas. When I changed the column header to manufacture, then Excel adds the extra commas. I can edit those out in the short-term. Thanks so much for the help!!

[ngreenwald]

Thanks for pointing this out, the updated version resolves this issue

[whitneyt1]

Hi! We're getting a different error at the same step. We tried with both a toffy formatted panel, and one downloaded directly from mibitracker. For the toffy formatted panel, we tried all of the different CSV options under excel's "save as"

Thanks!

Panel55_MousePancreas.csv
pancreas_panel.csv

[srivarra]

Hi Whitney, what version of Toffy are you using? I just attempted to open the files you posted, and Panel55_MousePancreas.csv was converted to the toffy format, while pancreas_panel.csv was already at the correct format. You should be able to get the version of Toffy by running pip list in the anaconda terminal.

[whitneyt1]

Hi Sri! We downloaded and installed toffy right before running the script, so it should be the most updated version.

…

On Mon, Oct 17, 2022 at 12:24 PM Sricharan Reddy Varra < ***@***.***> wrote: Hi Whitney, what version of Toffy are you using? I just attempted to open the files you posted, and Panel55_MousePancreas.csv was converted to the toffy format, while pancreas_panel.csv was already at the correct format. You should be able to get the version of Toffy by running pip list in the anaconda terminal. — Reply to this email directly, view it on GitHub <#245 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALDKSPDDEUGQ6AH2BBWQ37DWDWRYJANCNFSM6AAAAAAQHBKCGA> . You are receiving this because you commented.Message ID: ***@***.***>

[srivarra]

@whitneyt1 Sorry, not ark-analysis I meant toffy. Run git pull first, then try git checkout convert_utf.

[alex-l-kong]

@srivarra we just merged this PR in, so it should work on the main branch of toffy now.

[whitneyt1]

Thanks, I deleted toffy folder and environment, redownloaded but am still getting the same error.

when i try to run git checkout convert_utf:

[whitneyt1]

although if i run pip list, there is not toffy package attached

[whitneyt1]