Rename the output from mescore?

[zhouyi0812]

Hello! I wonder if we could rename the output in mescore? for example after motion correction the output file name is xxx motion correction rather than the uuid? Thank you!

[kushalkolar]

No, this is by design and there is no reason to do it. What are you trying to do?

On Fri, Jan 26, 2024, 13:09 Yi Zhou @.***> wrote:

Hello! I wonder if we could rename the output in mescore? for example after motion correction the output file name is xxx motion correction rather than the uuid? Thank you!

— Reply to this email directly, view it on GitHub https://github.com/nel-lab/mesmerize-core/issues/268, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACHXXRBAYUL2BCQVRZGHFI3YQPWMFAVCNFSM6AAAAABCMQZ6NKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGEYDENRWGY2TKNA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[zhouyi0812]

Because I have so many movies (1000) that need to segmentation. So I want to do a batch processing. For example, do motion correction for all first, and then segmentation, then examine the results, so I think if there is a more specific output name, it is easier to manage the file, delete other things and reuse the mmap file?

[kushalkolar]

You can manage all that with the DataFrame, you can give each item any name you want.

[zhouyi0812]

Thank you! Also I wonder if you know why when I do cnmfe algorithm, sometimes the it stops running like shows in the terminal. That the cpu is just not doing work, as this too long time to wait. Thank you!

[kushalkolar]

@EricThomson

[zhouyi0812]

You can manage all that with the DataFrame, you can give each item any name you want.

Could you please a little be specific so I could find more information about it? So far I am looping each video and save to individual file, in this case if I could integrate all motion correction movie into a dataframe and change the name at a time? Do you have more efficient way for that amount number of movie? Thank you very much!

[clewis7]

Hi @zhouyi0812,

What Kushal means is that every time you add a movie to your DataFrame to run motion correction or cnmfe, you can specify an item_name. This should allow you to more readily organize your movies.

For example:

import mesmerize_core as mc 

# set your batch_path
batch_path = "/path/to/where/you/want/to/store/dataframe/batch.pickle"

# create a batch
df = mc.create_batch(batch_path)

# set movie_path
movie_path = "/path/to/movie/movie.tif"

# set mcorr params
mcorr_params1 =\
{
  'main': 
    {
        'max_shifts': [24, 24],
        'strides': [48, 48],
        'overlaps': [24, 24],
        'max_deviation_rigid': 3,
        'border_nan': 'copy',
        'pw_rigid': True,
        'gSig_filt': None
    },
}

# add item with an item name
df.caiman.add_item(
    algo='mcorr',
    item_name = "movie1",
    input_movie_path=movie_path,
    params=mcorr_params1,
)

Here I am setting the item_name to be movie1, but this can be anything you want.

[kushalkolar]

Closing as this seems to be solved.