Closed lea-danics closed 5 months ago
LazyTiff is a mescore loader but I'd really just recommend using tiffit by @EricThomson (check his repo) to convert your tiff files so that they're memmapable (I'm assuming you don't have memmapable tiff files right now), which makes them much nicer to deal with.
Thank You! I installed tiffit as well. Than should I only modify the code? e.g. a = tiffit(df.iloc[0].caiman.get_input_movie_path()) 2 a.shape
Thanks for the help!
tiffit is a command line interface so at the command line you can convert your movies to a "good" format before you start your analysis, before you do anything in jupyter. So in your anaconda prompt (or whatever command line you initially use to run jupyter from), you activate your virtual environment. Then, if you have a "bad" tiff file named bad.tiff
, create a good tiff file with:
tiffit convert bad.tiff good.tiff
That creates a new tiff file named good.tiff
which behaves better for Caiman and mesmerize etc. Then you do your analysis on good.tiff
within jupyter as usual.
Thank You! I installed tiffit as well. Than should I only modify the code? e.g. a = tiffit(df.iloc[0].caiman.get_input_movie_path()) 2 a.shape
Thanks for the help!
Can you please tell us what you're trying to do, the full context.
Hi, I'm guessing you solved this, if not feel free to re-open :)
Dear Kushal,
I cannot overcome at the following point of cnmfe demo workbook: a = LazyTiff(df.iloc[0].caiman.get_input_movie_path()) 2 a.shape
NameError: name 'LazyTiff' is not defined
I couldn't import neither install LazyTiff.
When I tried to install I got ERROR: Could not find a version that satisfies the requirement lazytiff (from versions: none) ERROR: No matching distribution found for lazytiff
For installation I tried this code in (mescore) PS C: C:\Users\danic git clone https://github.com/plimkilde/lazytiff.git cd lazytiff pip install lazytiff
Thanks for the help in advance!!