added user given output directory #1
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tdincer
assigned ttngu207, guzman-raphael and jverswijver and unassigned guzman-raphael
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This modified pipeline was successfully run on a sample dataset. Let's try to push this to the |
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Looks great @tdincer! just one minor change with some whitespace at the end of a line. 👍
Co-authored-by: jverswijver <49455164+jverswijver@users.noreply.github.com>
| @@ -337,7 +342,7 @@ def fit_file(self, motion_correct=False, indices=None, include_eval=False): | |||
| logging.warning("Error: File not found, with file list:\n" + fnames[0]) | |||
| raise Exception('File not found!') | |||
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| base_name = pathlib.Path(fnames[0]).stem + "_memmap_" | |||
| base_name = (pathlib.Path(output_dir) / (pathlib.Path(fnames[0]).stem + "_memmap_")).as_posix() | |||
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I'd double check here on how base_name is used. I think base_name should not contain any path, but only a filename (or prefix to a filename), so we should not join output_dir here.
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@ttngu207 base_name is passed only to mmapping.save_memmap together with the full path file names in line 369 or 372, depending on a condition. Addition of another path related keyword looks excessive to me. There is only one caveat. The docstring in mmapping.save_memmap clearly states that the base_name must not contain underscore character. As long as this caveat is considered we should be good.
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We cannot guarantee base_name will not contain underscore especially when base_name is now a full path.
On second look, I do think you don't need to include the output_dir as part of the base_name here. And you don't need to pass output_dir into mmapping.save_memmap.
In the mmapping.save_memmap, the path is actually retrieved from fname, which, in this case, is passed in as fname_mc (line 369 below).
fname_mc is generated from the output of mc.motion_correct, which should already account for the correct output_dir.
Co-authored-by: Thinh Nguyen <thinhnguyen0405@gmail.com>
changed `if return_mc:` to ` if return_mc & motion_correct:` to make sure that motion correction is applied if we want to return the `motion correction object`
`base_name` line is changed to its original form.
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@ttngu207 This one is finally ready to merge (see adjusted .npz file output directory). |
Added:
cnmf.fit_filemethodcnmf.fit_fileto return movie correction object