Misc features #36
Misc features #36
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…entation threshold and TTA
| @@ -193,7 +193,7 @@ def extract_patches( | |||
| min_coords[0] : min_coords[0] + 160, | |||
| min_coords[1] : min_coords[1] + 160, | |||
| min_coords[2] : min_coords[2] + 160, | |||
| ] | |||
| ].copy() | |||
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When not adding the "copy", overlapping extracted patches will have the ignore-label padding in each other, because the original array is padded instead of the small patches.
| @@ -121,7 +128,7 @@ def convert_single_nrrd_files(labels_dir, corrections_dir, out_dir): | |||
| merged_corrections = get_corrections_from_folder( | |||
| cur_patch_corrections_folder, os.path.join(labels_dir, label_file) | |||
| ) | |||
| out_file = os.path.join(out_dir, label_file) | |||
| out_file = os.path.join(out_dir, token + ".nii.gz") | |||
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If not specifying .nii.gz format, it will take to data format of the inputs (which can also be e.g. .mrc)
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I'm not sure I follow. It looks like the output file path is hardcoded to .nii.gz.
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Yes, exactly. I hard-coded it to nii.gz s.t. it does not save out e.g. .mrc files. The input to the training is still nii.gz. We may want to change that at some point to something more common in Cryo-ET. This change here is to make everything compatible with the current training setup.
| @@ -95,3 +109,53 @@ def components( | |||
| os.path.splitext(os.path.basename(segmentation_path))[0] + "_components.mrc", | |||
| ) | |||
| store_tomogram(filename=out_file, tomogram=segmentation) | |||
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| @cli.command(name="thresholds", no_args_is_help=True) | |||
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This is a separate command for a function that
- takes as input a scoremap produced by MemBrain-seg, together with multiple float values
- thresholds the scoremap at each given float value and stores the resulting segmentation mask
| @@ -121,7 +128,7 @@ def convert_single_nrrd_files(labels_dir, corrections_dir, out_dir): | |||
| merged_corrections = get_corrections_from_folder( | |||
| cur_patch_corrections_folder, os.path.join(labels_dir, label_file) | |||
| ) | |||
| out_file = os.path.join(out_dir, label_file) | |||
| out_file = os.path.join(out_dir, token + ".nii.gz") | |||
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I'm not sure I follow. It looks like the output file path is hardcoded to .nii.gz.
Hi,
I have implemented a couple of potentially useful features from some user requests, and packed it together with some small bug fixes and documentation:
I think most things should be relatively straightforward, but feel free take a look and let me know if you spot anything :)