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pipeline:subtract:sp_mask [2021/02/01 16:08] shaikh |
pipeline:subtract:sp_mask [2021/10/11 17:07] shaikh |
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Generate and Apply Mask : Make a soft mask of the region to be excluded. | Generate and Apply Mask : Make a soft mask of the region to be excluded. | ||
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===== Usage ===== | ===== Usage ===== | ||
Usage in command line | Usage in command line | ||
- | sp_signalsubtract.py sp_mask --map2mask=map_to_make_mask_from --fullmap=full_map --outdir=output_subtraction_directory --mapthresh=threshold --verbosity=verbosity_level | + | < |
+ | | ||
+ | </ | ||
- | \\ | ||
===== Typical usage ===== | ===== Typical usage ===== | ||
- | sp_signalsubtract comprises the steps needed to subtract masked regions from a map in order to focus on the remaining features from that map. There are six steps for this process (five within SPHIRE): | + | sp_signalsubtract comprises the steps needed to subtract masked regions from a map in order to focus on the remaining features from that map. There are six steps for this process (five within SPHIRE): |
- | \\ __1. [[avgfilt|Average and low-pass filter a map for segmentation]] __ | + | \\ |
+ | __1. [[: | ||
- | \\ __2. Locate regions to be subtracted __ | + | \\ |
+ | __2. Locate regions to be subtracted __ | ||
- | \\ __3. Mask a soft mask of the region to be excluded __: | + | \\ |
+ | __3. Mask a soft mask of the region to be excluded __: | ||
+ | < | ||
- | | + | sp_signalsubtract.py sp_mask --map2mask=map_to_make_mask_from --outdir=output_subtraction_directory --fullmap=full_map --mapthresh=threshold |
- | The map to make a mask from (--map2mask) corresponds to the region that you want to subtract. | + | </ |
- | !!!IMPORTANT!!! | + | The map to make a mask from (–map2mask) corresponds |
- | + | ||
- | \\ __4. [[projsubtract|Compute re-projections of map to be subtracted, and subtract | + | |
- | \\ __5. [[pipeline: | + | !!!IMPORTANT!!! The full map which is to be multiplied by the mask (–fullmap) must NOT have been postprocessed (e.g., sharpened). Otherwise, re-projections will not be optimally comparable to the experimental images. |
- | \\ __6. [[centershift|Center map of the remaining density]] __ | + | [{{: |
\\ | \\ | ||
+ | __4. [[: | ||
+ | |||
+ | \\ | ||
+ | __5. [[: | ||
+ | |||
+ | \\ | ||
+ | __6. [[: | ||
+ | |||
===== Input ===== | ===== Input ===== | ||
+ | |||
=== Main Parameters === | === Main Parameters === | ||
- | | + | |
- | | + | ; ; < |
- | | + | |
- | | + | |
- | + | ||
- | \\ | + | |
=== Advanced Parameters === | === Advanced Parameters === | ||
- | | + | |
- | + | ; ; < | |
- | \\ | + | |
===== Output ===== | ===== Output ===== | ||
- | | + | |
- | | + | ; ; mask_final.hdf |
- | | + | |
- | + | ||
- | \\ | + | |
===== Description ===== | ===== Description ===== | ||
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==== Method ==== | ==== Method ==== | ||
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==== Reference ==== | ==== Reference ==== | ||
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==== Developer Notes ==== | ==== Developer Notes ==== | ||
- | \\ | ||
==== Author / Maintainer ==== | ==== Author / Maintainer ==== | ||
+ | |||
Tapu Shaikh | Tapu Shaikh | ||
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==== Keywords ==== | ==== Keywords ==== | ||
+ | |||
Category 1:: APPLICATIONS | Category 1:: APPLICATIONS | ||
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==== Files ==== | ==== Files ==== | ||
+ | |||
sphire/ | sphire/ | ||
- | \\ | ||
==== See also ==== | ==== See also ==== | ||
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==== Maturity ==== | ==== Maturity ==== | ||
+ | |||
Beta:: Under evaluation and testing. Please let us know if there are any bugs. | Beta:: Under evaluation and testing. Please let us know if there are any bugs. | ||
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==== Bugs ==== | ==== Bugs ==== | ||
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