Update/feature subsetting #504
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hamshkhawar
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Nicholas-Schaub and
NHotaling
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bengtl
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Jan 26, 2024
| @@ -38,19 +39,20 @@ If WIPP is running, navigate to the plugins page and add a new plugin. Paste the | |||
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| ## Options | |||
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| This plugin takes one input argument and one output argument: | |||
| This plugin takes twelve input arguments and one output argument: | |||
| 4. `imageFeature` - Tabular data featuring image filenames | ||
| 5. `tabularFeature` - Tabular feature that will be used to filter images | ||
| 6. `groupVar` - This is a mandatory input across which to subset data. This can take either 1 or 2 variables as input and if 2 variables are provided then the second variable will be treated as the minor grouping variable. In our example, if the `z` is provided as input, then within a subcollection, the mean of the feature value will be taken for all images with the same z. Then the z positions will be filtered out based on the input of `percentile` and `removeDirection` variables. Now if `z,c` are provided as input, then 'c' will be treated as the minor grouping variable which means that the mean will be taken for all images with the same z for each channel. Also, the plugin will ensures that the same values of z positions are filtered out across c. | ||
| 7. `percentile` and `removeDirection` - These two variables denote the critieria with which images are filtered. For example, if percentile is `0.1` and removeDirection is set to `Below` then images with feature value below the 10th percentile will be removed. On the other hand, if removeDirection is set to above then all images with feature value greater than the 10th pecentile will be removed. This enables data subsetting from both `brighfield` and `darkfield` microscopy images. |
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| 7. `percentile` and `removeDirection` - These two variables denote the critieria with which images are filtered. For example, if percentile is `0.1` and removeDirection is set to `Below` then images with feature value below the 10th percentile will be removed. On the other hand, if removeDirection is set to above then all images with feature value greater than the 10th pecentile will be removed. This enables data subsetting from both `brighfield` and `darkfield` microscopy images. | |
| 7. `percentile` and `removeDirection` - These two variables denote the critieria with which images are filtered. For example, if percentile is `0.1` and removeDirection is set to `Below` then images with feature value below the 10th percentile will be removed. On the other hand, if removeDirection is set to above then all images with feature value greater than the 10th pecentile will be removed. This enables data subsetting from both `brightfield` and `darkfield` microscopy images. |
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| CHUNK_SIZE = 10000 | ||
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| logger = logging.getLogger(__name__) |
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It seems the logger is initiated twice? It is already initiated in the main.py
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Nicholas-Schaub
requested changes
Aug 6, 2024
* fix merge conflicts * fix apply manifest * fix apply manifest * remove file * updated hdbscan-clustering-plugin * fix bug in tests * fixed random generation of floats * fixed docker file and shell script for running docker * fixed docker files * renamed plugin and fixed merged conflicts * fixed docker files
I fixed it and add CLT and ict.yaml file for this plugin |
bengtl
approved these changes
Sep 3, 2024
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This PR is updated to new plugin standards