usage: usage: e2spt_wedgefill <input stack> --options This program will identify and fill in the missing wedge in a stack of subtomograms (with a missing wedge) which have been aligned to an average (with no missing wedge). While in a sense this creates 'Frankenstien particles' it is assumed that having values from an average of many particles is better than having zero in the same areas, at least for certain purposes. You must provide an average volume from which to draw the missing values and it is critical that this volume be an average of the particles being corrected. The particles should also have been properly normalized prior to averaging to achieve the desired effect. #Specifically, this process is designed to make it possible to run PCA or other classification processes on the particles. Any missing values will all be at the same point near the center of the cloud defined by the entire population, rather than having zero values distorting the cloud. Once particles have been classified, the originals wihout filled wedge can be used for averaging. #.
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --input | str | this is redundant with supplying the image stack directly after the program name. |
| --output | str | optional file name to save the stack with a filled wedge. |
| --fillimage | str | the iamge to use to fill in the missing wedge of the images in --input. Ideally, this is the average of the aligned images in --input, or the reference the images in --input were aligned to. |
| --fillwithnoise | None | this will fill the missing wedge with gaussian noise. --matchto will be turned on by default if this option is supplied. |
| --matchto | None | this will match the power spectrum of each image in --input to that --fillimage so that things are properly normalized. |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |
| --subset | int | Default=0 (not used). Plot only this substet of transforms from the hdf stack or json file provided. |
| --verbose, -v | int | verbose level [0-9], higher number means higher level of verboseness |