|
Size: 1245
Comment:
|
Size: 1178
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 2: | Line 2: |
| ''''' Under Construction ''''' | '''''Under Construction''''' proc2d == This program performs various processing operations on images and sets of images (WARNING: auto normalization removed) == == Usage: == proc2d 3244.img start.hed invert apix=5 lp=18 proc2d start.hed start.hed invert inplace |
| Line 5: | Line 12: |
| Note: Despite the experimental tags, the 'phasecls' and 'fscls' almost always produce better results than the default linear variance classifier. Note that these options are mutually exclusive. | IMPORTANT NOTE: proc2d no longer automatically normalizes output images. Use the 'norm' or 'edgenorm' flag to re-enable this. |
| Line 7: | Line 14: |
| This is the main refinement command in EMAN. You should have your starting images in 'start.img' and your initial 3D model in threed.0a.mrc. The 'refine' command will then refine this model iteratively. Note that the 'total number of iterations' specifies the number of iterations the program will finish with. If 5 iterations have been run, then 'refine 8 ...' is run, the program will pick up after 5 iterations and run only 3 more cycles. If you want to start over again from the first iteration, you must remove all of the 'threed.?.mrc' files (except for 0a) and all of the 'classes.?.mrc' files. Most of the options are simply passed through to other programs. Typical options for this program can be determined by running [/eman/eman1/progs/eman.html eman] and following the reconstruction procedure it provides. The tree option may not work in certian parallel configurations, such as grid configurations where the filesystem isn't cross-mounted. |
This program is used to perform a variety of generic 2D image processing tasks. Like all of the EMAN programs, it will read any supported file format. By default it outputs to an Imagic file although there are options to change this. Note that, by default, images are appended to the end of the output file if it already exists. All images in one file MUST have the same size. ie - if you try to copy 50x50 images to the end of a file that already contains 100x100 images, an error will result. Note the 'first=' and 'last=' options allow a subset of the input file to be processed. The 'inplace' keyword may be used to cause output images to overwrite the input images rather than being appended to the end of the file. |
EMAN1 Individual Programs
Under Construction
- proc2d
This program performs various processing operations on images and sets of images (WARNING: auto normalization removed)
Usage:
proc2d 3244.img start.hed invert apix=5 lp=18
proc2d start.hed start.hed invert inplace
Description
IMPORTANT NOTE: proc2d no longer automatically normalizes output images. Use the 'norm' or 'edgenorm' flag to re-enable this.
This program is used to perform a variety of generic 2D image processing tasks. Like all of the EMAN programs, it will read any supported file format. By default it outputs to an Imagic file although there are options to change this. Note that, by default, images are appended to the end of the output file if it already exists. All images in one file MUST have the same size. ie - if you try to copy 50x50 images to the end of a file that already contains 100x100 images, an error will result. Note the 'first=' and 'last=' options allow a subset of the input file to be processed. The 'inplace' keyword may be used to cause output images to overwrite the input images rather than being appended to the end of the file.