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| Generic 2-D image processing program. The main tasks this program can be used for are: | |
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| See [[EMAN2/Programs/e2boxer#tipsandtricks|e3boxer Tips and Tricks]] for more. | * Convert images from one format to another * Perform basic image processing operations such as filters, masks, normalization, etc. * Resize/rescale images * Select subsets of image stacks |
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| == Convert MRC image's storage type == By default, the image will be saved as float type, i.e., 4 bytes (16 bit) for each pixel. For MRC format, we can save image as short (2 bytes/16bit) or byte. e2proc2d.py provide options to convert mrc image between these storage types. The following example is for 2D mrc image. You can do similar conversion to 3D mrc image by calling e2proc3d.py. |
This program operates on both single 2-D image files, image stacks, and EMAN2 BDB databases. It has many command-line options for specific tasks. The generic '--process' option is by far the most powerful, offering access to 180+ different image processing operations (for a list, type ''e2help.py processors''). |
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| For specific details on various options, use ''e2proc2d.py --help''. === Examples === convert IMAGIC format test.hed to HDF format: |
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| [someone@localhost]$e2proc2d.py --mrc16bit float-image.mrc short-image.mrc | e2proc2d.py test.hed test.hdf |
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apply a 10 A low-pass filter to a stack of particles and write output to a new file. |
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| [someone@localhost]$e2proc2d.py --mrc8bit float-image.mrc byte-image.mrc | e2proc2d.py ptcl.hdf ptcl.filt.hdf --process=filter.lowpass.gauss:cutoff_freq=0.1 |
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invert the contrast in a BDB database. Overwrite the original images {{{ e2proc2d.py bdb:particles#set1 bdb:particles#set1 --inplace --mult=-1 }}} |
e2proc2d
Generic 2-D image processing program. The main tasks this program can be used for are:
- Convert images from one format to another
- Perform basic image processing operations such as filters, masks, normalization, etc.
- Resize/rescale images
- Select subsets of image stacks
This program operates on both single 2-D image files, image stacks, and EMAN2 BDB databases. It has many command-line options for specific tasks. The generic '--process' option is by far the most powerful, offering access to 180+ different image processing operations (for a list, type e2help.py processors).
For specific details on various options, use e2proc2d.py --help.
Examples
convert IMAGIC format test.hed to HDF format:
e2proc2d.py test.hed test.hdf
apply a 10 A low-pass filter to a stack of particles and write output to a new file.
e2proc2d.py ptcl.hdf ptcl.filt.hdf --process=filter.lowpass.gauss:cutoff_freq=0.1
invert the contrast in a BDB database. Overwrite the original images
e2proc2d.py bdb:particles#set1 bdb:particles#set1 --inplace --mult=-1