This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Last revision Both sides next revision | ||
pipeline:utilities:e2proc3d [2018/02/16 10:11] 127.0.0.1 external edit |
pipeline:utilities:e2proc3d [2018/08/22 10:50] fmerino |
||
---|---|---|---|
Line 6: | Line 6: | ||
\\ | \\ | ||
===== Usage ===== | ===== Usage ===== | ||
+ | |||
Usage in command line | Usage in command line | ||
Line 12: | Line 13: | ||
\\ | \\ | ||
===== Typical usage ===== | ===== Typical usage ===== | ||
+ | |||
e2proc3d does not support MPI. | e2proc3d does not support MPI. | ||
Line 26: | Line 28: | ||
2. Apply a 10 A low-pass filter to a volume and write output to a new file. | 2. Apply a 10 A low-pass filter to a volume and write output to a new file. | ||
- | e2proc3d.py threed.hdf threed.filt.hdf --process=filter.lowpass.gauss: | + | e2proc3d.py threed.hdf threed.filt.hdf --process=filter.lowpass.gauss: |
3. Extract a reconstruction from a refinement directory as an HDF file usable with Chimera. | 3. Extract a reconstruction from a refinement directory as an HDF file usable with Chimera. | ||
- | e2proc3d.py bdb: | + | e2proc3d.py bdb: |
4. Create a new 64x64x64 volume, initialize it as 1, then apply a hard spherical mask to 0. | 4. Create a new 64x64x64 volume, initialize it as 1, then apply a hard spherical mask to 0. | ||
- | e2proc3d.py :64:64:64:1 myvol.hdf --process mask.sharp: | + | e2proc3d.py :64:64:64:1 myvol.hdf --process mask.sharp: |
' | ' | ||
Line 40: | Line 42: | ||
\\ | \\ | ||
===== Input ===== | ===== Input ===== | ||
- | === Main Options | + | === Main Parameters |
; input_volume : Input volume: Input volume file name. (default required string) | ; input_volume : Input volume: Input volume file name. (default required string) | ||
+ | ; output_file : Output file name: Type of output file depends on the option settings. (default required string) | ||
- | ; medianshrink : Downsample volume with median filter: Downsample the volume by a factor of '< | + | ; %%--%%medianshrink : Downsample volume with median filter: Downsample the volume by a factor of '< |
- | ; meanshrink : Downsample volume with averaging filter: Downsample the volume by a factor of '< | + | ; %%--%%meanshrink : Downsample volume with averaging filter: Downsample the volume by a factor of '< |
- | ; meanshrinkbig : Downsample large volume with averaging filter: Downsample the volume by a factor of '< | + | ; %%--%%meanshrinkbig : Downsample large volume with averaging filter: Downsample the volume by a factor of '< |
- | ; scale : Rescale volume: Rescale the volume by '< | + | ; %%--%%scale : Rescale volume: Rescale the volume by '< |
- | ; sym : Symmetry to impose: Point-group symmetry to impose. Choices are:' | + | ; %%--%%sym : Symmetry to impose: Point-group symmetry to impose. Choices are:' |
- | ; averager : Averager: Averager used for --average and --sym options. (default mean) | + | ; %%--%%averager : Averager: Averager used for --average and --sym options. (default mean) |
- | ; clip : Pad or clip volume to the specific dimensions. Specify 1, 3 or 6 arguments. (default none) | + | ; %%--%%clip : Window to specific size [Pixels]: Window (pad or clip) volume to the specific dimensions. Specify 1, 3 or 6 arguments; '< |
- | ; fftclip : Rescale by padding FFT: Make the output have this size with rescaling by padding FFT. The argument format is '< | + | ; %%--%%fftclip : Rescale by padding FFT: Make the output have this size with rescaling by padding FFT. The argument format is '< |
- | ; process : Apply processor: Apply a processor named ' | + | ; %%--%%process : Apply processor: Apply a processor named ' |
- | ; apix : Pixels size [A/pixel] for S scaling: Pixels size [A/pixel] for S scaling. (default 0.0) | + | ; %%--%%apix : Pixels size [A/pixel] for S scaling: Pixels size [A/pixel] for S scaling. (default 0.0) |
- | ; origin : Set origin of coordinates: | + | ; %%--%%origin : Set origin of coordinates: |
- | ; mult : Scale densities: Scale the densities by a fixed number in the output. (default 1.0) | + | ; %%--%%mult : Scale densities: Scale the densities by a fixed number in the output. (default 1.0) |
- | ; multfile : Multiply by another volume: Multiply the volume by another volume of identical size. This can be used to apply masks, etc. (default none) | + | ; %%--%%multfile : Multiply by another volume: Multiply the volume by another volume of identical size. This can be used to apply masks, etc. (default none) |
- | ; matchto : Match filtration: Match filtration of input volume to this specified volume. (default none) | + | ; %%--%%matchto : Match filtration: Match filtration of input volume to this specified volume. (default none) |
- | ; outmode : Use specific bit-depth: All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported (int8, int16, int32, uint8, uint16, uint32). Values are rescaled to fill MIN-MAX range. (default float) | + | ; %%--%%outmode : Use specific bit-depth: All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported (int8, int16, int32, uint8, uint16, uint32). Values are rescaled to fill MIN-MAX range. (default float) |
- | ; outnorescale : Do not rescale float values: If specified, floating point values will not be rescaled when writing data as integers. Values outside of range are truncated. (default False) | + | ; %%--%%outnorescale : Do not rescale float values: If specified, floating point values will not be rescaled when writing data as integers. Values outside of range are truncated. (default False) |
- | ; add : Add constant: Add a constant ' | + | ; %%--%%add : Add constant: Add a constant ' |
- | ; addfile : Add another volume: Add the volume to another volume of identical size. (default none) | + | ; %%--%%addfile : Add another volume: Add the volume to another volume of identical size. (default none) |
- | ; calcfsc : Calculate FSC: Calculate a FSC curve between two models. Output is a txt file. This option is the name of the second volume. (default none) | + | ; %%--%%calcfsc : Calculate FSC: Calculate a FSC curve between two models. Output is a txt file. This option is the name of the second volume. (default none) |
- | ; calcsf : Calculate radial structure factor: Calculate a radial structure factor. Must specify --apix option. (default none) | + | ; %%--%%calcsf : Calculate radial structure factor: Calculate a radial structure factor. Must specify --apix option. (default none) |
- | ; calcradial : Calculate radial density by shell: Calculate the radial density by shell. Output file is a text file. 0 - mean amp, 2 - min, 3 - max, 4- sigma. (default -1) | + | ; %%--%%calcradial : Calculate radial density by shell: Calculate the radial density by shell. Output file is a text file. 0 - mean amp, 2 - min, 3 - max, 4- sigma. (default -1) |
- | ; setsf : Set radial structure factor: Set the radial structure factor. Must specify --apix option. (default none) | + | ; %%--%%setsf : Set radial structure factor: Set the radial structure factor. Must specify --apix option. (default none) |
- | ; tophalf : Keep only top half map: The output only keeps the top half map. (default False) | + | ; %%--%%tophalf : Keep only top half map: The output only keeps the top half map. (default False) |
- | ; inputto1 : Set all voxels to 1: All voxels in the input file are set to 1 after reading. This can be used with mask.* processors to produce a mask file of the correct size. (default False) | + | ; %%--%%inputto1 : Set all voxels to 1: All voxels in the input file are set to 1 after reading. This can be used with mask.* processors to produce a mask file of the correct size. (default False) |
- | ; icos5fhalfmap : Input is icos 5f top half map: The input is the icos 5f top half map generated by the --tophalf option. (default False) | + | ; %%--%%icos5fhalfmap : Input is icos 5f top half map: The input is the icos 5f top half map generated by the --tophalf option. (default False) |
- | ; outtype : Output image format: Set output image format; mrc, imagic, hdf, and etc. (default none) | + | ; %%--%%outtype : Output image format: Set output image format; mrc, imagic, hdf, and etc. (default none) |
- | ; first : First image ID to process: The ID of the first image in the input to process [0 - n-1]. (default 0) | + | ; %%--%%first : First image ID to process: The ID of the first image in the input to process [0 - n-1]. (default 0) |
- | ; trans : Translate map: Translate map by dx,dy,dz. (default none) | + | ; %%--%%trans : Translate map: Translate map by dx,dy,dz. (default none) |
- | ; resetxf : Reset transform matrix: Reset an existing transform matrix to the identity matrix. (default False) | + | ; %%--%%resetxf : Reset transform matrix: Reset an existing transform matrix to the identity matrix. (default False) |
- | ; align : Align to reference: Align input map to reference specified with --alignref option. As with processors, a sequence of aligners is permitted. The argument format is '< | + | ; %%--%%align : Align to reference: Align input map to reference specified with --alignref option. As with processors, a sequence of aligners is permitted. The argument format is '< |
- | ; ralignzphi : Refine Z alignment: Refine Z alignment within +-10 pixels and phi +-15 degrees (for C symmetries). Specify name of alignment reference here not with --alignref option. (default none) | + | ; %%--%%ralignzphi : Refine Z alignment: Refine Z alignment within +-10 pixels and phi +-15 degrees (for C symmetries). Specify name of alignment reference here not with --alignref option. (default none) |
- | ; alignref : Reference volume file: Alignment to reference volume. May only be specified once. (default none) | + | ; %%--%%alignref : Reference volume file: Alignment to reference volume. May only be specified once. (default none) |
- | ; alignctod : Rotate C to D symmetry: Rotate a map already aligned for C symmetry so the best 2-fold is positioned for specified D symmetry. Does not impose specified symmetry. (default none) | + | ; %%--%%alignctod : Rotate C to D symmetry: Rotate a map already aligned for C symmetry so the best 2-fold is positioned for specified D symmetry. Does not impose specified symmetry. (default none) |
- | ; rot : Rotate: Rotate map. Specify '< | + | ; %%--%%rot : Rotate: Rotate map. Specify '< |
- | ; icos5to2 : Rotate icosahedral 5- to 2-fold: Rotate an icosahedral map from 5-fold on Z (EMAN standard) to 2-fold on Z (MRC standard) orientation. (default False) | + | ; %%--%%icos5to2 : Rotate icosahedral 5- to 2-fold: Rotate an icosahedral map from 5-fold on Z (EMAN standard) to 2-fold on Z (MRC standard) orientation. (default False) |
- | ; icos2to5 : Rotate icosahedral 2- to 5-fold: Rotate an icosahedral map from 2-fold on Z (MRC standard) to 5-fold on Z (EMAN standard) orientation. (default False) | + | ; %%--%%icos2to5 : Rotate icosahedral 2- to 5-fold: Rotate an icosahedral map from 2-fold on Z (MRC standard) to 5-fold on Z (EMAN standard) orientation. (default False) |
- | ; last : Last image ID to process: The ID of the last image in the input to process. (default -1) | + | ; %%--%%last : Last image ID to process: The ID of the last image in the input to process. (default -1) |
- | ; swap : Swap byte order: Swap the byte order. (default False) | + | ; %%--%%swap : Swap byte order: Swap the byte order. (default False) |
- | ; average : Computes global average: Computes the average of a stack of 3D volumes. (default False) | + | ; %%--%%average : Computes global average: Computes the average of a stack of 3D volumes. (default False) |
- | ; append : Append to stack: Append output volumes to a stack of volumes. i.e., do not write inplace (opposite of ' | + | ; %%--%%append : Append to stack: Append output volumes to a stack of volumes. i.e., do not write inplace (opposite of ' |
- | ; ppid : Set PID of parent process: Set the PID of the parent process, used for cross platform PPID. (default | + | ; %%--%%unstacking : Unstack output: Process a stack of 3D images, then output it as a series of numbered single image files. (default False) |
- | ; unstacking : Unstack output: Process a stack of 3D images, then output it as a series of numbered single image files. (default False) | + | ; %%--%%tomoprep : Prepare tomography annotation: Produce a special HDF file designed for rapid interactive tomography annotation. This option should be used alone. (default False) |
- | ; tomoprep : Prepare tomography annotation: Produce a special HDF file designed for rapid interactive tomography annotation. This option should be used alone. (default False) | + | ; %%--%%step : Processes only subset: Specify '< |
- | ; verbose : Verbose level [0-9]: Higher number means higher level of verboseness. (default 0) | + | |
- | ; step : Processes only subset: Specify '< | + | \\ |
+ | === Advanced Parameters === | ||
+ | ; %%--%%ppid : Set PID of parent process: Set the PID of the parent process, used for cross platform PPID. (default -2) | ||
+ | ; %%--%%verbose : Verbose level [0-9]: Higher number means higher level of verboseness. (default 0) | ||
\\ | \\ | ||
===== Output ===== | ===== Output ===== | ||
- | ; output_file : Output file name. Type of output file depends on the option settings. | + | Type of output file depends on the option settings. |
\\ | \\ | ||
===== Description ===== | ===== Description ===== | ||
- | This program operates on single 3D volume files, stacks of 3-D volume files, and EMAN2 BDB databases. It has many command-line options for specific tasks. The generic ' | + | This program operates on single 3D volume files, stacks of 3-D volume files, and EMAN2 bdb databases. It has many command-line options for specific tasks. The generic ' |
' | ' | ||
+ | |||
+ | \\ | ||
+ | ==== Method ==== | ||
+ | |||
+ | \\ | ||
+ | ==== Reference ==== | ||
+ | |||
+ | \\ | ||
+ | ==== Developer Notes ==== | ||
\\ | \\ | ||
Line 105: | Line 120: | ||
\\ | \\ | ||
==== Keywords ==== | ==== Keywords ==== | ||
- | category | + | Category |
- | | + | Category |
\\ | \\ | ||
==== Files ==== | ==== Files ==== | ||
- | e2proc3d.py | + | programs/e2proc3d.py |
\\ | \\ | ||
==== See also ==== | ==== See also ==== | ||
- | [[http:// | + | [[http:// |
- | [[http:// | + | [[http:// |
- | [[http:// | + | [[http:// |
\\ | \\ |