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NewNamesProposal
Adrian Quintana edited this page Dec 11, 2017
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Xmipp's new users would benefit from a coherent global naming scheme:
- easier to remember, more logic
- easier to type (shell autocompletion)
- improves overall impression -quality- of the package
Rules:
- all executables begin with $PREFIX,
xmippby default - separation by underscores
- all acronyms in lowercase
DELETED means
- not compiled by default
- not in main documentation
- not really supported
Alphabetical order as of 1.1 release:
| Old name | New name | Comment(s) |
|---|---|---|
| `2Dinterpolation` | `DELETED` | ... |
| `3DInterpolation` | `DELETED` | ... |
| `adapt_for_spider` | `DELETED` | ... |
| `add_noise` | `add_noise` | Wrapper not needed |
| `adjust_CTF` | `DELETED` | ... |
| `adjust_surface` | `DELETED` | ... |
| `adjust_volume` | `adjust_volume_grey_levels` | ... |
| `align2d` | `align2d` | Wrapper not needed |
| `align3D` | `align_volumes` | ... |
| `ang_distribution` | `angular_distribution_show` | ... |
| `angular_distance` | `angular_distance` | Wrapper not needed |
| `angular_predict` | `angular_discrete_assign` | ... |
| `angular_predict_continuous` | `angular_continuous_assign` | ... |
| `angular_predict_tomography` | `angular_assign_for_tomogram` | Changed from tomography (the image is a tomogram) |
| `angular_refinement` | `DELETED` | ... |
| `appenddocfile` | `docfile_append` | ... |
| `applygeo` | `header_apply` | ... |
| `are_different` | `DELETED` | ... |
| `art` | `reconstruct_art` | ... |
| `assign_angles` | `DELETED` | ... |
| `assign_CTF` | `ctf_estimate_from_micrograph` | ... |
| `assign_multiple_CTFs` | `DELETED` | ... |
| `batchsom` | `classify_batch_som` | ... |
| `break_sym` | `break_symmetry` | ... |
| `centilt` | `align_tilt_pairs` | ... |
| `codestatis` | `DELETED` | ... |
| `combine_stats` | `DELETED` | ... |
| `compare_selfiles` | `selfile_compare` | ... |
| `correctphase` | `ctf_correct_phase` | ... |
| `correlation` | `correlation` | Wrapper not needed |
| `cpsel` | `selfile_copy` | ... |
| `create_phantom` | `phantom_create` | ... |
| `create_surface` | `crystal_create_surface` | ... |
| `CTF_profile` | `ctf_profile` | ... |
| `ctfviewer` | `ctf_view` | ... |
| `data2img` | `convert_data2img` | ... |
| `data2vol` | `convert_data2vol` | ... |
| `deconvoluteCTF` | `DELETED` | ... |
| `deform` | `crystal_shear` | ... |
| `denoising` | `denoise` | ... |
| `denoising_micrograph` | `micrograph_denoise` | ... |
| `docfile_histogram` | `docfile_histogram` | Wrapper not needed |
| `do_selfile` | `selfile_create` | ... |
| `downsample` | `micrograph_downsample` | ... |
| `draw_surface` | `DELETED` | ... |
| `DWT` | `DELETED` | ... |
| `edit` | `edit` | Wrapper not needed |
| `EM2Angles` | `crystal_euler2mrc` | ... |
| `enhance_psd` | `psd_enhance` | .. |
| `euler` | `DELETED` | ... |
| `evaluate` | `foms_evaluate` | Changed from FOMs (all lowercase now) |
| `evaluate_FSCs` | `DELETED` | ... |
| `exp_shift_computation` | `DELETED` | ... |
| `fcmeans` | `classify_fcmeans` | ... |
| `FFT` | `DELETED` | ... |
| `findcenter` | `find_center2d` | ... |
| `findcenter3D` | `find_center3d` | ... |
| `fkcn` | `classify_fkcn` | ... |
| `flip` | `mirror` | ... |
| `fourierfilter` | `fourier_filter` | ... |
| `fsom` | `classify_fsom` | ... |
| `xmipp_gnuplot_mplot` | `DELETED` | ... |
| `xmipp_gnuplot_mprint` | `DELETED` | ... |
| `headerinfo` | `header_assign`,`header_reset`,`header_extract` | ... |
| `histogram` | `histogram` | Wrapper not needed |
| `idr_art` | `ctf_correct_idr` | ... |
| `IDWT` | `DELETED` | ... |
| `IFTT` | `DELETED` | ... |
| `img2data` | `convert_img2data` | ... |
| `infogeo` | `header_print` | header printing functionality |
| `infogeo` | `statistics` | -stats functionality |
| `iv` | `DELETED` | ... |
| `kcmeans` | `classify_kcmeans` | ... |
| `kerdensom` | `classify_kerdensom` | ... |
| `lattice_vectors` | `crystal_lattice_vectors` | ... |
| `look_at_FFT` | `DELETED` | ... |
| `makespectra` | `DELETED` | Correct version:`make_spectra` |
| `make_spectra` | `make_spectra` | Wrapper not needed |
| `mark` | `micrograph_mark` | ... |
| `markhan` | `try_symmetry` | ... |
| `mask` | `mask` | Wrapper not needed |
| `microscope` | `phantom_simulate_microscope` | ... |
| `MLalign2D` | `ml_align2d` | ... |
| `MLalign2D_combine` | `ml_align2d_combine` | ... |
| `MLrefine3D` | `ml_refine3d` | ... |
| `morphology` | `morphology` | Wrapper not needed |
| `mpi_art` | `mpi_art` | Wrapper not needed |
| `mpi_MLalign2D` | `mpi_ml_align2d` | ... |
| `mpi_MLrefine3D` | `mpi_ml_refine3d` | ... |
| `mpi_projection_matching` | `mpi_angular_projection_matching` | ... |
| `mpi_wbp` | `mpi_reconstruct_wbp` | ... |
| `mvsel` | `selfile_move` | ... |
| `normalize` | `normalize` | Wrapper not needed |
| `operate` | `operate` | Wrapper not needed |
| `pca` | `classify_pca` | ... |
| `PDB2descr` | `convert_pdb2descr` | ... |
| `pdb2surface` | `convert_pdb2surface` | ... |
| `pdbphantom` | `convert_pdb2vol` | ... |
| `PDBsidechain` | `extract_sidechain_from_pdb` | ... |
| `phantom_transform` | `phantom_transform` | Wrapper not needed |
| `project` | `project` | Wrapper not needed |
| `projection_matching` | `angular_projection_matching` | ... |
| `projection_neighbourhood` | `angular_neighbourhood` | ... |
| `projectpca` | `classify_project_pca` | ... |
| `pyramid` | `scale_pyramid` | ... |
| `radon_transform` | `DELETED` | ... |
| `random_mapping` | `DELETED` | ... |
| `random_phantom` | `phantom_create_random` | ... |
| `range_adjust` | `range_adjust` | Wrapper not needed |
| `raw22spi` | `convert_raw22spi` | ... |
| `recons_test` | `phantom_test_reconstruction` | ... |
| `resolution` | `resolution_fsc` | ... |
| `reverse_endian` | `reverse_endian` | Wrapper not needed |
| `rmsel` | `selfile_delete` | ... |
| `rotate` | `rotate` | Wrapper not needed |
| `rotate_descr` | `DELETED` | ... |
| `sammon` | `classify_sammon_projection` |
|
| `sample_size` | `DELETED` | ... |
| `scale` | `scale` | Wrapper not needed |
| `scissor` | `micrograph_scissor` | ... |
| `segment` | `volume_segment` | ... |
| `select_images` | `selfile_select` | ... |
| `sel_stats` | `selfile_statistics` | ... |
| `separate_objects` | `separate_objects` | Wrapper not needed |
| `shift` | `shift` | Wrapper not needed |
| `show` | `show` | Wrapper not needed |
| `show_sel` | `DELETED` | ... |
| `show_som` | `DELETED` | ... |
| `show_spectra` | `DELETED` | ... |
| `show_spectrasom` | `DELETED` | ... |
| `skew` | `crystal_skew` | ... |
| `som` | `classify_som` | ... |
| `sort_junk` | `sort_by_statistics` | ... |
| `spar` | `DELETED` | ... |
| `spARMA` | `DELETED` | ... |
| `spi22ccp4` | `convert_spi22ccp4` | ... |
| `spi22em` | `convert_spi22em` | ... |
| `split_selfile` | `selfile_split` | ... |
| `Spots2RealSpace2D` | `crystal_aph2img` | ... |
| `ssnr` | `resolution_ssnr` | ... |
| `statis` | `average` | ... |
| `surface` | `DELETED` | ... |
| `symmetrize` | `symmetrize` | Wrapper not needed |
| `threshold` | `threshold` | Wrapper not needed |
| `tiff2raw` | `convert_tiff2raw` | ... |
| `toPDB` | `convert_data2pdb` | ... |
| `toPhantom` | `convert_data2descr` | ... |
| `unbend` | `crystal_unbend` | ... |
| `visualize_fft` | `fourier_transform` | ... |
| `vol2data` | `convert_vol2data` | ... |
| `volsampler` | `convert_vol2pseudo` | ... |
| `voxels22blobs` | `convert_voxels22blobs` | ... |
| `wbp` | `reconstruct_wbp` | ... |
| `window` | `window` | Wrapper not needed |
| `window_micrograph` | `micrograph_window` | ... |
| `xmask` | `mask_design` | ... |
- convert
- micrograph
- classify
- docfile
- selfile
- ctf
- header
- phantom
- crystal
For developers it would be also recommended to change all directory names, so that there would be a direct match between the executables and the sources.
An auxiliary script -one that warns the user of the change and informs him of the new name- could be written to ease the transition. It could even be something as simple as:
#!/bin/sh
VERSION=1.2
NEW_NAME=bar
# Warn user
echo "** Warning! This program name is deprecated as of Xmipp version" $VERSION
echo "** Please use" $NEW_NAME "instead"
echo "** Continuing execution..."
# Call real program
$NEW_NAME "$@"
--Main.AlfredoSolano - 05 Feb 2007