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auto3dem:history [2015/03/29 15:41] gcardone [auto3dem v1.03] |
auto3dem:history [2015/12/22 12:59] (current) gcardone |
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| ====== Modification history ====== | ====== Modification history ====== | ||
| - | This document describes incremental modifications made to the Baker lab software suite. Since the image preprocessing, image reconstruction, format conversion, and utility programs are so tightly coupled (e.g. shared standards and libraries) and released as a single package, all modifications are described together in a single document. Owing to the complexity of the software, it is impractical to provide a line-by-line listing of alterations. Instead we focus primarily on modifications that impact the end user and on large-scale changes to the code. Starting on version 4.02, more details on some of the listed changes can be found in the file MINOR_RELEASE_NOTES, included in the software package. | + | This document describes incremental modifications made to the Baker lab software suite. Since the image preprocessing, image reconstruction, format conversion, and utility programs are so tightly coupled (e.g. shared standards and libraries) and released as a single package, all modifications are described together in a single document. Owing to the complexity of the software, it is impractical to provide a line-by-line listing of alterations. Instead we focus primarily on modifications that impact the end user and on large-scale changes to the code. Starting on version 4.02, more details on the changes in the latest version can be found in the file MINOR_RELEASE_NOTES, included in the software package. |
| + | |||
| + | ==== auto3dem v4.05.2 ==== | ||
| + | |||
| + | == New programs == | ||
| + | * **prj**: calculate projections from a reconstruction using orientations either random, uniform or from an input data set | ||
| + | * **a3dm_icosrotate**: rotate an icosahedral map from standard orientation to one with a pair of vertices positioned along the z axis | ||
| + | * **a3dm_dat_stats**: gather information on the results from a run at a given iteration | ||
| + | * **a3dm_sel_stableparts**: select only stable particles, i.e. with unchanged orientation with respect to a previous iteration, and generate a new stack parameter file | ||
| + | * **a3dm_plot_score**: generate a histogram of the particle scores at a given iteration | ||
| + | * **a3dm_mg_inspect_prepare**: generate auxiliary info and images for screening micrographs using //a3dm_mg_inspect// | ||
| + | * **a3dm_mg_inspect**: quickly inspect and screen micrographs by means of a graphical interface | ||
| + | * **avemaps**: compute average of input maps (replaces mergemaps and mergemaps2) | ||
| + | |||
| + | == General modifications== | ||
| + | * improved handling of cyclic and dihedral symmetries | ||
| + | * added program a3dm_snapshot to gather information about a run, to send to developers for troubleshooting | ||
| + | * particles read from stack files are now background-subtracted | ||
| + | |||
| + | == Random Model Computation == | ||
| + | * use inner radius given as input to **setup_rmc** to mask reference maps at each iteration | ||
| + | * suppressed non significant warnings | ||
| + | |||
| + | == auto3dem == | ||
| + | * added option //po2r mask_map// to specify a binary mask to use for mask-focused refinement | ||
| + | * added option //auto evod_parallel// to specify if processing of even- and odd-numbered particles to be done concurrently | ||
| + | * added option //p3dr cpu_sparse// to specify if to spread cpus among different nodes to optimize resources for large maps (works only on multi-node clusters with pbs/sge queue systems) | ||
| + | * modified approach to define radial mask on maps (only ppft and hollow procedures): search of outer radius starts from radius with minimum standard deviation | ||
| + | |||
| + | == autopp == | ||
| + | * :!: restored option //D// to original interpolation and moved binning procedure to option //H// | ||
| + | * options 5 and 6: keep all info in first line of .dat files | ||
| + | * option 6: fixed bug when processing stacks with only one particle | ||
| + | * option j: when scaling, adjust also pixel size in .dat files | ||
| + | |||
| + | == PPFT == | ||
| + | * figure of merit calculated in double precision | ||
| + | |||
| + | == POR == | ||
| + | * avoid overflow error with metric/funcmode 0 | ||
| + | * change metric 1 to normalized version | ||
| + | * use the same user-defined metric for origin refinement | ||
| + | |||
| + | == maskmap == | ||
| + | * added option to apply the inverse of input mask | ||
| + | |||
| + | == rot_map == | ||
| + | * input shifts now expected as pixels | ||
| + | * improved estimate of the background value | ||
| + | * write the map in a format compatible with **p3dr** | ||
| + | |||
| + | == a3dm_plot_fsc == | ||
| + | * estimate resolution at threshold value by linear interpolation | ||
| + | * added option //-c/--cutoff// to specify threshold value where to estimate the resolution | ||
| + | |||
| + | ==== auto3dem v4.05.1 ==== | ||
| + | |||
| + | == Installation == | ||
| + | * changed installation procedure: **auto3dem_install** is the new command | ||
| + | * made easy to add support for new compilers | ||
| + | |||
| + | == New programs == | ||
| + | * **maskmap**: apply an input binary mask after adding a soft edge | ||
| + | |||
| + | == Random Model Computation == | ||
| + | * a minimum number of micrographs is used to generate an initial model. This value can be controlled by option //-nmgmin// in **setup_rmc** | ||
| + | * initial master file contains commented line for limiting number of cpus used at reconstruction | ||
| + | |||
| + | == General modifications == | ||
| + | * provided binary for CTFFIND4 in the package (Linux only) | ||
| + | * at start programs will display if compiled in parallel or serial mode | ||
| + | * maps are flattened with a soft mask, using full map as reference for masking in gold standard | ||
| + | * inconsistency of pixel size in map header does not throw an error anymore | ||
| + | |||
| + | == auto3dem == | ||
| + | * added parameter to control the soft edge with solvent flattening (//auto flatten_falloff//) | ||
| + | * keep input/output files used by flatten and hollow procedure | ||
| + | * continue parameter file generated at end of each run has now unique name to avoid overwriting and to keep track of the processing | ||
| + | |||
| + | == autopp == | ||
| + | * :!: option //D// modified to perform binning of micrographs instead of interpolation | ||
| + | * added experimental option 3x in autopp for using ctffind4 | ||
| + | |||
| + | == robem == | ||
| + | * added option for performing binning in batch mode (//-bin//) | ||
| + | * improved font appearance | ||
| + | * remove unused read/write menus | ||
| + | * added warning if can not connect to display | ||
| + | * minor fixes on size of file names | ||
| + | * avoid including origin when calibrating maps for subtraction | ||
| + | |||
| + | ==== auto3dem v4.05 ==== | ||
| + | |||
| + | Implemented the gold standard approach, and set as default | ||
| + | |||
| + | == Installation == | ||
| + | * added installation script for Mac OSX | ||
| + | * added installation instructions for Mac OSX | ||
| + | |||
| + | == new programs == | ||
| + | * **a3dm_plot_fsc.py**: plot FSC curves from a given set of iterations | ||
| + | * **a3dm_fsc2xml.py**: convert FSC curve to EMDB-compatible XML format | ||
| + | |||
| + | == auto3dem == | ||
| + | * changed method to identify score to use for selection of particles | ||
| + | * setup_rmc now prepares parameter files for gold standard procedure | ||
| + | * map radial profile is avoided if new_ptles set | ||
| + | * move the parameter updates outside of even/odd loops | ||
| + | * make sure that parameter files are complete with particles for gold standard | ||
| + | * fixed bug when estimating mask radii and changed constant factor for outer radius | ||
| + | |||
| + | == autopp == | ||
| + | * added option 6 to split parameters into even and odd numbered particles | ||
| + | * option j: handle multistack parameter files | ||
| + | * option 6: check presence of 'dat' in parameter file names | ||
| + | * option 6: handle files not containing _ character when splitting into even/odd files | ||
| + | * option 6: make up particle parameters when splitting empty files | ||
| + | * options F and O: added option to delete input files once processed | ||
| + | * option 5: fixed split and join of parameter files | ||
| + | * option K: remove box size from first line of dat files | ||
| + | * added option for not masking corners when generating/processing stacks | ||
| + | * option j: remove box size info from first line of dat files | ||
| + | * option 3 (ctffind): remove unused variable pave | ||
| + | |||
| + | == P3DR == | ||
| + | * increased output format size for pixel count | ||
| + | |||
| + | == PSF == | ||
| + | * handle large maps | ||
| + | |||
| + | == PPFT == | ||
| + | * added warning messages during initialization | ||
| + | * fix error messages in get_info module | ||
| + | * constrained shift values in output dat files | ||
| + | * improved logs and check controls | ||
| + | * fixed index bug for compare_mode 1 (mode not currently used) | ||
| + | |||
| + | == POR == | ||
| + | * constrained shift values in output dat files | ||
| + | |||
| + | == tiff2pif == | ||
| + | * fixed interface and handle endianess | ||
| + | |||
| + | == dm32pif == | ||
| + | * accept unsigned integer format | ||
| + | |||
| + | == robem == | ||
| + | * added -fastload to avoid calculation of radial profiles | ||
| + | * calculate radial profile also for maps loaded for comparison (Subtract 3D Map menu) | ||
| + | * redefined //map_1d_rob// as //calc_map_1d_profile//, and simplified its interface | ||
| + | * allow initialization of large arrays | ||
| + | * allow opening of large maps | ||
| + | * allow large indexes when reading integer maps | ||
| + | * changed window parameters to avoid colored stripes in the gui | ||
| + | * fix radial projection for large maps | ||
| + | * increased buffer display | ||
| + | * open stack images even if in different directory than dat file | ||
| ==== auto3dem v4.04 ==== | ==== auto3dem v4.04 ==== | ||
| Line 281: | Line 437: | ||
| <WRAP center round box 60%> | <WRAP center round box 60%> | ||
| - | OLD: xbatch robem –pre infile [other options] | + | OLD: xbatch robem –pre infile [other options]\\ |
| NEW: robem –nogui –pre infile [other options] | NEW: robem –nogui –pre infile [other options] | ||
| </WRAP> | </WRAP> | ||
| - | * Fixed the feature that adds Gaussian noise to an image. This had been done incorrectly in previous versions as evidenced by the fact that adding Gaussian noise with mean=0 changed the mean intensity of the image. | + | * Fixed the feature that adds Gaussian noise to an image. This had been done incorrectly in previous versions as evidenced by the fact that adding Gaussian noise with mean=0 changed the mean intensity of the image. (This feature is found at Manipulate > Fix Values) |
| - | (This feature is found at Manipulate > Fix Values) | + | |
| * Fixed bug that caused robem to crash when clicking in drawing area of particle processing screen before particles had been loaded. | * Fixed bug that caused robem to crash when clicking in drawing area of particle processing screen before particles had been loaded. | ||
| * Fixed bug where display of radial projections would sometimes cause robem to crash. | * Fixed bug where display of radial projections would sometimes cause robem to crash. | ||
| Line 1181: | Line 1336: | ||
| setup_rmc | setup_rmc | ||
| * Script setup_rmc.pl modified so that default values for PPFT are overridden. | * Script setup_rmc.pl modified so that default values for PPFT are overridden. | ||
| - | + | ||
| - | delta_theta = 1° (default 0.5°) | + | delta_theta = 1° (default 0.5°) |
| - | verbose = -1 (default 2) | + | verbose = -1 (default 2) |
| auto3dem | auto3dem | ||
| * parameter file now accepts po2r for specifying PO2R input. por still works to allow back compatibility with v1.0, but all internal perl variables renamed to use po2r (e.g. %por_ref renamed internally to %po2r_ref) | * parameter file now accepts po2r for specifying PO2R input. por still works to allow back compatibility with v1.0, but all internal perl variables renamed to use po2r (e.g. %por_ref renamed internally to %po2r_ref) | ||