from __future__ import absolute_import, division, print_function from libtbx.phil.command_line import argument_interpreter as model_argument_interpreter from libtbx.utils import Sorry from spotfinder.command_line.signal_strength import additional_spotfinder_phil_defs # implicit import try: from dials.algorithms.integration.kapton_correction import absorption_defs except ImportError: absorption_defs = "" libtbx_misc_defs = """ predictions_file = "" .type = str .help = File has xds parameters for spot predictions in XDS XPARAM format. parallel = 0 .type = int integration { file_template = None .type = str .help = "Full path for the files to integrate, expressed as template like lyso_1_###.img" file_range = None .type = ints (value_min=1) .help = First and last file number to integrate, forming a contiguous INCLUSIVE range (not like Python range). rocking_curve = *none gh1982a .type = choice .help = gh1982a is the Greenhough & Helliwell 1982 section I model, with epsilon from eqn (V.6) mosaicity_deg = 0.0 .type = float .help = full width effective mosaicity, degrees, for specified rocking curve model such as gh1982a guard_width_sq = 11 .type = int .help = Guard is the reserved area around the Bragg spot mask that cannot be used for background .help = plane determination because the tail of the signal distribution may leak from the spot. .help = Value represents max disallowed squared hypotenuse between neighboring signal & background pixels, as integer px**2. detector_gain = 0.0 .type = float .help = Detector gain in units of Analog Digital Units per photon. .help = Future plan: this value overrides any given through the dxtbx format mechanism. .help = Present: this is a mandatory value, code throws an exception with the default value. background_factor = 1 .type = int (value_min=1) .help = require minimum number of pixels for background fit = background_factor x # spot pixels model = *rossmann1979jac12-225 use_case_3_simulated_annealing use_case_3_simulated_annealing_7 use_case_3_simulated_annealing_9 user_supplied .type = choice .help = algorithm for prediction of spots .help = Michael Rossman (1979) J. Appl. Cryst. 12, 225-238. use_subpixel_translations = None .type = floats .help = list slow,fast offsets for correcting tile positions to subpixel resolution (2 numbers for each tile) subpixel_joint_model { rotations = None .type=floats .help = joint-refined tile rotations & translations [along with per-image beam,dist,rotz,wavelength, not stored] translations = None .type=floats .help = joint-refined tile rotations & translations [along with per-image beam,dist,rotz,wavelength, not stored] } spot_shape_verbose = False .type = bool .help = analysis of radial and azimuthal spot shapes. signal_penetration = 0.5 .type = float .help = For computing parallax effect due to finite sensor thickness, fraction of signal to attenuate before .help = ignoring the remaining trailing parallax. Small value (0.0) means do not account for parallax. spotfinder_subset = *inlier_spots goodspots spots_non-ice .type = choice .help = which subset to use for parameter refinement and constructing integration profiles. .help = subsets are nested goodspots > spots_non-ice > inlier_spots mask_pixel_value = None .type = int .help = pixels set to this value will be ignored during integration mosaic { refinement_target = LSQ *ML .type = choice .help = Modeling of still shots, refinement of crystal physical parameters by one of two targets given in the paper .help = [Sauter et al. Acta D (2014) 70:3299-3309]: least squares (LSQ) or maximum likelihood (ML). .help = As the paper describes, ML gives superior results and is set to be the default as of 7/2017. kludge1 = 1 .type = float .help = bugfix 1 of 2 for protocol 6, equation 2. When matching obs and model reflections, .help = must increase the provisional model mosaicity so as to model enough spots. .help = default 1 might be too small for a bad model, aborting indexing with too few matches. .help = > 2 might be too large and could lead to misindexing. bugfix2_enable = True .type = bool .help = bugfix 2 of 2 for protocol 6, equation 2. Assure that the result of the arctan() .help = function call is placed in the correct principle value region. .help = choice of "False" preserves the ability to roll back program behavior .help = as promised to the Nature Methods editor. domain_size_lower_limit = 10 .type = float .help = Mosaic blocks must be at least this many unit cells on edge (refers to cube-root of cell volume) .help = used in simple_integration.py as an initial value .help = too-small value predicts too many spots, leading to misindexing. .help = too-large value doesn't predict enough spots .help = choose lowest value physically reasonable, 10 unit cells. enable_rotational_target_highsym = True .type = bool .help = Protocol 6, use equation 2 (true) or protocol 5, use equation 1 (false) for higher Bravais-setting refinement enable_rotational_target_triclinic = True .type = bool .help = Protocol 5, use equation 2 (true) or protocol 4, use equation 1 (false) for triclinic Bravais-setting refinement enable_simplex = False .type = bool .help = simplex_optimization enable_AD14F7B = False .type = bool .help = enable Sauter et al. Acta D (2014) 70:3299-3309, Fig. 7(b) plot, angular excursion vs two theta enable_polychromatic = False .type = bool .help = followup top hat wavelength dispersion ewald_proximal_volume_resolution_cutoff = 2.5 .type = float .help = Resolution cutoff in Angstroms. Set roughly to the apparent cutoff of bright spots for one or a group of images. .help = governs the cutoff resolution for teh ewald proximal volume: that volume of reciprocal space containing .help = spots predicted by the current mosaicity model. } initial_volume_factor = 1.8 .type = float .help = controls the initial integration limits before filtering by sig(I) durig merging .help = used in rstbx/new_horizons/oscillation_shots.py -- not fully understood .help = a larger volume factor integrates a larger volume of reciprocal space enable_residual_map = False .type = bool .help = x,y model vs. spotfinder residuals plotted vs. image position enable_residual_map_deltapsi = False .type = bool .help = if residual map is enabled, colorcode the Bragg spots by Delta-Psi .help = blue, negative delta psi, outside Ewald sphere. red, positive delta psi, inside Ewald sphere. .help = requires also setting enable_residual_map to True and spot_prediction to dials enable_residual_scatter = False .type = bool .help = x,y model vs. spotfinder residuals scatter plot graphics_backend = *screen pdf .type = choice .help = data plots are written to the terminal screen, or to pdf files pdf_output_dir = "." .type = str .help = plots are written to this directory montecarlo_integration_limit = None .type = float .help = use None to limit the integration resolution based on Wilson plot .help = alternatively set integration limit to a fixed value given in Angstroms. greedy_integration_limit = False .type = bool .help = governs the resolution limits used for higher Bravais settings .help = if true, use the expanded limiting_resolution used for the last triclinic round .help = if false, attempt to analyze triclinic integrated spots for limits (default until Feb 2015, not so reliable) combine_sym_constraints_and_3D_target = False .type = bool .help = enable redesigned refinement protocol from Acta D 2014 Sauter paper .help = if false (default as of Feb 2015) symmetry constraints are applied after eqn (1) positional refinement .help = but before indexing of high-Bravais symmetry spots, possibly leading to misindexing of high-angle spots .help = if true, spots are indexed once only, in triclinic setting. After application of high-symmetry constraints .help = dials is used to refine positions (eqn 1) and deltapsi angle (eqn 2). spot_prediction = *ucbp3 dials .type = choice .help = in high-symmetry integration protocol, predict with ucbp3 (CSPAD subpixel corrections) or dials (detector tilt, but unit translations) enable_one_to_one_safeguard = False .type = bool .help = Flag enables a safeguard within the stills integration algorithm, within the mapping of .help = predicted spots to observations prior to model refinement. The safeguard prevents .help = a many-to-one predicted-to-observation mapping, assuring that each prediction is mapped .help = to at most one observation, one that is closest. The legacy code did not include .help = this safeguard. It is expected that True should become the default after a testing period. dials_refinement{ strategy = *distance wavelength fix .type = choice .help = either refine the distance or the wavelength for XFEL stills, or fix them both in place }%s } """ % absorption_defs indexing_defs = """ include scope spotfinder.command_line.signal_strength.master_params spotfinder = *distl speck .type=choice .help = "Choose among spotfinder implementations [distl|speck]" speckfinder { dark_stddev = "" .type = str .help = Mandatory dark standard deviation image for gain correction. dark_adu_scale = 100 .type = int .help = "Mandatory scale at which dark was calculated; must be >1 on account of integer rounding." } indexing { data = None .type=str .multiple=True .help="Relative or absolute path names for raw image files to be indexed" indexing_pickle = None .type=str .help = "pickle file name for integration results subsequent to indexing." completeness_pickle = None .type=str .help = "pickle file name for HKL, I, SIGI, XY." open_wx_viewer = False .type = bool verbose_cv = False .type = bool .help = "screen printout of the obs vs predicted spot correction vectors," .help = "for empriical repositioning of the detector tiles." lattice_model_scoring_cutoff = 2.0 .type = float .help = Cutoff value for the over integrated signal from the model lattice. .help = Used for choosing the most accurate combination of candidate basis vectors. devel_algorithm = None .type = str .help = for development only, turn on whatever testing behavior outlier_detection { allow = True .type = bool .multiple=False .help="Algorithm (Sauter&Poon[2010] J Appl Cryst 43:611) provides superior positional fit with noisy data." switch=False .type=bool .multiple=False .help="Switch to the outlying spots to detect a second lattice. False==first lattice; True==second lattice" verbose=False .type=bool .multiple=False .help="Verbose output." pdf=None .type=str .multiple=False .help="Output file name for making graphs of |dr| vs spot number and dy vs dx." } plot_search_scope = False .type = bool .help = improvement of the model, plot target function of origin offset or S0 mm_search_scope = 4.0 .type = float .help = global radius of origin_offset search, used for plotting the search scope improve_local_scope = *origin_offset S0_vector .type = choice .help = improve 'beam position' according to Sauter et al (2004). Local minimum only .help = specifies which parameter to optimize. } """ iotbx_defs_viewer_detail = """ powder_arcs{ show = False .type=bool .help = "show powder arcs calculated from PDB file." code = None .type=str .help = "PDB code (4 characters) for file; fetch it from the Internet." } calibrate_silver = False .type=bool .help = "Open special GUI for distance/metrology from silver behenate." calibrate_pdb{ code = None .type=str .help = "Open pdb code (over Internet) to get unit cell & symmetry for powder rings." .help = "Most useful for calibrating low-Q rings on far detector." .help = "Option is mutually exclusive with calibrate silver, unit cell and powder arcs options." d_min = 20. .type=float .help = "Limiting resolution to calculate powder rings" } calibrate_unitcell{ unitcell = None .type=unit_cell .help = "Specify unit cell for powder rings." .help = "Option is mutually exclusive with calibrate silver, pdb and powder arcs options." d_min = 20. .type=float .help = "Limiting resolution to calculate powder rings" spacegroup = None .type=str .help = "Specify spacegroup for the unit cell" } """ iotbx_defs_viewer = """ viewer { %s } """%iotbx_defs_viewer_detail iotbx_defs_target = """ target_cell=None .type=unit_cell .multiple=False .help="Imperative unit cell applied at the level of DPS algorithm basis selection." target_cell_centring_type= *P C I R F .type=choice .multiple=False .help="Centring symbol for the target cell" isoforms .help=Constrain the unit cell to specific values during refinement .help=As presently implemented, applies only to dials_refinement_preceding_integration .help=and applies only to the higher-symmetry integration trial, not the initial triclinic .multiple=True { name=None .type=str cell=None .type=unit_cell lookup_symbol=None .type=str .help=The sgtbx lookup symbol of the reflections pointgroup rmsd_target_mm=None .type=float .help=Maximum acceptable DIALS positional rmsd, in mm beam_restraint=None .type=floats(size=2) .help=Known beam position in mm X,Y, rmsd_target_mm is reused here as a circle of confusion .help=to assure that no images are accepted where the lattice is misindexed by a unit shift. } """ libtbx_defs = indexing_defs + libtbx_misc_defs iotbx_defs = iotbx_defs_viewer + iotbx_defs_target indexing_api_defs = indexing_defs + iotbx_defs_target class EffectiveParamGenerator: def __init__(self,libtbx_defs,iotbx_defs): from libtbx import adopt_init_args adopt_init_args(self, locals()) def master(self,package = 'iotbx'): libselector = {'libtbx':self.libtbx_defs, 'iotbx':self.iotbx_defs+self.libtbx_defs, } [package] if (package == "libtbx"): from libtbx import phil else: from iotbx import phil return phil.parse(input_string=libselector, process_includes=True) def default(self,item = 'iotbx'): app_master = self.master(item) return app_master.fetch(sources=[app_master,]) def show(self, modpython): modified_params = self.master().format(python_object = modpython) modified_params.show() def merge(self, args): #future: this member function should be deprecated; replace with preferences.py effective_params = self.default() argument_interpreter = model_argument_interpreter( master_phil=self.master(), #home_scope = ) consume = [] for arg in args: try: command_line_params = argument_interpreter.process( arg=arg ) effective_params = effective_params.fetch(sources=[command_line_params,]) consume.append(arg) except Sorry as e: pass for item in consume: args.remove(item) # effective_params.show() params = effective_params.extract() self.validation(params) self.effective_params = effective_params return params def validation(self,trial_params): pass effective_param_generator = EffectiveParamGenerator(libtbx_defs,iotbx_defs) #singleton