''' Author : Lyubimov, A.Y. Created : 12/21/2017 Last Changed: 12/21/2017 Description : SIMTBX (nanoBragg) GUI Threads and PostEvents ''' from __future__ import absolute_import, division, print_function import os import wx from threading import Thread from libtbx import easy_run from scitbx.array_family import flex from simtbx.nanoBragg import nanoBragg from simtbx.nanoBragg import shapetype from iotbx import pdb from cctbx.eltbx import henke # ------------------------------ IMAGE SYNTHESIS ----------------------------- # tp_EVT_NBDONE = wx.NewEventType() EVT_NBDONE = wx.PyEventBinder(tp_EVT_NBDONE, 1) class nanoBraggAllDone(wx.PyCommandEvent): ''' Send event when finished all cycles ''' def __init__(self, etype, eid, pixels=None): wx.PyCommandEvent.__init__(self, etype, eid) self.pixels = pixels def GetValue(self): return self.pixels class nanoBraggThread(Thread): ''' Basic spotfinder (with defaults) that could be used to rapidly analyze images as they are collected ''' def __init__(self, parent, params, add_background=True, add_noise=True, randomize=True, pixel_scale=None, preview=True): Thread.__init__(self) self.SIM = nanoBragg(detpixels_slowfast=(1231, 1263), pixel_size_mm=0.344, Ncells_abc=(5, 5, 5)) self.parent = parent self.params = params self.add_background = add_background self.add_noise = add_noise self.randomize = randomize self.crystal_size = pixel_scale self.preview = preview def run(self): if self.preview: self.generate_image() else: self.generate_image_set() def generate_image_set(self): pass def generate_image(self): img_filename = 'test_image.{}'.format(self.params.image_format) self.img_file = os.path.join(self.params.output, img_filename) if self.params.reference_coordinates is None: self.SIM.default_F = 1000 print('DEBUG: GENERATING FCALC OF {}'.format(self.SIM.default_F)) else: print('DEBUG: GENERATING FCALC FROM COORDINATES') self.SIM.default_F = 0 sfall = self.fcalc_from_pdb(resolution=1.6, algorithm="fft", wavelength=self.SIM.wavelength_A) self.SIM.Fhkl = sfall # fastest option, least realistic self.SIM.xtal_shape = shapetype.Tophat # oversample = 1 is the fastest setting (speed inversely proportional to # square of oversample) self.SIM.oversample = 1 self.SIM.wavelength_A = 1.3 self.SIM.polarization = 1 self.SIM.distance_mm = 300 # default orientation is with a axis down the beam, lets pick a random one print('DEBUG: RANDOMIZE ORIENTATION - ', self.randomize) if self.randomize: self.SIM.randomize_orientation() # display randomly-picked missetting angles print('SIMTBX: MISSETTING ANGLES: ', self.SIM.missets_deg) # or an Arndt-Wonacott A matrix (U*B), same as used by mosflm print('SIMTBX: ARNDT-WONACOTT A MATRIX', self.SIM.Amatrix) # show all parameters print('SIMTBX: SHOWING PARAMETERS:') self.SIM.show_params() print('\n *** \n') # print 'SIMTBX: SETTING BEAM PARAMETERS' self.SIM.flux = 1e12 # assumes round beam self.SIM.beamsize_mm = 0.1 self.SIM.exposure_s = 1 print('SIMTBX: FLUX = ', self.SIM.flux) print('SIMTBX: BEAM SIZE = {} mm'.format(self.SIM.beamsize_mm)) print('SIMTBX: EXPOSURE = {} SEC'.format(self.SIM.exposure_s)) # now actually run the simulation print('SIMTBX: ADDING SPOTS...') self.SIM.add_nanoBragg_spots() if self.crystal_size is not None: scale = (self.crystal_size/1000)**3 / (self.SIM.xtal_size_mm[0] * self.SIM.xtal_size_mm[1] * self.SIM.xtal_size_mm[2]) print('SIMTBX: SCALING BY {} '.format(scale)) self.SIM.raw_pixels *= scale if self.add_background: print('SIMTBX: ADDING WATER BACKGROUND') # rough approximation to water: interpolation points for sin(theta/lambda) vs structure factor bg = flex.vec2_double( [(0, 2.57), (0.0365, 2.58), (0.07, 2.8), (0.12, 5), (0.162, 8), (0.2, 6.75), (0.18, 7.32), (0.216, 6.75), (0.236, 6.5), (0.28, 4.5), (0.3, 4.3), (0.345, 4.36), (0.436, 3.77), (0.5, 3.17)]) self.SIM.Fbg_vs_stol = bg self.SIM.amorphous_sample_thick_mm = 0.1 self.SIM.amorphous_density_gcm3 = 1 self.SIM.amorphous_molecular_weight_Da = 18 self.SIM.add_background() print('SIMTBX: ADDING AIR BACKGROUND') bg = flex.vec2_double( [(0, 14.1), (0.045, 13.5), (0.174, 8.35), (0.35, 4.78), (0.5, 4.22)]) self.SIM.Fbg_vs_stol = bg self.SIM.amorphous_sample_thick_mm = 35 # between beamstop and collimator self.SIM.amorphous_density_gcm3 = 1.2e-3 self.SIM.amorphous_sample_molecular_weight_Da = 28 # nitrogen = N2 self.SIM.add_background() # set this to 0 or -1 to trigger automatic radius. could be very slow with bright images self.SIM.detector_psf_kernel_radius_pixels = 5 self.SIM.detector_psf_fwhm_mm = 0.08 self.SIM.detector_psf_type = shapetype.Fiber if self.add_noise: print('SIMTBX: ADDING NOISE...') self.SIM.add_noise() # write out a file on arbitrary scale, header contains beam center in various conventions print('DEBUG: FILENAME = ', self.img_file) print('SIMTBX: CONVERTING TO SMV FORMAT...') self.SIM.to_smv_format(fileout="intimage_001.img") # output image file if self.img_file is not None: self.SIM.to_smv_format(fileout=self.img_file) print('IMAGE WRITTEN TO ', self.img_file) # send pixels back to GUI when done try: evt = nanoBraggAllDone(tp_EVT_NBDONE, -1, pixels=self.SIM.raw_pixels) wx.PostEvent(self.parent, evt) except Exception as e: print(e) def fcalc_from_pdb(self, resolution=None, algorithm=None, wavelength=0.9): ''' Generate FCalc from PDB-formatted coordinates ''' with open(self.params.reference_coordinates, 'r') as pdb_file: pdb_lines = pdb_file.readlines() # Read in coordinates pdb_inp = pdb.input(source_info=None, lines=pdb_lines) xray_structure = pdb_inp.xray_structure_simple() # take a detour to insist on calculating anomalous contribution of every atom scatterers = xray_structure.scatterers() for sc in scatterers: expected_henke = henke.table(sc.element_symbol()).at_angstrom(wavelength) sc.fp = expected_henke.fp() sc.fdp = expected_henke.fdp() # how do we do bulk solvent? primitive_xray_structure = xray_structure.primitive_setting() P1_primitive_xray_structure = primitive_xray_structure.expand_to_p1() fcalc = P1_primitive_xray_structure.structure_factors( d_min=resolution, anomalous_flag=True, algorithm=algorithm).f_calc() return fcalc.amplitudes() # ------------------------------- MISCELLANEOUS ------------------------------ # class ImageViewerThread(Thread): ''' Worker thread that will move the image viewer launch away from the GUI and hopefully will prevent the image selection dialog freezing on MacOS''' def __init__(self, parent, file_string, viewer='dials.image_viewer', img_type=None): Thread.__init__(self) self.parent = parent self.file_string = file_string self.viewer = viewer self.img_type = img_type def run(self): command = '{} {}'.format(self.viewer, self.file_string) easy_run.fully_buffered(command)