# -*- mode: python; coding: utf-8; indent-tabs-mode: nil; python-indent: 2 -*- # # $Id$ from __future__ import absolute_import, division, print_function from six.moves import range import os, sys, copy from iotbx.detectors.npy import NpyImage class empty: pass parameters=empty() def ImageFactory(filename): global parameters if type(filename)==type("") and os.path.isfile(filename): from dxtbx.format.FormatPYunspecified import FormatPYunspecified assert FormatPYunspecified.understand(filename) I = FormatPYunspecified(filename).get_detectorbase() else: print("This is not a file; assume the data are in the defined dictionary format") I = NpyImage(filename, source_data=parameters.horizons_phil.indexing.data) I.readHeader(parameters.horizons_phil) I.translate_tiles(parameters.horizons_phil) #from xfel.cxi.display_powder_arcs import apply_gaussian_noise #apply_gaussian_noise(I,parameters.horizons_phil) if (parameters.horizons_phil.viewer.powder_arcs.show): from xfel.cxi.display_powder_arcs import superimpose_powder_arcs superimpose_powder_arcs(I,parameters.horizons_phil) return I from iotbx import detectors detectors.ImageFactory = ImageFactory from spotfinder.diffraction.imagefiles import FileName FileName.exts.append("pickle") from spotfinder.applications.xfel import cxi_phil show_bg_boxes=True class wrapper_of_callback(object): def __init__(self, info=None): if info != None: self.spotfinder = info.S self.frames = info.frames self.Files = info.Files self.phil_params= info.phil_params def display(self,path): import wx from rstbx.viewer.frame import XrayFrame app = wx.App(0) frame = XrayFrame(None, -1, "X-ray image display", size=(1200,1080)) frame.SetSize((1024,780)) frame.load_image(path) frame.Show() app.MainLoop() def display_with_callback(self,path): from rstbx.viewer import display display.user_callback = self.user_callback self.display(path) def user_callback(self,dc,wxpanel,wx): # arguments are a wx Device Context, an Xray Frame, and the wx Module itself """ for spot in self.spotfinder.images[self.frames[0]]["spots_total"]: for pxl in spot.bodypixels: x,y = wxpanel._img.image_coords_as_screen_coords( pxl.y, pxl.x) dc.SetPen(wx.Pen('red')) dc.SetBrush(wx.RED_BRUSH) dc.DrawCircle(x,y,1) x,y = wxpanel._img.image_coords_as_screen_coords( spot.ctr_mass_y(), spot.ctr_mass_x()) dc.SetPen(wx.Pen('green')) dc.SetBrush(wx.GREEN_BRUSH) dc.DrawCircle(x,y,1) """ """ for spot in self.spotfinder.images[self.frames[0]]["lo_pass_resolution_spots"]: for pxl in spot.bodypixels: x,y = wxpanel._img.image_coords_as_screen_coords( pxl.y, pxl.x) dc.SetPen(wx.Pen('yellow')) dc.DrawCircle(x,y,1) """ for spot in self.spotfinder.images[self.frames[0]]["spots_inlier"]: for pxl in spot.bodypixels: x,y = wxpanel._img.image_coords_as_screen_coords( pxl.y, pxl.x) dc.SetPen(wx.Pen('cyan')) dc.DrawCircle(x,y,1) if show_bg_boxes: imgobj = self.Files.imageindex(self.frames[0]) from iotbx.detectors.npy import tile_manager aa = tile_manager(self.phil_params).effective_tiling_as_flex_int( reapply_peripheral_margin = True, beam = ( imgobj.beamx/imgobj.pixel_size,imgobj.beamy/imgobj.pixel_size)) dc.SetPen(wx.Pen('orange')) dc.SetBrush(wx.Brush('red', wx.TRANSPARENT)) for i in range(0, len(aa), 4): p = wxpanel._img.image_coords_as_screen_coords(aa[i + 1], aa[i + 0]) p2 = wxpanel._img.image_coords_as_screen_coords(aa[i + 3]-1, aa[i + 2]-1) dc.DrawRectangle(x=p[0], y=p[1], width=p2[0]-p[0],height=p2[1]-p[1]) if False: x, y = wxpanel._img.image_coords_as_screen_coords(850, 850) dc.SetPen(wx.Pen('red')) dc.SetBrush(wx.Brush('red', wx.TRANSPARENT)) for i in range(24): r, s = wxpanel._img.image_coords_as_screen_coords(850 + (i + 1) * 25, 850) dc.DrawCircle(x, y, r - x) def view_raw_image(path, *command_line, **kwargs): args = [path, "viewer.powder_arcs.show=False", "viewer.powder_arcs.code=3n9c", ] horizons_phil = cxi_phil.cxi_versioned_extract( copy.deepcopy(args),list(command_line)) global parameters parameters.horizons_phil = horizons_phil if horizons_phil.viewer.calibrate_pdb.code is not None: from rstbx.viewer.calibration import pdb_code_wrapper pdb_code_wrapper(horizons_phil).display(path) return elif horizons_phil.viewer.calibrate_unitcell.unitcell is not None: from rstbx.viewer.calibration import unit_cell_wrapper unit_cell_wrapper(horizons_phil).display(path) return elif horizons_phil.viewer.calibrate_silver==True: from rstbx.viewer.calibration import sb_wrapper sb_wrapper(horizons_phil).display(path) return wrapper_of_callback().display(path) def run_one(path, *command_line, **kwargs): args = ["distl.image=%s"%path, "distl.res.outer=2.1", "distl.detector_format_version=CXI 5.1", ] horizons_phil = cxi_phil.cxi_versioned_extract( copy.deepcopy(args),list(command_line)) global parameters parameters.horizons_phil = horizons_phil from spotfinder.applications import signal_strength info = signal_strength.run_signal_strength(horizons_phil) if kwargs.get("display",False): work = wrapper_of_callback(info) work.display_with_callback(path) def run_one_index_core(horizons_phil): global parameters parameters.horizons_phil = horizons_phil from rstbx.new_horizons.index import pre_indexing_validation,pack_names,new_horizons_state pre_indexing_validation(horizons_phil) imagefile_arguments = pack_names(horizons_phil) info = new_horizons_state(horizons_phil,imagefile_arguments) try: info.process() except Exception as e: e.info = info raise e info.S = info.spotfinder_results return info def run_one_index(path, *arguments, **kwargs): assert arguments[0].find("target=")==0 target = arguments[0].split("=")[1] from xfel.phil_preferences import load_cxi_phil if "--nodisplay" in arguments[1:]: display = False arguments = list(arguments) arguments.remove("--nodisplay") else: display = True args = ["indexing.data=%s"%path, "beam_search_scope=0.5", "lepage_max_delta = 3.0", "spots_pickle = None", "subgroups_pickle = None", "refinements_pickle = None", "rmsd_tolerance = 5.0", "mosflm_rmsd_tolerance = 5.0", "difflimit_sigma_cutoff=2.0", #"indexing.verbose_cv=True", "indexing.open_wx_viewer=%s"%display ] + list(arguments[1:]) horizons_phil = load_cxi_phil(target, args) info = run_one_index_core(horizons_phil) info.Files = info.organizer.Files info.phil_params = info.horizons_phil # The spotfinder view within cxi.index is an anachronism; no useful purpose anymore # therefore remove this option within cxi.index: return work = wrapper_of_callback(info) if kwargs.get("display",False): import wx from rstbx.viewer import display from rstbx.viewer.frame import XrayFrame display.user_callback = work.user_callback app = wx.App(0) frame = XrayFrame(None, -1, "X-ray image display", size=(1200,1080)) frame.SetSize((1024,780)) frame.load_image(path) frame.Show() app.MainLoop() if __name__ == "__main__": function = sys.argv[1] # either view, spots, or index selector = {"view":view_raw_image, "spots":run_one, "index":run_one_index} files = [arg for arg in sys.argv[2:] if os.path.isfile(arg)] arguments = [arg for arg in sys.argv[2:] if not os.path.isfile(arg)] for file in files: selector[function](file, *arguments, **({'display':True}))