Source code for sas.sascalc.calculator.sas_gen

# pylint: disable=invalid-name
"""
SAS generic computation and sld file readers
"""
import sas.sascalc.calculator.core.sld2i as mod
from sas.sascalc.calculator.BaseComponent import BaseComponent
from periodictable import formula
from periodictable import nsf
import numpy
import os
import copy
import sys
import logging

MFACTOR_AM = 2.853E-12
MFACTOR_MT = 2.3164E-9
METER2ANG = 1.0E+10
#Avogadro constant [1/mol]
NA = 6.02214129e+23

[docs]def mag2sld(mag, v_unit=None): """ Convert magnetization to magnatic SLD sldm = Dm * mag where Dm = gamma * classical elec. radius/(2*Bohr magneton) Dm ~ 2.853E-12 [A^(-2)] ==> Shouldn't be 2.90636E-12 [A^(-2)]??? """ if v_unit == "A/m": factor = MFACTOR_AM elif v_unit == "mT": factor = MFACTOR_MT else: raise ValueError, "Invalid valueunit" sld_m = factor * mag return sld_m
[docs]def transform_center(pos_x, pos_y, pos_z): """ re-center :return: posx, posy, posz [arrays] """ posx = pos_x - (min(pos_x) + max(pos_x)) / 2.0 posy = pos_y - (min(pos_y) + max(pos_y)) / 2.0 posz = pos_z - (min(pos_z) + max(pos_z)) / 2.0 return posx, posy, posz
[docs]class GenSAS(BaseComponent): """ Generic SAS computation Model based on sld (n & m) arrays """ def __init__(self): """ Init :Params sld_data: MagSLD object """ # Initialize BaseComponent BaseComponent.__init__(self) self.sld_data = None self.data_pos_unit = None self.data_x = None self.data_y = None self.data_z = None self.data_sldn = None self.data_mx = None self.data_my = None self.data_mz = None self.data_vol = None #[A^3] self.is_avg = False ## Name of the model self.name = "GenSAS" ## Define parameters self.params = {} self.params['scale'] = 1.0 self.params['background'] = 0.0 self.params['solvent_SLD'] = 0.0 self.params['total_volume'] = 1.0 self.params['Up_frac_in'] = 1.0 self.params['Up_frac_out'] = 1.0 self.params['Up_theta'] = 0.0 self.description = 'GenSAS' ## Parameter details [units, min, max] self.details = {} self.details['scale'] = ['', 0.0, numpy.inf] self.details['background'] = ['[1/cm]', 0.0, numpy.inf] self.details['solvent_SLD'] = ['1/A^(2)', -numpy.inf, numpy.inf] self.details['total_volume'] = ['A^(3)', 0.0, numpy.inf] self.details['Up_frac_in'] = ['[u/(u+d)]', 0.0, 1.0] self.details['Up_frac_out'] = ['[u/(u+d)]', 0.0, 1.0] self.details['Up_theta'] = ['[deg]', -numpy.inf, numpy.inf] # fixed parameters self.fixed = []
[docs] def set_pixel_volumes(self, volume): """ Set the volume of a pixel in (A^3) unit :Param volume: pixel volume [float] """ if self.data_vol == None: raise self.data_vol = volume
[docs] def set_is_avg(self, is_avg=False): """ Sets is_avg: [bool] """ self.is_avg = is_avg
def _gen(self, x, y, i): """ Evaluate the function :Param x: array of x-values :Param y: array of y-values :Param i: array of initial i-value :return: function value """ pos_x = self.data_x pos_y = self.data_y pos_z = self.data_z len_x = len(pos_x) if self.is_avg == None: len_x *= -1 pos_x, pos_y, pos_z = transform_center(pos_x, pos_y, pos_z) len_q = len(x) sldn = copy.deepcopy(self.data_sldn) sldn -= self.params['solvent_SLD'] model = mod.new_GenI(len_x, pos_x, pos_y, pos_z, sldn, self.data_mx, self.data_my, self.data_mz, self.data_vol, self.params['Up_frac_in'], self.params['Up_frac_out'], self.params['Up_theta']) if y == []: mod.genicom(model, len_q, x, i) else: mod.genicomXY(model, len_q, x, y, i) vol_correction = self.data_total_volume / self.params['total_volume'] return self.params['scale'] * vol_correction * i + \ self.params['background']
[docs] def set_sld_data(self, sld_data=None): """ Sets sld_data """ self.sld_data = sld_data self.data_pos_unit = sld_data.pos_unit self.data_x = sld_data.pos_x self.data_y = sld_data.pos_y self.data_z = sld_data.pos_z self.data_sldn = sld_data.sld_n self.data_mx = sld_data.sld_mx self.data_my = sld_data.sld_my self.data_mz = sld_data.sld_mz self.data_vol = sld_data.vol_pix self.data_total_volume = sum(sld_data.vol_pix) self.params['total_volume'] = sum(sld_data.vol_pix)
[docs] def getProfile(self): """ Get SLD profile : return: sld_data """ return self.sld_data
[docs] def run(self, x=0.0): """ Evaluate the model :param x: simple value :return: (I value) """ if x.__class__.__name__ == 'list': if len(x[1]) > 0: msg = "Not a 1D." raise ValueError, msg i_out = numpy.zeros_like(x[0]) # 1D I is found at y =0 in the 2D pattern out = self._gen(x[0], [], i_out) return out else: msg = "Q must be given as list of qx's and qy's" raise ValueError, msg
[docs] def runXY(self, x=0.0): """ Evaluate the model :param x: simple value :return: I value :Use this runXY() for the computation """ if x.__class__.__name__ == 'list': i_out = numpy.zeros_like(x[0]) out = self._gen(x[0], x[1], i_out) return out else: msg = "Q must be given as list of qx's and qy's" raise ValueError, msg
[docs] def evalDistribution(self, qdist): """ Evaluate a distribution of q-values. :param qdist: ndarray of scalar q-values (for 1D) or list [qx,qy] where qx,qy are 1D ndarrays (for 2D). """ if qdist.__class__.__name__ == 'list': if len(qdist[1]) < 1: out = self.run(qdist) else: out = self.runXY(qdist) return out else: mesg = "evalDistribution is expecting an ndarray of " mesg += "a list [qx,qy] where qx,qy are arrays." raise RuntimeError, mesg
[docs]class OMF2SLD(object): """ Convert OMFData to MAgData """ def __init__(self): """ Init """ self.pos_x = None self.pos_y = None self.pos_z = None self.mx = None self.my = None self.mz = None self.sld_n = None self.vol_pix = None self.output = None self.omfdata = None
[docs] def set_data(self, omfdata, shape='rectangular'): """ Set all data """ self.omfdata = omfdata length = int(omfdata.xnodes * omfdata.ynodes * omfdata.znodes) pos_x = numpy.arange(omfdata.xmin, omfdata.xnodes*omfdata.xstepsize + omfdata.xmin, omfdata.xstepsize) pos_y = numpy.arange(omfdata.ymin, omfdata.ynodes*omfdata.ystepsize + omfdata.ymin, omfdata.ystepsize) pos_z = numpy.arange(omfdata.zmin, omfdata.znodes*omfdata.zstepsize + omfdata.zmin, omfdata.zstepsize) self.pos_x = numpy.tile(pos_x, int(omfdata.ynodes * omfdata.znodes)) self.pos_y = pos_y.repeat(int(omfdata.xnodes)) self.pos_y = numpy.tile(self.pos_y, int(omfdata.znodes)) self.pos_z = pos_z.repeat(int(omfdata.xnodes * omfdata.ynodes)) self.mx = omfdata.mx self.my = omfdata.my self.mz = omfdata.mz self.sld_n = numpy.zeros(length) if omfdata.mx == None: self.mx = numpy.zeros(length) if omfdata.my == None: self.my = numpy.zeros(length) if omfdata.mz == None: self.mz = numpy.zeros(length) self._check_data_length(length) self.remove_null_points(False, False) mask = numpy.ones(len(self.sld_n), dtype=bool) if shape.lower() == 'ellipsoid': try: # Pixel (step) size included x_c = max(self.pos_x) + min(self.pos_x) y_c = max(self.pos_y) + min(self.pos_y) z_c = max(self.pos_z) + min(self.pos_z) x_d = max(self.pos_x) - min(self.pos_x) y_d = max(self.pos_y) - min(self.pos_y) z_d = max(self.pos_z) - min(self.pos_z) x_r = (x_d + omfdata.xstepsize) / 2.0 y_r = (y_d + omfdata.ystepsize) / 2.0 z_r = (z_d + omfdata.zstepsize) / 2.0 x_dir2 = ((self.pos_x - x_c / 2.0) / x_r) x_dir2 *= x_dir2 y_dir2 = ((self.pos_y - y_c / 2.0) / y_r) y_dir2 *= y_dir2 z_dir2 = ((self.pos_z - z_c / 2.0) / z_r) z_dir2 *= z_dir2 mask = (x_dir2 + y_dir2 + z_dir2) <= 1.0 except: logging.error(sys.exc_value) self.output = MagSLD(self.pos_x[mask], self.pos_y[mask], self.pos_z[mask], self.sld_n[mask], self.mx[mask], self.my[mask], self.mz[mask]) self.output.set_pix_type('pixel') self.output.set_pixel_symbols('pixel')
[docs] def get_omfdata(self): """ Return all data """ return self.omfdata
[docs] def get_output(self): """ Return output """ return self.output
def _check_data_length(self, length): """ Check if the data lengths are consistent :Params length: data length """ msg = "Error: Inconsistent data length." if len(self.pos_x) != length: raise ValueError, msg if len(self.pos_y) != length: raise ValueError, msg if len(self.pos_z) != length: raise ValueError, msg if len(self.mx) != length: raise ValueError, msg if len(self.my) != length: raise ValueError, msg if len(self.mz) != length: raise ValueError, msg
[docs] def remove_null_points(self, remove=False, recenter=False): """ Removes any mx, my, and mz = 0 points """ if remove: is_nonzero = (numpy.fabs(self.mx) + numpy.fabs(self.my) + numpy.fabs(self.mz)).nonzero() if len(is_nonzero[0]) > 0: self.pos_x = self.pos_x[is_nonzero] self.pos_y = self.pos_y[is_nonzero] self.pos_z = self.pos_z[is_nonzero] self.sld_n = self.sld_n[is_nonzero] self.mx = self.mx[is_nonzero] self.my = self.my[is_nonzero] self.mz = self.mz[is_nonzero] if recenter: self.pos_x -= (min(self.pos_x) + max(self.pos_x)) / 2.0 self.pos_y -= (min(self.pos_y) + max(self.pos_y)) / 2.0 self.pos_z -= (min(self.pos_z) + max(self.pos_z)) / 2.0
[docs] def get_magsld(self): """ return MagSLD """ return self.output
[docs]class OMFReader(object): """ Class to load omf/ascii files (3 columns w/header). """ ## File type type_name = "OMF ASCII" ## Wildcards type = ["OMF files (*.OMF, *.omf)|*.omf"] ## List of allowed extensions ext = ['.omf', '.OMF']
[docs] def read(self, path): """ Load data file :param path: file path :return: x, y, z, sld_n, sld_mx, sld_my, sld_mz """ desc = "" mx = numpy.zeros(0) my = numpy.zeros(0) mz = numpy.zeros(0) try: input_f = open(path, 'rb') buff = input_f.read() lines = buff.split('\n') input_f.close() output = OMFData() valueunit = None for line in lines: toks = line.split() # Read data try: _mx = float(toks[0]) _my = float(toks[1]) _mz = float(toks[2]) _mx = mag2sld(_mx, valueunit) _my = mag2sld(_my, valueunit) _mz = mag2sld(_mz, valueunit) mx = numpy.append(mx, _mx) my = numpy.append(my, _my) mz = numpy.append(mz, _mz) except: # Skip non-data lines logging.error(sys.exc_value) #Reading Header; Segment count ignored s_line = line.split(":", 1) if s_line[0].lower().count("oommf") > 0: oommf = s_line[1].lstrip() if s_line[0].lower().count("title") > 0: title = s_line[1].lstrip() if s_line[0].lower().count("desc") > 0: desc += s_line[1].lstrip() desc += '\n' if s_line[0].lower().count("meshtype") > 0: meshtype = s_line[1].lstrip() if s_line[0].lower().count("meshunit") > 0: meshunit = s_line[1].lstrip() if meshunit.count("m") < 1: msg = "Error: \n" msg += "We accept only m as meshunit" raise ValueError, msg if s_line[0].lower().count("xbase") > 0: xbase = s_line[1].lstrip() if s_line[0].lower().count("ybase") > 0: ybase = s_line[1].lstrip() if s_line[0].lower().count("zbase") > 0: zbase = s_line[1].lstrip() if s_line[0].lower().count("xstepsize") > 0: xstepsize = s_line[1].lstrip() if s_line[0].lower().count("ystepsize") > 0: ystepsize = s_line[1].lstrip() if s_line[0].lower().count("zstepsize") > 0: zstepsize = s_line[1].lstrip() if s_line[0].lower().count("xnodes") > 0: xnodes = s_line[1].lstrip() if s_line[0].lower().count("ynodes") > 0: ynodes = s_line[1].lstrip() if s_line[0].lower().count("znodes") > 0: znodes = s_line[1].lstrip() if s_line[0].lower().count("xmin") > 0: xmin = s_line[1].lstrip() if s_line[0].lower().count("ymin") > 0: ymin = s_line[1].lstrip() if s_line[0].lower().count("zmin") > 0: zmin = s_line[1].lstrip() if s_line[0].lower().count("xmax") > 0: xmax = s_line[1].lstrip() if s_line[0].lower().count("ymax") > 0: ymax = s_line[1].lstrip() if s_line[0].lower().count("zmax") > 0: zmax = s_line[1].lstrip() if s_line[0].lower().count("valueunit") > 0: valueunit = s_line[1].lstrip().rstrip() if s_line[0].lower().count("valuemultiplier") > 0: valuemultiplier = s_line[1].lstrip() if s_line[0].lower().count("valuerangeminmag") > 0: valuerangeminmag = s_line[1].lstrip() if s_line[0].lower().count("valuerangemaxmag") > 0: valuerangemaxmag = s_line[1].lstrip() if s_line[0].lower().count("end") > 0: output.filename = os.path.basename(path) output.oommf = oommf output.title = title output.desc = desc output.meshtype = meshtype output.xbase = float(xbase) * METER2ANG output.ybase = float(ybase) * METER2ANG output.zbase = float(zbase) * METER2ANG output.xstepsize = float(xstepsize) * METER2ANG output.ystepsize = float(ystepsize) * METER2ANG output.zstepsize = float(zstepsize) * METER2ANG output.xnodes = float(xnodes) output.ynodes = float(ynodes) output.znodes = float(znodes) output.xmin = float(xmin) * METER2ANG output.ymin = float(ymin) * METER2ANG output.zmin = float(zmin) * METER2ANG output.xmax = float(xmax) * METER2ANG output.ymax = float(ymax) * METER2ANG output.zmax = float(zmax) * METER2ANG output.valuemultiplier = valuemultiplier output.valuerangeminmag = mag2sld(float(valuerangeminmag), \ valueunit) output.valuerangemaxmag = mag2sld(float(valuerangemaxmag), \ valueunit) output.set_m(mx, my, mz) return output except: msg = "%s is not supported: \n" % path msg += "We accept only Text format OMF file." raise RuntimeError, msg
[docs]class PDBReader(object): """ PDB reader class: limited for reading the lines starting with 'ATOM' """ type_name = "PDB" ## Wildcards type = ["pdb files (*.PDB, *.pdb)|*.pdb"] ## List of allowed extensions ext = ['.pdb', '.PDB']
[docs] def read(self, path): """ Load data file :param path: file path :return: MagSLD :raise RuntimeError: when the file can't be opened """ pos_x = numpy.zeros(0) pos_y = numpy.zeros(0) pos_z = numpy.zeros(0) sld_n = numpy.zeros(0) sld_mx = numpy.zeros(0) sld_my = numpy.zeros(0) sld_mz = numpy.zeros(0) vol_pix = numpy.zeros(0) pix_symbol = numpy.zeros(0) x_line = [] y_line = [] z_line = [] x_lines = [] y_lines = [] z_lines = [] try: input_f = open(path, 'rb') buff = input_f.read() lines = buff.split('\n') input_f.close() num = 0 for line in lines: try: # check if line starts with "ATOM" if line[0:6].strip().count('ATM') > 0 or \ line[0:6].strip() == 'ATOM': # define fields of interest atom_name = line[12:16].strip() try: float(line[12]) atom_name = atom_name[1].upper() except: if len(atom_name) == 4: atom_name = atom_name[0].upper() elif line[12] != ' ': atom_name = atom_name[0].upper() + \ atom_name[1].lower() else: atom_name = atom_name[0].upper() _pos_x = float(line[30:38].strip()) _pos_y = float(line[38:46].strip()) _pos_z = float(line[46:54].strip()) pos_x = numpy.append(pos_x, _pos_x) pos_y = numpy.append(pos_y, _pos_y) pos_z = numpy.append(pos_z, _pos_z) try: val = nsf.neutron_sld(atom_name)[0] # sld in Ang^-2 unit val *= 1.0e-6 sld_n = numpy.append(sld_n, val) atom = formula(atom_name) # cm to A units vol = 1.0e+24 * atom.mass / atom.density / NA vol_pix = numpy.append(vol_pix, vol) except: print "Error: set the sld of %s to zero"% atom_name sld_n = numpy.append(sld_n, 0.0) sld_mx = numpy.append(sld_mx, 0) sld_my = numpy.append(sld_my, 0) sld_mz = numpy.append(sld_mz, 0) pix_symbol = numpy.append(pix_symbol, atom_name) elif line[0:6].strip().count('CONECT') > 0: toks = line.split() num = int(toks[1]) - 1 val_list = [] for val in toks[2:]: try: int_val = int(val) except: break if int_val == 0: break val_list.append(int_val) #need val_list ordered for val in val_list: index = val - 1 if (pos_x[index], pos_x[num]) in x_line and \ (pos_y[index], pos_y[num]) in y_line and \ (pos_z[index], pos_z[num]) in z_line: continue x_line.append((pos_x[num], pos_x[index])) y_line.append((pos_y[num], pos_y[index])) z_line.append((pos_z[num], pos_z[index])) if len(x_line) > 0: x_lines.append(x_line) y_lines.append(y_line) z_lines.append(z_line) except: logging.error(sys.exc_value) output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz) output.set_conect_lines(x_line, y_line, z_line) output.filename = os.path.basename(path) output.set_pix_type('atom') output.set_pixel_symbols(pix_symbol) output.set_nodes() output.set_pixel_volumes(vol_pix) output.sld_unit = '1/A^(2)' return output except: raise RuntimeError, "%s is not a sld file" % path
[docs] def write(self, path, data): """ Write """ print "Not implemented... "
[docs]class SLDReader(object): """ Class to load ascii files (7 columns). """ ## File type type_name = "SLD ASCII" ## Wildcards type = ["sld files (*.SLD, *.sld)|*.sld", "txt files (*.TXT, *.txt)|*.txt", "all files (*.*)|*.*"] ## List of allowed extensions ext = ['.sld', '.SLD', '.txt', '.TXT', '.*']
[docs] def read(self, path): """ Load data file :param path: file path :return MagSLD: x, y, z, sld_n, sld_mx, sld_my, sld_mz :raise RuntimeError: when the file can't be opened :raise ValueError: when the length of the data vectors are inconsistent """ try: pos_x = numpy.zeros(0) pos_y = numpy.zeros(0) pos_z = numpy.zeros(0) sld_n = numpy.zeros(0) sld_mx = numpy.zeros(0) sld_my = numpy.zeros(0) sld_mz = numpy.zeros(0) try: # Use numpy to speed up loading input_f = numpy.loadtxt(path, dtype='float', skiprows=1, ndmin=1, unpack=True) pos_x = numpy.array(input_f[0]) pos_y = numpy.array(input_f[1]) pos_z = numpy.array(input_f[2]) sld_n = numpy.array(input_f[3]) sld_mx = numpy.array(input_f[4]) sld_my = numpy.array(input_f[5]) sld_mz = numpy.array(input_f[6]) ncols = len(input_f) if ncols == 8: vol_pix = numpy.array(input_f[7]) elif ncols == 7: vol_pix = None except: # For older version of numpy input_f = open(path, 'rb') buff = input_f.read() lines = buff.split('\n') input_f.close() for line in lines: toks = line.split() try: _pos_x = float(toks[0]) _pos_y = float(toks[1]) _pos_z = float(toks[2]) _sld_n = float(toks[3]) _sld_mx = float(toks[4]) _sld_my = float(toks[5]) _sld_mz = float(toks[6]) pos_x = numpy.append(pos_x, _pos_x) pos_y = numpy.append(pos_y, _pos_y) pos_z = numpy.append(pos_z, _pos_z) sld_n = numpy.append(sld_n, _sld_n) sld_mx = numpy.append(sld_mx, _sld_mx) sld_my = numpy.append(sld_my, _sld_my) sld_mz = numpy.append(sld_mz, _sld_mz) try: _vol_pix = float(toks[7]) vol_pix = numpy.append(vol_pix, _vol_pix) except: vol_pix = None except: # Skip non-data lines logging.error(sys.exc_value) output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz) output.filename = os.path.basename(path) output.set_pix_type('pixel') output.set_pixel_symbols('pixel') if vol_pix != None: output.set_pixel_volumes(vol_pix) return output except: raise RuntimeError, "%s is not a sld file" % path
[docs] def write(self, path, data): """ Write sld file :Param path: file path :Param data: MagSLD data object """ if path == None: raise ValueError, "Missing the file path." if data == None: raise ValueError, "Missing the data to save." x_val = data.pos_x y_val = data.pos_y z_val = data.pos_z vol_pix = data.vol_pix length = len(x_val) sld_n = data.sld_n if sld_n == None: sld_n = numpy.zeros(length) sld_mx = data.sld_mx if sld_mx == None: sld_mx = numpy.zeros(length) sld_my = numpy.zeros(length) sld_mz = numpy.zeros(length) else: sld_my = data.sld_my sld_mz = data.sld_mz out = open(path, 'w') # First Line: Column names out.write("X Y Z SLDN SLDMx SLDMy SLDMz VOLUMEpix") for ind in range(length): out.write("\n%g %g %g %g %g %g %g %g" % \ (x_val[ind], y_val[ind], z_val[ind], sld_n[ind], sld_mx[ind], sld_my[ind], sld_mz[ind], vol_pix[ind])) out.close()
[docs]class OMFData(object): """ OMF Data. """ _meshunit = "A" _valueunit = "A^(-2)" def __init__(self): """ Init for mag SLD """ self.filename = 'default' self.oommf = '' self.title = '' self.desc = '' self.meshtype = '' self.meshunit = self._meshunit self.valueunit = self._valueunit self.xbase = 0.0 self.ybase = 0.0 self.zbase = 0.0 self.xstepsize = 6.0 self.ystepsize = 6.0 self.zstepsize = 6.0 self.xnodes = 10.0 self.ynodes = 10.0 self.znodes = 10.0 self.xmin = 0.0 self.ymin = 0.0 self.zmin = 0.0 self.xmax = 60.0 self.ymax = 60.0 self.zmax = 60.0 self.mx = None self.my = None self.mz = None self.valuemultiplier = 1. self.valuerangeminmag = 0 self.valuerangemaxmag = 0 def __str__(self): """ doc strings """ _str = "Type: %s\n" % self.__class__.__name__ _str += "File: %s\n" % self.filename _str += "OOMMF: %s\n" % self.oommf _str += "Title: %s\n" % self.title _str += "Desc: %s\n" % self.desc _str += "meshtype: %s\n" % self.meshtype _str += "meshunit: %s\n" % str(self.meshunit) _str += "xbase: %s [%s]\n" % (str(self.xbase), self.meshunit) _str += "ybase: %s [%s]\n" % (str(self.ybase), self.meshunit) _str += "zbase: %s [%s]\n" % (str(self.zbase), self.meshunit) _str += "xstepsize: %s [%s]\n" % (str(self.xstepsize), self.meshunit) _str += "ystepsize: %s [%s]\n" % (str(self.ystepsize), self.meshunit) _str += "zstepsize: %s [%s]\n" % (str(self.zstepsize), self.meshunit) _str += "xnodes: %s\n" % str(self.xnodes) _str += "ynodes: %s\n" % str(self.ynodes) _str += "znodes: %s\n" % str(self.znodes) _str += "xmin: %s [%s]\n" % (str(self.xmin), self.meshunit) _str += "ymin: %s [%s]\n" % (str(self.ymin), self.meshunit) _str += "zmin: %s [%s]\n" % (str(self.zmin), self.meshunit) _str += "xmax: %s [%s]\n" % (str(self.xmax), self.meshunit) _str += "ymax: %s [%s]\n" % (str(self.ymax), self.meshunit) _str += "zmax: %s [%s]\n" % (str(self.zmax), self.meshunit) _str += "valueunit: %s\n" % self.valueunit _str += "valuemultiplier: %s\n" % str(self.valuemultiplier) _str += "ValueRangeMinMag:%s [%s]\n" % (str(self.valuerangeminmag), self.valueunit) _str += "ValueRangeMaxMag:%s [%s]\n" % (str(self.valuerangemaxmag), self.valueunit) return _str
[docs] def set_m(self, mx, my, mz): """ Set the Mx, My, Mz values """ self.mx = mx self.my = my self.mz = mz
[docs]class MagSLD(object): """ Magnetic SLD. """ pos_x = None pos_y = None pos_z = None sld_n = None sld_mx = None sld_my = None sld_mz = None # Units _pos_unit = 'A' _sld_unit = '1/A^(2)' _pix_type = 'pixel' def __init__(self, pos_x, pos_y, pos_z, sld_n=None, sld_mx=None, sld_my=None, sld_mz=None, vol_pix=None): """ Init for mag SLD :params : All should be numpy 1D array """ self.is_data = True self.filename = '' self.xstepsize = 6.0 self.ystepsize = 6.0 self.zstepsize = 6.0 self.xnodes = 10.0 self.ynodes = 10.0 self.znodes = 10.0 self.has_stepsize = False self.has_conect = False self.pos_unit = self._pos_unit self.sld_unit = self._sld_unit self.pix_type = 'pixel' self.pos_x = pos_x self.pos_y = pos_y self.pos_z = pos_z self.sld_n = sld_n self.line_x = None self.line_y = None self.line_z = None self.sld_mx = sld_mx self.sld_my = sld_my self.sld_mz = sld_mz self.vol_pix = vol_pix self.sld_m = None self.sld_phi = None self.sld_theta = None self.pix_symbol = None if sld_mx != None and sld_my != None and sld_mz != None: self.set_sldms(sld_mx, sld_my, sld_mz) self.set_nodes() def __str__(self): """ doc strings """ _str = "Type: %s\n" % self.__class__.__name__ _str += "File: %s\n" % self.filename _str += "Axis_unit: %s\n" % self.pos_unit _str += "SLD_unit: %s\n" % self.sld_unit return _str
[docs] def set_pix_type(self, pix_type): """ Set pixel type :Param pix_type: string, 'pixel' or 'atom' """ self.pix_type = pix_type
[docs] def set_sldn(self, sld_n): """ Sets neutron SLD """ if sld_n.__class__.__name__ == 'float': if self.is_data: # For data, put the value to only the pixels w non-zero M is_nonzero = (numpy.fabs(self.sld_mx) + numpy.fabs(self.sld_my) + numpy.fabs(self.sld_mz)).nonzero() self.sld_n = numpy.zeros(len(self.pos_x)) if len(self.sld_n[is_nonzero]) > 0: self.sld_n[is_nonzero] = sld_n else: self.sld_n.fill(sld_n) else: # For non-data, put the value to all the pixels self.sld_n = numpy.ones(len(self.pos_x)) * sld_n else: self.sld_n = sld_n
[docs] def set_sldms(self, sld_mx, sld_my, sld_mz): r""" Sets (\|m\|, m_theta, m_phi) """ if sld_mx.__class__.__name__ == 'float': self.sld_mx = numpy.ones(len(self.pos_x)) * sld_mx else: self.sld_mx = sld_mx if sld_my.__class__.__name__ == 'float': self.sld_my = numpy.ones(len(self.pos_x)) * sld_my else: self.sld_my = sld_my if sld_mz.__class__.__name__ == 'float': self.sld_mz = numpy.ones(len(self.pos_x)) * sld_mz else: self.sld_mz = sld_mz sld_m = numpy.sqrt(sld_mx * sld_mx + sld_my * sld_my + \ sld_mz * sld_mz) self.sld_m = sld_m
[docs] def set_pixel_symbols(self, symbol='pixel'): """ Set pixel :Params pixel: str; pixel or atomic symbol, or array of strings """ if self.sld_n == None: return if symbol.__class__.__name__ == 'str': self.pix_symbol = numpy.repeat(symbol, len(self.sld_n)) else: self.pix_symbol = symbol
[docs] def set_pixel_volumes(self, vol): """ Set pixel volumes :Params pixel: str; pixel or atomic symbol, or array of strings """ if self.sld_n == None: return if vol.__class__.__name__ == 'ndarray': self.vol_pix = vol elif vol.__class__.__name__.count('float') > 0: self.vol_pix = numpy.repeat(vol, len(self.sld_n)) else: self.vol_pix = None
[docs] def get_sldn(self): """ Returns nuclear sld """ return self.sld_n
[docs] def set_nodes(self): """ Set xnodes, ynodes, and znodes """ self.set_stepsize() if self.pix_type == 'pixel': try: xdist = (max(self.pos_x) - min(self.pos_x)) / self.xstepsize ydist = (max(self.pos_y) - min(self.pos_y)) / self.ystepsize zdist = (max(self.pos_z) - min(self.pos_z)) / self.zstepsize self.xnodes = int(xdist) + 1 self.ynodes = int(ydist) + 1 self.znodes = int(zdist) + 1 except: self.xnodes = None self.ynodes = None self.znodes = None else: self.xnodes = None self.ynodes = None self.znodes = None
[docs] def set_stepsize(self): """ Set xtepsize, ystepsize, and zstepsize """ if self.pix_type == 'pixel': try: xpos_pre = self.pos_x[0] ypos_pre = self.pos_y[0] zpos_pre = self.pos_z[0] for x_pos in self.pos_x: if xpos_pre != x_pos: self.xstepsize = numpy.fabs(x_pos - xpos_pre) break for y_pos in self.pos_y: if ypos_pre != y_pos: self.ystepsize = numpy.fabs(y_pos - ypos_pre) break for z_pos in self.pos_z: if zpos_pre != z_pos: self.zstepsize = numpy.fabs(z_pos - zpos_pre) break #default pix volume self.vol_pix = numpy.ones(len(self.pos_x)) vol = self.xstepsize * self.ystepsize * self.zstepsize self.set_pixel_volumes(vol) self.has_stepsize = True except: self.xstepsize = None self.ystepsize = None self.zstepsize = None self.vol_pix = None self.has_stepsize = False else: self.xstepsize = None self.ystepsize = None self.zstepsize = None self.has_stepsize = True return self.xstepsize, self.ystepsize, self.zstepsize
[docs] def set_conect_lines(self, line_x, line_y, line_z): """ Set bonding line data if taken from pdb """ if line_x.__class__.__name__ != 'list' or len(line_x) < 1: return if line_y.__class__.__name__ != 'list' or len(line_y) < 1: return if line_z.__class__.__name__ != 'list' or len(line_z) < 1: return self.has_conect = True self.line_x = line_x self.line_y = line_y self.line_z = line_z
[docs]def test_load(): """ Test code """ from mpl_toolkits.mplot3d import Axes3D current_dir = os.path.abspath(os.path.curdir) print current_dir for i in range(6): current_dir, _ = os.path.split(current_dir) tfile = os.path.join(current_dir, "test", "CoreXY_ShellZ.txt") ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf") if os.path.isfile(tfile): tfpath = tfile ofpath = ofile break reader = SLDReader() oreader = OMFReader() output = reader.read(tfpath) ooutput = oreader.read(ofpath) foutput = OMF2SLD() foutput.set_data(ooutput) import matplotlib.pyplot as plt fig = plt.figure() ax = Axes3D(fig) ax.plot(output.pos_x, output.pos_y, output.pos_z, '.', c="g", alpha=0.7, markeredgecolor='gray', rasterized=True) gap = 7 max_mx = max(output.sld_mx) max_my = max(output.sld_my) max_mz = max(output.sld_mz) max_m = max(max_mx, max_my, max_mz) x2 = output.pos_x+output.sld_mx/max_m * gap y2 = output.pos_y+output.sld_my/max_m * gap z2 = output.pos_z+output.sld_mz/max_m * gap x_arrow = numpy.column_stack((output.pos_x, x2)) y_arrow = numpy.column_stack((output.pos_y, y2)) z_arrow = numpy.column_stack((output.pos_z, z2)) unit_x2 = output.sld_mx / max_m unit_y2 = output.sld_my / max_m unit_z2 = output.sld_mz / max_m color_x = numpy.fabs(unit_x2 * 0.8) color_y = numpy.fabs(unit_y2 * 0.8) color_z = numpy.fabs(unit_z2 * 0.8) colors = numpy.column_stack((color_x, color_y, color_z)) plt.show()
[docs]def test(): """ Test code """ current_dir = os.path.abspath(os.path.curdir) for i in range(3): current_dir, _ = os.path.split(current_dir) ofile = os.path.join(current_dir, "test", "A_Raw_Example-1.omf") if os.path.isfile(ofile): ofpath = ofile break oreader = OMFReader() ooutput = oreader.read(ofpath) foutput = OMF2SLD() foutput.set_data(ooutput) writer = SLDReader() writer.write(os.path.join(os.path.dirname(ofpath), "out.txt"), foutput.output) model = GenSAS() model.set_sld_data(foutput.output) x = numpy.arange(1000)/10000. + 1e-5 y = numpy.arange(1000)/10000. + 1e-5 i = numpy.zeros(1000) model.runXY([x, y, i])
if __name__ == "__main__": test() test_load()