| 1 | """ |
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| 2 | This module provide GUI for the neutron scattering length density calculator |
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| 3 | @author: Gervaise B. Alina |
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| 4 | """ |
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| 5 | |
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| 6 | import wx |
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| 7 | import math |
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| 8 | import sys |
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| 9 | |
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| 10 | from sans.guiframe.utils import format_number, check_float |
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| 11 | from sans.guicomm.events import StatusEvent |
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| 12 | |
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| 13 | # the calculator default value for wavelength is 6 |
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| 14 | import periodictable |
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| 15 | from periodictable import formula |
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| 16 | from periodictable.xsf import xray_energy, xray_sld_from_atoms |
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| 17 | from periodictable.constants import avogadro_number |
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| 18 | from periodictable.nsf import neutron_scattering |
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| 19 | |
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| 20 | WAVELENGTH = 6.0 |
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| 21 | _BOX_WIDTH = 76 |
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| 22 | _STATICBOX_WIDTH = 350 |
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| 23 | _SCALE = 1e-6 |
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| 24 | |
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| 25 | #SLD panel size |
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| 26 | if sys.platform.count("win32")>0: |
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| 27 | _STATICBOX_WIDTH = 350 |
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| 28 | PANEL_SIZE = 400 |
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| 29 | FONT_VARIANT = 0 |
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| 30 | else: |
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| 31 | _STATICBOX_WIDTH = 380 |
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| 32 | PANEL_SIZE = 430 |
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| 33 | FONT_VARIANT = 1 |
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| 34 | |
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| 35 | class SldPanel(wx.Panel): |
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| 36 | """ |
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| 37 | Provides the SLD calculator GUI. |
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| 38 | """ |
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| 39 | ## Internal nickname for the window, used by the AUI manager |
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| 40 | window_name = "SLD Calculator" |
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| 41 | ## Name to appear on the window title bar |
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| 42 | window_caption = "SLD Calculator" |
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| 43 | ## Flag to tell the AUI manager to put this panel in the center pane |
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| 44 | CENTER_PANE = True |
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| 45 | def __init__(self, parent, base=None, id=-1): |
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| 46 | wx.Panel.__init__(self, parent, id = id) |
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| 47 | #Font size |
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| 48 | self.SetWindowVariant(variant=FONT_VARIANT) |
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| 49 | # Object that receive status event |
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| 50 | self.base = base |
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| 51 | self.wavelength = WAVELENGTH |
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| 52 | #Draw the panel |
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| 53 | self._do_layout() |
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| 54 | self.SetAutoLayout(True) |
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| 55 | self.Layout() |
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| 56 | |
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| 57 | def _do_layout(self): |
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| 58 | """ |
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| 59 | Draw window content |
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| 60 | """ |
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| 61 | unit_a = '[A]' |
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| 62 | unit_density = '[g/cm^(3)]' |
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| 63 | unit_sld = '[1/A^(2)]' |
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| 64 | unit_cm1 ='[1/cm]' |
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| 65 | unit_cm ='[cm]' |
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| 66 | sizer_input = wx.GridBagSizer(5,5) |
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| 67 | sizer_output = wx.GridBagSizer(5,5) |
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| 68 | sizer_button = wx.BoxSizer(wx.HORIZONTAL) |
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| 69 | sizer1 = wx.BoxSizer(wx.HORIZONTAL) |
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| 70 | sizer2 = wx.BoxSizer(wx.HORIZONTAL) |
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| 71 | sizer3 = wx.BoxSizer(wx.HORIZONTAL) |
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| 72 | #---------inputs---------------- |
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| 73 | inputbox = wx.StaticBox(self, -1, "Input") |
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| 74 | boxsizer1 = wx.StaticBoxSizer(inputbox, wx.VERTICAL) |
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| 75 | boxsizer1.SetMinSize((_STATICBOX_WIDTH,-1)) |
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| 76 | |
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| 77 | compound_txt = wx.StaticText(self, -1, 'Compound ') |
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| 78 | self.compound_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 79 | density_txt = wx.StaticText(self, -1, 'Density ') |
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| 80 | self.density_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 81 | unit_density_txt = wx.StaticText(self, -1, unit_density) |
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| 82 | wavelength_txt = wx.StaticText(self, -1, 'Wavelength ') |
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| 83 | self.wavelength_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 84 | self.wavelength_ctl.SetValue(str(self.wavelength)) |
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| 85 | unit_a_txt = wx.StaticText(self, -1, unit_a) |
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| 86 | iy = 0 |
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| 87 | ix = 0 |
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| 88 | sizer_input.Add(compound_txt,(iy, ix),(1,1),\ |
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| 89 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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| 90 | ix +=1 |
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| 91 | sizer_input.Add(self.compound_ctl,(iy, ix),(1,1),\ |
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| 92 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 93 | iy += 1 |
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| 94 | ix = 0 |
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| 95 | sizer_input.Add(density_txt,(iy, ix),(1,1),\ |
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| 96 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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| 97 | ix += 1 |
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| 98 | sizer_input.Add(self.density_ctl, (iy, ix), (1,1),\ |
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| 99 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 100 | ix +=1 |
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| 101 | sizer_input.Add(unit_density_txt,(iy, ix),(1,1),\ |
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| 102 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 103 | iy += 1 |
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| 104 | ix = 0 |
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| 105 | sizer_input.Add(wavelength_txt, (iy, ix),(1,1),\ |
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| 106 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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| 107 | ix += 1 |
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| 108 | sizer_input.Add(self.wavelength_ctl,(iy, ix),(1,1),\ |
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| 109 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 110 | ix += 1 |
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| 111 | sizer_input.Add(unit_a_txt,(iy, ix),(1,1),\ |
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| 112 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 113 | boxsizer1.Add( sizer_input ) |
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| 114 | sizer1.Add(boxsizer1,0, wx.EXPAND | wx.ALL, 10) |
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| 115 | #---------Outputs sizer-------- |
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| 116 | outputbox = wx.StaticBox(self, -1, "Output") |
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| 117 | boxsizer2 = wx.StaticBoxSizer(outputbox, wx.VERTICAL) |
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| 118 | boxsizer2.SetMinSize((_STATICBOX_WIDTH,-1)) |
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| 119 | |
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| 120 | i_complex = '- i' |
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| 121 | neutron_sld_txt = wx.StaticText(self, -1, 'Neutron SLD') |
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| 122 | self.neutron_sld_reel_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 123 | self.neutron_sld_reel_ctl.SetEditable(False) |
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| 124 | self.neutron_sld_reel_ctl.SetToolTipString("Neutron SLD real.") |
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| 125 | self.neutron_sld_im_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 126 | self.neutron_sld_im_ctl.SetEditable(False) |
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| 127 | self.neutron_sld_im_ctl.SetToolTipString("Neutron SLD imaginary.") |
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| 128 | neutron_sld_units_txt = wx.StaticText(self, -1, unit_sld) |
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| 129 | |
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| 130 | cu_ka_sld_txt = wx.StaticText(self, -1, 'Cu Ka SLD') |
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| 131 | self.cu_ka_sld_reel_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 132 | self.cu_ka_sld_reel_ctl.SetEditable(False) |
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| 133 | self.cu_ka_sld_reel_ctl.SetToolTipString("Cu Ka SLD real.") |
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| 134 | self.cu_ka_sld_im_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 135 | self.cu_ka_sld_im_ctl.SetEditable(False) |
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| 136 | self.cu_ka_sld_im_ctl.SetToolTipString("Cu Ka SLD imaginary.") |
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| 137 | cu_ka_sld_units_txt = wx.StaticText(self, -1, unit_sld) |
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| 138 | |
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| 139 | mo_ka_sld_txt = wx.StaticText(self, -1, 'Mo Ka SLD') |
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| 140 | self.mo_ka_sld_reel_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 141 | self.mo_ka_sld_reel_ctl.SetEditable(False) |
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| 142 | self.mo_ka_sld_reel_ctl.SetToolTipString("Mo Ka SLD real.") |
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| 143 | self.mo_ka_sld_im_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 144 | self.mo_ka_sld_im_ctl.SetEditable(False) |
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| 145 | self.mo_ka_sld_im_ctl.SetToolTipString("Mo Ka SLD imaginary.") |
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| 146 | mo_ka_sld_units_txt = wx.StaticText(self, -1, unit_sld) |
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| 147 | |
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| 148 | neutron_inc_txt = wx.StaticText(self, -1, 'Neutron Inc. Xs') |
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| 149 | self.neutron_inc_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 150 | self.neutron_inc_ctl.SetEditable(False) |
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| 151 | self.neutron_inc_ctl.SetToolTipString("Neutron Inc. Xs") |
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| 152 | neutron_inc_units_txt = wx.StaticText(self, -1, unit_cm1) |
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| 153 | |
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| 154 | neutron_abs_txt = wx.StaticText(self, -1, 'Neutron Abs. Xs') |
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| 155 | self.neutron_abs_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 156 | self.neutron_abs_ctl.SetEditable(False) |
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| 157 | self.neutron_abs_ctl.SetToolTipString("Neutron Abs. Xs") |
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| 158 | neutron_abs_units_txt = wx.StaticText(self, -1, unit_cm1) |
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| 159 | |
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| 160 | neutron_length_txt = wx.StaticText(self, -1, 'Neutron 1/e length') |
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| 161 | self.neutron_length_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH,-1)) |
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| 162 | self.neutron_length_ctl.SetEditable(False) |
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| 163 | self.neutron_length_ctl.SetToolTipString("Neutron 1/e length") |
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| 164 | neutron_length_units_txt = wx.StaticText(self, -1, unit_cm) |
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| 165 | |
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| 166 | iy = 0 |
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| 167 | ix = 0 |
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| 168 | sizer_output.Add(neutron_sld_txt,(iy, ix),(1,1), |
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| 169 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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| 170 | ix += 1 |
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| 171 | sizer_output.Add(self.neutron_sld_reel_ctl,(iy, ix),(1,1), |
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| 172 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 173 | ix += 1 |
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| 174 | sizer_output.Add(wx.StaticText(self, -1, i_complex) |
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| 175 | ,(iy, ix),(1,1),wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 176 | ix +=1 |
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| 177 | sizer_output.Add(self.neutron_sld_im_ctl |
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| 178 | ,(iy, ix),(1,1),wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 179 | ix +=1 |
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| 180 | sizer_output.Add(neutron_sld_units_txt |
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| 181 | ,(iy, ix),(1,1),wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 182 | iy += 1 |
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| 183 | ix = 0 |
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| 184 | sizer_output.Add(cu_ka_sld_txt,(iy, ix),(1,1), |
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| 185 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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| 186 | ix +=1 |
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| 187 | sizer_output.Add(self.cu_ka_sld_reel_ctl,(iy, ix),(1,1), |
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| 188 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 189 | ix +=1 |
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| 190 | sizer_output.Add(wx.StaticText(self, -1, i_complex) |
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| 191 | ,(iy, ix),(1,1),wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 192 | ix += 1 |
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| 193 | sizer_output.Add(self.cu_ka_sld_im_ctl |
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| 194 | ,(iy, ix),(1,1),wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 195 | ix += 1 |
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| 196 | sizer_output.Add(cu_ka_sld_units_txt |
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| 197 | ,(iy, ix),(1,1),wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 198 | iy += 1 |
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| 199 | ix = 0 |
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| 200 | sizer_output.Add(mo_ka_sld_txt,(iy, ix),(1,1), |
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| 201 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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| 202 | ix +=1 |
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| 203 | sizer_output.Add(self.mo_ka_sld_reel_ctl,(iy, ix),(1,1), |
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| 204 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 205 | ix +=1 |
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| 206 | sizer_output.Add(wx.StaticText(self, -1, i_complex) |
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| 207 | ,(iy, ix),(1,1),wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 208 | ix += 1 |
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| 209 | sizer_output.Add(self.mo_ka_sld_im_ctl |
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| 210 | ,(iy, ix),(1,1),wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 211 | ix +=1 |
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| 212 | sizer_output.Add(mo_ka_sld_units_txt |
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| 213 | ,(iy, ix),(1,1),wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 214 | iy += 1 |
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| 215 | ix = 0 |
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| 216 | sizer_output.Add(neutron_inc_txt,(iy, ix),(1,1), |
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| 217 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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| 218 | ix += 1 |
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| 219 | sizer_output.Add(self.neutron_inc_ctl,(iy, ix),(1,1), |
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| 220 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 221 | ix += 2 |
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| 222 | sizer_output.Add(neutron_inc_units_txt,(iy, ix),(1,1), |
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| 223 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 224 | iy += 1 |
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| 225 | ix = 0 |
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| 226 | sizer_output.Add(neutron_abs_txt, (iy, ix), (1,1), |
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| 227 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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| 228 | ix += 1 |
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| 229 | sizer_output.Add(self.neutron_abs_ctl, (iy, ix), (1,1), |
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| 230 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 231 | ix +=2 |
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| 232 | sizer_output.Add(neutron_abs_units_txt, (iy, ix), (1,1), |
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| 233 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 234 | iy += 1 |
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| 235 | ix = 0 |
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| 236 | sizer_output.Add(neutron_length_txt, (iy, ix), (1,1), |
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| 237 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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| 238 | ix +=1 |
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| 239 | sizer_output.Add(self.neutron_length_ctl, (iy, ix), (1,1), |
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| 240 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 241 | ix += 2 |
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| 242 | sizer_output.Add(neutron_length_units_txt, (iy, ix), (1,1), |
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| 243 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 244 | boxsizer2.Add( sizer_output ) |
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| 245 | sizer2.Add(boxsizer2,0, wx.EXPAND|wx.ALL, 10) |
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| 246 | #-----Button sizer------------ |
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| 247 | |
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| 248 | id = wx.NewId() |
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| 249 | button_calculate = wx.Button(self, id, "Calculate") |
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| 250 | button_calculate.SetToolTipString("Calculate SLD.") |
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| 251 | self.Bind(wx.EVT_BUTTON, self.calculateSld, id = id) |
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| 252 | |
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| 253 | sizer_button.Add((250, 20), 1, wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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| 254 | sizer_button.Add(button_calculate, 0, wx.RIGHT|wx.ADJUST_MINSIZE,20) |
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| 255 | sizer3.Add(sizer_button) |
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| 256 | #---------layout---------------- |
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| 257 | vbox = wx.BoxSizer(wx.VERTICAL) |
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| 258 | vbox.Add(sizer1) |
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| 259 | vbox.Add(sizer2) |
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| 260 | vbox.Add(sizer3) |
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| 261 | vbox.Fit(self) |
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| 262 | self.SetSizer(vbox) |
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| 263 | |
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| 264 | def calculate_xray_sld(self, element): |
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| 265 | """ |
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| 266 | Get an element and compute the corresponding SLD for a given formula |
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| 267 | |
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| 268 | :param element: elements a string of existing atom |
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| 269 | |
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| 270 | """ |
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| 271 | myformula = formula(str(element)) |
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| 272 | if len(myformula.atoms) != 1: |
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| 273 | return |
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| 274 | element = myformula.atoms.keys()[0] |
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| 275 | energy = xray_energy(element.K_alpha) |
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| 276 | |
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| 277 | self.sld_formula = formula(str(user_formula), density=self.density) |
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| 278 | atom = self.sld_formula.atoms |
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| 279 | return xray_sld_from_atoms(atom, density=self.density, energy= energy) |
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| 280 | |
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| 281 | def check_inputs(self): |
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| 282 | """Check validity user inputs""" |
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| 283 | flag = True |
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| 284 | |
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| 285 | if check_float(self.density_ctl): |
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| 286 | self.density = float(self.density_ctl.GetValue()) |
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| 287 | else: |
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| 288 | flag = False |
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| 289 | raise ValueError,"Error for Density value :expect float" |
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| 290 | |
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| 291 | self.wavelength = self.wavelength_ctl.GetValue() |
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| 292 | if self.wavelength.lstrip().rstrip() == "": |
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| 293 | self.wavelength = WAVELENGTH |
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| 294 | else: |
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| 295 | if check_float(self.wavelength_ctl): |
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| 296 | self.wavelength = float(self.wavelength) |
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| 297 | else: |
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| 298 | flag = False |
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| 299 | raise ValueError,"Error for wavelength value :expect float" |
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| 300 | |
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| 301 | self.compound = self.compound_ctl.GetValue().lstrip().rstrip() |
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| 302 | if self.compound != "": |
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| 303 | self.compound_ctl.SetBackgroundColour(wx.WHITE) |
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| 304 | self.compound_ctl.Refresh() |
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| 305 | else: |
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| 306 | self.compound_ctl.SetBackgroundColour("pink") |
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| 307 | self.compound_ctl.Refresh() |
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| 308 | flag = False |
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| 309 | raise ValueError, "Enter a formula" |
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| 310 | return flag |
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| 311 | |
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| 312 | def calculate_sld_helper(self, element, density, molecule_formula): |
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| 313 | """ |
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| 314 | Get an element and compute the corresponding SLD for a given formula |
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| 315 | |
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| 316 | :param element: elements a string of existing atom |
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| 317 | |
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| 318 | """ |
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| 319 | element_formula = formula(str(element)) |
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| 320 | if len(element_formula.atoms) != 1: |
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| 321 | return |
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| 322 | element = element_formula.atoms.keys()[0] |
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| 323 | energy = xray_energy(element.K_alpha) |
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| 324 | atom = molecule_formula.atoms |
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| 325 | return xray_sld_from_atoms(atom, density=density, energy=energy) |
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| 326 | |
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| 327 | |
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| 328 | def calculateSld(self, event): |
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| 329 | """ |
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| 330 | Calculate the neutron scattering density length of a molecule |
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| 331 | """ |
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| 332 | try: |
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| 333 | #Check validity user inputs |
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| 334 | if self.check_inputs(): |
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| 335 | #get ready to compute |
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| 336 | try: |
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| 337 | self.sld_formula = formula(self.compound, density=self.density) |
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| 338 | except: |
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| 339 | if self.base is not None: |
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| 340 | msg = "SLD Calculator: %s" %(sys.exc_value) |
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| 341 | wx.PostEvent(self.base, StatusEvent(status=msg)) |
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| 342 | else: |
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| 343 | raise |
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| 344 | return |
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| 345 | |
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| 346 | |
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| 347 | (sld_real, sld_im, sld_inc), (coh,absorp,incoh), \ |
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| 348 | length = neutron_scattering(self.compound, |
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| 349 | self.density, self.wavelength) |
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| 350 | cu_real, cu_im = self.calculate_sld_helper(element="Cu", |
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| 351 | density=self.density, |
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| 352 | molecule_formula=self.sld_formula) |
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| 353 | mo_real, mo_im = self.calculate_sld_helper(element="Mo", |
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| 354 | density=self.density, |
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| 355 | molecule_formula=self.sld_formula) |
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| 356 | # set neutron sld values |
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| 357 | self.neutron_sld_reel_ctl.SetValue(format_number(sld_real * _SCALE)) |
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| 358 | self.neutron_sld_im_ctl.SetValue(format_number(math.fabs(sld_im) * _SCALE)) |
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| 359 | # Compute the Cu SLD |
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| 360 | self.cu_ka_sld_reel_ctl.SetValue(format_number(cu_real *_SCALE)) |
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| 361 | self.cu_ka_sld_im_ctl.SetValue(format_number(math.fabs(cu_im )* _SCALE)) |
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| 362 | # Compute the Mo SLD |
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| 363 | self.mo_ka_sld_reel_ctl.SetValue(format_number(mo_real *_SCALE)) |
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| 364 | self.mo_ka_sld_im_ctl.SetValue(format_number(math.fabs(mo_im)* _SCALE)) |
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| 365 | # set incoherence and absorption |
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| 366 | self.neutron_inc_ctl.SetValue(format_number(incoh)) |
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| 367 | self.neutron_abs_ctl.SetValue(format_number(absorp)) |
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| 368 | # Neutron length |
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| 369 | self.neutron_length_ctl.SetValue(format_number(length)) |
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| 370 | # display wavelength |
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| 371 | self.wavelength_ctl.SetValue(str(self.wavelength)) |
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| 372 | except: |
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| 373 | if self.base is not None: |
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| 374 | msg = "SLD Calculator: %s"%(sys.exc_value) |
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| 375 | wx.PostEvent(self.base, StatusEvent(status=msg)) |
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| 376 | else: |
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| 377 | raise |
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| 378 | return |
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| 379 | |
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| 380 | |
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| 381 | class SldWindow(wx.Frame): |
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| 382 | def __init__(self, parent=None, id=1, title="SLD Calculator",base=None): |
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| 383 | wx.Frame.__init__(self, parent, id, title, size=( PANEL_SIZE, PANEL_SIZE)) |
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| 384 | |
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| 385 | self.panel = SldPanel(self, base=base) |
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| 386 | self.Centre() |
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| 387 | self.Show(True) |
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| 388 | |
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| 389 | class ViewApp(wx.App): |
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| 390 | def OnInit(self): |
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| 391 | frame = SldWindow(None, -1, 'SLD Calculator') |
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| 392 | frame.Show(True) |
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| 393 | self.SetTopWindow(frame) |
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| 394 | |
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| 395 | return True |
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| 396 | |
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| 397 | |
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| 398 | if __name__ == "__main__": |
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| 399 | app = ViewApp(0) |
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| 400 | app.MainLoop() |
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