Ignore:
Timestamp:
Sep 5, 2017 2:53:09 PM (7 years ago)
Author:
Paul Kienzle <pkienzle@…>
Branches:
master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, magnetic_scatt, release-4.2.2, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload
Children:
96f00a0
Parents:
78d0a9b (diff), f9ba422 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

Merge branch 'master' into ticket-639-katex

Location:
src/sas/sasgui/perspectives/calculator
Files:
22 added
22 deleted
10 edited

Legend:

Unmodified
Added
Removed

  • src/sas/sasgui/perspectives/calculator/model_editor.py

    ra1b8fee r07ec714  
    643643        self.name_hsizer = None 
    644644        self.name_tcl = None 
     645        self.overwrite_cb = None 
    645646        self.desc_sizer = None 
    646647        self.desc_tcl = None 
    … …  
    657658        self.warning = "" 
    658659        #This does not seem to be used anywhere so commenting out for now 
    659         #    -- PDB 2/26/17  
     660        #    -- PDB 2/26/17 
    660661        #self._description = "New Plugin Model" 
    661662        self.function_tcl = None 
    … …  
    689690        #title name [string] 
    690691        name_txt = wx.StaticText(self, -1, 'Function Name : ') 
    691         overwrite_cb = wx.CheckBox(self, -1, "Overwrite existing plugin model of this name?", (10, 10)) 
    692         overwrite_cb.SetValue(False) 
    693         overwrite_cb.SetToolTipString("Overwrite it if already exists?") 
    694         wx.EVT_CHECKBOX(self, overwrite_cb.GetId(), self.on_over_cb) 
     692        self.overwrite_cb = wx.CheckBox(self, -1, "Overwrite existing plugin model of this name?", (10, 10)) 
     693        self.overwrite_cb.SetValue(False) 
     694        self.overwrite_cb.SetToolTipString("Overwrite it if already exists?") 
     695        wx.EVT_CHECKBOX(self, self.overwrite_cb.GetId(), self.on_over_cb) 
    695696        self.name_tcl = wx.TextCtrl(self, -1, size=(PANEL_WIDTH * 3 / 5, -1)) 
    696697        self.name_tcl.Bind(wx.EVT_TEXT_ENTER, self.on_change_name) 
    … …  
    700701        self.name_tcl.SetToolTipString(hint_name) 
    701702        self.name_hsizer.AddMany([(self.name_tcl, 0, wx.LEFT | wx.TOP, 0), 
    702                                   (overwrite_cb, 0, wx.LEFT, 20)]) 
     703                                  (self.overwrite_cb, 0, wx.LEFT, 20)]) 
    703704        self.name_sizer.AddMany([(name_txt, 0, wx.LEFT | wx.TOP, 10), 
    704705                                 (self.name_hsizer, 0, 
    … …  
    740741        self.param_sizer.AddMany([(param_txt, 0, wx.LEFT, 10), 
    741742                                  (self.param_tcl, 1, wx.EXPAND | wx.ALL, 10)]) 
    742          
     743 
    743744        # Parameters with polydispersity 
    744745        pd_param_txt = wx.StaticText(self, -1, 'Fit Parameters requiring ' + \ 
    … …  
    755756        self.pd_param_tcl.setDisplayLineNumbers(True) 
    756757        self.pd_param_tcl.SetToolTipString(pd_param_tip) 
    757          
     758 
    758759        self.param_sizer.AddMany([(pd_param_txt, 0, wx.LEFT, 10), 
    759760                                  (self.pd_param_tcl, 1, wx.EXPAND | wx.ALL, 10)]) 
    … …  
    995996            info = 'Error' 
    996997            color = 'red' 
     998            self.overwrite_cb.SetValue(True) 
     999            self.overwrite_name = True 
    9971000        else: 
    9981001            self._notes = result 
    … …  
    10301033        if has_scipy: 
    10311034            lines.insert(0, 'import scipy') 
    1032          
    1033         # Think about 2D later         
     1035 
     1036        # Think about 2D later 
    10341037        #self.is_2d = func_str.count("#self.ndim = 2") 
    10351038        #line_2d = '' 
    10361039        #if self.is_2d: 
    10371040        #    line_2d = CUSTOM_2D_TEMP.split('\n') 
    1038          
    1039         # Also think about test later         
     1041 
     1042        # Also think about test later 
    10401043        #line_test = TEST_TEMPLATE.split('\n') 
    10411044        #local_params = '' 
    … …  
    10431046        spaces4  = ' '*4 
    10441047        spaces13 = ' '*13 
    1045         spaces16 = ' '*16      
     1048        spaces16 = ' '*16 
    10461049        param_names = []    # to store parameter names 
    10471050        has_scipy = func_str.count("scipy.") 
    … …  
    10551058            out_f.write(line + '\n') 
    10561059            if line.count('#name'): 
    1057                 out_f.write('name = "%s" \n' % name)                
     1060                out_f.write('name = "%s" \n' % name) 
    10581061            elif line.count('#title'): 
    1059                 out_f.write('title = "User model for %s"\n' % name)                
     1062                out_f.write('title = "User model for %s"\n' % name) 
    10601063            elif line.count('#description'): 
    1061                 out_f.write('description = "%s"\n' % desc_str)                
     1064                out_f.write('description = "%s"\n' % desc_str) 
    10621065            elif line.count('#parameters'): 
    10631066                out_f.write('parameters = [ \n') 
    … …  
    10651068                    p_line = param_line.lstrip().rstrip() 
    10661069                    if p_line: 
    1067                         pname, pvalue = self.get_param_helper(p_line) 
     1070                        pname, pvalue, desc = self.get_param_helper(p_line) 
    10681071                        param_names.append(pname) 
    1069                         out_f.write("%s['%s', '', %s, [-numpy.inf, numpy.inf], '', ''],\n" % (spaces16, pname, pvalue)) 
     1072                        out_f.write("%s['%s', '', %s, [-numpy.inf, numpy.inf], '', '%s'],\n" % (spaces16, pname, pvalue, desc)) 
    10701073                for param_line in pd_param_str.split('\n'): 
    10711074                    p_line = param_line.lstrip().rstrip() 
    10721075                    if p_line: 
    1073                         pname, pvalue = self.get_param_helper(p_line) 
     1076                        pname, pvalue, desc = self.get_param_helper(p_line) 
    10741077                        param_names.append(pname) 
    1075                         out_f.write("%s['%s', '', %s, [-numpy.inf, numpy.inf], 'volume', ''],\n" % (spaces16, pname, pvalue)) 
     1078                        out_f.write("%s['%s', '', %s, [-numpy.inf, numpy.inf], 'volume', '%s'],\n" % (spaces16, pname, pvalue, desc)) 
    10761079                out_f.write('%s]\n' % spaces13) 
    1077              
     1080 
    10781081        # No form_volume or ER available in simple model editor 
    10791082        out_f.write('def form_volume(*arg): \n') 
    … …  
    10821085        out_f.write('def ER(*arg): \n') 
    10831086        out_f.write('    return 1.0 \n') 
    1084          
     1087 
    10851088        # function to compute 
    10861089        out_f.write('\n') 
    … …  
    10911094        for func_line in func_str.split('\n'): 
    10921095            out_f.write('%s%s\n' % (spaces4, func_line)) 
    1093          
     1096 
    10941097        Iqxy_string = 'return Iq(numpy.sqrt(x**2+y**2) ' 
    1095              
     1098 
    10961099        out_f.write('\n') 
    10971100        out_f.write('def Iqxy(x, y ') 
    … …  
    11131116        items = line.split(";") 
    11141117        for item in items: 
    1115             name = item.split("=")[0].lstrip().rstrip() 
     1118            name = item.split("=")[0].strip() 
     1119            description = "" 
    11161120            try: 
    1117                 value = item.split("=")[1].lstrip().rstrip() 
     1121                value = item.split("=")[1].strip() 
     1122                if value.count("#"): 
     1123                    # If line ends in a comment, remove it before parsing float 
     1124                    index = value.index("#") 
     1125                    description = value[(index + 1):].strip() 
     1126                    value = value[:value.index("#")].strip() 
    11181127                float(value) 
    1119             except: 
     1128            except ValueError: 
    11201129                value = 1.0 # default 
    11211130 
    1122         return name, value 
     1131        return name, value, description 
    11231132 
    11241133    def set_function_helper(self, line): 
    … …  
    12041213import numpy 
    12051214 
    1206 #name  
     1215#name 
    12071216 
    12081217#title 
    … …  
    12101219#description 
    12111220 
    1212 #parameters  
     1221#parameters 
    12131222 
    12141223""" 

  • src/sas/sasgui/perspectives/calculator/pyconsole.py

    r7432acb r4627657  
    3737    Iqxy = model.evalDistribution([qx, qy]) 
    3838 
    39     result = """ 
    40     Iq(%s) = %s 
    41     Iqxy(%s, %s) = %s 
    42     """%(q, Iq, qx, qy, Iqxy) 
     39    # check the model's unit tests run 
     40    from sasmodels.model_test import run_one 
     41    result = run_one(path) 
    4342 
    4443    return result 
    … …  
    8988        ok = wx.Button(self, wx.ID_OK, "OK") 
    9089 
    91         # Mysterious constraint layouts from  
     90        # Mysterious constraint layouts from 
    9291        # https://www.wxpython.org/docs/api/wx.lib.layoutf.Layoutf-class.html 
    9392        lc = layoutf.Layoutf('t=t5#1;b=t5#2;l=l5#1;r=r5#1', (self,ok)) 

  • src/sas/sasgui/perspectives/calculator/media/density_calculator_help.rst

    rd85c194 r6aad2e8  
    29294) Click the 'Calculate' button to perform the calculation. 
    3030 
    31 .. image:: density_tutor.gif 
     31.. image:: density_tutor.png 
    3232 
    3333.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 

  • src/sas/sasgui/perspectives/calculator/media/gen_sas_help.html

    rd85c194 r6aad2e8  
    1919by the particle  
    2020<p> 
    21 <img src="gen_i.gif"/> 
     21<img src="gen_i.png"/> 
    2222</p> 
    2323<br> 
    … …  
    2626of the j'th pixel respectively. And the total volume 
    2727<p> 
    28 <img src="v_j.gif"/> 
     28<img src="v_j.png"/> 
    2929</p> 
    3030<br> 
    … …  
    4444scattering length. (Figure below). 
    4545<p> 
    46 <img src="mag_vector.bmp"/> 
     46<img src="mag_vector.png"/> 
    4747</p> 
    4848<br> 
    4949The magnetic scattering length density is then 
    5050<p> 
    51 <img src="dm_eq.gif"/> 
     51<img src="dm_eq.png"/> 
    5252</p> 
    5353<br> 
    … …  
    6666<br> 
    6767<p> 
    68 <img src="gen_mag_pic.bmp"/> 
     68<img src="gen_mag_pic.png"/> 
    6969</p> 
    7070<br> 
    … …  
    7575densities , including the nuclear scattering length density (&#946; <sub>N</sub>) are given as, for non-spin-flips, 
    7676<p> 
    77 <img src="sld1.gif"/> 
     77<img src="sld1.png"/> 
    7878</p> 
    7979<br> 
    … …  
    8181for spin-flips, 
    8282<p> 
    83 <img src="sld2.gif"/> 
     83<img src="sld2.png"/> 
    8484</p> 
    8585<br> 
    … …  
    8787where 
    8888<p> 
    89 <img src="mxp.gif"/> 
     89<img src="mxp.png"/> 
    9090</p> 
    9191<p> 
    92 <img src="myp.gif"/> 
     92<img src="myp.png"/> 
    9393</p> 
    9494<p> 
    95 <img src="mzp.gif"/> 
     95<img src="mzp.png"/> 
    9696</p> 
    9797<p> 
    98 <img src="mqx.gif"/> 
     98<img src="mqx.png"/> 
    9999</p> 
    100100<p> 
    101 <img src="mqy.gif"/> 
     101<img src="mqy.png"/> 
    102102</p> 
    103103<br> 
    … …  
    110110<br> 
    111111<p> 
    112 <img src="gen_gui_help.bmp"/> 
     112<img src="gen_gui_help.png"/> 
    113113</p> 
    114114<br> 
    … …  
    136136in a 2D output, whileas the scattering calculation averaged over all the orientations uses the Debye equation providing a 1D output: 
    137137 <p> 
    138 <img src="gen_debye_eq.gif"/> 
     138<img src="gen_debye_eq.png"/> 
    139139</p> 
    140140<br> 

  • src/sas/sasgui/perspectives/calculator/media/image_viewer_help.rst

    rda456fb r6aad2e8  
    3434   will be displayed. 
    3535 
    36 .. image:: load_image.bmp 
     36.. image:: load_image.png 
    3737 
    38383) To save, print, or copy the image, or to apply a grid overlay, right-click  
    3939   anywhere in the plot. 
    4040 
    41 .. image:: pic_plot.bmp 
     41.. image:: pic_plot.png 
    4242 
    43434. If the image is taken from a 2D detector, SasView can attempt to convert  
    … …  
    5151   then click the OK. 
    5252 
    53 .. image:: pic_convert.bmp 
     53.. image:: pic_convert.png 
    5454 
    5555.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 

  • src/sas/sasgui/perspectives/calculator/media/kiessig_calculator_help.rst

    r7805458 r5ed76f8  
    1010----------- 
    1111 
    12 This tool is approximately estimates the thickness of a layer or the diameter  
    13 of particles from the position of the Kiessig fringe/Bragg peak in NR/SAS data  
    14 using the relation 
     12This tool estimates real space dimensions from the position or spacing of 
     13features in recipricol space.  In particular a particle of size $d$ will 
     14give rise to Bragg peaks with spacing $\Delta q$ according to the relation 
    1515 
    16 (thickness *or* size) = 2 * |pi| / (fringe_width *or* peak position) 
    17    
     16.. math:: 
     17 
     18    d = 2\pi / \Delta q 
     19 
     20Similarly, the spacing between the peaks in Kiessig fringes in reflectometry 
     21data arise from layers of thickness $d$. 
     22 
    1823.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    1924 
    … …  
    2126-------------- 
    2227 
    23 To get a rough thickness or particle size, simply type the fringe or peak  
     28To get a rough thickness or particle size, simply type the fringe or peak 
    2429position (in units of 1/|Ang|\) and click on the *Compute* button. 
    2530 
    2631.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    2732 
    28 .. note::  This help document was last changed by Steve King, 01May2015 
    29  
     33.. note::  This help document was last changed by Paul Kienzle, 05Apr2017 

  • src/sas/sasgui/perspectives/calculator/media/resolution_calculator_help.rst

    r7805458 r5ed76f8  
    1010----------- 
    1111 
    12 This tool is approximately estimates the resolution of Q from SAS instrumental  
    13 parameter values assuming that the detector is flat and normal to the  
     12This tool is approximately estimates the resolution of $Q$ from SAS instrumental 
     13parameter values assuming that the detector is flat and normal to the 
    1414incident beam. 
    1515 
    … …  
    23232) Select the source (Neutron or Photon) and source type (Monochromatic or TOF). 
    2424 
    25    *NOTE! The computational difference between the sources is only the  
     25   *NOTE! The computational difference between the sources is only the 
    2626   gravitational contribution due to the mass of the particles.* 
    2727 
    28 3) Change the default values of the instrumental parameters as required. Be  
     283) Change the default values of the instrumental parameters as required. Be 
    2929   careful to note that distances are specified in cm! 
    3030 
    31 4) Enter values for the source wavelength(s), |lambda|\ , and its spread (= FWHM/|lambda|\ ). 
    32     
    33    For monochromatic sources, the inputs are just one value. For TOF sources,  
    34    the minimum and maximum values should be separated by a '-' to specify a  
     314) Enter values for the source wavelength(s), $\lambda$, and its spread (= $\text{FWHM}/\lambda$). 
     32 
     33   For monochromatic sources, the inputs are just one value. For TOF sources, 
     34   the minimum and maximum values should be separated by a '-' to specify a 
    3535   range. 
    36     
    37    Optionally, the wavelength (BUT NOT of the wavelength spread) can be extended  
    38    by adding '; nn' where the 'nn' specifies the number of the bins for the  
    39    numerical integration. The default value is nn = 10. The same number of bins  
     36 
     37   Optionally, the wavelength (BUT NOT of the wavelength spread) can be extended 
     38   by adding '; nn' where the 'nn' specifies the number of the bins for the 
     39   numerical integration. The default value is nn = 10. The same number of bins 
    4040   will be used for the corresponding wavelength spread. 
    4141 
    42 5) For TOF, the default wavelength spectrum is flat. A custom spectral  
    43    distribution file (2-column text: wavelength (|Ang|\) vs Intensity) can also  
     425) For TOF, the default wavelength spectrum is flat. A custom spectral 
     43   distribution file (2-column text: wavelength (|Ang|\) vs Intensity) can also 
    4444   be loaded by selecting *Add new* in the combo box. 
    4545 
    46 6) When ready, click the *Compute* button. Depending on the computation the  
     466) When ready, click the *Compute* button. Depending on the computation the 
    4747   calculation time will vary. 
    4848 
    49 7) 1D and 2D dQ values will be displayed at the bottom of the panel, and a 2D  
    50    resolution weight distribution (a 2D elliptical Gaussian function) will also  
    51    be displayed in the plot panel even if the Q inputs are outside of the  
     497) 1D and 2D $dQ$ values will be displayed at the bottom of the panel, and a 2D 
     50   resolution weight distribution (a 2D elliptical Gaussian function) will also 
     51   be displayed in the plot panel even if the $Q$ inputs are outside of the 
    5252   detector limit (the red lines indicate the limits of the detector). 
    53     
    54    TOF only: green lines indicate the limits of the maximum Q range accessible  
     53 
     54   TOF only: green lines indicate the limits of the maximum $Q$ range accessible 
    5555   for the longest wavelength due to the size of the detector. 
    56      
    57    Note that the effect from the beam block/stop is ignored, so in the small Q  
    58    region near the beam block/stop  
    5956 
    60    [ie., Q < 2. |pi|\ .(beam block diameter) / (sample-to-detector distance) / |lambda|\_min]  
     57   Note that the effect from the beam block/stop is ignored, so in the small $Q$ 
     58   region near the beam block/stop 
     59 
     60   [i.e., $Q < (2 \pi \cdot \text{beam block diameter}) / (\text{sample-to-detector distance} \cdot \lambda_\text{min})$] 
    6161 
    6262   the variance is slightly under estimated. 
    6363 
    64 8) A summary of the calculation is written to the SasView *Console* at the  
     648) A summary of the calculation is written to the SasView *Console* at the 
    6565   bottom of the main SasView window. 
    6666 
    67 .. image:: resolution_tutor.gif 
     67.. image:: resolution_tutor.png 
    6868 
    6969.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    7474The scattering wave transfer vector is by definition 
    7575 
    76 .. image:: q.gif 
     76.. image:: q.png 
    7777 
    78 In the small-angle limit, the variance of Q is to a first-order  
     78In the small-angle limit, the variance of $Q$ is to a first-order 
    7979approximation 
    8080 
    81 .. image:: sigma_q.gif 
     81.. image:: sigma_q.png 
    8282 
    8383The geometric and gravitational contributions can then be summarised as 
    8484 
    85 .. image:: sigma_table.gif 
     85.. image:: sigma_table.png 
    8686 
    87 Finally, a Gaussian function is used to describe the 2D weighting distribution  
    88 of the uncertainty in Q. 
     87Finally, a Gaussian function is used to describe the 2D weighting distribution 
     88of the uncertainty in $Q$. 
    8989 
    9090.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    9393---------- 
    9494 
    95 D.F.R. Mildner and J.M. Carpenter  
     95D.F.R. Mildner and J.M. Carpenter 
    9696*J. Appl. Cryst.* 17 (1984) 249-256 
    9797 
    98 D.F.R. Mildner, J.M. Carpenter and D.L. Worcester  
     98D.F.R. Mildner, J.M. Carpenter and D.L. Worcester 
    9999*J. Appl. Cryst.* 19 (1986) 311-319 
    100100 

  • src/sas/sasgui/perspectives/calculator/media/sas_calculator_help.rst

    rda456fb r5ed76f8  
    1919------ 
    2020 
    21 In general, a particle with a volume *V* can be described by an ensemble  
    22 containing *N* 3-dimensional rectangular pixels where each pixel is much  
    23 smaller than *V*. 
     21In general, a particle with a volume $V$ can be described by an ensemble 
     22containing $N$ 3-dimensional rectangular pixels where each pixel is much 
     23smaller than $V$. 
    2424 
    25 Assuming that all the pixel sizes are the same, the elastic scattering  
     25Assuming that all the pixel sizes are the same, the elastic scattering 
    2626intensity from the particle is 
    2727 
    28 .. image:: gen_i.gif 
     28.. image:: gen_i.png 
    2929 
    3030Equation 1. 
    3131 
    32 where |beta|\ :sub:`j` and *r*\ :sub:`j` are the scattering length density and  
    33 the position of the j'th pixel respectively. 
     32where $\beta_j$ and $r_j$ are the scattering length density and 
     33the position of the $j^\text{th}$ pixel respectively. 
    3434 
    35 The total volume *V* 
     35The total volume $V$ 
    3636 
    37 .. image:: v_j.gif 
     37.. math:: 
    3838 
    39 for |beta|\ :sub:`j` |noteql|\0 where *v*\ :sub:`j` is the volume of the j'th  
    40 pixel (or the j'th natural atomic volume (= atomic mass / (natural molar  
     39    V = \sum_j^N v_j 
     40 
     41for $\beta_j \ne 0$ where $v_j$ is the volume of the $j^\text{th}$ 
     42pixel (or the $j^\text{th}$ natural atomic volume (= atomic mass / (natural molar 
    4143density * Avogadro number) for the atomic structures). 
    4244 
    43 *V* can be corrected by users. This correction is useful especially for an  
    44 atomic structure (such as taken from a PDB file) to get the right normalization.  
     45$V$ can be corrected by users. This correction is useful especially for an 
     46atomic structure (such as taken from a PDB file) to get the right normalization. 
    4547 
    46 *NOTE!* |beta|\ :sub:`j` *displayed in the GUI may be incorrect but this will not  
     48*NOTE! $\beta_j$ displayed in the GUI may be incorrect but this will not 
    4749affect the scattering computation if the correction of the total volume V is made.* 
    4850 
    49 The scattering length density (SLD) of each pixel, where the SLD is uniform, is  
    50 a combination of the nuclear and magnetic SLDs and depends on the spin states  
     51The scattering length density (SLD) of each pixel, where the SLD is uniform, is 
     52a combination of the nuclear and magnetic SLDs and depends on the spin states 
    5153of the neutrons as follows. 
    5254 
    … …  
    5456^^^^^^^^^^^^^^^^^^^ 
    5557 
    56 For magnetic scattering, only the magnetization component, *M*\ :sub:`perp`\ ,  
    57 perpendicular to the scattering vector *Q* contributes to the magnetic  
     58For magnetic scattering, only the magnetization component, $M_\perp$, 
     59perpendicular to the scattering vector $Q$ contributes to the magnetic 
    5860scattering length. 
    5961 
    60 .. image:: mag_vector.bmp 
     62.. image:: mag_vector.png 
    6163 
    6264The magnetic scattering length density is then 
    6365 
    64 .. image:: dm_eq.gif 
     66.. image:: dm_eq.png 
    6567 
    66 where the gyromagnetic ratio |gamma| = -1.913, |mu|\ :sub:`B` is the Bohr  
    67 magneton, *r*\ :sub:`0` is the classical radius of electron, and |sigma| is the  
     68where the gyromagnetic ratio is $\gamma = -1.913$, $\mu_B$ is the Bohr 
     69magneton, $r_0$ is the classical radius of electron, and $\sigma$ is the 
    6870Pauli spin. 
    6971 
    7072For a polarized neutron, the magnetic scattering is depending on the spin states. 
    7173 
    72 Let us consider that the incident neutrons are polarised both parallel (+) and   
    73 anti-parallel (-) to the x' axis (see below). The possible states after  
    74 scattering from the sample are then  
     74Let us consider that the incident neutrons are polarised both parallel (+) and 
     75anti-parallel (-) to the x' axis (see below). The possible states after 
     76scattering from the sample are then 
    7577 
    7678*  Non-spin flips: (+ +) and (- -) 
    7779*  Spin flips:     (+ -) and (- +) 
    7880 
    79 .. image:: gen_mag_pic.bmp 
     81.. image:: gen_mag_pic.png 
    8082 
    81 Now let us assume that the angles of the *Q* vector and the spin-axis (x')  
    82 to the x-axis are |phi| and |theta|\ :sub:`up` respectively (see above). Then,  
    83 depending upon the polarization (spin) state of neutrons, the scattering  
    84 length densities, including the nuclear scattering length density (|beta|\ :sub:`N`\ )  
     83Now let us assume that the angles of the *Q* vector and the spin-axis (x') 
     84to the x-axis are $\phi$ and $\theta_\text{up}$ respectively (see above). Then, 
     85depending upon the polarization (spin) state of neutrons, the scattering 
     86length densities, including the nuclear scattering length density ($\beta_N$) 
    8587are given as 
    8688 
    8789*  for non-spin-flips 
    8890 
    89    .. image:: sld1.gif 
     91   .. image:: sld1.png 
    9092 
    9193*  for spin-flips 
    9294 
    93    .. image:: sld2.gif 
     95   .. image:: sld2.png 
    9496 
    9597where 
    9698 
    97 .. image:: mxp.gif 
     99.. image:: mxp.png 
    98100 
    99 .. image:: myp.gif 
     101.. image:: myp.png 
    100102 
    101 .. image:: mzp.gif 
     103.. image:: mzp.png 
    102104 
    103 .. image:: mqx.gif 
     105.. image:: mqx.png 
    104106 
    105 .. image:: mqy.gif 
     107.. image:: mqy.png 
    106108 
    107 Here the *M0*\ :sub:`x`\ , *M0*\ :sub:`y` and *M0*\ :sub:`z` are the x, y and z  
    108 components of the magnetisation vector in the laboratory xyz frame.  
     109Here the $M0_x$, $M0_y$ and $M0_z$ are the $x$, $y$ and $z$ 
     110components of the magnetisation vector in the laboratory $xyz$ frame. 
    109111 
    110112.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    113115-------------- 
    114116 
    115 .. image:: gen_gui_help.bmp 
     117.. image:: gen_gui_help.png 
    116118 
    117 After computation the result will appear in the *Theory* box in the SasView   
     119After computation the result will appear in the *Theory* box in the SasView 
    118120*Data Explorer* panel. 
    119121 
    120 *Up_frac_in* and *Up_frac_out* are the ratio  
     122*Up_frac_in* and *Up_frac_out* are the ratio 
    121123 
    122124   (spin up) / (spin up + spin down) 
    123     
     125 
    124126of neutrons before the sample and at the analyzer, respectively. 
    125127 
    126 *NOTE 1. The values of* Up_frac_in *and* Up_frac_out *must be in the range  
     128*NOTE 1. The values of* Up_frac_in *and* Up_frac_out *must be in the range 
    1271290.0 to 1.0. Both values are 0.5 for unpolarized neutrons.* 
    128130 
    129 *NOTE 2. This computation is totally based on the pixel (or atomic) data fixed  
     131*NOTE 2. This computation is totally based on the pixel (or atomic) data fixed 
    130132in xyz coordinates. No angular orientational averaging is considered.* 
    131133 
    132 *NOTE 3. For the nuclear scattering length density, only the real component  
     134*NOTE 3. For the nuclear scattering length density, only the real component 
    133135is taken account.* 
    134136 
    … …  
    139141 
    140142The SANS Calculator tool can read some PDB, OMF or SLD files but ignores 
    141 polarized/magnetic scattering when doing so, thus related parameters such as  
     143polarized/magnetic scattering when doing so, thus related parameters such as 
    142144*Up_frac_in*, etc, will be ignored. 
    143145 
    144 The calculation for fixed orientation uses Equation 1 above resulting in a 2D  
    145 output, whereas the scattering calculation averaged over all the orientations  
     146The calculation for fixed orientation uses Equation 1 above resulting in a 2D 
     147output, whereas the scattering calculation averaged over all the orientations 
    146148uses the Debye equation below providing a 1D output 
    147149 
    148 .. image:: gen_debye_eq.gif 
     150.. image:: gen_debye_eq.png 
    149151 
    150 where *v*\ :sub:`j` |beta|\ :sub:`j` |equiv| *b*\ :sub:`j` is the scattering  
    151 length of the j'th atom. The calculation output is passed to the *Data Explorer*  
     152where $v_j \beta_j \equiv b_j$ is the scattering 
     153length of the $j^\text{th}$ atom. The calculation output is passed to the *Data Explorer* 
    152154for further use. 
    153155 

  • src/sas/sasgui/perspectives/calculator/media/sld_calculator_help.rst

    rf93b473f r5ed76f8  
    1010----------- 
    1111 
    12 The neutron scattering length density (SLD) is defined as 
     12The neutron scattering length density (SLD, $\beta_N$) is defined as 
    1313 
    14   SLD = (b_c1 + b_c2 + ... + b_cn) / Vm 
     14.. math:: 
    1515 
    16 where b_ci is the bound coherent scattering length of ith of n atoms in a molecule 
    17 with the molecular volume Vm 
     16  \beta_N = (b_{c1} + b_{c2} + ... + b_{cn}) / V_m 
     17 
     18where $b_{ci}$ is the bound coherent scattering length of ith of n atoms in a molecule 
     19with the molecular volume $V_m$. 
    1820 
    1921.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    2224---------------------------- 
    2325 
    24 To calculate scattering length densities enter the empirical formula of a  
     26To calculate scattering length densities enter the empirical formula of a 
    2527compound and its mass density and click "Calculate". 
    2628 
    27 Entering a wavelength value is optional (a default value of 6.0 |Ang| will  
     29Entering a wavelength value is optional (a default value of 6.0 |Ang| will 
    2830be used). 
    2931 
    … …  
    3840*  Parentheses can be nested, such as "(CaCO3(H2O)6)1". 
    3941 
    40 *  Isotopes are represented by their atomic number in *square brackets*, such  
     42*  Isotopes are represented by their atomic number in *square brackets*, such 
    4143   as "CaCO[18]3+6H2O", H[1], or H[2]. 
    4244 
    4345*  Numbers of atoms can be integer or decimal, such as "CaCO3+(3HO0.5)2". 
    4446 
    45 *  The SLD of mixtures can be calculated as well. For example, for a 70-30  
     47*  The SLD of mixtures can be calculated as well. For example, for a 70-30 
    4648   mixture of H2O/D2O write "H14O7+D6O3" or more simply "H7D3O5" (i.e. this says 
    4749   7 hydrogens, 3 deuteriums, and 5 oxygens) and enter a mass density calculated 
    4850   on the percentages of H2O and D2O. 
    4951 
    50 *  Type "C[13]6 H[2]12 O[18]6" for C(13)6H(2)12O(18)6 (6 Carbon-13 atoms, 12  
     52*  Type "C[13]6 H[2]12 O[18]6" for C(13)6H(2)12O(18)6 (6 Carbon-13 atoms, 12 
    5153   deuterium atoms, and 6 Oxygen-18 atoms). 
    52     
     54 
    5355.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    5456 
    55 .. note::  This help document was last changed by Steve King, 01May2015 
     57.. note::  This help document was last changed by Paul Kienzle, 05Apr2017 
    5658 

  • src/sas/sasgui/perspectives/calculator/media/slit_calculator_help.rst

    rf93b473f r5ed76f8  
    1111----------- 
    1212 
    13 This tool enables X-ray users to calculate the slit size (FWHM/2) for smearing  
     13This tool enables X-ray users to calculate the slit size (FWHM/2) for smearing 
    1414based on their half beam profile data. 
    1515 
    1616*NOTE! Whilst it may have some more generic applicability, the calculator has 
    17 only been tested with beam profile data from Anton-Paar SAXSess*\ |TM|\   
    18 *software.* 
     17only been tested with beam profile data from Anton-Paar SAXSess:sup:`TM` software.* 
    1918 
    2019.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ 
    … …  
    27262) Load a beam profile file in the *Data* field using the *Browse* button. 
    2827 
    29    *NOTE! To see an example of the beam profile file format, visit the file  
     28   *NOTE! To see an example of the beam profile file format, visit the file 
    3029   beam profile.DAT in your {installation_directory}/SasView/test folder.* 
    3130 
    32 3) Once a data is loaded, the slit size is automatically computed and displayed  
     313) Once a data is loaded, the slit size is automatically computed and displayed 
    3332   in the tool window. 
    3433 
    35 *NOTE! The beam profile file does not carry any information about the units of  
     34*NOTE! The beam profile file does not carry any information about the units of 
    3635the Q data. This calculator assumes the data has units of 1/\ |Ang|\ . If the 
    3736data is not in these units it must be manually converted beforehand.* 
Note: See TracChangeset for help on using the changeset viewer.