[f3d51f6] | 1 | # Make sure the option of saving each curve is available |
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| 2 | # Use the I(q) curve as input and compare the output to P(r) |
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| 3 | |
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| 4 | import os |
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[4a5de6f] | 5 | import sys |
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[f3d51f6] | 6 | import wx |
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[aa4b8379] | 7 | import logging |
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[ff7acff] | 8 | from danse.common.plottools import Data1D, Theory1D |
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[f3d51f6] | 9 | from sans.guicomm.events import NewPlotEvent, StatusEvent |
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| 10 | import math, numpy |
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| 11 | from sans.pr.invertor import Invertor |
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[aab8ad7] | 12 | from DataLoader.loader import Loader |
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[f3d51f6] | 13 | |
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[f1181977] | 14 | PR_FIT_LABEL = r"$P_{fit}(r)$" |
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| 15 | PR_LOADED_LABEL = r"$P_{loaded}(r)$" |
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| 16 | IQ_DATA_LABEL = r"$I_{obs}(q)$" |
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| 17 | IQ_FIT_LABEL = r"$I_{fit}(q)$" |
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| 18 | IQ_SMEARED_LABEL = r"$I_{smeared}(q)$" |
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[aa4b8379] | 19 | |
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| 20 | import wx.lib |
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| 21 | (NewPrFileEvent, EVT_PR_FILE) = wx.lib.newevent.NewEvent() |
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| 22 | |
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| 23 | |
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[f3d51f6] | 24 | class Plugin: |
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| 25 | |
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[b659551] | 26 | DEFAULT_ALPHA = 0.0001 |
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| 27 | DEFAULT_NFUNC = 10 |
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| 28 | DEFAULT_DMAX = 140.0 |
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| 29 | |
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[d2ee6f6] | 30 | def __init__(self, standalone=True): |
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[f3d51f6] | 31 | ## Plug-in name |
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| 32 | self.sub_menu = "Pr inversion" |
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| 33 | |
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| 34 | ## Reference to the parent window |
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| 35 | self.parent = None |
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| 36 | |
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| 37 | ## Simulation window manager |
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| 38 | self.simview = None |
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| 39 | |
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| 40 | ## List of panels for the simulation perspective (names) |
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| 41 | self.perspective = [] |
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| 42 | |
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| 43 | ## State data |
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[b659551] | 44 | self.alpha = self.DEFAULT_ALPHA |
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| 45 | self.nfunc = self.DEFAULT_NFUNC |
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| 46 | self.max_length = self.DEFAULT_DMAX |
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[634f1cf] | 47 | self.q_min = None |
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| 48 | self.q_max = None |
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[a4bd2ac] | 49 | self.has_bck = False |
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[2a92852] | 50 | self.slit_height = 0 |
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| 51 | self.slit_width = 0 |
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[f3d51f6] | 52 | ## Remember last plottable processed |
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| 53 | self.last_data = "sphere_60_q0_2.txt" |
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[0bae207] | 54 | self._current_file_data = None |
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[f3d51f6] | 55 | ## Time elapsed for last computation [sec] |
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| 56 | # Start with a good default |
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| 57 | self.elapsed = 0.022 |
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[aa4b8379] | 58 | self.iq_data_shown = False |
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[f3d51f6] | 59 | |
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| 60 | ## Current invertor |
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| 61 | self.invertor = None |
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[3fd1ebc] | 62 | self.pr = None |
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[feb21d8] | 63 | # Copy of the last result in case we need to display it. |
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| 64 | self._last_pr = None |
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| 65 | self._last_out = None |
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| 66 | self._last_cov = None |
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[f3d51f6] | 67 | ## Calculation thread |
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| 68 | self.calc_thread = None |
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| 69 | ## Estimation thread |
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| 70 | self.estimation_thread = None |
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| 71 | ## Result panel |
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| 72 | self.control_panel = None |
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| 73 | ## Currently views plottable |
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| 74 | self.current_plottable = None |
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[b659551] | 75 | ## Number of P(r) points to display on the output plot |
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| 76 | self._pr_npts = 51 |
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[aa4b8379] | 77 | ## Flag to let the plug-in know that it is running standalone |
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[d2ee6f6] | 78 | self.standalone = standalone |
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[feb21d8] | 79 | self._normalize_output = False |
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| 80 | self._scale_output_unity = False |
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[aa4b8379] | 81 | |
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[f1181977] | 82 | ## List of added P(r) plots |
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| 83 | self._added_plots = {} |
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| 84 | self._default_Iq = {} |
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| 85 | |
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[6f1f129] | 86 | # Associate the inversion state reader with .prv files |
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| 87 | from DataLoader.loader import Loader |
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| 88 | from inversion_state import Reader |
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| 89 | |
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[410aad8] | 90 | #TODO: get rid of the cansas flag |
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| 91 | self.state_reader = Reader(self.set_state, cansas = not self.standalone) |
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[6f1f129] | 92 | l = Loader() |
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[410aad8] | 93 | l.associate_file_reader('.prv', self.state_reader) |
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[6f1f129] | 94 | |
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[aa4b8379] | 95 | # Log startup |
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| 96 | logging.info("Pr(r) plug-in started") |
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| 97 | |
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[410aad8] | 98 | def set_state(self, state, datainfo=None): |
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[6f1f129] | 99 | """ |
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| 100 | Call-back method for the inversion state reader. |
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| 101 | This method is called when a .prv file is loaded. |
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| 102 | |
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| 103 | @param state: InversionState object |
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[410aad8] | 104 | @param datainfo: Data1D object [optional] |
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[6f1f129] | 105 | """ |
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[410aad8] | 106 | try: |
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| 107 | # If we are not in standalone mode, the panel will not |
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| 108 | # load any data file and we need to keep track of the |
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| 109 | # data here. |
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| 110 | if self.standalone == False: |
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| 111 | if datainfo is None: |
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| 112 | raise RuntimeError, "Pr.set_state: datainfo parameter cannot be None in standalone mode" |
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| 113 | |
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| 114 | self.current_plottable = datainfo |
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| 115 | self.current_plottable.group_id = datainfo.meta_data['prstate'].file |
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| 116 | |
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| 117 | # Load the P(r) results |
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| 118 | self.control_panel.set_state(state) |
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| 119 | |
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| 120 | # Make sure the user sees the P(r) panel after loading |
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| 121 | self.parent.set_perspective(self.perspective) |
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| 122 | |
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| 123 | except: |
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| 124 | logging.error("prview.set_state: %s" % sys.exc_value) |
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[f3d51f6] | 125 | |
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| 126 | def populate_menu(self, id, owner): |
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| 127 | """ |
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| 128 | Create a menu for the plug-in |
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| 129 | """ |
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[7cb0353] | 130 | return [] |
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[f3d51f6] | 131 | |
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[119a11d] | 132 | def help(self, evt): |
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| 133 | """ |
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| 134 | Show a general help dialog. |
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| 135 | TODO: replace the text with a nice image |
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| 136 | """ |
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| 137 | from inversion_panel import HelpDialog |
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| 138 | dialog = HelpDialog(None, -1) |
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| 139 | if dialog.ShowModal() == wx.ID_OK: |
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| 140 | dialog.Destroy() |
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| 141 | else: |
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| 142 | dialog.Destroy() |
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| 143 | |
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[f3d51f6] | 144 | def _fit_pr(self, evt): |
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| 145 | from sans.pr.invertor import Invertor |
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| 146 | import numpy |
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| 147 | import pylab |
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| 148 | import math |
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| 149 | from sans.guicomm.events import NewPlotEvent |
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[ff7acff] | 150 | from danse.common.plottools import Data1D, Theory1D |
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[f3d51f6] | 151 | |
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| 152 | # Generate P(r) for sphere |
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| 153 | radius = 60.0 |
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| 154 | d_max = 2*radius |
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| 155 | |
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| 156 | |
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| 157 | r = pylab.arange(0.01, d_max, d_max/51.0) |
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| 158 | M = len(r) |
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| 159 | y = numpy.zeros(M) |
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| 160 | pr_err = numpy.zeros(M) |
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| 161 | |
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| 162 | sum = 0.0 |
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| 163 | for j in range(M): |
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| 164 | value = self.pr_theory(r[j], radius) |
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| 165 | sum += value |
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| 166 | y[j] = value |
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| 167 | pr_err[j] = math.sqrt(y[j]) |
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| 168 | |
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| 169 | |
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| 170 | y = y/sum*d_max/len(r) |
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| 171 | |
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| 172 | |
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| 173 | |
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| 174 | # Perform fit |
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| 175 | pr = Invertor() |
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| 176 | pr.d_max = d_max |
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| 177 | pr.alpha = 0 |
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| 178 | pr.x = r |
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| 179 | pr.y = y |
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| 180 | pr.err = pr_err |
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| 181 | out, cov = pr.pr_fit() |
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| 182 | for i in range(len(out)): |
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| 183 | print "%g +- %g" % (out[i], math.sqrt(cov[i][i])) |
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| 184 | |
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| 185 | |
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| 186 | # Show input P(r) |
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[b659551] | 187 | new_plot = Data1D(pr.x, pr.y, dy=pr.err) |
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[f3d51f6] | 188 | new_plot.name = "P_{obs}(r)" |
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| 189 | new_plot.xaxis("\\rm{r}", 'A') |
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| 190 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
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| 191 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Pr")) |
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| 192 | |
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| 193 | # Show P(r) fit |
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| 194 | self.show_pr(out, pr) |
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| 195 | |
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| 196 | # Show I(q) fit |
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| 197 | q = pylab.arange(0.001, 0.1, 0.01/51.0) |
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| 198 | self.show_iq(out, pr, q) |
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| 199 | |
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| 200 | |
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| 201 | def show_shpere(self, x, radius=70.0, x_range=70.0): |
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| 202 | import numpy |
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| 203 | import pylab |
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| 204 | import math |
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| 205 | from sans.guicomm.events import NewPlotEvent |
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[ff7acff] | 206 | from danse.common.plottools import Data1D, Theory1D |
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[f3d51f6] | 207 | # Show P(r) |
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| 208 | y_true = numpy.zeros(len(x)) |
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| 209 | |
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| 210 | sum_true = 0.0 |
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| 211 | for i in range(len(x)): |
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| 212 | y_true[i] = self.pr_theory(x[i], radius) |
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| 213 | sum_true += y_true[i] |
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| 214 | |
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| 215 | y_true = y_true/sum_true*x_range/len(x) |
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| 216 | |
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| 217 | # Show the theory P(r) |
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| 218 | new_plot = Theory1D(x, y_true) |
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| 219 | new_plot.name = "P_{true}(r)" |
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| 220 | new_plot.xaxis("\\rm{r}", 'A') |
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| 221 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
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| 222 | |
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| 223 | |
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| 224 | #Put this call in plottables/guitools |
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| 225 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Sphere P(r)")) |
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| 226 | |
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[b659551] | 227 | def get_npts(self): |
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| 228 | """ |
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| 229 | Returns the number of points in the I(q) data |
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| 230 | """ |
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| 231 | try: |
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| 232 | return len(self.pr.x) |
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| 233 | except: |
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| 234 | return 0 |
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| 235 | |
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[f3d51f6] | 236 | def show_iq(self, out, pr, q=None): |
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| 237 | import numpy |
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| 238 | import pylab |
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| 239 | import math |
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| 240 | from sans.guicomm.events import NewPlotEvent |
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[ff7acff] | 241 | from danse.common.plottools import Data1D, Theory1D |
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[f3d51f6] | 242 | |
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| 243 | qtemp = pr.x |
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| 244 | if not q==None: |
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| 245 | qtemp = q |
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| 246 | |
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| 247 | # Make a plot |
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| 248 | maxq = -1 |
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| 249 | for q_i in qtemp: |
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| 250 | if q_i>maxq: |
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| 251 | maxq=q_i |
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| 252 | |
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[634f1cf] | 253 | minq = 0.001 |
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| 254 | |
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| 255 | # Check for user min/max |
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| 256 | if not pr.q_min==None: |
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| 257 | minq = pr.q_min |
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| 258 | if not pr.q_max==None: |
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| 259 | maxq = pr.q_max |
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| 260 | |
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| 261 | x = pylab.arange(minq, maxq, maxq/301.0) |
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[f3d51f6] | 262 | y = numpy.zeros(len(x)) |
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| 263 | err = numpy.zeros(len(x)) |
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| 264 | for i in range(len(x)): |
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| 265 | value = pr.iq(out, x[i]) |
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| 266 | y[i] = value |
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| 267 | try: |
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| 268 | err[i] = math.sqrt(math.fabs(value)) |
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| 269 | except: |
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| 270 | err[i] = 1.0 |
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| 271 | print "Error getting error", value, x[i] |
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| 272 | |
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| 273 | new_plot = Theory1D(x, y) |
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[2a92852] | 274 | new_plot.name = IQ_FIT_LABEL |
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[f3d51f6] | 275 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
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| 276 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
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[d2ee6f6] | 277 | |
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| 278 | title = "I(q)" |
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| 279 | # If we have a group ID, use it |
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| 280 | if pr.info.has_key("plot_group_id"): |
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| 281 | new_plot.group_id = pr.info["plot_group_id"] |
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| 282 | title = pr.info["plot_group_id"] |
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| 283 | |
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| 284 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title)) |
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[f3d51f6] | 285 | |
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[2a92852] | 286 | # If we have used slit smearing, plot the smeared I(q) too |
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| 287 | if pr.slit_width>0 or pr.slit_height>0: |
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| 288 | x = pylab.arange(minq, maxq, maxq/301.0) |
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| 289 | y = numpy.zeros(len(x)) |
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| 290 | err = numpy.zeros(len(x)) |
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| 291 | for i in range(len(x)): |
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| 292 | value = pr.iq_smeared(out, x[i]) |
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| 293 | y[i] = value |
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| 294 | try: |
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| 295 | err[i] = math.sqrt(math.fabs(value)) |
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| 296 | except: |
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| 297 | err[i] = 1.0 |
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| 298 | print "Error getting error", value, x[i] |
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| 299 | |
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| 300 | new_plot = Theory1D(x, y) |
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| 301 | new_plot.name = IQ_SMEARED_LABEL |
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| 302 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
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| 303 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
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| 304 | #new_plot.group_id = "test group" |
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| 305 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="I(q)")) |
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| 306 | |
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[f3d51f6] | 307 | |
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[b659551] | 308 | def _on_pr_npts(self, evt): |
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| 309 | """ |
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| 310 | Redisplay P(r) with a different number of points |
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| 311 | """ |
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| 312 | from inversion_panel import PrDistDialog |
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| 313 | dialog = PrDistDialog(None, -1) |
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| 314 | dialog.set_content(self._pr_npts) |
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| 315 | if dialog.ShowModal() == wx.ID_OK: |
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| 316 | self._pr_npts= dialog.get_content() |
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| 317 | dialog.Destroy() |
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[feb21d8] | 318 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
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[b659551] | 319 | else: |
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| 320 | dialog.Destroy() |
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[f3d51f6] | 321 | |
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| 322 | |
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| 323 | def show_pr(self, out, pr, cov=None): |
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| 324 | import numpy |
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| 325 | import pylab |
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| 326 | import math |
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| 327 | from sans.guicomm.events import NewPlotEvent |
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[ff7acff] | 328 | from danse.common.plottools import Data1D, Theory1D |
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[f3d51f6] | 329 | |
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| 330 | # Show P(r) |
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[b659551] | 331 | x = pylab.arange(0.0, pr.d_max, pr.d_max/self._pr_npts) |
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[f3d51f6] | 332 | |
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| 333 | y = numpy.zeros(len(x)) |
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| 334 | dy = numpy.zeros(len(x)) |
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| 335 | y_true = numpy.zeros(len(x)) |
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| 336 | |
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| 337 | sum = 0.0 |
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[feb21d8] | 338 | pmax = 0.0 |
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[dfb58f8] | 339 | cov2 = numpy.ascontiguousarray(cov) |
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| 340 | |
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[f3d51f6] | 341 | for i in range(len(x)): |
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[dfb58f8] | 342 | if cov2==None: |
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[f3d51f6] | 343 | value = pr.pr(out, x[i]) |
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| 344 | else: |
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[dfb58f8] | 345 | (value, dy[i]) = pr.pr_err(out, cov2, x[i]) |
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[660b1e6] | 346 | sum += value*pr.d_max/len(x) |
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[f3d51f6] | 347 | |
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[feb21d8] | 348 | # keep track of the maximum P(r) value |
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| 349 | if value>pmax: |
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| 350 | pmax = value |
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| 351 | |
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| 352 | y[i] = value |
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| 353 | |
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| 354 | if self._normalize_output==True: |
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| 355 | y = y/sum |
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| 356 | dy = dy/sum |
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| 357 | elif self._scale_output_unity==True: |
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| 358 | y = y/pmax |
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| 359 | dy = dy/pmax |
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[f3d51f6] | 360 | |
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[dfb58f8] | 361 | if cov2==None: |
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[f3d51f6] | 362 | new_plot = Theory1D(x, y) |
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| 363 | else: |
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| 364 | new_plot = Data1D(x, y, dy=dy) |
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[f1181977] | 365 | new_plot.name = PR_FIT_LABEL |
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[f3d51f6] | 366 | new_plot.xaxis("\\rm{r}", 'A') |
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| 367 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
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[d2ee6f6] | 368 | # Make sure that the plot is linear |
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| 369 | new_plot.xtransform="x" |
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| 370 | new_plot.ytransform="y" |
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[f3d51f6] | 371 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="P(r) fit")) |
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| 372 | |
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| 373 | return x, pr.d_max |
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| 374 | |
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| 375 | |
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[6f1f129] | 376 | def choose_file(self, path=None): |
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[f3d51f6] | 377 | """ |
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| 378 | |
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| 379 | """ |
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| 380 | #TODO: this should be in a common module |
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[6f1f129] | 381 | return self.parent.choose_file(path=path) |
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[f3d51f6] | 382 | |
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[0bae207] | 383 | |
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| 384 | def load(self, path): |
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| 385 | """ |
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| 386 | Load data. This will eventually be replaced |
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| 387 | by our standard DataLoader class. |
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| 388 | """ |
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| 389 | class FileData: |
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| 390 | x = None |
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| 391 | y = None |
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| 392 | err = None |
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| 393 | path = None |
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| 394 | |
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| 395 | def __init__(self, path): |
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| 396 | self.path = path |
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| 397 | |
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| 398 | self._current_file_data = FileData(path) |
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| 399 | |
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[aab8ad7] | 400 | # Use data loader to load file |
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| 401 | dataread = Loader().load(path) |
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| 402 | x = None |
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| 403 | y = None |
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| 404 | err = None |
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| 405 | if dataread.__class__.__name__ == 'Data1D': |
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| 406 | x = dataread.x |
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| 407 | y = dataread.y |
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| 408 | err = dataread.dy |
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| 409 | else: |
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[e43c012] | 410 | if isinstance(dataread, list) and len(dataread)>0: |
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| 411 | x = dataread[0].x |
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| 412 | y = dataread[0].y |
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| 413 | err = dataread[0].dy |
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| 414 | msg = "PrView only allows a single data set at a time. " |
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| 415 | msg += "Only the first data set was loaded." |
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| 416 | wx.PostEvent(self.parent, StatusEvent(status=msg)) |
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| 417 | else: |
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[6f1f129] | 418 | if dataread is None: |
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| 419 | return x, y, err |
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[e43c012] | 420 | raise RuntimeError, "This tool can only read 1D data" |
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[aab8ad7] | 421 | |
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[0bae207] | 422 | self._current_file_data.x = x |
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| 423 | self._current_file_data.y = y |
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| 424 | self._current_file_data.err = err |
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| 425 | return x, y, err |
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| 426 | |
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| 427 | def load_columns(self, path = "sphere_60_q0_2.txt"): |
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| 428 | """ |
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| 429 | Load 2- or 3- column ascii |
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| 430 | """ |
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[f3d51f6] | 431 | import numpy, math, sys |
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| 432 | # Read the data from the data file |
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| 433 | data_x = numpy.zeros(0) |
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| 434 | data_y = numpy.zeros(0) |
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| 435 | data_err = numpy.zeros(0) |
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[b659551] | 436 | scale = None |
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| 437 | min_err = 0.0 |
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[f3d51f6] | 438 | if not path == None: |
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| 439 | input_f = open(path,'r') |
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| 440 | buff = input_f.read() |
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| 441 | lines = buff.split('\n') |
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| 442 | for line in lines: |
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| 443 | try: |
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| 444 | toks = line.split() |
---|
| 445 | x = float(toks[0]) |
---|
| 446 | y = float(toks[1]) |
---|
[b659551] | 447 | if len(toks)>2: |
---|
| 448 | err = float(toks[2]) |
---|
| 449 | else: |
---|
| 450 | if scale==None: |
---|
| 451 | scale = 0.05*math.sqrt(y) |
---|
| 452 | #scale = 0.05/math.sqrt(y) |
---|
| 453 | min_err = 0.01*y |
---|
| 454 | err = scale*math.sqrt(y)+min_err |
---|
| 455 | #err = 0 |
---|
| 456 | |
---|
[4a5de6f] | 457 | data_x = numpy.append(data_x, x) |
---|
| 458 | data_y = numpy.append(data_y, y) |
---|
[b659551] | 459 | data_err = numpy.append(data_err, err) |
---|
[f3d51f6] | 460 | except: |
---|
[b659551] | 461 | pass |
---|
[f3d51f6] | 462 | |
---|
[357b79b] | 463 | if not scale==None: |
---|
| 464 | message = "The loaded file had no error bars, statistical errors are assumed." |
---|
| 465 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
| 466 | else: |
---|
| 467 | wx.PostEvent(self.parent, StatusEvent(status='')) |
---|
| 468 | |
---|
[b659551] | 469 | return data_x, data_y, data_err |
---|
[f3d51f6] | 470 | |
---|
[0bae207] | 471 | def load_abs(self, path): |
---|
| 472 | """ |
---|
| 473 | Load an IGOR .ABS reduced file |
---|
| 474 | @param path: file path |
---|
| 475 | @return: x, y, err vectors |
---|
| 476 | """ |
---|
| 477 | import numpy, math, sys |
---|
| 478 | # Read the data from the data file |
---|
| 479 | data_x = numpy.zeros(0) |
---|
| 480 | data_y = numpy.zeros(0) |
---|
| 481 | data_err = numpy.zeros(0) |
---|
| 482 | scale = None |
---|
| 483 | min_err = 0.0 |
---|
| 484 | |
---|
| 485 | data_started = False |
---|
| 486 | if not path == None: |
---|
| 487 | input_f = open(path,'r') |
---|
| 488 | buff = input_f.read() |
---|
| 489 | lines = buff.split('\n') |
---|
| 490 | for line in lines: |
---|
| 491 | if data_started==True: |
---|
| 492 | try: |
---|
| 493 | toks = line.split() |
---|
| 494 | x = float(toks[0]) |
---|
| 495 | y = float(toks[1]) |
---|
| 496 | if len(toks)>2: |
---|
| 497 | err = float(toks[2]) |
---|
| 498 | else: |
---|
| 499 | if scale==None: |
---|
| 500 | scale = 0.05*math.sqrt(y) |
---|
| 501 | #scale = 0.05/math.sqrt(y) |
---|
| 502 | min_err = 0.01*y |
---|
| 503 | err = scale*math.sqrt(y)+min_err |
---|
| 504 | #err = 0 |
---|
| 505 | |
---|
| 506 | data_x = numpy.append(data_x, x) |
---|
| 507 | data_y = numpy.append(data_y, y) |
---|
| 508 | data_err = numpy.append(data_err, err) |
---|
| 509 | except: |
---|
| 510 | pass |
---|
| 511 | elif line.find("The 6 columns")>=0: |
---|
| 512 | data_started = True |
---|
| 513 | |
---|
| 514 | if not scale==None: |
---|
| 515 | message = "The loaded file had no error bars, statistical errors are assumed." |
---|
| 516 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
| 517 | else: |
---|
| 518 | wx.PostEvent(self.parent, StatusEvent(status='')) |
---|
| 519 | |
---|
| 520 | return data_x, data_y, data_err |
---|
| 521 | |
---|
| 522 | |
---|
| 523 | |
---|
[f3d51f6] | 524 | def pr_theory(self, r, R): |
---|
| 525 | """ |
---|
| 526 | |
---|
| 527 | """ |
---|
| 528 | if r<=2*R: |
---|
| 529 | return 12.0* ((0.5*r/R)**2) * ((1.0-0.5*r/R)**2) * ( 2.0 + 0.5*r/R ) |
---|
| 530 | else: |
---|
| 531 | return 0.0 |
---|
| 532 | |
---|
[660b1e6] | 533 | def get_context_menu(self, graph=None): |
---|
[f3d51f6] | 534 | """ |
---|
| 535 | Get the context menu items available for P(r) |
---|
[660b1e6] | 536 | @param graph: the Graph object to which we attach the context menu |
---|
[f3d51f6] | 537 | @return: a list of menu items with call-back function |
---|
| 538 | """ |
---|
[660b1e6] | 539 | # Look whether this Graph contains P(r) data |
---|
[aa4b8379] | 540 | #if graph.selected_plottable==IQ_DATA_LABEL: |
---|
[660b1e6] | 541 | for item in graph.plottables: |
---|
[aa4b8379] | 542 | if item.name==PR_FIT_LABEL: |
---|
[feb21d8] | 543 | m_list = [["Add P(r) data", "Load a data file and display it on this plot", self._on_add_data], |
---|
[b659551] | 544 | ["Change number of P(r) points", "Change the number of points on the P(r) output", self._on_pr_npts]] |
---|
[aa4b8379] | 545 | |
---|
[900c787] | 546 | if self._scale_output_unity==True or self._normalize_output==True: |
---|
| 547 | m_list.append(["Disable P(r) scaling", |
---|
| 548 | "Let the output P(r) keep the scale of the data", |
---|
| 549 | self._on_disable_scaling]) |
---|
[feb21d8] | 550 | |
---|
| 551 | if self._scale_output_unity==False: |
---|
| 552 | m_list.append(["Scale P_max(r) to unity", |
---|
| 553 | "Scale P(r) so that its maximum is 1", |
---|
| 554 | self._on_scale_unity]) |
---|
| 555 | |
---|
| 556 | if self._normalize_output==False: |
---|
| 557 | m_list.append(["Normalize P(r) to unity", |
---|
| 558 | "Normalize the integral of P(r) to 1", |
---|
| 559 | self._on_normalize]) |
---|
| 560 | |
---|
| 561 | return m_list |
---|
| 562 | #return [["Add P(r) data", "Load a data file and display it on this plot", self._on_add_data], |
---|
| 563 | # ["Change number of P(r) points", "Change the number of points on the P(r) output", self._on_pr_npts]] |
---|
| 564 | |
---|
[aa4b8379] | 565 | elif item.name==graph.selected_plottable: |
---|
[d2ee6f6] | 566 | #TODO: we might want to check that the units are consistent with I(q) |
---|
| 567 | # before allowing this menu item |
---|
[aa4b8379] | 568 | return [["Compute P(r)", "Compute P(r) from distribution", self._on_context_inversion]] |
---|
[660b1e6] | 569 | |
---|
[aa4b8379] | 570 | return [] |
---|
[660b1e6] | 571 | |
---|
[feb21d8] | 572 | def _on_disable_scaling(self, evt): |
---|
| 573 | """ |
---|
| 574 | Disable P(r) scaling |
---|
| 575 | @param evt: Menu event |
---|
| 576 | """ |
---|
| 577 | self._normalize_output = False |
---|
| 578 | self._scale_output_unity = False |
---|
| 579 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
---|
| 580 | |
---|
[f1181977] | 581 | # Now replot the original added data |
---|
| 582 | for plot in self._added_plots: |
---|
| 583 | self._added_plots[plot].y = numpy.copy(self._default_Iq[plot]) |
---|
| 584 | wx.PostEvent(self.parent, NewPlotEvent(plot=self._added_plots[plot], |
---|
| 585 | title=self._added_plots[plot].name, |
---|
| 586 | update=True)) |
---|
| 587 | |
---|
| 588 | # Need the update flag in the NewPlotEvent to protect against |
---|
| 589 | # the plot no longer being there... |
---|
| 590 | |
---|
[feb21d8] | 591 | def _on_normalize(self, evt): |
---|
| 592 | """ |
---|
[f1181977] | 593 | Normalize the area under the P(r) curve to 1. |
---|
| 594 | This operation is done for all displayed plots. |
---|
| 595 | |
---|
[feb21d8] | 596 | @param evt: Menu event |
---|
| 597 | """ |
---|
| 598 | self._normalize_output = True |
---|
| 599 | self._scale_output_unity = False |
---|
| 600 | |
---|
| 601 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
---|
| 602 | |
---|
[f1181977] | 603 | # Now scale the added plots too |
---|
| 604 | for plot in self._added_plots: |
---|
| 605 | sum = numpy.sum(self._added_plots[plot].y) |
---|
| 606 | npts = len(self._added_plots[plot].x) |
---|
| 607 | sum *= self._added_plots[plot].x[npts-1]/npts |
---|
| 608 | y = self._added_plots[plot].y/sum |
---|
| 609 | |
---|
| 610 | new_plot = Theory1D(self._added_plots[plot].x, y) |
---|
| 611 | new_plot.name = self._added_plots[plot].name |
---|
| 612 | new_plot.xaxis("\\rm{r}", 'A') |
---|
| 613 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
---|
| 614 | |
---|
| 615 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, update=True, |
---|
| 616 | title=self._added_plots[plot].name)) |
---|
| 617 | |
---|
| 618 | |
---|
| 619 | |
---|
[feb21d8] | 620 | def _on_scale_unity(self, evt): |
---|
| 621 | """ |
---|
[f1181977] | 622 | Scale the maximum P(r) value on each displayed plot to 1. |
---|
| 623 | |
---|
[feb21d8] | 624 | @param evt: Menu event |
---|
| 625 | """ |
---|
| 626 | self._scale_output_unity = True |
---|
| 627 | self._normalize_output = False |
---|
| 628 | |
---|
| 629 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
---|
| 630 | |
---|
[f1181977] | 631 | # Now scale the added plots too |
---|
| 632 | for plot in self._added_plots: |
---|
| 633 | _max = 0 |
---|
| 634 | for y in self._added_plots[plot].y: |
---|
| 635 | if y>_max: |
---|
| 636 | _max = y |
---|
| 637 | y = self._added_plots[plot].y/_max |
---|
| 638 | |
---|
| 639 | new_plot = Theory1D(self._added_plots[plot].x, y) |
---|
| 640 | new_plot.name = self._added_plots[plot].name |
---|
| 641 | new_plot.xaxis("\\rm{r}", 'A') |
---|
| 642 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
---|
| 643 | |
---|
| 644 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, update=True, |
---|
| 645 | title=self._added_plots[plot].name)) |
---|
| 646 | |
---|
| 647 | |
---|
[660b1e6] | 648 | def _on_add_data(self, evt): |
---|
| 649 | """ |
---|
| 650 | Add a data curve to the plot |
---|
| 651 | WARNING: this will be removed once guiframe.plotting has its full functionality |
---|
| 652 | """ |
---|
| 653 | path = self.choose_file() |
---|
| 654 | if path==None: |
---|
| 655 | return |
---|
| 656 | |
---|
[14d05ba] | 657 | #x, y, err = self.parent.load_ascii_1D(path) |
---|
| 658 | # Use data loader to load file |
---|
| 659 | try: |
---|
| 660 | dataread = Loader().load(path) |
---|
| 661 | x = None |
---|
| 662 | y = None |
---|
| 663 | err = None |
---|
| 664 | if dataread.__class__.__name__ == 'Data1D': |
---|
| 665 | x = dataread.x |
---|
| 666 | y = dataread.y |
---|
| 667 | err = dataread.dy |
---|
| 668 | else: |
---|
[e43c012] | 669 | if isinstance(dataread, list) and len(dataread)>0: |
---|
| 670 | x = dataread[0].x |
---|
| 671 | y = dataread[0].y |
---|
| 672 | err = dataread[0].dy |
---|
| 673 | msg = "PrView only allows a single data set at a time. " |
---|
| 674 | msg += "Only the first data set was loaded." |
---|
| 675 | wx.PostEvent(self.parent, StatusEvent(status=msg)) |
---|
| 676 | else: |
---|
| 677 | wx.PostEvent(self.parent, StatusEvent(status="This tool can only read 1D data")) |
---|
| 678 | return |
---|
| 679 | |
---|
[14d05ba] | 680 | except: |
---|
| 681 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
| 682 | return |
---|
[660b1e6] | 683 | |
---|
[f1181977] | 684 | filename = os.path.basename(path) |
---|
| 685 | |
---|
[b659551] | 686 | #new_plot = Data1D(x, y, dy=err) |
---|
| 687 | new_plot = Theory1D(x, y) |
---|
[f1181977] | 688 | new_plot.name = filename |
---|
[660b1e6] | 689 | new_plot.xaxis("\\rm{r}", 'A') |
---|
| 690 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
---|
| 691 | |
---|
[f1181977] | 692 | # Store a ref to the plottable for later use |
---|
| 693 | self._added_plots[filename] = new_plot |
---|
| 694 | self._default_Iq[filename] = numpy.copy(y) |
---|
| 695 | |
---|
| 696 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=filename)) |
---|
[660b1e6] | 697 | |
---|
| 698 | |
---|
[f3d51f6] | 699 | |
---|
| 700 | def start_thread(self): |
---|
| 701 | from pr_thread import CalcPr |
---|
| 702 | from copy import deepcopy |
---|
| 703 | |
---|
| 704 | # If a thread is already started, stop it |
---|
| 705 | if self.calc_thread != None and self.calc_thread.isrunning(): |
---|
| 706 | self.calc_thread.stop() |
---|
| 707 | |
---|
| 708 | pr = self.pr.clone() |
---|
| 709 | self.calc_thread = CalcPr(pr, self.nfunc, error_func=self._thread_error, completefn=self._completed, updatefn=None) |
---|
| 710 | self.calc_thread.queue() |
---|
| 711 | self.calc_thread.ready(2.5) |
---|
| 712 | |
---|
| 713 | def _thread_error(self, error): |
---|
| 714 | wx.PostEvent(self.parent, StatusEvent(status=error)) |
---|
| 715 | |
---|
[32dffae4] | 716 | def _estimate_completed(self, alpha, message, elapsed): |
---|
[f3d51f6] | 717 | """ |
---|
| 718 | Parameter estimation completed, |
---|
| 719 | display the results to the user |
---|
| 720 | @param alpha: estimated best alpha |
---|
| 721 | @param elapsed: computation time |
---|
| 722 | """ |
---|
| 723 | # Save useful info |
---|
| 724 | self.elapsed = elapsed |
---|
| 725 | self.control_panel.alpha_estimate = alpha |
---|
[32dffae4] | 726 | if not message==None: |
---|
| 727 | wx.PostEvent(self.parent, StatusEvent(status=str(message))) |
---|
[35adaf6] | 728 | |
---|
| 729 | self.perform_estimateNT() |
---|
| 730 | |
---|
| 731 | |
---|
| 732 | |
---|
| 733 | def _estimateNT_completed(self, nterms, alpha, message, elapsed): |
---|
| 734 | """ |
---|
| 735 | Parameter estimation completed, |
---|
| 736 | display the results to the user |
---|
| 737 | @param alpha: estimated best alpha |
---|
| 738 | @param nterms: estimated number of terms |
---|
| 739 | @param elapsed: computation time |
---|
| 740 | """ |
---|
| 741 | # Save useful info |
---|
| 742 | self.elapsed = elapsed |
---|
| 743 | self.control_panel.nterms_estimate = nterms |
---|
| 744 | self.control_panel.alpha_estimate = alpha |
---|
| 745 | if not message==None: |
---|
| 746 | wx.PostEvent(self.parent, StatusEvent(status=str(message))) |
---|
[f3d51f6] | 747 | |
---|
| 748 | def _completed(self, out, cov, pr, elapsed): |
---|
| 749 | """ |
---|
| 750 | Method called with the results when the inversion |
---|
| 751 | is done |
---|
| 752 | |
---|
| 753 | @param out: output coefficient for the base functions |
---|
| 754 | @param cov: covariance matrix |
---|
| 755 | @param pr: Invertor instance |
---|
| 756 | @param elapsed: time spent computing |
---|
| 757 | """ |
---|
[dfb58f8] | 758 | from copy import deepcopy |
---|
[f3d51f6] | 759 | # Save useful info |
---|
| 760 | self.elapsed = elapsed |
---|
[feb21d8] | 761 | # Keep a copy of the last result |
---|
| 762 | self._last_pr = pr.clone() |
---|
| 763 | self._last_out = out |
---|
| 764 | self._last_cov = cov |
---|
| 765 | |
---|
[b659551] | 766 | # Save Pr invertor |
---|
| 767 | self.pr = pr |
---|
| 768 | |
---|
[d6113849] | 769 | #message = "Computation completed in %g seconds [chi2=%g]" % (elapsed, pr.chi2) |
---|
| 770 | #wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
[f3d51f6] | 771 | |
---|
[dfb58f8] | 772 | cov = numpy.ascontiguousarray(cov) |
---|
| 773 | |
---|
[f3d51f6] | 774 | # Show result on control panel |
---|
| 775 | self.control_panel.chi2 = pr.chi2 |
---|
| 776 | self.control_panel.elapsed = elapsed |
---|
| 777 | self.control_panel.oscillation = pr.oscillations(out) |
---|
| 778 | #print "OSCILL", pr.oscillations(out) |
---|
[d6113849] | 779 | #print "PEAKS:", pr.get_peaks(out) |
---|
[dfb58f8] | 780 | self.control_panel.positive = pr.get_positive(out) |
---|
| 781 | self.control_panel.pos_err = pr.get_pos_err(out, cov) |
---|
[a4bd2ac] | 782 | self.control_panel.rg = pr.rg(out) |
---|
| 783 | self.control_panel.iq0 = pr.iq0(out) |
---|
| 784 | self.control_panel.bck = pr.background |
---|
[f3d51f6] | 785 | |
---|
[aa4b8379] | 786 | if False: |
---|
[0bae207] | 787 | for i in range(len(out)): |
---|
| 788 | try: |
---|
| 789 | print "%d: %g +- %g" % (i, out[i], math.sqrt(math.fabs(cov[i][i]))) |
---|
| 790 | except: |
---|
| 791 | print sys.exc_value |
---|
| 792 | print "%d: %g +- ?" % (i, out[i]) |
---|
| 793 | |
---|
| 794 | # Make a plot of I(q) data |
---|
[aa4b8379] | 795 | new_plot = Data1D(self.pr.x, self.pr.y, dy=self.pr.err) |
---|
[f1181977] | 796 | new_plot.name = IQ_DATA_LABEL |
---|
[aa4b8379] | 797 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
---|
| 798 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
---|
| 799 | #new_plot.group_id = "test group" |
---|
| 800 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Iq")) |
---|
[f3d51f6] | 801 | |
---|
| 802 | # Show I(q) fit |
---|
| 803 | self.show_iq(out, self.pr) |
---|
| 804 | |
---|
| 805 | # Show P(r) fit |
---|
[dfb58f8] | 806 | x_values, x_range = self.show_pr(out, self.pr, cov) |
---|
[f3d51f6] | 807 | |
---|
| 808 | # Popup result panel |
---|
| 809 | #result_panel = InversionResults(self.parent, -1, style=wx.RAISED_BORDER) |
---|
| 810 | |
---|
[2a92852] | 811 | def show_data(self, path=None, reset=False): |
---|
| 812 | """ |
---|
| 813 | Show data read from a file |
---|
| 814 | @param path: file path |
---|
| 815 | @param reset: if True all other plottables will be cleared |
---|
| 816 | """ |
---|
| 817 | |
---|
| 818 | |
---|
[0bae207] | 819 | if path is not None: |
---|
[ea5551f] | 820 | try: |
---|
| 821 | pr = self._create_file_pr(path) |
---|
[6f1f129] | 822 | |
---|
| 823 | # If the file contains nothing, just return |
---|
| 824 | if pr is None: |
---|
| 825 | return |
---|
| 826 | |
---|
[ea5551f] | 827 | self.pr = pr |
---|
| 828 | except: |
---|
| 829 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
| 830 | return |
---|
[660b1e6] | 831 | |
---|
| 832 | # Make a plot of I(q) data |
---|
[357b79b] | 833 | if self.pr.err==None: |
---|
| 834 | new_plot = Theory1D(self.pr.x, self.pr.y) |
---|
| 835 | else: |
---|
| 836 | new_plot = Data1D(self.pr.x, self.pr.y, dy=self.pr.err) |
---|
[f1181977] | 837 | new_plot.name = IQ_DATA_LABEL |
---|
[660b1e6] | 838 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
---|
| 839 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
---|
[aa4b8379] | 840 | new_plot.interactive = True |
---|
[660b1e6] | 841 | #new_plot.group_id = "test group" |
---|
[2a92852] | 842 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="I(q)", reset=reset)) |
---|
[660b1e6] | 843 | |
---|
[aa4b8379] | 844 | # Get Q range |
---|
| 845 | self.control_panel.q_min = self.pr.x.min() |
---|
| 846 | self.control_panel.q_max = self.pr.x.max() |
---|
| 847 | |
---|
[410aad8] | 848 | def save_data(self, filepath, prstate=None): |
---|
| 849 | """ |
---|
| 850 | Save data in provided state object. |
---|
| 851 | TODO: move the state code away from inversion_panel and move it here. |
---|
| 852 | Then remove the "prstate" input and make this method private. |
---|
| 853 | |
---|
| 854 | @param filepath: path of file to write to |
---|
| 855 | @param prstate: P(r) inversion state |
---|
| 856 | """ |
---|
| 857 | #TODO: do we need this or can we use DataLoader.loader.save directly? |
---|
| 858 | |
---|
| 859 | # Add output data and coefficients to state |
---|
| 860 | prstate.coefficients = self._last_out |
---|
| 861 | prstate.covariance = self._last_cov |
---|
| 862 | |
---|
| 863 | # Write the output to file |
---|
| 864 | self.state_reader.write(filepath, self.current_plottable, prstate) |
---|
| 865 | |
---|
[660b1e6] | 866 | |
---|
[2a92852] | 867 | def setup_plot_inversion(self, alpha, nfunc, d_max, q_min=None, q_max=None, |
---|
| 868 | bck=False, height=0, width=0): |
---|
[f3d51f6] | 869 | self.alpha = alpha |
---|
| 870 | self.nfunc = nfunc |
---|
| 871 | self.max_length = d_max |
---|
[634f1cf] | 872 | self.q_min = q_min |
---|
| 873 | self.q_max = q_max |
---|
[a4bd2ac] | 874 | self.has_bck = bck |
---|
[2a92852] | 875 | self.slit_height = height |
---|
| 876 | self.slit_width = width |
---|
[f3d51f6] | 877 | |
---|
[4a5de6f] | 878 | try: |
---|
[2a92852] | 879 | pr = self._create_plot_pr() |
---|
| 880 | if not pr==None: |
---|
| 881 | self.pr = pr |
---|
| 882 | self.perform_inversion() |
---|
[4a5de6f] | 883 | except: |
---|
| 884 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
[f3d51f6] | 885 | |
---|
[2a92852] | 886 | def estimate_plot_inversion(self, alpha, nfunc, d_max, q_min=None, q_max=None, |
---|
| 887 | bck=False, height=0, width=0): |
---|
[f3d51f6] | 888 | self.alpha = alpha |
---|
| 889 | self.nfunc = nfunc |
---|
| 890 | self.max_length = d_max |
---|
[634f1cf] | 891 | self.q_min = q_min |
---|
| 892 | self.q_max = q_max |
---|
[a4bd2ac] | 893 | self.has_bck = bck |
---|
[2a92852] | 894 | self.slit_height = height |
---|
| 895 | self.slit_width = width |
---|
[f3d51f6] | 896 | |
---|
[4a5de6f] | 897 | try: |
---|
[2a92852] | 898 | pr = self._create_plot_pr() |
---|
| 899 | if not pr==None: |
---|
| 900 | self.pr = pr |
---|
| 901 | self.perform_estimate() |
---|
[4a5de6f] | 902 | except: |
---|
| 903 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
[f3d51f6] | 904 | |
---|
[2a92852] | 905 | def _create_plot_pr(self, estimate=False): |
---|
[f3d51f6] | 906 | """ |
---|
| 907 | Create and prepare invertor instance from |
---|
| 908 | a plottable data set. |
---|
| 909 | @param path: path of the file to read in |
---|
| 910 | """ |
---|
| 911 | # Get the data from the chosen data set and perform inversion |
---|
| 912 | pr = Invertor() |
---|
| 913 | pr.d_max = self.max_length |
---|
| 914 | pr.alpha = self.alpha |
---|
[634f1cf] | 915 | pr.q_min = self.q_min |
---|
| 916 | pr.q_max = self.q_max |
---|
[f3d51f6] | 917 | pr.x = self.current_plottable.x |
---|
| 918 | pr.y = self.current_plottable.y |
---|
[a4bd2ac] | 919 | pr.has_bck = self.has_bck |
---|
[2a92852] | 920 | pr.slit_height = self.slit_height |
---|
| 921 | pr.slit_width = self.slit_width |
---|
[f3d51f6] | 922 | |
---|
[d2ee6f6] | 923 | # Keep track of the plot window title to ensure that |
---|
| 924 | # we can overlay the plots |
---|
| 925 | if hasattr(self.current_plottable, "group_id"): |
---|
| 926 | pr.info["plot_group_id"] = self.current_plottable.group_id |
---|
| 927 | |
---|
[f3d51f6] | 928 | # Fill in errors if none were provided |
---|
[d2ee6f6] | 929 | err = self.current_plottable.dy |
---|
| 930 | all_zeros = True |
---|
| 931 | if err == None: |
---|
[d483799] | 932 | err = numpy.zeros(len(pr.y)) |
---|
[d2ee6f6] | 933 | else: |
---|
| 934 | for i in range(len(err)): |
---|
| 935 | if err[i]>0: |
---|
| 936 | all_zeros = False |
---|
| 937 | |
---|
| 938 | if all_zeros: |
---|
| 939 | scale = None |
---|
| 940 | min_err = 0.0 |
---|
[f3d51f6] | 941 | for i in range(len(pr.y)): |
---|
[d2ee6f6] | 942 | # Scale the error so that we can fit over several decades of Q |
---|
| 943 | if scale==None: |
---|
| 944 | scale = 0.05*math.sqrt(pr.y[i]) |
---|
| 945 | min_err = 0.01*pr.y[i] |
---|
| 946 | err[i] = scale*math.sqrt( math.fabs(pr.y[i]) ) + min_err |
---|
| 947 | message = "The loaded file had no error bars, statistical errors are assumed." |
---|
| 948 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
| 949 | |
---|
| 950 | pr.err = err |
---|
[2a92852] | 951 | |
---|
| 952 | return pr |
---|
[f3d51f6] | 953 | |
---|
| 954 | |
---|
[2a92852] | 955 | def setup_file_inversion(self, alpha, nfunc, d_max, path, q_min=None, q_max=None, |
---|
| 956 | bck=False, height=0, width=0): |
---|
[f3d51f6] | 957 | self.alpha = alpha |
---|
| 958 | self.nfunc = nfunc |
---|
| 959 | self.max_length = d_max |
---|
[634f1cf] | 960 | self.q_min = q_min |
---|
| 961 | self.q_max = q_max |
---|
[a4bd2ac] | 962 | self.has_bck = bck |
---|
[2a92852] | 963 | self.slit_height = height |
---|
| 964 | self.slit_width = width |
---|
[f3d51f6] | 965 | |
---|
[4a5de6f] | 966 | try: |
---|
[2a92852] | 967 | pr = self._create_file_pr(path) |
---|
| 968 | if not pr==None: |
---|
| 969 | self.pr = pr |
---|
[4a5de6f] | 970 | self.perform_inversion() |
---|
| 971 | except: |
---|
| 972 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
[f3d51f6] | 973 | |
---|
[2a92852] | 974 | def estimate_file_inversion(self, alpha, nfunc, d_max, path, q_min=None, q_max=None, |
---|
| 975 | bck=False, height=0, width=0): |
---|
[f3d51f6] | 976 | self.alpha = alpha |
---|
| 977 | self.nfunc = nfunc |
---|
| 978 | self.max_length = d_max |
---|
[634f1cf] | 979 | self.q_min = q_min |
---|
| 980 | self.q_max = q_max |
---|
[a4bd2ac] | 981 | self.has_bck = bck |
---|
[2a92852] | 982 | self.slit_height = height |
---|
| 983 | self.slit_width = width |
---|
[f3d51f6] | 984 | |
---|
[4a5de6f] | 985 | try: |
---|
[2a92852] | 986 | pr = self._create_file_pr(path) |
---|
| 987 | if not pr==None: |
---|
| 988 | self.pr = pr |
---|
[4a5de6f] | 989 | self.perform_estimate() |
---|
| 990 | except: |
---|
| 991 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
| 992 | |
---|
[f3d51f6] | 993 | |
---|
| 994 | def _create_file_pr(self, path): |
---|
| 995 | """ |
---|
| 996 | Create and prepare invertor instance from |
---|
| 997 | a file data set. |
---|
| 998 | @param path: path of the file to read in |
---|
| 999 | """ |
---|
| 1000 | # Load data |
---|
| 1001 | if os.path.isfile(path): |
---|
[357b79b] | 1002 | |
---|
[0bae207] | 1003 | if self._current_file_data is not None \ |
---|
| 1004 | and self._current_file_data.path==path: |
---|
[aab8ad7] | 1005 | # Protect against corrupted data from |
---|
| 1006 | # previous failed load attempt |
---|
| 1007 | if self._current_file_data.x is None: |
---|
| 1008 | return None |
---|
[0bae207] | 1009 | x = self._current_file_data.x |
---|
| 1010 | y = self._current_file_data.y |
---|
| 1011 | err = self._current_file_data.err |
---|
| 1012 | else: |
---|
[e43c012] | 1013 | # Reset the status bar so that we don't get mixed up |
---|
| 1014 | # with old messages. |
---|
| 1015 | #TODO: refactor this into a proper status handling |
---|
| 1016 | wx.PostEvent(self.parent, StatusEvent(status='')) |
---|
[0bae207] | 1017 | x, y, err = self.load(path) |
---|
[6f1f129] | 1018 | |
---|
| 1019 | # If the file contains no data, just return |
---|
| 1020 | #TODO: clean this up: we need a way to recognize that not all P(r) files are data |
---|
| 1021 | if x is None: |
---|
| 1022 | return None |
---|
[357b79b] | 1023 | |
---|
| 1024 | # If we have not errors, add statistical errors |
---|
[aab8ad7] | 1025 | if err==None and y is not None: |
---|
[357b79b] | 1026 | err = numpy.zeros(len(y)) |
---|
[aab8ad7] | 1027 | scale = None |
---|
| 1028 | min_err = 0.0 |
---|
[357b79b] | 1029 | for i in range(len(y)): |
---|
[aab8ad7] | 1030 | # Scale the error so that we can fit over several decades of Q |
---|
| 1031 | if scale==None: |
---|
| 1032 | scale = 0.05*math.sqrt(y[i]) |
---|
| 1033 | min_err = 0.01*y[i] |
---|
| 1034 | err[i] = scale*math.sqrt( math.fabs(y[i]) ) + min_err |
---|
[357b79b] | 1035 | message = "The loaded file had no error bars, statistical errors are assumed." |
---|
| 1036 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
[f3d51f6] | 1037 | |
---|
[aab8ad7] | 1038 | try: |
---|
| 1039 | # Get the data from the chosen data set and perform inversion |
---|
| 1040 | pr = Invertor() |
---|
| 1041 | pr.d_max = self.max_length |
---|
| 1042 | pr.alpha = self.alpha |
---|
| 1043 | pr.q_min = self.q_min |
---|
| 1044 | pr.q_max = self.q_max |
---|
| 1045 | pr.x = x |
---|
| 1046 | pr.y = y |
---|
| 1047 | pr.err = err |
---|
| 1048 | pr.has_bck = self.has_bck |
---|
| 1049 | pr.slit_height = self.slit_height |
---|
| 1050 | pr.slit_width = self.slit_width |
---|
| 1051 | return pr |
---|
| 1052 | except: |
---|
| 1053 | wx.PostEvent(self.parent, StatusEvent(status="Problem reading data: %s" % sys.exc_value)) |
---|
[2a92852] | 1054 | return None |
---|
[f3d51f6] | 1055 | |
---|
| 1056 | def perform_estimate(self): |
---|
| 1057 | from pr_thread import EstimatePr |
---|
| 1058 | from copy import deepcopy |
---|
| 1059 | |
---|
| 1060 | # If a thread is already started, stop it |
---|
| 1061 | if self.estimation_thread != None and self.estimation_thread.isrunning(): |
---|
| 1062 | self.estimation_thread.stop() |
---|
| 1063 | |
---|
| 1064 | pr = self.pr.clone() |
---|
| 1065 | self.estimation_thread = EstimatePr(pr, self.nfunc, error_func=self._thread_error, |
---|
| 1066 | completefn = self._estimate_completed, |
---|
| 1067 | updatefn = None) |
---|
| 1068 | self.estimation_thread.queue() |
---|
| 1069 | self.estimation_thread.ready(2.5) |
---|
[35adaf6] | 1070 | |
---|
| 1071 | def perform_estimateNT(self): |
---|
| 1072 | from pr_thread import EstimateNT |
---|
| 1073 | from copy import deepcopy |
---|
| 1074 | |
---|
| 1075 | # If a thread is already started, stop it |
---|
| 1076 | if self.estimation_thread != None and self.estimation_thread.isrunning(): |
---|
| 1077 | self.estimation_thread.stop() |
---|
| 1078 | |
---|
| 1079 | pr = self.pr.clone() |
---|
[2a92852] | 1080 | # Skip the slit settings for the estimation |
---|
| 1081 | # It slows down the application and it doesn't change the estimates |
---|
| 1082 | pr.slit_height = 0.0 |
---|
| 1083 | pr.slit_width = 0.0 |
---|
[35adaf6] | 1084 | self.estimation_thread = EstimateNT(pr, self.nfunc, error_func=self._thread_error, |
---|
| 1085 | completefn = self._estimateNT_completed, |
---|
| 1086 | updatefn = None) |
---|
| 1087 | self.estimation_thread.queue() |
---|
| 1088 | self.estimation_thread.ready(2.5) |
---|
[f3d51f6] | 1089 | |
---|
| 1090 | def perform_inversion(self): |
---|
| 1091 | |
---|
| 1092 | # Time estimate |
---|
| 1093 | #estimated = self.elapsed*self.nfunc**2 |
---|
[2a92852] | 1094 | #message = "Computation time may take up to %g seconds" % self.elapsed |
---|
| 1095 | #wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
[f3d51f6] | 1096 | |
---|
| 1097 | # Start inversion thread |
---|
| 1098 | self.start_thread() |
---|
| 1099 | return |
---|
| 1100 | |
---|
| 1101 | out, cov = self.pr.lstsq(self.nfunc) |
---|
| 1102 | |
---|
| 1103 | # Save useful info |
---|
| 1104 | self.elapsed = self.pr.elapsed |
---|
| 1105 | |
---|
| 1106 | for i in range(len(out)): |
---|
| 1107 | try: |
---|
| 1108 | print "%d: %g +- %g" % (i, out[i], math.sqrt(math.fabs(cov[i][i]))) |
---|
| 1109 | except: |
---|
| 1110 | print "%d: %g +- ?" % (i, out[i]) |
---|
| 1111 | |
---|
| 1112 | |
---|
| 1113 | |
---|
| 1114 | # Make a plot of I(q) data |
---|
| 1115 | new_plot = Data1D(self.pr.x, self.pr.y, dy=self.pr.err) |
---|
| 1116 | new_plot.name = "I_{obs}(q)" |
---|
| 1117 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
---|
| 1118 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
---|
| 1119 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Iq")) |
---|
| 1120 | |
---|
| 1121 | # Show I(q) fit |
---|
| 1122 | self.show_iq(out, self.pr) |
---|
| 1123 | |
---|
| 1124 | # Show P(r) fit |
---|
| 1125 | x_values, x_range = self.show_pr(out, self.pr, cov=cov) |
---|
| 1126 | |
---|
| 1127 | |
---|
| 1128 | |
---|
| 1129 | def _on_context_inversion(self, event): |
---|
| 1130 | panel = event.GetEventObject() |
---|
| 1131 | |
---|
| 1132 | from inversion_panel import InversionDlg |
---|
| 1133 | |
---|
| 1134 | # If we have more than one displayed plot, make the user choose |
---|
[aa4b8379] | 1135 | if len(panel.plots)>1 and panel.graph.selected_plottable in panel.plots: |
---|
| 1136 | dataset = panel.graph.selected_plottable |
---|
| 1137 | if False: |
---|
| 1138 | dialog = InversionDlg(None, -1, "P(r) Inversion", panel.plots, pars=False) |
---|
| 1139 | dialog.set_content(self.last_data, self.nfunc, self.alpha, self.max_length) |
---|
| 1140 | if dialog.ShowModal() == wx.ID_OK: |
---|
| 1141 | dataset = dialog.get_content() |
---|
| 1142 | dialog.Destroy() |
---|
| 1143 | else: |
---|
| 1144 | dialog.Destroy() |
---|
| 1145 | return |
---|
[f3d51f6] | 1146 | elif len(panel.plots)==1: |
---|
| 1147 | dataset = panel.plots.keys()[0] |
---|
| 1148 | else: |
---|
| 1149 | print "Error: No data is available" |
---|
| 1150 | return |
---|
| 1151 | |
---|
| 1152 | # Store a reference to the current plottable |
---|
[3fd1ebc] | 1153 | # If we have a suggested value, use it. |
---|
| 1154 | try: |
---|
| 1155 | estimate = float(self.control_panel.alpha_estimate) |
---|
| 1156 | self.control_panel.alpha = estimate |
---|
| 1157 | except: |
---|
| 1158 | self.control_panel.alpha = self.alpha |
---|
| 1159 | print "No estimate yet" |
---|
| 1160 | pass |
---|
[d6113849] | 1161 | try: |
---|
| 1162 | estimate = int(self.control_panel.nterms_estimate) |
---|
| 1163 | self.control_panel.nfunc = estimate |
---|
| 1164 | except: |
---|
| 1165 | self.control_panel.nfunc = self.nfunc |
---|
| 1166 | print "No estimate yet" |
---|
| 1167 | pass |
---|
[3fd1ebc] | 1168 | |
---|
[f3d51f6] | 1169 | self.current_plottable = panel.plots[dataset] |
---|
| 1170 | self.control_panel.plotname = dataset |
---|
[d6113849] | 1171 | #self.control_panel.nfunc = self.nfunc |
---|
[f3d51f6] | 1172 | self.control_panel.d_max = self.max_length |
---|
| 1173 | self.parent.set_perspective(self.perspective) |
---|
[aa4b8379] | 1174 | self.control_panel._on_invert(None) |
---|
[f3d51f6] | 1175 | |
---|
| 1176 | def get_panels(self, parent): |
---|
| 1177 | """ |
---|
| 1178 | Create and return a list of panel objects |
---|
| 1179 | """ |
---|
| 1180 | from inversion_panel import InversionControl |
---|
| 1181 | |
---|
| 1182 | self.parent = parent |
---|
[aa4b8379] | 1183 | self.control_panel = InversionControl(self.parent, -1, |
---|
| 1184 | style=wx.RAISED_BORDER, |
---|
| 1185 | standalone=self.standalone) |
---|
[f3d51f6] | 1186 | self.control_panel.set_manager(self) |
---|
| 1187 | self.control_panel.nfunc = self.nfunc |
---|
| 1188 | self.control_panel.d_max = self.max_length |
---|
| 1189 | self.control_panel.alpha = self.alpha |
---|
| 1190 | |
---|
| 1191 | self.perspective = [] |
---|
| 1192 | self.perspective.append(self.control_panel.window_name) |
---|
[aa4b8379] | 1193 | |
---|
| 1194 | self.parent.Bind(EVT_PR_FILE, self._on_new_file) |
---|
| 1195 | |
---|
[f3d51f6] | 1196 | return [self.control_panel] |
---|
| 1197 | |
---|
[aa4b8379] | 1198 | def _on_new_file(self, evt): |
---|
| 1199 | """ |
---|
| 1200 | Called when the application manager posted an |
---|
| 1201 | EVT_PR_FILE event. Just prompt the control |
---|
| 1202 | panel to load a new data file. |
---|
| 1203 | """ |
---|
| 1204 | self.control_panel._change_file(None) |
---|
| 1205 | |
---|
[f3d51f6] | 1206 | def get_perspective(self): |
---|
| 1207 | """ |
---|
| 1208 | Get the list of panel names for this perspective |
---|
| 1209 | """ |
---|
| 1210 | return self.perspective |
---|
| 1211 | |
---|
| 1212 | def on_perspective(self, event): |
---|
| 1213 | """ |
---|
| 1214 | Call back function for the perspective menu item. |
---|
| 1215 | We notify the parent window that the perspective |
---|
| 1216 | has changed. |
---|
| 1217 | """ |
---|
| 1218 | self.parent.set_perspective(self.perspective) |
---|
| 1219 | |
---|
| 1220 | def post_init(self): |
---|
| 1221 | """ |
---|
| 1222 | Post initialization call back to close the loose ends |
---|
| 1223 | [Somehow openGL needs this call] |
---|
| 1224 | """ |
---|
[d2ee6f6] | 1225 | if self.standalone==True: |
---|
| 1226 | self.parent.set_perspective(self.perspective) |
---|
[35adaf6] | 1227 | |
---|
| 1228 | if __name__ == "__main__": |
---|
| 1229 | i = Plugin() |
---|
| 1230 | print i.perform_estimateNT() |
---|
| 1231 | |
---|
| 1232 | |
---|
| 1233 | |
---|
[660b1e6] | 1234 | |
---|