[9ff861b] | 1 | |
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[7116b6e0] | 2 | ################################################################################ |
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| 3 | #This software was developed by the University of Tennessee as part of the |
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| 4 | #Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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| 5 | #project funded by the US National Science Foundation. |
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| 6 | # |
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| 7 | #See the license text in license.txt |
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| 8 | # |
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| 9 | #copyright 2009, University of Tennessee |
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| 10 | ################################################################################ |
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[9ff861b] | 11 | |
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| 12 | |
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[f3d51f6] | 13 | # Make sure the option of saving each curve is available |
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| 14 | # Use the I(q) curve as input and compare the output to P(r) |
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| 15 | |
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| 16 | import os |
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[4a5de6f] | 17 | import sys |
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[f3d51f6] | 18 | import wx |
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[aa4b8379] | 19 | import logging |
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[302510b] | 20 | import time |
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[75df58b] | 21 | import copy |
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| 22 | import math |
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| 23 | import numpy |
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| 24 | import pylab |
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| 25 | from sans.guiframe.dataFitting import Data1D |
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| 26 | from sans.guiframe.dataFitting import Theory1D |
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| 27 | from sans.guiframe.events import NewPlotEvent |
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| 28 | from sans.guiframe.events import StatusEvent |
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| 29 | |
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[f3d51f6] | 30 | from sans.pr.invertor import Invertor |
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[aab8ad7] | 31 | from DataLoader.loader import Loader |
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[75df58b] | 32 | from DataLoader.data_info import Data1D as LoaderData1D |
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[80d2872] | 33 | import DataLoader |
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[af91b68] | 34 | from pr_widgets import load_error |
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[75df58b] | 35 | from sans.guiframe.plugin_base import PluginBase |
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[f3d51f6] | 36 | |
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[0d88a09] | 37 | |
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[f1181977] | 38 | PR_FIT_LABEL = r"$P_{fit}(r)$" |
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| 39 | PR_LOADED_LABEL = r"$P_{loaded}(r)$" |
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| 40 | IQ_DATA_LABEL = r"$I_{obs}(q)$" |
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| 41 | IQ_FIT_LABEL = r"$I_{fit}(q)$" |
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| 42 | IQ_SMEARED_LABEL = r"$I_{smeared}(q)$" |
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[aa4b8379] | 43 | |
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[75df58b] | 44 | #import wx.lib |
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| 45 | #(NewPrFileEvent, EVT_PR_FILE) = wx.lib.newevent.NewEvent() |
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| 46 | |
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[aa4b8379] | 47 | |
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| 48 | |
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[3e41f43] | 49 | class Plugin(PluginBase): |
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[7116b6e0] | 50 | """ |
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| 51 | """ |
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[b659551] | 52 | DEFAULT_ALPHA = 0.0001 |
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| 53 | DEFAULT_NFUNC = 10 |
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| 54 | DEFAULT_DMAX = 140.0 |
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| 55 | |
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[d2ee6f6] | 56 | def __init__(self, standalone=True): |
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[3e41f43] | 57 | PluginBase.__init__(self, name="Pr inversion", standalone=standalone) |
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[f3d51f6] | 58 | ## Simulation window manager |
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| 59 | self.simview = None |
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[3e41f43] | 60 | |
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[f3d51f6] | 61 | ## State data |
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[b659551] | 62 | self.alpha = self.DEFAULT_ALPHA |
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| 63 | self.nfunc = self.DEFAULT_NFUNC |
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| 64 | self.max_length = self.DEFAULT_DMAX |
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[634f1cf] | 65 | self.q_min = None |
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| 66 | self.q_max = None |
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[a4bd2ac] | 67 | self.has_bck = False |
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[2a92852] | 68 | self.slit_height = 0 |
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| 69 | self.slit_width = 0 |
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[f3d51f6] | 70 | ## Remember last plottable processed |
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| 71 | self.last_data = "sphere_60_q0_2.txt" |
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[0bae207] | 72 | self._current_file_data = None |
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[f3d51f6] | 73 | ## Time elapsed for last computation [sec] |
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| 74 | # Start with a good default |
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| 75 | self.elapsed = 0.022 |
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[aa4b8379] | 76 | self.iq_data_shown = False |
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[f3d51f6] | 77 | |
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| 78 | ## Current invertor |
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| 79 | self.invertor = None |
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[3fd1ebc] | 80 | self.pr = None |
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[feb21d8] | 81 | # Copy of the last result in case we need to display it. |
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| 82 | self._last_pr = None |
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| 83 | self._last_out = None |
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| 84 | self._last_cov = None |
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[f3d51f6] | 85 | ## Calculation thread |
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| 86 | self.calc_thread = None |
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| 87 | ## Estimation thread |
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| 88 | self.estimation_thread = None |
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| 89 | ## Result panel |
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| 90 | self.control_panel = None |
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| 91 | ## Currently views plottable |
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| 92 | self.current_plottable = None |
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[b659551] | 93 | ## Number of P(r) points to display on the output plot |
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| 94 | self._pr_npts = 51 |
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[aa4b8379] | 95 | ## Flag to let the plug-in know that it is running standalone |
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[d2ee6f6] | 96 | self.standalone = standalone |
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[feb21d8] | 97 | self._normalize_output = False |
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| 98 | self._scale_output_unity = False |
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[aa4b8379] | 99 | |
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[f1181977] | 100 | ## List of added P(r) plots |
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| 101 | self._added_plots = {} |
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| 102 | self._default_Iq = {} |
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| 103 | |
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[6f1f129] | 104 | # Associate the inversion state reader with .prv files |
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| 105 | from DataLoader.loader import Loader |
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| 106 | from inversion_state import Reader |
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| 107 | |
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[0d88a09] | 108 | # Create a CanSAS/Pr reader |
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| 109 | self.state_reader = Reader(self.set_state) |
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[6f1f129] | 110 | l = Loader() |
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[410aad8] | 111 | l.associate_file_reader('.prv', self.state_reader) |
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[b35d3d1] | 112 | l.associate_file_reader(".sav", self.state_reader) |
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[6f1f129] | 113 | |
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[aa4b8379] | 114 | # Log startup |
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| 115 | logging.info("Pr(r) plug-in started") |
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| 116 | |
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[410aad8] | 117 | def set_state(self, state, datainfo=None): |
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[6f1f129] | 118 | """ |
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[7116b6e0] | 119 | Call-back method for the inversion state reader. |
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| 120 | This method is called when a .prv file is loaded. |
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| 121 | |
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| 122 | :param state: InversionState object |
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| 123 | :param datainfo: Data1D object [optional] |
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| 124 | |
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[6f1f129] | 125 | """ |
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[410aad8] | 126 | try: |
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[0d88a09] | 127 | if datainfo is None: |
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| 128 | raise RuntimeError, "Pr.set_state: datainfo parameter cannot be None in standalone mode" |
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[302510b] | 129 | |
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[0d88a09] | 130 | # Ensuring that plots are coordinated correctly |
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| 131 | t = time.localtime(datainfo.meta_data['prstate'].timestamp) |
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| 132 | time_str = time.strftime("%b %d %H:%M", t) |
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| 133 | |
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| 134 | # Check that no time stamp is already appended |
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| 135 | max_char = datainfo.meta_data['prstate'].file.find("[") |
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| 136 | if max_char < 0: |
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| 137 | max_char = len(datainfo.meta_data['prstate'].file) |
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| 138 | |
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| 139 | datainfo.meta_data['prstate'].file = datainfo.meta_data['prstate'].file[0:max_char] +' [' + time_str + ']' |
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| 140 | datainfo.filename = datainfo.meta_data['prstate'].file |
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[410aad8] | 141 | |
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[0d88a09] | 142 | self.current_plottable = datainfo |
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| 143 | self.current_plottable.group_id = datainfo.meta_data['prstate'].file |
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| 144 | |
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[410aad8] | 145 | # Load the P(r) results |
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| 146 | self.control_panel.set_state(state) |
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| 147 | |
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| 148 | # Make sure the user sees the P(r) panel after loading |
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| 149 | self.parent.set_perspective(self.perspective) |
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| 150 | |
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| 151 | except: |
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| 152 | logging.error("prview.set_state: %s" % sys.exc_value) |
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[f3d51f6] | 153 | |
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[8994b6b] | 154 | |
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[119a11d] | 155 | def help(self, evt): |
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| 156 | """ |
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[7116b6e0] | 157 | Show a general help dialog. |
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| 158 | |
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| 159 | :TODO: replace the text with a nice image |
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| 160 | |
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[119a11d] | 161 | """ |
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| 162 | from inversion_panel import HelpDialog |
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| 163 | dialog = HelpDialog(None, -1) |
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| 164 | if dialog.ShowModal() == wx.ID_OK: |
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| 165 | dialog.Destroy() |
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| 166 | else: |
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| 167 | dialog.Destroy() |
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| 168 | |
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[f3d51f6] | 169 | def _fit_pr(self, evt): |
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[7116b6e0] | 170 | """ |
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| 171 | """ |
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[f3d51f6] | 172 | from sans.pr.invertor import Invertor |
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[75df58b] | 173 | |
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| 174 | from danse.common.plottools import Data1D as PlotData1D |
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| 175 | from danse.common.plottools import Theory1D as Theory1D |
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[f3d51f6] | 176 | |
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| 177 | # Generate P(r) for sphere |
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| 178 | radius = 60.0 |
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| 179 | d_max = 2*radius |
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| 180 | |
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| 181 | r = pylab.arange(0.01, d_max, d_max/51.0) |
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| 182 | M = len(r) |
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| 183 | y = numpy.zeros(M) |
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| 184 | pr_err = numpy.zeros(M) |
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| 185 | |
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| 186 | sum = 0.0 |
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| 187 | for j in range(M): |
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| 188 | value = self.pr_theory(r[j], radius) |
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| 189 | sum += value |
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| 190 | y[j] = value |
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| 191 | pr_err[j] = math.sqrt(y[j]) |
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| 192 | |
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| 193 | y = y/sum*d_max/len(r) |
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| 194 | |
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| 195 | # Perform fit |
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| 196 | pr = Invertor() |
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| 197 | pr.d_max = d_max |
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| 198 | pr.alpha = 0 |
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| 199 | pr.x = r |
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| 200 | pr.y = y |
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| 201 | pr.err = pr_err |
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| 202 | out, cov = pr.pr_fit() |
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| 203 | for i in range(len(out)): |
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| 204 | print "%g +- %g" % (out[i], math.sqrt(cov[i][i])) |
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| 205 | |
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| 206 | # Show input P(r) |
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[75df58b] | 207 | new_plot = PlotData1D(pr.x, pr.y, dy=pr.err) |
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[f3d51f6] | 208 | new_plot.name = "P_{obs}(r)" |
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| 209 | new_plot.xaxis("\\rm{r}", 'A') |
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| 210 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
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[75df58b] | 211 | print "_fit_pr" |
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[f3d51f6] | 212 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Pr")) |
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| 213 | |
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| 214 | # Show P(r) fit |
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| 215 | self.show_pr(out, pr) |
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| 216 | |
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| 217 | # Show I(q) fit |
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| 218 | q = pylab.arange(0.001, 0.1, 0.01/51.0) |
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| 219 | self.show_iq(out, pr, q) |
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| 220 | |
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| 221 | def show_shpere(self, x, radius=70.0, x_range=70.0): |
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[7116b6e0] | 222 | """ |
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| 223 | """ |
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[75df58b] | 224 | from danse.common.plottools import Theory1D as PlotTheory1D |
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[f3d51f6] | 225 | # Show P(r) |
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| 226 | y_true = numpy.zeros(len(x)) |
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| 227 | |
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| 228 | sum_true = 0.0 |
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| 229 | for i in range(len(x)): |
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| 230 | y_true[i] = self.pr_theory(x[i], radius) |
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| 231 | sum_true += y_true[i] |
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| 232 | |
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| 233 | y_true = y_true/sum_true*x_range/len(x) |
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| 234 | |
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| 235 | # Show the theory P(r) |
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[75df58b] | 236 | new_plot = PlotTheory1D(x, y_true) |
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[f3d51f6] | 237 | new_plot.name = "P_{true}(r)" |
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| 238 | new_plot.xaxis("\\rm{r}", 'A') |
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| 239 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
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| 240 | |
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| 241 | #Put this call in plottables/guitools |
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| 242 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Sphere P(r)")) |
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[75df58b] | 243 | |
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[f3d51f6] | 244 | |
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[b659551] | 245 | def get_npts(self): |
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| 246 | """ |
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[7116b6e0] | 247 | Returns the number of points in the I(q) data |
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[b659551] | 248 | """ |
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| 249 | try: |
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| 250 | return len(self.pr.x) |
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| 251 | except: |
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| 252 | return 0 |
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| 253 | |
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[f3d51f6] | 254 | def show_iq(self, out, pr, q=None): |
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[7116b6e0] | 255 | """ |
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[75df58b] | 256 | """ |
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| 257 | from danse.common.plottools import Theory1D as PlotTheory1D |
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[f3d51f6] | 258 | |
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| 259 | qtemp = pr.x |
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| 260 | if not q==None: |
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| 261 | qtemp = q |
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| 262 | |
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| 263 | # Make a plot |
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| 264 | maxq = -1 |
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| 265 | for q_i in qtemp: |
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| 266 | if q_i>maxq: |
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| 267 | maxq=q_i |
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| 268 | |
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[634f1cf] | 269 | minq = 0.001 |
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| 270 | |
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| 271 | # Check for user min/max |
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| 272 | if not pr.q_min==None: |
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| 273 | minq = pr.q_min |
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| 274 | if not pr.q_max==None: |
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| 275 | maxq = pr.q_max |
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| 276 | |
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| 277 | x = pylab.arange(minq, maxq, maxq/301.0) |
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[f3d51f6] | 278 | y = numpy.zeros(len(x)) |
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| 279 | err = numpy.zeros(len(x)) |
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| 280 | for i in range(len(x)): |
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| 281 | value = pr.iq(out, x[i]) |
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| 282 | y[i] = value |
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| 283 | try: |
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| 284 | err[i] = math.sqrt(math.fabs(value)) |
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| 285 | except: |
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| 286 | err[i] = 1.0 |
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| 287 | print "Error getting error", value, x[i] |
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| 288 | |
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[75df58b] | 289 | new_plot = PlotTheory1D(x, y) |
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[2a92852] | 290 | new_plot.name = IQ_FIT_LABEL |
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[f3d51f6] | 291 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
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| 292 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
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[d2ee6f6] | 293 | |
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| 294 | title = "I(q)" |
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| 295 | # If we have a group ID, use it |
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| 296 | if pr.info.has_key("plot_group_id"): |
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| 297 | new_plot.group_id = pr.info["plot_group_id"] |
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| 298 | title = pr.info["plot_group_id"] |
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| 299 | |
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| 300 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title)) |
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[f3d51f6] | 301 | |
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[2a92852] | 302 | # If we have used slit smearing, plot the smeared I(q) too |
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| 303 | if pr.slit_width>0 or pr.slit_height>0: |
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| 304 | x = pylab.arange(minq, maxq, maxq/301.0) |
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| 305 | y = numpy.zeros(len(x)) |
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| 306 | err = numpy.zeros(len(x)) |
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| 307 | for i in range(len(x)): |
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| 308 | value = pr.iq_smeared(out, x[i]) |
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| 309 | y[i] = value |
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| 310 | try: |
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| 311 | err[i] = math.sqrt(math.fabs(value)) |
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| 312 | except: |
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| 313 | err[i] = 1.0 |
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| 314 | print "Error getting error", value, x[i] |
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| 315 | |
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| 316 | new_plot = Theory1D(x, y) |
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| 317 | new_plot.name = IQ_SMEARED_LABEL |
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| 318 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
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| 319 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
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[f0ff8d65] | 320 | # If we have a group ID, use it |
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| 321 | if pr.info.has_key("plot_group_id"): |
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| 322 | new_plot.group_id = pr.info["plot_group_id"] |
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| 323 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title)) |
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[2a92852] | 324 | |
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[f3d51f6] | 325 | |
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[b659551] | 326 | def _on_pr_npts(self, evt): |
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| 327 | """ |
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[7116b6e0] | 328 | Redisplay P(r) with a different number of points |
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[b659551] | 329 | """ |
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| 330 | from inversion_panel import PrDistDialog |
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| 331 | dialog = PrDistDialog(None, -1) |
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| 332 | dialog.set_content(self._pr_npts) |
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| 333 | if dialog.ShowModal() == wx.ID_OK: |
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| 334 | self._pr_npts= dialog.get_content() |
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| 335 | dialog.Destroy() |
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[feb21d8] | 336 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
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[b659551] | 337 | else: |
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| 338 | dialog.Destroy() |
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[f3d51f6] | 339 | |
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| 340 | |
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| 341 | def show_pr(self, out, pr, cov=None): |
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[7116b6e0] | 342 | """ |
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[75df58b] | 343 | """ |
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| 344 | from danse.common.plottools import Data1D as PlotData1D |
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| 345 | from danse.common.plottools import Theory1D as PlotTheory1D |
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[f3d51f6] | 346 | |
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| 347 | # Show P(r) |
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[b659551] | 348 | x = pylab.arange(0.0, pr.d_max, pr.d_max/self._pr_npts) |
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[f3d51f6] | 349 | |
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| 350 | y = numpy.zeros(len(x)) |
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| 351 | dy = numpy.zeros(len(x)) |
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| 352 | y_true = numpy.zeros(len(x)) |
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| 353 | |
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| 354 | sum = 0.0 |
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[feb21d8] | 355 | pmax = 0.0 |
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[dfb58f8] | 356 | cov2 = numpy.ascontiguousarray(cov) |
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| 357 | |
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[f3d51f6] | 358 | for i in range(len(x)): |
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[dfb58f8] | 359 | if cov2==None: |
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[f3d51f6] | 360 | value = pr.pr(out, x[i]) |
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| 361 | else: |
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[dfb58f8] | 362 | (value, dy[i]) = pr.pr_err(out, cov2, x[i]) |
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[660b1e6] | 363 | sum += value*pr.d_max/len(x) |
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[f3d51f6] | 364 | |
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[feb21d8] | 365 | # keep track of the maximum P(r) value |
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| 366 | if value>pmax: |
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| 367 | pmax = value |
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| 368 | |
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| 369 | y[i] = value |
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| 370 | |
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| 371 | if self._normalize_output==True: |
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| 372 | y = y/sum |
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| 373 | dy = dy/sum |
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| 374 | elif self._scale_output_unity==True: |
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| 375 | y = y/pmax |
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| 376 | dy = dy/pmax |
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[f3d51f6] | 377 | |
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[dfb58f8] | 378 | if cov2==None: |
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[75df58b] | 379 | new_plot = PlotTheory1D(x, y) |
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[f3d51f6] | 380 | else: |
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[75df58b] | 381 | new_plot = PlotData1D(x, y, dy=dy) |
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[f1181977] | 382 | new_plot.name = PR_FIT_LABEL |
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[f3d51f6] | 383 | new_plot.xaxis("\\rm{r}", 'A') |
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| 384 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
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[75df58b] | 385 | new_plot.title = "P(r) fit" |
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[d2ee6f6] | 386 | # Make sure that the plot is linear |
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| 387 | new_plot.xtransform="x" |
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| 388 | new_plot.ytransform="y" |
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[f3d51f6] | 389 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="P(r) fit")) |
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| 390 | |
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| 391 | return x, pr.d_max |
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| 392 | |
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| 393 | |
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[75df58b] | 394 | def load(self, data): |
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[0bae207] | 395 | """ |
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[7116b6e0] | 396 | Load data. This will eventually be replaced |
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| 397 | by our standard DataLoader class. |
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[0bae207] | 398 | """ |
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| 399 | class FileData: |
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| 400 | x = None |
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| 401 | y = None |
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| 402 | err = None |
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| 403 | path = None |
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| 404 | |
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| 405 | def __init__(self, path): |
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| 406 | self.path = path |
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| 407 | |
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[75df58b] | 408 | self._current_file_data = FileData(data.path) |
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[0bae207] | 409 | |
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[aab8ad7] | 410 | # Use data loader to load file |
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[75df58b] | 411 | #dataread = Loader().load(path) |
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| 412 | dataread = data |
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[ceaf16e] | 413 | # Notify the user if we could not read the file |
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| 414 | if dataread is None: |
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| 415 | raise RuntimeError, "Invalid data" |
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| 416 | |
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[aab8ad7] | 417 | x = None |
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| 418 | y = None |
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| 419 | err = None |
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| 420 | if dataread.__class__.__name__ == 'Data1D': |
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| 421 | x = dataread.x |
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| 422 | y = dataread.y |
---|
| 423 | err = dataread.dy |
---|
| 424 | else: |
---|
[e43c012] | 425 | if isinstance(dataread, list) and len(dataread)>0: |
---|
| 426 | x = dataread[0].x |
---|
| 427 | y = dataread[0].y |
---|
| 428 | err = dataread[0].dy |
---|
| 429 | msg = "PrView only allows a single data set at a time. " |
---|
| 430 | msg += "Only the first data set was loaded." |
---|
| 431 | wx.PostEvent(self.parent, StatusEvent(status=msg)) |
---|
| 432 | else: |
---|
[6f1f129] | 433 | if dataread is None: |
---|
| 434 | return x, y, err |
---|
[e43c012] | 435 | raise RuntimeError, "This tool can only read 1D data" |
---|
[aab8ad7] | 436 | |
---|
[0bae207] | 437 | self._current_file_data.x = x |
---|
| 438 | self._current_file_data.y = y |
---|
| 439 | self._current_file_data.err = err |
---|
| 440 | return x, y, err |
---|
| 441 | |
---|
| 442 | def load_columns(self, path = "sphere_60_q0_2.txt"): |
---|
| 443 | """ |
---|
[7116b6e0] | 444 | Load 2- or 3- column ascii |
---|
[0bae207] | 445 | """ |
---|
[f3d51f6] | 446 | import numpy, math, sys |
---|
| 447 | # Read the data from the data file |
---|
| 448 | data_x = numpy.zeros(0) |
---|
| 449 | data_y = numpy.zeros(0) |
---|
| 450 | data_err = numpy.zeros(0) |
---|
[b659551] | 451 | scale = None |
---|
| 452 | min_err = 0.0 |
---|
[f3d51f6] | 453 | if not path == None: |
---|
| 454 | input_f = open(path,'r') |
---|
| 455 | buff = input_f.read() |
---|
| 456 | lines = buff.split('\n') |
---|
| 457 | for line in lines: |
---|
| 458 | try: |
---|
| 459 | toks = line.split() |
---|
| 460 | x = float(toks[0]) |
---|
| 461 | y = float(toks[1]) |
---|
[b659551] | 462 | if len(toks)>2: |
---|
| 463 | err = float(toks[2]) |
---|
| 464 | else: |
---|
| 465 | if scale==None: |
---|
| 466 | scale = 0.05*math.sqrt(y) |
---|
| 467 | #scale = 0.05/math.sqrt(y) |
---|
| 468 | min_err = 0.01*y |
---|
| 469 | err = scale*math.sqrt(y)+min_err |
---|
| 470 | #err = 0 |
---|
| 471 | |
---|
[4a5de6f] | 472 | data_x = numpy.append(data_x, x) |
---|
| 473 | data_y = numpy.append(data_y, y) |
---|
[b659551] | 474 | data_err = numpy.append(data_err, err) |
---|
[f3d51f6] | 475 | except: |
---|
[b659551] | 476 | pass |
---|
[f3d51f6] | 477 | |
---|
[357b79b] | 478 | if not scale==None: |
---|
| 479 | message = "The loaded file had no error bars, statistical errors are assumed." |
---|
| 480 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
| 481 | else: |
---|
| 482 | wx.PostEvent(self.parent, StatusEvent(status='')) |
---|
| 483 | |
---|
[b659551] | 484 | return data_x, data_y, data_err |
---|
[f3d51f6] | 485 | |
---|
[0bae207] | 486 | def load_abs(self, path): |
---|
| 487 | """ |
---|
[7116b6e0] | 488 | Load an IGOR .ABS reduced file |
---|
| 489 | |
---|
| 490 | :param path: file path |
---|
| 491 | |
---|
| 492 | :return: x, y, err vectors |
---|
| 493 | |
---|
[0bae207] | 494 | """ |
---|
| 495 | import numpy, math, sys |
---|
| 496 | # Read the data from the data file |
---|
| 497 | data_x = numpy.zeros(0) |
---|
| 498 | data_y = numpy.zeros(0) |
---|
| 499 | data_err = numpy.zeros(0) |
---|
| 500 | scale = None |
---|
| 501 | min_err = 0.0 |
---|
| 502 | |
---|
| 503 | data_started = False |
---|
| 504 | if not path == None: |
---|
| 505 | input_f = open(path,'r') |
---|
| 506 | buff = input_f.read() |
---|
| 507 | lines = buff.split('\n') |
---|
| 508 | for line in lines: |
---|
| 509 | if data_started==True: |
---|
| 510 | try: |
---|
| 511 | toks = line.split() |
---|
| 512 | x = float(toks[0]) |
---|
| 513 | y = float(toks[1]) |
---|
| 514 | if len(toks)>2: |
---|
| 515 | err = float(toks[2]) |
---|
| 516 | else: |
---|
| 517 | if scale==None: |
---|
| 518 | scale = 0.05*math.sqrt(y) |
---|
| 519 | #scale = 0.05/math.sqrt(y) |
---|
| 520 | min_err = 0.01*y |
---|
| 521 | err = scale*math.sqrt(y)+min_err |
---|
| 522 | #err = 0 |
---|
| 523 | |
---|
| 524 | data_x = numpy.append(data_x, x) |
---|
| 525 | data_y = numpy.append(data_y, y) |
---|
| 526 | data_err = numpy.append(data_err, err) |
---|
| 527 | except: |
---|
| 528 | pass |
---|
| 529 | elif line.find("The 6 columns")>=0: |
---|
| 530 | data_started = True |
---|
| 531 | |
---|
| 532 | if not scale==None: |
---|
| 533 | message = "The loaded file had no error bars, statistical errors are assumed." |
---|
| 534 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
| 535 | else: |
---|
| 536 | wx.PostEvent(self.parent, StatusEvent(status='')) |
---|
| 537 | |
---|
| 538 | return data_x, data_y, data_err |
---|
| 539 | |
---|
[f3d51f6] | 540 | def pr_theory(self, r, R): |
---|
[7116b6e0] | 541 | """ |
---|
[f3d51f6] | 542 | """ |
---|
| 543 | if r<=2*R: |
---|
| 544 | return 12.0* ((0.5*r/R)**2) * ((1.0-0.5*r/R)**2) * ( 2.0 + 0.5*r/R ) |
---|
| 545 | else: |
---|
| 546 | return 0.0 |
---|
| 547 | |
---|
[660b1e6] | 548 | def get_context_menu(self, graph=None): |
---|
[f3d51f6] | 549 | """ |
---|
[7116b6e0] | 550 | Get the context menu items available for P(r) |
---|
| 551 | |
---|
| 552 | :param graph: the Graph object to which we attach the context menu |
---|
| 553 | |
---|
| 554 | :return: a list of menu items with call-back function |
---|
| 555 | |
---|
[f3d51f6] | 556 | """ |
---|
[660b1e6] | 557 | # Look whether this Graph contains P(r) data |
---|
[aa4b8379] | 558 | #if graph.selected_plottable==IQ_DATA_LABEL: |
---|
[660b1e6] | 559 | for item in graph.plottables: |
---|
[75df58b] | 560 | if item.name == PR_FIT_LABEL: |
---|
| 561 | #add_data_hint = "Load a data file and display it on this plot" |
---|
| 562 | #["Add P(r) data",add_data_hint , self._on_add_data], |
---|
| 563 | change_n_hint = "Change the number of" |
---|
| 564 | change_n_hint += " points on the P(r) output" |
---|
| 565 | change_n_label = "Change number of P(r) points" |
---|
| 566 | m_list = [[change_n_label, change_n_hint , self._on_pr_npts]] |
---|
[aa4b8379] | 567 | |
---|
[75df58b] | 568 | if self._scale_output_unity or self._normalize_output: |
---|
| 569 | hint = "Let the output P(r) keep the scale of the data" |
---|
| 570 | m_list.append(["Disable P(r) scaling", hint, |
---|
[900c787] | 571 | self._on_disable_scaling]) |
---|
[75df58b] | 572 | if not self._scale_output_unity: |
---|
[feb21d8] | 573 | m_list.append(["Scale P_max(r) to unity", |
---|
| 574 | "Scale P(r) so that its maximum is 1", |
---|
| 575 | self._on_scale_unity]) |
---|
[75df58b] | 576 | if not self._normalize_output: |
---|
[feb21d8] | 577 | m_list.append(["Normalize P(r) to unity", |
---|
| 578 | "Normalize the integral of P(r) to 1", |
---|
| 579 | self._on_normalize]) |
---|
| 580 | |
---|
| 581 | return m_list |
---|
[75df58b] | 582 | #return [["Add P(r) data", |
---|
| 583 | #"Load a data file and display it on this plot", |
---|
| 584 | # self._on_add_data], |
---|
| 585 | # ["Change number of P(r) points", |
---|
| 586 | # "Change the number of points on the P(r) output", |
---|
| 587 | # self._on_pr_npts]] |
---|
[feb21d8] | 588 | |
---|
[75df58b] | 589 | elif item.name == graph.selected_plottable: |
---|
| 590 | #TODO: we might want to check that the units are |
---|
| 591 | # consistent with I(q) before allowing this menu item |
---|
| 592 | if not self.standalone and \ |
---|
| 593 | issubclass(item.__class__, DataLoader.data_info.Data1D): |
---|
| 594 | return [["Compute P(r)", |
---|
| 595 | "Compute P(r) from distribution", |
---|
| 596 | self._on_context_inversion]] |
---|
[660b1e6] | 597 | |
---|
[aa4b8379] | 598 | return [] |
---|
[660b1e6] | 599 | |
---|
[feb21d8] | 600 | def _on_disable_scaling(self, evt): |
---|
| 601 | """ |
---|
[7116b6e0] | 602 | Disable P(r) scaling |
---|
| 603 | |
---|
| 604 | :param evt: Menu event |
---|
| 605 | |
---|
[feb21d8] | 606 | """ |
---|
| 607 | self._normalize_output = False |
---|
| 608 | self._scale_output_unity = False |
---|
| 609 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
---|
| 610 | |
---|
[f1181977] | 611 | # Now replot the original added data |
---|
| 612 | for plot in self._added_plots: |
---|
| 613 | self._added_plots[plot].y = numpy.copy(self._default_Iq[plot]) |
---|
[75df58b] | 614 | wx.PostEvent(self.parent, |
---|
| 615 | NewPlotEvent(plot=self._added_plots[plot], |
---|
| 616 | title=self._added_plots[plot].name, |
---|
[f1181977] | 617 | update=True)) |
---|
| 618 | |
---|
| 619 | # Need the update flag in the NewPlotEvent to protect against |
---|
| 620 | # the plot no longer being there... |
---|
| 621 | |
---|
[feb21d8] | 622 | def _on_normalize(self, evt): |
---|
| 623 | """ |
---|
[7116b6e0] | 624 | Normalize the area under the P(r) curve to 1. |
---|
| 625 | This operation is done for all displayed plots. |
---|
| 626 | |
---|
| 627 | :param evt: Menu event |
---|
| 628 | |
---|
[feb21d8] | 629 | """ |
---|
| 630 | self._normalize_output = True |
---|
| 631 | self._scale_output_unity = False |
---|
| 632 | |
---|
| 633 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
---|
| 634 | |
---|
[f1181977] | 635 | # Now scale the added plots too |
---|
| 636 | for plot in self._added_plots: |
---|
| 637 | sum = numpy.sum(self._added_plots[plot].y) |
---|
| 638 | npts = len(self._added_plots[plot].x) |
---|
| 639 | sum *= self._added_plots[plot].x[npts-1]/npts |
---|
| 640 | y = self._added_plots[plot].y/sum |
---|
| 641 | |
---|
| 642 | new_plot = Theory1D(self._added_plots[plot].x, y) |
---|
| 643 | new_plot.name = self._added_plots[plot].name |
---|
| 644 | new_plot.xaxis("\\rm{r}", 'A') |
---|
| 645 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
---|
| 646 | |
---|
[75df58b] | 647 | wx.PostEvent(self.parent, |
---|
| 648 | NewPlotEvent(plot=new_plot, update=True, |
---|
| 649 | title=self._added_plots[plot].name)) |
---|
[f1181977] | 650 | |
---|
[feb21d8] | 651 | def _on_scale_unity(self, evt): |
---|
| 652 | """ |
---|
[7116b6e0] | 653 | Scale the maximum P(r) value on each displayed plot to 1. |
---|
| 654 | |
---|
| 655 | :param evt: Menu event |
---|
| 656 | |
---|
[feb21d8] | 657 | """ |
---|
| 658 | self._scale_output_unity = True |
---|
| 659 | self._normalize_output = False |
---|
| 660 | |
---|
| 661 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
---|
| 662 | |
---|
[f1181977] | 663 | # Now scale the added plots too |
---|
| 664 | for plot in self._added_plots: |
---|
| 665 | _max = 0 |
---|
| 666 | for y in self._added_plots[plot].y: |
---|
| 667 | if y>_max: |
---|
| 668 | _max = y |
---|
| 669 | y = self._added_plots[plot].y/_max |
---|
| 670 | |
---|
| 671 | new_plot = Theory1D(self._added_plots[plot].x, y) |
---|
| 672 | new_plot.name = self._added_plots[plot].name |
---|
| 673 | new_plot.xaxis("\\rm{r}", 'A') |
---|
| 674 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
---|
| 675 | |
---|
[75df58b] | 676 | wx.PostEvent(self.parent, |
---|
| 677 | NewPlotEvent(plot=new_plot, update=True, |
---|
| 678 | title=self._added_plots[plot].name)) |
---|
[f1181977] | 679 | |
---|
| 680 | |
---|
[660b1e6] | 681 | def _on_add_data(self, evt): |
---|
| 682 | """ |
---|
[7116b6e0] | 683 | Add a data curve to the plot |
---|
| 684 | |
---|
| 685 | :WARNING: this will be removed once guiframe.plotting has |
---|
| 686 | its full functionality |
---|
[660b1e6] | 687 | """ |
---|
| 688 | path = self.choose_file() |
---|
| 689 | if path==None: |
---|
| 690 | return |
---|
| 691 | |
---|
[14d05ba] | 692 | #x, y, err = self.parent.load_ascii_1D(path) |
---|
| 693 | # Use data loader to load file |
---|
| 694 | try: |
---|
| 695 | dataread = Loader().load(path) |
---|
| 696 | x = None |
---|
| 697 | y = None |
---|
| 698 | err = None |
---|
| 699 | if dataread.__class__.__name__ == 'Data1D': |
---|
| 700 | x = dataread.x |
---|
| 701 | y = dataread.y |
---|
| 702 | err = dataread.dy |
---|
| 703 | else: |
---|
[e43c012] | 704 | if isinstance(dataread, list) and len(dataread)>0: |
---|
| 705 | x = dataread[0].x |
---|
| 706 | y = dataread[0].y |
---|
| 707 | err = dataread[0].dy |
---|
| 708 | msg = "PrView only allows a single data set at a time. " |
---|
| 709 | msg += "Only the first data set was loaded." |
---|
| 710 | wx.PostEvent(self.parent, StatusEvent(status=msg)) |
---|
| 711 | else: |
---|
[75df58b] | 712 | msg = "This tool can only read 1D data" |
---|
| 713 | wx.PostEvent(self.parent, StatusEvent(status=msg)) |
---|
[e43c012] | 714 | return |
---|
| 715 | |
---|
[14d05ba] | 716 | except: |
---|
| 717 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
| 718 | return |
---|
[660b1e6] | 719 | |
---|
[f1181977] | 720 | filename = os.path.basename(path) |
---|
| 721 | |
---|
[b659551] | 722 | #new_plot = Data1D(x, y, dy=err) |
---|
| 723 | new_plot = Theory1D(x, y) |
---|
[f1181977] | 724 | new_plot.name = filename |
---|
[660b1e6] | 725 | new_plot.xaxis("\\rm{r}", 'A') |
---|
| 726 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
---|
| 727 | |
---|
[f1181977] | 728 | # Store a ref to the plottable for later use |
---|
| 729 | self._added_plots[filename] = new_plot |
---|
| 730 | self._default_Iq[filename] = numpy.copy(y) |
---|
| 731 | |
---|
| 732 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=filename)) |
---|
[660b1e6] | 733 | |
---|
| 734 | |
---|
[f3d51f6] | 735 | |
---|
| 736 | def start_thread(self): |
---|
[7116b6e0] | 737 | """ |
---|
| 738 | """ |
---|
[f3d51f6] | 739 | from pr_thread import CalcPr |
---|
| 740 | from copy import deepcopy |
---|
| 741 | |
---|
| 742 | # If a thread is already started, stop it |
---|
| 743 | if self.calc_thread != None and self.calc_thread.isrunning(): |
---|
| 744 | self.calc_thread.stop() |
---|
| 745 | |
---|
| 746 | pr = self.pr.clone() |
---|
[75df58b] | 747 | self.calc_thread = CalcPr(pr, self.nfunc, |
---|
| 748 | error_func=self._thread_error, |
---|
| 749 | completefn=self._completed, updatefn=None) |
---|
[f3d51f6] | 750 | self.calc_thread.queue() |
---|
| 751 | self.calc_thread.ready(2.5) |
---|
| 752 | |
---|
| 753 | def _thread_error(self, error): |
---|
[7116b6e0] | 754 | """ |
---|
| 755 | """ |
---|
[f3d51f6] | 756 | wx.PostEvent(self.parent, StatusEvent(status=error)) |
---|
| 757 | |
---|
[32dffae4] | 758 | def _estimate_completed(self, alpha, message, elapsed): |
---|
[f3d51f6] | 759 | """ |
---|
[7116b6e0] | 760 | Parameter estimation completed, |
---|
| 761 | display the results to the user |
---|
| 762 | |
---|
| 763 | :param alpha: estimated best alpha |
---|
| 764 | :param elapsed: computation time |
---|
| 765 | |
---|
[f3d51f6] | 766 | """ |
---|
| 767 | # Save useful info |
---|
| 768 | self.elapsed = elapsed |
---|
| 769 | self.control_panel.alpha_estimate = alpha |
---|
[32dffae4] | 770 | if not message==None: |
---|
| 771 | wx.PostEvent(self.parent, StatusEvent(status=str(message))) |
---|
[35adaf6] | 772 | |
---|
| 773 | self.perform_estimateNT() |
---|
| 774 | |
---|
| 775 | |
---|
| 776 | |
---|
| 777 | def _estimateNT_completed(self, nterms, alpha, message, elapsed): |
---|
| 778 | """ |
---|
[7116b6e0] | 779 | Parameter estimation completed, |
---|
| 780 | display the results to the user |
---|
| 781 | |
---|
| 782 | :param alpha: estimated best alpha |
---|
| 783 | :param nterms: estimated number of terms |
---|
| 784 | :param elapsed: computation time |
---|
| 785 | |
---|
[35adaf6] | 786 | """ |
---|
| 787 | # Save useful info |
---|
| 788 | self.elapsed = elapsed |
---|
| 789 | self.control_panel.nterms_estimate = nterms |
---|
| 790 | self.control_panel.alpha_estimate = alpha |
---|
| 791 | if not message==None: |
---|
| 792 | wx.PostEvent(self.parent, StatusEvent(status=str(message))) |
---|
[f3d51f6] | 793 | |
---|
| 794 | def _completed(self, out, cov, pr, elapsed): |
---|
| 795 | """ |
---|
[7116b6e0] | 796 | Method called with the results when the inversion |
---|
| 797 | is done |
---|
| 798 | |
---|
| 799 | :param out: output coefficient for the base functions |
---|
| 800 | :param cov: covariance matrix |
---|
| 801 | :param pr: Invertor instance |
---|
| 802 | :param elapsed: time spent computing |
---|
| 803 | |
---|
[f3d51f6] | 804 | """ |
---|
[dfb58f8] | 805 | from copy import deepcopy |
---|
[f3d51f6] | 806 | # Save useful info |
---|
| 807 | self.elapsed = elapsed |
---|
[feb21d8] | 808 | # Keep a copy of the last result |
---|
| 809 | self._last_pr = pr.clone() |
---|
| 810 | self._last_out = out |
---|
| 811 | self._last_cov = cov |
---|
| 812 | |
---|
[b659551] | 813 | # Save Pr invertor |
---|
| 814 | self.pr = pr |
---|
| 815 | |
---|
[75df58b] | 816 | #message = "Computation completed in" |
---|
| 817 | #message += %g seconds [chi2=%g]" % (elapsed, pr.chi2) |
---|
[d6113849] | 818 | #wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
[f3d51f6] | 819 | |
---|
[dfb58f8] | 820 | cov = numpy.ascontiguousarray(cov) |
---|
| 821 | |
---|
[f3d51f6] | 822 | # Show result on control panel |
---|
| 823 | self.control_panel.chi2 = pr.chi2 |
---|
| 824 | self.control_panel.elapsed = elapsed |
---|
| 825 | self.control_panel.oscillation = pr.oscillations(out) |
---|
| 826 | #print "OSCILL", pr.oscillations(out) |
---|
[d6113849] | 827 | #print "PEAKS:", pr.get_peaks(out) |
---|
[dfb58f8] | 828 | self.control_panel.positive = pr.get_positive(out) |
---|
| 829 | self.control_panel.pos_err = pr.get_pos_err(out, cov) |
---|
[a4bd2ac] | 830 | self.control_panel.rg = pr.rg(out) |
---|
| 831 | self.control_panel.iq0 = pr.iq0(out) |
---|
| 832 | self.control_panel.bck = pr.background |
---|
[f3d51f6] | 833 | |
---|
[aa4b8379] | 834 | if False: |
---|
[0bae207] | 835 | for i in range(len(out)): |
---|
| 836 | try: |
---|
[75df58b] | 837 | print "%d: %g +- %g" % (i, out[i], |
---|
| 838 | math.sqrt(math.fabs(cov[i][i]))) |
---|
[0bae207] | 839 | except: |
---|
| 840 | print sys.exc_value |
---|
| 841 | print "%d: %g +- ?" % (i, out[i]) |
---|
| 842 | |
---|
| 843 | # Make a plot of I(q) data |
---|
[aa4b8379] | 844 | new_plot = Data1D(self.pr.x, self.pr.y, dy=self.pr.err) |
---|
[f1181977] | 845 | new_plot.name = IQ_DATA_LABEL |
---|
[aa4b8379] | 846 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
---|
| 847 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
---|
| 848 | #new_plot.group_id = "test group" |
---|
| 849 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Iq")) |
---|
[f3d51f6] | 850 | |
---|
| 851 | # Show I(q) fit |
---|
| 852 | self.show_iq(out, self.pr) |
---|
| 853 | |
---|
| 854 | # Show P(r) fit |
---|
[dfb58f8] | 855 | x_values, x_range = self.show_pr(out, self.pr, cov) |
---|
[f3d51f6] | 856 | |
---|
| 857 | # Popup result panel |
---|
[75df58b] | 858 | #result_panel = InversionResults(self.parent, |
---|
| 859 | #-1, style=wx.RAISED_BORDER) |
---|
[f3d51f6] | 860 | |
---|
[75df58b] | 861 | def show_data(self, path=None, data=None, reset=False): |
---|
[2a92852] | 862 | """ |
---|
[7116b6e0] | 863 | Show data read from a file |
---|
| 864 | |
---|
| 865 | :param path: file path |
---|
| 866 | :param reset: if True all other plottables will be cleared |
---|
| 867 | |
---|
[2a92852] | 868 | """ |
---|
[75df58b] | 869 | print "show_data", data.name |
---|
| 870 | #if path is not None: |
---|
| 871 | if data is not None: |
---|
[ea5551f] | 872 | try: |
---|
[75df58b] | 873 | #pr = self._create_file_pr(path) |
---|
| 874 | pr = self._create_file_pr(data) |
---|
[ceaf16e] | 875 | except: |
---|
[75df58b] | 876 | status = "Problem reading data: %s" % sys.exc_value |
---|
[ceaf16e] | 877 | wx.PostEvent(self.parent, StatusEvent(status=status)) |
---|
| 878 | raise RuntimeError, status |
---|
[6f1f129] | 879 | |
---|
[ceaf16e] | 880 | # If the file contains nothing, just return |
---|
| 881 | if pr is None: |
---|
| 882 | raise RuntimeError, "Loaded data is invalid" |
---|
| 883 | |
---|
| 884 | self.pr = pr |
---|
[75df58b] | 885 | |
---|
[660b1e6] | 886 | # Make a plot of I(q) data |
---|
[357b79b] | 887 | if self.pr.err==None: |
---|
| 888 | new_plot = Theory1D(self.pr.x, self.pr.y) |
---|
| 889 | else: |
---|
| 890 | new_plot = Data1D(self.pr.x, self.pr.y, dy=self.pr.err) |
---|
[f1181977] | 891 | new_plot.name = IQ_DATA_LABEL |
---|
[660b1e6] | 892 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
---|
| 893 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
---|
[aa4b8379] | 894 | new_plot.interactive = True |
---|
[660b1e6] | 895 | #new_plot.group_id = "test group" |
---|
[75df58b] | 896 | wx.PostEvent(self.parent, |
---|
| 897 | NewPlotEvent(plot=new_plot, title="I(q)", reset=reset)) |
---|
[660b1e6] | 898 | |
---|
[0d88a09] | 899 | self.current_plottable = new_plot |
---|
| 900 | self.current_plottable.group_id = IQ_DATA_LABEL |
---|
| 901 | |
---|
| 902 | |
---|
[aa4b8379] | 903 | # Get Q range |
---|
| 904 | self.control_panel.q_min = self.pr.x.min() |
---|
| 905 | self.control_panel.q_max = self.pr.x.max() |
---|
| 906 | |
---|
[410aad8] | 907 | def save_data(self, filepath, prstate=None): |
---|
| 908 | """ |
---|
[7116b6e0] | 909 | Save data in provided state object. |
---|
| 910 | |
---|
| 911 | :TODO: move the state code away from inversion_panel and move it here. |
---|
| 912 | Then remove the "prstate" input and make this method private. |
---|
| 913 | |
---|
| 914 | :param filepath: path of file to write to |
---|
| 915 | :param prstate: P(r) inversion state |
---|
| 916 | |
---|
[410aad8] | 917 | """ |
---|
| 918 | #TODO: do we need this or can we use DataLoader.loader.save directly? |
---|
| 919 | |
---|
| 920 | # Add output data and coefficients to state |
---|
| 921 | prstate.coefficients = self._last_out |
---|
| 922 | prstate.covariance = self._last_cov |
---|
| 923 | |
---|
| 924 | # Write the output to file |
---|
[0ab485b] | 925 | # First, check that the data is of the right type |
---|
[75df58b] | 926 | if issubclass(self.current_plottable.__class__, |
---|
| 927 | DataLoader.data_info.Data1D): |
---|
[0ab485b] | 928 | self.state_reader.write(filepath, self.current_plottable, prstate) |
---|
| 929 | else: |
---|
[75df58b] | 930 | msg = "pr.save_data: the data being saved is not a" |
---|
| 931 | msg += " DataLoader.data_info.Data1D object" |
---|
| 932 | raise RuntimeError, msg |
---|
[410aad8] | 933 | |
---|
[660b1e6] | 934 | |
---|
[2a92852] | 935 | def setup_plot_inversion(self, alpha, nfunc, d_max, q_min=None, q_max=None, |
---|
| 936 | bck=False, height=0, width=0): |
---|
[7116b6e0] | 937 | """ |
---|
| 938 | """ |
---|
[f3d51f6] | 939 | self.alpha = alpha |
---|
| 940 | self.nfunc = nfunc |
---|
| 941 | self.max_length = d_max |
---|
[634f1cf] | 942 | self.q_min = q_min |
---|
| 943 | self.q_max = q_max |
---|
[a4bd2ac] | 944 | self.has_bck = bck |
---|
[2a92852] | 945 | self.slit_height = height |
---|
| 946 | self.slit_width = width |
---|
[f3d51f6] | 947 | |
---|
[4a5de6f] | 948 | try: |
---|
[2a92852] | 949 | pr = self._create_plot_pr() |
---|
| 950 | if not pr==None: |
---|
| 951 | self.pr = pr |
---|
| 952 | self.perform_inversion() |
---|
[4a5de6f] | 953 | except: |
---|
| 954 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
[f3d51f6] | 955 | |
---|
[75df58b] | 956 | def estimate_plot_inversion(self, alpha, nfunc, d_max, |
---|
| 957 | q_min=None, q_max=None, |
---|
[2a92852] | 958 | bck=False, height=0, width=0): |
---|
[7116b6e0] | 959 | """ |
---|
| 960 | """ |
---|
[f3d51f6] | 961 | self.alpha = alpha |
---|
| 962 | self.nfunc = nfunc |
---|
| 963 | self.max_length = d_max |
---|
[634f1cf] | 964 | self.q_min = q_min |
---|
| 965 | self.q_max = q_max |
---|
[a4bd2ac] | 966 | self.has_bck = bck |
---|
[2a92852] | 967 | self.slit_height = height |
---|
| 968 | self.slit_width = width |
---|
[f3d51f6] | 969 | |
---|
[4a5de6f] | 970 | try: |
---|
[2a92852] | 971 | pr = self._create_plot_pr() |
---|
| 972 | if not pr==None: |
---|
| 973 | self.pr = pr |
---|
| 974 | self.perform_estimate() |
---|
[4a5de6f] | 975 | except: |
---|
| 976 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
[f3d51f6] | 977 | |
---|
[2a92852] | 978 | def _create_plot_pr(self, estimate=False): |
---|
[f3d51f6] | 979 | """ |
---|
[7116b6e0] | 980 | Create and prepare invertor instance from |
---|
| 981 | a plottable data set. |
---|
| 982 | |
---|
| 983 | :param path: path of the file to read in |
---|
| 984 | |
---|
[f3d51f6] | 985 | """ |
---|
[ceaf16e] | 986 | # Sanity check |
---|
| 987 | if self.current_plottable is None: |
---|
| 988 | msg = "Please load a valid data set before proceeding." |
---|
| 989 | wx.PostEvent(self.parent, StatusEvent(status=msg)) |
---|
| 990 | return None |
---|
| 991 | |
---|
[f3d51f6] | 992 | # Get the data from the chosen data set and perform inversion |
---|
| 993 | pr = Invertor() |
---|
| 994 | pr.d_max = self.max_length |
---|
| 995 | pr.alpha = self.alpha |
---|
[634f1cf] | 996 | pr.q_min = self.q_min |
---|
| 997 | pr.q_max = self.q_max |
---|
[f3d51f6] | 998 | pr.x = self.current_plottable.x |
---|
| 999 | pr.y = self.current_plottable.y |
---|
[a4bd2ac] | 1000 | pr.has_bck = self.has_bck |
---|
[2a92852] | 1001 | pr.slit_height = self.slit_height |
---|
| 1002 | pr.slit_width = self.slit_width |
---|
[f3d51f6] | 1003 | |
---|
[d2ee6f6] | 1004 | # Keep track of the plot window title to ensure that |
---|
| 1005 | # we can overlay the plots |
---|
| 1006 | if hasattr(self.current_plottable, "group_id"): |
---|
| 1007 | pr.info["plot_group_id"] = self.current_plottable.group_id |
---|
| 1008 | |
---|
[f3d51f6] | 1009 | # Fill in errors if none were provided |
---|
[d2ee6f6] | 1010 | err = self.current_plottable.dy |
---|
| 1011 | all_zeros = True |
---|
| 1012 | if err == None: |
---|
[d483799] | 1013 | err = numpy.zeros(len(pr.y)) |
---|
[d2ee6f6] | 1014 | else: |
---|
| 1015 | for i in range(len(err)): |
---|
| 1016 | if err[i]>0: |
---|
| 1017 | all_zeros = False |
---|
| 1018 | |
---|
| 1019 | if all_zeros: |
---|
| 1020 | scale = None |
---|
| 1021 | min_err = 0.0 |
---|
[f3d51f6] | 1022 | for i in range(len(pr.y)): |
---|
[d2ee6f6] | 1023 | # Scale the error so that we can fit over several decades of Q |
---|
| 1024 | if scale==None: |
---|
| 1025 | scale = 0.05*math.sqrt(pr.y[i]) |
---|
| 1026 | min_err = 0.01*pr.y[i] |
---|
| 1027 | err[i] = scale*math.sqrt( math.fabs(pr.y[i]) ) + min_err |
---|
[75df58b] | 1028 | message = "The loaded file had no error bars, " |
---|
| 1029 | message += "statistical errors are assumed." |
---|
[d2ee6f6] | 1030 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
| 1031 | |
---|
| 1032 | pr.err = err |
---|
[2a92852] | 1033 | |
---|
| 1034 | return pr |
---|
[f3d51f6] | 1035 | |
---|
| 1036 | |
---|
[75df58b] | 1037 | def setup_file_inversion(self, alpha, nfunc, d_max, data, |
---|
| 1038 | path=None, q_min=None, q_max=None, |
---|
[2a92852] | 1039 | bck=False, height=0, width=0): |
---|
[7116b6e0] | 1040 | """ |
---|
| 1041 | """ |
---|
[f3d51f6] | 1042 | self.alpha = alpha |
---|
| 1043 | self.nfunc = nfunc |
---|
| 1044 | self.max_length = d_max |
---|
[634f1cf] | 1045 | self.q_min = q_min |
---|
| 1046 | self.q_max = q_max |
---|
[a4bd2ac] | 1047 | self.has_bck = bck |
---|
[2a92852] | 1048 | self.slit_height = height |
---|
| 1049 | self.slit_width = width |
---|
[f3d51f6] | 1050 | |
---|
[4a5de6f] | 1051 | try: |
---|
[75df58b] | 1052 | #pr = self._create_file_pr(path) |
---|
| 1053 | pr = self._create_file_pr(data) |
---|
[2a92852] | 1054 | if not pr==None: |
---|
| 1055 | self.pr = pr |
---|
[4a5de6f] | 1056 | self.perform_inversion() |
---|
| 1057 | except: |
---|
| 1058 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
[f3d51f6] | 1059 | |
---|
[75df58b] | 1060 | def estimate_file_inversion(self, alpha, nfunc, d_max, data, |
---|
| 1061 | path=None, q_min=None, q_max=None, |
---|
[2a92852] | 1062 | bck=False, height=0, width=0): |
---|
[7116b6e0] | 1063 | """ |
---|
| 1064 | """ |
---|
[f3d51f6] | 1065 | self.alpha = alpha |
---|
| 1066 | self.nfunc = nfunc |
---|
| 1067 | self.max_length = d_max |
---|
[634f1cf] | 1068 | self.q_min = q_min |
---|
| 1069 | self.q_max = q_max |
---|
[a4bd2ac] | 1070 | self.has_bck = bck |
---|
[2a92852] | 1071 | self.slit_height = height |
---|
| 1072 | self.slit_width = width |
---|
[f3d51f6] | 1073 | |
---|
[4a5de6f] | 1074 | try: |
---|
[75df58b] | 1075 | pr = self._create_file_pr(data) |
---|
| 1076 | #pr = self._create_file_pr(path) |
---|
| 1077 | if not pr is None: |
---|
[2a92852] | 1078 | self.pr = pr |
---|
[4a5de6f] | 1079 | self.perform_estimate() |
---|
| 1080 | except: |
---|
| 1081 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
| 1082 | |
---|
[f3d51f6] | 1083 | |
---|
[75df58b] | 1084 | def _create_file_pr(self, data): |
---|
[f3d51f6] | 1085 | """ |
---|
[7116b6e0] | 1086 | Create and prepare invertor instance from |
---|
| 1087 | a file data set. |
---|
| 1088 | |
---|
| 1089 | :param path: path of the file to read in |
---|
| 1090 | |
---|
[f3d51f6] | 1091 | """ |
---|
| 1092 | # Load data |
---|
[75df58b] | 1093 | #if os.path.isfile(path): |
---|
| 1094 | """ |
---|
| 1095 | if self._current_file_data is not None \ |
---|
| 1096 | and self._current_file_data.path==path: |
---|
| 1097 | # Protect against corrupted data from |
---|
| 1098 | # previous failed load attempt |
---|
| 1099 | if self._current_file_data.x is None: |
---|
| 1100 | return None |
---|
| 1101 | x = self._current_file_data.x |
---|
| 1102 | y = self._current_file_data.y |
---|
| 1103 | err = self._current_file_data.err |
---|
[357b79b] | 1104 | |
---|
[75df58b] | 1105 | message = "The data from this file has already been loaded." |
---|
| 1106 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
| 1107 | else: |
---|
| 1108 | """ |
---|
| 1109 | # Reset the status bar so that we don't get mixed up |
---|
| 1110 | # with old messages. |
---|
| 1111 | #TODO: refactor this into a proper status handling |
---|
| 1112 | wx.PostEvent(self.parent, StatusEvent(status='')) |
---|
| 1113 | try: |
---|
| 1114 | class FileData: |
---|
| 1115 | x = None |
---|
| 1116 | y = None |
---|
| 1117 | err = None |
---|
| 1118 | path = None |
---|
| 1119 | def __init__(self, path): |
---|
| 1120 | self.path = path |
---|
[6f1f129] | 1121 | |
---|
[75df58b] | 1122 | self._current_file_data = FileData(data.path) |
---|
| 1123 | self._current_file_data.x = data.x |
---|
| 1124 | self._current_file_data.y = data.y |
---|
| 1125 | self._current_file_data.err = data.dy |
---|
| 1126 | x, y, err = data.x, data.y, data.dy |
---|
| 1127 | except: |
---|
| 1128 | load_error(sys.exc_value) |
---|
| 1129 | return None |
---|
| 1130 | |
---|
| 1131 | # If the file contains no data, just return |
---|
| 1132 | if x is None or len(x) == 0: |
---|
| 1133 | load_error("The loaded file contains no data") |
---|
| 1134 | return None |
---|
| 1135 | |
---|
| 1136 | # If we have not errors, add statistical errors |
---|
| 1137 | if err is not None and y is not None: |
---|
| 1138 | err = numpy.zeros(len(y)) |
---|
| 1139 | scale = None |
---|
| 1140 | min_err = 0.0 |
---|
| 1141 | for i in range(len(y)): |
---|
| 1142 | # Scale the error so that we can fit over several decades of Q |
---|
| 1143 | if scale == None: |
---|
| 1144 | scale = 0.05 * math.sqrt(y[i]) |
---|
| 1145 | min_err = 0.01 * y[i] |
---|
| 1146 | err[i] = scale * math.sqrt(math.fabs(y[i])) + min_err |
---|
| 1147 | message = "The loaded file had no error bars, " |
---|
| 1148 | message += "statistical errors are assumed." |
---|
| 1149 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
| 1150 | |
---|
| 1151 | try: |
---|
| 1152 | # Get the data from the chosen data set and perform inversion |
---|
| 1153 | pr = Invertor() |
---|
| 1154 | pr.d_max = self.max_length |
---|
| 1155 | pr.alpha = self.alpha |
---|
| 1156 | pr.q_min = self.q_min |
---|
| 1157 | pr.q_max = self.q_max |
---|
| 1158 | pr.x = x |
---|
| 1159 | pr.y = y |
---|
| 1160 | pr.err = err |
---|
| 1161 | pr.has_bck = self.has_bck |
---|
| 1162 | pr.slit_height = self.slit_height |
---|
| 1163 | pr.slit_width = self.slit_width |
---|
| 1164 | return pr |
---|
| 1165 | except: |
---|
| 1166 | load_error(sys.exc_value) |
---|
[2a92852] | 1167 | return None |
---|
[f3d51f6] | 1168 | |
---|
| 1169 | def perform_estimate(self): |
---|
[7116b6e0] | 1170 | """ |
---|
| 1171 | """ |
---|
[f3d51f6] | 1172 | from pr_thread import EstimatePr |
---|
| 1173 | from copy import deepcopy |
---|
| 1174 | |
---|
| 1175 | # If a thread is already started, stop it |
---|
[75df58b] | 1176 | if self.estimation_thread != None and \ |
---|
| 1177 | self.estimation_thread.isrunning(): |
---|
[f3d51f6] | 1178 | self.estimation_thread.stop() |
---|
| 1179 | |
---|
| 1180 | pr = self.pr.clone() |
---|
[75df58b] | 1181 | self.estimation_thread = EstimatePr(pr, self.nfunc, |
---|
| 1182 | error_func=self._thread_error, |
---|
| 1183 | completefn = self._estimate_completed, |
---|
[f3d51f6] | 1184 | updatefn = None) |
---|
| 1185 | self.estimation_thread.queue() |
---|
| 1186 | self.estimation_thread.ready(2.5) |
---|
[35adaf6] | 1187 | |
---|
| 1188 | def perform_estimateNT(self): |
---|
[7116b6e0] | 1189 | """ |
---|
| 1190 | """ |
---|
[35adaf6] | 1191 | from pr_thread import EstimateNT |
---|
| 1192 | from copy import deepcopy |
---|
| 1193 | |
---|
| 1194 | # If a thread is already started, stop it |
---|
| 1195 | if self.estimation_thread != None and self.estimation_thread.isrunning(): |
---|
| 1196 | self.estimation_thread.stop() |
---|
| 1197 | |
---|
| 1198 | pr = self.pr.clone() |
---|
[2a92852] | 1199 | # Skip the slit settings for the estimation |
---|
| 1200 | # It slows down the application and it doesn't change the estimates |
---|
| 1201 | pr.slit_height = 0.0 |
---|
| 1202 | pr.slit_width = 0.0 |
---|
[75df58b] | 1203 | self.estimation_thread = EstimateNT(pr, self.nfunc, |
---|
| 1204 | error_func=self._thread_error, |
---|
| 1205 | completefn = self._estimateNT_completed, |
---|
[35adaf6] | 1206 | updatefn = None) |
---|
| 1207 | self.estimation_thread.queue() |
---|
| 1208 | self.estimation_thread.ready(2.5) |
---|
[f3d51f6] | 1209 | |
---|
| 1210 | def perform_inversion(self): |
---|
[7116b6e0] | 1211 | """ |
---|
| 1212 | """ |
---|
[f3d51f6] | 1213 | # Time estimate |
---|
| 1214 | #estimated = self.elapsed*self.nfunc**2 |
---|
[2a92852] | 1215 | #message = "Computation time may take up to %g seconds" % self.elapsed |
---|
| 1216 | #wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
[f3d51f6] | 1217 | |
---|
| 1218 | # Start inversion thread |
---|
| 1219 | self.start_thread() |
---|
| 1220 | return |
---|
| 1221 | |
---|
| 1222 | out, cov = self.pr.lstsq(self.nfunc) |
---|
| 1223 | |
---|
| 1224 | # Save useful info |
---|
| 1225 | self.elapsed = self.pr.elapsed |
---|
| 1226 | |
---|
| 1227 | for i in range(len(out)): |
---|
| 1228 | try: |
---|
[75df58b] | 1229 | print "%d: %g +- %g" % (i, out[i], |
---|
| 1230 | math.sqrt(math.fabs(cov[i][i]))) |
---|
[f3d51f6] | 1231 | except: |
---|
| 1232 | print "%d: %g +- ?" % (i, out[i]) |
---|
| 1233 | |
---|
| 1234 | # Make a plot of I(q) data |
---|
| 1235 | new_plot = Data1D(self.pr.x, self.pr.y, dy=self.pr.err) |
---|
| 1236 | new_plot.name = "I_{obs}(q)" |
---|
| 1237 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
---|
| 1238 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
---|
| 1239 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Iq")) |
---|
| 1240 | # Show I(q) fit |
---|
| 1241 | self.show_iq(out, self.pr) |
---|
| 1242 | # Show P(r) fit |
---|
| 1243 | x_values, x_range = self.show_pr(out, self.pr, cov=cov) |
---|
| 1244 | |
---|
| 1245 | def _on_context_inversion(self, event): |
---|
[75df58b] | 1246 | """ |
---|
| 1247 | """ |
---|
[f3d51f6] | 1248 | panel = event.GetEventObject() |
---|
| 1249 | |
---|
| 1250 | # If we have more than one displayed plot, make the user choose |
---|
[75df58b] | 1251 | if len(panel.plots) > 1 and \ |
---|
| 1252 | panel.graph.selected_plottable in panel.plots: |
---|
[aa4b8379] | 1253 | dataset = panel.graph.selected_plottable |
---|
[75df58b] | 1254 | elif len(panel.plots) == 1: |
---|
[f3d51f6] | 1255 | dataset = panel.plots.keys()[0] |
---|
| 1256 | else: |
---|
[75df58b] | 1257 | logging.info("Prview Error: No data is available") |
---|
[f3d51f6] | 1258 | return |
---|
| 1259 | |
---|
| 1260 | # Store a reference to the current plottable |
---|
[3fd1ebc] | 1261 | # If we have a suggested value, use it. |
---|
| 1262 | try: |
---|
| 1263 | estimate = float(self.control_panel.alpha_estimate) |
---|
| 1264 | self.control_panel.alpha = estimate |
---|
| 1265 | except: |
---|
| 1266 | self.control_panel.alpha = self.alpha |
---|
[75df58b] | 1267 | logging.info("Prview :Alpha Not estimate yet") |
---|
[3fd1ebc] | 1268 | pass |
---|
[d6113849] | 1269 | try: |
---|
| 1270 | estimate = int(self.control_panel.nterms_estimate) |
---|
| 1271 | self.control_panel.nfunc = estimate |
---|
| 1272 | except: |
---|
| 1273 | self.control_panel.nfunc = self.nfunc |
---|
[75df58b] | 1274 | logging.info("Prview : ntemrs Not estimate yet") |
---|
[d6113849] | 1275 | pass |
---|
[3fd1ebc] | 1276 | |
---|
[f3d51f6] | 1277 | self.current_plottable = panel.plots[dataset] |
---|
| 1278 | self.control_panel.plotname = dataset |
---|
[d6113849] | 1279 | #self.control_panel.nfunc = self.nfunc |
---|
[f3d51f6] | 1280 | self.control_panel.d_max = self.max_length |
---|
| 1281 | self.parent.set_perspective(self.perspective) |
---|
[aa4b8379] | 1282 | self.control_panel._on_invert(None) |
---|
[f3d51f6] | 1283 | |
---|
| 1284 | def get_panels(self, parent): |
---|
| 1285 | """ |
---|
| 1286 | Create and return a list of panel objects |
---|
| 1287 | """ |
---|
| 1288 | from inversion_panel import InversionControl |
---|
| 1289 | |
---|
| 1290 | self.parent = parent |
---|
[aa4b8379] | 1291 | self.control_panel = InversionControl(self.parent, -1, |
---|
| 1292 | style=wx.RAISED_BORDER, |
---|
| 1293 | standalone=self.standalone) |
---|
[f3d51f6] | 1294 | self.control_panel.set_manager(self) |
---|
| 1295 | self.control_panel.nfunc = self.nfunc |
---|
| 1296 | self.control_panel.d_max = self.max_length |
---|
| 1297 | self.control_panel.alpha = self.alpha |
---|
| 1298 | self.perspective = [] |
---|
| 1299 | self.perspective.append(self.control_panel.window_name) |
---|
[75df58b] | 1300 | |
---|
[f3d51f6] | 1301 | return [self.control_panel] |
---|
| 1302 | |
---|
[75df58b] | 1303 | def set_data(self, data_list): |
---|
[aa4b8379] | 1304 | """ |
---|
[75df58b] | 1305 | receive a list of data to compute pr |
---|
[aa4b8379] | 1306 | """ |
---|
[75df58b] | 1307 | if len(data_list) > 1: |
---|
[75a7ece] | 1308 | msg = "Pr panel does not allow multiple Data.\n" |
---|
| 1309 | msg += "Please select one!\n" |
---|
| 1310 | from pr_widgets import DataDialog |
---|
| 1311 | dlg = DataDialog(data_list=data_list, text=msg) |
---|
| 1312 | if dlg.ShowModal() == wx.ID_OK: |
---|
| 1313 | data = dlg.get_data() |
---|
| 1314 | if issubclass(data.__class__, LoaderData1D): |
---|
| 1315 | self.control_panel._change_file(evt=None, data=data) |
---|
| 1316 | else: |
---|
| 1317 | msg = "Pr cannot be computed for data of " |
---|
| 1318 | msg += "type %s" % (data_list[0].__class__.__name__) |
---|
| 1319 | wx.PostEvent(self.parent, |
---|
| 1320 | StatusEvent(status=msg, info='error')) |
---|
[75df58b] | 1321 | elif len(data_list) == 1: |
---|
| 1322 | if issubclass(data_list[0].__class__, LoaderData1D): |
---|
| 1323 | self.control_panel._change_file(evt=None, data=data_list[0]) |
---|
| 1324 | else: |
---|
| 1325 | msg = "Pr cannot be computed for" |
---|
| 1326 | msg += " data of type %s" % (data_list[0].__class__.__name__) |
---|
[75a7ece] | 1327 | wx.PostEvent(self.parent, |
---|
| 1328 | StatusEvent(status=msg, info='error')) |
---|
| 1329 | else: |
---|
| 1330 | msg = "Pr contain no data" |
---|
| 1331 | wx.PostEvent(self.parent, StatusEvent(status=msg, info='warning')) |
---|
[75df58b] | 1332 | |
---|
[f3d51f6] | 1333 | def post_init(self): |
---|
| 1334 | """ |
---|
| 1335 | Post initialization call back to close the loose ends |
---|
| 1336 | [Somehow openGL needs this call] |
---|
| 1337 | """ |
---|
[3e41f43] | 1338 | if self.standalone: |
---|
[d2ee6f6] | 1339 | self.parent.set_perspective(self.perspective) |
---|
[35adaf6] | 1340 | |
---|
| 1341 | if __name__ == "__main__": |
---|
| 1342 | i = Plugin() |
---|
| 1343 | print i.perform_estimateNT() |
---|
| 1344 | |
---|
| 1345 | |
---|
| 1346 | |
---|
[660b1e6] | 1347 | |
---|