source: sasview/src/sas/qtgui/Perspectives/Inversion/InversionPerspective.py @ 5d14851a

ESS_GUIESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_opencl
Last change on this file since 5d14851a was a74dd016, checked in by wojciech, 6 years ago

Fixing faling P(r) on files without added errors
  • Property mode set to 100644
File size: 35.1 KB
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1import logging
2import numpy as np
3
4from PyQt5 import QtGui, QtCore, QtWidgets
5
6# sas-global
7import sas.qtgui.Utilities.GuiUtils as GuiUtils
8
9# pr inversion GUI elements
10from .InversionUtils import WIDGETS
11from .UI.TabbedInversionUI import Ui_PrInversion
12from .InversionLogic import InversionLogic
13
14# pr inversion calculation elements
15from sas.sascalc.pr.invertor import Invertor
16from sas.qtgui.Plotting.PlotterData import Data1D
17# Batch calculation display
18from sas.qtgui.Utilities.GridPanel import BatchInversionOutputPanel
19
20
21def is_float(value):
22    """Converts text input values to floats. Empty strings throw ValueError"""
23    try:
24        return float(value)
25    except ValueError:
26        return 0.0
27
28
29NUMBER_OF_TERMS = 10
30REGULARIZATION = 0.0001
31BACKGROUND_INPUT = 0.0
32MAX_DIST = 140.0
33DICT_KEYS = ["Calculator", "PrPlot", "DataPlot"]
34
35logger = logging.getLogger(__name__)
36
37
38class InversionWindow(QtWidgets.QDialog, Ui_PrInversion):
39    """
40    The main window for the P(r) Inversion perspective.
41    """
42
43    name = "Inversion"
44    estimateSignal = QtCore.pyqtSignal(tuple)
45    estimateNTSignal = QtCore.pyqtSignal(tuple)
46    estimateDynamicNTSignal = QtCore.pyqtSignal(tuple)
47    estimateDynamicSignal = QtCore.pyqtSignal(tuple)
48    calculateSignal = QtCore.pyqtSignal(tuple)
49
50    def __init__(self, parent=None, data=None):
51        super(InversionWindow, self).__init__()
52        self.setupUi(self)
53
54        self.setWindowTitle("P(r) Inversion Perspective")
55
56        self._manager = parent
57        #Needed for Batch fitting
58        self._parent = parent
59        self.communicate = parent.communicator()
60        self.communicate.dataDeletedSignal.connect(self.removeData)
61
62        self.logic = InversionLogic()
63
64        # The window should not close
65        self._allowClose = False
66
67        # Visible data items
68        # current QStandardItem showing on the panel
69        self._data = None
70        # Reference to Dmax window for self._data
71        self.dmaxWindow = None
72        # p(r) calculator for self._data
73        self._calculator = Invertor()
74        # Default to background estimate
75        self._calculator.est_bck = True
76        # plots of self._data
77        self.prPlot = None
78        self.dataPlot = None
79        # suggested nTerms
80        self.nTermsSuggested = NUMBER_OF_TERMS
81
82        # Calculation threads used by all data items
83        self.calcThread = None
84        self.estimationThread = None
85        self.estimationThreadNT = None
86        self.isCalculating = False
87
88        # Mapping for all data items
89        # Dictionary mapping data to all parameters
90        self._dataList = {}
91        if not isinstance(data, list):
92            data_list = [data]
93        if data is not None:
94            for datum in data_list:
95                self.updateDataList(datum)
96
97        self.dataDeleted = False
98
99        self.model = QtGui.QStandardItemModel(self)
100        self.mapper = QtWidgets.QDataWidgetMapper(self)
101
102        # Batch fitting parameters
103        self.isBatch = False
104        self.batchResultsWindow = None
105        self.batchResults = {}
106        self.batchComplete = []
107
108        # Add validators
109        self.setupValidators()
110        # Link user interactions with methods
111        self.setupLinks()
112        # Set values
113        self.setupModel()
114        # Set up the Widget Map
115        self.setupMapper()
116
117        #Hidding calculate all buton
118        self.calculateAllButton.setVisible(False)
119        # Set base window state
120        self.setupWindow()
121
122    ######################################################################
123    # Base Perspective Class Definitions
124
125    def communicator(self):
126        return self.communicate
127
128    def allowBatch(self):
129        return False
130
131    def setClosable(self, value=True):
132        """
133        Allow outsiders close this widget
134        """
135        assert isinstance(value, bool)
136        self._allowClose = value
137
138    def isClosable(self):
139        """
140        Allow outsiders close this widget
141        """
142        return self._allowClose
143
144    def closeEvent(self, event):
145        """
146        Overwrite QDialog close method to allow for custom widget close
147        """
148        # Close report widgets before closing/minimizing main widget
149        self.closeDMax()
150        self.closeBatchResults()
151        if self._allowClose:
152            # reset the closability flag
153            self.setClosable(value=False)
154            # Tell the MdiArea to close the container
155            self.parentWidget().close()
156            event.accept()
157        else:
158            event.ignore()
159            # Maybe we should just minimize
160            self.setWindowState(QtCore.Qt.WindowMinimized)
161
162    def closeDMax(self):
163        if self.dmaxWindow is not None:
164            self.dmaxWindow.close()
165
166    def closeBatchResults(self):
167        if self.batchResultsWindow is not None:
168            self.batchResultsWindow.close()
169
170    ######################################################################
171    # Initialization routines
172
173    def setupLinks(self):
174        """Connect the use controls to their appropriate methods"""
175        self.dataList.currentIndexChanged.connect(self.displayChange)
176        self.calculateAllButton.clicked.connect(self.startThreadAll)
177        self.calculateThisButton.clicked.connect(self.startThread)
178        self.stopButton.clicked.connect(self.stopCalculation)
179        self.removeButton.clicked.connect(self.removeData)
180        self.helpButton.clicked.connect(self.help)
181        self.estimateBgd.toggled.connect(self.toggleBgd)
182        self.manualBgd.toggled.connect(self.toggleBgd)
183        self.regConstantSuggestionButton.clicked.connect(self.acceptAlpha)
184        self.noOfTermsSuggestionButton.clicked.connect(self.acceptNoTerms)
185        self.explorerButton.clicked.connect(self.openExplorerWindow)
186
187        self.backgroundInput.textChanged.connect(
188            lambda: self.set_background(self.backgroundInput.text()))
189        self.minQInput.textChanged.connect(
190            lambda: self._calculator.set_qmin(is_float(self.minQInput.text())))
191        self.regularizationConstantInput.textChanged.connect(
192            lambda: self._calculator.set_alpha(is_float(self.regularizationConstantInput.text())))
193        self.maxDistanceInput.textChanged.connect(
194            lambda: self._calculator.set_dmax(is_float(self.maxDistanceInput.text())))
195        self.maxQInput.textChanged.connect(
196            lambda: self._calculator.set_qmax(is_float(self.maxQInput.text())))
197        self.slitHeightInput.textChanged.connect(
198            lambda: self._calculator.set_slit_height(is_float(self.slitHeightInput.text())))
199        self.slitWidthInput.textChanged.connect(
200            lambda: self._calculator.set_slit_width(is_float(self.slitWidthInput.text())))
201
202        self.model.itemChanged.connect(self.model_changed)
203        self.estimateNTSignal.connect(self._estimateNTUpdate)
204        self.estimateDynamicNTSignal.connect(self._estimateDynamicNTUpdate)
205        self.estimateDynamicSignal.connect(self._estimateDynamicUpdate)
206        self.estimateSignal.connect(self._estimateUpdate)
207        self.calculateSignal.connect(self._calculateUpdate)
208
209        self.maxDistanceInput.textEdited.connect(self.performEstimateDynamic)
210
211    def setupMapper(self):
212        # Set up the mapper.
213        self.mapper.setOrientation(QtCore.Qt.Vertical)
214        self.mapper.setModel(self.model)
215
216        # Filename
217        self.mapper.addMapping(self.dataList, WIDGETS.W_FILENAME)
218        # Background
219        self.mapper.addMapping(self.backgroundInput, WIDGETS.W_BACKGROUND_INPUT)
220        self.mapper.addMapping(self.estimateBgd, WIDGETS.W_ESTIMATE)
221        self.mapper.addMapping(self.manualBgd, WIDGETS.W_MANUAL_INPUT)
222
223        # Qmin/Qmax
224        self.mapper.addMapping(self.minQInput, WIDGETS.W_QMIN)
225        self.mapper.addMapping(self.maxQInput, WIDGETS.W_QMAX)
226
227        # Slit Parameter items
228        self.mapper.addMapping(self.slitWidthInput, WIDGETS.W_SLIT_WIDTH)
229        self.mapper.addMapping(self.slitHeightInput, WIDGETS.W_SLIT_HEIGHT)
230
231        # Parameter Items
232        self.mapper.addMapping(self.regularizationConstantInput, WIDGETS.W_REGULARIZATION)
233        self.mapper.addMapping(self.regConstantSuggestionButton, WIDGETS.W_REGULARIZATION_SUGGEST)
234        self.mapper.addMapping(self.explorerButton, WIDGETS.W_EXPLORE)
235        self.mapper.addMapping(self.maxDistanceInput, WIDGETS.W_MAX_DIST)
236        self.mapper.addMapping(self.noOfTermsInput, WIDGETS.W_NO_TERMS)
237        self.mapper.addMapping(self.noOfTermsSuggestionButton, WIDGETS.W_NO_TERMS_SUGGEST)
238
239        # Output
240        self.mapper.addMapping(self.rgValue, WIDGETS.W_RG)
241        self.mapper.addMapping(self.iQ0Value, WIDGETS.W_I_ZERO)
242        self.mapper.addMapping(self.backgroundValue, WIDGETS.W_BACKGROUND_OUTPUT)
243        self.mapper.addMapping(self.computationTimeValue, WIDGETS.W_COMP_TIME)
244        self.mapper.addMapping(self.chiDofValue, WIDGETS.W_CHI_SQUARED)
245        self.mapper.addMapping(self.oscillationValue, WIDGETS.W_OSCILLATION)
246        self.mapper.addMapping(self.posFractionValue, WIDGETS.W_POS_FRACTION)
247        self.mapper.addMapping(self.sigmaPosFractionValue, WIDGETS.W_SIGMA_POS_FRACTION)
248
249        # Main Buttons
250        self.mapper.addMapping(self.removeButton, WIDGETS.W_REMOVE)
251        self.mapper.addMapping(self.calculateAllButton, WIDGETS.W_CALCULATE_ALL)
252        self.mapper.addMapping(self.calculateThisButton, WIDGETS.W_CALCULATE_VISIBLE)
253        self.mapper.addMapping(self.helpButton, WIDGETS.W_HELP)
254
255        self.mapper.toFirst()
256
257    def setupModel(self):
258        """
259        Update boxes with initial values
260        """
261        bgd_item = QtGui.QStandardItem(str(BACKGROUND_INPUT))
262        self.model.setItem(WIDGETS.W_BACKGROUND_INPUT, bgd_item)
263        blank_item = QtGui.QStandardItem("")
264        self.model.setItem(WIDGETS.W_QMIN, blank_item)
265        blank_item = QtGui.QStandardItem("")
266        self.model.setItem(WIDGETS.W_QMAX, blank_item)
267        blank_item = QtGui.QStandardItem("")
268        self.model.setItem(WIDGETS.W_SLIT_WIDTH, blank_item)
269        blank_item = QtGui.QStandardItem("")
270        self.model.setItem(WIDGETS.W_SLIT_HEIGHT, blank_item)
271        no_terms_item = QtGui.QStandardItem(str(NUMBER_OF_TERMS))
272        self.model.setItem(WIDGETS.W_NO_TERMS, no_terms_item)
273        reg_item = QtGui.QStandardItem(str(REGULARIZATION))
274        self.model.setItem(WIDGETS.W_REGULARIZATION, reg_item)
275        max_dist_item = QtGui.QStandardItem(str(MAX_DIST))
276        self.model.setItem(WIDGETS.W_MAX_DIST, max_dist_item)
277        blank_item = QtGui.QStandardItem("")
278        self.model.setItem(WIDGETS.W_RG, blank_item)
279        blank_item = QtGui.QStandardItem("")
280        self.model.setItem(WIDGETS.W_I_ZERO, blank_item)
281        bgd_item = QtGui.QStandardItem(str(BACKGROUND_INPUT))
282        self.model.setItem(WIDGETS.W_BACKGROUND_OUTPUT, bgd_item)
283        blank_item = QtGui.QStandardItem("")
284        self.model.setItem(WIDGETS.W_COMP_TIME, blank_item)
285        blank_item = QtGui.QStandardItem("")
286        self.model.setItem(WIDGETS.W_CHI_SQUARED, blank_item)
287        blank_item = QtGui.QStandardItem("")
288        self.model.setItem(WIDGETS.W_OSCILLATION, blank_item)
289        blank_item = QtGui.QStandardItem("")
290        self.model.setItem(WIDGETS.W_POS_FRACTION, blank_item)
291        blank_item = QtGui.QStandardItem("")
292        self.model.setItem(WIDGETS.W_SIGMA_POS_FRACTION, blank_item)
293
294    def setupWindow(self):
295        """Initialize base window state on init"""
296        self.enableButtons()
297        self.estimateBgd.setChecked(True)
298
299    def setupValidators(self):
300        """Apply validators to editable line edits"""
301        self.noOfTermsInput.setValidator(QtGui.QIntValidator())
302        self.regularizationConstantInput.setValidator(GuiUtils.DoubleValidator())
303        self.maxDistanceInput.setValidator(GuiUtils.DoubleValidator())
304        self.minQInput.setValidator(GuiUtils.DoubleValidator())
305        self.maxQInput.setValidator(GuiUtils.DoubleValidator())
306        self.slitHeightInput.setValidator(GuiUtils.DoubleValidator())
307        self.slitWidthInput.setValidator(GuiUtils.DoubleValidator())
308
309    ######################################################################
310    # Methods for updating GUI
311
312    def enableButtons(self):
313        """
314        Enable buttons when data is present, else disable them
315        """
316        self.calculateAllButton.setEnabled(len(self._dataList) > 1
317                                           and not self.isBatch
318                                           and not self.isCalculating)
319        self.calculateThisButton.setEnabled(self.logic.data_is_loaded
320                                            and not self.isBatch
321                                            and not self.isCalculating)
322        self.removeButton.setEnabled(self.logic.data_is_loaded)
323        self.explorerButton.setEnabled(self.logic.data_is_loaded)
324        self.stopButton.setVisible(self.isCalculating)
325        self.regConstantSuggestionButton.setEnabled(
326            self.logic.data_is_loaded and
327            self._calculator.suggested_alpha != self._calculator.alpha)
328        self.noOfTermsSuggestionButton.setEnabled(
329            self.logic.data_is_loaded and
330            self._calculator.nfunc != self.nTermsSuggested)
331
332    def populateDataComboBox(self, filename, data_ref):
333        """
334        Append a new file name to the data combobox
335        :param filename: data filename
336        :param data_ref: QStandardItem reference for data set to be added
337        """
338        self.dataList.addItem(filename, data_ref)
339
340    def acceptNoTerms(self):
341        """Send estimated no of terms to input"""
342        self.model.setItem(WIDGETS.W_NO_TERMS, QtGui.QStandardItem(
343            self.noOfTermsSuggestionButton.text()))
344
345    def acceptAlpha(self):
346        """Send estimated alpha to input"""
347        self.model.setItem(WIDGETS.W_REGULARIZATION, QtGui.QStandardItem(
348            self.regConstantSuggestionButton.text()))
349
350    def displayChange(self, data_index=0):
351        """Switch to another item in the data list"""
352        if self.dataDeleted:
353            return
354        self.updateDataList(self._data)
355        self.setCurrentData(self.dataList.itemData(data_index))
356
357    ######################################################################
358    # GUI Interaction Events
359
360    def updateCalculator(self):
361        """Update all p(r) params"""
362        self._calculator.set_x(self.logic.data.x)
363        self._calculator.set_y(self.logic.data.y)
364        self._calculator.set_err(self.logic.data.dy)
365        self.set_background(self.backgroundInput.text())
366
367    def set_background(self, value):
368        self._calculator.background = is_float(value)
369
370    def model_changed(self):
371        """Update the values when user makes changes"""
372        if not self.mapper:
373            msg = "Unable to update P{r}. The connection between the main GUI "
374            msg += "and P(r) was severed. Attempting to restart P(r)."
375            logger.warning(msg)
376            self.setClosable(True)
377            self.close()
378            InversionWindow.__init__(self.parent(), list(self._dataList.keys()))
379            exit(0)
380        if self.dmaxWindow is not None:
381            self.dmaxWindow.nfunc = self.getNFunc()
382            self.dmaxWindow.pr_state = self._calculator
383        self.mapper.toLast()
384
385    def help(self):
386        """
387        Open the P(r) Inversion help browser
388        """
389        tree_location = "/user/qtgui/Perspectives/Inversion/pr_help.html"
390
391        # Actual file anchor will depend on the combo box index
392        # Note that we can be clusmy here, since bad current_fitter_id
393        # will just make the page displayed from the top
394        self._manager.showHelp(tree_location)
395
396    def toggleBgd(self):
397        """
398        Toggle the background between manual and estimated
399        """
400        if self.estimateBgd.isChecked():
401            self.manualBgd.setChecked(False)
402            self.backgroundInput.setEnabled(False)
403            self._calculator.set_est_bck = True
404        elif self.manualBgd.isChecked():
405            self.estimateBgd.setChecked(False)
406            self.backgroundInput.setEnabled(True)
407            self._calculator.set_est_bck = False
408        else:
409            pass
410
411    def openExplorerWindow(self):
412        """
413        Open the Explorer window to see correlations between params and results
414        """
415        from .DMaxExplorerWidget import DmaxWindow
416        self.dmaxWindow = DmaxWindow(pr_state=self._calculator,
417                                     nfunc=self.getNFunc(),
418                                     parent=self)
419        self.dmaxWindow.show()
420
421    def showBatchOutput(self):
422        """
423        Display the batch output in tabular form
424        :param output_data: Dictionary mapping filename -> P(r) instance
425        """
426        if self.batchResultsWindow is None:
427            self.batchResultsWindow = BatchInversionOutputPanel(
428                parent=self, output_data=self.batchResults)
429        else:
430            self.batchResultsWindow.setupTable(self.batchResults)
431        self.batchResultsWindow.show()
432
433    def stopCalculation(self):
434        """ Stop all threads, return to the base state and update GUI """
435        self.stopCalcThread()
436        self.stopEstimationThread()
437        self.stopEstimateNTThread()
438        # Show any batch calculations that successfully completed
439        if self.isBatch and self.batchResultsWindow is not None:
440            self.showBatchOutput()
441        self.isBatch = False
442        self.isCalculating = False
443        self.updateGuiValues()
444
445    ######################################################################
446    # Response Actions
447
448    def setData(self, data_item=None, is_batch=False):
449        """
450        Assign new data set(s) to the P(r) perspective
451        Obtain a QStandardItem object and parse it to get Data1D/2D
452        Pass it over to the calculator
453        """
454        assert data_item is not None
455
456        if not isinstance(data_item, list):
457            msg = "Incorrect type passed to the P(r) Perspective"
458            raise AttributeError(msg)
459
460        for data in data_item:
461            if data in self._dataList.keys():
462                # Don't add data if it's already in
463                continue
464            # Create initial internal mappings
465            self.logic.data = GuiUtils.dataFromItem(data)
466            if not isinstance(self.logic.data, Data1D):
467                msg = "P(r) perspective cannot be computed with 2D data."
468                logger.error(msg)
469                raise ValueError(msg)
470            # Estimate q range
471            qmin, qmax = self.logic.computeDataRange()
472            self._calculator.set_qmin(qmin)
473            self._calculator.set_qmax(qmax)
474            if np.size(self.logic.data.dy) == 0 or np.all(self.logic.data.dy) == 0:
475                self.logic.add_errors()
476            self.updateDataList(data)
477            self.populateDataComboBox(self.logic.data.filename, data)
478        self.dataList.setCurrentIndex(len(self.dataList) - 1)
479        #Checking for 1D again to mitigate the case when 2D data is last on the data list
480        if isinstance(self.logic.data, Data1D):
481            self.setCurrentData(data)
482
483    def updateDataList(self, dataRef):
484        """Save the current data state of the window into self._data_list"""
485        if dataRef is None:
486            return
487        self._dataList[dataRef] = {
488            DICT_KEYS[0]: self._calculator,
489            DICT_KEYS[1]: self.prPlot,
490            DICT_KEYS[2]: self.dataPlot
491        }
492        # Update batch results window when finished
493        self.batchResults[self.logic.data.filename] = self._calculator
494        if self.batchResultsWindow is not None:
495            self.showBatchOutput()
496
497    def getNFunc(self):
498        """Get the n_func value from the GUI object"""
499        try:
500            nfunc = int(self.noOfTermsInput.text())
501        except ValueError:
502            logger.error("Incorrect number of terms specified: %s"
503                          %self.noOfTermsInput.text())
504            self.noOfTermsInput.setText(str(NUMBER_OF_TERMS))
505            nfunc = NUMBER_OF_TERMS
506        return nfunc
507
508    def setCurrentData(self, data_ref):
509        """Get the data by reference and display as necessary"""
510        if data_ref is None:
511            return
512        if not isinstance(data_ref, QtGui.QStandardItem):
513            msg = "Incorrect type passed to the P(r) Perspective"
514            raise AttributeError(msg)
515        # Data references
516        self._data = data_ref
517        self.logic.data = GuiUtils.dataFromItem(data_ref)
518        self._calculator = self._dataList[data_ref].get(DICT_KEYS[0])
519        self.prPlot = self._dataList[data_ref].get(DICT_KEYS[1])
520        self.dataPlot = self._dataList[data_ref].get(DICT_KEYS[2])
521        self.performEstimate()
522
523    def updateDynamicGuiValues(self):
524        pr = self._calculator
525        alpha = self._calculator.suggested_alpha
526        self.model.setItem(WIDGETS.W_MAX_DIST,
527                            QtGui.QStandardItem("{:.4g}".format(pr.get_dmax())))
528        self.regConstantSuggestionButton.setText("{:-3.2g}".format(alpha))
529        self.noOfTermsSuggestionButton.setText(
530             "{:n}".format(self.nTermsSuggested))
531
532        self.enableButtons()
533
534    def updateGuiValues(self):
535        pr = self._calculator
536        out = self._calculator.out
537        cov = self._calculator.cov
538        elapsed = self._calculator.elapsed
539        alpha = self._calculator.suggested_alpha
540        self.model.setItem(WIDGETS.W_QMIN,
541                           QtGui.QStandardItem("{:.4g}".format(pr.get_qmin())))
542        self.model.setItem(WIDGETS.W_QMAX,
543                           QtGui.QStandardItem("{:.4g}".format(pr.get_qmax())))
544        self.model.setItem(WIDGETS.W_BACKGROUND_INPUT,
545                           QtGui.QStandardItem("{:.3g}".format(pr.background)))
546        self.model.setItem(WIDGETS.W_BACKGROUND_OUTPUT,
547                           QtGui.QStandardItem("{:.3g}".format(pr.background)))
548        self.model.setItem(WIDGETS.W_COMP_TIME,
549                           QtGui.QStandardItem("{:.4g}".format(elapsed)))
550        self.model.setItem(WIDGETS.W_MAX_DIST,
551                           QtGui.QStandardItem("{:.4g}".format(pr.get_dmax())))
552
553        if isinstance(pr.chi2, np.ndarray):
554            self.model.setItem(WIDGETS.W_CHI_SQUARED,
555                               QtGui.QStandardItem("{:.3g}".format(pr.chi2[0])))
556        if out is not None:
557            self.model.setItem(WIDGETS.W_RG,
558                               QtGui.QStandardItem("{:.3g}".format(pr.rg(out))))
559            self.model.setItem(WIDGETS.W_I_ZERO,
560                               QtGui.QStandardItem(
561                                   "{:.3g}".format(pr.iq0(out))))
562            self.model.setItem(WIDGETS.W_OSCILLATION, QtGui.QStandardItem(
563                "{:.3g}".format(pr.oscillations(out))))
564            self.model.setItem(WIDGETS.W_POS_FRACTION, QtGui.QStandardItem(
565                "{:.3g}".format(pr.get_positive(out))))
566            if cov is not None:
567                self.model.setItem(WIDGETS.W_SIGMA_POS_FRACTION,
568                                   QtGui.QStandardItem(
569                                       "{:.3g}".format(
570                                           pr.get_pos_err(out, cov))))
571        if self.prPlot is not None:
572            title = self.prPlot.name
573            self.prPlot.plot_role = Data1D.ROLE_RESIDUAL
574            GuiUtils.updateModelItemWithPlot(self._data, self.prPlot, title)
575            self.communicate.plotRequestedSignal.emit([self._data,self.prPlot], None)
576        if self.dataPlot is not None:
577            title = self.dataPlot.name
578            self.dataPlot.plot_role = Data1D.ROLE_DEFAULT
579            self.dataPlot.symbol = "Line"
580            self.dataPlot.show_errors = False
581            GuiUtils.updateModelItemWithPlot(self._data, self.dataPlot, title)
582            self.communicate.plotRequestedSignal.emit([self._data,self.dataPlot], None)
583        self.enableButtons()
584
585    def removeData(self, data_list=None):
586        """Remove the existing data reference from the P(r) Persepective"""
587        self.dataDeleted = True
588        self.batchResults = {}
589        if not data_list:
590            data_list = [self._data]
591        self.closeDMax()
592        for data in data_list:
593            self._dataList.pop(data)
594        self._data = None
595        length = len(self.dataList)
596        for index in reversed(range(length)):
597            if self.dataList.itemData(index) in data_list:
598                self.dataList.removeItem(index)
599        # Last file removed
600        self.dataDeleted = False
601        if len(self._dataList) == 0:
602            self.prPlot = None
603            self.dataPlot = None
604            self.logic.data = None
605            self._calculator = Invertor()
606            self.closeBatchResults()
607            self.nTermsSuggested = NUMBER_OF_TERMS
608            self.noOfTermsSuggestionButton.setText("{:n}".format(
609                self.nTermsSuggested))
610            self.regConstantSuggestionButton.setText("{:-3.2g}".format(
611                REGULARIZATION))
612            self.updateGuiValues()
613            self.setupModel()
614        else:
615            self.dataList.setCurrentIndex(0)
616            self.updateGuiValues()
617
618    ######################################################################
619    # Thread Creators
620
621    def startThreadAll(self):
622        self.isCalculating = True
623        self.isBatch = True
624        self.batchComplete = []
625        self.calculateAllButton.setText("Calculating...")
626        self.enableButtons()
627        self.batchResultsWindow = BatchInversionOutputPanel(
628            parent=self, output_data=self.batchResults)
629        self.performEstimate()
630
631    def startNextBatchItem(self):
632        self.isBatch = False
633        for index in range(len(self._dataList)):
634            if index not in self.batchComplete:
635                self.dataList.setCurrentIndex(index)
636                self.isBatch = True
637                # Add the index before calculating in case calculation fails
638                self.batchComplete.append(index)
639                break
640        if self.isBatch:
641            self.performEstimate()
642        else:
643            # If no data sets left, end batch calculation
644            self.isCalculating = False
645            self.batchComplete = []
646            self.calculateAllButton.setText("Calculate All")
647            self.showBatchOutput()
648            self.enableButtons()
649
650    def startThread(self):
651        """
652            Start a calculation thread
653        """
654        from .Thread import CalcPr
655
656        # Set data before running the calculations
657        self.isCalculating = True
658        self.enableButtons()
659        self.updateCalculator()
660        # Disable calculation buttons to prevent thread interference
661
662        # If the thread is already started, stop it
663        self.stopCalcThread()
664
665        pr = self._calculator.clone()
666        #Making sure that nfunc and alpha parameters are correctly initialized
667        pr.suggested_alpha = self._calculator.alpha
668        self.calcThread = CalcPr(pr, self.nTermsSuggested,
669                                 error_func=self._threadError,
670                                 completefn=self._calculateCompleted,
671                                 updatefn=None)
672        self.calcThread.queue()
673        self.calcThread.ready(2.5)
674
675    def stopCalcThread(self):
676        """ Stops a thread if it exists and is running """
677        if self.calcThread is not None and self.calcThread.isrunning():
678            self.calcThread.stop()
679
680    def performEstimateNT(self):
681        """
682        Perform parameter estimation
683        """
684        from .Thread import EstimateNT
685
686        self.updateCalculator()
687
688        # If a thread is already started, stop it
689        self.stopEstimateNTThread()
690
691        pr = self._calculator.clone()
692        # Skip the slit settings for the estimation
693        # It slows down the application and it doesn't change the estimates
694        pr.slit_height = 0.0
695        pr.slit_width = 0.0
696        nfunc = self.getNFunc()
697
698        self.estimationThreadNT = EstimateNT(pr, nfunc,
699                                             error_func=self._threadError,
700                                             completefn=self._estimateNTCompleted,
701                                             updatefn=None)
702        self.estimationThreadNT.queue()
703        self.estimationThreadNT.ready(2.5)
704
705    def performEstimateDynamicNT(self):
706        """
707        Perform parameter estimation
708        """
709        from .Thread import EstimateNT
710
711        self.updateCalculator()
712
713        # If a thread is already started, stop it
714        self.stopEstimateNTThread()
715
716        pr = self._calculator.clone()
717        # Skip the slit settings for the estimation
718        # It slows down the application and it doesn't change the estimates
719        pr.slit_height = 0.0
720        pr.slit_width = 0.0
721        nfunc = self.getNFunc()
722
723        self.estimationThreadNT = EstimateNT(pr, nfunc,
724                                             error_func=self._threadError,
725                                             completefn=self._estimateDynamicNTCompleted,
726                                             updatefn=None)
727        self.estimationThreadNT.queue()
728        self.estimationThreadNT.ready(2.5)
729
730    def stopEstimateNTThread(self):
731        if (self.estimationThreadNT is not None and
732                self.estimationThreadNT.isrunning()):
733            self.estimationThreadNT.stop()
734
735    def performEstimate(self):
736        """
737            Perform parameter estimation
738        """
739        from .Thread import EstimatePr
740
741        # If a thread is already started, stop it
742        self.stopEstimationThread()
743
744        self.estimationThread = EstimatePr(self._calculator.clone(),
745                                           self.getNFunc(),
746                                           error_func=self._threadError,
747                                           completefn=self._estimateCompleted,
748                                           updatefn=None)
749        self.estimationThread.queue()
750        self.estimationThread.ready(2.5)
751
752    def performEstimateDynamic(self):
753        """
754            Perform parameter estimation
755        """
756        from .Thread import EstimatePr
757
758        # If a thread is already started, stop it
759        self.stopEstimationThread()
760
761        self.estimationThread = EstimatePr(self._calculator.clone(),
762                                           self.getNFunc(),
763                                           error_func=self._threadError,
764                                           completefn=self._estimateDynamicCompleted,
765                                           updatefn=None)
766        self.estimationThread.queue()
767        self.estimationThread.ready(2.5)
768
769    def stopEstimationThread(self):
770        """ Stop the estimation thread if it exists and is running """
771        if (self.estimationThread is not None and
772                self.estimationThread.isrunning()):
773            self.estimationThread.stop()
774
775    ######################################################################
776    # Thread Complete
777
778    def _estimateCompleted(self, alpha, message, elapsed):
779        ''' Send a signal to the main thread for model update'''
780        self.estimateSignal.emit((alpha, message, elapsed))
781
782    def _estimateDynamicCompleted(self, alpha, message, elapsed):
783        ''' Send a signal to the main thread for model update'''
784        self.estimateDynamicSignal.emit((alpha, message, elapsed))
785
786    def _estimateUpdate(self, output_tuple):
787        """
788        Parameter estimation completed,
789        display the results to the user
790
791        :param alpha: estimated best alpha
792        :param elapsed: computation time
793        """
794        alpha, message, elapsed = output_tuple
795        self._calculator.alpha = alpha
796        self._calculator.elapsed += self._calculator.elapsed
797        if message:
798            logger.info(message)
799        self.performEstimateNT()
800        self.performEstimateDynamicNT()
801
802    def _estimateDynamicUpdate(self, output_tuple):
803        """
804        Parameter estimation completed,
805        display the results to the user
806
807        :param alpha: estimated best alpha
808        :param elapsed: computation time
809        """
810        alpha, message, elapsed = output_tuple
811        self._calculator.alpha = alpha
812        self._calculator.elapsed += self._calculator.elapsed
813        if message:
814            logger.info(message)
815        self.performEstimateDynamicNT()
816
817    def _estimateNTCompleted(self, nterms, alpha, message, elapsed):
818        ''' Send a signal to the main thread for model update'''
819        self.estimateNTSignal.emit((nterms, alpha, message, elapsed))
820
821    def _estimateDynamicNTCompleted(self, nterms, alpha, message, elapsed):
822        ''' Send a signal to the main thread for model update'''
823        self.estimateDynamicNTSignal.emit((nterms, alpha, message, elapsed))
824
825    def _estimateNTUpdate(self, output_tuple):
826        """
827        Parameter estimation completed,
828        display the results to the user
829
830        :param alpha: estimated best alpha
831        :param nterms: estimated number of terms
832        :param elapsed: computation time
833        """
834        nterms, alpha, message, elapsed = output_tuple
835        self._calculator.elapsed += elapsed
836        self._calculator.suggested_alpha = alpha
837        self.nTermsSuggested = nterms
838        # Save useful info
839        self.updateGuiValues()
840        if message:
841            logger.info(message)
842        if self.isBatch:
843            self.acceptAlpha()
844            self.acceptNoTerms()
845            self.startThread()
846
847    def _estimateDynamicNTUpdate(self, output_tuple):
848        """
849        Parameter estimation completed,
850        display the results to the user
851
852        :param alpha: estimated best alpha
853        :param nterms: estimated number of terms
854        :param elapsed: computation time
855        """
856        nterms, alpha, message, elapsed = output_tuple
857        self._calculator.elapsed += elapsed
858        self._calculator.suggested_alpha = alpha
859        self.nTermsSuggested = nterms
860        # Save useful info
861        self.updateDynamicGuiValues()
862        if message:
863            logger.info(message)
864        if self.isBatch:
865            self.acceptAlpha()
866            self.acceptNoTerms()
867            self.startThread()
868
869    def _calculateCompleted(self, out, cov, pr, elapsed):
870        ''' Send a signal to the main thread for model update'''
871        self.calculateSignal.emit((out, cov, pr, elapsed))
872
873    def _calculateUpdate(self, output_tuple):
874        """
875        Method called with the results when the inversion is done
876
877        :param out: output coefficient for the base functions
878        :param cov: covariance matrix
879        :param pr: Invertor instance
880        :param elapsed: time spent computing
881        """
882        out, cov, pr, elapsed = output_tuple
883        # Save useful info
884        cov = np.ascontiguousarray(cov)
885        pr.cov = cov
886        pr.out = out
887        pr.elapsed = elapsed
888
889        # Save Pr invertor
890        self._calculator = pr
891
892        # Update P(r) and fit plots
893        self.prPlot = self.logic.newPRPlot(out, self._calculator, cov)
894        self.prPlot.filename = self.logic.data.filename
895        self.dataPlot = self.logic.new1DPlot(out, self._calculator)
896        self.dataPlot.filename = self.logic.data.filename
897
898        # Udpate internals and GUI
899        self.updateDataList(self._data)
900        if self.isBatch:
901            self.batchComplete.append(self.dataList.currentIndex())
902            self.startNextBatchItem()
903        else:
904            self.isCalculating = False
905        self.updateGuiValues()
906
907    def _threadError(self, error):
908        """
909            Call-back method for calculation errors
910        """
911        logger.error(error)
912        if self.isBatch:
913            self.startNextBatchItem()
914        else:
915            self.stopCalculation()
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