source: sasview/src/sas/qtgui/Perspectives/Inversion/InversionPerspective.py @ 28965e9

ESS_GUIESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalc
Last change on this file since 28965e9 was 28965e9, checked in by wojciech, 13 months ago

Fixes for the perform estimate. Dmax explorer still not functional

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File size: 34.1 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
16# Batch calculation display
17from sas.qtgui.Utilities.GridPanel import BatchInversionOutputPanel
18
19
20def is_float(value):
21    """Converts text input values to floats. Empty strings throw ValueError"""
22    try:
23        return float(value)
24    except ValueError:
25        return 0.0
26
27
28NUMBER_OF_TERMS = 10
29REGULARIZATION = 0.0001
30BACKGROUND_INPUT = 0.0
31MAX_DIST = 140.0
32DICT_KEYS = ["Calculator", "PrPlot", "DataPlot"]
33
34logger = logging.getLogger(__name__)
35
36
37class InversionWindow(QtWidgets.QDialog, Ui_PrInversion):
38    """
39    The main window for the P(r) Inversion perspective.
40    """
41
42    name = "Inversion"
43    estimateSignal = QtCore.pyqtSignal(tuple)
44    estimateNTSignal = QtCore.pyqtSignal(tuple)
45    estimateDynamicNTSignal = QtCore.pyqtSignal(tuple)
46    estimateDynamicSignal = QtCore.pyqtSignal(tuple)
47    calculateSignal = QtCore.pyqtSignal(tuple)
48
49    def __init__(self, parent=None, data=None):
50        super(InversionWindow, self).__init__()
51        self.setupUi(self)
52
53        self.setWindowTitle("P(r) Inversion Perspective")
54
55        self._manager = parent
56        self.communicate = parent.communicator()
57        self.communicate.dataDeletedSignal.connect(self.removeData)
58
59        self.logic = InversionLogic()
60
61        # The window should not close
62        self._allowClose = False
63
64        # Visible data items
65        # current QStandardItem showing on the panel
66        self._data = None
67        # Reference to Dmax window for self._data
68        self.dmaxWindow = None
69        # p(r) calculator for self._data
70        self._calculator = Invertor()
71        # Default to background estimate
72        self._calculator.est_bck = True
73        # plots of self._data
74        self.prPlot = None
75        self.dataPlot = None
76        # suggested nTerms
77        self.nTermsSuggested = NUMBER_OF_TERMS
78
79        # Calculation threads used by all data items
80        self.calcThread = None
81        self.estimationThread = None
82        self.estimationThreadNT = None
83        self.isCalculating = False
84
85        # Mapping for all data items
86        # Dictionary mapping data to all parameters
87        self._dataList = {}
88        if not isinstance(data, list):
89            data_list = [data]
90        if data is not None:
91            for datum in data_list:
92                self.updateDataList(datum)
93
94        self.dataDeleted = False
95
96        self.model = QtGui.QStandardItemModel(self)
97        self.mapper = QtWidgets.QDataWidgetMapper(self)
98
99        # Batch fitting parameters
100        self.isBatch = False
101        self.batchResultsWindow = None
102        self.batchResults = {}
103        self.batchComplete = []
104
105        # Add validators
106        self.setupValidators()
107        # Link user interactions with methods
108        self.setupLinks()
109        # Set values
110        self.setupModel()
111        # Set up the Widget Map
112        self.setupMapper()
113        # Set base window state
114        self.setupWindow()
115
116    ######################################################################
117    # Base Perspective Class Definitions
118
119    def communicator(self):
120        return self.communicate
121
122    def allowBatch(self):
123        return True
124
125    def setClosable(self, value=True):
126        """
127        Allow outsiders close this widget
128        """
129        assert isinstance(value, bool)
130        self._allowClose = value
131
132    def isClosable(self):
133        """
134        Allow outsiders close this widget
135        """
136        return self._allowClose
137
138    def closeEvent(self, event):
139        """
140        Overwrite QDialog close method to allow for custom widget close
141        """
142        # Close report widgets before closing/minimizing main widget
143        self.closeDMax()
144        self.closeBatchResults()
145        if self._allowClose:
146            # reset the closability flag
147            self.setClosable(value=False)
148            # Tell the MdiArea to close the container
149            self.parentWidget().close()
150            event.accept()
151        else:
152            event.ignore()
153            # Maybe we should just minimize
154            self.setWindowState(QtCore.Qt.WindowMinimized)
155
156    def closeDMax(self):
157        if self.dmaxWindow is not None:
158            self.dmaxWindow.close()
159
160    def closeBatchResults(self):
161        if self.batchResultsWindow is not None:
162            self.batchResultsWindow.close()
163
164    ######################################################################
165    # Initialization routines
166
167    def setupLinks(self):
168        """Connect the use controls to their appropriate methods"""
169        self.dataList.currentIndexChanged.connect(self.displayChange)
170        self.calculateAllButton.clicked.connect(self.startThreadAll)
171        self.calculateThisButton.clicked.connect(self.startThread)
172        self.stopButton.clicked.connect(self.stopCalculation)
173        self.removeButton.clicked.connect(self.removeData)
174        self.helpButton.clicked.connect(self.help)
175        self.estimateBgd.toggled.connect(self.toggleBgd)
176        self.manualBgd.toggled.connect(self.toggleBgd)
177        self.regConstantSuggestionButton.clicked.connect(self.acceptAlpha)
178        self.noOfTermsSuggestionButton.clicked.connect(self.acceptNoTerms)
179        self.explorerButton.clicked.connect(self.openExplorerWindow)
180
181        self.backgroundInput.textChanged.connect(
182            lambda: self.set_background(self.backgroundInput.text()))
183        self.minQInput.textChanged.connect(
184            lambda: self._calculator.set_qmin(is_float(self.minQInput.text())))
185        self.regularizationConstantInput.textChanged.connect(
186            lambda: self._calculator.set_alpha(is_float(self.regularizationConstantInput.text())))
187        self.maxDistanceInput.textChanged.connect(
188            lambda: self._calculator.set_dmax(is_float(self.maxDistanceInput.text())))
189        self.maxQInput.textChanged.connect(
190            lambda: self._calculator.set_qmax(is_float(self.maxQInput.text())))
191        self.slitHeightInput.textChanged.connect(
192            lambda: self._calculator.set_slit_height(is_float(self.slitHeightInput.text())))
193        self.slitWidthInput.textChanged.connect(
194            lambda: self._calculator.set_slit_width(is_float(self.slitWidthInput.text())))
195
196        self.model.itemChanged.connect(self.model_changed)
197        self.estimateNTSignal.connect(self._estimateNTUpdate)
198        self.estimateDynamicNTSignal.connect(self._estimateDynamicNTUpdate)
199        self.estimateDynamicSignal.connect(self._estimateDynamicUpdate)
200        self.estimateSignal.connect(self._estimateUpdate)
201        self.calculateSignal.connect(self._calculateUpdate)
202
203        self.maxDistanceInput.textEdited.connect(self.performEstimateDynamic)
204
205    def setupMapper(self):
206        # Set up the mapper.
207        self.mapper.setOrientation(QtCore.Qt.Vertical)
208        self.mapper.setModel(self.model)
209
210        # Filename
211        self.mapper.addMapping(self.dataList, WIDGETS.W_FILENAME)
212        # Background
213        self.mapper.addMapping(self.backgroundInput, WIDGETS.W_BACKGROUND_INPUT)
214        self.mapper.addMapping(self.estimateBgd, WIDGETS.W_ESTIMATE)
215        self.mapper.addMapping(self.manualBgd, WIDGETS.W_MANUAL_INPUT)
216
217        # Qmin/Qmax
218        self.mapper.addMapping(self.minQInput, WIDGETS.W_QMIN)
219        self.mapper.addMapping(self.maxQInput, WIDGETS.W_QMAX)
220
221        # Slit Parameter items
222        self.mapper.addMapping(self.slitWidthInput, WIDGETS.W_SLIT_WIDTH)
223        self.mapper.addMapping(self.slitHeightInput, WIDGETS.W_SLIT_HEIGHT)
224
225        # Parameter Items
226        self.mapper.addMapping(self.regularizationConstantInput, WIDGETS.W_REGULARIZATION)
227        self.mapper.addMapping(self.regConstantSuggestionButton, WIDGETS.W_REGULARIZATION_SUGGEST)
228        self.mapper.addMapping(self.explorerButton, WIDGETS.W_EXPLORE)
229        self.mapper.addMapping(self.maxDistanceInput, WIDGETS.W_MAX_DIST)
230        self.mapper.addMapping(self.noOfTermsInput, WIDGETS.W_NO_TERMS)
231        self.mapper.addMapping(self.noOfTermsSuggestionButton, WIDGETS.W_NO_TERMS_SUGGEST)
232
233        # Output
234        self.mapper.addMapping(self.rgValue, WIDGETS.W_RG)
235        self.mapper.addMapping(self.iQ0Value, WIDGETS.W_I_ZERO)
236        self.mapper.addMapping(self.backgroundValue, WIDGETS.W_BACKGROUND_OUTPUT)
237        self.mapper.addMapping(self.computationTimeValue, WIDGETS.W_COMP_TIME)
238        self.mapper.addMapping(self.chiDofValue, WIDGETS.W_CHI_SQUARED)
239        self.mapper.addMapping(self.oscillationValue, WIDGETS.W_OSCILLATION)
240        self.mapper.addMapping(self.posFractionValue, WIDGETS.W_POS_FRACTION)
241        self.mapper.addMapping(self.sigmaPosFractionValue, WIDGETS.W_SIGMA_POS_FRACTION)
242
243        # Main Buttons
244        self.mapper.addMapping(self.removeButton, WIDGETS.W_REMOVE)
245        self.mapper.addMapping(self.calculateAllButton, WIDGETS.W_CALCULATE_ALL)
246        self.mapper.addMapping(self.calculateThisButton, WIDGETS.W_CALCULATE_VISIBLE)
247        self.mapper.addMapping(self.helpButton, WIDGETS.W_HELP)
248
249        self.mapper.toFirst()
250
251    def setupModel(self):
252        """
253        Update boxes with initial values
254        """
255        bgd_item = QtGui.QStandardItem(str(BACKGROUND_INPUT))
256        self.model.setItem(WIDGETS.W_BACKGROUND_INPUT, bgd_item)
257        blank_item = QtGui.QStandardItem("")
258        self.model.setItem(WIDGETS.W_QMIN, blank_item)
259        blank_item = QtGui.QStandardItem("")
260        self.model.setItem(WIDGETS.W_QMAX, blank_item)
261        blank_item = QtGui.QStandardItem("")
262        self.model.setItem(WIDGETS.W_SLIT_WIDTH, blank_item)
263        blank_item = QtGui.QStandardItem("")
264        self.model.setItem(WIDGETS.W_SLIT_HEIGHT, blank_item)
265        no_terms_item = QtGui.QStandardItem(str(NUMBER_OF_TERMS))
266        self.model.setItem(WIDGETS.W_NO_TERMS, no_terms_item)
267        reg_item = QtGui.QStandardItem(str(REGULARIZATION))
268        self.model.setItem(WIDGETS.W_REGULARIZATION, reg_item)
269        max_dist_item = QtGui.QStandardItem(str(MAX_DIST))
270        self.model.setItem(WIDGETS.W_MAX_DIST, max_dist_item)
271        blank_item = QtGui.QStandardItem("")
272        self.model.setItem(WIDGETS.W_RG, blank_item)
273        blank_item = QtGui.QStandardItem("")
274        self.model.setItem(WIDGETS.W_I_ZERO, blank_item)
275        bgd_item = QtGui.QStandardItem(str(BACKGROUND_INPUT))
276        self.model.setItem(WIDGETS.W_BACKGROUND_OUTPUT, bgd_item)
277        blank_item = QtGui.QStandardItem("")
278        self.model.setItem(WIDGETS.W_COMP_TIME, blank_item)
279        blank_item = QtGui.QStandardItem("")
280        self.model.setItem(WIDGETS.W_CHI_SQUARED, blank_item)
281        blank_item = QtGui.QStandardItem("")
282        self.model.setItem(WIDGETS.W_OSCILLATION, blank_item)
283        blank_item = QtGui.QStandardItem("")
284        self.model.setItem(WIDGETS.W_POS_FRACTION, blank_item)
285        blank_item = QtGui.QStandardItem("")
286        self.model.setItem(WIDGETS.W_SIGMA_POS_FRACTION, blank_item)
287
288    def setupWindow(self):
289        """Initialize base window state on init"""
290        self.enableButtons()
291        self.estimateBgd.setChecked(True)
292
293    def setupValidators(self):
294        """Apply validators to editable line edits"""
295        self.noOfTermsInput.setValidator(QtGui.QIntValidator())
296        self.regularizationConstantInput.setValidator(GuiUtils.DoubleValidator())
297        self.maxDistanceInput.setValidator(GuiUtils.DoubleValidator())
298        self.minQInput.setValidator(GuiUtils.DoubleValidator())
299        self.maxQInput.setValidator(GuiUtils.DoubleValidator())
300        self.slitHeightInput.setValidator(GuiUtils.DoubleValidator())
301        self.slitWidthInput.setValidator(GuiUtils.DoubleValidator())
302
303    ######################################################################
304    # Methods for updating GUI
305
306    def enableButtons(self):
307        """
308        Enable buttons when data is present, else disable them
309        """
310        self.calculateAllButton.setEnabled(len(self._dataList) > 1
311                                           and not self.isBatch
312                                           and not self.isCalculating)
313        self.calculateThisButton.setEnabled(self.logic.data_is_loaded
314                                            and not self.isBatch
315                                            and not self.isCalculating)
316        self.removeButton.setEnabled(self.logic.data_is_loaded)
317        self.explorerButton.setEnabled(self.logic.data_is_loaded)
318        self.stopButton.setVisible(self.isCalculating)
319        self.regConstantSuggestionButton.setEnabled(
320            self.logic.data_is_loaded and
321            self._calculator.suggested_alpha != self._calculator.alpha)
322        self.noOfTermsSuggestionButton.setEnabled(
323            self.logic.data_is_loaded and
324            self._calculator.nfunc != self.nTermsSuggested)
325
326    def populateDataComboBox(self, filename, data_ref):
327        """
328        Append a new file name to the data combobox
329        :param filename: data filename
330        :param data_ref: QStandardItem reference for data set to be added
331        """
332        self.dataList.addItem(filename, data_ref)
333
334    def acceptNoTerms(self):
335        """Send estimated no of terms to input"""
336        self.model.setItem(WIDGETS.W_NO_TERMS, QtGui.QStandardItem(
337            self.noOfTermsSuggestionButton.text()))
338
339    def acceptAlpha(self):
340        """Send estimated alpha to input"""
341        self.model.setItem(WIDGETS.W_REGULARIZATION, QtGui.QStandardItem(
342            self.regConstantSuggestionButton.text()))
343
344    def displayChange(self, data_index=0):
345        """Switch to another item in the data list"""
346        if self.dataDeleted:
347            return
348        self.updateDataList(self._data)
349        self.setCurrentData(self.dataList.itemData(data_index))
350
351    ######################################################################
352    # GUI Interaction Events
353
354    def updateCalculator(self):
355        """Update all p(r) params"""
356        self._calculator.set_x(self.logic.data.x)
357        self._calculator.set_y(self.logic.data.y)
358        self._calculator.set_err(self.logic.data.dy)
359        self.set_background(self.backgroundInput.text())
360
361    def set_background(self, value):
362        self._calculator.background = is_float(value)
363
364    def model_changed(self):
365        """Update the values when user makes changes"""
366        if not self.mapper:
367            msg = "Unable to update P{r}. The connection between the main GUI "
368            msg += "and P(r) was severed. Attempting to restart P(r)."
369            logger.warning(msg)
370            self.setClosable(True)
371            self.close()
372            InversionWindow.__init__(self.parent(), list(self._dataList.keys()))
373            exit(0)
374        if self.dmaxWindow is not None:
375            self.dmaxWindow.nfunc = self.getNFunc()
376            self.dmaxWindow.pr_state = self._calculator
377        self.mapper.toLast()
378
379    def help(self):
380        """
381        Open the P(r) Inversion help browser
382        """
383        tree_location = "/user/qtgui/Perspectives/Inversion/pr_help.html"
384
385        # Actual file anchor will depend on the combo box index
386        # Note that we can be clusmy here, since bad current_fitter_id
387        # will just make the page displayed from the top
388        self._manager.showHelp(tree_location)
389
390    def toggleBgd(self):
391        """
392        Toggle the background between manual and estimated
393        """
394        if self.estimateBgd.isChecked():
395            self.manualBgd.setChecked(False)
396            self.backgroundInput.setEnabled(False)
397            self._calculator.set_est_bck = True
398        elif self.manualBgd.isChecked():
399            self.estimateBgd.setChecked(False)
400            self.backgroundInput.setEnabled(True)
401            self._calculator.set_est_bck = False
402        else:
403            pass
404
405    def openExplorerWindow(self):
406        """
407        Open the Explorer window to see correlations between params and results
408        """
409        from .DMaxExplorerWidget import DmaxWindow
410        self.dmaxWindow = DmaxWindow(pr_state=self._calculator,
411                                     nfunc=self.getNFunc(),
412                                     parent=self)
413        self.dmaxWindow.show()
414
415    def showBatchOutput(self):
416        """
417        Display the batch output in tabular form
418        :param output_data: Dictionary mapping filename -> P(r) instance
419        """
420        if self.batchResultsWindow is None:
421            self.batchResultsWindow = BatchInversionOutputPanel(
422                parent=self, output_data=self.batchResults)
423        else:
424            self.batchResultsWindow.setupTable(self.batchResults)
425        self.batchResultsWindow.show()
426
427    def stopCalculation(self):
428        """ Stop all threads, return to the base state and update GUI """
429        self.stopCalcThread()
430        self.stopEstimationThread()
431        self.stopEstimateNTThread()
432        # Show any batch calculations that successfully completed
433        if self.isBatch and self.batchResultsWindow is not None:
434            self.showBatchOutput()
435        self.isBatch = False
436        self.isCalculating = False
437        self.updateGuiValues()
438
439    ######################################################################
440    # Response Actions
441
442    def setData(self, data_item=None, is_batch=False):
443        """
444        Assign new data set(s) to the P(r) perspective
445        Obtain a QStandardItem object and parse it to get Data1D/2D
446        Pass it over to the calculator
447        """
448        assert data_item is not None
449
450        if not isinstance(data_item, list):
451            msg = "Incorrect type passed to the P(r) Perspective"
452            raise AttributeError(msg)
453
454        for data in data_item:
455            if data in self._dataList.keys():
456                # Don't add data if it's already in
457                continue
458            # Create initial internal mappings
459            self.logic.data = GuiUtils.dataFromItem(data)
460            # Estimate q range
461            qmin, qmax = self.logic.computeDataRange()
462            self._calculator.set_qmin(qmin)
463            self._calculator.set_qmax(qmax)
464            self.updateDataList(data)
465            self.populateDataComboBox(self.logic.data.filename, data)
466        self.dataList.setCurrentIndex(len(self.dataList) - 1)
467        self.setCurrentData(data)
468
469    def updateDataList(self, dataRef):
470        """Save the current data state of the window into self._data_list"""
471        if dataRef is None:
472            return
473        self._dataList[dataRef] = {
474            DICT_KEYS[0]: self._calculator,
475            DICT_KEYS[1]: self.prPlot,
476            DICT_KEYS[2]: self.dataPlot
477        }
478        # Update batch results window when finished
479        self.batchResults[self.logic.data.filename] = self._calculator
480        if self.batchResultsWindow is not None:
481            self.showBatchOutput()
482
483    def getNFunc(self):
484        """Get the n_func value from the GUI object"""
485        try:
486            nfunc = int(self.noOfTermsInput.text())
487        except ValueError:
488            logger.error("Incorrect number of terms specified: %s"
489                          %self.noOfTermsInput.text())
490            self.noOfTermsInput.setText(str(NUMBER_OF_TERMS))
491            nfunc = NUMBER_OF_TERMS
492        return nfunc
493
494    def setCurrentData(self, data_ref):
495        """Get the data by reference and display as necessary"""
496        if data_ref is None:
497            return
498        if not isinstance(data_ref, QtGui.QStandardItem):
499            msg = "Incorrect type passed to the P(r) Perspective"
500            raise AttributeError(msg)
501        # Data references
502        self._data = data_ref
503        self.logic.data = GuiUtils.dataFromItem(data_ref)
504        self._calculator = self._dataList[data_ref].get(DICT_KEYS[0])
505        self.prPlot = self._dataList[data_ref].get(DICT_KEYS[1])
506        self.dataPlot = self._dataList[data_ref].get(DICT_KEYS[2])
507        self.performEstimate()
508
509    def updateDynamicGuiValues(self):
510        pr = self._calculator
511        alpha = self._calculator.suggested_alpha
512        self.model.setItem(WIDGETS.W_MAX_DIST,
513                            QtGui.QStandardItem("{:.4g}".format(pr.get_dmax())))
514        self.regConstantSuggestionButton.setText("{:-3.2g}".format(alpha))
515        self.noOfTermsSuggestionButton.setText(
516             "{:n}".format(self.nTermsSuggested))
517
518        self.enableButtons()
519
520    def updateGuiValues(self):
521        pr = self._calculator
522        out = self._calculator.out
523        cov = self._calculator.cov
524        elapsed = self._calculator.elapsed
525        alpha = self._calculator.suggested_alpha
526        self.model.setItem(WIDGETS.W_QMIN,
527                           QtGui.QStandardItem("{:.4g}".format(pr.get_qmin())))
528        self.model.setItem(WIDGETS.W_QMAX,
529                           QtGui.QStandardItem("{:.4g}".format(pr.get_qmax())))
530        self.model.setItem(WIDGETS.W_BACKGROUND_INPUT,
531                           QtGui.QStandardItem("{:.3g}".format(pr.background)))
532        self.model.setItem(WIDGETS.W_BACKGROUND_OUTPUT,
533                           QtGui.QStandardItem("{:.3g}".format(pr.background)))
534        self.model.setItem(WIDGETS.W_COMP_TIME,
535                           QtGui.QStandardItem("{:.4g}".format(elapsed)))
536        self.model.setItem(WIDGETS.W_MAX_DIST,
537                           QtGui.QStandardItem("{:.4g}".format(pr.get_dmax())))
538
539        if isinstance(pr.chi2, np.ndarray):
540            self.model.setItem(WIDGETS.W_CHI_SQUARED,
541                               QtGui.QStandardItem("{:.3g}".format(pr.chi2[0])))
542        if out is not None:
543            self.model.setItem(WIDGETS.W_RG,
544                               QtGui.QStandardItem("{:.3g}".format(pr.rg(out))))
545            self.model.setItem(WIDGETS.W_I_ZERO,
546                               QtGui.QStandardItem(
547                                   "{:.3g}".format(pr.iq0(out))))
548            self.model.setItem(WIDGETS.W_OSCILLATION, QtGui.QStandardItem(
549                "{:.3g}".format(pr.oscillations(out))))
550            self.model.setItem(WIDGETS.W_POS_FRACTION, QtGui.QStandardItem(
551                "{:.3g}".format(pr.get_positive(out))))
552            if cov is not None:
553                self.model.setItem(WIDGETS.W_SIGMA_POS_FRACTION,
554                                   QtGui.QStandardItem(
555                                       "{:.3g}".format(
556                                           pr.get_pos_err(out, cov))))
557        if self.prPlot is not None:
558            title = self.prPlot.name
559            GuiUtils.updateModelItemWithPlot(self._data, self.prPlot, title)
560            self.communicate.plotRequestedSignal.emit([self.prPlot], None)
561        if self.dataPlot is not None:
562            title = self.dataPlot.name
563            GuiUtils.updateModelItemWithPlot(self._data, self.dataPlot, title)
564            self.communicate.plotRequestedSignal.emit([self.dataPlot], None)
565        self.enableButtons()
566
567    def removeData(self, data_list=None):
568        """Remove the existing data reference from the P(r) Persepective"""
569        self.dataDeleted = True
570        self.batchResults = {}
571        if not data_list:
572            data_list = [self._data]
573        self.closeDMax()
574        for data in data_list:
575            self._dataList.pop(data)
576        self._data = None
577        length = len(self.dataList)
578        for index in reversed(range(length)):
579            if self.dataList.itemData(index) in data_list:
580                self.dataList.removeItem(index)
581        # Last file removed
582        self.dataDeleted = False
583        if len(self._dataList) == 0:
584            self.prPlot = None
585            self.dataPlot = None
586            self.logic.data = None
587            self._calculator = Invertor()
588            self.closeBatchResults()
589            self.nTermsSuggested = NUMBER_OF_TERMS
590            self.noOfTermsSuggestionButton.setText("{:n}".format(
591                self.nTermsSuggested))
592            self.regConstantSuggestionButton.setText("{:-3.2g}".format(
593                REGULARIZATION))
594            self.updateGuiValues()
595            self.setupModel()
596        else:
597            self.dataList.setCurrentIndex(0)
598            self.updateGuiValues()
599
600    ######################################################################
601    # Thread Creators
602
603    def startThreadAll(self):
604        self.isCalculating = True
605        self.isBatch = True
606        self.batchComplete = []
607        self.calculateAllButton.setText("Calculating...")
608        self.enableButtons()
609        self.batchResultsWindow = BatchInversionOutputPanel(
610            parent=self, output_data=self.batchResults)
611        self.performEstimate()
612
613    def startNextBatchItem(self):
614        self.isBatch = False
615        for index in range(len(self._dataList)):
616            if index not in self.batchComplete:
617                self.dataList.setCurrentIndex(index)
618                self.isBatch = True
619                # Add the index before calculating in case calculation fails
620                self.batchComplete.append(index)
621                break
622        if self.isBatch:
623            self.performEstimate()
624        else:
625            # If no data sets left, end batch calculation
626            self.isCalculating = False
627            self.batchComplete = []
628            self.calculateAllButton.setText("Calculate All")
629            self.showBatchOutput()
630            self.enableButtons()
631
632    def startThread(self):
633        """
634            Start a calculation thread
635        """
636        from .Thread import CalcPr
637
638        # Set data before running the calculations
639        self.isCalculating = True
640        self.enableButtons()
641        self.updateCalculator()
642        # Disable calculation buttons to prevent thread interference
643
644        # If the thread is already started, stop it
645        self.stopCalcThread()
646
647        pr = self._calculator.clone()
648        nfunc = self.getNFunc()
649        self.calcThread = CalcPr(pr, nfunc,
650                                 error_func=self._threadError,
651                                 completefn=self._calculateCompleted,
652                                 updatefn=None)
653        self.calcThread.queue()
654        self.calcThread.ready(2.5)
655
656    def stopCalcThread(self):
657        """ Stops a thread if it exists and is running """
658        if self.calcThread is not None and self.calcThread.isrunning():
659            self.calcThread.stop()
660
661    def performEstimateNT(self):
662        """
663        Perform parameter estimation
664        """
665        from .Thread import EstimateNT
666
667        self.updateCalculator()
668
669        # If a thread is already started, stop it
670        self.stopEstimateNTThread()
671
672        pr = self._calculator.clone()
673        # Skip the slit settings for the estimation
674        # It slows down the application and it doesn't change the estimates
675        pr.slit_height = 0.0
676        pr.slit_width = 0.0
677        nfunc = self.getNFunc()
678
679        self.estimationThreadNT = EstimateNT(pr, nfunc,
680                                             error_func=self._threadError,
681                                             completefn=self._estimateNTCompleted,
682                                             updatefn=None)
683        self.estimationThreadNT.queue()
684        self.estimationThreadNT.ready(2.5)
685
686    def performEstimateDynamicNT(self):
687        """
688        Perform parameter estimation
689        """
690        from .Thread import EstimateNT
691
692        self.updateCalculator()
693
694        # If a thread is already started, stop it
695        self.stopEstimateNTThread()
696
697        pr = self._calculator.clone()
698        # Skip the slit settings for the estimation
699        # It slows down the application and it doesn't change the estimates
700        pr.slit_height = 0.0
701        pr.slit_width = 0.0
702        nfunc = self.getNFunc()
703
704        self.estimationThreadNT = EstimateNT(pr, nfunc,
705                                             error_func=self._threadError,
706                                             completefn=self._estimateDynamicNTCompleted,
707                                             updatefn=None)
708        self.estimationThreadNT.queue()
709        self.estimationThreadNT.ready(2.5)
710
711    def stopEstimateNTThread(self):
712        if (self.estimationThreadNT is not None and
713                self.estimationThreadNT.isrunning()):
714            self.estimationThreadNT.stop()
715
716    def performEstimate(self):
717        """
718            Perform parameter estimation
719        """
720        from .Thread import EstimatePr
721
722        # If a thread is already started, stop it
723        self.stopEstimationThread()
724
725        self.estimationThread = EstimatePr(self._calculator.clone(),
726                                           self.getNFunc(),
727                                           error_func=self._threadError,
728                                           completefn=self._estimateCompleted,
729                                           updatefn=None)
730        self.estimationThread.queue()
731        self.estimationThread.ready(2.5)
732
733    def performEstimateDynamic(self):
734        """
735            Perform parameter estimation
736        """
737        from .Thread import EstimatePr
738
739        # If a thread is already started, stop it
740        self.stopEstimationThread()
741
742        self.estimationThread = EstimatePr(self._calculator.clone(),
743                                           self.getNFunc(),
744                                           error_func=self._threadError,
745                                           completefn=self._estimateDynamicCompleted,
746                                           updatefn=None)
747        self.estimationThread.queue()
748        self.estimationThread.ready(2.5)
749
750    def stopEstimationThread(self):
751        """ Stop the estimation thread if it exists and is running """
752        if (self.estimationThread is not None and
753                self.estimationThread.isrunning()):
754            self.estimationThread.stop()
755
756    ######################################################################
757    # Thread Complete
758
759    def _estimateCompleted(self, alpha, message, elapsed):
760        ''' Send a signal to the main thread for model update'''
761        self.estimateSignal.emit((alpha, message, elapsed))
762
763    def _estimateDynamicCompleted(self, alpha, message, elapsed):
764        ''' Send a signal to the main thread for model update'''
765        self.estimateDynamicSignal.emit((alpha, message, elapsed))
766
767    def _estimateUpdate(self, output_tuple):
768        """
769        Parameter estimation completed,
770        display the results to the user
771
772        :param alpha: estimated best alpha
773        :param elapsed: computation time
774        """
775        alpha, message, elapsed = output_tuple
776        self._calculator.alpha = alpha
777        self._calculator.elapsed += self._calculator.elapsed
778        if message:
779            logger.info(message)
780        self.performEstimateNT()
781        self.performEstimateDynamicNT()
782
783    def _estimateDynamicUpdate(self, output_tuple):
784        """
785        Parameter estimation completed,
786        display the results to the user
787
788        :param alpha: estimated best alpha
789        :param elapsed: computation time
790        """
791        alpha, message, elapsed = output_tuple
792        self._calculator.alpha = alpha
793        self._calculator.elapsed += self._calculator.elapsed
794        if message:
795            logger.info(message)
796        self.performEstimateDynamicNT()
797
798    def _estimateNTCompleted(self, nterms, alpha, message, elapsed):
799        ''' Send a signal to the main thread for model update'''
800        self.estimateNTSignal.emit((nterms, alpha, message, elapsed))
801
802    def _estimateDynamicNTCompleted(self, nterms, alpha, message, elapsed):
803        ''' Send a signal to the main thread for model update'''
804        self.estimateDynamicNTSignal.emit((nterms, alpha, message, elapsed))
805
806    def _estimateNTUpdate(self, output_tuple):
807        """
808        Parameter estimation completed,
809        display the results to the user
810
811        :param alpha: estimated best alpha
812        :param nterms: estimated number of terms
813        :param elapsed: computation time
814        """
815        nterms, alpha, message, elapsed = output_tuple
816        self._calculator.elapsed += elapsed
817        self._calculator.suggested_alpha = alpha
818        self.nTermsSuggested = nterms
819        # Save useful info
820        self.updateGuiValues()
821        if message:
822            logger.info(message)
823        if self.isBatch:
824            self.acceptAlpha()
825            self.acceptNoTerms()
826            self.startThread()
827
828    def _estimateDynamicNTUpdate(self, output_tuple):
829        """
830        Parameter estimation completed,
831        display the results to the user
832
833        :param alpha: estimated best alpha
834        :param nterms: estimated number of terms
835        :param elapsed: computation time
836        """
837        nterms, alpha, message, elapsed = output_tuple
838        self._calculator.elapsed += elapsed
839        self._calculator.suggested_alpha = alpha
840        self.nTermsSuggested = nterms
841        # Save useful info
842        self.updateDynamicGuiValues()
843        if message:
844            logger.info(message)
845        if self.isBatch:
846            self.acceptAlpha()
847            self.acceptNoTerms()
848            self.startThread()
849
850    def _calculateCompleted(self, out, cov, pr, elapsed):
851        ''' Send a signal to the main thread for model update'''
852        self.calculateSignal.emit((out, cov, pr, elapsed))
853
854    def _calculateUpdate(self, output_tuple):
855        """
856        Method called with the results when the inversion is done
857
858        :param out: output coefficient for the base functions
859        :param cov: covariance matrix
860        :param pr: Invertor instance
861        :param elapsed: time spent computing
862        """
863        out, cov, pr, elapsed = output_tuple
864        # Save useful info
865        cov = np.ascontiguousarray(cov)
866        pr.cov = cov
867        pr.out = out
868        pr.elapsed = elapsed
869
870        # Save Pr invertor
871        self._calculator = pr
872
873        # Update P(r) and fit plots
874        self.prPlot = self.logic.newPRPlot(out, self._calculator, cov)
875        self.prPlot.filename = self.logic.data.filename
876        self.dataPlot = self.logic.new1DPlot(out, self._calculator)
877        self.dataPlot.filename = self.logic.data.filename
878
879        # Udpate internals and GUI
880        self.updateDataList(self._data)
881        if self.isBatch:
882            self.batchComplete.append(self.dataList.currentIndex())
883            self.startNextBatchItem()
884        else:
885            self.isCalculating = False
886        self.updateGuiValues()
887
888    def _threadError(self, error):
889        """
890            Call-back method for calculation errors
891        """
892        logger.error(error)
893        if self.isBatch:
894            self.startNextBatchItem()
895        else:
896            self.stopCalculation()
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